Genome-Wide Association Analysis Identifies the <i>PMEL</i> Gene Affecting Coat Color and Birth Weight in Simmental × Holstein
Coat color and birth weight, as easily selected traits in cattle, play important roles in cattle breeding. Therefore, we carried out a genome-wide association study on birth weight and coat color to identify loci or potential linkage regions in 233 Simmental × Holstein crossbred beef cattle. The res...
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MDPI AG
2023-12-01
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| Online Access: | https://www.mdpi.com/2076-2615/13/24/3821 |
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| author | Jing Wang Tingting Fan Zhenwei Du Lingyang Xu Yan Chen Lupei Zhang Huijiang Gao Junya Li Yi Ma Xue Gao |
| author_facet | Jing Wang Tingting Fan Zhenwei Du Lingyang Xu Yan Chen Lupei Zhang Huijiang Gao Junya Li Yi Ma Xue Gao |
| author_sort | Jing Wang |
| collection | DOAJ |
| description | Coat color and birth weight, as easily selected traits in cattle, play important roles in cattle breeding. Therefore, we carried out a genome-wide association study on birth weight and coat color to identify loci or potential linkage regions in 233 Simmental × Holstein crossbred beef cattle. The results revealed that nine SNPs were significantly associated with coat color (<i>rs137169378</i>, <i>rs110022687</i>, <i>rs136002689</i>, <i>Hypotrichosis_PMel17</i>, <i>PMEL_1</i>, <i>rs134930689</i>, <i>rs383170073</i>, <i>rs109924971</i>, and <i>rs109146332</i>), and these were in <i>RNF41</i>, <i>ZC3H10</i>, <i>ERBB3</i>, <i>PMEL</i>, and <i>OR10A7</i> on BTA5. Interestingly, <i>rs137169378</i>, <i>rs110022687</i>, <i>rs136002689</i>, <i>Hypotrichosis_PMel17</i>, and <i>PMEL_1</i> showed strong linkage disequilibrium (<i>r</i><sup>2</sup> > 0.8) and were significantly associated with coat color. Notably, <i>Hypotrichosis_PMel17</i> and <i>PMEL_1</i> were located in the gene <i>PMEL</i> (<i>p</i> = 2.22 × 10<sup>−18</sup>). Among the five significant SNPs associated with coat color, the birth weight of heterozygous individuals (AB) was greater than that of homozygous individuals (AA). Notably, the birth weight of heterozygous individuals with <i>Hypotrichosis_PMel17</i> and <i>PMEL_1</i> genotypes was significantly greater than that of homozygous individuals (0.01 < <i>p</i> < 0.05). Interestingly, the two loci were homozygous in black/white individuals and heterozygous in gray/white individuals, and the birth weight of heterozygous brown/white individuals (43.82 ± 5.25 kg) was greater than that of homozygous individuals (42.58 ± 3.09 kg). The birth weight of calves with the parental color (41.95 ± 3.53 kg) was significantly lower than that of calves with a non-parental color (43.54 ± 4.78 kg) (<i>p</i> < 0.05), and the birth weight of gray/white individuals (49.40 ± 7.11 kg) was the highest. Overall, <i>PMEL</i> appears to be a candidate gene affecting coat color in cattle, and coat color may have a selective effect on birth weight. This study provides a foundation for the breeding of beef cattle through GWAS for coat color and birth weight. |
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| spelling | doaj.art-53662a4dcec4448c8209c46d68c4f6e92023-12-22T13:47:30ZengMDPI AGAnimals2076-26152023-12-011324382110.3390/ani13243821Genome-Wide Association Analysis Identifies the <i>PMEL</i> Gene Affecting Coat Color and Birth Weight in Simmental × HolsteinJing Wang0Tingting Fan1Zhenwei Du2Lingyang Xu3Yan Chen4Lupei Zhang5Huijiang Gao6Junya Li7Yi Ma8Xue Gao9Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaLaboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaLaboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaLaboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaLaboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaLaboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaLaboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaLaboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaAnimal Husbandry Institute, Tianjin Academy of Agricultural Sciences, Tianjin 300384, ChinaLaboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaCoat color and birth weight, as easily selected traits in cattle, play important roles in cattle breeding. Therefore, we carried out a genome-wide association study on birth weight and coat color to identify loci or potential linkage regions in 233 Simmental × Holstein crossbred beef cattle. The results revealed that nine SNPs were significantly associated with coat color (<i>rs137169378</i>, <i>rs110022687</i>, <i>rs136002689</i>, <i>Hypotrichosis_PMel17</i>, <i>PMEL_1</i>, <i>rs134930689</i>, <i>rs383170073</i>, <i>rs109924971</i>, and <i>rs109146332</i>), and these were in <i>RNF41</i>, <i>ZC3H10</i>, <i>ERBB3</i>, <i>PMEL</i>, and <i>OR10A7</i> on BTA5. Interestingly, <i>rs137169378</i>, <i>rs110022687</i>, <i>rs136002689</i>, <i>Hypotrichosis_PMel17</i>, and <i>PMEL_1</i> showed strong linkage disequilibrium (<i>r</i><sup>2</sup> > 0.8) and were significantly associated with coat color. Notably, <i>Hypotrichosis_PMel17</i> and <i>PMEL_1</i> were located in the gene <i>PMEL</i> (<i>p</i> = 2.22 × 10<sup>−18</sup>). Among the five significant SNPs associated with coat color, the birth weight of heterozygous individuals (AB) was greater than that of homozygous individuals (AA). Notably, the birth weight of heterozygous individuals with <i>Hypotrichosis_PMel17</i> and <i>PMEL_1</i> genotypes was significantly greater than that of homozygous individuals (0.01 < <i>p</i> < 0.05). Interestingly, the two loci were homozygous in black/white individuals and heterozygous in gray/white individuals, and the birth weight of heterozygous brown/white individuals (43.82 ± 5.25 kg) was greater than that of homozygous individuals (42.58 ± 3.09 kg). The birth weight of calves with the parental color (41.95 ± 3.53 kg) was significantly lower than that of calves with a non-parental color (43.54 ± 4.78 kg) (<i>p</i> < 0.05), and the birth weight of gray/white individuals (49.40 ± 7.11 kg) was the highest. Overall, <i>PMEL</i> appears to be a candidate gene affecting coat color in cattle, and coat color may have a selective effect on birth weight. This study provides a foundation for the breeding of beef cattle through GWAS for coat color and birth weight.https://www.mdpi.com/2076-2615/13/24/3821coat colorbirth weightSimmental × HolsteinGWAS<i>PMEL</i> |
| spellingShingle | Jing Wang Tingting Fan Zhenwei Du Lingyang Xu Yan Chen Lupei Zhang Huijiang Gao Junya Li Yi Ma Xue Gao Genome-Wide Association Analysis Identifies the <i>PMEL</i> Gene Affecting Coat Color and Birth Weight in Simmental × Holstein Animals coat color birth weight Simmental × Holstein GWAS <i>PMEL</i> |
| title | Genome-Wide Association Analysis Identifies the <i>PMEL</i> Gene Affecting Coat Color and Birth Weight in Simmental × Holstein |
| title_full | Genome-Wide Association Analysis Identifies the <i>PMEL</i> Gene Affecting Coat Color and Birth Weight in Simmental × Holstein |
| title_fullStr | Genome-Wide Association Analysis Identifies the <i>PMEL</i> Gene Affecting Coat Color and Birth Weight in Simmental × Holstein |
| title_full_unstemmed | Genome-Wide Association Analysis Identifies the <i>PMEL</i> Gene Affecting Coat Color and Birth Weight in Simmental × Holstein |
| title_short | Genome-Wide Association Analysis Identifies the <i>PMEL</i> Gene Affecting Coat Color and Birth Weight in Simmental × Holstein |
| title_sort | genome wide association analysis identifies the i pmel i gene affecting coat color and birth weight in simmental holstein |
| topic | coat color birth weight Simmental × Holstein GWAS <i>PMEL</i> |
| url | https://www.mdpi.com/2076-2615/13/24/3821 |
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