Joint Genomic and Transcriptomic Analysis Reveals Candidate Genes Associated with Plumage Color Traits in Matahu Ducks
Plumage color is a key trait for identifying waterfowl breeds with significant economic importance. A white-feathered group has recently emerged within the native Matahu duck population, presenting an opportunity for breeding new lines. However, the genetic basis for this plumage variation is still...
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2024-10-01
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| author | Pengwei Ren Liu Yang Muhammad Zahoor Khan Yadi Jing Meixia Zhang Chao Qi Xin Zhang Xiang Liu Zhansheng Liu Shuer Zhang Mingxia Zhu |
| author_facet | Pengwei Ren Liu Yang Muhammad Zahoor Khan Yadi Jing Meixia Zhang Chao Qi Xin Zhang Xiang Liu Zhansheng Liu Shuer Zhang Mingxia Zhu |
| author_sort | Pengwei Ren |
| collection | DOAJ |
| description | Plumage color is a key trait for identifying waterfowl breeds with significant economic importance. A white-feathered group has recently emerged within the native Matahu duck population, presenting an opportunity for breeding new lines. However, the genetic basis for this plumage variation is still unknown, necessitating further research. This study aims to identify the genetic mechanisms underlying the emergence of white-feathered individuals in the Matahu duck population through combined genome and transcriptome analysis, providing insights for selective breeding and the development of new white-feathered lines. In this study, a total of 1344 selected genes and 1406 significantly differentially expressed genes were identified through selection signal analysis and transcriptomic analysis, respectively. The functional enrichment of these genes revealed several key signaling pathways, including those related to cGMP-PKG, cAMP, PI3K-Akt, and MAPK. Furthermore, important candidate genes involved in melanin biosynthesis, such as <i>MITF</i>, <i>MC1R</i>, <i>TYR</i>, <i>TYRP1</i>, and <i>ABCB6</i>, were identified. Notably, 107 genes were detected by both methods, and, among these, <i>DGKI</i>, <i>GPRC5B</i>, <i>HMX1</i>, <i>STS</i>, <i>ADGRA1</i>, <i>PRKAR2B</i>, and <i>HOXB9</i> are suggested to play a role in melanin formation and potentially influence plumage traits. Through the integrative approach combining genomic selection signals and transcriptomic analyses, we identified several candidate genes directly associated with plumage color, including <i>MITF</i>, <i>TYR</i>, <i>TYRP1</i>, and <i>MC1R</i>, along with multiple signaling pathways linked to melanin formation. We hypothesize that the expression of <i>DGKI</i>, <i>GPRC5B</i>, <i>HMX1</i>, <i>STS</i>, <i>ADGRA1</i>, <i>PRKAR2B</i>, and <i>HOXB9</i>, detected by both methods, may be closely related to the regulation of plumage color traits. These findings provide a foundational basis for further research aimed at elucidating the genetic mechanisms governing plumage color variation in ducks. |
| format | Article |
| id | doaj-art-253b32fe73b84cdf8ccf9b88c790c52d |
| institution | Kabale University |
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| publishDate | 2024-10-01 |
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| spelling | doaj-art-253b32fe73b84cdf8ccf9b88c790c52d2024-11-08T14:32:36ZengMDPI AGAnimals2076-26152024-10-011421311110.3390/ani14213111Joint Genomic and Transcriptomic Analysis Reveals Candidate Genes Associated with Plumage Color Traits in Matahu DucksPengwei Ren0Liu Yang1Muhammad Zahoor Khan2Yadi Jing3Meixia Zhang4Chao Qi5Xin Zhang6Xiang Liu7Zhansheng Liu8Shuer Zhang9Mingxia Zhu10College of Agriculture and Biology, Liaocheng University, Liaocheng 252000, ChinaCollege of Agriculture and Biology, Liaocheng University, Liaocheng 252000, ChinaCollege of Agriculture and Biology, Liaocheng University, Liaocheng 252000, ChinaCollege of Agriculture and Biology, Liaocheng University, Liaocheng 252000, ChinaCollege of Agriculture and Biology, Liaocheng University, Liaocheng 252000, ChinaShandong Animal Husbandry Station, Jinan 250010, ChinaJining Animal Husbandry and Veterinary Career Development Centre, Jining 272002, ChinaCollege of Agriculture and Biology, Liaocheng University, Liaocheng 252000, ChinaShandong Animal Husbandry Station, Jinan 250010, ChinaShandong Animal Husbandry Station, Jinan 250010, ChinaCollege of Agriculture and Biology, Liaocheng University, Liaocheng 252000, ChinaPlumage color is a key trait for identifying waterfowl breeds with significant economic importance. A white-feathered group has recently emerged within the native Matahu duck population, presenting an opportunity for breeding new lines. However, the genetic basis for this plumage variation is still unknown, necessitating further research. This study aims to identify the genetic mechanisms underlying the emergence of white-feathered individuals in the Matahu duck population through combined genome and transcriptome analysis, providing insights for selective breeding and the development of new white-feathered lines. In this study, a total of 1344 selected genes and 1406 significantly differentially expressed genes were identified through selection signal analysis and transcriptomic analysis, respectively. The functional enrichment of these genes revealed several key signaling pathways, including those related to cGMP-PKG, cAMP, PI3K-Akt, and MAPK. Furthermore, important candidate genes involved in melanin biosynthesis, such as <i>MITF</i>, <i>MC1R</i>, <i>TYR</i>, <i>TYRP1</i>, and <i>ABCB6</i>, were identified. Notably, 107 genes were detected by both methods, and, among these, <i>DGKI</i>, <i>GPRC5B</i>, <i>HMX1</i>, <i>STS</i>, <i>ADGRA1</i>, <i>PRKAR2B</i>, and <i>HOXB9</i> are suggested to play a role in melanin formation and potentially influence plumage traits. Through the integrative approach combining genomic selection signals and transcriptomic analyses, we identified several candidate genes directly associated with plumage color, including <i>MITF</i>, <i>TYR</i>, <i>TYRP1</i>, and <i>MC1R</i>, along with multiple signaling pathways linked to melanin formation. We hypothesize that the expression of <i>DGKI</i>, <i>GPRC5B</i>, <i>HMX1</i>, <i>STS</i>, <i>ADGRA1</i>, <i>PRKAR2B</i>, and <i>HOXB9</i>, detected by both methods, may be closely related to the regulation of plumage color traits. These findings provide a foundational basis for further research aimed at elucidating the genetic mechanisms governing plumage color variation in ducks.https://www.mdpi.com/2076-2615/14/21/3111Matahu duckwhite plumage traitsgenometranscriptomegenetic markers |
| spellingShingle | Pengwei Ren Liu Yang Muhammad Zahoor Khan Yadi Jing Meixia Zhang Chao Qi Xin Zhang Xiang Liu Zhansheng Liu Shuer Zhang Mingxia Zhu Joint Genomic and Transcriptomic Analysis Reveals Candidate Genes Associated with Plumage Color Traits in Matahu Ducks Animals Matahu duck white plumage traits genome transcriptome genetic markers |
| title | Joint Genomic and Transcriptomic Analysis Reveals Candidate Genes Associated with Plumage Color Traits in Matahu Ducks |
| title_full | Joint Genomic and Transcriptomic Analysis Reveals Candidate Genes Associated with Plumage Color Traits in Matahu Ducks |
| title_fullStr | Joint Genomic and Transcriptomic Analysis Reveals Candidate Genes Associated with Plumage Color Traits in Matahu Ducks |
| title_full_unstemmed | Joint Genomic and Transcriptomic Analysis Reveals Candidate Genes Associated with Plumage Color Traits in Matahu Ducks |
| title_short | Joint Genomic and Transcriptomic Analysis Reveals Candidate Genes Associated with Plumage Color Traits in Matahu Ducks |
| title_sort | joint genomic and transcriptomic analysis reveals candidate genes associated with plumage color traits in matahu ducks |
| topic | Matahu duck white plumage traits genome transcriptome genetic markers |
| url | https://www.mdpi.com/2076-2615/14/21/3111 |
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