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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #365676
Research Project: Database Tools for Managing and Analyzing Big Data Sets to Enhance Small Grains Breeding

Location: Plant, Soil and Nutrition Research

Title: A Low resolution epistasis mapping approach to identify chromosome arm interactions in allohexaploid wheat

Author
item SANTANTONIA, NICHOLAS - Cornell University
item Jannink, Jean-Luc
item SORRELS, MARK - Cornell University

Submitted to: Genes, Genomes, Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/5/2018
Publication Date: 11/19/2018
Citation: Santantonia, N., Jannink, J., Sorrels, M. 2018. A Low resolution epistasis mapping approach to identify chromosome arm interactions in allohexaploid wheat. Genes, Genomes, Genetics. 9:675-684. https://doi.org/10.25387/g3.7311797.
DOI: https://doi.org/10.25387/g3.7311797

Interpretive Summary: Besides their direct effects, genes may affect crop performance through their interactions with other genes. These interactions are difficult to detect. We developed a method to look for interactions not between pairs of genes but between pairs of chromosome arms. We tested this method in wheat. Interactions across evolutionarily-related chromosome arms were identified, but were less abundant than other chromosome arm pair interactions. We showed that are method is robust and may help identify underlying interacting genes, making their selection possible.

Technical Abstract: Epistasis is an important contributor to genetic variance. In inbred populations, pairwise epistasis is present as additive by additive interactions. Testing for epistasis presents a multiple testing problem as the pairwise search space for modest numbers of markers is large. Single markers do not necessarily track functional units of interacting chromatin as well as haplotype based methods do. To harness the power of multiple markers while minimizing the number of tests conducted, we present a low resolution test for epistatic interactions across whole chromosome arms. Epistasis covariance matrices were constructed from the additive covariances of individual chromosome arms. These covariances were subsequently used to estimate an epistatic variance parameter while correcting for background additive and epistatic effects. We find significant epistasis for 2% of the interactions tested for four agronomic traits in a winter wheat breeding population. Interactions across homeologous chromosome arms were identified, but were less abundant than other chromosome arm pair interactions. The homeologous chromosome arm pair 4BL/4DL showed a strong negative relationship between additive and interaction effects that may be indicative of functional redundancy. Several chromosome arms appeared to act as hubs in an interaction network, suggesting that they may contain important regulatory factors. The differential patterns of epistasis across different traits demonstrate that detection of epistatic interactions is robust when correcting for background additive and epistatic effects in the population. The low resolution epistasis mapping method presented here identifies important epistatic interactions with a limited number of statistical tests at the cost of low precision.