Genomic predictive ability for foliar nutritive traits in perennial ryegrass

Abstract

Forage nutritive value impacts animal nutrition, which underpins livestock productivity, reproduction and health. Genetic improvement for nutritive traits has been limited, as they are typically expensive and time-consuming to measure through conventional methods. Genomic selection is appropriate for such complex and expensive traits, enabling cost-effective prediction of breeding values using genome-wide markers. The aims of the present study were to assess the potential of genomic selection for a range of nutritive traits in a multi-population training set, and to quantify contributions of genotypic, environmental and genotype-by-environment (G x E) variance components to trait variation and heritability for nutritive traits. The training set consisted of a total of 517 half-sibling (half-sib) families, from five advanced breeding populations, evaluated in two distinct New Zealand grazing environments. Autumn-harvested samples were analyzed for 18 nutritive traits and maternal parents of the half-sib families were genotyped using genotyping-by-sequencing. Significant (P<0.05) genotypic variation was detected for all nutritive traits and genomic heritability (h2g) was moderate to high (0.20 to 0.74). G x E interactions were significant and particularly large for water soluble carbohydrate (WSC), crude fat, phosphorus (P) and crude protein. GBLUP, KGD-GBLUP and BayesC genomic prediction models displayed similar predictive ability, estimated by 10-fold cross validation, for all nutritive traits with values ranging from r = 0.16 to 0.45 using phenotypes from across two environments. High predictive ability was observed for the mineral traits sulphur (0.44), sodium (0.45) and magnesium (0.45) and the lowest values were observed for P (0.16), digestibility (0.22) and high molecular weight WSC (0.23). Predictive ability estimates for most nutritive traits were retained when marker number was reduced from 1 million to as few as 50,000. The moderate to high predictive abilities observed suggests implementation of genomic selection is feasible for most of the nutritive traits examined. For traits with lower predictive ability, multi-trait genomic prediction approaches that exploit the strong genetic correlations observed amongst some nutritive traits may be useful. This appears to be particularly important for WSC, considered one of the primary constituent of nutritive value for forages.