Variance heterogeneity genome-wide mapping for cadmium in bread wheat reveals novel genomic loci and epistatic interactions

Authors

Waseem Hussain, University of Nebraska-LincolnFollow
Malachy T. Campbell, Virginia Polytechnic Institute and State UniversityFollow
Diego Jarquin, University of Nebraska-LincolnFollow
Harkamal Walia, University of Nebraska-LincolnFollow
Gota Morota, Virginia Polytechnic Institute and State University, BlacksburgFollow

ORCID IDs

Waseem Hussain https://orcid.org/0000-0002-6861-0193

Malachy T. Campbell https://orcid.org/0000-0002-8257-3595

Gota Morota https://orcid.org/0000-0002-3567-6911

Document Type

Article

Date of this Version

4-11-2020

Citation

Plant Genome. 2020;13:e20011.

doi:10.1002/tpg2.20011

Comments

This is an open access article under the terms of the Creative Commons Attribution License. © 2020 The Authors.

Abstract

Genome-wide association mapping identifies quantitative trait loci (QTL) that influence the mean differences between the marker genotypes for a given trait. While most loci influence the mean value of a trait, certain loci, known as variance heterogeneity QTL (vQTL) determine the variability of the trait instead of the mean trait value (mQTL). In the present study, we performed a variance heterogeneity genome-wide association study (vGWAS) for grain cadmium (Cd) concentration in bread wheat. We used double generalized linear model and hierarchical generalized linear model to identify vQTL associated with grain Cd. We identified novel vQTL regions on chromosomes 2A and 2B that contribute to the Cd variation and loci that affect both mean and variance heterogeneity (mvQTL) on chromosome 5A. In addition, our results demonstrated the presence of epistatic interactions between vQTL and mvQTL, which could explain variance heterogeneity. Overall, we provide novel insights into the genetic architecture of grain Cd concentration and report the first application of vGWAS in wheat. Moreover, our findings indicated that epistasis is an important mechanism underlying natural variation for grain Cd concentration.