Genetic dissection of domestication-related traits in soybean through genotyping-by-sequencing of two interspecific mapping populations
- 162 Downloads
A total of 132 domestication-related QTLs, of which 41 were novel, were identified through genotyping-by-sequencing of two Glycine max × Glycine soja populations.
Soybean [Glycine max (L.) Merr.] was domesticated in East Asia from the wild progenitor Glycine soja. The domestication process led to many distinct morphological changes that adapt it to cultivation. These include larger seeds, erect growth, larger stem diameter, reduced pod shattering, and altered growth habit. The objective of this study was to identify QTLs controlling key domestication-related traits (DRTs) using interspecific mapping populations. A total of 151 RILs from Williams 82 × PI 468916 and 510 RILs from Williams 82 × PI 479752 were utilized for QTL mapping. These lines were genotyped using a genotyping-by-sequencing protocol which resulted in approximately 5000 polymorphic SNP markers. The number of QTLs detected for each of the eleven DRTs ranged between 0–4 QTLs in the smaller Williams 82 × PI 468916 population and 3–16 QTLs in the larger Williams 82 × PI 479752 population. A total of 132 QTLs were detected, of which 51 are associated with selective sweeps previously related to soybean domestication. These QTLs were detected across all 20 chromosomes within 42 genomic regions. This study identifies 41 novel QTLs not detected in previous studies using smaller populations while also confirming the quantitative nature for several of the important DRTs in soybeans. These results would enable more effective use of the wild germplasm for soybean improvement.
Funding for this work was from the North Central Soybean Research Program (FY17–18) and Indiana Soybean Alliance of the United States (FY17–18).
Compliance with ethical standards
Conflict of interest
On behalf of all authors, the corresponding authors state that there is no conflict of interest.
The data that support the findings of this study are shown in Supplementary Data.
- Beavis WD (1998) QTL analyses: power, precision, and accuracy. In: Paterson AH (ed) Molecular dissection of complex traits. CRC Press, Boca Raton, pp 145–162Google Scholar
- Bernard RL (1975) The inheritance of appressed pubescence. Soybean Genet Newsl 2:34–36Google Scholar
- Carter TE, Nelson RL, Sneller CH, Cui Z (2004) Genetic diversity in soybean. In: Boerma HR, Specht JE (eds) Soybeans: improvement, production, and uses. American Society of Agronomy, Madison, pp 303–416Google Scholar
- Palmer RG, Pfeiffer TW, Buss GR, Kilen TC (2004) Qualitative genetics. In: Boerma HR, Specht JE (eds) Soybeans: improvement, production, and uses, 3rd edn. American Society of Agronomy, Madison, pp 137–233Google Scholar
- R Core Team (2014) R: A language and environment for statistical computing. R Foundation for Statistical Computing, ViennaGoogle Scholar
- Song Q, Hyten DL, Jia G, Quigley CV, Fickus EW, Nelson RL, Cregan PB (2013) Development and evaluation of SoySNP50K, a high-density genotyping array for soybean. PLoS ONE 8(1):1–12Google Scholar
- Swarts K, Li H, Romero Navarro JA, An D, Romay MC, Hearne S, Acharya C, Glaubitz JC, Mitchell S, Elshire RJ, Buckler ES, Bradbury PJ (2014) Novel methods to optimize genotypic imputation for low-coverage, next-generation sequence data in crop plants. Plant Genome. https://doi.org/10.18637/jss.v069.i01 CrossRefGoogle Scholar
- Xia Z, Watanabe S, Yamada T, Tsubokura Y, Nakashima H, Zhai H, Anai T, Sato S, Yamazaki T, Lu S, Wu H, Tabata S, Harada K (2012) Positional cloning and characterization reveal the molecular basis for soybean maturity locus E1 that regulates photoperiodic flowering. Proc Natl Acad Sci 109(32):E2155–E2164CrossRefGoogle Scholar
- 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 (2015) Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean. Nat Biotechnol 33(4):408–414CrossRefGoogle Scholar