Public Data Files

Next Generation Sequencing

Accession NumberData infoLiteraturePaper LinkLink to Data
SoyKB_Public_Dataset_001_2013-07-08 Magellan_x_PI438489B_GBS Xu X, Zeng L, Tao Y, Vuong T, Wan J, Boerma R, Noe J, Li Z, Finnerty S, Pathan SM, Shannon JG, Nguyen HT
Pinpointing genes underlying the quantitative trait loci for root-knot nematode resistance in palaeopolyploid soybean by whole genome resequencing.
Proc Natl Acad Sci U S A. 2013 Aug 13;110(33):13469-74. doi: 10.1073/pnas.1222368110. Epub 2013 Jul 29.


SNP

Data Conditions Sample Name Reference Genome Literature Paper Link Link to Data
41 NAM parentsRef
IA3023
J105_3_4
M20_2_5_2
CL0J095_4_6
CL0J173_6_8
HS6_3976
LD00_3309
LD01_5907
LD02_4485
LD02_9050
LG00_3372
LG03_2979
LG03_3191
LG04_4717
LG04_6000
LG05_4292
LG05_4317
LG05_4464
LG05_4832
LG90_2550
LG92_1255
LG94_1128
LG94_1906
LG97_7012
LG98_1605
MAGELLAN
MAVERICK
NE3001
PI398881
PI404188A
PI427136
PI437169B
PI507681B
PI518751
PI561370
PI574486
PROHIO
S06_13640
SKYLLA
TN05_3027
U03_100612
Bilyeu Lab (unpublished)
GWAS
(32 genomes from BGI)
Wild and Cultivated SoybeanLam HM, Xu X, Liu X, Chen W, Yang G, Wong FL, Li MW, He W, Qin N, Wang B, Li J, Jian M, Wang J, Shao G, Wang J, Sun SS, Zhang G. Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nat Genet. 2010 Dec;42(12):1053-9. Epub 2010 Nov 14.
G.SojaRefer Base
Consensus Base
Kim MY, Lee S, Van K, Kim TH, Jeong SC, Choi IY, Kim DS, Lee YS, Park D, Ma J, Kim WY, Kim BC, Park S, Lee KA, Kim DH, Kim KH, Shin JH, Jang YE, Kim KD, Liu WX, Chaisan T, Kang YJ, Lee YH, Kim KH, Moon JK, Schmutz J, Jackson SA, Bhak J, Lee SH. Whole-genome sequencing and intensive analysis of the undomesticated soybean (Glycine soja Sieb. and Zucc.) genome.Proc Natl Acad Sci U S A. 2010 Dec 21;107(51):22032-7. Epub 2010 Dec 3.
SoySNP50KClick to view sample namesSong Q, Hyten DL, Jia G, Quigley CV, Fickus EW, Nelson RL, et al. (2013) Development and Evaluation of SoySNP50K, a High-Density Genotyping Array for Soybean. PLoS ONE 8(1): e54985. https://doi.org/10.1371/journal.pone.0054985
MSMCClick to view sample namesValliyodan, Babu & Nguyen, Henry. (2006). Valliyodan, B. & Nguyen, H. T. Understanding regulatory networks and engineering for enhanced drought tolerance in plants. Curr. Opin. Plant Biol. 9, 189-195. Current opinion in plant biology. 9. 189-95. 10.1016/j.pbi.2006.01.019.
USB-15x
USB-40x
Zhou302v1Wm82.a1Zhou, Z., Jiang, Y., Wang, Z. et al. Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean. Nat Biotechnol 33, 408–414 (2015). https://doi.org/10.1038/nbt.3096
Zhou302v2Click to view sample namesWm82.a2Zhou, Z., Jiang, Y., Wang, Z. et al. Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean. Nat Biotechnol 33, 408–414 (2015). https://doi.org/10.1038/nbt.3096
USB481Click to view sample namesWm82.a2
Soy775Click to view sample namesWm82.a2
Soy1066Click to view sample namesWm82.a2