Theoretical and Applied Genetics

, Volume 132, Issue 4, pp 1195–1209 | Cite as

Genetic dissection of domestication-related traits in soybean through genotyping-by-sequencing of two interspecific mapping populations

  • Stephen A. Swarm
  • Lianjun Sun
  • Xutong Wang
  • Weidong Wang
  • Patrick J. Brown
  • Jianxin MaEmail author
  • Randall L. NelsonEmail author
Original Article


Key message

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.

Data availability

The data that support the findings of this study are shown in Supplementary Data.

Supplementary material

122_2018_3272_MOESM1_ESM.pdf (600 kb)
Supplementary Fig. S1 Discrimination of RILs into the Williams 82 × PI 468916 population (‘PI468916’) and Williams 82 × PI 479752 (‘PI479752’) based on 35,303 SNPs and five SSR markers. The first two principal components are plotted for each RIL and colored according to the k-means cluster analysis. The number of RILs classified into each group is indicated in parentheses. (PDF 600 kb)
122_2018_3272_MOESM2_ESM.pdf (349 kb)
Supplementary Fig. S2 Genetic distance (cM) versus physical distance (Mb based on Wm82.a2.v1) in WP468 (green), WP479 (red), and the combined populations (blue). (PDF 349 kb)
122_2018_3272_MOESM3_ESM.pdf (2.9 mb)
Supplementary Fig. S3 Matrix of scatter plots of phenotypic traits (upper panel) and Pearson correlations (lower panel, with p-values in blue). Density distributions are given on the diagonal. aFirst flowering (days after planting); bmaturity date (days after May 31); cstem diameter (mm); dmain stem length (cm); eshattering (1 to 6 rating); fgrowth habit (1 to 5 rating); glodging (1 to 9 rating); g100-seed weight (g); hleaflet size (1 to 5 rating); ileaflet shape (1 to 3 rating). (PDF 3002 kb)
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Supplementary material 4 (XLSX 70 kb)
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Supplementary material 5 (XLSX 24 kb)
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Supplementary material 8 (XLSX 19 kb)


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Copyright information

© This is a U.S. government work and its text is not subject to copyright protection in the United States; however, its text may be subject to foreign copyright protection 2019

Authors and Affiliations

  1. 1.Department of Crop SciencesUniversity of Illinois at Urbana–ChampaignUrbanaUSA
  2. 2.Department of Agronomy and Center for Plant BiologyPurdue UniversityWest LafayetteUSA
  3. 3.Soybean/Maize Germplasm, Pathology, and Genetics Research UnitUS Department of Agriculture-Agricultural Research ServiceUrbanaUSA
  4. 4.Beck’s Superior HybridsAtlantaUSA
  5. 5.College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
  6. 6.Department of Plant SciencesUniversity of California, DavisDavisUSA

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