Genomic Inbreeding and Runs of Homozygosity Analysis of Cashmere Goat
Author:
Zhao Qian12, Huang Chang12ORCID, Chen Qian2, Su Yingxiao2, Zhang Yanjun3, Wang Ruijun3, Su Rui3ORCID, Xu Huijuan4, Liu Shucai4, Ma Yuehui2ORCID, Zhao Qianjun2, Ye Shaohui1
Affiliation:
1. Department of Animal Breeding and Reproduction, College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China 2. State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China 3. College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China 4. Chifeng Hanshan White Cashmere Goat Breeding Farm, Chifeng 024506, China
Abstract
Cashmere goats are valuable genetic resources which are famous worldwide for their high-quality fiber. Runs of homozygosity (ROHs) have been identified as an efficient tool to assess inbreeding level and identify related genes under selection. However, there is limited research on ROHs in cashmere goats. Therefore, we investigated the ROH pattern, assessed genomic inbreeding levels and examined the candidate genes associated with the cashmere trait using whole-genome resequencing data from 123 goats. Herein, the Inner Mongolia cashmere goat presented the lowest inbreeding coefficient of 0.0263. In total, we identified 57,224 ROHs. Seventy-four ROH islands containing 50 genes were detected. Certain identified genes were related to meat, fiber and milk production (FGF1, PTPRM, RERE, GRID2, RARA); fertility (BIRC6, ECE2, CDH23, PAK1); disease or cold resistance and adaptability (PDCD1LG2, SVIL, PRDM16, RFX4, SH3BP2); and body size and growth (TMEM63C, SYN3, SDC1, STRBP, SMG6). 135 consensus ROHs were identified, and we found candidate genes (FGF5, DVL3, NRAS, KIT) were associated with fiber length or color. These findings enhance our comprehension of inbreeding levels in cashmere goats and the genetic foundations of traits influenced by selective breeding. This research contributes significantly to the future breeding, reservation and use of cashmere goats and other goat breeds.
Funder
Major Science and Technology Program of Inner Mongolia Autonomous Region National Key Research and Development Program of China Ministry of Agriculture and Rural of the People’s Republic of China Modern Agro-industry Technology Research System
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