Assessment of Genetic Diversity in Azerbaijani Buffalo Population in Iran Based on Runs of Homozygosity Stretches
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NIMAL GENETICS
Assessment of Genetic Diversity in Azerbaijani Buffalo Population in Iran Based on Runs of Homozygosity Stretches M. H. Fallahia, H. Moradi Shahrbabaka, *, M. Moradi Shahrbabaka, R. Abdollahi Arpanahib, and S. Gholamia aDepartment
of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran Department of Animal and Poultry Sciences, College of Aburaihan, University of Tehran, Tehran, Iran *e-mail: [email protected]
b
Received September 28, 2019; revised February 10, 2020; accepted February 20, 2020
Abstract—Quantifying human, plant and livestock inbreeding has been an important goal of evolutionary biologists and agricultural scientists for nearly a century. Comprehensive identification of the breed characteristics is a critical factor for the effective management of farm animal genetic resources. The objective of this study was to estimate inbreeding coefficients derived from runs of homozygosity islands from 243 Iranian Azerbaijani buffalos using dense SNP markers (Axiom® Buffalo Genotyping 90K). After quality control, 62,141 SNP markers remained for computation of inbreeding coefficients. The amount of estimated inbreeding coefficient using four methods including genomic relationship matrix (FGRM), excess of homozygosity (FHOM), correlation of uniting gametes (FUNI) and FIS was similar (0.026) and it was estimated 0.0163 using Run of homozygosity procedure. Low levels of FROH in Azerbaijan buffalo population can be due to the traditional rural breeding system, random mating, high recombination rate and small population of ancestors. Keywords: inbreeding, Buffalo, SNP, run of homozygosity DOI: 10.1134/S102279542010004X
INTRODUCTION The size of buffalo population is increasing at about 1.3 percent annually worldwide, while on the contrary in some countries such as Iraq and Bulgaria, the numbers are dropping. Some of the main reasons for this decline may be industrialization, the increasing demand for buffalo meat but a lack of replacement of the slaughtered animals and farming diversification and income. The buffalo is a native animal of Iran, with over 80 percent of its population concentrated in the north and north-west (Azerbaijan province) and 20 percent in the south of the country. Official neglect and pro-Holstein propaganda have caused a significant decrease in buffalo numbers in Iran in recent decades [1]. In 1930s, there were 1,500,000 buffaloes in Iran and by 1995 this number had decreased to 500,000. The buffalo farming system in Iran is based on smallholders (99 percent); most of the herds have an average of five animals; a few herds have between 20 and 50 buffaloes and some of them have 300 buffaloes. Smallholders manage their animals according to the opportunities offered by the environment: on pasture, stubble, shrubs and grass. Most of them obtain their feeding by grazing along water sources: streams, rivers, ponds, lakes, integrated with the following products: citrus peels and pulp, sugar cane wastage and etc. In
Khuzestan, buff
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