Suitability of existing commercial single nucleotide polymorphism chips for genomic studies in Bos indicus cattle breeds and their Bos taurus crosses

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  • Nilesh Nayee, National Dairy Development Board, Anand-388001, Gujarat, India
  • ,
  • Goutam Sahana
  • Swapnil Gajjar, National Dairy Development Board, Anand-388001, Gujarat, India
  • ,
  • Ananthasayanam Sudhakar, National Dairy Development Board, Anand-388001, Gujarat, India
  • ,
  • Kamlesh Trivedi, National Dairy Development Board, Anand-388001, Gujarat, India
  • ,
  • Mogens Sandø Lund
  • Bernt Guldbrandtsen
Bos indicus cattle breeds are genetically distinct from Bos taurus breeds. We examined
the performance of three SNP arrays, the Illumina BovineHD BeadChip
(777k; Illumina Inc.), the Illumina BovineSNP50 BeadChip (50k) and the Gene-
Seek 70k Indicus chip (75Ki; GeneSeek) in four B. indicus breeds (Gir, Kankrej,
Sahiwal and Red Sindhi) and their B. taurus crosses, along with two B. taurus
breeds, Holstein and Jersey. More SNPs on both Illumina SNP chips were
monomorphic in B. indicus breeds (average 20.3%–29.3% on the 777k chip,
35.5%–45.5% on the 50k chip) than in Holstein (19.7% on the 777k chip, 17.1% on
the 50k chip). The proportion of monomorphic SNPs on the 75Ki chip was much
lower, 4% (2.8%–7%) in B. indicus breeds, while it was 33.5% in Holstein. With on
average 164,357 heterozygous loci in B. indicus breeds, the 777k SNP chip has sufficient
heterozygous loci to design a chip customized for B. indicus breeds. Principal
component analysis clearly differentiated B. indicus from B. taurus breeds.
Differentiation among B. indicus breeds was only achieved by plotting the third
and fifth principal components using 777k genotype data. Admixture analysis
showed that many B. indicus animals, previously believed to be of pure origin, are
in fact had mixed ancestry. The extent of linkage disequilibrium showed comparatively
higher effective population sizes in four B. indicus breeds compared to two
B. taurus breeds. The results of admixture analyses show that it is important to
assess the genomic composition of a bull before using it in a breeding programme.
Original languageEnglish
JournalJournal of Animal Breeding and Genetics (Online)
Pages (from-to)432-441
Number of pages10
Publication statusPublished - 16 Aug 2018

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