Glycine max
The Williams82 soybean cultivar was sequenced in 2006 by the DOE-JGI Community Sequencing Program (CSP), and the soybean genome was completed in 2010 [2]. In 2015, the new assembly (Wm82.a2.v1) was finished [3]. The Wm82.a2.v1 contains the following data:
● Number of Chromosomes: 20
● Number of Unplaced Scaffolds: 1170
● Number of Protein-coding Genes: 56044
● Number of transcripts: 88674
● 2014 - Anderson JE et al. 40 genetically diverse soybean lines.[5]
● 2014 - Chung WH et al. 15 wild and cultivated accessions.[6]
● 2014 - Cook DE et al. 3 cultivated accessions.[7]
● 2014 - Qiu J et al. 11 wild and semi-wild accessions.[8]
● 2015 - Zhou et al. 302 wild and cultivated accessions.[9]
● 2016 - Valliyodan B et al. 104 wild, landraces, and elite lines.[10]
● 2016 - Maldonado dos Santos JV et al. 28 Brazilian soybean cultivars.[11]
● 2017 - Chao Fang et al. 569 landraces and cultivars.[12]
● 2020 - Yucheng Liu et al. 2053 wild and cultivated lines.[13]
● 2020 - Sijia Lu et al. 85 wild soybeans, 153 landraces and 186 improved cultivars. [14]
● 2020 - Cong Li et al. A diverse soybean landrace panel consisting of 279 accessions. [15]
● 2021 - Hiromi Kajiya-Kanegae et al. 170 accessions from Japanese and world soybean mini-core collections. [16]
● 2021 - Myung-Shin Kim et al. 855 soybean individuals which includes domesticated, wild, and natural hybrid (G. max/G. soja) accessions. [17]
● 2022 - Philipp E Bayer et al. 990 wild and cultivated lines.[18]
● 2022 - Huilong Hong et al. 1674 soybean improved cultivars and landraces from Asia, America, Europe and Africa.[19]
● 2022 - Chunming Yang et al. 250 soybean landraces and cultivars from China, America, and Europe.[20]
● 2022 - Jiao Wang et al. 181 diverse wild soybean accessions collected from three major agro-ecological zones in China.[21]
● 2022 - Guang Yang et al. 372 wild and cultivated lines.[22]
[1] Li YH, Zhao SC, Ma JX, Li D, Yan L, Li J, Qi XT, Guo XS, Zhang L, He WM, Chang RZ, Liang QS, Guo Y, Ye C, Wang XB, Tao Y, Guan RX, Wang JY, Liu YL, Jin LG, Zhang XQ, Liu ZX, Zhang LJ, Chen J, Wang KJ, Nielsen R, Li RQ, Chen PY, Li WB, Reif JC, Purugganan M, Wang J, Zhang MC, Qiu LJ: Molecular footprints of domestication and improvement in soybean revealed by whole genome re-sequencing. BMC Genomics, 14:579. [PMID=23984715]
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[3] Song Q, Jenkins J, Jia G, Hyten DL, Pantalone V, Jackson SA, Schmutz J, Cregan PB: Construction of high resolution genetic linkage maps to improve the soybean genome sequence assembly Glyma1.01. BMC Genomics, 17:33. [PMID=26739042]
[4] 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. Nature genetics 2010, 42(12):1053-1059.[PMID=21076406]
[5] Anderson JE, Kantar MB, Kono TY, Fu F, Stec AO, Song Q, Cregan PB, Specht JE, Diers BW, Cannon SB, McHale LK, Stupar RM: A roadmap for functional structural variants in the soybean genome. G3 (Bethesda, Md) 2014, 4(7):1307-1318.[PMID=24855315]
[6] Chung WH, Jeong N,Kim J, Lee WK, Lee YG, Lee SH, Yoon W, Kim JH, Choi IY, Choi HK, Moon JK, Kim N, Jeong SC: Population structure and domestication revealed by high-depth resequencing of Korean cultivated and wild soybean genomes. DNA research : an international journal for rapid publication of reports on genes and genomes 2014, 21(2):153-167. [PMID=24271940]
[7] Cook DE, Bayless AM, Wang K, Guo X, Song Q, Jiang J, Bent AF: Distinct Copy Number, Coding Sequence, and Locus Methylation Patterns Underlie Rhg1-Mediated Soybean Resistance to Soybean Cyst Nematode. Plant physiology 2014, 165(2):630-647. [PMID=24733883]
[8] Qiu J, Wang Y, Wu S, Wang YY, Ye CY, Bai X, Li Z, Yan C, Wang W, Wang Z, Shu Q, Xie J, Lee, SH, Fan L: Genome re-sequencing of semi-wild soybean reveals a complex Soja population structure and deep introgression. PloS one 2014, 9(9):e108479. [PMID=25265539]
[9] Zhou Z, Jiang Y, Wang Z, Gou Z, Lyu J, Li W, Yu Y, Shu L, Zhao Y, Ma Y, Fang C, Shen Y, Liu T, Li C, Li Q, Wu M, Wang M, Wu Y, Dong Y, Wan W, Wang X, Ding Z, Gao Y, Xiang H, Zhu B, Lee SH, Wang W, Tian Z: Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean. Nat Biotechnol 2015, 33(4):408-414.[PMID=25643055]
[10] Valliyodan B, Dan Q, Patil G, Zeng P, Huang J, Dai L, Chen C, Li Y, Joshi T, Song L, Vuong TD, Musket TA, Xu D, Shannon JG, Shifeng C, Liu X, Nguyen HT: Landscape of genomic diversity and trait discovery in soybean. Sci Rep 2016, 6:23598.[PMID=27029319]
[11] Maldonado dos Santos JV, Valliyodan B, Joshi T, Khan SM, Liu Y, Wang J, Vuong TD, de Oliveira MF, Marcelino-Guimarães FC, Xu D, Nguyen HT, Abdelnoor RV: Evaluation of genetic variation among Brazilian soybean cultivars through genome resequencing. BMC genomics 2016, 17:110.[PMID=26872939]
[12] Fang C, Ma Y, Wu S,Liu Z, Wang Z, Yang R, Hu G, Zhou Z, Yu H, Zhang M, Pan Y, Zhou G, Ren H, Du W, Yan H, Wang Y, Han D, Shen Y, Liu S, Liu T, Zhang J, Qin H, Yuan J, Yuan X, Kong F, Liu B, Li J, Zhang Z, Wang G, Zhu B, Tian Z: Genome-wide association studies dissect the genetic networks underlying agronomical traits in soybean. Genome biology 2017, 18(1):161.[PMID=28838319]
[13] Liu Y, Du H, Li P,Shen Y, Peng H, Liu S, Zhou GA, Zhang H, Liu Z, Shi M, Huang X, Li Y, Zhang M, Wang Z, Zhu B, Han B, Liang C, Tian Z: Pan-Genome of Wild and Cultivated Soybeans. Cell 2020, 182(1):162-176.e113. [PMID=32553274]
[14]Lu S, Dong L, Fang C, Liu S, Kong L, Cheng Q, Chen L, Su T, Nan H, Zhang D, Zhang L, Wang Z, Yang Y, Yu D, Liu X, Yang Q, Lin X, Tang Y, Zhao X, Yang X, Tian C, Xie Q, Li X, Yuan X, Tian Z, Liu B, Weller JL, Kong F: Stepwise selection on homeologous PRR genes controlling flowering and maturity during soybean domestication. Nature genetics 2020, 52(4):428-436. [PMID=32231277]
[15] Li C, Li YH, Li Y, Lu H, Hong H, Tian Y, Li H, Zhao T, Zhou X, Liu J, Zhou X, Jackson SA, Liu B, Qiu LJ: A Domestication-Associated Gene GmPRR3b Regulates the Circadian Clock and Flowering Time in Soybean. Molecular plant 2020, 13(5):745-759. [PMID=32017998]
[16] Kajiya-Kanegae H,Nagasaki H, Kaga A, Hirano K, Ogiso-Tanaka E, Matsuoka M, Ishimori M, Ishimoto M, Hashiguchi M, Tanaka H, Akashi R, Isobe S, Iwata H: Whole-genome sequence diversity and association analysis of 198 soybean accessions in mini-core collections. DNA research : an international journal for rapid publication of reports on genes and genomes 2021, 28(1). [PMID=33492369]
[17] Kim MS, Lozano R, Kim JH, Bae DN, Kim ST, Park JH, Choi MS, Kim J, Ok HC, Park SK, Gore MA, Moon JK, Jeong SC: The patterns of deleterious mutations during the domestication of soybean. Nature communications 2021, 12(1):97. [PMID=33397978]
[18] Bayer PE, Valliyodan B, Hu H, Marsh JI, Yuan Y, Vuong TD, Patil G, Song Q, Batley J, Varshney RK, Lam HM, Edwards D, Nguyen HT: Sequencing the USDA core soybean collection reveals gene loss during domestication and breeding. The plant genome 2022, 15(1):e20109.[PMID=34169673]
[19] Hong H, Li M, Chen Y, Wang H, Wang J, Guo B, Gao H, Ren H, Yuan M, Han Y, Qiu L: Genome-wide association studies for soybean epicotyl length in two environments using 3VmrMLM. Frontiers in plant science 2022, 13:1033120.[PMID=36452100]
[20] Yang C, Yan J,Jiang S, Li X, Min H, Wang X, Hao D: Resequencing 250 Soybean Accessions: New Insights into Genes Associated with Agronomic Traits and Genetic Networks. Genomics, proteomics & bioinformatics 2022, 20(1):29-41.[PMID=34314874]
[21] Wang J, Hu Z, Liao X, Wang Z, Li W, Zhang P, Cheng H, Wang Q, Bhat JA, Wang H, Liu B, Zhang H, Huang F, Yu D: Whole-genome resequencing reveals signature of local adaptation and divergence in wild soybean. Evolutionary applications 2022,15(11):1820-1833. [ PMID=36426120]
[22] Yang G, Li W, Fan C, Liu M, Liu J, Liang W, Wang L, Di S, Fang C, Li H, Ding G, Bi Y, Lai Y: Genome-wide association study uncovers major genetic loci associated with flowering time in response to active accumulated temperature in wild soybean population. BMC genomics 2022, 23(1):749. [PMID=36368932]