Genomic Prediction and Genome-Wide Association Studies of Flour Yield and Alveograph Quality Traits Using Advanced Winter Wheat Breeding Material

Peter S Kristensen,Just Jensen,Carlos Guzmán,Ahmed Jahoor,Jeppe R Andersen,Jihad Orabi

doi:10.3390/genes10090669

Peter S Kristensen, Just Jensen + Show 4 more

Open Access

https://doi.org/10.3390/genes10090669

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Abstract

Use of genetic markers and genomic prediction might improve genetic gain for quality traits in wheat breeding programs. Here, flour yield and Alveograph quality traits were inspected in 635 F6 winter wheat breeding lines from two breeding cycles. Genome-wide association studies revealed single nucleotide polymorphisms (SNPs) on chromosome 5D significantly associated with flour yield, Alveograph P (dough tenacity), and Alveograph W (dough strength). Additionally, SNPs on chromosome 1D were associated with Alveograph P and W, SNPs on chromosome 1B were associated with Alveograph P, and SNPs on chromosome 4A were associated with Alveograph L (dough extensibility). Predictive abilities based on genomic best linear unbiased prediction (GBLUP) models ranged from 0.50 for flour yield to 0.79 for Alveograph W based on a leave-one-out cross-validation strategy. Predictive abilities were negatively affected by smaller training set sizes, lower genetic relationship between lines in training and validation sets, and by genotype–environment (G×E) interactions. Bayesian Power Lasso models and genomic feature models resulted in similar or slightly improved predictions compared to GBLUP models. SNPs with the largest effects can be used for screening large numbers of lines in early generations in breeding programs to select lines that potentially have good quality traits. In later generations, genomic predictions might be used for a more accurate selection of high quality wheat lines.

Highlights

Baking quality of wheat is a complex trait controlled by many genes with minor effects and few genes with larger effects [1,2]
Phenotypic variation was higher for the Alveograph traits than for flour yield (Table 1)
A dendrogram based on the G-matrix showed that the lines were genetically related both within and between sets (Figure 2)

Summary

Introduction

Baking quality of wheat is a complex trait controlled by many genes with minor effects and few genes with larger effects [1,2]. The amount and the composition of gluten proteins have large effects on baking quality of wheat. The major gluten loci are the high molecular weight glutenins (HMWGs). To a large extent, controlled by the Hardness locus on chromosome 5D, consisting of the genes Pina-D1, Pinb-D1, and Gsp-1 [5,6]. Breeding for improved wheat quality is challenging, because phenotyping of most quality traits requires laborious analyses of relatively large amounts of grain using expensive equipment. Baking tests can be used for evaluating the quality of wheat lines by determining bread loaf volume and texture. Breeding programs typically do not have the resources to perform baking tests with

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