Use of SNP genotyping to determine pedigree and breed composition of dairy cattle in Kenya

D M Gorbach, M L Makgahlela, J M Reecy, S J Kemp, I Baltenweck, R Ouma, O Mwai, K Marshall, B Murdoch, S Moore, M F Rothschild

Research output: Contribution to journalArticlepeer-review

Abstract

High levels of inbreeding in East African dairy cattle are a potential concern because of use of a limited range of imported germplasm coupled with strong selection, especially by disease, and sparse performance recording. To address this, genetic relationships and breed composition in an admixed population of Kenyan dairy cattle were estimated by means of a 50K SNP scan. Genomic DNA from 3 worldwide Holstein and 20 Kenyan bulls, 71 putative cow-calf pairs, 25 cows from a large ranch and 5 other Kenyan animals were genotyped for 37 238 informative SNPs. Sires were predicted and 89% of putative dam-calf relationships were supported by genotype data. Animals were clustered with the HapMap population using Structure software to assess breed composition. Cows from a large ranch primarily clustered with Holsteins, while animals from smaller farms were generally crosses between Holstein and Guernsey. Coefficients of relatedness were estimated and showed evidence of heavy use of one AI bull. We conclude that little native germplasm exists within the genotyped populations and mostly European ancestry remains.

Original languageEnglish
Pages (from-to)348-51
Number of pages4
JournalJournal of Animal Breeding and Genetics
Volume127
Issue number5
DOIs
Publication statusPublished - Oct 2010

Keywords

  • Animal Husbandry
  • Animals
  • Breeding
  • Cattle
  • Female
  • Genotype
  • Kenya
  • Male
  • Pedigree
  • Polymorphism, Single Nucleotide

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