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Prioritization for conservation of Iranian native cattle breeds based on genome-wide SNP data

Karimi, Karim, Esmailizadeh Koshkoiyeh, Ali, Asadi Fozi, Masood, Porto-Neto, Laercio R., Gondro, Cedric
Conservation genetics 2016 v.17 no.1 pp. 77-89
cattle, cattle breeds, conservation status, extinction, farm management, genetic variation, genotyping, homozygosity, inbreeding, population size, prioritization, quality control, risk, single nucleotide polymorphism
Comprehensive identification of the breed characteristics is essential for the effective management of farm animal genetic resources. The objective of this study was to estimate effective population size, genomic inbreeding coefficients, autozygosity derived from runs of homozygosity, and genetic diversity in Iranian native cattle using dense SNP markers. Ten samples per breed were collected from eight Iranian native cattle breeds representing the Sarabi, Kurdi, Najdi, Taleshi, Mazandarani, Pars, Kermani, and Sistani breeds. Samples were genotyped for 777,962 SNPs using the Illumina BovineHD BeadChip, and after quality control 450,341 SNPs were kept for further analyses. The estimated effective population size (Ne) was relatively small for all breeds, varying from Ne = 13 (Sarabi) to Ne = 107 (Mazandarani). Analysis of runs of homozygosity in different cut-off lengths was applied to provide information on the recent and ancient inbreeding occurrences in each population. The inbreeding coefficients estimated by runs of homozygosity varied between breeds. Sarabi, Pars, and Sistani breeds had higher proportion of long runs of homozygosity, likely to reflect recent inbreeding, while Kermani breed had the higher number of short runs of homozygosity. Some breeds such as Sarabi, Sistani, Pars, Taleshi, and Kermani are exposed to serious risk of extinction and other breeds, except Mazandarani, have no promising situations. Higher priority should be given to conservation programming in Sarabi and Sistani breeds due to unique genetic composition and critical conservation status.