Genotype-by-environment interaction of fertility traits in Danish Holstein cattle using a single-step genomic reaction norm model

Zhe Zhang,Jørn Rind Thomasen,Morten Kargo,Guosheng Su,Aoxing Liu,Yuchun Pan

doi:10.1038/s41437-019-0192-4

Zhe Zhang, Jørn Rind Thomasen + Show 4 more

Open Access

https://doi.org/10.1038/s41437-019-0192-4

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Abstract

Genotype-by-environment (G × E) interactions could play an important role in cattle populations, and it should be considered in breeding programmes to select the best sires for different environments. The objectives of this study were to study G × E interactions for female fertility traits in the Danish Holstein dairy cattle population using a reaction norm model (RNM), and to detect the particular genomic regions contributing to the performance of these traits and the G × E interactions. In total 4534 bulls were genotyped by an Illumina BovineSNP50 BeadChip. An RNM with a pedigree-based relationship matrix and a pedigree-genomic combined relationship matrix was used to explore the existence of G × E interactions. In the RNM, the environmental gradient (EG) was defined as herd effect. Further, the genomic regions affecting interval from calving to first insemination (ICF) and interval from first to last insemination (IFL) were detected using single-step genome-wide association study (ssGWAS). The genetic correlations between extreme EGs indicated that G × E interactions were sizable for ICF and IFL. The genomic RNM (pedigree-genomic combined relationship matrix) had higher prediction accuracy than the conventional RNM (pedigree-based relationship matrix). The top genomic regions affecting the slope of the reaction norm included immunity-related genes (IL17, IL17F and LIF), and growth-related genes (MC4R and LEP), while the top regions influencing the intercept of the reaction norm included fertility-related genes such as EREG, AREG and SMAD4. In conclusion, our findings validated the G × E interactions for fertility traits across different herds and were helpful in understanding the genetic background of G × E interactions for these traits.

Highlights

Supplementary information The online version of this article contains supplementary material, which is available to authorized users.In the dairy cattle industry, fertility traits are some of the most influential components, as declining fertility prolongs the resume cycles after calving and increases veterinary costs (De Vries 2006; Schneider et al 2005)
The other one is the reaction norm model (RNM) (Falconer et al 1996), which models the trajectory of animal performance as a function of the environmental gradient (EG), and the breeding value of an animal is partitioned into an environment-independent part and an environment-dependent part
The objective of this study was to use the RNM with information on genomic markers and pedigrees to explore the G × E interaction of female fertility for Danish Holstein dairy cows and to map the genomic regions contributing to the fertility phenotypes across different EGs

Summary

Introduction

Some previous studies have emphasized the importance of genetic evaluation and the improvement of fertility traits in spite of their low heritability (below 5%) (Liu et al 2017; Sun et al 2010), and more balanced selection indices including production, longevity, health and fertility have been used instead of indices which focused on yield Another issue regarding selection for improved fertility is that a wide range of environments often contribute to the phenomenon of genotype-by-environment (G × E) interaction, which is defined as different performances of animals and their offspring in different environments than those where they were raised or selected (Falconer et al 1996). RNMs are able to explore G × E interactions in a range of continuous environments and quantify the G × E interaction at any environment within the range

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