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Single nucleotide polymorphism and haplotype effects associated with somatic cell score in German Holstein cattle
BACKGROUND: To better understand the genetic determination of udder health, we performed a genome-wide association study (GWAS) on a population of 2354 German Holstein bulls for which daughter yield deviations (DYD) for somatic cell score (SCS) were available. For this study, we used genetic informa...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4078941/ https://www.ncbi.nlm.nih.gov/pubmed/24898131 http://dx.doi.org/10.1186/1297-9686-46-35 |
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author | Abdel-Shafy, Hamdy Bortfeldt, Ralf H Tetens, Jens Brockmann, Gudrun A |
author_facet | Abdel-Shafy, Hamdy Bortfeldt, Ralf H Tetens, Jens Brockmann, Gudrun A |
author_sort | Abdel-Shafy, Hamdy |
collection | PubMed |
description | BACKGROUND: To better understand the genetic determination of udder health, we performed a genome-wide association study (GWAS) on a population of 2354 German Holstein bulls for which daughter yield deviations (DYD) for somatic cell score (SCS) were available. For this study, we used genetic information of 44 576 informative single nucleotide polymorphisms (SNPs) and 11 725 inferred haplotype blocks. RESULTS: When accounting for the sub-structure of the analyzed population, 16 SNPs and 10 haplotypes in six genomic regions were significant at the Bonferroni threshold of P ≤ 1.14 × 10(-6). The size of the identified regions ranged from 0.05 to 5.62 Mb. Genomic regions on chromosomes 5, 6, 18 and 19 coincided with known QTL affecting SCS, while additional genomic regions were found on chromosomes 13 and X. Of particular interest is the region on chromosome 6 between 85 and 88 Mb, where QTL for mastitis traits and significant SNPs for SCS in different Holstein populations coincide with our results. In all identified regions, except for the region on chromosome X, significant SNPs were present in significant haplotypes. The minor alleles of identified SNPs on chromosomes 18 and 19, and the major alleles of SNPs on chromosomes 6 and X were favorable for a lower SCS. Differences in somatic cell count (SCC) between alternative SNP alleles reached 14 000 cells/mL. CONCLUSIONS: The results support the polygenic nature of the genetic determination of SCS, confirm the importance of previously reported QTL, and provide evidence for the segregation of additional QTL for SCS in Holstein cattle. The small size of the regions identified here will facilitate the search for causal genetic variations that affect gene functions. |
format | Online Article Text |
id | pubmed-4078941 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-40789412014-07-03 Single nucleotide polymorphism and haplotype effects associated with somatic cell score in German Holstein cattle Abdel-Shafy, Hamdy Bortfeldt, Ralf H Tetens, Jens Brockmann, Gudrun A Genet Sel Evol Research BACKGROUND: To better understand the genetic determination of udder health, we performed a genome-wide association study (GWAS) on a population of 2354 German Holstein bulls for which daughter yield deviations (DYD) for somatic cell score (SCS) were available. For this study, we used genetic information of 44 576 informative single nucleotide polymorphisms (SNPs) and 11 725 inferred haplotype blocks. RESULTS: When accounting for the sub-structure of the analyzed population, 16 SNPs and 10 haplotypes in six genomic regions were significant at the Bonferroni threshold of P ≤ 1.14 × 10(-6). The size of the identified regions ranged from 0.05 to 5.62 Mb. Genomic regions on chromosomes 5, 6, 18 and 19 coincided with known QTL affecting SCS, while additional genomic regions were found on chromosomes 13 and X. Of particular interest is the region on chromosome 6 between 85 and 88 Mb, where QTL for mastitis traits and significant SNPs for SCS in different Holstein populations coincide with our results. In all identified regions, except for the region on chromosome X, significant SNPs were present in significant haplotypes. The minor alleles of identified SNPs on chromosomes 18 and 19, and the major alleles of SNPs on chromosomes 6 and X were favorable for a lower SCS. Differences in somatic cell count (SCC) between alternative SNP alleles reached 14 000 cells/mL. CONCLUSIONS: The results support the polygenic nature of the genetic determination of SCS, confirm the importance of previously reported QTL, and provide evidence for the segregation of additional QTL for SCS in Holstein cattle. The small size of the regions identified here will facilitate the search for causal genetic variations that affect gene functions. BioMed Central 2014-06-04 /pmc/articles/PMC4078941/ /pubmed/24898131 http://dx.doi.org/10.1186/1297-9686-46-35 Text en Copyright © 2014 Abdel-Shafy et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. |
spellingShingle | Research Abdel-Shafy, Hamdy Bortfeldt, Ralf H Tetens, Jens Brockmann, Gudrun A Single nucleotide polymorphism and haplotype effects associated with somatic cell score in German Holstein cattle |
title | Single nucleotide polymorphism and haplotype effects associated with somatic cell score in German Holstein cattle |
title_full | Single nucleotide polymorphism and haplotype effects associated with somatic cell score in German Holstein cattle |
title_fullStr | Single nucleotide polymorphism and haplotype effects associated with somatic cell score in German Holstein cattle |
title_full_unstemmed | Single nucleotide polymorphism and haplotype effects associated with somatic cell score in German Holstein cattle |
title_short | Single nucleotide polymorphism and haplotype effects associated with somatic cell score in German Holstein cattle |
title_sort | single nucleotide polymorphism and haplotype effects associated with somatic cell score in german holstein cattle |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4078941/ https://www.ncbi.nlm.nih.gov/pubmed/24898131 http://dx.doi.org/10.1186/1297-9686-46-35 |
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