Genome‐wide marker effect heterogeneity is associated with a large effect dormancy locus in winter malting barley

Abstract

Prediction of trait values in plant breeding populations typically relies on assumptions about marker effect homogeneity across populations. Evidence is presented for winter malting barley (Hordeum vulgare L.) germination traits that a single, causative, largeeffect gene in the Seed dormancy 1 region on Chromosome 5H, HvAlaAT1 (Qsd1), leads to heterogeneous estimated marker effects genome wide between groups of otherwise related individuals carrying different Qsd1 alleles. This led to reduced prediction accuracy across alleles when a model was trained either on individuals carrying both alleles or one allele. Several genomic prediction models were tested to increase prediction accuracy within the Qsd1 allele groups. Small gains (5-12%) in prediction accuracy were realized using structured genomic best linear unbiased predictor models when information about the Qsd1 allele was used to stratify the population. We concluded that a single large-effect locus can lead to heterogeneous marker effects in the same breeding family. Variance partitioning based on largeeffect loci can be used to inform best practices in designing genomic prediction models; however, there are likely few cases for which it may be practical to do this.For malting barley, if germination traits are highly associated with malting quality traits, then similar steps should be considered for malting quality trait prediction.

Malting quality and preharvest sprouting traits are genetically correlated in spring malting barley

“…Model 9 was compared to an equivalent model with a diagonal variance structure assuming no correlations between traits for the line effect with a likelihood ratio test to assess improvements in model fit and significance of correlation. HvMKK3 is associated with differences in germination phenotypes and large effect loci can lead to changes in marker effects genome wide (Rooney et al 2022). It is also possible substantial correlations can be driven by a large effect locus.…”