Linkage disequilibrium, SNP frequency change due to selection, and association mapping in popcorn chromosome regions containing QTLs for quality traits.

Geísa Pinheiro Paes,Fabyano Fonseca E Silva,Gabriel Borges Mundim,José Marcelo Soriano Viana

doi:10.1590/1678-4685-gmb-2015-0126

Geísa Pinheiro Paes, Fabyano Fonseca E Silva + Show 2 more

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https://doi.org/10.1590/1678-4685-gmb-2015-0126

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Abstract

The objectives of this study were to assess linkage disequilibrium (LD) and selection-induced changes in single nucleotide polymorphism (SNP) frequency, and to perform association mapping in popcorn chromosome regions containing quantitative trait loci (QTLs) for quality traits. Seven tropical and two temperate popcorn populations were genotyped for 96 SNPs chosen in chromosome regions containing QTLs for quality traits. The populations were phenotyped for expansion volume, 100-kernel weight, kernel sphericity, and kernel density. The LD statistics were the difference between the observed and expected haplotype frequencies (D), the proportion of D relative to the expected maximum value in the population, and the square of the correlation between the values of alleles at two loci. Association mapping was based on least squares and Bayesian approaches. In the tropical populations, D-values greater than 0.10 were observed for SNPs separated by 100-150 Mb, while most of the D-values in the temperate populations were less than 0.05. Selection for expansion volume indirectly led to increase in LD values, population differentiation, and significant changes in SNP frequency. Some associations were observed for expansion volume and the other quality traits. The candidate genes are involved with starch, storage protein, lipid, and cell wall polysaccharides synthesis.

Highlights

Selection for expansion volume indirectly led to increase in Linkage disequilibrium (LD) values, population differentiation, and significant changes in single nucleotide polymorphism (SNP) frequency
Linkage disequilibrium (LD) or gametic phase disequilibrium is the difference between haplotype frequency products (P(AB).P(ab) – P(Ab).P(aB)) (Kempthorne, 1957)
Because this difference corresponds to the covariance between values of alleles at two loci (Weir, 2008), LD is commonly defined as the non-random association of alleles at different loci

Summary

Introduction

Linkage disequilibrium (LD) or gametic phase disequilibrium is the difference between haplotype frequency products (P(AB).P(ab) – P(Ab).P(aB)) (Kempthorne, 1957). Because this difference corresponds to the covariance between values of alleles at two loci (Weir, 2008), LD is commonly defined as the non-random association of alleles at different loci. With respect to biallelic markers, the most common statistics to measure LD in a population are the difference between the observed and expected (under linkage equilibrium) haplotype frequencies (D), the proportion of D relative to the expected maximum value in the population (D’), and the square of the correlation between the values of alleles at two loci (r2) (Flint-Garcia et al., 2003). Its main advantages relative to QTL mapping are the use of breeding population instead of population derived by crossing two inbred or pure lines and more precise identification of candidate genes (Flint-Garcia et al, 2005)

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