Identification of Candidate Genes Associated with Yak Body Size Using a Genome-Wide Association Study and Multiple Populations of Information
Yaks have evolved several breeds or genetic resources owing to their geographical and ecological environment, and investigating the genetic construction of body size among breeds is key for breeding. Here, a genome-wide association study (GWAS) was performed for five body size traits in 31 yak breed...
| Main Authors: | , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2023-04-01
|
| Series: | Animals |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2076-2615/13/9/1470 |
| _version_ | 1797603077782503424 |
|---|---|
| author | Xinrui Liu Mingxiu Wang Jie Qin Yaxin Liu Zhixin Chai Wei Peng Yixi Kangzhu Jincheng Zhong Jiabo Wang |
| author_facet | Xinrui Liu Mingxiu Wang Jie Qin Yaxin Liu Zhixin Chai Wei Peng Yixi Kangzhu Jincheng Zhong Jiabo Wang |
| author_sort | Xinrui Liu |
| collection | DOAJ |
| description | Yaks have evolved several breeds or genetic resources owing to their geographical and ecological environment, and investigating the genetic construction of body size among breeds is key for breeding. Here, a genome-wide association study (GWAS) was performed for five body size traits in 31 yak breeds and genetic resources. The information from clustering individuals according to their habitats was used for kinship grouping in the compressed mixed linear model (CMLM). We named this approach the pCMLM method. A total of 3,584,464 high-quality single nucleotide polymorphisms (SNPs) were obtained, and six markers were found to be significantly associated with height by pCMLM. Four candidate genes, including <i>FXYD6</i>, <i>SOHLH2</i>, <i>ADGRB2</i>, and <i>OSBPL6</i>, were identified. Our results show that when CMLM cannot identify optimal clustering groups, pCMLM can provide sufficient associated results based on population information. Moreover, this study provides basic information on the gene localization of quantitative traits of body size among yak breeds. |
| first_indexed | 2024-03-11T04:25:17Z |
| format | Article |
| id | doaj.art-92ff7b3439744afd92ca62b2224995de |
| institution | Directory Open Access Journal |
| issn | 2076-2615 |
| language | English |
| last_indexed | 2024-03-11T04:25:17Z |
| publishDate | 2023-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Animals |
| spelling | doaj.art-92ff7b3439744afd92ca62b2224995de2023-11-17T22:29:32ZengMDPI AGAnimals2076-26152023-04-01139147010.3390/ani13091470Identification of Candidate Genes Associated with Yak Body Size Using a Genome-Wide Association Study and Multiple Populations of InformationXinrui Liu0Mingxiu Wang1Jie Qin2Yaxin Liu3Zhixin Chai4Wei Peng5Yixi Kangzhu6Jincheng Zhong7Jiabo Wang8Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education and Sichuan Province, Southwest Minzu University, Chengdu 610041, ChinaKey Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education and Sichuan Province, Southwest Minzu University, Chengdu 610041, ChinaKey Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education and Sichuan Province, Southwest Minzu University, Chengdu 610041, ChinaKey Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education and Sichuan Province, Southwest Minzu University, Chengdu 610041, ChinaKey Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education and Sichuan Province, Southwest Minzu University, Chengdu 610041, ChinaQinghai Academy of Animal Science and Veterinary Science, Qinghai University, Xining 810016, ChinaKey Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education and Sichuan Province, Southwest Minzu University, Chengdu 610041, ChinaKey Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education and Sichuan Province, Southwest Minzu University, Chengdu 610041, ChinaKey Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education and Sichuan Province, Southwest Minzu University, Chengdu 610041, ChinaYaks have evolved several breeds or genetic resources owing to their geographical and ecological environment, and investigating the genetic construction of body size among breeds is key for breeding. Here, a genome-wide association study (GWAS) was performed for five body size traits in 31 yak breeds and genetic resources. The information from clustering individuals according to their habitats was used for kinship grouping in the compressed mixed linear model (CMLM). We named this approach the pCMLM method. A total of 3,584,464 high-quality single nucleotide polymorphisms (SNPs) were obtained, and six markers were found to be significantly associated with height by pCMLM. Four candidate genes, including <i>FXYD6</i>, <i>SOHLH2</i>, <i>ADGRB2</i>, and <i>OSBPL6</i>, were identified. Our results show that when CMLM cannot identify optimal clustering groups, pCMLM can provide sufficient associated results based on population information. Moreover, this study provides basic information on the gene localization of quantitative traits of body size among yak breeds.https://www.mdpi.com/2076-2615/13/9/1470yakgenetic resourcegenome-wide association studybody size traitgenetic characteristicextended model |
| spellingShingle | Xinrui Liu Mingxiu Wang Jie Qin Yaxin Liu Zhixin Chai Wei Peng Yixi Kangzhu Jincheng Zhong Jiabo Wang Identification of Candidate Genes Associated with Yak Body Size Using a Genome-Wide Association Study and Multiple Populations of Information Animals yak genetic resource genome-wide association study body size trait genetic characteristic extended model |
| title | Identification of Candidate Genes Associated with Yak Body Size Using a Genome-Wide Association Study and Multiple Populations of Information |
| title_full | Identification of Candidate Genes Associated with Yak Body Size Using a Genome-Wide Association Study and Multiple Populations of Information |
| title_fullStr | Identification of Candidate Genes Associated with Yak Body Size Using a Genome-Wide Association Study and Multiple Populations of Information |
| title_full_unstemmed | Identification of Candidate Genes Associated with Yak Body Size Using a Genome-Wide Association Study and Multiple Populations of Information |
| title_short | Identification of Candidate Genes Associated with Yak Body Size Using a Genome-Wide Association Study and Multiple Populations of Information |
| title_sort | identification of candidate genes associated with yak body size using a genome wide association study and multiple populations of information |
| topic | yak genetic resource genome-wide association study body size trait genetic characteristic extended model |
| url | https://www.mdpi.com/2076-2615/13/9/1470 |
| work_keys_str_mv | AT xinruiliu identificationofcandidategenesassociatedwithyakbodysizeusingagenomewideassociationstudyandmultiplepopulationsofinformation AT mingxiuwang identificationofcandidategenesassociatedwithyakbodysizeusingagenomewideassociationstudyandmultiplepopulationsofinformation AT jieqin identificationofcandidategenesassociatedwithyakbodysizeusingagenomewideassociationstudyandmultiplepopulationsofinformation AT yaxinliu identificationofcandidategenesassociatedwithyakbodysizeusingagenomewideassociationstudyandmultiplepopulationsofinformation AT zhixinchai identificationofcandidategenesassociatedwithyakbodysizeusingagenomewideassociationstudyandmultiplepopulationsofinformation AT weipeng identificationofcandidategenesassociatedwithyakbodysizeusingagenomewideassociationstudyandmultiplepopulationsofinformation AT yixikangzhu identificationofcandidategenesassociatedwithyakbodysizeusingagenomewideassociationstudyandmultiplepopulationsofinformation AT jinchengzhong identificationofcandidategenesassociatedwithyakbodysizeusingagenomewideassociationstudyandmultiplepopulationsofinformation AT jiabowang identificationofcandidategenesassociatedwithyakbodysizeusingagenomewideassociationstudyandmultiplepopulationsofinformation |