From pj37 at cornell.edu Mon Jun 5 15:09:34 2006 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Mon, 05 Jun 2006 15:09:34 -0400 Subject: new terms / synonyms for citrus terms Message-ID: <4484816E.1050100@cornell.edu> Hi, In the just concluded POC workshop at Cornell, certain term requirements came in from Citrus functional genomics project. The following plant structures that need either a new term or added as synonyms are. Albedo. Definition: White, spongy inner part of citrus fruit rind. comment: IS THIS SAME AS ENDOCARP if so we can add as synonym. Flavedo. Definition: Outer part of the rind of citrus fruit, bearing oil glands and pigments. comment: IS THIS SAME AS EXOCARP if so we can add as synonym.. Rind Definition: The outer covering of certain fruit; also referred to as peel or skin comment: IS THIS SAME AS PERICARP if so we can add as synonym.. Juice sac Definition ?? More info at http://www.chineseplantscience.com/earticle_read.asp?id=12171 Thanks Pankaj From peter.stevens at mobot.org Mon Jun 5 15:15:18 2006 From: peter.stevens at mobot.org (Peter Stevens) Date: Mon, 5 Jun 2006 15:15:18 -0400 Subject: new terms / synonyms for citrus terms In-Reply-To: <4484816E.1050100@cornell.edu> References: <4484816E.1050100@cornell.edu> Message-ID: >Hi, > >In the just concluded POC workshop at Cornell, certain term requirements >came in from Citrus functional genomics project. > >The following plant structures that need either a new term or added as >synonyms are. > >Albedo. > Definition: White, spongy inner part of citrus fruit rind. > comment: IS THIS SAME AS ENDOCARP if so we can add as synonym. OK, or endocarp is strictly applied to the inner epidermis of the fruit wall. > >Flavedo. > Definition: Outer part of the rind of citrus fruit, bearing oil > glands and pigments. > comment: IS THIS SAME AS EXOCARP if so we can add as synonym.. OK, or exocarp is strictly applied to the outer epidermis of the fruit wall. > >Rind > Definition: The outer covering of certain fruit; also referred > to as peel or skin > comment: IS THIS SAME AS PERICARP if so we can add as synonym.. This would have to be looked at on a case-by-case basis. The rind of a citrus = pericarp, but there is also another definition which means "the tough outer wall of a fruit you have to cut off to get to the innards". P. >Juice sac > Definition ?? > More info at >http://www.chineseplantscience.com/earticle_read.asp?id=12171 > >Thanks >Pankaj -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.alercia at cgiar.org Tue Jun 6 02:51:42 2006 From: a.alercia at cgiar.org (Alercia, Adriana (IPGRI - Rome)) Date: Tue, 6 Jun 2006 08:51:42 +0200 Subject: new terms / synonyms for citrus terms In-Reply-To: Message-ID: Hello, Am not quite convinced that Albedo is a synonym of Endocarp.... I think that 'Albedo' is related to MESOCARP (white tissue of rind of citrus) while ENDOCARP is related to the pulp. Adriana ________________________________ From: owner-po-dev at plantontology.org [mailto:owner-po-dev at plantontology.org] On Behalf Of Peter Stevens Sent: Monday, June 05, 2006 9:15 PM To: po-dev at plantontology.org; Pankaj Jaiswal Subject: Re: new terms / synonyms for citrus terms Hi, In the just concluded POC workshop at Cornell, certain term requirements came in from Citrus functional genomics project. The following plant structures that need either a new term or added as synonyms are. Albedo. Definition: White, spongy inner part of citrus fruit rind. comment: IS THIS SAME AS ENDOCARP if so we can add as synonym. OK, or endocarp is strictly applied to the inner epidermis of the fruit wall. Flavedo. Definition: Outer part of the rind of citrus fruit, bearing oil glands and pigments. comment: IS THIS SAME AS EXOCARP if so we can add as synonym.. OK, or exocarp is strictly applied to the outer epidermis of the fruit wall. Rind Definition: The outer covering of certain fruit; also referred to as peel or skin comment: IS THIS SAME AS PERICARP if so we can add as synonym.. This would have to be looked at on a case-by-case basis. The rind of a citrus = pericarp, but there is also another definition which means "the tough outer wall of a fruit you have to cut off to get to the innards". P. Juice sac Definition ?? More info at http://www.chineseplantscience.com/earticle_read.asp?id=12171 Thanks Pankaj -------------- next part -------------- An HTML attachment was scrubbed... URL: From pj37 at cornell.edu Tue Jun 6 16:20:55 2006 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Tue, 06 Jun 2006 16:20:55 -0400 Subject: new terms / synonyms for citrus terms In-Reply-To: References: Message-ID: <4485E3A7.1000608@cornell.edu> Dear Adriana, I did browse the literature and see that citrus community do call the Albedo equivalent to mesocarp. If so I would take your word. Whereas for Endocarp being pulp, is not very clear. Seems that there is a very thin layer of endocarp (innermost epidermis) may/may not be visible in the developed fruit. The citation at http://www.chineseplantscience.com/earticle_read.asp?id=12171 refers that juice sac is a multicellular structure that develops from the innermost epidermis of the carpel which I see is equivalent to endocarp. This means that juice sac being a derivation cannot be referred as endocarp. If you can confirm isn't the pulp equivalent to juice sac. Based on this can you provide us a definition of 'juice sac'. Pankaj Alercia, Adriana (IPGRI - Rome) wrote: > Hello, > > Am not quite convinced that Albedo is a synonym of Endocarp.... I think > that 'Albedo' is related to MESOCARP (white tissue of rind of citrus) > while ENDOCARP is related to the pulp. > > Adriana > ------------------------------------------------------------------------ > From: owner-po-dev at plantontology.org > [mailto:owner-po-dev at plantontology.org] On Behalf Of Peter Stevens > Sent: Monday, June 05, 2006 9:15 PM > To: po-dev at plantontology.org; Pankaj Jaiswal > Subject: Re: new terms / synonyms for citrus terms > >> Hi, > >> In the just concluded POC workshop at Cornell, certain term requirements >> came in from Citrus functional genomics project. > >> The following plant structures that need either a new term or added as >> synonyms are. > >> Albedo. >> Definition: White, spongy inner part of citrus fruit rind. > >> comment: IS THIS SAME AS ENDOCARP if so we can add as synonym. > > > OK, or endocarp is strictly applied to the inner epidermis of the fruit > wall. > > >> >> Flavedo. >> Definition: Outer part of the rind of citrus fruit, bearing oil >> glands and pigments. >> comment: IS THIS SAME AS EXOCARP if so we can add as synonym.. > > > OK, or exocarp is strictly applied to the outer epidermis of the fruit wall. > > >> >> Rind >> Definition: The outer covering of certain fruit; also referred >> to as peel or skin >> comment: IS THIS SAME AS PERICARP if so we can add as synonym.. > > > This would have to be looked at on a case-by-case basis. The rind of a > citrus = pericarp, but there is also another definition which means "the > tough outer wall of a fruit you have to cut off to get to the innards". > > P. > >> Juice sac >> Definition ?? >> More info at >> http://www.chineseplantscience.com/earticle_read.asp?id=12171 >> > >> Thanks >> Pankaj > > -- Pankaj Jaiswal G-15, Bradfield Hall Dept. of Plant Breeding and Genetics Cornell University Ithaca, NY-14853, USA Ph. +1-607-255-3103 / 4199 fax: +1-607-255-6683 From a.alercia at cgiar.org Thu Jun 8 08:15:25 2006 From: a.alercia at cgiar.org (Alercia, Adriana (IPGRI - Rome)) Date: Thu, 8 Jun 2006 14:15:25 +0200 Subject: new terms / synonyms for citrus terms In-Reply-To: <4485E3A7.1000608@cornell.edu> Message-ID: Dear Pankaj, Sorry, if this took time but I wanted to double check with one of the world international expert on citrus, Dr Roland Cottin, who provided the following definitions which I hope will be useful for this exercise which I think is really important for our community. They are as follows: QUOTE In my opinion : - Albedo = mesocarp of Citrus fruits, inner part of peel (skin, rind) often spongious and almost always white (Albedo word come from Alba = white) - Flavedo = epicarp of Citrus fruits, outer part of peel (skin, rind) that contains oil glands, and almost always brightly coloured (Flavedo word come from Flavour) - Pulp = common name for endocarp in Citrus fruits (also called flesh) - Endocarp = Inner part of the citrus fruit, composed of less than 5 to more than 15 segments and a central axis, less or more hollow - Segment = type of bag in pulp which contains juice vesicles (also called juice bags) and seeds (in case of seedy fruits) - Juice bag = little bag, gathered in a bigger one (segment) that may contains generally coloured juice. Some relatives to Citrus fruits have "Juice bag" but without juice, only membrane ! UNQUOTE Hope this helps and please do not hesitate to contact Roland should you require further information. Adriana -----Original Message----- From: Pankaj Jaiswal [mailto:pj37 at cornell.edu] Sent: Tuesday, June 06, 2006 10:21 PM To: po-dev at plantontology.org; Alercia, Adriana (IPGRI - Rome) Cc: Peter Stevens Subject: Re: new terms / synonyms for citrus terms Dear Adriana, I did browse the literature and see that citrus community do call the Albedo equivalent to mesocarp. If so I would take your word. Whereas for Endocarp being pulp, is not very clear. Seems that there is a very thin layer of endocarp (innermost epidermis) may/may not be visible in the developed fruit. The citation at http://www.chineseplantscience.com/earticle_read.asp?id=12171 refers that juice sac is a multicellular structure that develops from the innermost epidermis of the carpel which I see is equivalent to endocarp. This means that juice sac being a derivation cannot be referred as endocarp. If you can confirm isn't the pulp equivalent to juice sac. Based on this can you provide us a definition of 'juice sac'. Pankaj Alercia, Adriana (IPGRI - Rome) wrote: > Hello, > > Am not quite convinced that Albedo is a synonym of Endocarp.... I > think that 'Albedo' is related to MESOCARP (white tissue of rind of > citrus) while ENDOCARP is related to the pulp. > > Adriana > ---------------------------------------------------------------------- > -- > From: owner-po-dev at plantontology.org > [mailto:owner-po-dev at plantontology.org] On Behalf Of Peter Stevens > Sent: Monday, June 05, 2006 9:15 PM > To: po-dev at plantontology.org; Pankaj Jaiswal > Subject: Re: new terms / synonyms for citrus terms > >> Hi, > >> In the just concluded POC workshop at Cornell, certain term >> requirements came in from Citrus functional genomics project. > >> The following plant structures that need either a new term or added >> as synonyms are. > >> Albedo. >> Definition: White, spongy inner part of citrus fruit rind. > >> comment: IS THIS SAME AS ENDOCARP if so we can add as synonym. > > > OK, or endocarp is strictly applied to the inner epidermis of the > fruit wall. > > >> >> Flavedo. >> Definition: Outer part of the rind of citrus fruit, bearing oil >> glands and pigments. >> comment: IS THIS SAME AS EXOCARP if so we can add as synonym.. > > > OK, or exocarp is strictly applied to the outer epidermis of the fruit wall. > > >> >> Rind >> Definition: The outer covering of certain fruit; also referred >> to as peel or skin >> comment: IS THIS SAME AS PERICARP if so we can add as synonym.. > > > This would have to be looked at on a case-by-case basis. The rind of a > citrus = pericarp, but there is also another definition which means > "the tough outer wall of a fruit you have to cut off to get to the innards". > > P. > >> Juice sac >> Definition ?? >> More info at >> http://www.chineseplantscience.com/earticle_read.asp?id=12171 >> > >> Thanks >> Pankaj > > -- Pankaj Jaiswal G-15, Bradfield Hall Dept. of Plant Breeding and Genetics Cornell University Ithaca, NY-14853, USA Ph. +1-607-255-3103 / 4199 fax: +1-607-255-6683 -------------- next part -------------- An HTML attachment was scrubbed... URL: From pj37 at cornell.edu Thu Jun 8 11:12:06 2006 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Thu, 08 Jun 2006 11:12:06 -0400 Subject: archesporial cell Need feedback Message-ID: <44883E46.4020804@cornell.edu> refer to http://www.plantontology.org/amigo/go.cgi?action=query&view=query&session_id=7037b1149707476&query=archesporial+cell&search_constraint=terms Hi Can you suggest the best usage of the name 'archesporial cell' and its definition. I am doing the ontology updates now and will be able to add them this week. It appear that the term 'archesporial cell' is used as a precursor for both the microsporocyte and megasporocyte. Whereas in PO the term 'archesporial cell' appears as a synonym for 'megasporocyte'. THE USE OF THIS SYNONYM IS INAPPRORIATE. On the other hand the same term (from synonym as above) is used in describing a developmental stage of the anther development. This is inconsistent with its usage as synonym in anatomy section. ----------------------- WE NEED TWO TERMS FOR 'archesporial cell' representing its location in either the ANTHER and OVULE. These will be children of 'cell' SUGGEST new term names?? Delete the synonym from 'megasporocyte'. ----------------------------- For further reading http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=10465788&dopt=Abstract In arabidopsis anther of wild-type flowers, hypodermal cells at the four corners of the anther expand radially and differentiate into archesporial cells at stage 2 of anther development in stage 7 flowers (Fig. 1C; Sanders et al. 1999). Archesporial cells undergo periclinal divisions, giving rise to an inner primary sporogenous cell (PSC) layer and an outer primary parietal cell (PPC) layer at stage 3 anthers (Fig. 1D). In Arabidopsis stage 10-11 flowers, an archesporial cell forms from a single hypodermal cell at the top of the ovule primordium, becoming more prominent than neighboring cells because of its slightly larger size, denser cytoplasm, and more conspicuous nucleus (Fig. 2A). In some flowering plants, the archesporial cell of the ovule undergoes a periclinal division, and subsequently the inner cell differentiates into the megasporocyte. However, in the majority of flowering plants including Arabidopsis, the archesporial cell elongates and polarizes longitudinally, and directly differentiates into the megasporocyte or megaspore mother cell (MMC) with obvious change in cell shape from near rectangular to teardrop (Figs. 2B and 7B, below; Willemse 1981; Grossniklaus and Schneitz 1998) From peter.stevens at mobot.org Thu Jun 8 10:30:18 2006 From: peter.stevens at mobot.org (Peter Stevens) Date: Thu, 8 Jun 2006 10:30:18 -0400 Subject: archesporial cell Need feedback In-Reply-To: <44883E46.4020804@cornell.edu> References: <44883E46.4020804@cornell.edu> Message-ID: >refer to >http://www.plantontology.org/amigo/go.cgi?action=query&view=query&session_id=7037b1149707476&query=archesporial+cell&search_constraint=terms > > >Hi > >Can you suggest the best usage of the name 'archesporial cell' and its >definition. I am doing the ontology updates now and will be able to add >them this week. > >It appear that the term 'archesporial cell' is used as a precursor for >both the microsporocyte and megasporocyte. Whereas in PO the term >'archesporial cell' appears as a synonym for 'megasporocyte'. THE USE OF >THIS SYNONYM IS INAPPRORIATE. Well, Esau certainly uses it in this latter sense, so it is a synonym of megasporocyte. . > >On the other hand the same term (from synonym as above) is used in >describing a developmental stage of the anther development. This is >inconsistent with its usage as synonym in anatomy section. > >----------------------- > >WE NEED TWO TERMS FOR 'archesporial cell' representing its location in >either the ANTHER and OVULE. These will be children of 'cell' > >SUGGEST new term names?? I think megasporocyte and microsporocyte will do perfectly well for the cells that undergo meiosis and produce megaspores and microspores. The latter terms are also clearer than 'archespore". P. > >Delete the synonym from 'megasporocyte'. > >----------------------------- > >For further reading ><>http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=10465788&dopt=Abstract > >In arabidopsis anther of wild-type flowers, hypodermal cells at the four >corners of the anther expand radially and differentiate into >archesporial cells at stage 2 of anther development in stage 7 flowers >(Fig. 1C; Sanders et al. 1999). Archesporial cells undergo periclinal >divisions, giving rise to an inner primary sporogenous cell (PSC) layer >and an outer primary parietal cell (PPC) layer at stage 3 anthers (Fig. >1D). > >In Arabidopsis stage 10-11 flowers, an archesporial cell forms from a >single hypodermal cell at the top of the ovule primordium, becoming more >prominent than neighboring cells because of its slightly larger size, >denser cytoplasm, and more conspicuous nucleus (Fig. 2A). In some >flowering plants, the archesporial cell of the ovule undergoes a >periclinal division, and subsequently the inner cell differentiates into >the megasporocyte. However, in the majority of flowering plants >including Arabidopsis, the archesporial cell elongates and polarizes >longitudinally, and directly differentiates into the megasporocyte or >megaspore mother cell (MMC) with obvious change in cell shape from near >rectangular to teardrop (Figs. 2B and 7B, below; Willemse 1981; >Grossniklaus and Schneitz 1998) -------------- next part -------------- An HTML attachment was scrubbed... URL: From pj37 at cornell.edu Thu Jun 8 11:45:38 2006 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Thu, 08 Jun 2006 11:45:38 -0400 Subject: archesporial cell Need feedback In-Reply-To: References: <44883E46.4020804@cornell.edu> Message-ID: <44884622.9040207@cornell.edu> Peter, I am not sure on your suggestions. I need specific instances of archesporial cell present in anther and ovule to annotate gene expression profiles. Also the microsporocyte and megasporocyte have a derivation from (develops from) these specific instances of archesporial cell. Not to mention primary parietal cell is also derived from archesporial cell. Therefore we cannnot put them as synonyms of the microsporocyte and megasporocyte. Please take a look at the text from one of the papers I cited at the end of my previous (or this mail). Pankaj Peter Stevens wrote: >> refer to >> http://www.plantontology.org/amigo/go.cgi?action=query&view=query&session_id=7037b1149707476&query=archesporial+cell&search_constraint=terms >> > >> >> Hi > >> Can you suggest the best usage of the name 'archesporial cell' and its >> definition. I am doing the ontology updates now and will be able to add >> them this week. > >> It appear that the term 'archesporial cell' is used as a precursor for >> both the microsporocyte and megasporocyte. Whereas in PO the term >> 'archesporial cell' appears as a synonym for 'megasporocyte'. THE USE OF >> THIS SYNONYM IS INAPPRORIATE. > > > > Well, Esau certainly uses it in this latter sense, so it is a synonym of > megasporocyte. . > >> >> On the other hand the same term (from synonym as above) is used in >> describing a developmental stage of the anther development. This is >> inconsistent with its usage as synonym in anatomy section. > >> ----------------------- > >> WE NEED TWO TERMS FOR 'archesporial cell' representing its location in >> either the ANTHER and OVULE. These will be children of 'cell' > >> SUGGEST new term names?? > > > > I think megasporocyte and microsporocyte will do perfectly well for the > cells that undergo meiosis and produce megaspores and microspores. The > latter terms are also clearer than 'archespore". > > P. > >> >> Delete the synonym from 'megasporocyte'. > >> ----------------------------- > >> For further reading >> http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=10465788&dopt=Abstract > >> In arabidopsis anther of wild-type flowers, hypodermal cells at the four >> corners of the anther expand radially and differentiate into >> archesporial cells at stage 2 of anther development in stage 7 flowers >> (Fig. 1C; Sanders et al. 1999). Archesporial cells undergo periclinal >> divisions, giving rise to an inner primary sporogenous cell (PSC) layer >> and an outer primary parietal cell (PPC) layer at stage 3 anthers (Fig. >> 1D). > >> In Arabidopsis stage 10-11 flowers, an archesporial cell forms from a >> single hypodermal cell at the top of the ovule primordium, becoming more >> prominent than neighboring cells because of its slightly larger size, >> denser cytoplasm, and more conspicuous nucleus (Fig. 2A). In some >> flowering plants, the archesporial cell of the ovule undergoes a >> periclinal division, and subsequently the inner cell differentiates into >> the megasporocyte. However, in the majority of flowering plants >> including Arabidopsis, the archesporial cell elongates and polarizes >> longitudinally, and directly differentiates into the megasporocyte or >> megaspore mother cell (MMC) with obvious change in cell shape from near >> rectangular to teardrop (Figs. 2B and 7B, below; Willemse 1981; >> Grossniklaus and Schneitz 1998) > > -- Pankaj Jaiswal G-15, Bradfield Hall Dept. of Plant Breeding and Genetics Cornell University Ithaca, NY-14853, USA Ph. +1-607-255-3103 / 4199 fax: +1-607-255-6683 From pj37 at cornell.edu Thu Jun 8 12:07:15 2006 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Thu, 08 Jun 2006 12:07:15 -0400 Subject: new terms / synonyms for citrus terms In-Reply-To: References: Message-ID: <44884B33.9070607@cornell.edu> Dear Adriana, Thank you so much for the information. I appreciate your help. Please see my suggestions inserted below and let me know your feedback. -Pankaj Alercia, Adriana (IPGRI - Rome) wrote: > Dear Pankaj, > > Sorry, if this took time but I wanted to double check with one of the > world international expert on citrus, Dr Roland Cottin, who provided > the following definitions which I hope will be useful for this exercise > which I think is really important for our community. They are as follows: > > QUOTE > > In my opinion : > > - Albedo = mesocarp of Citrus fruits, inner part of peel (skin, rind) > often spongious and almost always white (Albedo word come from Alba = white) Okay > - Flavedo = epicarp of Citrus fruits, outer part of peel (skin, rind) > that contains oil glands, and almost always brightly coloured (Flavedo > word come from Flavour) Okay > - Pulp = common name for endocarp in Citrus fruits (also called flesh) May be not. Do you mean all the tissue that you get after squeezing the juice from a fruit without peel (rind). If true then everything inside a segment (your definition below) including itself is pulp. > - Endocarp = Inner part of the citrus fruit, composed of less than 5 to > more than 15 segments and a central axis, less or more hollow This is equivalent to fruit locule. We might have to look at it. The central axis is PO:0004540 : fruit columella. Therefore your description of endocarp may need revision. May be that it is the same as what you call below a 'segment'. > - Segment = type of bag in pulp which contains juice vesicles (also > called juice bags) and seeds (in case of seedy fruits) See above. It may be something different. > - Juice bag = little bag, gathered in a bigger one (segment) that may > contains generally coloured juice. Some relatives to Citrus fruits have > "Juice bag" but without juice, only membrane ! Okay. > UNQUOTE > > Hope this helps and please do not hesitate to contact Roland should you > require further information. > > Adriana > From pj37 at cornell.edu Tue Jun 13 10:40:52 2006 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Tue, 13 Jun 2006 10:40:52 -0400 Subject: Question GRO term In-Reply-To: <004501c68e8e$9152c9e0$b4971a96@NECVA70J> References: <004501c68e8e$9152c9e0$b4971a96@NECVA70J> Message-ID: <448ECE74.3080202@cornell.edu> Hello, Can you help Dr. Kikuchi find an appropriate Plant structure and growth stage term to define the tissue and stages he used for making the cDNA library. Dr. Kikuchi is very much interested in using the PO in the rice expression database his lab hosts. -Pankaj Shoshi Kikuchi wrote: > Dear Pankaj > > We are now preparing for the ontology-based description of our full-length > cDNA clones. > > I have a question. What is the appropriate description of embryogenic > callus. Many of our full-length cDNA libraries are originated from rice > callus induced from mature seed. > > 21 day-old callus after induction on the medium containing 2,4-D as auxin > from a mature seed. > > What kind of GRO term is the most appropriate one? > > Sincerely yours, > > Shoshi > *********************************** > Shoshi Kikuchi Ph.D > Plant Genome Research Unit > Division of Genome and Biodiversity Research > National Institute of Agrobilogical Sciences (NIAS) > Kan'non dai 2-1-2 > Tsukuba Ibaraki 305-8602 Japan > TEL/FAX +81-29-838-7007 > Email: skikuchi at nias.affrc.go.jp > WEB: ?(RMOS) http://microarray.rice.dna.affrc.go.jp > (KOME) http://cdna01.dna.affrc.go.jp/cDNA/ > ************************************ > > -- Pankaj Jaiswal G-15, Bradfield Hall Dept. of Plant Breeding and Genetics Cornell University Ithaca, NY-14853, USA Ph. +1-607-255-3103 / 4199 fax: +1-607-255-6683 From katica at acoma.Stanford.EDU Tue Jun 13 13:26:57 2006 From: katica at acoma.Stanford.EDU (katica at acoma.Stanford.EDU) Date: Tue, 13 Jun 2006 10:26:57 -0700 (PDT) Subject: Question GRO term In-Reply-To: <448ECE74.3080202@cornell.edu> References: <004501c68e8e$9152c9e0$b4971a96@NECVA70J> <448ECE74.3080202@cornell.edu> Message-ID: Dear Kikuchi, Pankaj Jaiswal forwarded your request to POC. Currently, we only have term 'cultured callus' and 'cultured embryo' in Plant structure ontology (PSO). New term, embryogenic callus, would need to be introduced to PSO. I have question for you: you described the callus as embryogenic, does this refer to callus that will give rise to somatic embryos, or to the callus induced from embryo tissue within seed, or both? I don't know enough about callus induction from rice seeds, some clarification would help with defining parent terms for the new term 'embryogenic callus'. Also, there are no Growth stage terms for in vitro cultures. Since Plant Growth Stages are pertinent to a whole plant, we intentionally ommitted dealing with staging for tissue culture entities. Best Regards, Katica > Shoshi Kikuchi wrote: >> Dear Pankaj >> >> We are now preparing for the ontology-based description of our full-length >> cDNA clones. >> >> I have a question. What is the appropriate description of embryogenic >> callus. Many of our full-length cDNA libraries are originated from rice >> callus induced from mature seed. >> >> 21 day-old callus after induction on the medium containing 2,4-D as auxin >> from a mature seed. >> >> What kind of GRO term is the most appropriate one? >> >> Sincerely yours, >> >> Shoshi >> *********************************** >> Shoshi Kikuchi Ph.D >> Plant Genome Research Unit >> Division of Genome and Biodiversity Research >> National Institute of Agrobilogical Sciences (NIAS) >> Kan'non dai 2-1-2 >> Tsukuba Ibaraki 305-8602 Japan >> TEL/FAX +81-29-838-7007 >> Email: skikuchi at nias.affrc.go.jp >> WEB: ??(RMOS) http://microarray.rice.dna.affrc.go.jp >> (KOME) http://cdna01.dna.affrc.go.jp/cDNA/ >> ************************************ >> >> > > > -- -------------------------------------------------------------------------- Katica Ilic katica at acoma.stanford.edu The Arabidopsis Information Resource Tel: (650) 325-1521 ext. 253 Carnegie Institution of Washington FAX: (650) 325-6857 Department of Plant Biology URL: http://arabidopsis.org/ 260 Panama St. Stanford, CA 94305 U.S.A. -------------------------------------------------------------------------- From katica at acoma.Stanford.EDU Wed Jun 14 13:38:19 2006 From: katica at acoma.Stanford.EDU (katica at acoma.Stanford.EDU) Date: Wed, 14 Jun 2006 10:38:19 -0700 (PDT) Subject: Question GRO term In-Reply-To: References: Message-ID: Dear Satoh, On Wed, 14 Jun 2006, SATOH, Kouji wrote: .... > I have question for you: you described the callus as embryogenic, does >> this refer to callus that will give rise to somatic embryos, or >> to the callus >> induced from embryo tissue within seed, or both? I don't know >> enough about >> callus induction from rice seeds, some clarification would help with >> defining parent terms for the new term 'embryogenic callus'. > > "Embryogenic callus" is the callus is able to generate somatic embryo, does > not indicate the callus derived from embryo tissue. OK, 'embryogenic calus' refers to callus with demonstrable morphogenetic competence (either organogenesis or embryogenesis). Coincidentally, in the particular case of the callus induced from rice seeds, it originated from embryonic tissue too (which is relevant for placing the new term under proper parent term). > And I think "Embryogenic callus" is one of organogenic callus. > Three type of tissues are generated from callus.They are adventitious shoot, > root, and embryo(same as soamtic embryo). > Because plant call has "totipotency". > Therefore the methods of re-diffrerentiation of plant from callus are two. > One is direct induced somatic embryo from callus. > This callus is embryogenic callus > > Other is two step method, at first, the induction of adventitious shoot (or > root), and after that, induced root (or shoot). > This callus is "organogenic callus" > > Can I answer the your question? Yes, you did. Thank you very much for clarification. Best regards, Katica > > best regards > Satoh > > ++++++++++++++++++++++++++++++++++++ > SATOH, Kouji (????????) Ph. D > Unit of Plant Genome Research > National Institute of Agrobiological Sciences > Mail: ksatoh at nias.affrc.go.jp > Tel: 029-838-7007 > ++++++++++++++++++++++++++++++++++++ > >> -----Original Message----- >> From: katica at acoma.stanford.edu [mailto:katica at acoma.stanford.edu] >> Sent: Wednesday, June 14, 2006 2:27 AM >> To: POC-dev; Pankaj Jaiswal >> Cc: Shoshi Kikuchi; ???? ???? >> Subject: Re: Question GRO term >> >> >> Dear Kikuchi, >> >> Pankaj Jaiswal forwarded your request to POC. Currently, we only >> have term >> 'cultured callus' and 'cultured embryo' in Plant structure ontology (PSO). >> New term, embryogenic callus, would need to be introduced to PSO. >> >> I have question for you: you described the callus as embryogenic, does >> this refer to callus that will give rise to somatic embryos, or >> to the callus >> induced from embryo tissue within seed, or both? I don't know >> enough about >> callus induction from rice seeds, some clarification would help with >> defining parent terms for the new term 'embryogenic callus'. >> >> Also, there are no Growth stage terms for in vitro cultures. Since Plant >> Growth Stages are pertinent to a whole plant, we intentionally >> ommitted dealing with staging for tissue culture entities. >> >> Best Regards, >> >> Katica >> >>> Shoshi Kikuchi wrote: >>>> Dear Pankaj >>>> >>>> We are now preparing for the ontology-based description of our >> full-length >>>> cDNA clones. >>>> >>>> I have a question. What is the appropriate description of embryogenic >>>> callus. Many of our full-length cDNA libraries are originated from rice >>>> callus induced from mature seed. >>>> >>>> 21 day-old callus after induction on the medium containing >> 2,4-D as auxin >>>> from a mature seed. >>>> >>>> What kind of GRO term is the most appropriate one? >>>> >>>> Sincerely yours, >>>> >>>> Shoshi >>>> *********************************** >>>> Shoshi Kikuchi Ph.D >>>> Plant Genome Research Unit >>>> Division of Genome and Biodiversity Research >>>> National Institute of Agrobilogical Sciences (NIAS) >>>> Kan'non dai 2-1-2 >>>> Tsukuba Ibaraki 305-8602 Japan >>>> TEL/FAX +81-29-838-7007 >>>> Email: skikuchi at nias.affrc.go.jp >>>> WEB: ????(RMOS) http://microarray.rice.dna.affrc.go.jp >>>> (KOME) http://cdna01.dna.affrc.go.jp/cDNA/ >>>> ************************************ >>>> >>>> >>> >>> >>> >> >> -- >> -------------------------------------------------------------------------- >> Katica Ilic katica at acoma.stanford.edu >> The Arabidopsis Information Resource Tel: (650) 325-1521 ext. 253 >> Carnegie Institution of Washington FAX: (650) 325-6857 >> Department of Plant Biology URL: http://arabidopsis.org/ >> 260 Panama St. >> Stanford, CA 94305 >> U.S.A. >> -------------------------------------------------------------------------- >> > -- -------------------------------------------------------------------------- Katica Ilic katica at acoma.stanford.edu The Arabidopsis Information Resource Tel: (650) 325-1521 ext. 253 Carnegie Institution of Washington FAX: (650) 325-6857 Department of Plant Biology URL: http://arabidopsis.org/ 260 Panama St. Stanford, CA 94305 U.S.A. -------------------------------------------------------------------------- From katica at acoma.Stanford.EDU Wed Jun 14 13:56:26 2006 From: katica at acoma.Stanford.EDU (katica at acoma.Stanford.EDU) Date: Wed, 14 Jun 2006 10:56:26 -0700 (PDT) Subject: Question GRO term In-Reply-To: References: Message-ID: Satoh, Sorry I wasn't specific enough regardng embryogenic callus, 'embryogenic callus' should describe callus with demonstrable competence to form somatic embryos. 'organogenic callus' has competence to form roots and/or shoots. I vaguely remember that some people referred to embryogenic callus even though regeneration of shoots/roots took place from such callus. My recollection goes back to literature that was published some 12 or more years ago. Is there a clear distinction in plant tissue culture community regarding proper use of this terminology, 'embryogenic callus' and 'organogenic callus'? Katica On Wed, 14 Jun 2006 katica at acoma.stanford.edu wrote: > Dear Satoh, > > On Wed, 14 Jun 2006, SATOH, Kouji wrote: > .... >> I have question for you: you described the callus as embryogenic, does >>> this refer to callus that will give rise to somatic embryos, or >>> to the callus >>> induced from embryo tissue within seed, or both? I don't know >>> enough about >>> callus induction from rice seeds, some clarification would help with >>> defining parent terms for the new term 'embryogenic callus'. >> >> "Embryogenic callus" is the callus is able to generate somatic embryo, does >> not indicate the callus derived from embryo tissue. > > OK, 'embryogenic calus' refers to callus with demonstrable morphogenetic > competence (either organogenesis or embryogenesis). Coincidentally, in the > particular case of the callus induced from rice seeds, it originated from > embryonic tissue too (which is relevant for placing the new term under proper > parent term). > >> And I think "Embryogenic callus" is one of organogenic callus. >> Three type of tissues are generated from callus.They are adventitious >> shoot, >> root, and embryo(same as soamtic embryo). >> Because plant call has "totipotency". >> Therefore the methods of re-diffrerentiation of plant from callus are two. >> One is direct induced somatic embryo from callus. >> This callus is embryogenic callus >> >> Other is two step method, at first, the induction of adventitious shoot (or >> root), and after that, induced root (or shoot). >> This callus is "organogenic callus" >> >> Can I answer the your question? > > Yes, you did. Thank you very much for clarification. > Best regards, > > Katica >> >> best regards >> Satoh >> >> ++++++++++++++++++++++++++++++++++++ >> SATOH, Kouji (????????) Ph. D >> Unit of Plant Genome Research >> National Institute of Agrobiological Sciences >> Mail: ksatoh at nias.affrc.go.jp >> Tel: 029-838-7007 >> ++++++++++++++++++++++++++++++++++++ >> >>> -----Original Message----- >>> From: katica at acoma.stanford.edu [mailto:katica at acoma.stanford.edu] >>> Sent: Wednesday, June 14, 2006 2:27 AM >>> To: POC-dev; Pankaj Jaiswal >>> Cc: Shoshi Kikuchi; ???? ???? >>> Subject: Re: Question GRO term >>> >>> >>> Dear Kikuchi, >>> >>> Pankaj Jaiswal forwarded your request to POC. Currently, we only >>> have term >>> 'cultured callus' and 'cultured embryo' in Plant structure ontology (PSO). >>> New term, embryogenic callus, would need to be introduced to PSO. >>> >>> I have question for you: you described the callus as embryogenic, does >>> this refer to callus that will give rise to somatic embryos, or >>> to the callus >>> induced from embryo tissue within seed, or both? I don't know >>> enough about >>> callus induction from rice seeds, some clarification would help with >>> defining parent terms for the new term 'embryogenic callus'. >>> >>> Also, there are no Growth stage terms for in vitro cultures. Since Plant >>> Growth Stages are pertinent to a whole plant, we intentionally >>> ommitted dealing with staging for tissue culture entities. >>> >>> Best Regards, >>> >>> Katica >>> >>>> Shoshi Kikuchi wrote: >>>>> Dear Pankaj >>>>> >>>>> We are now preparing for the ontology-based description of our >>> full-length >>>>> cDNA clones. >>>>> >>>>> I have a question. What is the appropriate description of embryogenic >>>>> callus. Many of our full-length cDNA libraries are originated from rice >>>>> callus induced from mature seed. >>>>> >>>>> 21 day-old callus after induction on the medium containing >>> 2,4-D as auxin >>>>> from a mature seed. >>>>> >>>>> What kind of GRO term is the most appropriate one? >>>>> >>>>> Sincerely yours, >>>>> >>>>> Shoshi >>>>> *********************************** >>>>> Shoshi Kikuchi Ph.D >>>>> Plant Genome Research Unit >>>>> Division of Genome and Biodiversity Research >>>>> National Institute of Agrobilogical Sciences (NIAS) >>>>> Kan'non dai 2-1-2 >>>>> Tsukuba Ibaraki 305-8602 Japan >>>>> TEL/FAX +81-29-838-7007 >>>>> Email: skikuchi at nias.affrc.go.jp >>>>> WEB: ????(RMOS) http://microarray.rice.dna.affrc.go.jp >>>>> (KOME) http://cdna01.dna.affrc.go.jp/cDNA/ >>>>> ************************************ >>>>> >>>>> >>>> >>>> >>>> >>> >>> -- >>> -------------------------------------------------------------------------- >>> Katica Ilic katica at acoma.stanford.edu >>> The Arabidopsis Information Resource Tel: (650) 325-1521 ext. 253 >>> Carnegie Institution of Washington FAX: (650) 325-6857 >>> Department of Plant Biology URL: http://arabidopsis.org/ >>> 260 Panama St. >>> Stanford, CA 94305 >>> U.S.A. >>> -------------------------------------------------------------------------- >>> >> > > -- -------------------------------------------------------------------------- Katica Ilic katica at acoma.stanford.edu The Arabidopsis Information Resource Tel: (650) 325-1521 ext. 253 Carnegie Institution of Washington FAX: (650) 325-6857 Department of Plant Biology URL: http://arabidopsis.org/ 260 Panama St. Stanford, CA 94305 U.S.A. -------------------------------------------------------------------------- From alice.clara.augustine at monsanto.com Wed Jun 14 22:58:57 2006 From: alice.clara.augustine at monsanto.com (AUGUSTINE, ALICE CLARA [AG/8042]) Date: Wed, 14 Jun 2006 21:58:57 -0500 Subject: Question GRO term Message-ID: Katica and all, There is a clear distinction between embryogenic callus and organogenic callus and the usage is pretty consistent amidst the tissue culture community. Organogenic - has competence to form any organ (root, leaf, shoot, leafless shoot/bare stem etc). In the embryogenic callus type, embryo-like structures develop, called somatic embryos, that then simultaneously develop shoots and roots. Then there is also the question of "meristematic callus". This type of callus that produces meristemoids (meristematic cell masses) Meristemoid: A localized group of callus cells, characterized by their accumulation of starch, RNA and protein, and giving rise to adventitious shoots or roots. Would it make sense to put organogenic callus and meristematic callus as synonyms? Another point to note is Meristemoids occur in 2 contexts: One as progenitors of stomata and the other as defined above. Cheers Regards, Alice Clara Augustine -----Original Message----- From: owner-po-dev at plantontology.org [mailto:owner-po-dev at plantontology.org] On Behalf Of katica at acoma.Stanford.EDU Sent: Wednesday, June 14, 2006 11:26 PM To: POC-dev; katica at acoma.Stanford.EDU Cc: SATOH, Kouji; Pankaj Jaiswal; Shoshi Kikuchi Subject: RE: Question GRO term Satoh, Sorry I wasn't specific enough regardng embryogenic callus, 'embryogenic callus' should describe callus with demonstrable competence to form somatic embryos. 'organogenic callus' has competence to form roots and/or shoots. I vaguely remember that some people referred to embryogenic callus even though regeneration of shoots/roots took place from such callus. My recollection goes back to literature that was published some 12 or more years ago. Is there a clear distinction in plant tissue culture community regarding proper use of this terminology, 'embryogenic callus' and 'organogenic callus'? Katica On Wed, 14 Jun 2006 katica at acoma.stanford.edu wrote: > Dear Satoh, > > On Wed, 14 Jun 2006, SATOH, Kouji wrote: > .... >> I have question for you: you described the callus as embryogenic, does >>> this refer to callus that will give rise to somatic embryos, or >>> to the callus >>> induced from embryo tissue within seed, or both? I don't know >>> enough about >>> callus induction from rice seeds, some clarification would help with >>> defining parent terms for the new term 'embryogenic callus'. >> >> "Embryogenic callus" is the callus is able to generate somatic embryo, does >> not indicate the callus derived from embryo tissue. > > OK, 'embryogenic calus' refers to callus with demonstrable morphogenetic > competence (either organogenesis or embryogenesis). Coincidentally, in the > particular case of the callus induced from rice seeds, it originated from > embryonic tissue too (which is relevant for placing the new term under proper > parent term). > >> And I think "Embryogenic callus" is one of organogenic callus. >> Three type of tissues are generated from callus.They are adventitious >> shoot, >> root, and embryo(same as soamtic embryo). >> Because plant call has "totipotency". >> Therefore the methods of re-diffrerentiation of plant from callus are two. >> One is direct induced somatic embryo from callus. >> This callus is embryogenic callus >> >> Other is two step method, at first, the induction of adventitious shoot (or >> root), and after that, induced root (or shoot). >> This callus is "organogenic callus" >> >> Can I answer the your question? > > Yes, you did. Thank you very much for clarification. > Best regards, > > Katica >> >> best regards >> Satoh >> >> ++++++++++++++++++++++++++++++++++++ >> SATOH, Kouji (????????) Ph. D >> Unit of Plant Genome Research >> National Institute of Agrobiological Sciences >> Mail: ksatoh at nias.affrc.go.jp >> Tel: 029-838-7007 >> ++++++++++++++++++++++++++++++++++++ >> >>> -----Original Message----- >>> From: katica at acoma.stanford.edu [mailto:katica at acoma.stanford.edu] >>> Sent: Wednesday, June 14, 2006 2:27 AM >>> To: POC-dev; Pankaj Jaiswal >>> Cc: Shoshi Kikuchi; ???? ???? >>> Subject: Re: Question GRO term >>> >>> >>> Dear Kikuchi, >>> >>> Pankaj Jaiswal forwarded your request to POC. Currently, we only >>> have term >>> 'cultured callus' and 'cultured embryo' in Plant structure ontology (PSO). >>> New term, embryogenic callus, would need to be introduced to PSO. >>> >>> I have question for you: you described the callus as embryogenic, does >>> this refer to callus that will give rise to somatic embryos, or >>> to the callus >>> induced from embryo tissue within seed, or both? I don't know >>> enough about >>> callus induction from rice seeds, some clarification would help with >>> defining parent terms for the new term 'embryogenic callus'. >>> >>> Also, there are no Growth stage terms for in vitro cultures. Since Plant >>> Growth Stages are pertinent to a whole plant, we intentionally >>> ommitted dealing with staging for tissue culture entities. >>> >>> Best Regards, >>> >>> Katica >>> >>>> Shoshi Kikuchi wrote: >>>>> Dear Pankaj >>>>> >>>>> We are now preparing for the ontology-based description of our >>> full-length >>>>> cDNA clones. >>>>> >>>>> I have a question. What is the appropriate description of embryogenic >>>>> callus. Many of our full-length cDNA libraries are originated from rice >>>>> callus induced from mature seed. >>>>> >>>>> 21 day-old callus after induction on the medium containing >>> 2,4-D as auxin >>>>> from a mature seed. >>>>> >>>>> What kind of GRO term is the most appropriate one? >>>>> >>>>> Sincerely yours, >>>>> >>>>> Shoshi >>>>> *********************************** >>>>> Shoshi Kikuchi Ph.D >>>>> Plant Genome Research Unit >>>>> Division of Genome and Biodiversity Research >>>>> National Institute of Agrobilogical Sciences (NIAS) >>>>> Kan'non dai 2-1-2 >>>>> Tsukuba Ibaraki 305-8602 Japan >>>>> TEL/FAX +81-29-838-7007 >>>>> Email: skikuchi at nias.affrc.go.jp >>>>> WEB: ????(RMOS) http://microarray.rice.dna.affrc.go.jp >>>>> (KOME) http://cdna01.dna.affrc.go.jp/cDNA/ >>>>> ************************************ >>>>> >>>>> >>>> >>>> >>>> >>> >>> -- >>> -------------------------------------------------------------------------- >>> Katica Ilic katica at acoma.stanford.edu >>> The Arabidopsis Information Resource Tel: (650) 325-1521 ext. 253 >>> Carnegie Institution of Washington FAX: (650) 325-6857 >>> Department of Plant Biology URL: http://arabidopsis.org/ >>> 260 Panama St. >>> Stanford, CA 94305 >>> U.S.A. >>> -------------------------------------------------------------------------- >>> >> > > -- -------------------------------------------------------------------------- Katica Ilic katica at acoma.stanford.edu The Arabidopsis Information Resource Tel: (650) 325-1521 ext. 253 Carnegie Institution of Washington FAX: (650) 325-6857 Department of Plant Biology URL: http://arabidopsis.org/ 260 Panama St. Stanford, CA 94305 U.S.A. -------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------- This e-mail message may contain privileged and/or confidential information, and is intended to be received only by persons entitled to receive such information. If you have received this e-mail in error, please notify the sender immediately. Please delete it and all attachments from any servers, hard drives or any other media. Other use of this e-mail by you is strictly prohibited. All e-mails and attachments sent and received are subject to monitoring, reading and archival by Monsanto. The recipient of this e-mail is solely responsible for checking for the presence of "Viruses" or other "Malware". Monsanto accepts no liability for any damage caused by any such code transmitted by or accompanying this e-mail or any attachment. --------------------------------------------------------------------------------------------------------- From katica at acoma.Stanford.EDU Thu Jun 15 14:19:05 2006 From: katica at acoma.Stanford.EDU (katica at acoma.Stanford.EDU) Date: Thu, 15 Jun 2006 11:19:05 -0700 (PDT) Subject: Question GRO term In-Reply-To: References: Message-ID: Hi Clare, Thanks for explanation. Based on the responses we got so far, my suggestion would be to add two terms, 'embryogenic callus' and 'organogenic callus': PO:0000004 : in vitro cultured cell, tissue and organ (i) PO:0000009 : cultured callus (i) embryogenic callus (i) organogenic callus (syn. meristematic callus) I need to double check about the synonym for the latter term. Since both callus types can originate (be induced) from a variety of tissues, I would ignore this aspect, it can get really complicated, (triggering large proliferation of terms). Also, at this point, I would suggest not to propagate term 'meristemoid' under 'in vitro cultured cell, tissue and organ' node. This term is already in the PSO, PO:meristemoid, PO:0000070, Def: A cell or a group of cells constituting an active locus of meristematic activity in a tissue composed of somewhat older, differentiating cells. The definition describes all meristemoid cell, regardless of location. However, if 'in vitro meristemoid cell' is required for accurate annotations (in cases where term' meristemoid' is not sufficiently granular), we will add it to PSO. Dr. Kikuchi (and others), please let me know if this would work for annotation purposes. Best regards, Katica On Wed, 14 Jun 2006, AUGUSTINE, ALICE CLARA [AG/8042] wrote: > Katica and all, > > There is a clear distinction between embryogenic callus and organogenic > callus and the usage is pretty consistent amidst the tissue culture > community. > > Organogenic - has competence to form any organ (root, leaf, shoot, leafless > shoot/bare stem etc). In the embryogenic callus type, embryo-like structures > develop, called somatic embryos, that then simultaneously develop shoots and > roots. > > Then there is also the question of "meristematic callus". This type of > callus that produces meristemoids (meristematic cell masses) > Meristemoid: A localized group of callus cells, characterized by their > accumulation of starch, RNA and protein, and giving rise to adventitious > shoots or roots. > Would it make sense to put organogenic callus and meristematic callus as > synonyms? > > Another point to note is Meristemoids occur in 2 contexts: > One as progenitors of stomata and the other as defined above. > > Cheers > Regards, > Alice Clara Augustine > > -----Original Message----- > From: owner-po-dev at plantontology.org [mailto:owner-po-dev at plantontology.org] > On Behalf Of katica at acoma.Stanford.EDU > Sent: Wednesday, June 14, 2006 11:26 PM > To: POC-dev; katica at acoma.Stanford.EDU > Cc: SATOH, Kouji; Pankaj Jaiswal; Shoshi Kikuchi > Subject: RE: Question GRO term > > Satoh, > > Sorry I wasn't specific enough regardng embryogenic callus, > 'embryogenic callus' should describe callus with demonstrable competence > to form somatic embryos. 'organogenic callus' has competence to form roots > and/or shoots. > > I vaguely remember that some people referred to embryogenic callus even > though regeneration of shoots/roots took place from such callus. My > recollection goes back to literature that was published some 12 or more > years ago. > > Is there a clear distinction in plant tissue culture community regarding > proper use of this terminology, 'embryogenic callus' and 'organogenic > callus'? > > Katica > > > On Wed, 14 Jun 2006 katica at acoma.stanford.edu wrote: > >> Dear Satoh, >> >> On Wed, 14 Jun 2006, SATOH, Kouji wrote: >> .... >>> I have question for you: you described the callus as embryogenic, does >>>> this refer to callus that will give rise to somatic embryos, or >>>> to the callus >>>> induced from embryo tissue within seed, or both? I don't know >>>> enough about >>>> callus induction from rice seeds, some clarification would help with >>>> defining parent terms for the new term 'embryogenic callus'. >>> >>> "Embryogenic callus" is the callus is able to generate somatic embryo, > does >>> not indicate the callus derived from embryo tissue. >> >> OK, 'embryogenic calus' refers to callus with demonstrable morphogenetic >> competence (either organogenesis or embryogenesis). Coincidentally, in the > >> particular case of the callus induced from rice seeds, it originated from >> embryonic tissue too (which is relevant for placing the new term under > proper >> parent term). >> >>> And I think "Embryogenic callus" is one of organogenic callus. >>> Three type of tissues are generated from callus.They are adventitious >>> shoot, >>> root, and embryo(same as soamtic embryo). >>> Because plant call has "totipotency". >>> Therefore the methods of re-diffrerentiation of plant from callus are > two. >>> One is direct induced somatic embryo from callus. >>> This callus is embryogenic callus >>> >>> Other is two step method, at first, the induction of adventitious shoot > (or >>> root), and after that, induced root (or shoot). >>> This callus is "organogenic callus" >>> >>> Can I answer the your question? >> >> Yes, you did. Thank you very much for clarification. >> Best regards, >> >> Katica >>> >>> best regards >>> Satoh >>> >>> ++++++++++++++++++++++++++++++++++++ >>> SATOH, Kouji (????????) Ph. D >>> Unit of Plant Genome Research >>> National Institute of Agrobiological Sciences >>> Mail: ksatoh at nias.affrc.go.jp >>> Tel: 029-838-7007 >>> ++++++++++++++++++++++++++++++++++++ >>> >>>> -----Original Message----- >>>> From: katica at acoma.stanford.edu [mailto:katica at acoma.stanford.edu] >>>> Sent: Wednesday, June 14, 2006 2:27 AM >>>> To: POC-dev; Pankaj Jaiswal >>>> Cc: Shoshi Kikuchi; ???? ???? >>>> Subject: Re: Question GRO term >>>> >>>> >>>> Dear Kikuchi, >>>> >>>> Pankaj Jaiswal forwarded your request to POC. Currently, we only >>>> have term >>>> 'cultured callus' and 'cultured embryo' in Plant structure ontology > (PSO). >>>> New term, embryogenic callus, would need to be introduced to PSO. >>>> >>>> I have question for you: you described the callus as embryogenic, does >>>> this refer to callus that will give rise to somatic embryos, or >>>> to the callus >>>> induced from embryo tissue within seed, or both? I don't know >>>> enough about >>>> callus induction from rice seeds, some clarification would help with >>>> defining parent terms for the new term 'embryogenic callus'. >>>> >>>> Also, there are no Growth stage terms for in vitro cultures. Since Plant >>>> Growth Stages are pertinent to a whole plant, we intentionally >>>> ommitted dealing with staging for tissue culture entities. >>>> >>>> Best Regards, >>>> >>>> Katica >>>> >>>>> Shoshi Kikuchi wrote: >>>>>> Dear Pankaj >>>>>> >>>>>> We are now preparing for the ontology-based description of our >>>> full-length >>>>>> cDNA clones. >>>>>> >>>>>> I have a question. What is the appropriate description of embryogenic >>>>>> callus. Many of our full-length cDNA libraries are originated from > rice >>>>>> callus induced from mature seed. >>>>>> >>>>>> 21 day-old callus after induction on the medium containing >>>> 2,4-D as auxin >>>>>> from a mature seed. >>>>>> >>>>>> What kind of GRO term is the most appropriate one? >>>>>> >>>>>> Sincerely yours, >>>>>> >>>>>> Shoshi >>>>>> *********************************** >>>>>> Shoshi Kikuchi Ph.D >>>>>> Plant Genome Research Unit >>>>>> Division of Genome and Biodiversity Research >>>>>> National Institute of Agrobilogical Sciences (NIAS) >>>>>> Kan'non dai 2-1-2 >>>>>> Tsukuba Ibaraki 305-8602 Japan >>>>>> TEL/FAX +81-29-838-7007 >>>>>> Email: skikuchi at nias.affrc.go.jp >>>>>> WEB: ????(RMOS) http://microarray.rice.dna.affrc.go.jp >>>>>> (KOME) http://cdna01.dna.affrc.go.jp/cDNA/ >>>>>> ************************************ >>>>>> >>>>>> >>>>> >>>>> >>>>> >>>> >>>> -- >>>> > -------------------------------------------------------------------------- >>>> Katica Ilic katica at acoma.stanford.edu >>>> The Arabidopsis Information Resource Tel: (650) 325-1521 ext. 253 >>>> Carnegie Institution of Washington FAX: (650) 325-6857 >>>> Department of Plant Biology URL: http://arabidopsis.org/ >>>> 260 Panama St. >>>> Stanford, CA 94305 >>>> U.S.A. >>>> > -------------------------------------------------------------------------- >>>> >>> >> >> > > -- -------------------------------------------------------------------------- Katica Ilic katica at acoma.stanford.edu The Arabidopsis Information Resource Tel: (650) 325-1521 ext. 253 Carnegie Institution of Washington FAX: (650) 325-6857 Department of Plant Biology URL: http://arabidopsis.org/ 260 Panama St. Stanford, CA 94305 U.S.A. -------------------------------------------------------------------------- From skikuchi at nias.affrc.go.jp Thu Jun 15 21:19:02 2006 From: skikuchi at nias.affrc.go.jp (Shoshi Kikuchi) Date: Fri, 16 Jun 2006 10:19:02 +0900 Subject: Question GRO term References: Message-ID: <00f501c690e2$da615ba0$b4971a96@NECVA70J> Dear Katica and all > Dr. Kikuchi (and others), please let me know if this would work for > annotation purposes. Thank you very much for your discusiion and very quick arrangement. We agree the annotation and it will work. Sincerely yours, Shoshi Kikuchi *********************************** Shoshi Kikuchi Ph.D Plant Genome Research Unit Division of Genome and Biodiversity Research National Institute of Agrobilogical Sciences (NIAS) Kan'non dai 2-1-2 Tsukuba Ibaraki 305-8602 Japan TEL/FAX +81-29-838-7007 Email: skikuchi at nias.affrc.go.jp WEB: ?(RMOS) http://microarray.rice.dna.affrc.go.jp (KOME) http://cdna01.dna.affrc.go.jp/cDNA/ ************************************ ----- Original Message ----- From: To: "AUGUSTINE, ALICE CLARA [AG/8042]" Cc: ; "SATOH, Kouji" ; "Pankaj Jaiswal" ; "Shoshi Kikuchi" Sent: Friday, June 16, 2006 3:19 AM Subject: RE: Question GRO term > > Hi Clare, > > Thanks for explanation. > > Based on the responses we got so far, my suggestion would be to add two > terms, 'embryogenic callus' and 'organogenic callus': > > PO:0000004 : in vitro cultured cell, tissue and organ > (i) PO:0000009 : cultured callus > (i) embryogenic callus > (i) organogenic callus (syn. meristematic callus) > > I need to double check about the synonym for the latter term. > > Since both callus types can originate (be induced) from a variety of > tissues, I would ignore this aspect, it can get really complicated, > (triggering large proliferation of terms). > Also, at this point, I would suggest not to propagate term 'meristemoid' > under 'in vitro cultured cell, tissue and organ' node. This term is already > in the PSO, > > PO:meristemoid, PO:0000070, > > Def: A cell or a group of cells constituting an active locus of > meristematic activity in a tissue composed of somewhat older, differentiating > cells. > > The definition describes all meristemoid cell, regardless of location. > However, if 'in vitro meristemoid cell' is required for accurate > annotations (in cases where term' meristemoid' is not sufficiently > granular), we will add it to PSO. > > Dr. Kikuchi (and others), please let me know if this would work for > annotation purposes. > > Best regards, > > Katica > > On Wed, 14 Jun 2006, AUGUSTINE, ALICE CLARA [AG/8042] wrote: > > > Katica and all, > > > > There is a clear distinction between embryogenic callus and organogenic > > callus and the usage is pretty consistent amidst the tissue culture > > community. > > > > Organogenic - has competence to form any organ (root, leaf, shoot, leafless > > shoot/bare stem etc). In the embryogenic callus type, embryo-like structures > > develop, called somatic embryos, that then simultaneously develop shoots and > > roots. > > > > Then there is also the question of "meristematic callus". This type of > > callus that produces meristemoids (meristematic cell masses) > > Meristemoid: A localized group of callus cells, characterized by their > > accumulation of starch, RNA and protein, and giving rise to adventitious > > shoots or roots. > > Would it make sense to put organogenic callus and meristematic callus as > > synonyms? > > > > Another point to note is Meristemoids occur in 2 contexts: > > One as progenitors of stomata and the other as defined above. > > > > Cheers > > Regards, > > Alice Clara Augustine > > > > -----Original Message----- > > From: owner-po-dev at plantontology.org [mailto:owner-po-dev at plantontology.org] > > On Behalf Of katica at acoma.Stanford.EDU > > Sent: Wednesday, June 14, 2006 11:26 PM > > To: POC-dev; katica at acoma.Stanford.EDU > > Cc: SATOH, Kouji; Pankaj Jaiswal; Shoshi Kikuchi > > Subject: RE: Question GRO term > > > > Satoh, > > > > Sorry I wasn't specific enough regardng embryogenic callus, > > 'embryogenic callus' should describe callus with demonstrable competence > > to form somatic embryos. 'organogenic callus' has competence to form roots > > and/or shoots. > > > > I vaguely remember that some people referred to embryogenic callus even > > though regeneration of shoots/roots took place from such callus. My > > recollection goes back to literature that was published some 12 or more > > years ago. > > > > Is there a clear distinction in plant tissue culture community regarding > > proper use of this terminology, 'embryogenic callus' and 'organogenic > > callus'? > > > > Katica > > > > > > On Wed, 14 Jun 2006 katica at acoma.stanford.edu wrote: > > > >> Dear Satoh, > >> > >> On Wed, 14 Jun 2006, SATOH, Kouji wrote: > >> .... > >>> I have question for you: you described the callus as embryogenic, does > >>>> this refer to callus that will give rise to somatic embryos, or > >>>> to the callus > >>>> induced from embryo tissue within seed, or both? I don't know > >>>> enough about > >>>> callus induction from rice seeds, some clarification would help with > >>>> defining parent terms for the new term 'embryogenic callus'. > >>> > >>> "Embryogenic callus" is the callus is able to generate somatic embryo, > > does > >>> not indicate the callus derived from embryo tissue. > >> > >> OK, 'embryogenic calus' refers to callus with demonstrable morphogenetic > >> competence (either organogenesis or embryogenesis). Coincidentally, in the > > > >> particular case of the callus induced from rice seeds, it originated from > >> embryonic tissue too (which is relevant for placing the new term under > > proper > >> parent term). > >> > >>> And I think "Embryogenic callus" is one of organogenic callus. > >>> Three type of tissues are generated from callus.They are adventitious > >>> shoot, > >>> root, and embryo(same as soamtic embryo). > >>> Because plant call has "totipotency". > >>> Therefore the methods of re-diffrerentiation of plant from callus are > > two. > >>> One is direct induced somatic embryo from callus. > >>> This callus is embryogenic callus > >>> > >>> Other is two step method, at first, the induction of adventitious shoot > > (or > >>> root), and after that, induced root (or shoot). > >>> This callus is "organogenic callus" > >>> > >>> Can I answer the your question? > >> > >> Yes, you did. Thank you very much for clarification. > >> Best regards, > >> > >> Katica > >>> > >>> best regards > >>> Satoh > >>> > >>> ++++++++++++++++++++++++++++++++++++ > >>> SATOH, Kouji (????????) Ph. D > >>> Unit of Plant Genome Research > >>> National Institute of Agrobiological Sciences > >>> Mail: ksatoh at nias.affrc.go.jp > >>> Tel: 029-838-7007 > >>> ++++++++++++++++++++++++++++++++++++ > >>> > >>>> -----Original Message----- > >>>> From: katica at acoma.stanford.edu [mailto:katica at acoma.stanford.edu] > >>>> Sent: Wednesday, June 14, 2006 2:27 AM > >>>> To: POC-dev; Pankaj Jaiswal > >>>> Cc: Shoshi Kikuchi; ???? ???? > >>>> Subject: Re: Question GRO term > >>>> > >>>> > >>>> Dear Kikuchi, > >>>> > >>>> Pankaj Jaiswal forwarded your request to POC. Currently, we only > >>>> have term > >>>> 'cultured callus' and 'cultured embryo' in Plant structure ontology > > (PSO). > >>>> New term, embryogenic callus, would need to be introduced to PSO. > >>>> > >>>> I have question for you: you described the callus as embryogenic, does > >>>> this refer to callus that will give rise to somatic embryos, or > >>>> to the callus > >>>> induced from embryo tissue within seed, or both? I don't know > >>>> enough about > >>>> callus induction from rice seeds, some clarification would help with > >>>> defining parent terms for the new term 'embryogenic callus'. > >>>> > >>>> Also, there are no Growth stage terms for in vitro cultures. Since Plant > >>>> Growth Stages are pertinent to a whole plant, we intentionally > >>>> ommitted dealing with staging for tissue culture entities. > >>>> > >>>> Best Regards, > >>>> > >>>> Katica > >>>> > >>>>> Shoshi Kikuchi wrote: > >>>>>> Dear Pankaj > >>>>>> > >>>>>> We are now preparing for the ontology-based description of our > >>>> full-length > >>>>>> cDNA clones. > >>>>>> > >>>>>> I have a question. What is the appropriate description of embryogenic > >>>>>> callus. Many of our full-length cDNA libraries are originated from > > rice > >>>>>> callus induced from mature seed. > >>>>>> > >>>>>> 21 day-old callus after induction on the medium containing > >>>> 2,4-D as auxin > >>>>>> from a mature seed. > >>>>>> > >>>>>> What kind of GRO term is the most appropriate one? > >>>>>> > >>>>>> Sincerely yours, > >>>>>> > >>>>>> Shoshi > >>>>>> *********************************** > >>>>>> Shoshi Kikuchi Ph.D > >>>>>> Plant Genome Research Unit > >>>>>> Division of Genome and Biodiversity Research > >>>>>> National Institute of Agrobilogical Sciences (NIAS) > >>>>>> Kan'non dai 2-1-2 > >>>>>> Tsukuba Ibaraki 305-8602 Japan > >>>>>> TEL/FAX +81-29-838-7007 > >>>>>> Email: skikuchi at nias.affrc.go.jp > >>>>>> WEB: ????(RMOS) http://microarray.rice.dna.affrc.go.jp > >>>>>> (KOME) http://cdna01.dna.affrc.go.jp/cDNA/ > >>>>>> ************************************ > >>>>>> > >>>>>> > >>>>> > >>>>> > >>>>> > >>>> > >>>> -- > >>>> > > -------------------------------------------------------------------------- > >>>> Katica Ilic katica at acoma.stanford.edu > >>>> The Arabidopsis Information Resource Tel: (650) 325-1521 ext. 253 > >>>> Carnegie Institution of Washington FAX: (650) 325-6857 > >>>> Department of Plant Biology URL: http://arabidopsis.org/ > >>>> 260 Panama St. > >>>> Stanford, CA 94305 > >>>> U.S.A. > >>>> > > -------------------------------------------------------------------------- > >>>> > >>> > >> > >> > > > > > > -- > -------------------------------------------------------------------------- > Katica Ilic katica at acoma.stanford.edu > The Arabidopsis Information Resource Tel: (650) 325-1521 ext. 253 > Carnegie Institution of Washington FAX: (650) 325-6857 > Department of Plant Biology URL: http://arabidopsis.org/ > 260 Panama St. > Stanford, CA 94305 > U.S.A. > -------------------------------------------------------------------------- > From kellogge at msx.umsl.edu Mon Jun 19 12:12:07 2006 From: kellogge at msx.umsl.edu (kellogge) Date: Mon, 19 Jun 2006 11:12:07 -0500 Subject: terms for roots Message-ID: Hi folks - Mary and I have had a discussion about terms for roots in maize, which has led to the suggestion of the following terms: Under each type of root, she has requested terms defining the central axis and also the lateral root. An example for crown root is: crown root ---part-of central axis of crown root ---part-of lateral root from crown root She has also run into the problem that grass embryos are well enough differentiated to have multiple nodes, such "nodal root" can apply within the embryo as well as on the germinated plant. Here's a proposed solution: embryonic root ---is-a primary root ---is-a embryonic nodal root ------is-a seminal root ------is-a root from node above scutellum shoot-borne root ---is-a nodal root ------is-a embryonic nodal root ---------is-a seminal root ---------is-a root from node above scutellum ------is-a prop root ------is-a crown root Toby Elizabeth A. Kellogg E. Desmond Lee and Family Professor of Botanical Studies Department of Biology University of Missouri-St. Louis St. Louis, MO 63121 Tel: 314-516-6217; FAX: 314-516-6233 http://www.umsl.edu/services/kellogg/ This message is for the designated recipient(s) only and may contain privileged or confidential information.? If you received it in error, please notify the sender immediately and delete the original.? Thank you.? From msachs at uiuc.edu Mon Jun 19 12:57:15 2006 From: msachs at uiuc.edu (Marty Sachs) Date: Mon, 19 Jun 2006 11:57:15 -0500 Subject: terms for roots In-Reply-To: References: Message-ID: Toby, This looks fine to me except for: >embryonic root >---is-a primary root >---is-a embryonic nodal root >------is-a seminal root >------is-a root from node above scutellum These roots which are also called 'secondary roots' or 'lateral seminal roots' are actually from the scutellar node, not from a node above the scutellum. See: http://aob.oxfordjournals.org/cgi/content/full/93/4/359/MCH056F1 http://maize.agron.iastate.edu/images/corn/fig1.gif The crown (a.k.a, nodal) roots are the first ones that form above the scutellem. -Marty At 11:12 AM -0500 6/19/06, kellogge wrote: >Hi folks - > Mary and I have had a discussion about terms for roots in maize, >which has led to the suggestion of the following terms: > >Under each type of root, she has requested terms defining the >central axis and also the lateral root. >An example for crown root is: >crown root >---part-of central axis of crown root >---part-of lateral root from crown root > >She has also run into the problem that grass embryos are well enough >differentiated to have multiple nodes, such "nodal root" can apply >within the embryo as well as on the germinated plant. >Here's a proposed solution: > >embryonic root >---is-a primary root >---is-a embryonic nodal root >------is-a seminal root >------is-a root from node above scutellum > >shoot-borne root >---is-a nodal root >------is-a embryonic nodal root >---------is-a seminal root >---------is-a root from node above scutellum >------is-a prop root >------is-a crown root > >Toby > >Elizabeth A. Kellogg >E. Desmond Lee and Family Professor of Botanical Studies >Department of Biology >University of Missouri-St. Louis >St. Louis, MO 63121 >Tel: 314-516-6217; FAX: 314-516-6233 >http://www.umsl.edu/services/kellogg/ >This message is for the designated recipient(s) only and may contain >privileged or confidential information. If you received it in >error, please notify the sender immediately and delete the original. >Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: From SchaefferM at missouri.edu Mon Jun 19 14:01:41 2006 From: SchaefferM at missouri.edu (Mary (Polacco) Schaeffer) Date: Mon, 19 Jun 2006 13:01:41 -0500 Subject: terms for roots In-Reply-To: Message-ID: Marty, Here is the photo I sent earlier to Toby and PO-DEV ? not sure if it made it to you, where an embryonic root is emerging from the embryo, above the scutellar node. Me, I?m no morphology expert, but I did check with my betters (Leszek, Ed Coe) before bringing this up. Image was from Hund et al TAG 109:618-629 (2004) _ root architecture QTL paper It fits with Kiesselbach description, p. 17 [in maize there is a class of lateral seminal roots in maize that come off the main 'stem':] "at the base of the first internode of the stem, just above the scutellar node" (Kiesselbach p.17). mary From: Marty Sachs Reply-To: po-dev at plantontology.org, Marty Sachs Date: Mon, 19 Jun 2006 11:57:15 -0500 To: po-dev at plantontology.org, kellogge Subject: Re: terms for roots Toby, This looks fine to me except for: > embryonic root > ---is-a primary root > ---is-a embryonic nodal root > ------is-a seminal root > ------is-a root from node above scutellum These roots which are also called 'secondary roots' or 'lateral seminal roots' are actually from the scutellar node, not from a node above the scutellum. See: http://aob.oxfordjournals.org/cgi/content/full/93/4/359/MCH056F1 http://maize.agron.iastate.edu/images/corn/fig1.gif The crown (a.k.a, nodal) roots are the first ones that form above the scutellem. -Marty At 11:12 AM -0500 6/19/06, kellogge wrote: > Hi folks - > Mary and I have had a discussion about terms for roots in maize, which has > led to the suggestion of the following terms: > > Under each type of root, she has requested terms defining the central axis and > also the lateral root. > An example for crown root is: > crown root > ---part-of central axis of crown root > ---part-of lateral root from crown root > > She has also run into the problem that grass embryos are well enough > differentiated to have multiple nodes, such "nodal root" can apply within the > embryo as well as on the germinated plant. > Here's a proposed solution: > embryonic root > ---is-a primary root > ---is-a embryonic nodal root > ------is-a seminal root > ------is-a root from node above scutellum > > shoot-borne root > ---is-a nodal root > ------is-a embryonic nodal root > ---------is-a seminal root > ---------is-a root from node above scutellum > ------is-a prop root > ------is-a crown root > > Toby > > Elizabeth A. Kellogg > E. Desmond Lee and Family Professor of Botanical Studies > Department of Biology > University of Missouri-St. Louis > St. Louis, MO 63121 > Tel: 314-516-6217; FAX: 314-516-6233 > http://www.umsl.edu/services/kellogg/ > This message is for the designated recipient(s) only and may contain > privileged or confidential information. If you received it in error, please > notify the sender immediately and delete the original. Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: maizeSeminalRoots.tiff Type: application/octet-stream Size: 37300 bytes Desc: not available URL: From msachs at uiuc.edu Mon Jun 19 14:12:45 2006 From: msachs at uiuc.edu (Marty Sachs) Date: Mon, 19 Jun 2006 13:12:45 -0500 Subject: terms for roots In-Reply-To: References: Message-ID: Mary, It looks like it, but I'm guessing not. I've seen this in some lines. I found the image that I was looking for: http://schnablelab.plantgenomics.iastate.edu/images/research/hypothesis/cornrootwild.html I've looked at a lot of these roots in my day, and it is true that in some backgrounds, they tend to grow upwards and appear as if they're emerging above the scutellum. However, they're really originating from within the scutellum (or the embryo axis proper). -Marty At 1:01 PM -0500 6/19/06, Mary (Polacco) Schaeffer wrote: >Marty, >Here is the photo I sent earlier to Toby and PO-DEV - not sure if it >made it to you, where an embryonic root is emerging from the embryo, >above the scutellar node. Me, I'm no morphology expert, but I did >check with my betters (Leszek, Ed Coe) before bringing this up. > >Image was from Hund et al TAG 109:618-629 (2004) _ root >architecture QTL paper > >It fits with Kiesselbach description, p. 17 >[in maize there is a class of lateral seminal roots in maize that >come off the main 'stem':] >"at the base of the first internode of the stem, just above the >scutellar node" (Kiesselbach p.17). > > mary > > >From: Marty Sachs >Reply-To: po-dev at plantontology.org, Marty Sachs >Date: Mon, 19 Jun 2006 11:57:15 -0500 >To: po-dev at plantontology.org, kellogge >Subject: Re: terms for roots > >Toby, > >This looks fine to me except for: > >embryonic root >---is-a primary root >---is-a embryonic nodal root >------is-a seminal root >------is-a root from node above scutellum > > >These roots which are also called 'secondary roots' or 'lateral >seminal roots' are actually from the scutellar node, not from a node >above the scutellum. > >See: >http://aob.oxfordjournals.org/cgi/content/full/93/4/359/MCH056F1 > >http://maize.agron.iastate.edu/images/corn/fig1.gif > >The crown (a.k.a, nodal) roots are the first ones that form above >the scutellem. > > -Marty > >At 11:12 AM -0500 6/19/06, kellogge wrote: > >Hi folks - > Mary and I have had a discussion about terms for roots in maize, >which has led to the suggestion of the following terms: > >Under each type of root, she has requested terms defining the >central axis and also the lateral root. >An example for crown root is: >crown root >---part-of central axis of crown root >---part-of lateral root from crown root > >She has also run into the problem that grass embryos are well enough >differentiated to have multiple nodes, such "nodal root" can apply >within the embryo as well as on the germinated plant. >Here's a proposed solution: >embryonic root >---is-a primary root >---is-a embryonic nodal root >------is-a seminal root >------is-a root from node above scutellum > >shoot-borne root >---is-a nodal root >------is-a embryonic nodal root >---------is-a seminal root >---------is-a root from node above scutellum >------is-a prop root >------is-a crown root > >Toby > >Elizabeth A. Kellogg >E. Desmond Lee and Family Professor of Botanical Studies >Department of Biology >University of Missouri-St. Louis >St. Louis, MO 63121 >Tel: 314-516-6217; FAX: 314-516-6233 >http://www.umsl.edu/services/kellogg/ >This message is for the designated recipient(s) only and may contain >privileged or confidential information. If you received it in >error, please notify the sender immediately and delete the original. >Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: From msachs at uiuc.edu Mon Jun 19 14:49:14 2006 From: msachs at uiuc.edu (Marty Sachs) Date: Mon, 19 Jun 2006 13:49:14 -0500 Subject: terms for roots In-Reply-To: References: Message-ID: Mary, About the best I could find is in; Kiesselbach TA (1949) The Structure and Reproduction of Corn. Nebr Agric Exp Stn Ann Rep 161:1-96 http://www.maizegdb.org/cgi-bin/displayrefrecord.cgi?id=59445 I'm attaching Figure 6 (page 14). The seminal (secondary) root here is also growing upwards, but clearly emerging from the scultellar node (embryo axis). On page 16-17 in a description of the root system, it says: "The root system of corn, as of other grasses, consists of two sets of roots: (1) seminal roots whose initials are present in the embryo, and (2) adventitious roots, which arise from stem tissue after germination...." -Marty At 1:17 PM -0500 6/19/06, Mary (Polacco) Schaeffer wrote: >Marty, >That was my concern but since there seems to be some dispute here >amongst my betters: >Do you have a picture or published reference I could go to for this? > m > > >From: Marty Sachs >Date: Mon, 19 Jun 2006 13:12:45 -0500 >To: "Mary (Polacco) Schaeffer" , POC-dev > >Subject: Re: terms for roots >... >I've looked at a lot of these roots in my day, and it is true that >in some backgrounds, they tend to grow upwards and appear as if >they're emerging above the scutellum. However, they're really >originating from within the scutellum (or the embryo axis proper). -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: %Kiesselbach-roots.jpg Type: application/applefile Size: 131 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Kiesselbach-roots.jpg Type: image/jpeg Size: 120372 bytes Desc: not available URL: From Leszek at missouri.edu Mon Jun 19 15:37:46 2006 From: Leszek at missouri.edu (Vincent, Leszek) Date: Mon, 19 Jun 2006 14:37:46 -0500 Subject: terms for roots In-Reply-To: Message-ID: <2BC371D49E5C86418135172EE7C130371D2627@UM-XMAIL08.um.umsystem.edu> Marty, Mary & others - The more I also try & gain clarity on the origin(s) of seminal roots - from the scutellar node or above the scutellar node, the more I need to see some images of longitudinal sections through the germinating kernel so as to really see where these seminal roots arise. The external morphology images & drawings just don't provide enough granularity for me. The work by Hochholdinger et al. (http://aob.oxfordjournals.org/cgi/content/full/93/4/359#SEC3) provides some persuasive DESCRIPTION of the embryonic origin of seminal roots which align with Marty's comments about the origin being from within the scutellar node region - although the exsertion/emergence of the seminal roots from the kernel tissue make the seminal roots seem to appear from above the scutellum - the origin & emergence sites not being spatially equivalent. I'd suggest the needed tweaking should be "------ is a root emerging from the scutellar node". This implies that Kiesselbach's description ((... just above the scutellar node." p.17) is a little 'off' but I sense that his description is focusing more on the apparent emergence of the seminal root than the origin. - Leszek *=*=*=*=*=*=*=*=*=*=*=*=*=*=*=* P. Leszek D. Vincent Ph.D., FLS Division of Plant Sciences 215 Curtis Hall University of Missouri-Columbia Columbia MO 65211-7020 USA Ph: (573) 884-3716; Skype VoIP: phytosynergy; Fax:(573) 884-7850; Email: Leszek at missouri.edu Associate Curator, Dunn-Palmer Herbarium (UMO); Research Associate, Missouri Botanical Garden (MO), USA; Plant Systematist on The Plant Ontology Consortium - NSF award 0321666 (www.plantontology.org) *=*=*=*=*=*=*=*=*=*=*=*=*=*=*=* ________________________________ From: owner-po-dev at plantontology.org [mailto:owner-po-dev at plantontology.org] On Behalf Of Marty Sachs Sent: Monday, June 19, 2006 1:49 PM To: Schaeffer, Mary L.; POC-dev Subject: Re: terms for roots Mary, About the best I could find is in; Kiesselbach TA (1949) The Structure and Reproduction of Corn. Nebr Agric Exp Stn Ann Rep 161:1-96 http://www.maizegdb.org/cgi-bin/displayrefrecord.cgi?id=59445 I'm attaching Figure 6 (page 14). The seminal (secondary) root here is also growing upwards, but clearly emerging from the scultellar node (embryo axis). On page 16-17 in a description of the root system, it says: "The root system of corn, as of other grasses, consists of two sets of roots: (1) seminal roots whose initials are present in the embryo, and (2) adventitious roots, which arise from stem tissue after germination...." -Marty At 1:17 PM -0500 6/19/06, Mary (Polacco) Schaeffer wrote: Marty, That was my concern but since there seems to be some dispute here amongst my betters: Do you have a picture or published reference I could go to for this? m From: Marty Sachs Date: Mon, 19 Jun 2006 13:12:45 -0500 To: "Mary (Polacco) Schaeffer" , POC-dev Subject: Re: terms for roots ... I've looked at a lot of these roots in my day, and it is true that in some backgrounds, they tend to grow upwards and appear as if they're emerging above the scutellum. However, they're really originating from within the scutellum (or the embryo axis proper). -------------- next part -------------- An HTML attachment was scrubbed... URL: From pj37 at cornell.edu Thu Jun 22 14:50:34 2006 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Thu, 22 Jun 2006 14:50:34 -0400 Subject: terms for roots [Leszek, Mary, Marty] In-Reply-To: References: Message-ID: <449AE67A.9040006@cornell.edu> Leszek, Mary, Marty Can you come up with a final decision and let me know. I will add the terms accrodingly. If the 'root from node above scutellum' is called as 'lateral seminal root'. I would rather use the later as term name. We need definitions as well. Pankaj Marty Sachs wrote: > Toby, > > This looks fine to me except for: > >> embryonic root >> ---is-a primary root >> ---is-a embryonic nodal root > >> ------is-a seminal root > >> ------is-a root from node above scutellum > > > These roots which are also called 'secondary roots' or 'lateral seminal > roots' are actually from the scutellar node, not from a node above the > scutellum. > > See: http://aob.oxfordjournals.org/cgi/content/full/93/4/359/MCH056F1 > > http://maize.agron.iastate.edu/images/corn/fig1.gif > > The crown (a.k.a, nodal) roots are the first ones that form above the > scutellem. > > -Marty > > At 11:12 AM -0500 6/19/06, kellogge wrote: > >> Hi folks - >> Mary and I have had a discussion about terms for roots in maize, >> which has led to the suggestion of the following terms: >> >> Under each type of root, she has requested terms defining the central >> axis and also the lateral root. >> An example for crown root is: >> crown root >> ---part-of central axis of crown root >> ---part-of lateral root from crown root >> >> She has also run into the problem that grass embryos are well enough >> differentiated to have multiple nodes, such "nodal root" can apply >> within the embryo as well as on the germinated plant. >> Here's a proposed solution: > >> embryonic root >> ---is-a primary root >> ---is-a embryonic nodal root >> ------is-a seminal root >> ------is-a root from node above scutellum > >> >> shoot-borne root >> ---is-a nodal root >> ------is-a embryonic nodal root >> ---------is-a seminal root >> ---------is-a root from node above scutellum >> ------is-a prop root >> ------is-a crown root From msachs at uiuc.edu Thu Jun 22 15:06:30 2006 From: msachs at uiuc.edu (Marty Sachs) Date: Thu, 22 Jun 2006 14:06:30 -0500 Subject: terms for roots [Leszek, Mary, Marty] In-Reply-To: <449AE67A.9040006@cornell.edu> References: <449AE67A.9040006@cornell.edu> Message-ID: Pankaj, These roots are called a variety of names by different people (seminal roots, lateral seminal roots, secondary roots, scutellar nodal roots, etc). As long as all the synonyms are given, I don't care which name becomes the primary name. However, I think that Leszek and I are convinced that they originate from the scutellar node proper. So, the definition needs to be changed. They are not 'root from node above scutellum', they originate within the scutellar node. -Marty At 2:50 PM -0400 6/22/06, Pankaj Jaiswal wrote: >Leszek, Mary, Marty > >Can you come up with a final decision and let me know. I will add >the terms accrodingly. > >If the 'root from node above scutellum' is called as 'lateral >seminal root'. I would rather use the later as term name. > >We need definitions as well. > >Pankaj > > >Marty Sachs wrote: > >>Toby, >> >>This looks fine to me except for: >> >>>embryonic root >>>---is-a primary root >>>---is-a embryonic nodal root >> >>>------is-a seminal root >> >>>------is-a root from node above scutellum >> >> >>These roots which are also called 'secondary roots' or 'lateral >>seminal roots' are actually from the scutellar node, not from a >>node above the scutellum. >> >>See: http://aob.oxfordjournals.org/cgi/content/full/93/4/359/MCH056F1 >> >>http://maize.agron.iastate.edu/images/corn/fig1.gif >> >>The crown (a.k.a, nodal) roots are the first ones that form above >>the scutellem. >> >> -Marty >> >>At 11:12 AM -0500 6/19/06, kellogge wrote: >> >>>Hi folks - >>> Mary and I have had a discussion about terms for roots in maize, >>>which has led to the suggestion of the following terms: >>> >>>Under each type of root, she has requested terms defining the >>>central axis and also the lateral root. >>>An example for crown root is: >>>crown root >>>---part-of central axis of crown root >>>---part-of lateral root from crown root >>> >>>She has also run into the problem that grass embryos are well >>>enough differentiated to have multiple nodes, such "nodal root" >>>can apply within the embryo as well as on the germinated plant. >>>Here's a proposed solution: >> >>>embryonic root >>>---is-a primary root >>>---is-a embryonic nodal root >>>------is-a seminal root >>>------is-a root from node above scutellum >> >>> >>>shoot-borne root >>>---is-a nodal root >>>------is-a embryonic nodal root >>>---------is-a seminal root >>>---------is-a root from node above scutellum >>>------is-a prop root >>>------is-a crown root From tkellogg at umsl.edu Thu Jun 22 15:25:56 2006 From: tkellogg at umsl.edu (Kellogg, Elizabeth A.) Date: Thu, 22 Jun 2006 14:25:56 -0500 Subject: terms for roots [Leszek, Mary, Marty] References: <449AE67A.9040006@cornell.edu> Message-ID: Certainly if these roots are really from the scutellar node, then the additional terms that I suggested are not needed, and the ontology does not need to be modified. Cheers - Toby Elizabeth A. Kellogg E. Desmond Lee and Family Professor of Botanical Studies Department of Biology University of Missouri-St. Louis One University Boulevard St. Louis, MO 63121 USA Tel.: 314-516-6217 FAX: 314-516-6233 -----Original Message----- From: owner-po-dev at plantontology.org on behalf of Marty Sachs Sent: Thu 6/22/2006 2:06 PM To: po-dev at plantontology.org; Pankaj Jaiswal Subject: Re: terms for roots [Leszek, Mary, Marty] Pankaj, These roots are called a variety of names by different people (seminal roots, lateral seminal roots, secondary roots, scutellar nodal roots, etc). As long as all the synonyms are given, I don't care which name becomes the primary name. However, I think that Leszek and I are convinced that they originate from the scutellar node proper. So, the definition needs to be changed. They are not 'root from node above scutellum', they originate within the scutellar node. -Marty At 2:50 PM -0400 6/22/06, Pankaj Jaiswal wrote: >Leszek, Mary, Marty > >Can you come up with a final decision and let me know. I will add >the terms accrodingly. > >If the 'root from node above scutellum' is called as 'lateral >seminal root'. I would rather use the later as term name. > >We need definitions as well. > >Pankaj > > >Marty Sachs wrote: > >>Toby, >> >>This looks fine to me except for: >> >>>embryonic root >>>---is-a primary root >>>---is-a embryonic nodal root >> >>>------is-a seminal root >> >>>------is-a root from node above scutellum >> >> >>These roots which are also called 'secondary roots' or 'lateral >>seminal roots' are actually from the scutellar node, not from a >>node above the scutellum. >> >>See: http://aob.oxfordjournals.org/cgi/content/full/93/4/359/MCH056F1 >> >>http://maize.agron.iastate.edu/images/corn/fig1.gif >> >>The crown (a.k.a, nodal) roots are the first ones that form above >>the scutellem. >> >> -Marty >> >>At 11:12 AM -0500 6/19/06, kellogge wrote: >> >>>Hi folks - >>> Mary and I have had a discussion about terms for roots in maize, >>>which has led to the suggestion of the following terms: >>> >>>Under each type of root, she has requested terms defining the >>>central axis and also the lateral root. >>>An example for crown root is: >>>crown root >>>---part-of central axis of crown root >>>---part-of lateral root from crown root >>> >>>She has also run into the problem that grass embryos are well >>>enough differentiated to have multiple nodes, such "nodal root" >>>can apply within the embryo as well as on the germinated plant. >>>Here's a proposed solution: >> >>>embryonic root >>>---is-a primary root >>>---is-a embryonic nodal root >>>------is-a seminal root >>>------is-a root from node above scutellum >> >>> >>>shoot-borne root >>>---is-a nodal root >>>------is-a embryonic nodal root >>>---------is-a seminal root >>>---------is-a root from node above scutellum >>>------is-a prop root >>>------is-a crown root -------------- next part -------------- A non-text attachment was scrubbed... Name: winmail.dat Type: application/ms-tnef Size: 4210 bytes Desc: not available URL: From feedback_submission at filetta.cshl.edu Mon Jun 26 14:47:12 2006 From: feedback_submission at filetta.cshl.edu (feedback_submission at filetta.cshl.edu) Date: Mon, 26 Jun 2006 14:47:12 -0400 Subject: Feedback on POC Message-ID: <200606261847.k5QIlBht011659@filetta.cshl.org> *** Feedback from Plant Ontology Live Site *** refer_to_url: http://www.plantontology.org/index.html comments: Hello, I am searching for a term for the initial of the cortex/endodermis in the root tip, but cannot find one, has it been forgotten or is it another term that I should use? name: Juliette Colinas email: jhc16 at duke.edu organization: Duke University/ Benfey lab send_feedback: Send your feedback From pj37 at cornell.edu Fri Jun 30 11:31:04 2006 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Fri, 30 Jun 2006 11:31:04 -0400 Subject: terms for roots [Leszek, Mary, Marty, Toby] In-Reply-To: References: <449AE67A.9040006@cornell.edu> Message-ID: <44A543B8.9090104@cornell.edu> Sorry for a delayed response, we already have a term 'seminal root'. Its definition says : Root formed at the scutelar node of the embryo in some monocotyledonous plants. Looks like we are all calling the same things as Toby suggested. NO need to change the ontology. If so is it okay for me to go ahead and add all the following as synonyms of 'seminal root'. synonyms are: lateral seminal roots, secondary roots, scutellar nodal roots Toby, Is it okay if I assign a second parent 'nodal root' to a 'seminal root'. like root --isa--embryonic root -----isa--seminal root --isa--shoot borne root -----isa--seminal root Also the relationship between radicle and primary root is totally wrong. By our definition primary root develops from radicle, whereas the ontology says it IS_A instance of primary root. If you all agree I will make the changes. Accordingly only seminal root and radicle are the only two instances of the embryonic root. Primary root is a root that develops from the radicle which is a type of embryonic root. root --isa--embryonic root -----isa--radicle --------developsfrom--primary root --isa--primary root Pankaj Marty Sachs wrote: > Pankaj, > > These roots are called a variety of names by different people (seminal > roots, lateral seminal roots, secondary roots, scutellar nodal roots, > etc). As long as all the synonyms are given, I don't care which name > becomes the primary name. However, I think that Leszek and I are > convinced that they originate from the scutellar node proper. So, the > definition needs to be changed. They are not 'root from node above > scutellum', they originate within the scutellar node. > > -Marty > > At 2:50 PM -0400 6/22/06, Pankaj Jaiswal wrote: > >> Leszek, Mary, Marty >> >> Can you come up with a final decision and let me know. I will add the >> terms accrodingly. >> >> If the 'root from node above scutellum' is called as 'lateral seminal >> root'. I would rather use the later as term name. >> >> We need definitions as well. >> >> Pankaj >> >> >> Marty Sachs wrote: >> >>> Toby, >>> >>> This looks fine to me except for: >>> >>>> embryonic root >>>> ---is-a primary root >>>> ---is-a embryonic nodal root >>> >>> >>>> ------is-a seminal root >>> >>> >>>> ------is-a root from node above scutellum >>> >>> >>> >>> These roots which are also called 'secondary roots' or 'lateral >>> seminal roots' are actually from the scutellar node, not from a node >>> above the scutellum. >>> >>> See: http://aob.oxfordjournals.org/cgi/content/full/93/4/359/MCH056F1 >>> >>> http://maize.agron.iastate.edu/images/corn/fig1.gif >>> >>> The crown (a.k.a, nodal) roots are the first ones that form above the >>> scutellem. >>> >>> -Marty >>> >>> At 11:12 AM -0500 6/19/06, kellogge wrote: >>> >>>> Hi folks - >>>> Mary and I have had a discussion about terms for roots in maize, >>>> which has led to the suggestion of the following terms: >>>> >>>> Under each type of root, she has requested terms defining the >>>> central axis and also the lateral root. >>>> An example for crown root is: >>>> crown root >>>> ---part-of central axis of crown root >>>> ---part-of lateral root from crown root >>>> >>>> She has also run into the problem that grass embryos are well enough >>>> differentiated to have multiple nodes, such "nodal root" can apply >>>> within the embryo as well as on the germinated plant. >>>> Here's a proposed solution: >>> >>> >>>> embryonic root >>>> ---is-a primary root >>>> ---is-a embryonic nodal root >>>> ------is-a seminal root >>>> ------is-a root from node above scutellum >>> >>> >>>> >>>> shoot-borne root >>>> ---is-a nodal root >>>> ------is-a embryonic nodal root >>>> ---------is-a seminal root >>>> ---------is-a root from node above scutellum >>>> ------is-a prop root >>>> ------is-a crown root > > > -- Pankaj Jaiswal G-15, Bradfield Hall Dept. of Plant Breeding and Genetics Cornell University Ithaca, NY-14853, USA Ph. +1-607-255-3103 / 4199 fax: +1-607-255-6683 From Leszek at missouri.edu Fri Jun 30 18:05:59 2006 From: Leszek at missouri.edu (Vincent, Leszek) Date: Fri, 30 Jun 2006 17:05:59 -0500 Subject: terms for roots [Leszek, Mary, Marty, Toby] In-Reply-To: <44A543B8.9090104@cornell.edu> Message-ID: <2BC371D49E5C86418135172EE7C130371D2685@UM-XMAIL08.um.umsystem.edu> Hi Pankaj - You're correct regarding your initial query. But I suggest you tweak the definition of 'seminal root' to: 'Root formed within the scutellar node of the embryo in some monocotyledonous plants.' Over to Toby & others. - Leszek *=*=*=*=*=*=*=*=*=*=*=*=*=*=*=* P. Leszek D. Vincent Ph.D., FLS Division of Plant Sciences 215 Curtis Hall University of Missouri-Columbia Columbia MO 65211-7020 USA Ph: (573) 884-3716; Skype VoIP: phytosynergy; Fax:(573) 884-7850; Email: Leszek at missouri.edu Associate Curator, Dunn-Palmer Herbarium (UMO); Research Associate, Missouri Botanical Garden (MO), USA; Plant Systematist on The Plant Ontology Consortium - NSF award 0321666 - www.plantontology.org *=*=*=*=*=*=*=*=*=*=*=*=*=*=*=* -----Original Message----- From: owner-po-dev at plantontology.org [mailto:owner-po-dev at plantontology.org] On Behalf Of Pankaj Jaiswal Sent: Friday, June 30, 2006 10:31 AM To: POC-dev Subject: Re: terms for roots [Leszek, Mary, Marty, Toby] Sorry for a delayed response, we already have a term 'seminal root'. Its definition says : Root formed at the scutelar node of the embryo in some monocotyledonous plants. Looks like we are all calling the same things as Toby suggested. NO need to change the ontology. If so is it okay for me to go ahead and add all the following as synonyms of 'seminal root'. synonyms are: lateral seminal roots, secondary roots, scutellar nodal roots Toby, Is it okay if I assign a second parent 'nodal root' to a 'seminal root'. like root --isa--embryonic root -----isa--seminal root --isa--shoot borne root -----isa--seminal root Also the relationship between radicle and primary root is totally wrong. By our definition primary root develops from radicle, whereas the ontology says it IS_A instance of primary root. If you all agree I will make the changes. Accordingly only seminal root and radicle are the only two instances of the embryonic root. Primary root is a root that develops from the radicle which is a type of embryonic root. root --isa--embryonic root -----isa--radicle --------developsfrom--primary root --isa--primary root Pankaj Marty Sachs wrote: > Pankaj, > > These roots are called a variety of names by different people (seminal > roots, lateral seminal roots, secondary roots, scutellar nodal roots, > etc). As long as all the synonyms are given, I don't care which name > becomes the primary name. However, I think that Leszek and I are > convinced that they originate from the scutellar node proper. So, the > definition needs to be changed. They are not 'root from node above > scutellum', they originate within the scutellar node. > > -Marty > > At 2:50 PM -0400 6/22/06, Pankaj Jaiswal wrote: > >> Leszek, Mary, Marty >> >> Can you come up with a final decision and let me know. I will add the >> terms accrodingly. >> >> If the 'root from node above scutellum' is called as 'lateral seminal >> root'. I would rather use the later as term name. >> >> We need definitions as well. >> >> Pankaj >> >> >> Marty Sachs wrote: >> >>> Toby, >>> >>> This looks fine to me except for: >>> >>>> embryonic root >>>> ---is-a primary root >>>> ---is-a embryonic nodal root >>> >>> >>>> ------is-a seminal root >>> >>> >>>> ------is-a root from node above scutellum >>> >>> >>> >>> These roots which are also called 'secondary roots' or 'lateral >>> seminal roots' are actually from the scutellar node, not from a node >>> above the scutellum. >>> >>> See: http://aob.oxfordjournals.org/cgi/content/full/93/4/359/MCH056F1 >>> >>> http://maize.agron.iastate.edu/images/corn/fig1.gif >>> >>> The crown (a.k.a, nodal) roots are the first ones that form above the >>> scutellem. >>> >>> -Marty >>> >>> At 11:12 AM -0500 6/19/06, kellogge wrote: >>> >>>> Hi folks - >>>> Mary and I have had a discussion about terms for roots in maize, >>>> which has led to the suggestion of the following terms: >>>> >>>> Under each type of root, she has requested terms defining the >>>> central axis and also the lateral root. >>>> An example for crown root is: >>>> crown root >>>> ---part-of central axis of crown root >>>> ---part-of lateral root from crown root >>>> >>>> She has also run into the problem that grass embryos are well enough >>>> differentiated to have multiple nodes, such "nodal root" can apply >>>> within the embryo as well as on the germinated plant. >>>> Here's a proposed solution: >>> >>> >>>> embryonic root >>>> ---is-a primary root >>>> ---is-a embryonic nodal root >>>> ------is-a seminal root >>>> ------is-a root from node above scutellum >>> >>> >>>> >>>> shoot-borne root >>>> ---is-a nodal root >>>> ------is-a embryonic nodal root >>>> ---------is-a seminal root >>>> ---------is-a root from node above scutellum >>>> ------is-a prop root >>>> ------is-a crown root > > > -- Pankaj Jaiswal G-15, Bradfield Hall Dept. of Plant Breeding and Genetics Cornell University Ithaca, NY-14853, USA Ph. +1-607-255-3103 / 4199 fax: +1-607-255-6683