Gramene mutant database format
Jun Jian Ni
jn66 at cornell.edu
Wed Jun 27 10:47:15 EDT 2001
Hi everyone,
I sent my email to Gramene mailing list yesterday and however it seems
unsuccessful. Pankaj told me it might be caused by too big attachment
file. Now I am sending them as text file. Sorry for inconvinience to
read them.
The first file (Rice_mutant_database.txt) was prepared by Pankaj, Doreen
and me. Susan also gave us a lot of suggestions. Now, we are planning to
use it as Gramene mutant database format. Considering more convenient
for discussion, I keep current file situation with some question and
comments on it.
The second file (Detail_mutant_database.txt) was prepared by me while
preparing the format. It has some information that cannot be included in
the first file. I am also sending it to you for your background and
comments.
Hope to get your suggestion and comments. Thank you very much.
Junjian
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Rice mutant database
( version for discussion and comments)
(06-26-2001)
1. Name: abbreviated symbol (evidence).
2. Gramene ID: unique identifier(evidence).
3. Description: a text defining the mutant (maximum two sentences,
INCLUCING WHETHER IT IS A DOMINANT OR RECESSIVE MUTATION) (evidence)
4. Synonym: we may not need to categorize as following, instead we
have only one column where the synonyms start with rice followed by other
grasses/monocots/Arabidopsis (evidence) EITHER WAY IS FINE, BUT I WONDER
IF THERE ARE NO SYNONMS, WILL THIS FIELD APPEAR, OR WILL IT APPEAR ONLY IF
THERE IS SOMETHING IN IT? (This question is relevant for all fields listed
below, and is especially relevant where you have a long list of diseases
or other specific "sub-trait" classes.)
(I think this will be optional, and it will appear only there is sthg in
it.)
a. From rice
b. From other crops (start with the closest relative among grasses and
if possible include Arabidopsis)
5. Key words
6. Picture: jpeg format (evidence)
7. Plant trait ontology: give several GO numbers (evidence)
8. Plant morphology: give several GO numbers (evidence)
9. Plant anatomy: give several GO numbers (evidence)
I AM NOT VERY CLEAR ON THE DIFFERENCE BETWEEN MORPHOLOGY AND ANATOMY-
CAN YOU CLARIFY YOUR THOUGHTS ON THIS? According to traditional
classfication in rice, morphological traits and anatomy traits are included
into same category. However, there are two different categories
in current GO. According my understanding, comparing to morphology
(outside, easy to be observed), anatomy traits are: 1) related with
structure; 2) inside; 3) should be examined with specific instruments.
10. Gene ontology (evidence)
a. Molecular function
b. Biological process
11. Linkage map information (evidence)
a. Chromosome no.
b. Location on chromosome (cM)
WE NEED TO BE VERY CAREFUL IF WE CITE A CM LOCATION BASED ON THE
MORPHOLOGICAL MUTANT MAP BECAUSE THIS WILL N0T COINCIDE WITH A LOCATION
ON GRAMENE?S RICE TEMPLATE MAP (BASED ON THE HIGH RESOLUTION GENETIC AND
PHYSICAL MAPPING DATA). THEREFORE, WE NEED TO DISCUSS HOW TO PROVIDE CM
INFORMATION THAT ALLOWS THESE MUTANT POSITIONS TO BE OVERLAYED ON THE HIGH
RESOLUTIO MAP. It is really an important and also very difficult question.
It related the information conform (shift) among different marker types
(molecular, morphological markers) and different populations. Up to now,
I still have no satisfied answer to that. I will keep this question in
mind and will also discuss it with related persons.
C. Linked marker(s) (if any)
12. Sequence information (if any)
a. ALLELE [I AM NOT SURE WHERE TO PUT "ALLELE" BUT IF WE HAVE SEQUENCE
INFORMATION, IT WILL BE IMPORTANT TO DISTINGUISH EXACTLY WHERE IN THE
SEQUENCE THE MUTANT DIFFERS FROM THE WILD TYPE. IN MY OPINION THIS INFO
ABOUT "ALLELES".
b. FUNCTIONAL NUCLEOTIDE POLYMORPHISM (FNP) (IF KNOWN)
13. RELATED GENE AND QTL INFORMATION IN RICE (IF ANY) (EVIDENCE)
14. Comparative map information: give unique identifier from
different crops (Should we have unique identifier for each crop in Gramene
[YES, I THINK WE NEED TO HAVE A GRAMENE ID SO WE ARE SURE IT IS UNIQUE] or
we take the identifier from publication/respective database?) Can we
provide links to databases? (evidence) WE SHOULD ALSO PROVIDE LINKS TO
OTHER DATABASES, AND WE WILL PROBABLY WANT TO PROVIDE AN EQUIVALENCE TABLE
SO IT IS EASY TO LINK OUR GRAMENE ID'S WITH ID'S IN OTHER DATABASES.
Pankaj said that we maybe should get the permission for link to other
databases.
15. Mutagenesis type: PJ will try to give the GO ID (evidence)
[PLEASE CLARIFY WHY THE GO ID IS RELEVANT TO MUTAGENESIS TYPE- I DON'T
UNDERSTAND YOUR THINKING HERE.] Pankaj suggested he will use the
information to curate the control vocabulary for Mutagenesis type so that
I can take that ID.
16. Germplasm information: IRIS Ac no. And web link to IRIS (evidence)
[YOU WILL ALSO WANT TO LINK TO THE USDA DATABASE, "GRIN" AND OTHER NATIONAL
GERMPLASM DATABASES, INCLUDING THE MAFF GERMPLASM COLLECTION IN JAPAN,
THE COLLECTIONS IN KOREA, CHINA, INDIA, ETC. , WHEREVER POSSIBLE. That is
very good suggestion!
17. List of references: a combined list of all the above evidences.
Can be done by parsing !
18. Comments field: a simple text if any?
19. Curator's name: ID of person validating the entry
6/26/01
10:46 AM
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Some details for mutant database
(revised version)
06-26-2001
1. Name of the mutant
2. Phenotypic description
a. Photos
b. Morphological and anatomy descriptions
Leaf
Leaf length (long, short)
Leaf width
Leaf blade pubescence
Leaf blade color
Basal leaf sheath color
Leaf angel (erect, droopy)
Flag leaf angle
Ligule length
Ligule color
Ligule shape
Collar color
Auricle color
Leaf senescence
Leaf thickness (thick, thin)
Leaf structure (rolled, stiff, wrinkled)
Secondary leaf sheath elongation
Stem and culms
Culm length
Culm number (Tillering ability)
Culm angle
Diameter of basal internode
Culm strength
Culm internode color
Internode length
Root
Root number
Root length
Root weight
Root/Shoot ratio
Root thickness
Root penetration index
Root branching profile
Panicle and spikelets
Panicle length
Panicle type
Secondary branching of panicles
Panicle axis (straight or not)
Panicle exsertion
Awning (no, short, long)
Awn color
Apiculus color
Stigma color
Lemma and Palea color
Lemma and palea pubescence
Sterile lemma color
Sterile lemma length
Panicle threshability
Grain and seeds
Grain length
Grain width
Size (big, small)
Shape (round, slender)
Shattering
c. Related physiological feature (if any)
d. Related biochemical feature (if any)
e. Specific growth and developmental stages
Germination
Seedling
Tillering
Stem elongation
Booting
Heading
Milk stage
Dough stage
Mature grain
3. Agronomic performance
a. a. Yield and yield components
Yield
Grain yield
Biomass
Yield components
Panicles per plant
Grains per panicle
1000 grain weight
Spikelets per panicle
Seed set percentage
Grains per plant
Harvest index (the ratio of grain dry weight to whole plant dry weight)
b. Resistance to biotic stress
i. Diseases:
Leaf blast (LB)
Panicle blast (PB)
Brown spot (BS)
Narrow brown leaf spot (NBLS)
Bacterial leaf streak (BLS)
Leaf scald (LSc)
Bacterial blight (BB)
Rice disease caused by viruses and mycoplasma-like organism (MLO)
Rice tungro disease (RTD)
Rice grassy stunt 1 and 2 disease (RGSV1 and RGSV2)
Rice ragged stunt disease
Yellow dwarf (YD)
Rice yellow mottle (RYMV)
Rice hoja blanca (RHBV)
Sheath blight (ShB)
Sheath rot (ShR)
Grain discoloration (Gd)
False smut (FSm)
Kernel smut (KSm)
Udbatta disease (Udb)
Bakanae disease (Bak)
Stem rot (SR)
Ufra (U)
ii. Insects:
Brown planthopper (BPH)
Green leafhopper (GLH)
Whitebacked planthopper (WBPH)
Rice delphacid (RDel)
Stem borers (SB)
Leaffolder (LF)
Gall midge (GM)
Caseworm (CW)
Rice whorl maggot (RWM)
Rice bug (RB)
Thrips
iii. Weeds
iv. Rats
v. Birds
c. Resistance to abiotic stress
Alkali injury (Alk) and salt injury (Sal)
Drought sensitivity (DRS)
Deepwater tolerance
Elongation (Elon)
submergence tolerance (Sub)
Kneeling ability (KnA)
Cold tolerance (Ctol)
Heat tolerance (Htol)
Nutrient deficiency and ion toxicity
iron toxicity (FeTox)
Phosphorus def (Pdef)
Zinc def (Zdef)
Lodging incidence X
d. Fertility, sterility and heterosis Spikelet fertility
Spikelet sterility
Pollen sterility
e. Heterosis
Male sterility
Male sterility group
Cytoplasmic-nuclear interaction type
Thermosensitive-genic type (TGMS)
Photoperiod-sensitive genic type (PGMS)
Thermo-photoperiod genic type (TPGMS)
Genetically engineered (transgenic) type
Nuclear type
Degree of male sterility
Completely sterile
Highly sterile
Sterile
Partially sterile
Partially fertile to fertile
Abortion pattern
Pollen free
Abortion at uni-nucleate stage of pollen
Abortion at binucleate stage of pollen
Abortion at trinucleate stage of pollen
Abortion at later stage and pollen looks like a fertile pollen
e. Grain Quality:
Endosperm type
Chalkiness of endosperm
Brown rice length
Brown rice shape (length-width ratio)
100-grain weight
Seed coat color
Scent AROMA
Amylose content of the grain (Amy)
Alkali digestion
Gel consistency (GelC)
PROTEIN CONTENT
OIL CONTENT
f. Maturity
Flowering date
Maturity date
g. Plant height
h. Seedling
Seedling height
Seedling vigor
4. Related gene and QTLs IN RICE.
5. Linkage map information:
Allele
Chromosome number
Location on chromosome (cM) [SAME PROBLEM NOTED AS ON PREVIOUS DOCUMENT REGARDING LINKING MORPHOLOGICAL MUTANTS TO THE HIGH RESOLUTION GENETIC/PHYSICAL MAP IN GRAMENE. WE NEED TO DISCUSS IN SOME DEPTH HOW TO DO THIS]
CloseLY linked marker(s)
6. Sequence information if any.
ALLELES
FUNCTIONAL NUCLEOTIDE POLYMORPHISM(S)
7. Comparative map information, including related mutants, traits, genes in maize, sorghum, wheat, etc.
Grasses (EVIDENCE)
Other sources (EVIDENCE)
8. Germplasm information (genetic stocks).
Name (GENUS, SPECIES, CULTIVAR)
ACCESSION (GERMPLASM COLLECTION AND ACCESSION #)
Related wild type
SUB-SPECIES Group (EVIDENCE- THIS IS VERY IMPORTANT HERE)
Indica
Japonica
Javanica
Intermediate
Wild relative
Others
9. Mutagenesis
Mutant type
Spontaneous mutant
Induced mutant
Chemical agent
Incorporation of base analogs
5-bromouracil (5-BU)
2-aminopurine (2-AP)
Specific mispairing
Ethyl methanesulfonate (EMS)
Nitrosoguanidine (NG)
Hyfroxylamine (HA)
HydrazineBisulfite ions
Nitrous acid (NA)
Proflavin
Acridine orange
ICR-191
Loss of specific pairing
Aflatoxin B1 (AFB1)
Benzo(a) pyrene
Physical
Ultraviolet(UV)
X-rays
(-rays
Cosmic rays
Electron ((-prticle)
Positron (positive (-prticle)
Proton (nucleus of common isotope of hydrogen)
Deuteron (nucleus of heavy isotope of hydrogen)
( (nucleus of helium)
Neutron
Molecular biological methods
Mutagenesis of regulatory regions
BAL 31 (Digestion)
Uni- directional deletion mutations at specific sits
bi-directional deletion mutations at specific sits
Exonuclease III (Generate nested deletion by digestion)
Linker-scanning mutagenesis
Exonuclease III
Oligonucleotide ligation
PCR
Mutagenesis of coding sequences
Random mutagenesis
Chemical mutagenesis
Cassette mutagenesis
Misincorporation mutagenesis
Spiked Oligonucleotide Primers
Alanine-scanning mutagenesis
Site-directed mutagenesis (mutagenic oligonucleotides)
Conventional site-directed mutagenesis
PCR site-directed mutagenesis
10. References:
Title
Author
Journal
Resources on line
11. Other information
6/26/01
5:22 PM
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