Next Generation Sequencing
SNP
| Data Conditions | Sample Name | Reference Genome | Literature | Paper Link | Link to Data |
|---|---|---|---|---|---|
| Williams vs Forrest (7947) | Refer Base Consensus Base | Wu X, Ren C, Joshi T, Vuong T, Xu D, Nguyen HT. SNP discovery by high-throughput sequencing in soybean. BMC Genomics. 2010 Aug 11;11:469. | |||
| Magellan vs PI567516C | Refer Base Consensus Base | Nguyen Lab (unpublished) | |||
| 41 NAM parents | Ref 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PI427136 PI437169B PI507681B PI518751 PI561370 PI574486 PROHIO S06_13640 SKYLLA TN05_3027 U03_100612 | Bilyeu Lab (unpublished) | |||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 Soybean | Lam 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.Soja | Refer 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. | |||
| GBS Nguyen BGI 25Sample GATK | Ref C HN001 PI518664(Hutcheson) HN002 PI548402(Peking) HN003 PI089772 HN004 PI090763 HN005 PI404166 HN006 PI407788A HN007 PI424298 HN008 PI437655 HN009 PI495017C HN010 PI468915 HN011 PI507354 HN012 PI567305 HN013 S05-11482 HN014 PI548667 (Essex) HN015 PI437654 HN018 PI437690 HN019 PI548402 HN020 PI088788 HN021 PI209332 HN022 PI404198B HN023 PI424608A HN024 PI548316 HN026 PI612611 HN027 S10-11227 | ||||
| SoySNP50K | Click to view sample names | Song 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 | |||
| MSMC | Click to view sample names | Valliyodan, 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 | |||||
| Zhou302v1 | Wm82.a1 | Zhou, 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 | |||
| Zhou302v2 | Click to view sample names | Wm82.a2 | Zhou, 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 | ||
| USB481 | Click to view sample names | Wm82.a2 | |||
| Soy775 | Click to view sample names | Wm82.a2 | |||
| Soy1066 | Click to view sample names | Wm82.a2 | |||
| KB100 | Click to view sample names | Wm82.a2 |