Abstract
Soybean is one of the world's major vegetative oil sources, while oleic acid and linolenic acid content are the major quality traits of soybean oil. The restricted two-stage multi-locus genome-wide association analysis (RTM-GWAS), characterized with error and false-positive control, has provided a potential approach for a relatively thorough detection of whole-genome QTL-alleles. The Chinese soybean landrace population (CSLRP) composed of 366 accessions was tested under four environments to identify the QTL-allele constitution of seed oil, oleic acid and linolenic acid content (SOC, OAC, and LAC). Using RTM-GWAS with 29,119 SNPLDBs (SNP linkage disequilibrium blocks) as genomic markers, 50, 98, and 50 QTLs with 136, 283, and 154 alleles (2–9 per locus) were detected, with their contribution 82.52, 90.31, and 83.86% to phenotypic variance, corresponding to their heritability 91.29, 90.97, and 90.24% for SOC, OAC, and LAC, respectively. The RTM-GWAS was shown to be more powerful and efficient than previous single-locus model GWAS procedures. For each trait, the detected QTL-alleles were organized into a QTL-allele matrix as the population genetic constitution. From which the genetic differentiation among 6 eco-populations was characterized as significant allele frequency differentiation on 28, 56, and 30 loci for the three traits, respectively. The QTL-allele matrices were also used for genomic selection for optimal crosses, which predicted transgressive potential up to 24.76, 40.30, and 2.37% for the respective traits, respectively. From the detected major QTLs, 38, 27, and 25 candidate genes were annotated for the respective traits, and two common QTL covering eight genes were identified for further study.
Highlights
To overcome these limitations, He et al (2017) proposed an innovative restricted two-stage multi-locus genomewide association study (GWAS) procedure (RTM-GWAS) for a relatively thorough detection of QTL and their multiple alleles in a germplasm population
That might be due to the enhancement of soybean improvement on seed oil traits in this region during the recent decades
RTM-GWAS is based on multi-allelic SNPs are grouped intoSNP linkage disequilibrium blocks (SNPLDBs) marker rather than bi-allelic SNP marker used by other GWAS methods
Summary
To overcome these limitations, He et al (2017) proposed an innovative restricted two-stage multi-locus GWAS procedure (RTM-GWAS) for a relatively thorough detection of QTL and their multiple alleles in a germplasm population. SNP linkage disequilibrium blocks (SNPLDBs) to form genomic markers with multiple haplotypes as alleles, and it utilizes two-stage association analysis based on a multi-locus multi-allele model for genome-wide QTL identification along with their multiple alleles. The RTMGWAS procedure has been applied to identify QTL-allele system of 100-seed weight (Zhang et al, 2015) and seed isoflavone content (Meng et al, 2016) in CSLRP. (2017) applied the RTM-GWAS procedure to a soybean nested association mapping population, and identified 139 flowering date QTLs with 496 alleles, which cover almost all QTLs detected by four other mapping procedures.
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