Favored single nucleotide variants identified using whole genome Re-sequencing of Austrian and Chinese cattle breeds
Cattle have been essential for the development of human civilization since their first domestication few thousand years ago. Since then, they have spread across vast geographic areas following human activities. Throughout generations, the cattle genome has been shaped with detectable signals induced...
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Frontiers Media S.A.
2022-09-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2022.974787/full |
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| author | Maulana M. Naji Yifan Jiang Yuri T. Utsunomiya Benjamin D. Rosen Johann Sölkner Chuduan Wang Li Jiang Qin Zhang Yi Zhang Xiangdong Ding Gábor Mészáros |
| author_facet | Maulana M. Naji Yifan Jiang Yuri T. Utsunomiya Benjamin D. Rosen Johann Sölkner Chuduan Wang Li Jiang Qin Zhang Yi Zhang Xiangdong Ding Gábor Mészáros |
| author_sort | Maulana M. Naji |
| collection | DOAJ |
| description | Cattle have been essential for the development of human civilization since their first domestication few thousand years ago. Since then, they have spread across vast geographic areas following human activities. Throughout generations, the cattle genome has been shaped with detectable signals induced by various evolutionary processes, such as natural and human selection processes and demographic events. Identifying such signals, called selection signatures, is one of the primary goals of population genetics. Previous studies used various selection signature methods and normalized the outputs score using specific windows, in kbp or based on the number of SNPs, to identify the candidate regions. The recent method of iSAFE claimed for high accuracy in pinpointing the candidate SNPs. In this study, we analyzed whole-genome resequencing (WGS) data of ten individuals from Austrian Fleckvieh (Bos taurus) and fifty individuals from 14 Chinese indigenous breeds (Bos taurus, Bos taurus indicus, and admixed). Individual WGS reads were aligned to the cattle reference genome of ARS. UCD1.2 and subsequently undergone single nucleotide variants (SNVs) calling pipeline using GATK. Using these SNVs, we examined the population structure using principal component and admixture analysis. Then we refined selection signature candidates using the iSAFE program and compared it with the classical iHS approach. Additionally, we run Fst population differentiation from these two cattle groups. We found gradual changes of taurine in north China to admixed and indicine to the south. Based on the population structure and the number of individuals, we grouped samples to Fleckvieh, three Chinese taurines (Kazakh, Mongolian, Yanbian), admixed individuals (CHBI_Med), indicine individuals (CHBI_Low), and a combination of admixed and indicine (CHBI) for performing iSAFE and iHS tests. There were more significant SNVs identified using iSAFE than the iHS for the candidate of positive selection and more detectable signals in taurine than in indicine individuals. However, combining admixed and indicine individuals decreased the iSAFE signals. From both within-population tests, significant SNVs are linked to the olfactory receptors, production, reproduction, and temperament traits in taurine cattle, while heat and parasites tolerance in the admixed individuals. Fst test suggests similar patterns of population differentiation between Fleckvieh and three Chinese taurine breeds against CHBI. Nevertheless, there are genes shared only among the Chinese taurine, such as PAX5, affecting coat color, which might drive the differences between these yellowish coated breeds, and those in the greater Far East region. |
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| last_indexed | 2024-04-12T18:12:32Z |
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| spelling | doaj.art-d7a7cf81e59e4956b19e54ecfaf1d53f2022-12-22T03:21:46ZengFrontiers Media S.A.Frontiers in Genetics1664-80212022-09-011310.3389/fgene.2022.974787974787Favored single nucleotide variants identified using whole genome Re-sequencing of Austrian and Chinese cattle breedsMaulana M. Naji0Yifan Jiang1Yuri T. Utsunomiya2Benjamin D. Rosen3Johann Sölkner4Chuduan Wang5Li Jiang6Qin Zhang7Yi Zhang8Xiangdong Ding9Gábor Mészáros10University of Natural Resources and Life Sciences, Vienna, AustriaChina Agricultural University, Beijing, ChinaDepartment of Production and Animal Health, School of Veterinary Medicine, São Paulo State University (Unesp), Araçatuba, BrazilAnimal Genomics and Improvement Laboratory, USDA‐ARS, Beltsville, MD, United StatesUniversity of Natural Resources and Life Sciences, Vienna, AustriaChina Agricultural University, Beijing, ChinaChina Agricultural University, Beijing, ChinaChina Agricultural University, Beijing, ChinaChina Agricultural University, Beijing, ChinaChina Agricultural University, Beijing, ChinaUniversity of Natural Resources and Life Sciences, Vienna, AustriaCattle have been essential for the development of human civilization since their first domestication few thousand years ago. Since then, they have spread across vast geographic areas following human activities. Throughout generations, the cattle genome has been shaped with detectable signals induced by various evolutionary processes, such as natural and human selection processes and demographic events. Identifying such signals, called selection signatures, is one of the primary goals of population genetics. Previous studies used various selection signature methods and normalized the outputs score using specific windows, in kbp or based on the number of SNPs, to identify the candidate regions. The recent method of iSAFE claimed for high accuracy in pinpointing the candidate SNPs. In this study, we analyzed whole-genome resequencing (WGS) data of ten individuals from Austrian Fleckvieh (Bos taurus) and fifty individuals from 14 Chinese indigenous breeds (Bos taurus, Bos taurus indicus, and admixed). Individual WGS reads were aligned to the cattle reference genome of ARS. UCD1.2 and subsequently undergone single nucleotide variants (SNVs) calling pipeline using GATK. Using these SNVs, we examined the population structure using principal component and admixture analysis. Then we refined selection signature candidates using the iSAFE program and compared it with the classical iHS approach. Additionally, we run Fst population differentiation from these two cattle groups. We found gradual changes of taurine in north China to admixed and indicine to the south. Based on the population structure and the number of individuals, we grouped samples to Fleckvieh, three Chinese taurines (Kazakh, Mongolian, Yanbian), admixed individuals (CHBI_Med), indicine individuals (CHBI_Low), and a combination of admixed and indicine (CHBI) for performing iSAFE and iHS tests. There were more significant SNVs identified using iSAFE than the iHS for the candidate of positive selection and more detectable signals in taurine than in indicine individuals. However, combining admixed and indicine individuals decreased the iSAFE signals. From both within-population tests, significant SNVs are linked to the olfactory receptors, production, reproduction, and temperament traits in taurine cattle, while heat and parasites tolerance in the admixed individuals. Fst test suggests similar patterns of population differentiation between Fleckvieh and three Chinese taurine breeds against CHBI. Nevertheless, there are genes shared only among the Chinese taurine, such as PAX5, affecting coat color, which might drive the differences between these yellowish coated breeds, and those in the greater Far East region.https://www.frontiersin.org/articles/10.3389/fgene.2022.974787/fullcattlewhole-genome sequence (WGS)selection signatureBos taurusbos indicusiSAFE |
| spellingShingle | Maulana M. Naji Yifan Jiang Yuri T. Utsunomiya Benjamin D. Rosen Johann Sölkner Chuduan Wang Li Jiang Qin Zhang Yi Zhang Xiangdong Ding Gábor Mészáros Favored single nucleotide variants identified using whole genome Re-sequencing of Austrian and Chinese cattle breeds Frontiers in Genetics cattle whole-genome sequence (WGS) selection signature Bos taurus bos indicus iSAFE |
| title | Favored single nucleotide variants identified using whole genome Re-sequencing of Austrian and Chinese cattle breeds |
| title_full | Favored single nucleotide variants identified using whole genome Re-sequencing of Austrian and Chinese cattle breeds |
| title_fullStr | Favored single nucleotide variants identified using whole genome Re-sequencing of Austrian and Chinese cattle breeds |
| title_full_unstemmed | Favored single nucleotide variants identified using whole genome Re-sequencing of Austrian and Chinese cattle breeds |
| title_short | Favored single nucleotide variants identified using whole genome Re-sequencing of Austrian and Chinese cattle breeds |
| title_sort | favored single nucleotide variants identified using whole genome re sequencing of austrian and chinese cattle breeds |
| topic | cattle whole-genome sequence (WGS) selection signature Bos taurus bos indicus iSAFE |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2022.974787/full |
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