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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.

Abstract Background Native cattle breeds are an important source of genetic variation because they might carry alleles that enable them to adapt to local environment and tough feeding conditions. Jiaxian Red, a Chinese native cattle breed, is reported to have originated from crossbreeding between taurine and indicine cattle; their history as a draft and meat animal dates back at least 30 years. Using whole-genome sequencing (WGS) data of 30 animals from the core breeding farm, we investigated the genetic diversity, population structure and genomic regions under selection of Jiaxian Red cattle. Furthermore, we used 131 published genomes of world-wide cattle to characterize the genomic variation of Jiaxian Red cattle. Results The population structure analysis revealed that Jiaxian Red cattle harboured the ancestry with East Asian taurine (0.493), Chinese indicine (0.379), European taurine (0.095) and Indian indicine (0.033). Three methods (nucleotide diversity, linkage disequilibrium decay and runs of homozygosity) implied the relatively high genomic diversity in Jiaxian Red cattle. We used θπ, CLR, F ST and XP-EHH methods to look for the candidate signatures of positive selection in Jiaxian Red cattle. A total number of 171 (θπ and CLR) and 17 (F ST and XP-EHH) shared genes were identified using different detection strategies. Functional annotation analysis revealed that these genes are potentially responsible for growth and feed efficiency (CCSER1), meat quality traits (ROCK2, PPP1R12A, CYB5R4, EYA3, PHACTR1), fertility (RFX4, SRD5A2) and immune system response (SLAMF1, CD84 and SLAMF6). Conclusion We provide a comprehensive overview of sequence variations in Jiaxian Red cattle genomes. Selection signatures were detected in genomic regions that are possibly related to economically important traits in Jiaxian Red cattle. We observed a high level of genomic diversity and low inbreeding in Jiaxian Red cattle. These results provide a basis for further resource protection and breeding improvement of this breed.