Runs of Homozygosity Analysis Reveals Genomic Diversity and Population Structure of an Indigenous Cattle Breed in Southwest China
In aiming to achieve sustainable development goals in the livestock industry, it is becoming increasingly necessary and important for the effective conservation of genetic resources. There are some indigenous cattle breeds in Sichuan, southwest China, for which, however, the genetic diversity and po...
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MDPI AG
2022-11-01
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| author | Wei Wang Yi Shi Fang He Donghui Fang Jia Gan Fuqiu Wu Yueda AG Xiaodong Deng Qi Cao Chu Duo Wangdeng RZ Maozhong Fu Jun Yi |
| author_facet | Wei Wang Yi Shi Fang He Donghui Fang Jia Gan Fuqiu Wu Yueda AG Xiaodong Deng Qi Cao Chu Duo Wangdeng RZ Maozhong Fu Jun Yi |
| author_sort | Wei Wang |
| collection | DOAJ |
| description | In aiming to achieve sustainable development goals in the livestock industry, it is becoming increasingly necessary and important for the effective conservation of genetic resources. There are some indigenous cattle breeds in Sichuan, southwest China, for which, however, the genetic diversity and population structures still remain unknown because of the unavailability of systematic breeding programs and pedigree information. Xieka cattle are an indigenous breed locally distributed in southeastern Sichuan and have a long-term evolutionary adaptation to local environments and climates. In this study, we obtained 796,828 single nucleotide polymorphisms (SNPs) through sequencing the genomes of 30 Xieka cattle and used them for analyzing the genetic diversity and runs of homozygosity (ROH). The mean nucleotide diversity was 0.28 and 72% of SNPs were found to be in the heterozygous states. A total of 4377 ROH were detected with even distribution among all autosomes, and 74% of them were lower than 1 Mb in length. Meanwhile, only five ROH were found longer than 5 Mb. We further determined 19 significant genomic regions that were obviously enriched by ROH, in which 35 positional candidate genes were found. Some of these genes have been previously reported to be significantly associated with various production traits in cattle, such as meat quality, carcass performances, and diseases. In conclusion, the relatively high degree of genetic diversity of Xieka cattle was revealed using the genomic information, and the proposed candidate genes will help us optimize the breeding programs regarding this indigenous breed. |
| first_indexed | 2024-03-09T17:55:26Z |
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| language | English |
| last_indexed | 2024-03-09T17:55:26Z |
| publishDate | 2022-11-01 |
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| series | Animals |
| spelling | doaj.art-9bb9a7d108ff4379bc930deac43c19112023-11-24T10:23:49ZengMDPI AGAnimals2076-26152022-11-011223323910.3390/ani12233239Runs of Homozygosity Analysis Reveals Genomic Diversity and Population Structure of an Indigenous Cattle Breed in Southwest ChinaWei Wang0Yi Shi1Fang He2Donghui Fang3Jia Gan4Fuqiu Wu5Yueda AG6Xiaodong Deng7Qi Cao8Chu Duo9Wangdeng RZ10Maozhong Fu11Jun Yi12Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu 610066, ChinaAnimal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu 610066, ChinaAnimal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu 610066, ChinaAnimal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu 610066, ChinaAnimal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu 610066, ChinaJiulong County Agriculture, Animal Husbandry and Science and Technology Bureau, Jiulong 626200, ChinaAnimal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu 610066, ChinaAnimal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu 610066, ChinaJiulong County Agriculture, Animal Husbandry and Science and Technology Bureau, Jiulong 626200, ChinaJiulong County Agriculture, Animal Husbandry and Science and Technology Bureau, Jiulong 626200, ChinaJiulong County Agriculture, Animal Husbandry and Science and Technology Bureau, Jiulong 626200, ChinaAnimal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu 610066, ChinaAnimal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu 610066, ChinaIn aiming to achieve sustainable development goals in the livestock industry, it is becoming increasingly necessary and important for the effective conservation of genetic resources. There are some indigenous cattle breeds in Sichuan, southwest China, for which, however, the genetic diversity and population structures still remain unknown because of the unavailability of systematic breeding programs and pedigree information. Xieka cattle are an indigenous breed locally distributed in southeastern Sichuan and have a long-term evolutionary adaptation to local environments and climates. In this study, we obtained 796,828 single nucleotide polymorphisms (SNPs) through sequencing the genomes of 30 Xieka cattle and used them for analyzing the genetic diversity and runs of homozygosity (ROH). The mean nucleotide diversity was 0.28 and 72% of SNPs were found to be in the heterozygous states. A total of 4377 ROH were detected with even distribution among all autosomes, and 74% of them were lower than 1 Mb in length. Meanwhile, only five ROH were found longer than 5 Mb. We further determined 19 significant genomic regions that were obviously enriched by ROH, in which 35 positional candidate genes were found. Some of these genes have been previously reported to be significantly associated with various production traits in cattle, such as meat quality, carcass performances, and diseases. In conclusion, the relatively high degree of genetic diversity of Xieka cattle was revealed using the genomic information, and the proposed candidate genes will help us optimize the breeding programs regarding this indigenous breed.https://www.mdpi.com/2076-2615/12/23/3239Xieka cattleROHSNPsinbreedingSichuan |
| spellingShingle | Wei Wang Yi Shi Fang He Donghui Fang Jia Gan Fuqiu Wu Yueda AG Xiaodong Deng Qi Cao Chu Duo Wangdeng RZ Maozhong Fu Jun Yi Runs of Homozygosity Analysis Reveals Genomic Diversity and Population Structure of an Indigenous Cattle Breed in Southwest China Animals Xieka cattle ROH SNPs inbreeding Sichuan |
| title | Runs of Homozygosity Analysis Reveals Genomic Diversity and Population Structure of an Indigenous Cattle Breed in Southwest China |
| title_full | Runs of Homozygosity Analysis Reveals Genomic Diversity and Population Structure of an Indigenous Cattle Breed in Southwest China |
| title_fullStr | Runs of Homozygosity Analysis Reveals Genomic Diversity and Population Structure of an Indigenous Cattle Breed in Southwest China |
| title_full_unstemmed | Runs of Homozygosity Analysis Reveals Genomic Diversity and Population Structure of an Indigenous Cattle Breed in Southwest China |
| title_short | Runs of Homozygosity Analysis Reveals Genomic Diversity and Population Structure of an Indigenous Cattle Breed in Southwest China |
| title_sort | runs of homozygosity analysis reveals genomic diversity and population structure of an indigenous cattle breed in southwest china |
| topic | Xieka cattle ROH SNPs inbreeding Sichuan |
| url | https://www.mdpi.com/2076-2615/12/23/3239 |
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