Selection signatures in geographically separated Hereford populations

Abstract

Genomic differences between geographically separated Hereford populations may be characterised by using genomic diversity parameters, providing insight into different genes responsible for variation in traits of economic importance and adaptability to each population’s relevant production environment. This study aimed to develop a better understanding of the local adaptation and selection of South African, Irish, Uruguayan, and New Zealand Hereford populations in their respective environments. A total of 1 538 individuals for the four populations remained after quality control for further downstream data analyses. Descriptive genomic diversity parameters were estimated as HE, HO, FIS, MAF, and LD using PLINK v 1.9. All populations showed a moderate level of heterozygosity with HE values ranging from 0.359 to 0.391, and HO values ranging from 0.352 to 0.388. FIS values were -0.00475 to 0.0189 with MAF values ranging from 0.24 to 0.29 and LD ranging from 0.41 to 0.70. Population structure was visualised through principal component analysis. Each population showed to have a distinct cluster with some overlap between clusters. Intra-population genomic relatedness was determined through ROH. The detectRUNS package was used in R and a consecutive runs method was applied. The Irish and New Zealand populations showed to have the lowest degree of intra-population relatedness. A high level of genetic differentiation was observed in all populations. Selection signatures and candidate genes were identified using ROH for an intra-population approach and Pairwise Wright’s FST for an inter-population approach. Most notably, intra-population candidate genes related to traits of adaptation where the KDR and KIT genes were identified. Inter-population comparisons revealed 60 candidate genes related to traits of adaptation, production, and quality. The most common trait identified was that of bovine respiratory disease susceptibility. Five candidate genes, namely ARL6, ENOPH1, PPARGC1A, SCD5, and SNCA, were found to overlap between four of the six inter-population comparisons. Production and quality-related traits aligned with the breeding objectives of each population. The candidate genes related to adaptability traits showed that each population is adapted to its environment. Overall, each population showed to be genomically diverse and adapted to its geographically separated production region.