Identification of Loci and Candidate Genes Analyses for Tocopherol Concentration of Soybean Seed.

Meinan Sui,Hongkun Zheng,Jian Luo,Yan Jing,Lijuan Qiu,Weili Teng,Xue Zhao,Haiyan Li,Yingpeng Han,Wenbin Li,Yuhang Zhan

doi:10.3389/fpls.2020.539460

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.

Highlights

Soybean (Glycine max (L.) Merr.) is a major crop for oil and food
Of the recombinant inbred lines (RILs) population, these concentrations varied over a wide range with averages of 68.95, TABLE 1 | Basic genetic parameter statistics for tocopherol in the tested soybean population (n =180)
The results showed that the expression levels of Glyma.02G099800, Glyma.02G100800 and Glyma.02G102900 in pods were significantly correlated with total Toc content or its components, and Glyma.02G101300 showed no significant correlation with Toc content (Table S7)

Summary

Introduction

Soybean (Glycine max (L.) Merr.) is a major crop for oil and food. Soybean oil accounts for 30% of vegetable oil consumption. Tocopherols (Tocs) are extracted with soybean oil during seed processing. Toc concentrations account only 1.5% of the total oil, but they are important for providing oxidative stability (Tavva et al, 2007). The biological activities of four individual Tocs vary with the number and position of methyl groups on the chromanol ring (Bramley et al, 2000). The proportion of a-Toc is usually less than 10% of the total Toc in soybean seeds (Park et al, 2019). The biological activities of Toc that were synthesized by chemical account for only 50% of the natural a-Toc (Dwiyanti et al, 2007). Increasing a-Toc proportion and total Toc concentration of soybean seeds is important for soybean breeding programs

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