Genetic diversity and selection signatures in Jianchang Black goats revealed by whole-genome sequencing data

Authors: SUN, XUELIANG - Sichuan Agricultural University; GUO, JIAZHONG - Sichuan Agricultural University; LI, LI - Sichuan Agricultural University; ZHONG, TAO - Sichuan Agricultural University; WANG, LINJIE - Sichuan Agricultural University; ZHAN, SIYUAN - Sichuan Agricultural University; DAI, DINGHUI - Sichuan Agricultural University; LU, JUAN - Sichuan Agricultural University; WANG, DEHENG - Bureau Of Agriculture And Rural Affairs Of Wucheng County; Liu, Ge - George; ZHENG, HONGPING - Sichuan Agricultural University

Submitted to: Animals
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/7/2022
Publication Date: 9/10/2022
Citation: Sun, X., Guo, J., Li, L., Zhong, T., Wang, L., Zhan, S., Dai, D., Lu, J., Wang, D., Liu, G., Zheng, H. 2022. Genetic diversity and selection signatures in Jianchang Black goats revealed by whole-genome sequencing data. Animals. 12(18):2365. https://doi.org/10.3390/ani12182365.
DOI: https://doi.org/10.3390/ani12182365

Interpretive Summary: Breed diversity is important for adaptation to future changes in climate and consumer demand and for continual genetic improvement of economically important traits. We studied the genetic diversity and selection signatures of a local Jianchang Black goat breed using whole genome sequencing data. These results fill our knowledge gaps and provide the foundation for its conservation and utilization. Farmers, scientists, and policy planners who need to improve animal health and production based on genome-enable animal selection will benefit from this study.

Technical Abstract: Understanding the genetic composition of indigenous goats is essential to promote scientific conservation and sustainable utilization of these breeds. The Jianchang Black (JC) goat, a Chinese native breed, has the characteristics of solid black and crude feed tolerance but a low growth rate and small body size. In this study, we investigated the genetic composition of JC goats by conducting population structure, runs of homozygosity (ROHs), genomic inbreeding, and selection signature analyses based on the whole-genome sequencing data for 30 JC, 41 Jintang Black (JT), and Yunshang Black (YS) goats and 21 Bezoar ibexes. Our results revealed that JT and YS showed a close genetic relationship with gene flow but were genetically distant to JC, apart from Bezoars. A total of 61,184 ROHs were identified in the autosomal genome of 30 JC goats, with an average value of 2,039 per individual. The ROH-based inbreeding estimates in JC goats generally showed moderate values with a range from 0.134 to 0.264, mainly due to rapid declines in the effective population size during recent generations. The annotated genes (e.g., IL2, IL7, and KIT) overlapping with ROH islands were significantly enriched in immune-related biological processes. We further found 61 genes (e.g., STIM1, MYO9A, and KHDRBS2) under positive selection in JC goats via three complementary approaches, which may underly genetic adaptations to local environmental conditions. Our findings provided references for the conservation and sustainable utilization of JC goats.