Evolutionary relationships and signatures of selection in cattle established using genome-wide single nucleotide polymorphisms

Title from PDF of title page (University of Missouri--Columbia, viewed on August 28, 2012).The entire thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file; a non-technical public abstract appears in the public.pdf file.Dissertation advisor: Dr. Jeremy F. TaylorIncludes bibliographical references.Vita.Ph. D. University of Missouri--Columbia 2012"May 2012"Although high-throughput single nucleotide polymorphism (SNP) microarray assays were primarily developed for association studies, they are a powerful tool in the study of evolution and population genetics. The applications of SNP genotypes to phylogenomics and population genetics were extended in this dissertation. Using SNP probes designed in a single species, a well-resolved phylogeny of 61 species was produced. Ancestral relationships between cattle breeds were analyzed using parsimony analysis of homozygous genotypes, parsimony analysis of all genotypes, network analysis using FST estimates, principal component analysis, and admixture analysis. A novel method to identify molecular signatures of selection was deployed. In this method, birth date was analyzed as the dependent variable in a mixed model framework to identify SNP loci which predict birth date. It was shown that predictive loci changed in allele frequency much more than theoretically expected due to genetic drift alone; thus, these loci are in linkage disequilibrium with selected casual variants. In addition to identifying loci under artificial selection, loci putatively responding to natural selection were also identified.Includes bibliographical reference

Associations between 44 gene-associated markers and meat tenderness in Limousin steers [abstract]

Abstract only availableFaculty Mentor: Jerry Taylor, Animal ScienceBeef tenderness is a major factor influencing consumer satisfaction which can only be quantitatively measured using Warner-Bratzler Shear Force (WBSF) after carcasses are harvested and samples have been aged for fourteen days and then cooked.  Because of the logistic difficulty and cost of this process, researchers have begun developing genetic markers which identify beef cattle with the propensity to produce tender meat.  In this project, 44 single nucleotide polymorphisms (SNPs) representing 11 genes were scored in 131 Limousin steers with available WBSF, growth and carcass composition data.  Genotypes were determined using a Beckman Coulter GenomeLab SNPStream system.  The primary genes of interest in this study were CAPN1 which encodes the µ-calpain protein which posthumously degrades myofibrils and CAST which encodes the calpain inhibitor, calpastatin.  While SNP loci in both of these genes are currently being commercialized to the beef industry, none appear to be causal for effects on meat tenderness.  This project was designed to examine alternate SNPs within these genes to identify markers that may have greater commercial value.  SNPs located within the genes: LOX, OPN, ABCG2, DGAT1, GHR, LEP, TG, SST and APM were also analyzed, since these genes have previously been associated with variation in growth and carcass composition traits in beef cattle.  A commercial test which combines several of these SNPs would greatly benefit the industry by effectively identifying genetically superior breeding and slaughter animals

What's in your next-generation sequence data? An exploration of unmapped DNA and RNA sequence reads from the bovine reference individual.

BackgroundNext-generation sequencing projects commonly commence by aligning reads to a reference genome assembly. While improvements in alignment algorithms and computational hardware have greatly enhanced the efficiency and accuracy of alignments, a significant percentage of reads often remain unmapped.ResultsWe generated de novo assemblies of unmapped reads from the DNA and RNA sequencing of the Bos taurus reference individual and identified the closest matching sequence to each contig by alignment to the NCBI non-redundant nucleotide database using BLAST. As expected, many of these contigs represent vertebrate sequence that is absent, incomplete, or misassembled in the UMD3.1 reference assembly. However, numerous additional contigs represent invertebrate species. Most prominent were several species of Spirurid nematodes and a blood-borne parasite, Babesia bigemina. These species are either not present in the US or are not known to infect taurine cattle and the reference animal appears to have been host to unsequenced sister species.ConclusionsWe demonstrate the importance of exploring unmapped reads to ascertain sequences that are either absent or misassembled in the reference assembly and for detecting sequences indicative of parasitic or commensal organisms

Diversity and evolution of 11 innate immune genes in Bos taurus taurus and Bos taurus indicus cattle

The Toll-like receptor (TLR) and peptidoglycan recognition protein 1 (PGLYRP1) genes play key roles in the innate immune systems of mammals. While the TLRs recognize a variety of invading pathogens and induce innate immune responses, PGLYRP1 is directly microbicidal. We used custom allele-specific assays to genotype and validate 220 diallelic variants, including 54 nonsynonymous SNPs in 11 bovine innate immune genes (TLR1-TLR10, PGLYRP1) for 37 cattle breeds. Bayesian haplotype reconstructions and median joining networks revealed haplotype sharing between Bos taurus taurus and Bos taurus indicus breeds at every locus, and we were unable to differentiate between the specialized B. t. taurus beef and dairy breeds, despite an average polymorphism density of one locus per 219 bp. Ninety-nine tagSNPs and one tag insertion-deletion polymorphism were sufficient to predict 100% of the variation at all 11 innate immune loci in both subspecies and their hybrids, whereas 58 tagSNPs captured 100% of the variation at 172 loci in B. t. taurus. PolyPhen and SIFT analyses of nonsynonymous SNPs encoding amino acid replacements indicated that the majority of these substitutions were benign, but up to 31% were expected to potentially impact protein function. Several diversity-based tests provided support for strong purifying selection acting on TLR10 in B. t. taurus cattle. These results will broadly impact efforts related to bovine translational genomics

Detection of selective sweeps in cattle using genome-wide SNP data

Background: The domestication and subsequent selection by humans to create breeds and biological types of cattle undoubtedly altered the patterning of variation within their genomes. Strong selection to fix advantageous large-effect mutations underlying domesticability, breed characteristics or productivity created selective sweeps in which variation was lost in the chromosomal region flanking the selected allele. Selective sweeps have now been identified in the genomes of many animal species including humans, dogs, horses, and chickens. Here, we attempt to identify and characterise regions of the bovine genome that have been subjected to selective sweeps.Results: Two datasets were used for the discovery and validation of selective sweeps via the fixation of alleles at a series of contiguous SNP loci. BovineSNP50 data were used to identify 28 putative sweep regions among 14 diverse cattle breeds. Affymetrix BOS 1 prescreening assay data for five breeds were used to identify 85 regions and validate 5 regions identified using the BovineSNP50 data. Many genes are located within these regions and the lack of sequence data for the analysed breeds precludes the nomination of selected genes or variants and limits the prediction of the selected phenotypes. However, phenotypes that we predict to have historically been under strong selection include horned-polled, coat colour, stature, ear morphology, and behaviour.Conclusions: The bias towards common SNPs in the design of the BovineSNP50 assay led to the identification of recent selective sweeps associated with breed formation and common to only a small number of breeds rather than ancient events associated with domestication which could potentially be common to all European taurines. The limited SNP density, or marker resolution, of the BovineSNP50 assay significantly impacted the rate of false discovery of selective sweeps, however, we found sweeps in common between breeds which were confirmed using an ultra-high-density assay scored in a small number of animals from a subset of the breeds. No sweep regions were shared between indicine and taurine breeds reflecting their divergent selection histories and the very different environmental habitats to which these sub-species have adapted.Peer reviewedAnimal Scienc

Comparison of Bayesian models to estimate direct genomic values in multi-breed commercial beef cattle

Background: While several studies have examined the accuracy of direct genomic breeding values (DGV) within and across purebred cattle populations, the accuracy of DGV in crossbred or multi-breed cattle populations has been less well examined. Interest in the use of genomic tools for both selection and management has increased within the hybrid seedstock and commercial cattle sectors and research is needed to determine their efficacy. We predicted DGV for six traits using training populations of various sizes and alternative Bayesian models for a population of 3240 crossbred animals. Our objective was to compare alternate models with different assumptions regarding the distributions of single nucleotide polymorphism (SNP) effects to determine the optimal model for enhancing feasibility of multi-breed DGV prediction for the commercial beef industry.Results: Realized accuracies ranged from 0.40 to 0.78. Randomly assigning 60 to 70% of animals to training (n is about 2000 records) yielded DGV accuracies with the smallest coefficients of variation. Mixture models (BayesB95, BayesC[pi]) and models that allow SNP effects to be sampled from distributions with unequal variances (BayesA, BayesB95) were advantageous for traits that appear or are known to be influenced by large-effect genes. For other traits, models differed little in prediction accuracy (~0.3 to 0.6%), suggesting that they are mainly controlled by small-effect loci.Conclusions: The proportion (60 to 70%) of data allocated to training that optimized DGV accuracy and minimized the coefficient of variation of accuracy was similar to large dairy populations. Larger effects were estimated for some SNPs using BayesA and BayesB95 models because they allow unequal SNP variances. This substantially increased DGV accuracy for Warner-Bratzler Shear Force, for which large-effect quantitative trait loci (QTL) are known, while no loss in accuracy was observed for traits that appear to follow the infinitesimal model. Large decreases in accuracy (up to 0.07) occurred when SNPs that presumably tag large-effect QTL were over-regressed towards the mean in BayesC0 analyses. The DGV accuracies achieved here indicate that genomic selection has predictive utility in the commercial beef industry and that using models that reflect the genomic architecture of the trait can have predictive advantages in multi-breed populations.Peer reviewedAnimal Scienc

Accuracies of genomic breeding values in American Angus beef cattle using K-means clustering for cross-validation

<p>Abstract</p> <p>Background</p> <p>Genomic selection is a recently developed technology that is beginning to revolutionize animal breeding. The objective of this study was to estimate marker effects to derive prediction equations for direct genomic values for 16 routinely recorded traits of American Angus beef cattle and quantify corresponding accuracies of prediction.</p> <p>Methods</p> <p>Deregressed estimated breeding values were used as observations in a weighted analysis to derive direct genomic values for 3570 sires genotyped using the Illumina BovineSNP50 BeadChip. These bulls were clustered into five groups using K-means clustering on pedigree estimates of additive genetic relationships between animals, with the aim of increasing within-group and decreasing between-group relationships. All five combinations of four groups were used for model training, with cross-validation performed in the group not used in training. Bivariate animal models were used for each trait to estimate the genetic correlation between deregressed estimated breeding values and direct genomic values.</p> <p>Results</p> <p>Accuracies of direct genomic values ranged from 0.22 to 0.69 for the studied traits, with an average of 0.44. Predictions were more accurate when animals within the validation group were more closely related to animals in the training set. When training and validation sets were formed by random allocation, the accuracies of direct genomic values ranged from 0.38 to 0.85, with an average of 0.65, reflecting the greater relationship between animals in training and validation. The accuracies of direct genomic values obtained from training on older animals and validating in younger animals were intermediate to the accuracies obtained from K-means clustering and random clustering for most traits. The genetic correlation between deregressed estimated breeding values and direct genomic values ranged from 0.15 to 0.80 for the traits studied.</p> <p>Conclusions</p> <p>These results suggest that genomic estimates of genetic merit can be produced in beef cattle at a young age but the recurrent inclusion of genotyped sires in retraining analyses will be necessary to routinely produce for the industry the direct genomic values with the highest accuracy.</p

Controlo integrado da Lagarta das Pastagens Mythimna unipuncta (Haworth)

II Jornadas Agronómicas Açorianas, Outubro, 1991, Ponta Delgada, Açores.No Arquipélago dos Açores, desde 1970 e com maior incidência na ilha de S. Miguel, devido ao aumento da área de pastagem, com vista ao desenvolvimento da bovinocultura, uma das espécies de Noctuídeos, Mythimna unipuncta (Haworth) (Lepidoptera, Noctuidae), assinalada na região desde 1810 por GODMAN, tornou-se num grave problema económico, estimando-se os seus prejuízos em cerça de 8% da produção anual das pastagens (TAVARES, 1989)