Advertisement

Genomics for the Improvement of Productivity and Robustness of South African Goat Breeds

  • Edgar F. Dzomba
  • Khanyisile Mdladla
  • Keabetswe T. Ncube
  • Farai C. Muchadeyi
Chapter

Abstract

South Africa is one of the major goat-producing countries with over 6 million goats, 63% of which are farmed under smallholder communal farming systems where poor nutrition, disease infestation, and harsh climatic conditions are common. The Boer, Kalahari Red, and Savanna breeds were developed in South Africa and have turned out to be regionally and internationally relevant. Adaptation and tolerance to local conditions are crucial for survival of these goat genetic resources in suboptimal conditions. The full genetic potential of veld goat populations is not yet fully unraveled. Complete mtDNA sequencing and diversity analysis revealed multiple maternal lineages in South African goat populations that were shared amongst the breeds and populations with absence of population sub-structuring. Median joining network analysis using different mtDNA genes suggests that South African populations have multiple maternal lineages that are shared with other global populations. Caprine SNP50K panel data analysis highlighted elevated levels of genetic diversity in South African indigenous goats compared to industrial breeds as well as the utility of the genome-wide SNP marker panels in population genetic studies. Landscape genomic analysis suggests a strong role of environmental factors in shaping the genetic diversity of South African indigenous goats. Selected loci responsible for the adaption of goat populations to local production systems may be targeted in breed improvement programs particularly under marginalized communal production systems. Successful sequencing and analysis of the Tankwa and other South African goat genomes could screen for potentially numerous genomic variants such as copy number variants. Community-based breeding programs would be the appropriate tool for breed improvement allowing sharing of production capital, pooling of resources and services and enabling joint processes of decision-making. Genomics could complement breed improvement efforts by providing pedigree estimates and can be useful in monitoring and control of inbreeding and genetic gain.

References

  1. AGRINC (2013) Tankwa feral goats a real cliffhanger or the end of the road! Retrieved from http://www.karoofoundation.co.za/images/Parliament/The%20feral%20goats%20of%20Tankwa%20-11%20October%202013.pdf
  2. Almeida A, Schwalbach L, De Waal H et al (2006) The effect of supplementation on productive performance of Boer goat bucks fed winter veld hay. Trop Anim Health Prod 38(5):443–449CrossRefPubMedGoogle Scholar
  3. Bester J, Ramsay KA, Scholtz MM (2009) Goat farming in South Africa: findings of a national livestock survey. Appl Anim Husb Rural Develop 2:9–13Google Scholar
  4. Bickhart DM, Hou Y, Schroeder SG et al (2012) Copy number variation of individual cattle genomes using next-generation sequencing. Genome Res 22(4):778–790CrossRefPubMedPubMedCentralGoogle Scholar
  5. Campbell QP (2003) The origin and description of southern Africa’s indigenous goats. S Afr J Anim Sci 4(1):18–22Google Scholar
  6. DAFF (2012) A profile of the South African goat market value chain. Retrieved 06 Sept 2016, from http://www.daff.gov.za/docs/AMCP/Goat2012.pdf
  7. DAFF (2014) Newsletter: livestock statistics, estimated livestock numbers in RSA (August 2013 and February 2014). Retrieved 22 Sept 2014, from http://www.daff.gov.za/daffweb3/Resource-Centre
  8. Dong Y, Xie M, Jiang Y et al (2013) Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus). Nat Biotechnol 31(2):135–141CrossRefPubMedGoogle Scholar
  9. Dong Y, Zhang X, Xie M et al (2015) Reference genome of wild goat (Capra aegagrus) and sequencing of goat breeds provide insight into genic basis of goat domestication. BMC Genom 16(1):431.  https://doi.org/10.1186/s12864-015-1606-1 CrossRefGoogle Scholar
  10. Doro MG, Piras D, Leoni GG et al (2014) Phylogeny and patterns of diversity of goat mtDNA haplogroup A revealed by resequencing complete mitogenomes. PloS One 9(4):e95969.  https://doi.org/10.1371/journal.pone.0095969
  11. Food and Agriculture Organization of the United Nations (FAOSTAT) (2013) FAOSTAT database, FAO, Rome, Italy. http://faostat3.fao.org/
  12. Garrine CMLP (2007) Genetic characterization of indigenous goat populations of Mozambique. Doctoral dissertation, Department of Production Animal Studies in Faculty of Veterinary Science, University of PretoriaGoogle Scholar
  13. Geng R, Yuan C, Chen Y (2013) Exploring differentially expressed genes by RNA-Seq in cashmere goat (Capra hircus) skin during hair follicle development and cycling. PloS One 8(4):e62704.  https://doi.org/10.1371/journal.pone.0062704
  14. Gwaze FR, Chimonyo M, Dzama K (2009a) Variation in the functions of village goats in Zimbabwe and South Africa. Trop Anim Health Prod 41(7):1381–1391CrossRefGoogle Scholar
  15. Gwaze FR, Chimonyo M, Dzama K (2009b) Communal goat production in Southern Africa: a review. Trop Anim Health Prod 41(7):1157–1168Google Scholar
  16. Ilatsia ED, Roessler R, Kahi AK et al (2012) Production objectives and breeding goals of Sahiwal cattle keepers in Kenya and implications for a breeding programme. Trop Anim Health Prod 44(3):519–530CrossRefPubMedGoogle Scholar
  17. Joost S, Bonin A, Bruford MW et al (2007) A spatial analysis method (SAM) to detect candidate loci for selection: towards a landscape genomics approach to adaptation. Mol Ecol 16(18):3955–3969CrossRefPubMedGoogle Scholar
  18. Kijas JW, Ortiz JS, McCulloch R et al (2013) Genetic diversity and investigation of polledness in divergent goat populations using 52 088 SNPs. Anim Genet 44(3):325–335CrossRefPubMedGoogle Scholar
  19. Kotze A, Grobler JP, van Marle-Köster E, Jonker T, Dalton DL (2014) The Tankwa Karoo National Park feral goat population: a unique genetic resource. S Afri J Anim Sci 44:43–48Google Scholar
  20. Kristensen TN, Hoffmann AA, Pertoldi C et al (2015) What can livestock breeders learn from conservation genetics and vice versa? Front Genet 6:38.  https://doi.org/10.3389/fgene.2015.00038 CrossRefPubMedPubMedCentralGoogle Scholar
  21. Lashmar S, Visser C, van Marle-Köster E (2016) SNP-based genetic diversity of South African commercial dairy and fiber goat breeds. Small Rumin Res 136:65–71CrossRefGoogle Scholar
  22. Lebbie S (2004) Goats under household conditions. Small Rumin Res 51:131–136CrossRefGoogle Scholar
  23. Livestock Health and Production Group (LHPG) (2013) General disease trends and discussion as informally reported by veterinarians during June and July 2013. Monthly report on livestock disease trends as informally reported by veterinarians in South Africa June and July 2013. From http://www.rpofs.co.za/images/Dieregesondheid/DiseasereportJuneJuly2013.pdf
  24. Livestock Health and Production Group (LHPG) (2014a) Disease distribution report as reported by veterinarians. Monthly report on livestock disease trends as informally reported by veterinarians in South Africa February 2014. From http://www.landbou.com/content/uploads/ArticleDocument/Monthly_disease_report_February_20140.pdf
  25. Livestock Health and Production Group (LHPG) (2014b) General disease trends and discussion as informally reported by veterinarians during January 2014. Monthly report on livestock disease trends as informally reported by veterinarians in South Africa January 2014. From http://landbou.com/wp-content/uploads/2014/05/Monthly_Disease_report_January_2014_.pdf
  26. Mamabolo MJ (1999) Dietary, seasonal and environmental influences on the semen quality and fertility status of indigenous goats in Mpumalanga Province (South Africa). Msc thesis, University of Pretoria, South AfricaGoogle Scholar
  27. Mdladla K (2017) Landscape genomic approach to investigate genetic adaptation in South African indigenous goat populations. PhD thesis, Genetics School of Life Sciences College of Agriculture, Engineering and Science, University of KwaZulu-Natal, Pietermaritzburg, South Africa, 244 ppGoogle Scholar
  28. Mdladla K, Dzomba EF, Huson H et al (2016a) Population genomic structure and linkage disequilibrium analysis of South African goat breeds using genome-wide SNP data. Anim Genet 47(4):471–482CrossRefPubMedGoogle Scholar
  29. Mdladla K, Dzomba EF, Muchadeyi FC (2016b) Seroprevalence of Ehrlichia ruminantium antibodies and its associated risk factors in indigenous goats of South Africa. Prev Vet Med 125:99–105CrossRefPubMedGoogle Scholar
  30. Miles G (2007) Indigenous veld goats: made for Africa. Retrieved 12 Sept 2016, from http://www.farmersweekly.co.za/article.aspx?id=673&h=Indigenous-Veld-Goats:-made-for-Africa
  31. Mohlatlole RP, Dzomba EF, Muchadeyi FC (2015) Addressing production challenges in goat production systems of South Africa: the genomics approach. Small Rumin Res 131:43–49CrossRefGoogle Scholar
  32. Mohlatlole RP, Dzomba EF, Muchadeyi FC (2017) Whole-genome sequence and genetic variant analysis of the Tankwa feral goat of South Africa. Abstract. Plant and animal genome conference, San Diego, USA, 13–17 January 2017Google Scholar
  33. Morrison J (2007) A guide to the identification of the natural indigenous goats of Southern Africa. Indigenous Veld Goat Club. Retrieved 09 Sept 2016, from http://landbou.com/wp-content/uploads/2014/03/f2297405-a93f-4399-bdb7-6f3de538d75d.pdf
  34. National Department of Agriculture (NDA) (2012) A profile of the South African goat market value chain. Retrieved January 2016, from http://www.nda.agric.za/docs/AMCP/Goat2012.pdf
  35. Ncube K (2016) Maternal lineages and diversity of the growth hormone gene of South African goat populations. MSc dissertation, University of South AfricaGoogle Scholar
  36. Norris D, Ngambi J, Benyi K et al (2011) Milk production of three exotic dairy goat genotypes in Limpopo province, South Africa. Asian J Anim Vet Adv 6(3):274–281CrossRefGoogle Scholar
  37. Piras D, Doro MG, Casu G et al (2012) Haplotype affinities resolve a major component of goat (Capra hircus) MtDNA D-loop diversity and reveal specific features of the Sardinian stock. PloS One 7(2):e30785.  https://doi.org/10.1371/journal.pone.0030785
  38. Roets M, Kirsten JF (2005) Commercialisation of goat production in South Africa. Small Rumin Res 60(1):187–196CrossRefGoogle Scholar
  39. Tosser-Klopp G, Bardou P, Bouchez O et al (2014) Design and characterization of a 52K SNP chip for goats. PloS One 9(1):e86227.  https://doi.org/10.1371/journal.pone.0086227
  40. van Vuren D, Hedrick PW (1989) Genetic conservation in feral populations of livestock. Conserv Biol 3:312–317Google Scholar
  41. Visser C, Lashmar SF, Van Marle-Köster E et al (2016) Genetic diversity and population structure in South African, French and Argentinian Angora goats from genome-wide SNP data. PloS One 11(5):e0154353.  https://doi.org/10.1371/journal.pone.0154353
  42. Wang MD, Dzama K, Hefer CA et al (2015) Genomic population structure and prevalence of copy number variations in South African Nguni cattle. BMC Genom 16:894.  https://doi.org/10.1186/s12864-015-2122-z CrossRefGoogle Scholar
  43. Webb EC, Mamabolo M (2004) Production and reproduction characteristics of South African indigenous goats in communal farming systems. S Afr J Anim Sci 34(suppl 1):236–239Google Scholar

Copyright information

© Springer International Publishing AG 2017

Authors and Affiliations

  • Edgar F. Dzomba
    • 1
  • Khanyisile Mdladla
    • 1
    • 2
  • Keabetswe T. Ncube
    • 1
    • 2
  • Farai C. Muchadeyi
    • 2
  1. 1.Discipline of Genetics, School of Life SciencesUniversity of KwaZulu-NatalPietermaritzburgSouth Africa
  2. 2.Biotechnology Platform, Agricultural Research CouncilOnderstepoortSouth Africa

Personalised recommendations