Landscape genomics in South Africa

Genomic technologies for the improvement of South African beef cattle

Industry Sector: Cattle and Small Stock

Research Focus Area: Livestock production with global competitiveness: Breeding,physiology and management

Research Institute: Agriculture Research Institute – OVI

Researcher: Dr. Pranisha Omduth Soma

Title Initials Surname Highest Qualification
Prof. A.N. Maiwashe PhD
Dr F.C. Muchadeyi PhD
Prof. E. van-Marle Koster PhD
Prof. M.M. Makgahlela PhD
Dr M. MacNeil PhD
Dr S.O. Makina PhD

Final Report Approved: 23 August 2018

Aims Of The Project

  • To estimate linkage disequilibrium within South African beef cattle
  • To perform a genome wide scan for signatures of selection in beef cattle
  • To sequence genomic regions targeted by selection in order to identify possible polymorphisms

Executive Summary

South African indigenous and locally developed cattle breeds possess adaptive traits that are usually associated with tolerance to various diseases, extreme temperatures and humidity, and to change in feed availability. These breeds are also adapted to low-input management systems and have shown the ability to survive, produce and reproduce under harsh environments. Thus, these breeds hold potential in the changing South African production environments. However, little is known about the nature or extent of the genetic variation underlying these breeds.

The aim of this study was to conduct a genome wide scan for signatures of selection among Afrikaner, Nguni, Drakensberger, Bonsmara, Angus and Holstein cattle breeds of South Africa using data generated from the Bovine SNP50k BeadChip. The Angus and Holstein breeds were included as reference breeds since they have been extensively characterized using similar tools.

Therefore, in this project, the Bovine SNP50 BeadChip was used to characterize the genetic diversity and population structure of SA cattle breeds, determine the linkage disequilibrium and conduct a genome wide scan for signatures of selection among the Afrikaner (n=44), Nguni (n=54), Drakensberger (n=47) and Bonsmara (n=46)., using the Angus (n=31) and Holstein (n=29) cattle reference groups.

The first experiment performed included the evaluation of the Bovine SNP50 BeadChip to determine its utility for genome wide studies of South African cattle. Results of this experiment revealed that over 50 % of the SNPs were polymorphic (eg. Nguni = 35 843), indicating that the Bovine SNP50 assay would be useful for genome wide studies among South African cattle breeds.

Information about genetic diversity and population structure among cattle breeds is essential for genetic improvement, understanding of environmental adaptation as well as utilization and conservation of cattle breeds. Genetic diversity within the cattle breeds was analyzed using three measures of genetic diversity namely allelic richness, expected heterozygosity and inbreeding coefficient. The genetic diversity and population structure analyses indicated that the Afrikaner cattle had the lowest level of genetic diversity (He=0.24) while the Drakensberger cattle (He=0.30) had the highest among indigenous and locally-developed breeds. As expected, the average genetic distance was the greatest between indigenous breeds and Bos Taurus breeds but the lowest among indigenous and locally-developed breeds. Model-based clustering revealed some level of admixture among indigenous and locally-developed breeds and supported the clustering of the breeds according to their history of origin. Clear genetic divergence between South African (indigenous and locally-developed cattle breeds) and Bos Taurus cattle breeds was observed which suggested distinct genetic resources in South African cattle breeds which should be conserved in order to cope with unpredictable environments.

The extent of linkage disequilibrium (LD) is important for determining the minimum distance between markers for effective genome coverage for genome wide association studies. It can also provide insight into the evolutionary history of a population. The analyses of the extent of linkage disequilibrium (LD) showed that Afrikaner, Angus and Holstein had higher LD compared to Nguni, Drakensberger and Bonsmara cattle at all tested genomic distances. The higher LD within the Afrikaner cattle suggested that this breed has experienced considerable selection forces in contrast to what is expected of indigenous breeds and would require lower marker (50 000) density relative to what will be required for the Nguni, Drakensberger (150 000) and Bonsmara (75 000) cattle for genome wide studies. New breeding strategies may be required for the Afrikaner cattle breed to ensure future fitness of the breed. The effective population size for the Nguni, Drakensberger and Bonsmara were above the FAO recommended level.

The detection of selection signatures among cattle breeds may assist in locating regions of the genome that are, or have been, functionally important and targeted by selection. In this study, two approaches were employed. The first was based on the detection of genomic regions for which haplotypes have been driven towards complete

Fixation within breeds. The second approach identified regions of the genome exhibiting elevated population differentiation (Fst). A total of 47 genomic regions were identified as harboring potential signatures of selection using both methods. Thirty three of these regions were successfully annotated to identify candidate genes. Among these, were keratin genes (KRT222, KRT24, KRT25, KRT26 and KRT27) and one heat shock protein (HSPB9) on chromosome 19 (BTA) at 41,447,971-41,926,734 bp in the Nguni that have been previously associated with adaptation to tropical environments in Zebu cattle.

Furthermore, a number of genes associated with nervous system (WNT5B, FMOD, PRELP, ATP2B), immune response (CYM, CDC6, CDK10), production (MTPN, IGFBP4, TGFBI, AJAPI) and reproductive (ADIPOR2, OVOS2, RBBP8) performances were detected to be under selection in this study.

Target probes for enrichment were designed from exome and 5’ and 3’ untranslated regions of the cattle genome. Many SNP’s were identified in regulatory regions, leading to conformational changes in factor-binding sites. Gene ontology enrichment and clustering, resulted in the enrichment of gene ontology terms involved in fertility-related categories. Taking advantage of the availability of the fully sequenced bovine genome, the South African beef breeds were sequenced to detect genetic variants, in particular, large-scale SNP’s, which may contribute to the beef cattle genomics in South Africa.

The results presented in this study, forms the basis for effective management of South African cattle breeds and provides a useful foundation for the detection of mutations underlying genetic variation in traits of economic importance in South African cattle breeds.

This study produced one PhD thesis, 12 peer reviewed scientific articles and one popular article.

Please contact the Primary Researcher if you need a copy of the comprehensive report of this project – Pranisha Soma on pranisha@arc.agric.za