Data for a mapping population
Susan McCouch
srm4 at cornell.edu
Thu Jan 30 11:58:03 EST 2003
Hi Adam,
It was nice to catch site of you at PAGXI, however briefly.
Thank you very much for this communication about the mapping data
from your drought QTL work on the Bala x Azucena population. We are
currently altering our data models and database schema to be able to
store and provide access to raw mapping data files.
Do you still have the raw data that was used to map the QTLs? If so,
we are interested in offering it a home within Gramene. If you agree
to donate that data, it would be one of the first submissions of raw
marker and phenotype data to a public database. We aim to establish
collaborations with authors of QTL papers so that they can help
annotate their work for submission to our database in the future. We
have only begun to develop the process that will facilite this kind
of relationship, but we would be interested in working with you to
improve and streamline a mechanism for:
a) submission of raw data
b) author-based extraction of information from your published work to
be integrated into Gramene
c) final quality-check on curated information that you have donated,
once the Gramene curators have made all the internal and external
links required for full functionality to query the information you
have donated.
Please let us know if you are interested in working with us on these
points, and if you have the original, raw mapping scores for both
markers and phenotypes (in each environment), please let us know if
you are willing to make those public.
We are very happy to hear from you and look forward to working with
you to get your data integrated into our database.
Best regards,
Susan
>Dear Gramene,
>
>Contained below this email and as a Word attachment are details of
>mapping data on the Bala x Azucena mapping population of rice that I
>have been using for QTL mapping drought traits. I email it to you
>in the hope that it might be interesting for you to include it in
>the web site. Please let me know if it is interesting, if you will
>use it, if you need it in another format or if there is other
>information regarding the population tht would be useful.
>
>Yours sincerely,
>
>
>Adam Price
>
>------------------------------------------------
>The mapping population is an F6 recombinant inbred population
>derived from a cross between rice (Oryza sativa) varieties Bala and
>Azucena. 205 lines were evaluated, using a LOD threshold of 3.0. The
>map now contains 102 (RGP and Cornell) RFLP, 35 AFLP and 17
>microsatellites markers. The original version of the map was
>published in Price et al. (2000) TAG 100:49-56 (2000). To date the
>population has been used to identify QTLs for root penetration
>ability (Price et al. 2000, TAG 100:49-56), root morphological
>traits (Price et al. 2002, Field Crops Research 76: 25-43) and
>drought avoidance in the field (Price et al. 2002 Plant Molecular
>Biology 48: 683-695).
>
>The map as produced in mapmaker is given below. Note:
>1/ Here are presented the distance between markers (3rd column) and
>the distance from the top of the chromosome.
>2/ Chromosome 12 is split into two linkage groups (12t and 12b).
>3/ AFLP markers are named by the EcoR1 primer (e.g. E12) followed by
>the Mse primer (e.g. M36) followed by a full stop and a number
>representing the order of the polymorphic bands from the top of the
>gel; e.g. E18M43.7 was the 7th polymorphic band from the top of the
>gel using the EcoR1 primer 18 and Mse primer 43.
>4/ Two gaps exceed the 40 cM threshold (on chromosomes 2 and 6) but
>these markers are linked due to reasonably high LOD scores and known
>marker positions.
>
>=====================================================================
>c1 framework:
>
> Markers Distance
> 23 RG532 28.4 0
> 8 RG173 8 28.4
> 37 RZ995 11.1 36.4
> 160 E18M43.7 12.3 47.5
> 159 E18M43.6 7.6 59.8
> 146 E12M45.4 1.9 67.4
> 45 C178 22 69.3
> 249 RM5 2.7 91.3
> 106 R2635 33.5 94
> 239 RM246 14.9 127.5
> 63 C1370 6.8 142.4
> 81 G393 1.4 149.2
> 105 R2417 23.8 150.6
> 241 RM212 23.6 174.4
> 43 C86 19.3 198
> 60 C949 0.7 217.3
> 30 RZ14 32.8 218
> 90 R117 ---------- 250.8
> 250.5 cM 18 markers log-likelihood= -597.94
>
>
>c2 framework:
>
> Markers Distance
> 21 RG509 20.1 0
> 3 RG83 34.4 20.1
> 7 RG171 42.5 54.5
> 68 G45 18.9 97
> 161 E18M43.8 16.4 115.9
> 66 G39 0 132.3
> 5 RG139 3.2 132.3
> 254 RM221 5.3 135.5
> 69 G57 11.4 140.8
> 250 RM6 5 152.2
> 54 C601 35.7 157.2
> 13 RG256 ---------- 192.9
> 192.8 cM 12 markers log-likelihood= -432.44
>
>c3 framework:
>
> Markers Distance
> 132 E12M37.4 26.5 0
> 56 C643 2.7 26.5
> 19 RG409 11.7 29.2
> 11 RG191 33.1 40.9
> 143 E12M45.1 18 74
> 28 RG745 10 92
> 118 E12M36.10 5.1 102
> 75 G144 12.2 107.1
> 125 E12M36.16 22.6 119.3
> 34 RZ474 14.1 141.9
> 44 C136 32.9 156
> 101 R1618 25.5 188.9
> 76 G164 ---------- 214.4
> 214.6 cM 13 markers log-likelihood= -525.89
>
>c4 framework:
>
> Markers Distance
> 169 E18M43.17 14.6 0
> 10 RG190 12 14.6
> 58 C734 6.7 26.6
> 20 RG449 37 33.3
> 53 C513 13.6 70.3
> 235 RM252 10.7 83.9
> 6 RG163 39 94.6
> 61 C1016 5.3 133.6
> 237 RM349 1.3 138.9
> 236 RM348 13.2 140.2
> 26 RG620 ---------- 153.4
> 153.5 cM 11 log-likelihood= -400.88
>
>c5 framework:
>
> Markers Distance
> 33 RZ390 30.1 0
> 104 R2232 14.9 30.1
> 93 R569 28.3 45
> 2 RG13 17.3 73.3
> 55 C624 12 90.6
> 41 C43 13 102.6
> 31 RZ70 14.8 115.6
> 251 RM26 24.1 130.4
> 4 RG119 5.3 154.5
> 16 RG346 ---------- 159.8
> 159.8 cM 10 log-likelihood= -426.4
>
>c6 framework:
>
> Markers Distance
> 42 C76 2.4 0
> 35 RZ516 30.1 2.4
> 110 E12M36.1 12.0 32.5
> 12 RG213 7.3 44.5
> 248 MRG6488 41.9 51.8
> 127 E12M36.18 8.4 93.7
> 107 R2654 26.3 102.1
> 135 E12M37.7 4.0 128.4
> 134 E12M37.6 1.6 132.4
> 29 RG778 3.4 134.0
> 36 RZ682 ----------
> 137.4 cM 11 markers log-likelihood= -360.56
>
>c7 framework:
>
> Markers Distance
> 62 C1057 17.8 0
> 247 L538T7 26.7 17.8
> 218 E12M39.11 6.5 44.5
> 79 G338 4 51
> 40 C39 5.8 55
> 71 G89b 4.4 60.8
> 100 R1440 2.4 65.2
> 64 G20 22.3 67.6
> 50 C451 22.9 89.9
> 99 R1357 19 112.8
> 27 RG650 18.9 131.8
> 238 RM234 14.5 150.7
> 52 C507 14.5 165.2
> 142 E12M37.14 2.5 179.7
> 120 E12M36.12 3.8 182.2
> 17 RG351 ---------- 186
> 185.9 cM 16 markers log-likelihood= -531.39
>
>c8 framework:
>
> Markers Distance
> 97 R902 15.4 0
> 116 E12M36.7 7.1 15.4
> 83 G1010b 6.6 22.5
> 48 C225 1.7 29.1
> 138 E12M37.10 2.6 30.8
> 156 E18M43.4 11.3 33.4
> 88 G2132 11.7 44.7
> 84 G1073 19.7 56.4
> 77 G187 2 76.1
> 108 R2676 13.4 78.1
> 91 R202 20.4 91.5
> 25 RG598 2.5 111.9
> 96 R662 ---------- 114.4
> 114.2 cM 13 markers log-likelihood= -380.4
>
>c9 framework:
>
> Markers Distance
> 98 R1164 8.6 0
> 102 R1687 19.2 8.6
> 89 R79 26.2 27.8
> 80 G385 9.7 54
> 209 E12M39.1 5.4 63.7
> 246 RM242 15.3 69.1
> 181 E18M43.26 21.5 84.4
> 122 E12M36.13 3.2 105.9
> 86 G1085 4.1 109.1
> 180 E18M43.25 5.4 113.2
> 113 E12M36.4 17.2 118.6
> 51 C506 ---------- 135.8
> 136 cM 12 log-likelihood= -406.24
>
>c10 framework:
>
> Markers Distance
> 57 C701 7.9 0
> 73 G89d 33.8 7.9
> 14 RG257 16.1 41.7
> 130 E12M37.2 9.2 57.8
> 85 G1082 40.4 67
> 39 C16 35.7 107.4
> 47 C223 ---------- 143.1
> 143.2 cM 7 log-likelihood= -321.71
>
>c11 framework:
>
> Markers Distance
> 95 R642 26.1 0
> 32 RZ141 11.5 26.1
> 175 E18M43.z 5.1 37.6
> 111 E12M36.2 3.5 42.7
> 78 G320 8.8 46.2
> 230 E15M35.14 2.5 55
> 67 G44 2.7 57.5
> 124 E12M36.15 3.8 60.2
> 149 E12M45.y 10.5 64
> 255 RM229 0 74.5
> 1 RG2 20.1 74.5
> 253 RM206 2.8 94.6
> 46 C189 10.2 97.4
> 115 E12M36.6 5.4 107.6
> 87 G1465 5.7 113
> 140 E12M37.12 ---------- 118.7
> 118.9 cM 16 markers log-likelihood= -439.99
>
>c12t framework:
>
> Markers Distance
> 244 RM20A 4.9 0
> 65 G24 9.4 4.9
> 38 CDO127 6.7 14.3
> 141 E12M37.13 4 21
> 240 RM247 4.9 25
> 74 G124 ---------- 29.9
> 30 cM 6 markers log-likelihood= -183.87
>
>c12b framework:
>
> Markers Distance
> 94 R617 3.7 0
> 15 RG341 3.7 3.7
> 123 E12M36.14 8.6 7.4
> 103 R1933 9.9 16
> 49 C449 19.5 25.9
> 24 RG543 28.9 45.4
> 9 RG181 0 74.3
> 59 C901 ---------- 74.3
> 74.4 cM 8 markers log-likelihood= -257.02
>
>
>Attachment converted: Macintosh HD:Bala x Azucena.doc (WDBN/MSWD) (0003D642)
>
>------------
>Adam Price
>Lecturer in Plant Molecular Genetics
>School of Biological Sciences
>(Department of Plant and Soil Science)
>University of Aberdeen
>Aberdeen AB24 3UU, UK
>Tel; 01224 272690 Fax; 01224 272703
>e.mail a.price at abdn.ac.uk
--
******************************************
Susan McCouch
Dept of Plant Breeding
418 Bradfield Hall
Cornell University
Ithaca, NY 14853-1901
Phone: 607-255-0420
Fax: 607-255-6683
E-Mail: srm4 at cornell.edu
******************************************
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