Genome-Wide Association Study for Screening and Identifying Potential Shin Color Loci in Ducks
Shin color diversity is a widespread phenomenon in birds. In this study, ducks were assessed to identify candidate genes for yellow, black, and spotted tibiae. For this purpose, we performed whole-genome resequencing of an F<sub>2</sub> population consisting of 275 ducks crossed between...
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MDPI AG
2022-08-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/13/8/1391 |
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| author | Qixin Guo Yong Jiang Zhixiu Wang Yulin Bi Guohong Chen Hao Bai Guobin Chang |
| author_facet | Qixin Guo Yong Jiang Zhixiu Wang Yulin Bi Guohong Chen Hao Bai Guobin Chang |
| author_sort | Qixin Guo |
| collection | DOAJ |
| description | Shin color diversity is a widespread phenomenon in birds. In this study, ducks were assessed to identify candidate genes for yellow, black, and spotted tibiae. For this purpose, we performed whole-genome resequencing of an F<sub>2</sub> population consisting of 275 ducks crossed between Runzhou crested-white ducks and Cherry Valley ducks. We obtained 12.6 Mb of single nucleotide polymorphism (SNP) data, and the three shin colors were subsequently genotyped. Genome-wide association studies (GWASs) were performed to identify candidate and potential SNPs for the three shin colors. According to the results, 2947 and 3451 significant SNPs were associated with black and yellow shins, respectively, and six potential SNPs were associated with spotted shins. Based on the SNP annotations, the <i>MITF</i>, <i>EDNRB2</i>, POU family members, and the SLC superfamily were the candidate genes regulating pigmentation. In addition, the isoforms of <i>EDNRB2</i>, <i>TYR</i>, <i>TYRP1</i>, and MITF-M were significantly different between the black and yellow tibiae. <i>MITF</i> and <i>EDNRB2</i> may have synergistic roles in the regulation of melanin synthesis, and their mutations may lead to phenotypic differences in the melanin deposition between individuals. This study provides new insights into the genetic factors that may influence tibia color diversity in birds. |
| first_indexed | 2024-03-09T04:24:19Z |
| format | Article |
| id | doaj.art-dbdd7429beba4a6b9c8d4e5d8a7d78e1 |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-09T04:24:19Z |
| publishDate | 2022-08-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-dbdd7429beba4a6b9c8d4e5d8a7d78e12023-12-03T13:42:55ZengMDPI AGGenes2073-44252022-08-01138139110.3390/genes13081391Genome-Wide Association Study for Screening and Identifying Potential Shin Color Loci in DucksQixin Guo0Yong Jiang1Zhixiu Wang2Yulin Bi3Guohong Chen4Hao Bai5Guobin Chang6College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, ChinaCollege of Animal Science and Technology, Yangzhou University, Yangzhou 225009, ChinaCollege of Animal Science and Technology, Yangzhou University, Yangzhou 225009, ChinaCollege of Animal Science and Technology, Yangzhou University, Yangzhou 225009, ChinaCollege of Animal Science and Technology, Yangzhou University, Yangzhou 225009, ChinaCollege of Animal Science and Technology, Yangzhou University, Yangzhou 225009, ChinaCollege of Animal Science and Technology, Yangzhou University, Yangzhou 225009, ChinaShin color diversity is a widespread phenomenon in birds. In this study, ducks were assessed to identify candidate genes for yellow, black, and spotted tibiae. For this purpose, we performed whole-genome resequencing of an F<sub>2</sub> population consisting of 275 ducks crossed between Runzhou crested-white ducks and Cherry Valley ducks. We obtained 12.6 Mb of single nucleotide polymorphism (SNP) data, and the three shin colors were subsequently genotyped. Genome-wide association studies (GWASs) were performed to identify candidate and potential SNPs for the three shin colors. According to the results, 2947 and 3451 significant SNPs were associated with black and yellow shins, respectively, and six potential SNPs were associated with spotted shins. Based on the SNP annotations, the <i>MITF</i>, <i>EDNRB2</i>, POU family members, and the SLC superfamily were the candidate genes regulating pigmentation. In addition, the isoforms of <i>EDNRB2</i>, <i>TYR</i>, <i>TYRP1</i>, and MITF-M were significantly different between the black and yellow tibiae. <i>MITF</i> and <i>EDNRB2</i> may have synergistic roles in the regulation of melanin synthesis, and their mutations may lead to phenotypic differences in the melanin deposition between individuals. This study provides new insights into the genetic factors that may influence tibia color diversity in birds.https://www.mdpi.com/2073-4425/13/8/1391duckshin colorGWASmelanin |
| spellingShingle | Qixin Guo Yong Jiang Zhixiu Wang Yulin Bi Guohong Chen Hao Bai Guobin Chang Genome-Wide Association Study for Screening and Identifying Potential Shin Color Loci in Ducks Genes duck shin color GWAS melanin |
| title | Genome-Wide Association Study for Screening and Identifying Potential Shin Color Loci in Ducks |
| title_full | Genome-Wide Association Study for Screening and Identifying Potential Shin Color Loci in Ducks |
| title_fullStr | Genome-Wide Association Study for Screening and Identifying Potential Shin Color Loci in Ducks |
| title_full_unstemmed | Genome-Wide Association Study for Screening and Identifying Potential Shin Color Loci in Ducks |
| title_short | Genome-Wide Association Study for Screening and Identifying Potential Shin Color Loci in Ducks |
| title_sort | genome wide association study for screening and identifying potential shin color loci in ducks |
| topic | duck shin color GWAS melanin |
| url | https://www.mdpi.com/2073-4425/13/8/1391 |
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