Single nucleotide polymorphism arrays have created new possibilities for performing genome-wide studies to detect genomic regions harboring sequence variants that affect complex traits. However, the majority of validated SNPs for which allele frequencies have been estimated are limited primarily to European breeds. The objective of this study to perform SNP discovery in three South African indigenous breeds (Afrikaner, Drakensberger and Nguni) using whole genome sequencing. DNA was extracted from blood and hair samples, quantified and prepared at 50ng/µl concentration for sequencing at the Agricultural Research Council Biotechnology Platform using an Illumina HiSeq 2500. The fastq files were used to call the variants using the Genome Analysis Tool Kit. A total of 1,678,360 were identified as novel using Run 6 of 1000 Bull Genomes Project. Annotation of the identified variants classified them into functional categories. Within the coding regions, about 30% of the SNPs were nonsynonymous substitutions that encode for alternate amino acids. The study of distribution of SNP across the genome identified regions showing notable differences in the densities of SNPs among the breeds and highlighted many regions of functional significance. Gene ontology terms identified genes such as MLANA, SYT10 and CDC42EP5 that have been associated with coat colour in mouse, and ADAMS3, DNAJC3 and PAG5 genes have been associated with fertility in cattle. Further analysis of the variants detected 688 candidate selective sweeps (ZHp Z-scores ≤ -4) across all three breeds, of which 223 regions were assigned as being putative selective sweeps (ZHp scores ≤ -5). We also identified 96 regions with extremely low ZHp Z-scores (≤ -6) in Afrikaner and Nguni. Genes such as KIT and MITF that have been associated with skin pigmentation in cattle and CACNA1C, which has been associated with biopolar disorder in human, were identified in these regions. This study provides the first analysis of sequence data to discover SNPs in indigenous South African cattle breeds. The information will play an important role in our efforts to understand the genetic history of our cattle and in designing appropriate breed improvement programmes.
The availability of high-density SNP assays including the BovineSNP50 (50 K) enables the identification of novel quantitative trait loci (QTL) and improvement of the resolution of the locations of previously mapped QTL. We performed a series of genome-wide association studies (GWAS) using 50 K genotypes scored in 18,274 animals from 10 US beef cattle breeds with observations for twelve body weights, calving ease and carcass traits. A total of 159 large-effects QTL (defined as 1-Mb genome windows explaining more than 1% of additive genetic variance) were identified. In general, more QTL were identified in analyses with bigger sample sizes. Four large-effect pleiotropic or closely linked QTLs located on BTA6 at 37–42 Mb (primarily at 38 Mb), on BTA7 at 93 Mb, on BTA14 at 23–26 Mb (primarily at 25 Mb) and on BTA20 at 4 Mb were identified in more than one breed. Several breed-specific large-effect pleiotropic or closely linked QTL were also identified. Some identified QTL regions harbor genes known to have large effects on a variety of traits in cattle such as PLAG1 and MSTN and others harbor promising candidate genes including NCAPG, ARRDC3, ERGIC1, SH3PXD2B, HMGA2, MSRB3, LEMD3, TIGAR, SEPT7, and KIRREL3. Gene ontology analysis revealed that genes involved in ossification and in adipose tissue development were over-represented in the identified pleiotropic QTL. Also, the MAPK signaling pathway was identified as a common pathway affected by the genes located near the pleiotropic QTL. This largest GWAS ever performed in beef cattle, led us to discover several novel across-breed and breed-specific large-effect pleiotropic QTL that cumulatively account for a significant percentage of additive genetic variance (e.g. more than a third of additive genetic variance of birth and mature weights; and calving ease direct in Hereford). These results will improve our understanding of the biology of growth and body composition in cattle.
Journal Article Rapid communication: mapping of the bovine stearoyl-coenzyme A desaturase (SCD) gene to BTA26 Get access E. M. G. Campbell, E. M. G. Campbell 3Department of Animal Science, Texas Agricultural Experiment Station, Texas A&M University, College Station 77843-2471, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar D. S. Gallagher, D. S. Gallagher 3Department of Animal Science, Texas Agricultural Experiment Station, Texas A&M University, College Station 77843-2471, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar S. K. Davis, S. K. Davis 3Department of Animal Science, Texas Agricultural Experiment Station, Texas A&M University, College Station 77843-2471, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar J. F. Taylor, J. F. Taylor 3Department of Animal Science, Texas Agricultural Experiment Station, Texas A&M University, College Station 77843-2471, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar S. B. Smith S. B. Smith 3Department of Animal Science, Texas Agricultural Experiment Station, Texas A&M University, College Station 77843-2471, USA 2Correspondence: 2471 TAMU(phone: 979-845-3939; fax: 979-458-2702; E-mail: sbsmith@tamu.edu). Search for other works by this author on: Oxford Academic PubMed Google Scholar Journal of Animal Science, Volume 79, Issue 7, July 2001, Pages 1954–1955, https://doi.org/10.2527/2001.7971954x Published: 01 July 2001 Article history Received: 05 October 2000 Accepted: 21 February 2001 Published: 01 July 2001
The objective of this research was to evaluate the consumer-controlled factors of cooking method and degree of doneness on Top Choice, Low Choice, High Select, and Low Select top loin steaks. The in-home product test was conducted in Chicago, Houston, Philadelphia, and San Francisco. Consumers (n = 2,212) evaluated each top loin steak for overall like (OLIKE), tenderness (TEND), juiciness (JUIC), flavor desirability (DFLAV), and flavor intensity (IFLAV) using 23-point hedonic scales. Respondents in San Francisco and Philadelphia cooked their top loin steaks to lower degrees of doneness than those in Chicago and Houston. Outdoor grilling was the most common method of cookery for top loin steaks in all cities. Consumers had the highest preference for Top Choice steaks (P < .05) and the lowest preference for Low Select steaks (P < .05). Consumer OLIKE scores were the highest (P < .05) for steaks cooked to a medium rare or lesser degree of doneness. Consumers preferred (P < .05) medium and well done or more degrees of doneness over medium well. The interaction of city × cooking method was significant for all steak palatability attributes. The differences in consumer preparation techniques among cities present challenges for the beef industry to develop market-specific promotional campaigns.
Abstract beta-Mannosidosis is a lethal lysosomal storage disease inherited as an autosomal recessive in man, cattle and goats. Laboratory assay data of plasma beta-mannosidase activity represent a mixture of homozygous normal and carrier genotype distributions in a proportion determined by genotype frequency. A maximum likelihood approach employing data transformations for each genotype distribution and assuming a diallelic model of inheritance is described. Estimates of the transformation and genotype distribution parameters, gene frequency, genotype fitness and carrier probability were obtained simultaneously from a sample of 2,812 observations on U.S. purebred Salers cattle with enzyme activity, age, gender, month of pregnancy, month of testing, and parents identified. Transformations to normality were not required, estimated gene and carrier genotype frequencies of 0.074 and 0.148 were high, and the estimated relative fitness of heterozygotes was 1.36. The apparent overdominance in fitness may be due to a nonrandom sampling of progeny genotypes within families. The mean of plasma enzyme activity was higher for males than females, higher in winter months, lower in summer months and decreased with increased age. Estimates of carrier probabilities indicate that the test is most effective when animals are sampled as calves, although effectiveness of the plasma assay was less for males than females. Test effectiveness was enhanced through averaging repeated assays of enzyme activity on each animal. Our approach contributes to medical diagnostics in several ways. Rather than assume underlying normality for the distributions comprising the mixture, we estimate transformations to normality for each genotype distribution simultaneously with all other model parameters. This process also excludes potential biases due to data preadjustment for systematic effects. We also provide a method for partitioning phenotypic variation within each genotypic distribution which allows an assessment of the value of repeat measurements of the predictive variable for genotype assignment.
Genomic selection is emerging as a powerful tool for the estimation of breeding values in plant and animal breeding. While many analytical approaches have been proposed for the joint estimation of high-density single nucleotide polymorphism (SNP) effects, within the framework of best linear unbiased estimation, genomic selection is equivalent to the prediction of breeding values for individuals with no phenotypes, for which the theoretical solution was first published in 1974. Genomic selection simply replaces the pedigree-derived numerator relationship matrix with the marker-derived realized genomic relationship matrix, an approach first proposed in 1997. The advance facilitated by the availability of high-density SNP genotypes is the ability to precisely estimate realized relationship coefficients among individuals regardless of the availability of pedigree information or the history of selection that has been applied to the population. However, genomic relationship coefficients are usually estimated assuming the independence of SNP genotypes, thus ignoring the effects of linkage disequilibrium, and the utilized SNPs are invariably ascertained to be common variants within the specie's genome which leads to the overestimation of relationship coefficients. The accuracy of the produced genomic estimated breeding values (GEBV) is often evaluated using variously formed validation populations incorporating individuals with genotypes and phenotypes that were not used for the estimation of SNP effects in the training population. However, GEBV accuracies are shown here to be a function of the accuracy of training population GEBV and the magnitudes of genomic relationships between individuals in the training and validation populations. Consequently, genomic selection is ideally suited to populations in which highly accurate GEBV are available for training population individuals and whose marker-selected progeny go on to produce phenotypes and reenter the training population which then becomes dynamic. Conversely, genomic selection is not well suited to the identification of elite individuals within families that have not historically contributed to breeding programs, to static training populations, or to training and implementation in distantly related populations. Thus, the implementation of genomic selection for costly or difficult to measure phenotypes such as feed efficiency or disease resistance will require the periodic regeneration of phenotyped populations for the retraining of GEBV prediction equations or the identification of the causal variants which underlie variation in these traits. The exponentially reducing cost of whole genome resequencing may soon allow the identification of at least the large effect variants.
The purpose of this study was to identify loci associated with Mycobacterium avium subspecies paratuberculosis (Map) infection status in US Holsteins using the Illumina BovineSNP50 BeadChip whole genome single nucleotide polymorphism (SNP) assay. Two hundred forty-five cows from dairies in New York, Pennsylvania and Vermont enrolled in longitudinal herd studies between January 1999 and November 2007 were assessed for the presence of Map in both faecal and tissue samples. An animal was considered tissue infected if any sample contained at least one colony forming unit of Map per gram of tissue (CFU/g) and the same definition was employed for faecal samples. Each animal was genotyped with the Illumina BovineSNP50 BeadChip and after quality assurance filtering, 218 animals and 45 683 SNPs remained. We sought to identify loci associated with four different case/control classifications: presence of Map in the tissue, presence of Map in faeces, presence of Map in both tissue and faeces and presence of Map in tissue but not faeces. A case-control genome wide association study was conducted to test the four different classifications of Map infection status (cases) when compared with a Map-negative control group (control). Regions on chromosomes 1, 5, 7, 8, 16, 21 and 23 were identified with moderate significance (P < 5 x 10(-5)). Two regions, one on chromosome 3 (near EDN2) and another on chromosome 9 (no positional gene candidates), were identified with a high level of association to the presence of Map in tissue and both tissue and faeces respectively (P < 5 x 10(-7), genome-wide Bonferonni P < 0.05).
Bovine respiratory disease complex (BRDC) is an infectious disease of cattle that is caused by a combination of viral and/or bacterial pathogens. Selection for cattle with reduced susceptibility to respiratory disease would provide a permanent tool for reducing the prevalence of BRDC. The objective of this study was to identify BRDC susceptibility loci in pre-weaned Holstein calves as a prerequisite to using genetic improvement as a tool for decreasing the prevalence of BRDC. High density SNP genotyping with the Illumina BovineHD BeadChip was conducted on 1257 male and 757 female Holstein calves from California (CA), and 767 calves identified as female from New Mexico (NM). Of these, 1382 were classified as BRDC cases, and 1396 were classified as controls, with all phenotypes assigned using the McGuirk health scoring system. During the acquisition of blood for DNA isolation, two deep pharyngeal and one mid-nasal diagnostic swab were obtained from each calf for the identification of bacterial and viral pathogens. Genome-wide association analyses were conducted using four analytical approaches (EIGENSTRAT, EMMAX-GRM, GBLUP and FvR). The most strongly associated SNPs from each individual analysis were ranked and evaluated for concordance. The heritability of susceptibility to BRDC in pre-weaned Holstein calves was estimated.The four statistical approaches produced highly concordant results for 373 top ranked SNPs that defined 126 chromosomal regions for the CA population. Similarly, in NM, 370 SNPs defined 138 genomic regions that were identified by all four approaches. When the two populations were combined (i.e., CA + NM) and analyzed, 324 SNPs defined 116 genomic regions that were associated with BRDC across all analytical methods. Heritability estimates for BRDC were 21% for both CA and NM as individual populations, but declined to 13% when the populations were combined.Four analytical approaches utilizing both single and multi-marker association methods revealed common genomic regions associated with BRDC susceptibility that can be further characterized and used for genomic selection. Moderate heritability estimates were observed for BRDC susceptibility in pre-weaned Holstein calves, thereby supporting the application of genomic selection to reduce the prevalence of BRDC in U.S. Holsteins.
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