Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, Engineering Key Laboratory of Haikou, School of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, Hainan Province, China.
BMC Genom Data. 2024 May 7;25(1):44. doi: 10.1186/s12863-024-01228-8.
China has thousands years of goat breeding and abundant goat genetic resources. Additionally, the Hainan black goat is one of the high-quality local goat breeds in China. In order to conserve the germplasm resources of the Hainan black goat, facilitate its genetic improvement and further protect the genetic diversity of goats, it is urgent to develop a single nucleotide polymorphism (SNP) chip for Hainan black goat.
In this study, we aimed to design a 10K liquid chip for Hainan black goat based on genotyping by pinpoint sequencing of liquid captured targets (cGPS). A total of 45,588 candidate SNP sites were obtained, 10,677 of which representative SNP sites were selected to design probes, which finally covered 9,993 intervals and formed a 10K cGPS liquid chip for Hainan black goat. To verify the 10K cGPS liquid chip, some southern Chinese goat breeds and a sheep breed with similar phenotype to the Hainan black goat were selected. A total of 104 samples were used to verify the clustering ability of the 10K cGPS liquid chip for Hainan black goat. The results showed that the detection rate of sites was 97.34% -99.93%. 84.5% of SNP sites were polymorphic. The heterozygosity rate was 3.08%-36.80%. The depth of more than 99.4% sites was above 10X. The repetition rate was 99.66%-99.82%. The average consistency between cGPS liquid chip results and resequencing results was 85.58%. In addition, the phylogenetic tree clustering analysis verified that the SNP sites on the chip had better clustering ability.
These results indicate that we have successfully realized the development and verification of the 10K cGPS liquid chip for Hainan black goat, which provides a useful tool for the genome analysis of Hainan black goat. Moreover, the 10K cGPS liquid chip is conducive to the research and protection of Hainan black goat germplasm resources and lays a solid foundation for its subsequent breeding work.
中国养羊历史悠久，拥有丰富的山羊遗传资源。海南黑山羊是中国优质地方山羊品种之一。为了保护海南黑山羊的种质资源，促进其遗传改良，进一步保护山羊的遗传多样性，迫切需要开发海南黑山羊的单核苷酸多态性（SNP）芯片。
本研究旨在基于靶向测序的液滴数字基因（cGPS）技术设计海南黑山羊 10K 液相芯片。共获得 45588 个候选 SNP 位点，从中筛选出 10677 个代表性 SNP 位点设计探针，最终覆盖 9993 个区间，形成了海南黑山羊 10K cGPS 液相芯片。为了验证该 10K cGPS 液相芯片，选择了一些中国南方山羊品种和与海南黑山羊表型相似的绵羊品种，共 104 个样本对其进行验证。结果表明，该 10K cGPS 液相芯片对海南黑山羊的检测率为 97.34%-99.93%，SNP 位点的多态性为 84.5%，杂合度为 3.08%-36.80%，99.4%以上的位点深度大于 10X，重复率为 99.66%-99.82%，cGPS 液相芯片结果与重测序结果的平均一致性为 85.58%。此外，系统进化树聚类分析验证了芯片上 SNP 位点具有更好的聚类能力。
本研究成功实现了海南黑山羊 10K cGPS 液相芯片的开发与验证，为海南黑山羊基因组分析提供了有效的工具。此外，10K cGPS 液相芯片有利于海南黑山羊种质资源的研究与保护，为其后续的选育工作奠定了坚实的基础。
