Abstract
Soybean provides abundant dietary proteins for humans and livestock. However, the low content of sulfur-containing amino acids [SAA, including methionine (Met) and cysteine (Cys)] in soybean protein limits the quality and prevents it from becoming an ideal food and feed ingredient. Thus, the exploration of novel high-SAA soybean germplasm and identification of related genes is necessary. In this study, a genome-wide association study (GWAS) was conducted for Cys, Met and SAA in 165 soybean materials genotyped with a high-density SNP array. A total of 138 significant SNPs associated with three traits were identified. Moreover, one SNP on chromosome 7 was identified in three environments. Glyma.07g175700 and Glyma.07g176000 at the LD of AX-94036794 were considered candidate genes. Quantitative real-time PCR showed that different expression levels of these genes were observed in high-SAA and low-SAA material, which suggested that these two genes may be involved in SAA synthesis. These results will help to increase our understanding of the genetic mechanisms of SAA and improve nutritional quality through molecular marker-assisted selection breeding in soybeans.
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Abbreviations
- SAA:
-
Sulfur-containing amino acids
- Cys:
-
Cysteine
- Met:
-
Methionine
- QTL:
-
Quantitative trait locus/loci
- SNP:
-
Single nucleotide polymorphism
- GWAS:
-
Genome-wide association study
- MAS:
-
Marker-assisted selection
- RIL:
-
Recombinant inbred lines
- EMS:
-
Ethyl methanesulfonate
- MAF:
-
Minor allele frequency
- GLM:
-
General linear model
- LD:
-
Linkage disequilibrium
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Acknowledgements
This work was supported in part by Ministry of Science and Technology (2016YFD0100504, 2017YFE0111000), Natural Science Foundation of Jiangsu Provence (BK20191313), National Natural Science Foundation of China (31671715) and the Fundamental Research Funds for the Central Universities (KYZ201705).
Funding
Author Deyue Yu received Funding from Ministry of Science and Technology Grant 2016YFD0100504 and Grant 2017YFE0111000. Author Hui Wang received Funding from National Natural Science Foundation of China Grant 31671715. Author Guizhen Kan received Funding from Fundamental Research Funds for the Central Universities Grant KYZ201705 and Natural Science Foundation of Jiangsu Provence BK20191313.
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This study was designed by GK and DY. WY conducted the experiments, including phenotypic data evaluation, GWAS analysis. WY wrote this manuscript. ZW extracted RNA. ZW, YZ, RY, and HW carried out the qRT-PCR analysis. DY and GK revised the manuscript. All authors read and approved the final version to be published.
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Supplementary Figure 1
Boxplot of Cys, Met, and SAA content for Subpopulation I and Subpopulation II. This shows the average of the measurements over 3 years (TIF 7782 kb)
Supplementary Figure 2
Manhattan plots of the GWAS with the general linear model (GLM) plus the Q (population structure) model in BLUP. The blue horizontal threshold line is used to distinguish significant SNPs (− log10 P > 6.09). (a) SNPs associated with Cys; (b) SNPs associated with Met; (c) SNPs associated with SAA (TIF 64302 kb)
Supplementary Table 1
The significant SNP identified in three environments (XLSX 16 kb)
Supplementary Table 2
Genes detected in the 1Mb flanking region of the significant SNP AX-94036794 (XLSX 10 kb)
Supplementary Table 3
The homologous genes of Glyma.07g175700 in other plant genes’ Information (XLSX 9 kb)
Supplementary Table 4
The homologous genes of Glyma.07g176000 in other plant genes’ information (XLSX 9 kb)
Supplementary Table 5
The expression patterns of 21 genes in RNA-Seq data (XLSX 10 kb)
Supplementary Table 6
The sequences of primers using for tissue expression (XLSX 8 kb)
Supplementary Table 7
The information for 165 accessions (XLSX 12 kb)
Supplementary Table 8
Average value of phenotypic data for 165 accessions in three environments (XLSX 23 kb)
Supplementary Table 9
The significant SNP identified in BLUP (XLSX 26 kb)
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Yuan, W., Wu, Z., Zhang, Y. et al. Genome-wide association studies for sulfur-containing amino acids in soybean seeds. Euphytica 217, 155 (2021). https://doi.org/10.1007/s10681-021-02888-8
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DOI: https://doi.org/10.1007/s10681-021-02888-8