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

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.

Figure 1

Distribution of Cys (a), Met (b) and (c) Cys + Met content (g/kg of total protein) in the seed of 137 Canadian soybean lines.

Figure 2

(a) Classification into seven populations using fastSTRUCTURE where each individual (from 1 to 137) is represented by a single vertical line and each color represents one cluster. (b) Bootstrap consensus phylogenetic tree (2000 replicates) constructed using MEGA 7; each color represents a subgroup and seven subgroups were found in total and (c) PCA eigenvalues computed using GAPIT.

Figure 3

Manhattan plots for (a) Cys, (b) Met, and (c) Cys + Met content in a core set of 137 Canadian soybean accessions using MLM.

Figure 4

Total number of significant SNPs detected using six multi-locus methods.

Figure 5

Degree of significance (p-value) of the contrast between phenotypic means for lines carrying different alleles at candidate QTLs for sulfur-containing amino acid content in whole soybean seeds. Cys, Met, and Cys + Met content was measured in a core set of 137 Canadian soybean accessions in three environments (indicated by coloured symbols). A t-test was performed to compare the mean trait value for lines sharing one or the other allele at the nine QTLs discovered in the MLM method. Each coloured symbol represents the p-value for this comparison of means. The red horizontal bar indicates the adjusted Bonferroni significance threshold at alpha ≤  − log10(0.05/8 QTLs) for Cys, alpha ≤  − log10(0.05/4 QTLs) for Met and alpha ≤  − log10(0.05/7 QTLs) for Cys + Met content.

Figure 6

Identification of candidate genes within the haplotype block codetected by both MLM and the multi-locus methods (QTL #9 and QTN #17) on chromosome 20.

Figure 7

Expression profile of Glyma.20g129700 based on previous transcriptomic analysis in soybeans. Expression strength coded by color: yellow = low, red = high. As shown, Glyma.20g129700 is most highly expressed in flowers, pods, roots, pod shells and in the seed. Data derived from RNA-seq of Glycine max, published by Severin et al. and download from eFP browser (www.bar.utoronto.ca).