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Abstract
Knowledge on the extent of linkage disequilibrium (LD) in livestock populations is essential to determine the minimum distance between markers required for effective coverage when conducting genome-wide association studies (GWAS). This study evaluated the extent of LD, persistence of allelic phase and effective population size (Ne) for four Sanga cattle breeds in South Africa including the Afrikaner (n = 44), Nguni (n = 54), Drakensberger (n = 47), and Bonsmara breeds (n = 46), using Angus (n = 31) and Holstein (n = 29) as reference populations. We found that moderate LD extends up to inter-marker distances of 40–60 kb in Angus (0.21) and Holstein (0.21) and up to 100 kb in Afrikaner (0.20). This suggests that genomic selection and association studies performed within these breeds using an average inter-marker r2≥ 0.20 would require about 30,000–50,000 SNPs. However, r2≥ 0.20 extended only up to 10–20 kb in the Nguni and Drakensberger and 20–40 kb in the Bonsmara indicating that 75,000 to 150,000 SNPs would be necessary for GWAS in these breeds. Correlation between alleles at contiguous loci indicated that phase was not strongly preserved between breeds. This suggests the need for breed-specific reference populations in which a much greater density of markers should be scored to identify breed specific haplotypes which may then be imputed into multi-breed commercial populations. Analysis of effective population size based on the extent of LD, revealed Ne = 95 (Nguni), Ne = 87 (Drakensberger), Ne = 77 (Bonsmara), and Ne = 41 (Afrikaner). Results of this study form the basis for implementation of genomic selection programs in the Sanga breeds of South Africa.
Highlights
Conventional selection programs based on quantitative principles have worked remarkably well and have allowed for significant genetic progress in South African beef cattle breeds over many decades (Scholtz, 2010)
The greatest average physical distance between single nucleotide polymorphism (SNP) was observed for Afrikaner (81.65 kb) whilst the smallest average inter-marker interval was observed in Drakensberger (61.09 kb) and Holstein (61.08 kb)
The lower percentage of polymorphic loci among South African cattle breeds has previously been attributed to the ascertainment bias associated with the design of the BovineSNP50 BeadChip (Qwabe et al, 2013), as the SNP used in the design of this assay were detected in European B. taurus breeds, resulting in the minor allele frequency (MAF) being lower in B. indicus breeds
Summary
Conventional selection programs based on quantitative principles have worked remarkably well and have allowed for significant genetic progress in South African beef cattle breeds over many decades (Scholtz, 2010). Markers in LD with causal variants provide an alternative approach to the implementation of MAS in livestock populations and may be discovered in genome-wide association studies (GWAS) by searching for genomic regions that are associated with traits of economic importance (Goddard and Hayes, 2007). Discovery of these regions has been enabled by advances in genomic technologies, including sequencing of whole genomes of livestock species that include cattle, chickens, sheep, and goats (Hayes et al, 2009)
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