Identification of Loci and Candidate Genes Analyses for Tocopherol Concentration of Soybean Seed - PubMed (original) (raw)
Identification of Loci and Candidate Genes Analyses for Tocopherol Concentration of Soybean Seed
Meinan Sui et al. Front Plant Sci. 2020.
Abstract
Tocopherol (Toc) occurs in soybean seeds and is extracted together with the soybean oil. Toc is utilized as an antioxidant in food and an additive in animal feed. A total of 180 representative accessions and 144 recombinant inbred lines (RILs) from the cross of 'Hefeng 25' and 'OAC Bayfield' were selected to evaluate individuals and total Toc concentrations in soybean seeds. The 180 soybean samples were sequenced by the approach of Specific Locus Amplified Fragment Sequencing (SLAF-seq). A total of 22,611 single nucleotide polymorphisms (SNPs) were developed. Nineteen quantitative trait nucleotides (QTNs) were identified associated with individual or total-Toc based on genome-wide association analysis (GWAS). Among them, three QTNs located near known QTLs, and 16 were novel. Eighteen QTLs and nine eQTLs were also detected by linkage mapping. The QTN rs9337368 on Chr.02 was colocalized according to the linkage mapping of the RILs and genome-wide association analysis and regarded as a stable locus for mining the candidate genes in association with Toc. A total of 42 candidate genes near the 200 kbp flanking region of this identified locus were found. Upon a gene-based association, 11 SNPs from five genes out of the 42 candidates were detected. Expression level analysis of five candidate genes revealed that two genes were significantly related to Toc content. The identified loci, along with the candidate genes, might be valuable for increasing the Toc concentration in soybean seeds and improving the nutritional value of soybean oil.
Keywords: candidate genes; genome-wide association analysis; linkage mapping; soybean seed; tocopherol concentration.
Copyright © 2020 Sui, Jing, Li, Zhan, Luo, Teng, Qiu, Zheng, Li, Zhao and Han.
Figures
Figure 1
Distribution of tocopherol content among 180 soybean accessions in four tested environments.
Figure 2
SNP density and distribution across the 20 soybean chromosomes.
Figure 3
Summary of eQTL and QTL locations detected in the soybean genome.
Figure 4
The linkage disequilibrium (LD), principal component, and kinship analyses of soybean genetic data. (A) The linkage disequilibrium (LD) decay of genome-wide association study (GWAS) population. (B) The first three principal components of the more than 20,000 SNPs used in the GWAS. (C) Population structure of soybean germplasm collection as reflected by principal components. (D) A heatmap of the kinship matrix of the 180 soybean accessions calculated from the same SNPs.
Figure 5
Candidate gene-based association. Gene-based association analysis of candidate genes with SNPs that were significantly correlated to tocopherol content. Horizontal line indicated that the threshold was set to 2.0.
Figure 6
Haplotypes analysis of genes that related to tocopherol content. The * and ** was significance at p < 0.05 and p < 0.01, respectively.
Figure 7
Tocopherol content of 16 germplasms at R7 growth period. “High” represent the higher accessions (Line 1–Line 8), “Low” represent the lower accessions (Line 9–Line 16).
Figure 8
Expression levels of candidate genes in 16 soybean germplasms at R7 growth period.
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