Genetic analysis carried out in population tails reveals diverse two-loci interactions as a basic factor of quantitative traits variation in rye

Abstract

Bidirectional selective genotyping carried out independently for five quantitative traits within a biparental population of recombinant inbred lines of rye has revealed dramatic changes in alleles distribution in the population tails. A given allele, predominant in the lower tail, is often neutral for reversely directed selection or associates with the upper tail following divergent selection for a related trait. Such radical changes in the alleles distribution cannot be explained by differences in genotypic values within a single locus. This paper presents the theoretical model of a genetic mechanism underlying observed responses of individual loci to divergent selection. The presented model refers to the specific interactions between alleles at two loci. Its wider application in genetic analysis will open up new possibilities for testing positions of genes in the hierarchical structure of interacting loci revealed under selection pressure.

QTL mapping for benzoxazinoid content, preharvest sprouting, α-amylase activity, and leaf rust resistance in rye (Secale cereale L.)

“…This is a common conclusion from many QTL studies based on the whole mapping populations where phenotypic differences between lines are most often small and prone to environmental factors. This problem is overcome in bidirectional selective genotyping (BSG) studies where only extreme phenotypes, derived through divergent selection and much more independent of environmental changes, are analyzed [ 22 – 24 ]. These studies show that the individual effects of QTL are usually low, but their impact on the trait due to their interactions with other QTL may be substantial.…”

A complex network of QTL for thousand-kernel weight in the rye genome

“…Distributions of genotypic values for two-loci homozygous genotypes representing particular pairs of QTL (Tables 4,5,6,7,and 8,Fig. 3) corresponded to those described in the model of two-loci interactions (Masojć et al 2016). Individual QTL were involved in various types of two-loci interactions.…”

“…Differences between genotypic values of the two double homozygotes lower than 5% (below a 4.5% threshold) were assumed to be insignificant or ineffective for divergent selection. Distribution of significant and insignificant genotypic differences between four double homozygotes was related to the type of two-loci interaction and alleles distribution in selected subpopulations, as shown in the model (Masojć et al 2016). An additive relationship between two QTL (D-D type of interaction) was declared when significant allelic effects found at individual loci were also detectable on the level of two-loci genotypes (genotypic differences above a 4.5% threshold).…”

“…This hypothesis is based on frequent detection of QTL representing R and E classes showing alleles-trait association only in one of the two population tails (i.e., that representing desirable phenotype (R class loci) or the opposite, gathering lines of negative characteristics (E class locus)). As shown in a recently developed genetic model (Masojć et al 2016), QTL of R and E classes reflect epistatic interaction with QTL of class D (directional), revealing alleles-trait association within both Communicated by: Izabela Pawłowicz Electronic supplementary material The online version of this article (https://doi.org/10.1007/s13353-020-00559-3) contains supplementary material, which is available to authorized users. population tails.…”

“…population tails. The method of QTL classification is known as genes interaction assorting by divergent selection (GIABDS) (Masojć et al 2016) and represents further development of bidirectional selective genotyping (BSG), used by many authors for QTL identification (Gallais et al 2007;Navabi et al 2009;Sun et al 2010;Farkhari et al 2013;Myśków and Stojałowski 2016). Both methods apply the divergent selection to generate two subpopulations with contrasting phenotypes and look for significant differences in allele frequencies to disclose QTL.…”