EXPLORING THE STRUCTURE OF HAPLOTYPE BLOCKS, RUNS OF HOMOZYGOSITY AND EFFECTIVE POPULATION SIZE IN KHUZESTANI RIVER BUFFALO

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Pourya Davoudi
Hossein Moradi-Shahrbabak
Hassan Mehrabani-Yeganeh
Seyed Mohammad Ghoreishifar
Sajad Gholami
Rostam Abdollahi-Arpanahi

Abstract

Buffalo is considered as one of the most important species of livestock in many developing countries for milk and meat production. Knowledge about the characterization of haplotype block structure and about the genetic diversity of a population are fundamental factors for the success of genome-wide association and genomic selection studies. Parameters such as effective population size (Ne), Heterozygosity, runs of homozygosity (ROH) and inbreeding based on ROH (FROH) can give new insight about the level of genetic diversity for the population under selection. The main objective of this study was to investigate the haplotypic structure and genetic diversity in Iranian river buffalo (n = 123) using the Axiom Buffalo 90 K Genotyping Array. Analysis revealed 1726 haplo-blocks spanning 8.2 % of the genome and containing 12.4 % of all Single-nucleotide polymorphism (SNPs). The contemporary (5 generations ago) effective population size was approximately 240 animals. Totally, 992 ROH were identified, most of which were short (59 %) and had a length less than 10 Mb. Average observed heterozygosity and ROH-based inbreeding were 0.387 and 0.045, respectively. Our results will provide practical information to assist the genomic selection (GS) and genome-wide association study (GWAS) in buffaloes. Furthermore, the results of Ne, heterozygosity and ROH analyses displayed new knowledge about the level of genetic diversity in the Khuzestani river buffalo population.

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