Genome-Wide Association Study of Birth Wool Length, Birth Weight, and Head Color in Chinese Tan Sheep Through Whole-Genome Re-Sequencing
The Chinese Tan sheep is a unique breed of sheep that is typical throughout China, mainly used for fur and meat production. They are widely distributed in northwestern China and are famous for their lambskin and shiny white curly wool. In this study, the phenotypic traits of wool length, birth weigh...
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2024-12-01
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| author | Lina Ma Wei Zhao Qing Ma Jin Wang Zhengwei Zhao Juan Zhang Yaling Gu |
| author_facet | Lina Ma Wei Zhao Qing Ma Jin Wang Zhengwei Zhao Juan Zhang Yaling Gu |
| author_sort | Lina Ma |
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| description | The Chinese Tan sheep is a unique breed of sheep that is typical throughout China, mainly used for fur and meat production. They are widely distributed in northwestern China and are famous for their lambskin and shiny white curly wool. In this study, the phenotypic traits of wool length, birth weight, and head coat color were evaluated in 256 Chinese Tan sheep breeds. Whole genome sequencing generated 23.67 million high-quality SNPs for genome-wide association studies (GWAS). We identified 208 significant SNPs associated with birth wool length, implicating <i>RAD50</i>, <i>MACROD2</i>, <i>SAMD5</i>, <i>SASH1</i>, and <i>SPTLC3</i> as potential candidate genes for this trait. For birth weight, 1056 significant SNPs, with 76.89% of them located on chromosome 2, were identified by GWAS, and <i>XPA</i>, <i>INVS</i>, <i>LOC121818504</i>, <i>GABBR2</i>, <i>LOC101114941</i>, and <i>LOC106990096</i> were identified as potential candidate genes for birth weight. The GWAS for head coat color identified 1424 significant SNPs across three chromosomes, with 99.65% on chromosome 14, and <i>SPIRE2</i>, <i>TCF25</i>, and <i>MC1R</i> as candidate genes were found to be possibly involved in the development of the black-headed coat color in sheep. Furthermore, we selected head coat color as a representative trait and performed an independent test of our GWAS findings through multiplex PCR SNP genotyping. The findings validated five mutation sites in chromosome 14 (14,251,947 T>A, 14,252,090 G>A, 14,252,158 C>T, 14,252,329 T>G, and 14,252,464 C>T) within the exon1 of the <i>MC1R</i> gene (517 bp), as identified by GWAS in an additional 102 Tan sheep individuals, and revealed that black-headed sheep predominantly exhibited heterozygous genotypes, possibly contributing to their color change. Our results provide a valuable foundation for further study of these three economically important traits, and enhance our understanding of genetic structure and variation in Chinese Tan sheep. |
| format | Article |
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| publishDate | 2024-12-01 |
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| spelling | doaj-art-70a827f3eb4a4708964a4f5d80ee79ad2025-08-20T01:55:41ZengMDPI AGAnimals2076-26152024-12-011423349510.3390/ani14233495Genome-Wide Association Study of Birth Wool Length, Birth Weight, and Head Color in Chinese Tan Sheep Through Whole-Genome Re-SequencingLina Ma0Wei Zhao1Qing Ma2Jin Wang3Zhengwei Zhao4Juan Zhang5Yaling Gu6College of Animal Science and Technology, Ningxia University, Yinchuan 750021, ChinaCollege of Animal Science and Technology, Ningxia University, Yinchuan 750021, ChinaInstitute of Animal Science, Ningxia Academy of Agricultural and Forestry Sciences, Yinchuan 750002, ChinaInstitute of Animal Science, Ningxia Academy of Agricultural and Forestry Sciences, Yinchuan 750002, ChinaInstitute of Animal Science, Ningxia Academy of Agricultural and Forestry Sciences, Yinchuan 750002, ChinaCollege of Animal Science and Technology, Ningxia University, Yinchuan 750021, ChinaCollege of Animal Science and Technology, Ningxia University, Yinchuan 750021, ChinaThe Chinese Tan sheep is a unique breed of sheep that is typical throughout China, mainly used for fur and meat production. They are widely distributed in northwestern China and are famous for their lambskin and shiny white curly wool. In this study, the phenotypic traits of wool length, birth weight, and head coat color were evaluated in 256 Chinese Tan sheep breeds. Whole genome sequencing generated 23.67 million high-quality SNPs for genome-wide association studies (GWAS). We identified 208 significant SNPs associated with birth wool length, implicating <i>RAD50</i>, <i>MACROD2</i>, <i>SAMD5</i>, <i>SASH1</i>, and <i>SPTLC3</i> as potential candidate genes for this trait. For birth weight, 1056 significant SNPs, with 76.89% of them located on chromosome 2, were identified by GWAS, and <i>XPA</i>, <i>INVS</i>, <i>LOC121818504</i>, <i>GABBR2</i>, <i>LOC101114941</i>, and <i>LOC106990096</i> were identified as potential candidate genes for birth weight. The GWAS for head coat color identified 1424 significant SNPs across three chromosomes, with 99.65% on chromosome 14, and <i>SPIRE2</i>, <i>TCF25</i>, and <i>MC1R</i> as candidate genes were found to be possibly involved in the development of the black-headed coat color in sheep. Furthermore, we selected head coat color as a representative trait and performed an independent test of our GWAS findings through multiplex PCR SNP genotyping. The findings validated five mutation sites in chromosome 14 (14,251,947 T>A, 14,252,090 G>A, 14,252,158 C>T, 14,252,329 T>G, and 14,252,464 C>T) within the exon1 of the <i>MC1R</i> gene (517 bp), as identified by GWAS in an additional 102 Tan sheep individuals, and revealed that black-headed sheep predominantly exhibited heterozygous genotypes, possibly contributing to their color change. Our results provide a valuable foundation for further study of these three economically important traits, and enhance our understanding of genetic structure and variation in Chinese Tan sheep.https://www.mdpi.com/2076-2615/14/23/3495Chinese Tan sheepbirth wool lengthbirth weighthead coat colorgenome-wide association study<i>MC1R</i> |
| spellingShingle | Lina Ma Wei Zhao Qing Ma Jin Wang Zhengwei Zhao Juan Zhang Yaling Gu Genome-Wide Association Study of Birth Wool Length, Birth Weight, and Head Color in Chinese Tan Sheep Through Whole-Genome Re-Sequencing Animals Chinese Tan sheep birth wool length birth weight head coat color genome-wide association study <i>MC1R</i> |
| title | Genome-Wide Association Study of Birth Wool Length, Birth Weight, and Head Color in Chinese Tan Sheep Through Whole-Genome Re-Sequencing |
| title_full | Genome-Wide Association Study of Birth Wool Length, Birth Weight, and Head Color in Chinese Tan Sheep Through Whole-Genome Re-Sequencing |
| title_fullStr | Genome-Wide Association Study of Birth Wool Length, Birth Weight, and Head Color in Chinese Tan Sheep Through Whole-Genome Re-Sequencing |
| title_full_unstemmed | Genome-Wide Association Study of Birth Wool Length, Birth Weight, and Head Color in Chinese Tan Sheep Through Whole-Genome Re-Sequencing |
| title_short | Genome-Wide Association Study of Birth Wool Length, Birth Weight, and Head Color in Chinese Tan Sheep Through Whole-Genome Re-Sequencing |
| title_sort | genome wide association study of birth wool length birth weight and head color in chinese tan sheep through whole genome re sequencing |
| topic | Chinese Tan sheep birth wool length birth weight head coat color genome-wide association study <i>MC1R</i> |
| url | https://www.mdpi.com/2076-2615/14/23/3495 |
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