Abstract
BackgroundBi-parental mapping populations have been commonly utilized to identify and characterize quantitative trait loci (QTL) controlling resistance to soybean cyst nematode (SCN, Heterodera glycines Ichinohe). Although this approach successfully mapped a large number of SCN resistance QTL, it captures only limited allelic diversity that exists in parental lines, and it also has limitations for genomic resolution. In this study, a genome-wide association study (GWAS) was performed using a diverse set of 553 soybean plant introductions (PIs) belonging to maturity groups from III to V to detect QTL/genes associated with SCN resistance to HG Type 0.ResultsOver 45,000 single nucleotide polymorphism (SNP) markers generated by the SoySNP50K iSelect BeadChip (http//www.soybase.org) were utilized for analysis. GWAS identified 14 loci distributed over different chromosomes comprising 60 SNPs significantly associated with SCN resistance. Results also confirmed six QTL that were previously mapped using bi-parental populations, including the rhg1 and Rhg4 loci. GWAS identified eight novel QTL, including QTL on chromosome 10, which we have previously mapped by using a bi-parental population. In addition to the known loci for four simple traits, such as seed coat color, flower color, pubescence color, and stem growth habit, two traits, like lodging and pod shattering, having moderately complex inheritance have been confirmed with great precision by GWAS.ConclusionsThe study showed that GWAS can be employed as an effective strategy for identifying complex traits in soybean and for narrowing GWAS-defined genomic regions, which facilitates positional cloning of the causal gene(s).Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1811-y) contains supplementary material, which is available to authorized users.
Highlights
Bi-parental mapping populations have been commonly utilized to identify and characterize quantitative trait loci (QTL) controlling resistance to soybean cyst nematode (SCN, Heterodera glycines Ichinohe). this approach successfully mapped a large number of SCN resistance QTL, it captures only limited allelic diversity that exists in parental lines, and it has limitations for genomic resolution
The objectives of the present study were (i) to conduct a genome-wide association study (GWAS) to detect novel QTL and to confirm the known QTL associated with resistance to SCN in the diverse panel of soybean germplasm accessions and, (ii) to identify candidate genes harbored in the causative genomic locations aiming to enhancing understanding molecular mechanism of SCN resistance and facilitating map-based cloning of the genes identified
24 genotypes showed a high level of resistance (FI
Summary
Bi-parental mapping populations have been commonly utilized to identify and characterize quantitative trait loci (QTL) controlling resistance to soybean cyst nematode (SCN, Heterodera glycines Ichinohe). This approach successfully mapped a large number of SCN resistance QTL, it captures only limited allelic diversity that exists in parental lines, and it has limitations for genomic resolution. A genome-wide association study (GWAS) was performed using a diverse set of 553 soybean plant introductions (PIs) belonging to maturity groups from III to V to detect QTL/genes associated with SCN resistance to HG Type 0. Soybean cyst nematode (SCN, Heterodera glycines Ichinohe) is one of the most devastating plant-parasitic nematode species causing severe annual soybean yield losses worldwide. Diers and Arelli [1] reported over 80 % of public cultivars released during the 1990s with SCN-resistance were derived from
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