Simulation of QTL by sequencing for agronomic quantitative trait loci detection in small to medium population size in soybean

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Quantitative Trait Loci by sequencing (QTL-seq) is a QTL detection method that utilizes the principles of Bulked Segregants Analysis. It detects alleles with extreme frequencies in whole-genome sequence data from two bulked populations with contrasting phenotypes. This approach is less laborious than QTL detection using linkage mapping, and the result had been shown to be comparable in the same mapping population. However, since the genomes of the two bulked populations are completely sequenced, it can facilitate further characterization of the QTL segment and the genes underlying the QTLs. In this study, QTLseq was simulated using high-density SNP genotyping data from a recombinant inbred population consisting of 188 individuals. The genomes of both parents had been sequenced, and the SNP genotyping identified 2,207 SNP markers that were polymorphic and segregating in the population. Since the markers are dense enough and well distributed across the genome, they can be used to represent the alleles that can be obtained from whole genome resequencing of bulked individuals. The availability of genotype data for each individual in the mapping population also enabled the detection of QTL via linkage mapping. Using data generated from both approaches, various simulations were conducted to compare the results that could be obtained under ideal conditions, as well as less ideal ones such as when the QTL effects are small, the presence of skewed phenotype distribution, and a small number of bulked samples..
SNP genotyping, quantitative trait locus detection, QTL-seq, whole-genome resequencing.