A Genome-Wide Association Study of the Chest Circumference Trait in Xinjiang Donkeys Based on Whole-Genome Sequencing Technology
Animal genotyping by means of genome-wide association studies is important for connecting phenotypes of interest with their underlying genetics in livestock. However, the use of whole genome sequencing to investigate chest circumference (CC) in donkeys has rarely been reported. We aimed to use the g...
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-05-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/14/5/1081 |
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| author | Ling-Ling Liu Bin Chen Sheng-Lei Chen Wu-Jun Liu |
| author_facet | Ling-Ling Liu Bin Chen Sheng-Lei Chen Wu-Jun Liu |
| author_sort | Ling-Ling Liu |
| collection | DOAJ |
| description | Animal genotyping by means of genome-wide association studies is important for connecting phenotypes of interest with their underlying genetics in livestock. However, the use of whole genome sequencing to investigate chest circumference (CC) in donkeys has rarely been reported. We aimed to use the genome-wide association study approach to detect significant single nucleotide polymorphisms (SNPs) and key genes associated with chest circumference traits in Xinjiang donkeys. We assessed 112 Xinjiang donkeys in this study. The chest circumference of each was measured 2 h before milking. We re-sequenced blood samples from the Xinjiang donkeys, and genome-wide association study analyses were performed using a mixed model with the PLINK, GEMMA, and REGENIE programs. We tested 38 donkeys for candidate SNPs for genome-wide association study using three software programs. Additionally, 18 SNP markers reached genome-wide significance (<i>p</i> < 1.61 × 10<sup>−9</sup>). On the basis of these, 41 genes were identified. Previously proposed candidate genes for CC traits were supported by this study, including <i>NFATC2</i> (Nuclear Factor of Activated T Cells 2), <i>PROP1</i> (PROP Paired-Like Homeobox 1), <i>UBB</i> (Ubiquitin B), and <i>HAND2</i> (Heart and Neural Crest Derivatives Expressed 2). These promising candidates provide a valuable resource for validating potential meat production genes and will facilitate the development of high-yielding Xinjiang donkey breeds through marker-assisted selection or gene editing. |
| first_indexed | 2024-03-11T03:42:59Z |
| format | Article |
| id | doaj.art-c53c8674bf0b41c1a9a531a40dcae754 |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-11T03:42:59Z |
| publishDate | 2023-05-01 |
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| record_format | Article |
| series | Genes |
| spelling | doaj.art-c53c8674bf0b41c1a9a531a40dcae7542023-11-18T01:30:12ZengMDPI AGGenes2073-44252023-05-01145108110.3390/genes14051081A Genome-Wide Association Study of the Chest Circumference Trait in Xinjiang Donkeys Based on Whole-Genome Sequencing TechnologyLing-Ling Liu0Bin Chen1Sheng-Lei Chen2Wu-Jun Liu3Department of Animal Science, Xinjiang Agricultural University, Urumqi 830052, ChinaDepartment of Animal Science, Xinjiang Agricultural University, Urumqi 830052, ChinaDepartment of Animal Science, Xinjiang Agricultural University, Urumqi 830052, ChinaDepartment of Animal Science, Xinjiang Agricultural University, Urumqi 830052, ChinaAnimal genotyping by means of genome-wide association studies is important for connecting phenotypes of interest with their underlying genetics in livestock. However, the use of whole genome sequencing to investigate chest circumference (CC) in donkeys has rarely been reported. We aimed to use the genome-wide association study approach to detect significant single nucleotide polymorphisms (SNPs) and key genes associated with chest circumference traits in Xinjiang donkeys. We assessed 112 Xinjiang donkeys in this study. The chest circumference of each was measured 2 h before milking. We re-sequenced blood samples from the Xinjiang donkeys, and genome-wide association study analyses were performed using a mixed model with the PLINK, GEMMA, and REGENIE programs. We tested 38 donkeys for candidate SNPs for genome-wide association study using three software programs. Additionally, 18 SNP markers reached genome-wide significance (<i>p</i> < 1.61 × 10<sup>−9</sup>). On the basis of these, 41 genes were identified. Previously proposed candidate genes for CC traits were supported by this study, including <i>NFATC2</i> (Nuclear Factor of Activated T Cells 2), <i>PROP1</i> (PROP Paired-Like Homeobox 1), <i>UBB</i> (Ubiquitin B), and <i>HAND2</i> (Heart and Neural Crest Derivatives Expressed 2). These promising candidates provide a valuable resource for validating potential meat production genes and will facilitate the development of high-yielding Xinjiang donkey breeds through marker-assisted selection or gene editing.https://www.mdpi.com/2073-4425/14/5/1081chest circumferenceXinjiang donkeyGWASPLINKkey genes |
| spellingShingle | Ling-Ling Liu Bin Chen Sheng-Lei Chen Wu-Jun Liu A Genome-Wide Association Study of the Chest Circumference Trait in Xinjiang Donkeys Based on Whole-Genome Sequencing Technology Genes chest circumference Xinjiang donkey GWAS PLINK key genes |
| title | A Genome-Wide Association Study of the Chest Circumference Trait in Xinjiang Donkeys Based on Whole-Genome Sequencing Technology |
| title_full | A Genome-Wide Association Study of the Chest Circumference Trait in Xinjiang Donkeys Based on Whole-Genome Sequencing Technology |
| title_fullStr | A Genome-Wide Association Study of the Chest Circumference Trait in Xinjiang Donkeys Based on Whole-Genome Sequencing Technology |
| title_full_unstemmed | A Genome-Wide Association Study of the Chest Circumference Trait in Xinjiang Donkeys Based on Whole-Genome Sequencing Technology |
| title_short | A Genome-Wide Association Study of the Chest Circumference Trait in Xinjiang Donkeys Based on Whole-Genome Sequencing Technology |
| title_sort | genome wide association study of the chest circumference trait in xinjiang donkeys based on whole genome sequencing technology |
| topic | chest circumference Xinjiang donkey GWAS PLINK key genes |
| url | https://www.mdpi.com/2073-4425/14/5/1081 |
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