The genome landscape of the Xinglong buffalo
Abstract Background Xinglong buffalo, as an indigenous breed in Hainan province of China, possesses characteristics such as high humidity tolerance, disease resistance and high reproductive capacity. Combined with whole genome sequencing technology, comprehensive investigation can be undertaken to e...
Saved in:
| Main Authors: | , , , , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2024-11-01
|
| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12864-024-10941-8 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1850061838175174656 |
|---|---|
| author | Yuan Chai Shiyuan Li Hui Wu Yong Meng Yujing Fu Hong Li Guansheng Wu Junming Jiang Taoyu Chen Yuqing Jiao Qiaoling Chen Li Du Lianbin Li Churiga Man Si Chen Hongyan Gao Wenguang Zhang Fengyang Wang |
| author_facet | Yuan Chai Shiyuan Li Hui Wu Yong Meng Yujing Fu Hong Li Guansheng Wu Junming Jiang Taoyu Chen Yuqing Jiao Qiaoling Chen Li Du Lianbin Li Churiga Man Si Chen Hongyan Gao Wenguang Zhang Fengyang Wang |
| author_sort | Yuan Chai |
| collection | DOAJ |
| description | Abstract Background Xinglong buffalo, as an indigenous breed in Hainan province of China, possesses characteristics such as high humidity tolerance, disease resistance and high reproductive capacity. Combined with whole genome sequencing technology, comprehensive investigation can be undertaken to elucidate the genomic characteristics, functions and genetic variation of Xinglong buffalo population. Results Xinglong buffalo has the highest genetic diversity, lowest runs of homozygosity average length, and fasted decay of linkage disequilibrium in our study population. Phylogenetic tree results revealed that Xinglong buffalo was gathered together with Fuzhong buffalo firstly. The population genetic structure analysis indicates that at K = 3, the Xinglong buffalo for the first time showed a distinct ancestral origin from other water buffalo. Furthermore, compared to different populations, candidate genes displaying significantly distinct patterns of single nucleotide polymorphisms (SNPs) (e.g., RYR2, COX15, PCDH9, DTWD2, FCRL5) distribution have been identified in the Xinglong buffalo. Conclusions Based on the whole genome sequencing data, this study identified a substantial number of SNPs and assessed the genetic diversity and selection signatures within the Xinglong buffalo population. These results contribute to understanding the genomic characteristics of Xinglong buffalo and their genetic evolutionary status. However, the practical significance of these signatures for genetic enhancement still requires confirmation through additional samples and further experimental validation. |
| format | Article |
| id | doaj-art-d4b610d11c894fcd9761e5aa4aeff38f |
| institution | DOAJ |
| issn | 1471-2164 |
| language | English |
| publishDate | 2024-11-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj-art-d4b610d11c894fcd9761e5aa4aeff38f2025-08-20T02:50:05ZengBMCBMC Genomics1471-21642024-11-0125111210.1186/s12864-024-10941-8The genome landscape of the Xinglong buffaloYuan Chai0Shiyuan Li1Hui Wu2Yong Meng3Yujing Fu4Hong Li5Guansheng Wu6Junming Jiang7Taoyu Chen8Yuqing Jiao9Qiaoling Chen10Li Du11Lianbin Li12Churiga Man13Si Chen14Hongyan Gao15Wenguang Zhang16Fengyang Wang17Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, Hainan UniversityHainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, Hainan UniversityHainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, Hainan UniversityHainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, Hainan UniversityHainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, Hainan UniversityHainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, Hainan UniversityHainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, Hainan UniversityHainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, Hainan UniversityHainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, Hainan UniversityHainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, Hainan UniversityHainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, Hainan UniversityHainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, Hainan UniversityHainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, Hainan UniversityHainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, Hainan UniversityHainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, Hainan UniversityHainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, Hainan UniversityCollege of Animal Science, Inner Mongolia Agricultural UniversityHainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, Hainan UniversityAbstract Background Xinglong buffalo, as an indigenous breed in Hainan province of China, possesses characteristics such as high humidity tolerance, disease resistance and high reproductive capacity. Combined with whole genome sequencing technology, comprehensive investigation can be undertaken to elucidate the genomic characteristics, functions and genetic variation of Xinglong buffalo population. Results Xinglong buffalo has the highest genetic diversity, lowest runs of homozygosity average length, and fasted decay of linkage disequilibrium in our study population. Phylogenetic tree results revealed that Xinglong buffalo was gathered together with Fuzhong buffalo firstly. The population genetic structure analysis indicates that at K = 3, the Xinglong buffalo for the first time showed a distinct ancestral origin from other water buffalo. Furthermore, compared to different populations, candidate genes displaying significantly distinct patterns of single nucleotide polymorphisms (SNPs) (e.g., RYR2, COX15, PCDH9, DTWD2, FCRL5) distribution have been identified in the Xinglong buffalo. Conclusions Based on the whole genome sequencing data, this study identified a substantial number of SNPs and assessed the genetic diversity and selection signatures within the Xinglong buffalo population. These results contribute to understanding the genomic characteristics of Xinglong buffalo and their genetic evolutionary status. However, the practical significance of these signatures for genetic enhancement still requires confirmation through additional samples and further experimental validation.https://doi.org/10.1186/s12864-024-10941-8Xinglong buffaloWhole-genome sequencingGenetic diversitySelection signature |
| spellingShingle | Yuan Chai Shiyuan Li Hui Wu Yong Meng Yujing Fu Hong Li Guansheng Wu Junming Jiang Taoyu Chen Yuqing Jiao Qiaoling Chen Li Du Lianbin Li Churiga Man Si Chen Hongyan Gao Wenguang Zhang Fengyang Wang The genome landscape of the Xinglong buffalo BMC Genomics Xinglong buffalo Whole-genome sequencing Genetic diversity Selection signature |
| title | The genome landscape of the Xinglong buffalo |
| title_full | The genome landscape of the Xinglong buffalo |
| title_fullStr | The genome landscape of the Xinglong buffalo |
| title_full_unstemmed | The genome landscape of the Xinglong buffalo |
| title_short | The genome landscape of the Xinglong buffalo |
| title_sort | genome landscape of the xinglong buffalo |
| topic | Xinglong buffalo Whole-genome sequencing Genetic diversity Selection signature |
| url | https://doi.org/10.1186/s12864-024-10941-8 |
| work_keys_str_mv | AT yuanchai thegenomelandscapeofthexinglongbuffalo AT shiyuanli thegenomelandscapeofthexinglongbuffalo AT huiwu thegenomelandscapeofthexinglongbuffalo AT yongmeng thegenomelandscapeofthexinglongbuffalo AT yujingfu thegenomelandscapeofthexinglongbuffalo AT hongli thegenomelandscapeofthexinglongbuffalo AT guanshengwu thegenomelandscapeofthexinglongbuffalo AT junmingjiang thegenomelandscapeofthexinglongbuffalo AT taoyuchen thegenomelandscapeofthexinglongbuffalo AT yuqingjiao thegenomelandscapeofthexinglongbuffalo AT qiaolingchen thegenomelandscapeofthexinglongbuffalo AT lidu thegenomelandscapeofthexinglongbuffalo AT lianbinli thegenomelandscapeofthexinglongbuffalo AT churigaman thegenomelandscapeofthexinglongbuffalo AT sichen thegenomelandscapeofthexinglongbuffalo AT hongyangao thegenomelandscapeofthexinglongbuffalo AT wenguangzhang thegenomelandscapeofthexinglongbuffalo AT fengyangwang thegenomelandscapeofthexinglongbuffalo AT yuanchai genomelandscapeofthexinglongbuffalo AT shiyuanli genomelandscapeofthexinglongbuffalo AT huiwu genomelandscapeofthexinglongbuffalo AT yongmeng genomelandscapeofthexinglongbuffalo AT yujingfu genomelandscapeofthexinglongbuffalo AT hongli genomelandscapeofthexinglongbuffalo AT guanshengwu genomelandscapeofthexinglongbuffalo AT junmingjiang genomelandscapeofthexinglongbuffalo AT taoyuchen genomelandscapeofthexinglongbuffalo AT yuqingjiao genomelandscapeofthexinglongbuffalo AT qiaolingchen genomelandscapeofthexinglongbuffalo AT lidu genomelandscapeofthexinglongbuffalo AT lianbinli genomelandscapeofthexinglongbuffalo AT churigaman genomelandscapeofthexinglongbuffalo AT sichen genomelandscapeofthexinglongbuffalo AT hongyangao genomelandscapeofthexinglongbuffalo AT wenguangzhang genomelandscapeofthexinglongbuffalo AT fengyangwang genomelandscapeofthexinglongbuffalo |