Genome-Wide Association Study towards Genomic Predictive Power for High Production and Quality of Milk in American Alpine Goats
This paper reports an exploratory study based on quantitative genomic analysis in dairy traits of American Alpine goats. The dairy traits are quality-determining components in goat milk, cheese, ice cream, etc. Alpine goat phenotypes for quality components have been routinely recorded for many years...
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| Format: | Article |
| Language: | English |
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Wiley
2020-01-01
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| Series: | International Journal of Genomics |
| Online Access: | http://dx.doi.org/10.1155/2020/6035694 |
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| author | Y. Tilahun T. A. Gipson T. Alexander M. L. McCallum P. R. Hoyt |
| author_facet | Y. Tilahun T. A. Gipson T. Alexander M. L. McCallum P. R. Hoyt |
| author_sort | Y. Tilahun |
| collection | DOAJ |
| description | This paper reports an exploratory study based on quantitative genomic analysis in dairy traits of American Alpine goats. The dairy traits are quality-determining components in goat milk, cheese, ice cream, etc. Alpine goat phenotypes for quality components have been routinely recorded for many years and deposited in the Council on Dairy Cattle Breeding (CDCB) repository. The data collected were used to conduct an exploratory genome-wide association study (GWAS) from 72 female Alpine goats originating from locations throughout the U.S. Genotypes were identified with the Illumina Goat 50K single-nucleotide polymorphisms (SNP) BeadChip. The analysis used a polygenic model where the dropping criterion was a call rate≥0.95. The initial dataset was composed of ~60,000 rows of SNPs and 21 columns of phenotypic traits and composed of 53,384 scaffolds containing other informative data points used for genomic predictive power. Phenotypic association with the 50K BeadChip revealed 26,074 reads of candidate genes. These candidate genes segregated as separate novel SNPs and were identified as statistically significant regions for genome and chromosome level trait associations. Candidate genes associated differently for each of the following phenotypic traits: test day milk yield (13,469 candidate genes), test day protein yield (25,690 candidate genes), test day fat yield (25,690 candidate genes), percentage protein (25,690 candidate genes), percentage fat (25,690 candidate genes), and percentage lactose content (25,690 candidate genes). The outcome of this study supports elucidation of novel genes that are important for livestock species in association to key phenotypic traits. Validation towards the development of marker-based selection that provides precision breeding methods will thereby increase the breeding value. |
| format | Article |
| id | doaj-art-e88417dcbf3643d8a0473aa4b96660bd |
| institution | Kabale University |
| issn | 2314-436X 2314-4378 |
| language | English |
| publishDate | 2020-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | International Journal of Genomics |
| spelling | doaj-art-e88417dcbf3643d8a0473aa4b96660bd2025-02-03T01:24:56ZengWileyInternational Journal of Genomics2314-436X2314-43782020-01-01202010.1155/2020/60356946035694Genome-Wide Association Study towards Genomic Predictive Power for High Production and Quality of Milk in American Alpine GoatsY. Tilahun0T. A. Gipson1T. Alexander2M. L. McCallum3P. R. Hoyt4American Institute for Goats Research, Langston University, Langston, Oklahoma, USAAmerican Institute for Goats Research, Langston University, Langston, Oklahoma, USAAmerican Institute for Goats Research, Langston University, Langston, Oklahoma, USAAmerican Institute for Goats Research, Langston University, Langston, Oklahoma, USABiochemistry and Molecular Biology, Oklahoma State University, Stillwater, Oklahoma, USAThis paper reports an exploratory study based on quantitative genomic analysis in dairy traits of American Alpine goats. The dairy traits are quality-determining components in goat milk, cheese, ice cream, etc. Alpine goat phenotypes for quality components have been routinely recorded for many years and deposited in the Council on Dairy Cattle Breeding (CDCB) repository. The data collected were used to conduct an exploratory genome-wide association study (GWAS) from 72 female Alpine goats originating from locations throughout the U.S. Genotypes were identified with the Illumina Goat 50K single-nucleotide polymorphisms (SNP) BeadChip. The analysis used a polygenic model where the dropping criterion was a call rate≥0.95. The initial dataset was composed of ~60,000 rows of SNPs and 21 columns of phenotypic traits and composed of 53,384 scaffolds containing other informative data points used for genomic predictive power. Phenotypic association with the 50K BeadChip revealed 26,074 reads of candidate genes. These candidate genes segregated as separate novel SNPs and were identified as statistically significant regions for genome and chromosome level trait associations. Candidate genes associated differently for each of the following phenotypic traits: test day milk yield (13,469 candidate genes), test day protein yield (25,690 candidate genes), test day fat yield (25,690 candidate genes), percentage protein (25,690 candidate genes), percentage fat (25,690 candidate genes), and percentage lactose content (25,690 candidate genes). The outcome of this study supports elucidation of novel genes that are important for livestock species in association to key phenotypic traits. Validation towards the development of marker-based selection that provides precision breeding methods will thereby increase the breeding value.http://dx.doi.org/10.1155/2020/6035694 |
| spellingShingle | Y. Tilahun T. A. Gipson T. Alexander M. L. McCallum P. R. Hoyt Genome-Wide Association Study towards Genomic Predictive Power for High Production and Quality of Milk in American Alpine Goats International Journal of Genomics |
| title | Genome-Wide Association Study towards Genomic Predictive Power for High Production and Quality of Milk in American Alpine Goats |
| title_full | Genome-Wide Association Study towards Genomic Predictive Power for High Production and Quality of Milk in American Alpine Goats |
| title_fullStr | Genome-Wide Association Study towards Genomic Predictive Power for High Production and Quality of Milk in American Alpine Goats |
| title_full_unstemmed | Genome-Wide Association Study towards Genomic Predictive Power for High Production and Quality of Milk in American Alpine Goats |
| title_short | Genome-Wide Association Study towards Genomic Predictive Power for High Production and Quality of Milk in American Alpine Goats |
| title_sort | genome wide association study towards genomic predictive power for high production and quality of milk in american alpine goats |
| url | http://dx.doi.org/10.1155/2020/6035694 |
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