Dataset Information

Construction of a large collection of small genome variations in French dairy and beef breeds using whole-genome sequences.

ABSTRACT: In recent years, several bovine genome sequencing projects were carried out with the aim of developing genomic tools to improve dairy and beef production efficiency and sustainability.In this study, we describe the first French cattle genome variation dataset obtained by sequencing 274 whole genomes representing several major dairy and beef breeds. This dataset contains over 28 million single nucleotide polymorphisms (SNPs) and small insertions and deletions. Comparisons between sequencing results and SNP array genotypes revealed a very high genotype concordance rate, which indicates the good quality of our data.To our knowledge, this is the first large-scale catalog of small genomic variations in French dairy and beef cattle. This resource will contribute to the study of gene functions and population structure and also help to improve traits through genotype-guided selection.

SUBMITTER: Boussaha M

PROVIDER: S-EPMC5111192 | biostudies-literature | 2016 Nov

REPOSITORIES: biostudies-literature

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Construction of a large collection of small genome variations in French dairy and beef breeds using whole-genome sequences.

Boussaha Mekki M Michot Pauline P Letaief Rabia R Hozé Chris C Fritz Sébastien S Grohs Cécile C Esquerré Diane D Duchesne Amandine A Philippe Romain R Blanquet Véronique V Phocas Florence F Floriot Sandrine S Rocha Dominique D Klopp Christophe C Capitan Aurélien A Boichard Didier D

Genetics, selection, evolution : GSE 20161115 1

<h4>Background</h4>In recent years, several bovine genome sequencing projects were carried out with the aim of developing genomic tools to improve dairy and beef production efficiency and sustainability.<h4>Results</h4>In this study, we describe the first French cattle genome variation dataset obtained by sequencing 274 whole genomes representing several major dairy and beef breeds. This dataset contains over 28 million single nucleotide polymorphisms (SNPs) and small insertions and deletions. C ...[more]

PMID: 27846802

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Project description:BackgroundQuantitative genetic studies suggest the existence of variation at the genome level that affects the ability of cattle to resist to parasitic diseases. The objective of the current study was to identify regions of the bovine genome that are associated with resistance to endo-parasites.MethodsIndividual cattle records were available for Fasciola hepatica-damaged liver from 18 abattoirs. Deregressed estimated breeding values (EBV) for F. hepatica-damaged liver were generated for genotyped animals with a record for F. hepatica-damaged liver and for genotyped sires with a least one progeny record for F. hepatica-damaged liver; 3702 animals were available. In addition, individual cow records for antibody response to F. hepatica on 6388 genotyped dairy cows, antibody response to Ostertagia ostertagi on 8334 genotyped dairy cows and antibody response to Neospora caninum on 4597 genotyped dairy cows were adjusted for non-genetic effects. Genotypes were imputed to whole-sequence; after edits, 14,190,141 single nucleotide polymorphisms (SNPs) and 16,603,644 SNPs were available for cattle with deregressed EBV for F. hepatica-damaged liver and cows with an antibody response to a parasitic disease, respectively. Association analyses were undertaken using linear regression on one SNP at a time, in which a genomic relationship matrix accounted for the relationships between animals.ResultsGenomic regions for F. hepatica-damaged liver were located on Bos taurus autosomes (BTA) 1, 8, 11, 16, 17 and 18; each region included at least one SNP with a p value lower than 10-6. Five SNPs were identified as significant (q value < 0.05) for antibody response to N. caninum and were located on BTA21 or 25. For antibody response to F. hepatica and O. ostertagi, six and nine quantitative trait loci (QTL) regions that included at least one SNP with a p value lower than 10-6 were identified, respectively. Gene set enrichment analysis revealed a significant association between functional annotations related to the olfactory system and QTL that were suggestively associated with endo-parasite phenotypes.ConclusionsA number of novel genomic regions were suggestively associated with endo-parasite phenotypes across the bovine genome and two genomic regions on BTA21 and 25 were associated with antibody response to N. caninum.

Project description:While many association studies exist that have attempted to relate genomic markers to phenotypic performance in cattle, very few have considered gestation length as a phenotype, and of those that did, none used whole genome sequence data from multiple breeds. The objective of the present study was therefore to relate imputed whole genome sequence data to estimated breeding values for gestation length using 22,566 sires (representing 2,262,706 progeny) of multiple breeds [Angus (AA), Charolais (CH), Holstein-Friesian (HF), and Limousin (LM)]. The associations were undertaken within breed using linear mixed models that accounted for genomic relatedness among sires; a separate association analysis was undertaken with all breeds analysed together but with breed included as a fixed effect in the model. Furthermore, the genome was divided into 500 kb segments and whether or not segments harboured a single nucleotide polymorphism (SNP) with a P ? 1 × 10-4 common to different combinations of breeds was determined. Putative quantitative trait loci (QTL) regions associated with gestation length were detected in all breeds; significant associations with gestation length were only detected in the HF population and in the across-breed analysis of all 22,566 sires. Twenty-five SNPs were significantly associated (P ? 5 × 10-8) with gestation length in the HF population. Of the 25 significant SNPs, 18 were located within three QTLs on Bos taurus autosome number (BTA) 18, six were in two QTL on BTA19, and one was located within a QTL on BTA7. The strongest association was rs381577268, a downstream variant of ZNF613 located within a QTL spanning from 58.06 to 58.19 Mb on BTA18; it accounted for 1.37% of the genetic variance in gestation length. Overall there were 11 HF animals within the edited dataset that were homozygous for the T allele at rs381577268 and these had a 3.3 day longer (P < 0.0001) estimated breeding value (EBV) for gestation length than the heterozygous animals and a 4.7 day longer (P < 0.0001) EBV for gestation length than the homozygous CC animals. The majority of the 500 kb windows harboring a SNP with a P ? 1 × 10-4 were unique to a single breed and no window was shared among all four breeds for gestation length, suggesting any QTLs identified are breed-specific associations.

Project description:BackgroundIn France, implementation of genomic evaluations in dairy cattle breeds started in 2009 and this has modified the breeding schemes drastically. In this context, the goal of our study was to understand the impact of genomic selection on the genetic diversity of bulls from three French dairy cattle breeds born between 2005 and 2015 (Montbéliarde, Normande and Holstein) and the factors that are involved.MethodsWe compared annual genetic gains, inbreeding rates based on runs of homozygosity (ROH) and pedigree data, and mean ROH length within breeds, before and after the implementation of genomic selection.ResultsGenomic selection induced an increase in mean annual genetic gains of 50, 71 and 33% for Montbéliarde, Normande and Holstein bulls, respectively, and in parallel, the generation intervals were reduced by a factor of 1.7, 1.9 and 2, respectively. We found no significant change in inbreeding rate for the two national breeds, Montbéliarde and Normande, and a significant increase in inbreeding rate for the Holstein international breed, which is now as high as 0.55% per year based on ROH and 0.49% per year based on pedigree data (equivalent to a rate of 1.36 and 1.39% per generation, respectively). The mean ROH length was longer for bulls from the Holstein breed than for those from the other two breeds.ConclusionsWith the implementation of genomic selection, the annual genetic gain increased for bulls from the three major French dairy cattle breeds. At the same time, the annual loss of genetic diversity increased for Holstein bulls, possibly because of the massive use of a few elite bulls in this breed, but not for Montbéliarde and Normande bulls. The increase in mean ROH length in Holstein may reflect the occurrence of recent inbreeding. New strategies in breeding schemes, such as female donor stations and embryo transfer, and recent implementation of genomic evaluations in small regional breeds should be studied carefully in order to ensure the sustainability of breeding schemes in the future.

Dataset Information

Construction of a large collection of small genome variations in French dairy and beef breeds using whole-genome sequences.

Publications

Construction of a large collection of small genome variations in French dairy and beef breeds using whole-genome sequences.

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