Dataset Information

CRUMBLER: A tool for the prediction of ancestry in cattle.

ABSTRACT: In many beef and some dairy production systems, crossbreeding is used to take advantage of breed complementarity and heterosis. Admixed animals are frequently identified by their coat color and body conformation phenotypes, however, without pedigree information it is not possible to identify the expected breed composition of an admixed animal and in the presence of selection, the actual composition may differ from expectation. As the roles of DNA and genotype data become more pervasive in animal agriculture, a systematic method for estimating the breed composition (the proportions of an animal's genome originating from ancestral pure breeds) has utility for a variety of downstream analyses including the estimation of genomic breeding values for crossbred animals, the estimation of quantitative trait locus effects, and heterosis and heterosis retention in advanced generation composite animals. Currently, there is no automated or semi-automated ancestry estimation platform for cattle and the objective of this study was to evaluate the utility of extant public software for ancestry estimation and determine the effects of reference population size and composition and number of utilized single nucleotide polymorphism loci on ancestry estimation. We also sought to develop an analysis pipeline that would simplify this process for members of the livestock genomics research community. We developed and tested a tool, "CRUMBLER", to estimate the global ancestry of cattle using ADMIXTURE and SNPweights based on a defined reference panel. CRUMBLER, was developed and evaluated in cattle, but is a species agnostic pipeline that facilitates the streamlined estimation of breed composition for individuals with potentially complex ancestries using publicly available global ancestry software and a specified reference population SNP dataset. We developed the reference panel from a large cattle genotype data set and breed association pedigree information using iterative analyses to identify purebred individuals that were representative of each breed. We also evaluated the numbers of markers necessary for breed composition estimation and simulated genotypes for advanced generation composite animals to evaluate the precision of the developed tool. The developed CRUMBLER pipeline extracts a specified subset of genotypes that is common to all current commercially available genotyping platforms, processes these into the file formats required for the analysis software, and predicts admixture proportions using the specified reference population allele frequencies.

SUBMITTER: Crum TE

PROVIDER: S-EPMC6709893 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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CRUMBLER: A tool for the prediction of ancestry in cattle.

Crum Tamar E TE Schnabel Robert D RD Decker Jared E JE Regitano Luciana C A LCA Taylor Jeremy F JF

PloS one 20190826 8

In many beef and some dairy production systems, crossbreeding is used to take advantage of breed complementarity and heterosis. Admixed animals are frequently identified by their coat color and body conformation phenotypes, however, without pedigree information it is not possible to identify the expected breed composition of an admixed animal and in the presence of selection, the actual composition may differ from expectation. As the roles of DNA and genotype data become more pervasive in animal ...[more]

PMID: 31449539

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Project description:Cattle are bred for, amongst other factors, specific traits, including parasite resistance and adaptation to climate. However, the influence and inheritance of mitochondrial DNA (mtDNA) are not usually considered in breeding programmes. In this study, we analysed the mtDNA profiles of cattle from Victoria (VIC), southern Australia, which is a temperate climate, and the Northern Territory (NT), the northern part of Australia, which has a tropical climate, to determine if the mtDNA profiles of these cattle are indicative of breed and phenotype, and whether these profiles are appropriate for their environments.A phylogenetic tree of the full mtDNA sequences of different breeds of cattle, which were obtained from the NCBI database, showed that the mtDNA profiles of cattle do not always reflect their phenotype as some cattle with Bos taurus phenotypes had Bos indicus mtDNA, whilst some cattle with Bos indicus phenotypes had Bos taurus mtDNA. Using D-loop sequencing, we were able to contrast the phenotypes and mtDNA profiles from different species of cattle from the 2 distinct cattle breeding regions of Australia. We found that 67 of the 121 cattle with Bos indicus phenotypes from NT (55.4%) had Bos taurus mtDNA. In VIC, 92 of the 225 cattle with Bos taurus phenotypes (40.9%) possessed Bos indicus mtDNA. When focusing on oocytes from cattle with the Bos taurus phenotype in VIC, their respective oocytes with Bos indicus mtDNA had significantly lower levels of mtDNA copy number compared with oocytes possessing Bos taurus mtDNA (P < 0.01). However, embryos derived from oocytes with Bos indicus mtDNA had the same ability to develop to the blastocyst stage and the levels of mtDNA copy number in their blastocysts were similar to blastocysts derived from oocytes harbouring Bos taurus mtDNA. Nevertheless, oocytes originating from the Bos indicus phenotype exhibited lower developmental potential due to low mtDNA copy number when compared with oocytes from cattle with a Bos taurus phenotype.The phenotype of cattle is not always related to their mtDNA profiles. MtDNA profiles should be considered for breeding programmes as they also influence phenotypic traits and reproductive capacity in terms of oocyte quality.

Project description:BackgroundPrevious research programmes have described muscle biochemical traits and gene expression levels associated with beef tenderness. One of our results concerning the DNAJA1 gene (an Hsp40) was patented. This study aims to confirm the relationships previously identified between two gene families (heat shock proteins and energy metabolism) and beef quality.ResultsWe developed an Agilent chip with specific probes for bovine muscular genes. More than 3000 genes involved in muscle biology or meat quality were selected from genetic, proteomic or transcriptomic studies, or from scientific publications. As far as possible, several probes were used for each gene (e.g. 17 probes for DNAJA1). RNA from Longissimus thoracis muscle samples was hybridised on the chips. Muscles samples were from four groups of Charolais cattle: two groups of young bulls and two groups of steers slaughtered in two different years. Principal component analysis, simple correlation of gene expression levels with tenderness scores, and then multiple regression analysis provided the means to detect the genes within two families (heat shock proteins and energy metabolism) which were the most associated with beef tenderness. For the 25 Charolais young bulls slaughtered in year 1, expression levels of DNAJA1 and other genes of the HSP family were related to the initial or overall beef tenderness. Similarly, expression levels of genes involved in fat or energy metabolism were related with the initial or overall beef tenderness but in the year 1 and year 2 groups of young bulls only. Generally, the genes individually correlated with tenderness are not consistent across genders and years indicating the strong influence of rearing conditions on muscle characteristics related to beef quality. However, a group of HSP genes, which explained about 40% of the variability in tenderness in the group of 25 young bulls slaughtered in year 1 (considered as the reference group), was validated in the groups of 30 Charolais young bulls slaughtered in year 2, and in the 21 Charolais steers slaughtered in year 1, but not in the group of 19 steers slaughtered in year 2 which differ from the reference group by two factors (gender and year). When the first three groups of animals were analysed together, this subset of genes explained a 4-fold higher proportion of the variability in tenderness than muscle biochemical traits.ConclusionThis study underlined the relevance of the GENOTEND chip to identify markers of beef quality, mainly by confirming previous results and by detecting other genes of the heat shock family as potential markers of beef quality. However, it was not always possible to extrapolate the relevance of these markers to all animal groups which differ by several factors (such as gender or environmental conditions of production) from the initial population of reference in which these markers were identified.

Dataset Information

CRUMBLER: A tool for the prediction of ancestry in cattle.

Publications

CRUMBLER: A tool for the prediction of ancestry in cattle.

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