GWAS-Based Identification of New Loci for Milk Yield, Fat, and Protein in Holstein Cattle
High-yield and high-quality of milk are the primary goals of dairy production. Understanding the genetic architecture underlying these milk-related traits is beneficial so that genetic variants can be targeted toward the genetic improvement. In this study, we measured five milk production and qualit...
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MDPI AG
2020-11-01
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| Online Access: | https://www.mdpi.com/2076-2615/10/11/2048 |
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| author | Liyuan Liu Jinghang Zhou Chunpeng James Chen Juan Zhang Wan Wen Jia Tian Zhiwu Zhang Yaling Gu |
| author_facet | Liyuan Liu Jinghang Zhou Chunpeng James Chen Juan Zhang Wan Wen Jia Tian Zhiwu Zhang Yaling Gu |
| author_sort | Liyuan Liu |
| collection | DOAJ |
| description | High-yield and high-quality of milk are the primary goals of dairy production. Understanding the genetic architecture underlying these milk-related traits is beneficial so that genetic variants can be targeted toward the genetic improvement. In this study, we measured five milk production and quality traits in Holstein cattle population from China. These traits included milk yield, fat, and protein. We used the estimated breeding values as dependent variables to conduct the genome-wide association studies (GWAS). Breeding values were estimated through pedigree relationships by using a linear mixed model. Genotyping was carried out on the individuals with phenotypes by using the Illumina BovineSNP150 BeadChip. The association analyses were conducted by using the fixed and random model Circulating Probability Unification (FarmCPU) method. A total of ten single-nucleotide polymorphisms (SNPs) were detected above the genome-wide significant threshold (<i>p</i> < 4.0 × 10<sup>−7</sup>), including six located in previously reported quantitative traits locus (QTL) regions. We found eight candidate genes within distances of 120 kb upstream or downstream to the associated SNPs. The study not only identified the effect of <i>DGAT1</i> gene on milk fat and protein, but also discovered novel genetic loci and candidate genes related to milk traits. These novel genetic loci would be an important basis for molecular breeding in dairy cattle. |
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| language | English |
| last_indexed | 2024-03-09T06:04:21Z |
| publishDate | 2020-11-01 |
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| spelling | doaj.art-68efbc6fd8b94be1b07f755d23fdf8162023-12-03T12:05:21ZengMDPI AGAnimals2076-26152020-11-011011204810.3390/ani10112048GWAS-Based Identification of New Loci for Milk Yield, Fat, and Protein in Holstein CattleLiyuan Liu0Jinghang Zhou1Chunpeng James Chen2Juan Zhang3Wan Wen4Jia Tian5Zhiwu Zhang6Yaling Gu7School of Agriculture, Ningxia University, Yinchuan 750021, Ningxia, ChinaSchool of Agriculture, Ningxia University, Yinchuan 750021, Ningxia, ChinaDepartment of Crop and Soil Sciences, Washington State University, Pullman, Washington, DC 99164, USASchool of Agriculture, Ningxia University, Yinchuan 750021, Ningxia, ChinaAnimal Husbandry Workstation, Yinchuan 750001, Ningxia, ChinaAnimal Husbandry Workstation, Yinchuan 750001, Ningxia, ChinaDepartment of Crop and Soil Sciences, Washington State University, Pullman, Washington, DC 99164, USASchool of Agriculture, Ningxia University, Yinchuan 750021, Ningxia, ChinaHigh-yield and high-quality of milk are the primary goals of dairy production. Understanding the genetic architecture underlying these milk-related traits is beneficial so that genetic variants can be targeted toward the genetic improvement. In this study, we measured five milk production and quality traits in Holstein cattle population from China. These traits included milk yield, fat, and protein. We used the estimated breeding values as dependent variables to conduct the genome-wide association studies (GWAS). Breeding values were estimated through pedigree relationships by using a linear mixed model. Genotyping was carried out on the individuals with phenotypes by using the Illumina BovineSNP150 BeadChip. The association analyses were conducted by using the fixed and random model Circulating Probability Unification (FarmCPU) method. A total of ten single-nucleotide polymorphisms (SNPs) were detected above the genome-wide significant threshold (<i>p</i> < 4.0 × 10<sup>−7</sup>), including six located in previously reported quantitative traits locus (QTL) regions. We found eight candidate genes within distances of 120 kb upstream or downstream to the associated SNPs. The study not only identified the effect of <i>DGAT1</i> gene on milk fat and protein, but also discovered novel genetic loci and candidate genes related to milk traits. These novel genetic loci would be an important basis for molecular breeding in dairy cattle.https://www.mdpi.com/2076-2615/10/11/2048dairymilk productionquality traits<i>DGAT1</i>FarmCPU |
| spellingShingle | Liyuan Liu Jinghang Zhou Chunpeng James Chen Juan Zhang Wan Wen Jia Tian Zhiwu Zhang Yaling Gu GWAS-Based Identification of New Loci for Milk Yield, Fat, and Protein in Holstein Cattle Animals dairy milk production quality traits <i>DGAT1</i> FarmCPU |
| title | GWAS-Based Identification of New Loci for Milk Yield, Fat, and Protein in Holstein Cattle |
| title_full | GWAS-Based Identification of New Loci for Milk Yield, Fat, and Protein in Holstein Cattle |
| title_fullStr | GWAS-Based Identification of New Loci for Milk Yield, Fat, and Protein in Holstein Cattle |
| title_full_unstemmed | GWAS-Based Identification of New Loci for Milk Yield, Fat, and Protein in Holstein Cattle |
| title_short | GWAS-Based Identification of New Loci for Milk Yield, Fat, and Protein in Holstein Cattle |
| title_sort | gwas based identification of new loci for milk yield fat and protein in holstein cattle |
| topic | dairy milk production quality traits <i>DGAT1</i> FarmCPU |
| url | https://www.mdpi.com/2076-2615/10/11/2048 |
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