Genomic Selection and Genome-Wide Association Studies for Grain Protein Content Stability in a Nested Association Mapping Population of Wheat

Karansher S Sandhu,Michael O Pumphrey,Paul D Mihalyov,Arron H Carter,Megan J Lewien

doi:10.3390/agronomy11122528

Karansher S Sandhu, Michael O Pumphrey + Show 3 more

Open Access

https://doi.org/10.3390/agronomy11122528

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Abstract

Grain protein content (GPC) is controlled by complex genetic systems and their interactions and is an important quality determinant for hard spring wheat as it has a positive effect on bread and pasta quality. GPC is variable among genotypes and strongly influenced by the environment. Thus, understanding the genetic control of wheat GPC and identifying genotypes with improved stability is an important breeding goal. The objectives of this research were to identify genetic backgrounds with less variation for GPC across environments and identify quantitative trait loci (QTLs) controlling the stability of GPC. A spring wheat nested association mapping (NAM) population of 650 recombinant inbred lines (RIL) derived from 26 diverse founder parents crossed to one common parent, ‘Berkut’, was phenotyped over three years of field trials (2014–2016). Genomic selection models were developed and compared based on predictions of GPC and GPC stability. After observing variable genetic control of GPC within the NAM population, seven RIL families displaying reduced marker-by-environment interaction were selected based on a stability index derived from a Finlay–Wilkinson regression. A genome-wide association study identified eighteen significant QTLs for GPC stability with a Bonferroni-adjusted p-value < 0.05 using four different models and out of these eighteen QTLs eight were identified by two or more GWAS models simultaneously. This study also demonstrated that genome-wide prediction of GPC with ridge regression best linear unbiased estimates reached up to r = 0.69. Genomic selection can be used to apply selection pressure for GPC and improve genetic gain for GPC.

Highlights

Grain protein content (GPC) is a high-priority determinant of end-use quality for most cereals [1], including pasta (Triticum turgidum L.) and bread wheat (Triticum aestivum L.), for which higher GPC is preferred
The GPC values of the NAM population of 650 RILs (NAM650) population ranged from 11.2–18.0% in 2014, 8.7–16.8% in 2015, and 9.7–17.0% in 2016 (Figure 1), with 2014 having the highest mean GPC
Selection for GPC is often secondary to grain yield in terms of breeding objectives for spring wheat, it is a primary trait that producers consider when selecting varieties

Summary

Introduction

Grain protein content (GPC) is a high-priority determinant of end-use quality for most cereals [1], including pasta (Triticum turgidum L.) and bread wheat (Triticum aestivum L.), for which higher GPC is preferred. Improved understanding of genotypes and environmental interactions could provide new strategies for breeding crop varieties that stably perform between changing environments [7]. There are various approaches for measuring environmental stability, including the use of variance components of individuals across environments (represented by a coefficient of variation), the comparison of mean responses of genotypes to the overall mean of individuals in the trial (calculated as a coefficient of regression on an environment index) [9,10], and expected change in the performance of a genotype as a function of environmental effect [11]. Various biparental and association mapping studies have identified QTLs controlling GPC, but none of them has focused on the stability of GPC [14,15]

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