Heritability Estimated Using 50K SNPs Indicates Missing Heritability Problem in Holstein Breeding
Previous studies in Holstein have shown 35% to 51.8% heritability in milk production traits, such as milk yield, fat, and protein, using pedigree data. Other studies in complex human traits could be captured by common single-nucleotide polymorphisms (SNPs), and their genetic variations, attributed t...
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BioMed Central
2015-12-01
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| Series: | Genomics & Informatics |
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| Online Access: | http://genominfo.org/upload/pdf/gni-13-146.pdf |
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| author | Donghyun Shin Kyoung-Do Park Sojoeng Ka Heebal Kim Kwang-hyeon Cho |
| author_facet | Donghyun Shin Kyoung-Do Park Sojoeng Ka Heebal Kim Kwang-hyeon Cho |
| author_sort | Donghyun Shin |
| collection | DOAJ |
| description | Previous studies in Holstein have shown 35% to 51.8% heritability in milk production traits, such as milk yield, fat, and protein, using pedigree data. Other studies in complex human traits could be captured by common single-nucleotide polymorphisms (SNPs), and their genetic variations, attributed to chromosomes, are in proportion to their length. Using genome-wide estimation and partitioning approaches, we analyzed three quantitative Holstein traits relevant to milk production in Korean Holstein data harvested from 462 individuals genotyped for 54,609 SNPs. For all three traits (milk yield, fat, and protein), we estimated a nominally significant (p = 0.1) proportion of variance explained by all SNPs on the Illumina BovineSNP50 Beadchip (h2G). These common SNPs explained approximately most of the narrow-sense heritability. Longer genomic regions tended to provide more phenotypic variation information, with a correlation of 0.46~0.53 between the estimate of variance explained by individual chromosomes and their physical length. These results suggested that polygenicity was ubiquitous for Holstein milk production traits. These results will expand our knowledge on recent animal breeding, such as genomic selection in Holstein. |
| format | Article |
| id | doaj-art-e49ef5e603f44a1d9b4616b21b080b75 |
| institution | Kabale University |
| issn | 1598-866X 2234-0742 |
| language | English |
| publishDate | 2015-12-01 |
| publisher | BioMed Central |
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| series | Genomics & Informatics |
| spelling | doaj-art-e49ef5e603f44a1d9b4616b21b080b752025-02-02T17:02:16ZengBioMed CentralGenomics & Informatics1598-866X2234-07422015-12-0113414615110.5808/GI.2015.13.4.146140Heritability Estimated Using 50K SNPs Indicates Missing Heritability Problem in Holstein BreedingDonghyun Shin0Kyoung-Do Park1Sojoeng Ka2Heebal Kim3Kwang-hyeon Cho4Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea.Genomic Informatics Center, Hankyong National University, Anseong 17579, Korea.Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea.Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea.Division of Animal Breeding and Genetics, National Institute of Animal Science, Rural Development Administration, Cheonan 31001, Korea.Previous studies in Holstein have shown 35% to 51.8% heritability in milk production traits, such as milk yield, fat, and protein, using pedigree data. Other studies in complex human traits could be captured by common single-nucleotide polymorphisms (SNPs), and their genetic variations, attributed to chromosomes, are in proportion to their length. Using genome-wide estimation and partitioning approaches, we analyzed three quantitative Holstein traits relevant to milk production in Korean Holstein data harvested from 462 individuals genotyped for 54,609 SNPs. For all three traits (milk yield, fat, and protein), we estimated a nominally significant (p = 0.1) proportion of variance explained by all SNPs on the Illumina BovineSNP50 Beadchip (h2G). These common SNPs explained approximately most of the narrow-sense heritability. Longer genomic regions tended to provide more phenotypic variation information, with a correlation of 0.46~0.53 between the estimate of variance explained by individual chromosomes and their physical length. These results suggested that polygenicity was ubiquitous for Holstein milk production traits. These results will expand our knowledge on recent animal breeding, such as genomic selection in Holstein.http://genominfo.org/upload/pdf/gni-13-146.pdfbreedinggenomic selectionHolsteinheritabilitysingle-nucleotide polymorphism |
| spellingShingle | Donghyun Shin Kyoung-Do Park Sojoeng Ka Heebal Kim Kwang-hyeon Cho Heritability Estimated Using 50K SNPs Indicates Missing Heritability Problem in Holstein Breeding Genomics & Informatics breeding genomic selection Holstein heritability single-nucleotide polymorphism |
| title | Heritability Estimated Using 50K SNPs Indicates Missing Heritability Problem in Holstein Breeding |
| title_full | Heritability Estimated Using 50K SNPs Indicates Missing Heritability Problem in Holstein Breeding |
| title_fullStr | Heritability Estimated Using 50K SNPs Indicates Missing Heritability Problem in Holstein Breeding |
| title_full_unstemmed | Heritability Estimated Using 50K SNPs Indicates Missing Heritability Problem in Holstein Breeding |
| title_short | Heritability Estimated Using 50K SNPs Indicates Missing Heritability Problem in Holstein Breeding |
| title_sort | heritability estimated using 50k snps indicates missing heritability problem in holstein breeding |
| topic | breeding genomic selection Holstein heritability single-nucleotide polymorphism |
| url | http://genominfo.org/upload/pdf/gni-13-146.pdf |
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