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

Patil, Gunvant and Vuong, T D and Kale, S M and Valliyodan, B and Deshmukh, R and Zhu, C and Wu, X and Bai, Y and Yungbluth, D and Lu, F and Kumpatla, S and Shannon, J G and Varshney, R K and Nguyen, H T (2018) Dissecting genomic hotspots underlying seed protein, oil, and sucrose content in an interspecific mapping population of soybean using high-density linkage mapping. Plant Biotechnology Journal (TSI). pp. 1-15. ISSN 14677644

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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 inter-specific 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 0.3x depth. Based on 91,342 single nucleotide polymorphisms (SNPs), recombination events in RILs were defined, and a high-resolution bin map was developed (4,070 bins). In addition to bin mapping, QTL analysis for protein, oil and sucrose was performed using 3,343 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 Kb to 50 Kb). A total of 5, 9 and 4 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 was mapped on Chr. 20 (qPro_20) and suggested negative correlation between oil and protein. In terms of sucrose content, a novel and major QTL was identified on Chr. 8 (qSuc_08) and harbors putative genes involved in sugar transport. In addition, genome-wide association (GWAS) 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.

Item Type: Article
Divisions: Research Program : Genetic Gains
Uncontrolled Keywords: soybean (Glycine max), seed composition traits, genomic hotspot, bin map, whole‐genome resequencing, quantitative trait loci, genomic‐wide association study
Subjects: Others > Food Legumes
Others > Genetics and Genomics
Others > Legume Crops
Depositing User: Mr Ramesh K
Date Deposited: 16 Apr 2018 09:27
Last Modified: 06 Aug 2018 08:23
URI: http://oar.icrisat.org/id/eprint/10577
Official URL: http://dx.doi.org/10.1111/pbi.12929
Acknowledgement: 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
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