Genomic Inbreeding and Runs of Homozygosity Analysis of Cashmere Goat

文献类型： 外文期刊

第一作者： Zhao, Qian

作者： Zhao, Qian;Huang, Chang;Ye, Shaohui;Zhao, Qian;Huang, Chang;Chen, Qian;Su, Yingxiao;Ma, Yuehui;Zhao, Qianjun;Zhang, Yanjun;Wang, Ruijun;Su, Rui;Xu, Huijuan;Liu, Shucai

作者机构：

关键词： cashmere goat; runs of homozygosity; inbreeding coefficient; genetic diversity; selection signatures

期刊名称：ANIMALS （ 影响因子：3.0； 五年影响因子：3.2 ）

ISSN： 2076-2615

年卷期： 2024 年 14 卷 8 期

页码：

收录情况： SCI

摘要： Simple Summary Cashmere goats are valuable genetic resources which are famous for their high-quality fiber. Runs of homozygosity (ROHs) refer to uninterrupted sequences of homozygous genotypes present within the DNA sequence of an individual. To enhance the preservation, improvement and enduring utilization of this valuable genetic resource, we performed a comprehensive study on the genetic variance, degree of inbreeding, patterns of ROHs and selected genes situated in ROH islands which are associated with economic attributes in goats via whole-genome sequencing analysis. Our research showed that the Inner Mongolia cashmere goat possesses a notably high level of genetic diversity and presented the lowest inbreeding coefficient. On the contrary, the highest Froh and lowest levels of diversity were observed in wild goats compared to domesticated goats. The analysis of selection signal through ROHs identified some genes related to meat, fiber and milk production; fertility, disease and cold resistance and adaptability; and body size and growth.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.

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