Dissecting genomic hotspots underlying seed protein, oil, and sucrose content in an interspecific mapping population of soybean using high-density linkage mapping

Gunvant Patil, Tri D. Vuong, Sandip Kale, Babu Valliyodan, Rupesh Deshmukh, Chengsong Zhu, Xiaolei Wu, Yonghe Bai, Dennis Yungbluth, Fang Lu, Siva Kumpatla, J. Grover Shannon, Rajeev K. Varshney, Henry T. Nguyen

Research output: Contribution to journalArticlepeer-review

70 Scopus citations


The cultivated [Glycine max (L) Merr.] and wild [Glycine soja Siebold & Zucc.] soybean species comprise wide variation in seed composition traits. Compared to wild soybean, cultivated soybean contains low protein, high oil, and high sucrose. In this study, an interspecific population was derived from a cross between G. max (Williams 82) and G. soja (PI 483460B). This recombinant inbred line (RIL) population of 188 lines was sequenced at 0.3× depth. Based on 91 342 single nucleotide polymorphisms (SNPs), recombination events in RILs were defined, and a high-resolution bin map was developed (4070 bins). In addition to bin mapping, quantitative trait loci (QTL) analysis for protein, oil, and sucrose was performed using 3343 polymorphic SNPs (3K-SNP), derived from Illumina Infinium BeadChip sequencing platform. The QTL regions from both platforms were compared, and a significant concordance was observed between bin and 3K-SNP markers. Importantly, the bin map derived from next-generation sequencing technology enhanced mapping resolution (from 1325 to 50 Kb). A total of five, nine, and four QTLs were identified for protein, oil, and sucrose content, respectively, and some of the QTLs coincided with soybean domestication-related genomic loci. The major QTL for protein and oil were mapped on Chr. 20 (qPro_20) and suggested negative correlation between oil and protein. In terms of sucrose content, a novel and major QTL were identified on Chr. 8 (qSuc_08) and harbours putative genes involved in sugar transport. In addition, genome-wide association using 91 342 SNPs confirmed the genomic loci derived from QTL mapping. A QTL-based haplotype using whole-genome resequencing of 106 diverse soybean lines identified unique allelic variation in wild soybean that could be utilized to widen the genetic base in cultivated soybean.

Original languageEnglish (US)
Pages (from-to)1939-1953
Number of pages15
JournalPlant Biotechnology Journal
Issue number11
StatePublished - Nov 2018

Bibliographical note

Funding Information:
The authors gratefully acknowledge the financial support for this study provided by United Soybean Board. The authors acknowledge Haiying Shi, Division of Plant Sciences, University of Missouri, for her technical assistance.

Publisher Copyright:
© 2018 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.


  • bin map
  • genomic hotspot
  • genomic-wide association study
  • quantitative trait loci
  • seed composition traits
  • soybean (Glycine max)
  • whole-genome resequencing


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