Runs of Homozygosity Revealed Reproductive Traits of Hu Sheep

Abstract

Hu sheep, a famous breed in the Taihu Basin, has the advantages of non-seasonal estrus, multiple fetuses, coarse feeding tolerance, and suitability for house feeding. Runs of homozygosity (ROHs) were found to be an effective tool to detect the animal population structure and economic traits. The detection of ROHs is beneficial for reducing the incidence of inbreeding as well as identifying harmful variants in the genome. However, there is a lack of systemic reports on ruminants in previous studies of ROHs. Here, we sequenced 108 Hu sheep, detected ROHs in Hu sheep to calculate their inbreeding coefficient, and selected genes of Hu sheep breeds within the ROH islands which are relevant to agricultural economic characteristics. Then, we compared the characteristics of the occurrences of SNPs between Hu sheep and other sheep breeds, and also investigated the distribution of the frequencies of SNPs within specific gene regions of Hu sheep breeds to select their breed-specific genes. Furthermore, we performed a comparative genome and transcriptome analysis in human and sheep breeds to identify important reproduction-related genes. In this way, we found some significant SNPs, and mapped these with a set of interesting candidate genes which are related to the productive value of livestock (FGF9, BMPR1B, EFNB3, MICU2, GFRA3), healthy characteristics (LGSN, EPHA5, ALOX15B), and breed specificity (FGF9, SAP18, MICU2). These results in our study describe various production traits of Hu sheep from a genetic perspective, and provide insights into the genetic management and complementary understanding of Hu sheep.

Identification of Runs of Homozygosity Islands and Functional Variants in Wenchang Chicken

“…Nowadays, more and more researchers perform ROH to reveal genetic mechanisms of important traits, and it has been widely used in a variety of animals, such as cattle [7], pigs [8], and sheep [9]. For example, Li et al detected ROH in Hu sheep based on sequencing data and identified selected genes within the ROH islands relevant to agricultural economic characteristics [10]. However, these types of studies are seen less commonly in chickens, especially Chinese indigenous chickens such as the Wenchang chicken.…”

Whole-genome resequencing of major populations revealed domestication-related genes in yaks

“…In contrast to in previous studies, GRID2 was strongly associated with dry matter intake, average daily gain, birth weight, and milk fat yield in cattle [ 25 – 28 ]. SMARCAL1 (SWI/SNF related, matrix-associated, actin-dependent regulator of chromatin, subfamily a-like 1) is an SNF2 family member and can increase 8-cell development in human, mice, and cattle embryos [ 29 ]. Zhe et al identified EPHB2 (EPH receptor B2) as a candidate gene associated with litter weight during weaning in Duroc pigs [ 30 ].…”

DIA-Based Proteomic Analysis Reveals MYOZ2 as a Key Protein Affecting Muscle Growth and Development in Hybrid Sheep

“…The Hu sheep breed is highly regarded in China for its advantageous features of non-seasonal estrus, multiple births, tolerance to roughage, and suitability for domestic breeding [ 13 , 14 ]. Southdown sheep and Suffolk sheep have the characteristics of early development and easy fattening, and their rams are suitable for hybridization to obtain good growth and carcass characteristics [ 15 , 16 , 17 ].…”