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

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.

High‐throughput NGS‐based genotyping and phenotyping: Role in genomics‐assisted breeding for soybean improvement

“…For example, Yu et al (2019) utilized the RAD‐seq approach and identified candidate gene underlying the major QTL regulating flooding tolerance in soybean. Similarly, many other studies have demonstrated NGS‐based genotyping mediated candidate gene identification such as nitrogen fixation (Torkamaneh et al, 2020), plant height and primary branches in soybean (Borah et al, 2018), agronomic traits (Sonah et al, 2015), disease resistance (Zhao et al, 2015), and protein content (Sui et al, 2020). The NGS‐based WGRS has considerably increased the power of bulk segregant analysis (BSA) and its modified approaches and is being widely used in many plant species including soybean.…”

Genetic mapping of loci involved in oil tocopherol composition control in Russian sunflower (Helianthus annuus L.) lines

“…Since altered tocopherol composition is of high interest for plant breeders, genetic loci associated with tocopherol composition control were mapped in most important oilseed crops including rapeseed, soybean, and sunflower ( Haddadi et al 2012 ; Wang et al 2012 ; Sui et al 2020 ). For sunflower, two major genes encoding MPBQ-MT and γ-TMT have been described, mutations in which may lead to altered tocopherol composition.…”

Identification of Genomic Loci and Candidate Genes Related to Seed Tocopherol Content in Soybean

“…Tocopherols are present in relatively high concentrations in soybeans. In soybean and other oilseed crop species, tocopherol is extracted together with oil [16] and contributes significantly to the oil quality. Tocopherol composition is inherited as a quantitative trait and thus can be genetically dissected [17].…”

“…Recent research has seen the frequent application of the BSA-seq technique in soybean genetic and molecular studies, with a suite of candidate genes currently available for molecular breeding of the crop. However, many previous studies involving candidate gene detection focused on the use of mutant libraries and segregating populations [16,19], with only a few reported works that targeted variations present in natural mapping populations [22]. Additionally, several previous reports on candidate gene identification in the crop have been designed to target plant shoot architecture-related traits, with only minimal work conducted on nutritional composition attributes.…”

“…The past few years have seen a growing research interest in mapping causal genes and discovering the genetic mechanisms conditioning nutritional composition traits in crops [1,2,6,30,31]. For instance, based on recombinant inbred lines (RILs), QTLs associated with VE composition in soybean have been identified in multiple locations [2,16]. For the present experimental investigation, we used a natural population of global soybean collections to construct two separate DNA pools for BSA-seq and detected some novel candidate genes associated with seed tocopherols in soybean.…”