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

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.

Genome‐based prediction of multiple wheat quality traits in multiple years

“…In contrast, the two alveograph parameters ALVL and ALVPL indicative of dough extensibility and of the balance between dough extensibil-ity and strength, respectively, were more difficult to predict and were also associated with greater MAAPE values (lower prediction accuracy). Similar results were reported in the study of Battenfield et al (2016) and Juliana et al (2019), where the parameter ALVPL was associated with the lowest correlation values, and by Kristensen et al (2019), where ALVL was associated with the lowest predictive ability among the alveograph parameters. Together, the results reported here and in previous studies suggest that dough extensibility, as expressed by the alveograph parameters ALVL and ALVPL, is hard to predict and highly affected by several factors other than genetics.…”

“…When analyzing the prediction accuracies associated with each quality trait, we found that the results obtained in the present study exceeded (Battenfield et al, 2016;Kristensen et al, 2019) or were comparable to (Haile et al, 2018;Juliana et al, 2019) the results reported in previous studies.…”

“…(2016), Kristensen et al. (2018), 2019) and Juliana et al. (2019), where among the quality traits analyzed, the ones associated with gluten strength appeared to be associated with high Pearson's correlation values compared to the other analyzed traits.…”

“…Wheat quality traits mostly exhibit moderate to high narrow‐sense heritability ( h 2 ) values. For example, gluten strength, as indicated by the alveograph deformation energy (W), exhibited h 2 values ranging from 0.65 to 0.72 (Battenfield et al., 2016; Kristensen et al., 2019), whereas h 2 values ranging from 0.51 to 0.60 were identified for dough extensibility (Hayes et al., 2017; Kristensen et al., 2019). In general, both grain and protein content proved to be less heritable, with h 2 values between 0.17 and 0.57 (Battenfield et al., 2016; Hayes et al., 2017), whereas traits such as flour yellowness appeared to be almost completely genetically controlled ( h 2 = 0.93, Hayes et al., 2017).…”

Breeding, Selection, and Quality of Partial Waxy Wheat: An Australian Perspective

“…Perhaps it is no coincidence that the first molecular marker developed for wheat quality was one for a waxy gene, and the research was conducted in Western Australia, where there were ongoing efforts to breed for udon noodle wheats. This work has been developed further by researchers to expand the characterization of this gene and its homologues in wheat and other associated genes for granule-bound starch synthase I (GBSSI) proteins that are responsible for amylose synthesis and the three starch synthase II (SSIIa) enzymes involved in amylopectin synthesis (11,12). Molecular markers for these loci have been used extensively as an efficient approach to both maintain the quality characteristics of the noodle program, as well as facilitate the incorporation of new genetics into the program without large detrimental impacts on noodle quality.…”