Genomic inbreeding estimation and effective population size of four South African dairy breeds

Abstract

In this study 1002 dairy cattle, representing four South African dairy breeds (Ayrshire, Holstein, Jersey and SA Dairy Swiss) were genotyped at the ARC-Biotechnology Platform (Onderstepoort, 0110) with the Infinium Bovine SNP 50-24 V3.0 Beadchip. Genotypes for these animals originated from the Dairy Genomics Program (DGP) as part of an ongoing study aimed at integrating genomic information into the selection of South African dairy cattle. Genotypic data for all registered, genotyped animals participating in Logix Milk Recording was received from SA Stud Book, representing the Ayrshire, Holstein and Jersey breeds. The SA Dairy Swiss had no genotypic data available, thus hair samples from 62 individual animals were collected from three registered breeders to represent this breed. Raw Illumina genotype files were received via a downstream link from the ARC. These files were converted into PLINK (Purcell et al., 2007) files using SNP Convert v1.0 (Nicolazzi et al., 2016) for further analysis. The aim of the study was to estimate genomic inbreeding and effective population sizes for these breeds. The average call rate obtained across the samples was 99%. The observed heterozygosity values obtained for the populations were 0.355, 0.359, 0.340 and 0.345 for the Ayrshire, Holstein, Jersey and SA Dairy Swiss, respectively. Linkage disequilibrium (LD) estimation revealed average r2 values of 0.181 (Ayrshire), 0.311 (Holstein), 0.349 (Jersey) and 0.291 (SA Dairy Swiss). Two different inbreeding estimates were calculated individual inbreeding coefficients (FIS) and runs of homozygosity (FROH) and correlations were estimated between the inbreeding estimates. Pedigree-based inbreeding (FPED) estimates were received from SA Stud Book for the Ayrshire, Holstein and Jersey and compared to the genomic inbreeding estimates. The mean individual inbreeding coefficient (FIS) was -0.039 (Ayrshire), -0.007 (Holstein), -0.010 (Jersey) and -0.019 (SA Dairy Swiss), which indicates effective on farm management against inbreeding in the populations in this study. FROH > 16 Mb ranged from 0.227 to 0.255 (Ayrshire and Holstein). These relatively high FROH values indicate recent inbreeding in these populations. The strongest correlations were observed between FIS and FROH>1 ranging from 0.454 to 0.686 (SA Dairy Swiss and Jersey) respectively, while lower correlations were found between FIS and FROH>16, ranging from 0.071 to 0.377 (SA Dairy Swiss and Jersey) respectively. Very low correlations were found between FPED and FROH, which may have been due to shallow pedigree depth. The highest correlation between FPED and FROH (0.186) was observed for the Holstein at an ROH length of 4000kb. The Ne for the four populations included in the study has decreased to 117, 133, 120 and 112 for the Ayrshire, Holstein, Jersey and SA Dairy Swiss, respectively from approximately five generations ago. The four populations were separated into four separate clusters using principal component analysis (PCA). This corresponded with ADMIXTURE where the populations were also separated into the four respective populations. This indicates that the four populations are genetically distinct and were developed as separate breeds which is also consistent with the history of the four breeds. The high levels of genomic inbreeding could be explained by the increased use of artificial insemination in the populations studied. This is a concern as an increase in inbreeding leads to a reduction in the effective population size which was also evident in the populations included in the study.