Estimation of effective population size using 70K SNP-CHIP chips in Kurdish horse
Subject Areas : Journal of Animal BiologyBahareh Safaei 1 , Hossein Moradi-Shahrbabak 2
1 - دانشکده کشاورزی و منابع طبیعی دانشگاه تهران- کرج
2 - Department of Animal Science, University of Tehran, Karaj, Iran
Keywords: effective population size, linkage disequilibrium, Single Nucleotide Polymorphism, Kurdish horse.,
Abstract :
Native breeds of each region should be given particular consideration, and we should put excessive effort in preserving these breeds. Studying and evaluating the population structure and diversity is a technique to protect the genetic reserves of indigenous breeds. In this study, regarding the importance of preserving diverse breeds of Iranian horses, we investigated the effective population size of Kurdish horses. One of the significant variables for examining the population structure is the effective population size. For this purpose, we estimated linkage disequilibrium using Single Nucleotide Polymorphism information obtained from 70k SNPchips in Kurdish horses. At first, data quality control procedures were performed on the initial 65157 SNPs by Plink software (mind>0.05، geno>0.05، MAF<0.01، hwe<10-6), and then some data were removed posteriorly, and ultimately the number of 56012 SNPs on autosomal chromosomes were left for further analyses. linkage disequilibrium was calculated using the r2 statistic, and we employed this information to estimate the effective population size. r2 had the highest value in the distance from 0 to 2.5 kb, which decreased with increasing distance between markers. The average r2 was estimated at 0.046 in all chromosomes, and ranged from 0.041 to 0.052 among chromosomes. Likewise, the effective population size was predicted to be 6674 in 4463 previous generations, which reached 26 in the current generation.
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