Homeologous epistasis in wheat: the search for an immortal hybrid

Authors: SANTANTONIO, NICHOLAS - Cornell University; Jannink, Jean-Luc; SORRELS, MARK - Cornell University

Submitted to: Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/16/2019
Publication Date: 1/23/2019
Citation: Santantonio, N., Jannink, J., Sorrels, M. 2019. Homeologous epistasis in wheat: the search for an immortal hybrid. Genetics. 211:1105-1122. https://doi.org/10.25386/genetics.6913253.
DOI: https://doi.org/10.25386/genetics.6913253

Interpretive Summary: Hybridization between related species can result in the formation of a new species with multiple subgenomes. Genes in these subgenomes may interact, and it would then be possible to fix favorable interactions through breeding. We developed a model to estimate interaction between evolutionarily related genes and a statistical framework to determine their importance within a population. We showed that interactions between evolutionarily-related genes explain a portion of the interaction signal, but are less important than interactions between non-related genes.

Technical Abstract: Hybridization between related species results in the formation of an allopolyploid with multiple subgenomes. These subgenomes will each contain complete, yet evolutionarily divergent, sets of genes. Like a diploid hybrid, allopolyploids will have two versions, or homeoalleles, for every gene. Partial functional redundancy between homeologous genes should result in a deviation from additivity. These epistatic interactions between homeoalleles are analogous to dominance effects, but are fixed across subgenomes through self pollination. An allopolyploid can be viewed as an immortalized hybrid, with the opportunity to select and fix favorable homeoallelic interactions within inbred varieties. We present a subfunctionalization epistasis model to estimate the degree of functional redundancy between homeoallelic loci and a statistical framework to determine their importance within a population. We provide an example using the homeologous dwarfing genes of allohexaploid wheat, Rht-1, and search for genome-wide patterns indicative of homeoallelic subfunctionalization in a breeding population. Using the IWGSC RefSeq v1.0 sequence, 23,796 homeoallelic gene sets were identified and anchored to the nearest DNA marker to form 10,172 homeologous marker sets. Interaction predictors constructed from products of marker scores were used to fit the homeologous main and interaction effects, as well as estimate whole genome genetic values. Some traits displayed a pattern indicative of homeoallelic subfunctionalization, while other traits showed a less clear pattern or were not affected. Using genomic prediction accuracy to evaluate importance of marker interactions, we show that homeologous interactions explain a portion of the nonadditive genetic signal, but are less important than other epistatic interactions.