Genome-wide association identifies several QTLs controlling cysteine and methionine content in soybean seed including some promising candidate genes

Sidiki Malle,Malcolm Morrison,François Belzile,Milad Eskandari

doi:10.1038/s41598-020-78907-w

Sidiki Malle, Malcolm Morrison + Show 2 more

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https://doi.org/10.1038/s41598-020-78907-w

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Abstract

Soybean is an important source of protein, oil and carbohydrates, as well as other beneficial nutrients. A major function of proteins in nutrition is to supply adequate amounts of amino acids. Although they are essential for human nutrition, the sulfur-containing amino acids cysteine (Cys) and methionine (Met) are often limited and the genetic control of their content in soybean seeds is poorly characterized. This study aimed to characterize the phenotypic variation and identify quantitative trait loci (QTL) associated with Cys and Met content in a core set of 137 soybean lines, representative of the genetic diversity among Canadian short-season soybean, spanning maturity groups 000-II (MG000-II). Significant phenotypic differences were found among these lines for Cys, Met and Cys + Met content. Using both a mixed linear model and six multi-locus methods with a catalogue of 2.18 M SNPs, we report a total of nine QTLs and seventeen QTNs of which seven comprise promising candidate genes. This work allowed us to reproducibly detect multiple novel loci associated with sulfur-containing amino acid content. The markers and genes identified in this study may be useful for soybean genetic improvement aiming to increase Cys and Met content.

Highlights

Soybean is an important source of protein, oil and carbohydrates, as well as other beneficial nutrients
Fallen et al.[14] detected two quantitative trait loci (QTL) on chromosomes (Gm13 and 20) associated with both Cys and Met content in progeny of Essex x Williams 82 (282 F 5:9 recombinant inbred lines (RILs)). All these QTLs were reported as a result of QTL mapping in biparental populations and resulted in a poor overlap between the QTLs/QTNs reported in these studies
It can be seen that the amino acid content varied from 13.5 to 15.0 g/kg on total protein basis (TP) for Cys and from 12.6 to 13.6 g/kg TP for Met

Summary

Introduction

Soybean is an important source of protein, oil and carbohydrates, as well as other beneficial nutrients. A major function of proteins in nutrition is to supply adequate amounts of amino acids They are essential for human nutrition, the sulfur-containing amino acids cysteine (Cys) and methionine (Met) are often limited and the genetic control of their content in soybean seeds is poorly characterized. Synteny between 113 genes from a gene mining of sulfur-containing amino acid metabolic enzymes in soybean These authors identified many QTLs related to the 7S (β-conglycinin), 11S (glycinin) fractions and Cys/ Met content soybean on chromosomes 1, 3, 4, 6, 10, 13, 16, 17, 19 and 20. Fallen et al.[14] detected two QTLs on chromosomes (Gm13 and 20) associated with both Cys and Met content in progeny of Essex x Williams 82 (282 F 5:9 RILs) All these QTLs were reported as a result of QTL mapping in biparental populations and resulted in a poor overlap between the QTLs/QTNs reported in these studies. The major limitation of this approach is that they offer poor resolution in detecting Q TLs15 and the large confidence intervals surrounding the detected QTLs limits their utility for identifying candidate g enes[16]

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