Genetic diversity and reproductive trait selection signal analysis of Bohuai goats based on whole genome sequencing
Abstract Bohuai goat is a crossbreeding breed between Huai goat and Boer goat, which has higher meat yield and reproductive efficiency. To explore the genetic basis of these traits, we sequenced the whole genome of 289 samples from 8 Chinese local goat populations and Boer goats. Through variation d...
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BMC
2025-07-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-025-11878-2 |
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| author | Yuqiao Zhang Hua He Qinwei Yu Xingya Song Jun Ma Jiamei Wang Yongpan Wang Yu Jiang Zejun Xu Xianwei Wang Yongzhen Huang |
| author_facet | Yuqiao Zhang Hua He Qinwei Yu Xingya Song Jun Ma Jiamei Wang Yongpan Wang Yu Jiang Zejun Xu Xianwei Wang Yongzhen Huang |
| author_sort | Yuqiao Zhang |
| collection | DOAJ |
| description | Abstract Bohuai goat is a crossbreeding breed between Huai goat and Boer goat, which has higher meat yield and reproductive efficiency. To explore the genetic basis of these traits, we sequenced the whole genome of 289 samples from 8 Chinese local goat populations and Boer goats. Through variation detection and genetic diversity analysis, we identified 68,166,098 SNPs and assessed genetic diversity parameters such as nucleotide diversity, linkage disequilibrium, and homozygous regions (ROH). The analysis of population structure showed that there was a close genetic relationship between Bohuai goat and Boer goat, which was significantly different from that of Chinese native breeds. Fst, Pi_ratio and XPEHH methods were used to analyze the low reproduction rate population of Bohuai goat.. We found a strong selection in a region of BMPR1B on chr6, which may be associated with the high fertility of Bohuai goats and was also detected in the Vst. In addition, a CNVR fragment (GLIS3 gene) was found to be associated with spermatogenesis in the detection of CNV analysis. Our results provide insights for understanding the genetic diversity and selection of reproductive traits of Bohuai goats. They also offer evidence for the correlation between the BMPR1B gene and reproductive traits and provide information for molecular breeding strategies of other goat breeds. |
| format | Article |
| id | doaj-art-584632dfa6f1498abf2a4f0d5fdd5af9 |
| institution | Kabale University |
| issn | 1471-2164 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | BMC |
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| series | BMC Genomics |
| spelling | doaj-art-584632dfa6f1498abf2a4f0d5fdd5af92025-08-20T03:42:40ZengBMCBMC Genomics1471-21642025-07-0126111110.1186/s12864-025-11878-2Genetic diversity and reproductive trait selection signal analysis of Bohuai goats based on whole genome sequencingYuqiao Zhang0Hua He1Qinwei Yu2Xingya Song3Jun Ma4Jiamei Wang5Yongpan Wang6Yu Jiang7Zejun Xu8Xianwei Wang9Yongzhen Huang10College of Animal Science and Technology, Northwest A&F UniversityCollege of Veterinary Medicine, Northwest A&F UniversityInternational Exchange and Cooperation Division, Northwest A&F UniversityCollege of Animal Science and Technology, Northwest A&F UniversityCollege of Animal Science and Technology, Northwest A&F UniversityCollege of Animal Science and Technology, Northwest A&F UniversityCollege of Animal Science and Technology, Northwest A&F UniversityCollege of Animal Science and Technology, Northwest A&F UniversityHenan Provincial Animal Husbandry Technology Promotion StationHenan Provincial Animal Husbandry Technology Promotion StationCollege of Animal Science and Technology, Northwest A&F UniversityAbstract Bohuai goat is a crossbreeding breed between Huai goat and Boer goat, which has higher meat yield and reproductive efficiency. To explore the genetic basis of these traits, we sequenced the whole genome of 289 samples from 8 Chinese local goat populations and Boer goats. Through variation detection and genetic diversity analysis, we identified 68,166,098 SNPs and assessed genetic diversity parameters such as nucleotide diversity, linkage disequilibrium, and homozygous regions (ROH). The analysis of population structure showed that there was a close genetic relationship between Bohuai goat and Boer goat, which was significantly different from that of Chinese native breeds. Fst, Pi_ratio and XPEHH methods were used to analyze the low reproduction rate population of Bohuai goat.. We found a strong selection in a region of BMPR1B on chr6, which may be associated with the high fertility of Bohuai goats and was also detected in the Vst. In addition, a CNVR fragment (GLIS3 gene) was found to be associated with spermatogenesis in the detection of CNV analysis. Our results provide insights for understanding the genetic diversity and selection of reproductive traits of Bohuai goats. They also offer evidence for the correlation between the BMPR1B gene and reproductive traits and provide information for molecular breeding strategies of other goat breeds.https://doi.org/10.1186/s12864-025-11878-2Bohuai goatPopulation structureSelectionReproduction |
| spellingShingle | Yuqiao Zhang Hua He Qinwei Yu Xingya Song Jun Ma Jiamei Wang Yongpan Wang Yu Jiang Zejun Xu Xianwei Wang Yongzhen Huang Genetic diversity and reproductive trait selection signal analysis of Bohuai goats based on whole genome sequencing BMC Genomics Bohuai goat Population structure Selection Reproduction |
| title | Genetic diversity and reproductive trait selection signal analysis of Bohuai goats based on whole genome sequencing |
| title_full | Genetic diversity and reproductive trait selection signal analysis of Bohuai goats based on whole genome sequencing |
| title_fullStr | Genetic diversity and reproductive trait selection signal analysis of Bohuai goats based on whole genome sequencing |
| title_full_unstemmed | Genetic diversity and reproductive trait selection signal analysis of Bohuai goats based on whole genome sequencing |
| title_short | Genetic diversity and reproductive trait selection signal analysis of Bohuai goats based on whole genome sequencing |
| title_sort | genetic diversity and reproductive trait selection signal analysis of bohuai goats based on whole genome sequencing |
| topic | Bohuai goat Population structure Selection Reproduction |
| url | https://doi.org/10.1186/s12864-025-11878-2 |
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