Genetic diversity and signatures of selection in BoHuai goat revealed by whole-genome sequencing

Abstract

Background Cross breeding is an important way to improve livestock performance. As an important livestock and poultry resource in Henan Province of China, Bohuai goat was formed by crossing Boer goat and Huai goat. After more than 20 years of breeding, BoHuai goats showed many advantages, such as fast growth, good reproductive performance, and high meat yield. In order to better develop and protect Bohuai goats, we sequenced the whole genomes of 30 BoHuai goats and 5 Huai goats to analyze the genetic diversity, population structure and genomic regions under selection of BoHuai goat. Furthermore, we used 126 published genomes of world-wide goat to characterize the genomic variation of BoHuai goat. Results The results showed that the nucleotide diversity of BoHuai goats was lower and the degree of linkage imbalance was higher than that of other breeds. The analysis of population structure showed that BoHuai goats have obvious differences from other goat breeds. In addition, the BoHuai goat is more closely related to the Boer goat than the Huai goat and is highly similar to the Boer goat. Group by selection signal in the BoHuai goat study, we found that one region on chromosome 7 shows a very strong selection signal, which suggests that it could well be the segment region under the intense artificial selection results. Through selective sweeps, we detected some genes related to important traits such as lipid metabolism (LDLR, STAR, ANGPTL8), fertility (STAR), and disease resistance (CD274, DHPS, PDCD1LG2). Conclusion In this paper, we elucidated the genomic variation, ancestry composition, and selective signals related to important economic traits in BoHuai goats. Our studies on the genome of BoHuai goats will not only help to understand the characteristics of the crossbred but also provide a basis for the improvement of cross-breeding programs.

Evaluation of the Genetic Diversity and Population Structure of Four Native Pig Populations in Gansu Province

“…This study aimed to determine the population structure and genetic diversity to provide rational scientific conservation strategies for HX, MX, BM, and HZ pig populations. More and more studies have investigated the genetic diversity and population structure of various species of livestock (e.g., Min pig, Tongcheng pig, Tibetan sheep, Hainan cattle, and BoHuai goat) using whole-genome sequencing or SNP chips [14,[22][23][24][25][26][27]. For instance, Meng et al used a KPS porcine breeding chip v1 50K for SNP to study the genetic diversity of the Min pig-conserved population.…”

Genomic Inbreeding and Runs of Homozygosity Analysis of Cashmere Goat

“…PDCD1LG2 (PDCD1 ligand 2) and SVIL are immunostimulatory genes. It has been reported that PDCD1LG2 in Bohuai goats and SVIL in Bos indicus are related to immunity [69,70]. PRDM16 is key in regulating the formation of brown fat cells and the production of brown fat [71][72][73].…”

Advancements in copy number variation screening in herbivorous livestock genomes and their association with phenotypic traits

“…To date, several methodologies have been commonly employed for CNV detection, including comparative genome hybridization, extracting CNV data from SNP arrays, and whole-genome sequencing (WGS) approaches ( 24 – 26 ). Notably, recent research endeavors have delved into the investigation of the association between CNV in specific genes and a variety of phenotypic traits in animals, including growth characteristics in cattle ( 27 , 28 ), goats ( 29 – 31 ), sheep ( 32 ) and horses ( 33 – 38 ). These studies have also extended their focus to examine the link between CNVs and other vital phenotypes, such as reproduction traits ( 39 , 40 ) and disease resistance ( 7 , 41 ).…”