Biology subjects

Tessele, A.

Publications and source records attributed to Tessele, A..

2 recordsLinked to original sources

bioRxiv2025

Interchromosomal Linkage Disequilibrium Analysis Reveals Strong Indications of Sign Epistasis in Wheat Breeding Families

Additive gene action is assumed to underly quantitative traits, but the eventual poor performance of elite wheat lines as parents suggests that epistasis could be the underlying genetic architecture. Sign epistasis is characterized by alleles having either a beneficial or detrimental effect depending on the genetic background, which can result in elite lines that fail as parents in certain parental combinations. Hence, the objective of this study were to test the existence of sign epistasis and examine its consequences to wheat breeding. The presence of sign epistasis is expected to distort the allele frequency distribution between two interacting genes compared to neutral sites, creating strong linkage disequilibrium (LD). To test this hypothesis, analysis of interchromosomal LD in breeding families was performed and detected 19 regions in strong disequilibrium, whose allele frequency distribution matched the sign epistasis prediction and falsified the competing hypothesis of additive selection. To validate these candidate interactions while avoiding the biases of a circular analysis and the confounding effects of genetic drift, two independent sets of populations were analyzed. Genetic drift was attributed to creating the sign epistasis patterns observed in eleven interactions, but there was not sufficient evidence to reject the sign epistasis hypothesis in eight interactions. Sign epistasis may explain the poor performance of elite lines as parents, as crossing lines with complementary allelic combination re-establishes epistatic variance in the offspring. Reduction in the effective population size in certain crosses may also occur when unfavorable sign epistatic combinations are deleterious. The potential existence of di-genic and higher order epistatic interactions in elite germplasm can tremendously impact breeding strategies as managing epistasis becomes imperative for success.

genetics↗

bioRxiv2024

Improving genomic selection in hexaploid wheat with sub-genome additive and epistatic models

The goal of wheat breeding is the development of superior cultivars tailored to specific environments, and the identification of promising crosses is crucial for the success of breeding programs. Although genomic estimated breeding values were developed to estimate additive effects of genotypes before testing as parents, application has focused on predicting performance of candidate lines, ignoring non-additive genetic effects. However, non-additive genetic effects are hypothesized to be especially importance in allopolyploid species due to the interaction between homeologous genes. The objectives of this study were to model additive and additive-by-additive epistatic effects to better delineate the genetic architecture of grain yield in wheat and to the improve accuracy of genomewide predictions. The dataset utilized consisted of 3740 F5:6 experimental lines tested in the K-State wheat breeding program across the years 2016 and 2018. Covariance matrices were calculated based on whole and sub-genome marker data and the natural and orthogonal interaction approach (NOIA) was used to estimate variance components for additive and additive-by-additive epistatic effects. Incorporating epistatic effects in additive models resulted in non-orthogonal partitioning of genetic effects but increased total genetic variance and reduced deviance information criteria. Estimation of sub-genome effects indicated that genotypes with the greatest whole genome effects often combine sub-genomes with intermediate to high effects, suggesting potential for crossing parental lines which have complementary sub-genome effects. Modeling epistasis in either whole-genome or sub-genome models led to a marginal (3%) but significant improvement in genomic prediction accuracy, which could result in significant genetic gains across multiple cycles of breeding.

genetics↗