Skin transcriptomic and selection signature analyses identify ASIP as a key gene in cattle coat color determination
ObjectiveCoat color is a complex trait and plays an important role in breed identification. However, information regarding genes associated with coat color in cattle is limited, especially at the skin transcriptome level.MethodsWe investigated the differential expressed genes (DEGs) and genomic sele...
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Frontiers Media S.A.
2025-04-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2025.1577647/full |
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| author | Xin Wang Longxin Xu Di Zhou Yanli Lv Junda Wu Yuanfeng Zhao Mengmeng Ni Wenzhang Zhou Kaikai Zhang Hua Wang Jipan Zhang |
| author_facet | Xin Wang Longxin Xu Di Zhou Yanli Lv Junda Wu Yuanfeng Zhao Mengmeng Ni Wenzhang Zhou Kaikai Zhang Hua Wang Jipan Zhang |
| author_sort | Xin Wang |
| collection | DOAJ |
| description | ObjectiveCoat color is a complex trait and plays an important role in breed identification. However, information regarding genes associated with coat color in cattle is limited, especially at the skin transcriptome level.MethodsWe investigated the differential expressed genes (DEGs) and genomic selection signal underlying the coat color variation between black and brown cattle breeds. A total of 19 cattle (Brangus, Angus, Simmental, and Guanling) were performed skin transcriptome analysis and 262 cattle (Angus and Simmental) were performed whole genome analysis.ResultsAngus cattle (black coat) had a significantly higher melanin content in both their hair and skin compared to that of Simmental and Guanling cattle (brown coat). Transcriptomic analysis identified 14,118 expressed genes, with principal component analysis and hierarchical clustering revealing clear differences between black and brown cattle. DEGs analysis across four pairwise breed comparisons highlighted 343 downregulated and 54 upregulated genes common to all comparisons, with the ASIP gene (agouti signaling protein) emerging as a key gene linked to melanogenesis. The ASIP expression was several dozen-fold higher in brown cattle than in black cattle, suggesting a crucial role in coat color determination. Path-way enrichment and gene set enrichment analysis (GSEA) identified the “Melanogenesis” pathway as significantly enriched and central to coat color variation. Genes such as FZD10, WNT6, and ASIP showed differential expression patterns that correlated with coat color. Genomic analysis revealed strong selection signals in the ASIP gene region, with several SNPs exhibiting high linkage disequilibrium. Notably, the mutation type was predominant in Simmental cattle, while the reference allele was more common in Angus cattle.ConclusionBased on the skin transcriptomic and genomic analyses, we found that ASIP was significantly differential expressed between black and brown cattle breeds and under strong positive selection. These findings provide valuable insights into the genetic basis of coat color variation in cattle and highlight the ASIP gene as a critical determinant of this trait. |
| format | Article |
| id | doaj-art-009033735ff047188fa29395b7048ebc |
| institution | Kabale University |
| issn | 1664-8021 |
| language | English |
| publishDate | 2025-04-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Genetics |
| spelling | doaj-art-009033735ff047188fa29395b7048ebc2025-08-20T03:53:43ZengFrontiers Media S.A.Frontiers in Genetics1664-80212025-04-011610.3389/fgene.2025.15776471577647Skin transcriptomic and selection signature analyses identify ASIP as a key gene in cattle coat color determinationXin Wang0Longxin Xu1Di Zhou2Yanli Lv3Junda Wu4Yuanfeng Zhao5Mengmeng Ni6Wenzhang Zhou7Kaikai Zhang8Hua Wang9Jipan Zhang10Institute of Animal Husbandry and Veterinary Medicine, Guizhou Academy of Agricultural Sciences, Guiyang, ChinaInstitute of Animal Husbandry and Veterinary Medicine, Guizhou Academy of Agricultural Sciences, Guiyang, ChinaGuizhou Provincial Breeding Livestock and Poultry Germplasm Determination Center, Guiyang, ChinaGuizhou Provincial Breeding Livestock and Poultry Germplasm Determination Center, Guiyang, ChinaInstitute of Animal Husbandry and Veterinary Medicine, Guizhou Academy of Agricultural Sciences, Guiyang, ChinaInstitute of Animal Husbandry and Veterinary Medicine, Guizhou Academy of Agricultural Sciences, Guiyang, ChinaCollege of Animal Sciences, Guizhou University, Guiyang, ChinaInstitute of Animal Husbandry and Veterinary Medicine, Guizhou Academy of Agricultural Sciences, Guiyang, ChinaInstitute of Animal Husbandry and Veterinary Medicine, Guizhou Academy of Agricultural Sciences, Guiyang, ChinaInstitute of Animal Husbandry and Veterinary Medicine, Guizhou Academy of Agricultural Sciences, Guiyang, ChinaCollege of Animal Science and Technology, Southwest University, Chongqing, ChinaObjectiveCoat color is a complex trait and plays an important role in breed identification. However, information regarding genes associated with coat color in cattle is limited, especially at the skin transcriptome level.MethodsWe investigated the differential expressed genes (DEGs) and genomic selection signal underlying the coat color variation between black and brown cattle breeds. A total of 19 cattle (Brangus, Angus, Simmental, and Guanling) were performed skin transcriptome analysis and 262 cattle (Angus and Simmental) were performed whole genome analysis.ResultsAngus cattle (black coat) had a significantly higher melanin content in both their hair and skin compared to that of Simmental and Guanling cattle (brown coat). Transcriptomic analysis identified 14,118 expressed genes, with principal component analysis and hierarchical clustering revealing clear differences between black and brown cattle. DEGs analysis across four pairwise breed comparisons highlighted 343 downregulated and 54 upregulated genes common to all comparisons, with the ASIP gene (agouti signaling protein) emerging as a key gene linked to melanogenesis. The ASIP expression was several dozen-fold higher in brown cattle than in black cattle, suggesting a crucial role in coat color determination. Path-way enrichment and gene set enrichment analysis (GSEA) identified the “Melanogenesis” pathway as significantly enriched and central to coat color variation. Genes such as FZD10, WNT6, and ASIP showed differential expression patterns that correlated with coat color. Genomic analysis revealed strong selection signals in the ASIP gene region, with several SNPs exhibiting high linkage disequilibrium. Notably, the mutation type was predominant in Simmental cattle, while the reference allele was more common in Angus cattle.ConclusionBased on the skin transcriptomic and genomic analyses, we found that ASIP was significantly differential expressed between black and brown cattle breeds and under strong positive selection. These findings provide valuable insights into the genetic basis of coat color variation in cattle and highlight the ASIP gene as a critical determinant of this trait.https://www.frontiersin.org/articles/10.3389/fgene.2025.1577647/fullcattlecoat colorASIPmelanogenesismRNA-seqselection signal |
| spellingShingle | Xin Wang Longxin Xu Di Zhou Yanli Lv Junda Wu Yuanfeng Zhao Mengmeng Ni Wenzhang Zhou Kaikai Zhang Hua Wang Jipan Zhang Skin transcriptomic and selection signature analyses identify ASIP as a key gene in cattle coat color determination Frontiers in Genetics cattle coat color ASIP melanogenesis mRNA-seq selection signal |
| title | Skin transcriptomic and selection signature analyses identify ASIP as a key gene in cattle coat color determination |
| title_full | Skin transcriptomic and selection signature analyses identify ASIP as a key gene in cattle coat color determination |
| title_fullStr | Skin transcriptomic and selection signature analyses identify ASIP as a key gene in cattle coat color determination |
| title_full_unstemmed | Skin transcriptomic and selection signature analyses identify ASIP as a key gene in cattle coat color determination |
| title_short | Skin transcriptomic and selection signature analyses identify ASIP as a key gene in cattle coat color determination |
| title_sort | skin transcriptomic and selection signature analyses identify asip as a key gene in cattle coat color determination |
| topic | cattle coat color ASIP melanogenesis mRNA-seq selection signal |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2025.1577647/full |
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