Analysis of genomic selection characteristics of local cattle breeds in Gansu
Abstract Background The distinctive geography and climate of Gansu Province have given rise to three indigenous cattle breeds—Zaosheng, Anxi, and Yangba. Renowned for their superior meat quality and remarkable adaptability, these breeds are crucial for maintaining genetic diversity. However, they ar...
Saved in:
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2025-07-01
|
| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12864-025-11753-0 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849402961299505152 |
|---|---|
| author | Bao Cai Yandong Kang Lin Xiong Jie Pei Qianyun Ge Xiaoyun Wu Manyu Gan Xian Guo |
| author_facet | Bao Cai Yandong Kang Lin Xiong Jie Pei Qianyun Ge Xiaoyun Wu Manyu Gan Xian Guo |
| author_sort | Bao Cai |
| collection | DOAJ |
| description | Abstract Background The distinctive geography and climate of Gansu Province have given rise to three indigenous cattle breeds—Zaosheng, Anxi, and Yangba. Renowned for their superior meat quality and remarkable adaptability, these breeds are crucial for maintaining genetic diversity. However, they are under threat from intensive farming practices, environmental degradation, and genetic drift, which could lead to an irreversible loss of genetic resources. Thanks to natural and artificial selection, these breeds possess genetic markers that enhance their adaptation to extreme environments and improve key economic traits. By integrating comprehensive genome data from multiple breeds, this study aims to analyze population genetics, detect composite selection signals, and perform functional enrichment to uncover the mechanisms behind genetic differentiation and adaptive evolution. This research is pivotal for developing resilient breeds and ensuring sustainable resource management. Results The genetic background of local cattle breeds in Gansu shows a mix between indicine cattle (Bos indicus) and taurine cattle (Bos taurus), with geographical differentiation: Yangba cattle in the southeast mainly exhibit indicine ancestry (54.43%), while Anxi and Zaosheng cattle in the northwest show a predominance of taurine ancestry (86.51% and 74.81%, respectively). This divergence is closely related to historical ethnic migrations, geographic barriers, and gene flow along the Silk Road. Selection signal analysis has revealed specific adaptation mechanisms in different populations: Yangba cattle exhibit strong selection signals in the T-cell receptor pathway (FYN, FYB1) and skeletal development genes (SOX6), which may be related to their adaptation to hot and humid environments and mountainous terrain; Anxi cattle show adaptive evolution in nitrogen metabolism (CA8, CA10) and adherens junction pathways (CTNNA2), possibly reflecting the genetic basis for their adaptation to arid conditions; Zaosheng cattle display strong selection signals in muscle development (LARGE1, SGCZ) and immune regulation genes (SLAMF family), likely associated with enhanced meat production performance and increased pathogen resistance driven by artificial breeding. Conclusion This study explores the drivers of genetic diversity and adaptive evolution in Gansu’s native cattle breeds, emphasizing the impact of geography and human activity on genetic divergence. It provides a theoretical basis for conserving breed resources, identifying functional genes, and developing breeding strategies. |
| format | Article |
| id | doaj-art-100a70f4d99a4a6fb9560298caefe599 |
| institution | Kabale University |
| issn | 1471-2164 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj-art-100a70f4d99a4a6fb9560298caefe5992025-08-20T03:37:23ZengBMCBMC Genomics1471-21642025-07-0126111210.1186/s12864-025-11753-0Analysis of genomic selection characteristics of local cattle breeds in GansuBao Cai0Yandong Kang1Lin Xiong2Jie Pei3Qianyun Ge4Xiaoyun Wu5Manyu Gan6Xian Guo7Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural SciencesKey Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural SciencesKey Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural SciencesKey Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural SciencesKey Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural SciencesKey Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural SciencesSubei Mongolian Autonomous County Animal Husbandry Service CenterKey Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural SciencesAbstract Background The distinctive geography and climate of Gansu Province have given rise to three indigenous cattle breeds—Zaosheng, Anxi, and Yangba. Renowned for their superior meat quality and remarkable adaptability, these breeds are crucial for maintaining genetic diversity. However, they are under threat from intensive farming practices, environmental degradation, and genetic drift, which could lead to an irreversible loss of genetic resources. Thanks to natural and artificial selection, these breeds possess genetic markers that enhance their adaptation to extreme environments and improve key economic traits. By integrating comprehensive genome data from multiple breeds, this study aims to analyze population genetics, detect composite selection signals, and perform functional enrichment to uncover the mechanisms behind genetic differentiation and adaptive evolution. This research is pivotal for developing resilient breeds and ensuring sustainable resource management. Results The genetic background of local cattle breeds in Gansu shows a mix between indicine cattle (Bos indicus) and taurine cattle (Bos taurus), with geographical differentiation: Yangba cattle in the southeast mainly exhibit indicine ancestry (54.43%), while Anxi and Zaosheng cattle in the northwest show a predominance of taurine ancestry (86.51% and 74.81%, respectively). This divergence is closely related to historical ethnic migrations, geographic barriers, and gene flow along the Silk Road. Selection signal analysis has revealed specific adaptation mechanisms in different populations: Yangba cattle exhibit strong selection signals in the T-cell receptor pathway (FYN, FYB1) and skeletal development genes (SOX6), which may be related to their adaptation to hot and humid environments and mountainous terrain; Anxi cattle show adaptive evolution in nitrogen metabolism (CA8, CA10) and adherens junction pathways (CTNNA2), possibly reflecting the genetic basis for their adaptation to arid conditions; Zaosheng cattle display strong selection signals in muscle development (LARGE1, SGCZ) and immune regulation genes (SLAMF family), likely associated with enhanced meat production performance and increased pathogen resistance driven by artificial breeding. Conclusion This study explores the drivers of genetic diversity and adaptive evolution in Gansu’s native cattle breeds, emphasizing the impact of geography and human activity on genetic divergence. It provides a theoretical basis for conserving breed resources, identifying functional genes, and developing breeding strategies.https://doi.org/10.1186/s12864-025-11753-0Gansu local breedsPopulation geneticsGenetic evolutionWhole-genome re-sequencing |
| spellingShingle | Bao Cai Yandong Kang Lin Xiong Jie Pei Qianyun Ge Xiaoyun Wu Manyu Gan Xian Guo Analysis of genomic selection characteristics of local cattle breeds in Gansu BMC Genomics Gansu local breeds Population genetics Genetic evolution Whole-genome re-sequencing |
| title | Analysis of genomic selection characteristics of local cattle breeds in Gansu |
| title_full | Analysis of genomic selection characteristics of local cattle breeds in Gansu |
| title_fullStr | Analysis of genomic selection characteristics of local cattle breeds in Gansu |
| title_full_unstemmed | Analysis of genomic selection characteristics of local cattle breeds in Gansu |
| title_short | Analysis of genomic selection characteristics of local cattle breeds in Gansu |
| title_sort | analysis of genomic selection characteristics of local cattle breeds in gansu |
| topic | Gansu local breeds Population genetics Genetic evolution Whole-genome re-sequencing |
| url | https://doi.org/10.1186/s12864-025-11753-0 |
| work_keys_str_mv | AT baocai analysisofgenomicselectioncharacteristicsoflocalcattlebreedsingansu AT yandongkang analysisofgenomicselectioncharacteristicsoflocalcattlebreedsingansu AT linxiong analysisofgenomicselectioncharacteristicsoflocalcattlebreedsingansu AT jiepei analysisofgenomicselectioncharacteristicsoflocalcattlebreedsingansu AT qianyunge analysisofgenomicselectioncharacteristicsoflocalcattlebreedsingansu AT xiaoyunwu analysisofgenomicselectioncharacteristicsoflocalcattlebreedsingansu AT manyugan analysisofgenomicselectioncharacteristicsoflocalcattlebreedsingansu AT xianguo analysisofgenomicselectioncharacteristicsoflocalcattlebreedsingansu |