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A putative functional mutation (rs109231213) near PLAG1 (BTA14) associated with stature was studied in beef cattle. Data from 8199 Bos taurus, Bos indicus and Tropical Composite cattle were used to test the associations between rs109231213 and various phenotypes. Further, 23 496 SNPs located on BTA14 were tested for association with these phenotypes, both independently and fitted together with rs109231213. The C allele of rs109231213 significantly increased hip height, weight, net food intake, age at puberty in males and females and decreased IGF-I concentration in blood and fat depth. When rs109231213 was fitted as a fixed effect in the model, there was an overall reduction in associations between other SNPs and these traits but some SNPs remained associated (P

The aim of this study was to assess the accuracy of genomic predictions for 19 traits including feed efficiency, growth, and carcass and meat quality traits in beef cattle. The 10,181 cattle in our study had real or imputed genotypes for 729,068 SNP although not all cattle were measured for all traits. Animals included Bos taurus, Brahman, composite, and crossbred animals. Genomic EBV (GEBV) were calculated using 2 methods of genomic prediction (BayesR and genomic BLUP (GBLUP)) either using a common training dataset for all breeds or using a training dataset comprising only animals of the same breed. Accuracies of GEBV were assessed using 5-fold cross-validation. The accuracy of genomic prediction varied by trait and by method. Traits with a large number of recorded and genotyped animals and with high heritability gave the greatest accuracy of GEBV. Using GBLUP, the average accuracy was 0.27 across traits and breeds, but the accuracies between breeds and between traits varied widely. When the training population was restricted to animals from the same breed as the validation population, GBLUP accuracies declined by an average of 0.04. The greatest decline in accuracy was found for the 4 composite breeds. The BayesR accuracies were greater by an average of 0.03 than GBLUP accuracies, particularly for traits with known genes of moderate to large effect mutations segregating. The accuracies of 0.43 to 0.48 for IGF-I traits were among the greatest in the study. Although accuracies are low compared with those observed in dairy cattle, genomic selection would still be beneficial for traits that are hard to improve by conventional selection, such as tenderness and residual feed intake. BayesR identified many of the same quantitative trait loci as a genomewide association study but appeared to map them more precisely. All traits appear to be highly polygenic with thousands of SNP independently associated with each trait.

Variation in the XK, Kell blood group complex subunit-related family, member 4 (XKR4) gene on BTA14 was associated with rump fat thickness in a recent genome-wide association study. This region is also of interest because it is known to show evidence of a signature of population genetic selection. In this study, additional variation in this gene was genotyped in a sample of a total of 1283 animals of the Belmont Red (BEL) and Santa Gertrudis (SGT) breeds. The SNP rs41724387 was significantly (P < 0.001) associated with rump fat thickness and explained 5.9% of the genetic variance for the trait in this sample. Using the 4466 genotypes for the SNP rs42646708 from several data sets to estimate effects in seven breeds, this relatively large quantitative trait locus effect appears to be a result of the variation in indicine and taurine-indicine composite cattle. However, the only DNA variant found in Brahman cattle that altered the predicted amino acid sequence of XKR4 was not associated with rump fat thickness. This suggests that causative mutations lie outside the coding sequence of this gene.

Ticks and tick-borne diseases have a detrimental impact on livestock production causing estimated losses of around $200 million per year in Australia alone. Host resistance to ticks is heritable, within-breed heritability estimates being around 0.35, and with large differences between breeds. Previously a QTL for tick burden was detected on BTA14 at ~72 Mb distal to the centromere, near the gene receptor-interacting serine-threonine kinase 2 (RIPK2). To identify polymorphisms in this region, we sequenced all exons of the RIPK2 gene, identifying 46 single nucleotide polymorphism (SNP). Using SNP from RIPK2 as well as SNP from the bovine genome sequence, we genotyped two samples, one of 1,122 taurine dairy cattle and one of 761 zebu and zebu composite beef cattle. We confirmed that SNP and haplotypes from this region, including from RIPK2, were associated with tick burden in both dairy and beef cattle. To determine whether RIPK2 influences response to tick salivary gland extract (SGE), an immunisation experiment with tick SGE in a RIPK2 knockout (RIPK2 −/−) mouse strain was conducted. There was a significant (P < 0.05) reduction in IgG production in the RIPK2 −/− mouse in response to the SGE compared to its background strain C57BL/6 as well as the outbred CD1 mouse strain. In addition, antibodies generated by RIPK2 −/− mice recognised a different set of antigens within SGE when compared to parental-derived antibodies. In summary, the SNP association with tick burden at BTA14 was confirmed and quantitative and qualitative differences in antibody production were observed between RIPK2 −/− and wild-type mice.

Chromosomal regions containing DNA variation affecting the traits intramuscular fat percentage (IMF), meat tenderness measured as peak force to shear the LM (LLPF), and rump fat measured at the sacro-iliac crest in the chiller (CHILLP8) were identified using a set of 53,798 SNP genotyped on 940 taurine and indicine cattle sampled from a large progeny test experiment. Of these SNP, 87, 64, and 63 were significantly (P G SNP, was used to confirm these locations. In total, 37 SNP were significantly (P < 0.05) associated with the same trait and with the same favorable homozygote in both data sets, representing 27 chromosomal regions. For the trait IMF, the effect of SNP in the confirmation data set was predicted from the discovery set by multiplying the estimated allele effect of each SNP in the discovery set by the number of copies of the reference allele of each SNP in the confirmation set. These weighted effects were then summed over all SNP to generate a molecular breeding value (MBV) for each animal in the confirmation data set. Using a bivariate analysis of MBV and IMF phenotypes of animals in the confirmation set, a panel of 14 SNP explained 5.6 and 15.6% of the phenotypic and genetic variance of IMF, respectively, in the confirmation data set. The amount of variation did not increase as more SNP were added to the MBV and instead decreased to 1.2 and 3.8% of the phenotypic and genetic variance of IMF, respectively, when 329 SNP were included in the analysis.

Ticks and tick-born diseases are major constraints on cattle production in tropical and subtropical regions in the world. Previously, we identified single nucleotide polymorphisms (SNPs) associated with tick resistance on bovine chromosome 3 at approximately 70 Mb. In this study, we genotyped a dairy (n = 1133) and a beef (n = 774) sample to confirm the association of the intronic SNP rs29019303 and its gene (ELTD1) with tick burden. We genotyped 18 additional SNPs in a region of 181 kb and found that rs29019303 was significantly (P < 0.05) associated with tick burden in both samples with the same favourable allele. A second SNP in this same genomic region was also significantly associated with tick burden in each sample. The associations using haplotypes were stronger than for single markers, including a haplotype of nine tag SNPs that was highly significantly (P = 0.0008) associated with tick counts in the dairy animals. This haplotype and two others were significant after Bonferroni correction for multiple testing. The estimated size of the effects was close to 0.9% of the residual variance in both samples tested.

Variation at the retinoic acid receptor-related orphan receptor C (RORC) gene was previously associated with marbling score in a large sample of Australian taurine feedlot cattle of Angus and Shorthorn breeds. The T allele at the SNP RORC:g.3290T > G increased marbling score in Angus and Shorthorn cattle. We genotyped this SNP in an independent sample of 2,741 Australian cattle of Angus, Brahman, and Hereford breeds, and tested the association of this SNP with marbling score in all animals and with intramuscular fat (IMF) measurements in 2,104 animals. We found an allele frequency of the G allele of p G = 0.57 in Angus, p G = 0.09 in Hereford, and p G = 0.64 in Brahman. The regression of marbling score against number of copies of the G allele was significant (P = 0.033) in the combined sample after accounting for ancestry, breed, and the contemporary group structure of the data. All breeds had the same favorable homozygote; the regression on alleles showed a trend in Angus and Brahman cattle (P < 0.1), but not in Hereford cattle (P = 0.912). The regression of IMF against number of copies of the G allele was significant (P = 0.018) after accounting for ancestry, breed, and contemporary group structure. All breeds had the same favorable homozygote and the regression on alleles was significant (P = 0.024) in the Angus breed. In all breeds tested in this study, the T allele increased both marbling score and IMF. This polymorphism explained 0.3% of the phenotypic variance for IMF in this sample.

The calpain gene family and its inhibitors have diverse effects, many related to protein turnover, which appear to affect a range of phenotypes such as diabetes, exercise-induced muscle injury, and pathological events associated with degenerative neural diseases in humans, fertility, longevity, and postmortem effects on meat tenderness in livestock species. The calpains are inhibited by calpastatin, which binds directly to calpain. Here we report the direct measurement of epistatic interactions of causative mutations for quantitative trait loci (QTL) at calpain 1 (CAPN1), located on chromosome 29, with causative mutations for QTL variation at calpastatin (CAST), located on chromosome 7, in cattle. First we identified potential causative mutations at CAST and then genotyped these along with putative causative mutations at CAPN1 in >1500 cattle of seven breeds. The maximum allele substitution effect on the phenotype of the CAPN1:c.947G>C single nucleotide polymorphism (SNP) was 0.14 σp (P = 0.0003) and of the CAST:c.155C>T SNP was also 0.14 σp (P = 0.0011) when measured across breeds. We found significant epistasis between SNPs at CAPN1 and CAST in both taurine and zebu derived breeds. There were more additive × dominance components of epistasis than additive × additive and dominance × dominance components combined. A minority of breed comparisons did not show epistasis, suggesting that genetic variation at other genes may influence the degree of epistasis found in this system.

Cattle diverged during the Pleistocene into two subspecies, one in temperate and one in tropical environments. Here we have used next generation sequencing of the indicine subspecies of cattle and compared it to the taurine subspecies. Although 23.8 million single nucleotide polymorphisms (SNP) were found, the number of fixed amino acid substitutions between the taurine and indicine subspecies was low and consistent with the Haldane predictions for adaptive selection rather than with Neutral Theory. We noted 33 regions of enhanced divergence of nonsynonymous SNP between the subspecies, which included an increased rate of deleterious variants. Signals of positive selection were found for genes associated with immunity, including the Bovine Major Histocompatibility Complex, which also showed an increased rate of deleterious amino acid variants. The genes important in sensing the environment, especially the olfactory system, showed a network wide signal of positive selection.

The GH1:c.457CG exon 5 missense mutation in the bovine growth hormone 1 (GH1) gene that causes the replacement of leucine (L) with valine (V) was investigated in 1027 cattle with primarily Angus and Shorthorn breeding from Australian feedlots. The allele frequency of the GH1:c.457C allele was 0.77 in Angus and 0.76 in Shorthorn. The GH1:c.457C allele was associated with lower marbling (P = 0.0472), and the average effect of allele substitution was -0.22 of a phenotypic standard deviation. This allele was also associated with slightly higher rump fat (P = 0.0541) and the average effect of allele substitution was 0.11 SD. Marbling and rump fat were not strongly correlated (r = 0.097, P0.01) in this data set. This mutation had no significant effect on eye muscle area or hot dressed carcass weight (P0.1). Given these relationships, the differences between GH1 alleles could be the result of differential deposition of fat in fat depots.

Single nucleotide polymorphisms (SNPs) have become the marker of choice for genetic studies in organisms of conservation, commercial or biological interest. Most SNP discovery projects in nonmodel organisms apply a strategy for identifying putative SNPs based on filtering rules that account for random sequencing errors. Here, we analyse data used to develop 4723 novel SNPs for the commercially important deep-sea fish, orange roughy (Hoplostethus atlanticus), to assess the impact of not accounting for systematic sequencing errors when filtering identified polymorphisms when discovering SNPs. We used SAMtools to identify polymorphisms in a velvet assembly of genomic DNA sequence data from seven individuals. The resulting set of polymorphisms were filtered to minimize 'bycatch'-polymorphisms caused by sequencing or assembly error. An Illumina Infinium SNP chip was used to genotype a final set of 7714 polymorphisms across 1734 individuals. Five predictors were examined for their effect on the probability of obtaining an assayable SNP: depth of coverage, number of reads that support a variant, polymorphism type (e.g. A/C), strand-bias and Illumina SNP probe design score. Our results indicate that filtering out systematic sequencing errors could substantially improve the efficiency of SNP discovery. We show that BLASTX can be used as an efficient tool to identify single-copy genomic regions in the absence of a reference genome. The results have implications for research aiming to identify assayable SNPs and build SNP genotyping assays for nonmodel organisms.

Background Previous genome-wide association studies have identified significant regions of the X chromosome associated with reproductive traits in two Bos indicus-influenced breeds: Brahman cattle and Tropical Composites. Two QTL regions on this chromosome were identified in both breeds as strongly associated with scrotal circumference measurements, a reproductive trait previously shown to be useful for selection of young bulls. Scrotal circumference is genetically correlated with early age at puberty in both male and female offspring. These QTL were located at positions 69–77 and 81–92 Mb respectively, large areas each to which a significant number of potential candidate genes were mapped. Results To further characterise these regions, a bioinformatic approach was undertaken to identify novel non-synonymous SNP within the QTL regions of interest in Brahman cattle. After SNP discovery, we used conventional molecular assay technologies to perform studies of two candidate genes in both breeds. Non-synonymous SNP mapped to Testis-expressed gene 11 (Tex11) were associated (P

The POLL locus has been mapped to the centromeric region of bovine chromosome 1 (BTA1) in both taurine breeds and taurine-indicine crosses in an interval of approximately 1 Mb. It has not yet been mapped in pure-bred zebu cattle. Despite several efforts, neither causative mutations in candidate genes nor a singular diagnostic DNA marker has been identified. In this study, we genotyped a total of 68 Brahman cattle and 20 Hereford cattle informative for the POLL locus for 33 DNA microsatellites, 16 of which we identified de novo from the bovine genome sequence, mapping the POLL locus to the region of the genes IFNAR2 and SYNJ1. The 303-bp allele of the new microsatellite, CSAFG29, showed strong association with the POLL allele. We then genotyped 855 Brahman cattle for CSAFG29 and confirmed the association between the 303-bp allele and POLL. To determine whether the same association was found in taurine breeds, we genotyped 334 animals of the Angus, Hereford and Limousin breeds and 376 animals of the Brangus, Droughtmaster and Santa Gertrudis composite taurine-zebu breeds. The association between the 303-bp allele and POLL was confirmed in these breeds; however, an additional allele (305 bp) was also associated but not fully predictive of POLL. Across the data, CSAFG29 was in sufficient linkage disequilibrium to the POLL allele in Australian Brahman cattle that it could potentially be used as a diagnostic marker in that breed, but this may not be the case in other breeds. Further, we provide confirmatory evidence that the scur phenotype generally occurs in animals that are heterozygous for the POLL allele.

Copy number variation (CNV) is likely to be an important component of heritable variation in livestock. To characterise CNVs in cattle, we performed a genome wide survey to determine the number, location and gene content of these genomic features. A tiling oligonucleotide array with ~385,000 probes was used for comparative genomic hybridisation of both taurine and zebu cattle. Using a conservative set of calling criteria, a total of 51 CNV were detected that collectively spanned approximately half of one percent of the bovine genome. The size of the average CNV within each animal ranged from 213 kb up to 335 kb. Half of the CNV were detected in a single animal only, whilst the remainder was independently identified in multiple individuals. Analysis was performed to determine the gene content for each CNV region. This revealed that the majority of CNV (82%) spanned at least one gene, with a number of CNV containing genes which are known to control aspects of phenotypic variation in cattle. Whilst additional studies are required to determine the impact of individual CNV, this study confirmed them as an important class of genomic variation in cattle.

The genetic factors that contribute to efficient food conversion are largely unknown. Several physiological systems are likely to be important, including basal metabolic rate, the generation of ATP, the regulation of growth and development, and the homeostatic control of body mass. Using whole-genome association, we found that DNA variants in or near proteins contributing to the background use of energy of the cell were 10 times as common as those affecting appetite and body-mass homeostasis. In addition, there was a genic contribution from the extracellular matrix and tissue structure, suggesting a trade-off between efficiency and tissue construction. Nevertheless, the largest group consisted of those involved in gene regulation or control of the phenotype. We found that the distribution of micro-RNA motifs was significantly different for the genetic variants associated with residual feed intake than for the genetic variants in total, although the distribution of promoter sequence motifs was not different. This suggests that certain subsets of micro-RNA are more important for the regulation of this trait. Successful validation depended on the sign of the allelic association in different populations rather than on the strength of the initial association or its size of effect.

A medium-density linkage map of the ovine genome has been developed. Marker data for 550 new loci were generated and merged with the previous sheep linkage map. The new map comprises 1093 markers representing 1062 unique loci (941 anonymous loci, 121 genes) and spans 3500 cM (sex-averaged) for the autosomes and 132 cM (female) on the X chromosome. There is an average spacing of 3.4 cM between autosomal loci and 8.3 cM between highly polymorphic [polymorphic information content (PIC) ≥ 0.7] autosomal loci. The largest gap between markers is 32.5 cM, and the number of gaps of >20 cM between loci, or regions where loci are missing from chromosome ends, has been reduced from 40 in the previous map to 6. Five hundred and seventy-three of the loci can be ordered on a framework map with odds of >1000 : 1. The sheep linkage map contains strong links to both the cattle and goat maps. Five hundred and seventy-two of the loci positioned on the sheep linkage map have also been mapped by linkage analysis in cattle, and 209 of the loci mapped on the sheep linkage map have also been placed on the goat linkage map. Inspection of ruminant linkage maps indicates that the genomic coverage by the current sheep linkage map is comparable to that of the available cattle maps. The sheep map provides a valuable resource to the international sheep, cattle, and goat gene mapping community.

The ovine map is not yet well-developed, which represents a problem when looking for markers of a region of interest in sheep. A means of circumventing this is to use comparative mapping. In this study primers were determined using consensus sequences for the epidermal growth factor gene of humans, rats and mice, and an ovine epidermal growth factor gene fragment was amplified by polymerase chain reaction (PCR). A new set of specific ovine primers was chosen to study the polymorphism of this DNA fragment by denaturing gradient gel electrophoresis. Eighty-four individuals belonging to seven sheep breeds were studied with this technique and four alleles were detected. The heterozygosity rate was 0.57. Family analysis showed mendelian inheritance of the alleles. Usually, genetic analysis of type-I loci used in the comparative mapping is based on the detection of restriction fragment length polymorphisms in sheep DNA using cDNA probes from other species. Our work shows that another method, based on PCR and denaturing gradient gel electrophoresis techniques, can be efficiently used.

We sequenced the genomes of a Brahman, an Africander and a Tuli bull because tropically adapted breeds of cattle have so far not been well characterised at the level of DNA variation. In excess of 16 Gb of Illumina GA-II sequence was obtained for each animal in the form of 75-bp paired-end reads, generating more than 6× coverage of each genome, and between 86.7 and 88.8% of the bases of each genome sequence was covered by one or more sequence reads. A total of 6.35 million single nucleotide polymorphisms (SNP) were discovered in the three animals, adding 3.56 million new SNP to dbSNP. The Brahman animal had nearly twice as many SNP as either the Tuli or the Africander. Comparing genome sequence to genotypic array data, genotype accuracy from sequencing was more than 98% for homozygotes that had at least six high quality sequence reads and for heterozygotes that had at least two high quality reads containing the alternative allele. Intergenic and intronic SNP were found at higher densities closer to coding sequences, and there was a reduction in numbers of SNP within 5 bp of a splice site, features consistent with genetic selection. On average, slightly more SNP per Mb, and slightly higher average reads per SNP per Mb, were found towards the ends of chromosomes, especially towards the telomeric end of the chromosome. At least one autosome in each animal showed a large stretch of homozygosity, the largest was 58 Mb long in the Tuli, although the animals are not known to have recent inbreeding.

Genetic progress depends on accurate knowledge of the genetic composition of a population or herd including level of inbreeding and parentage. However, in many circumstances, such as at an individual property level, the relationships between animals may be unknown, or at best, only partly known. In this study, we used DNA from 938 animals and genotypes from ~54 000 single nucleotide polymorphisms (SNP) to determine the genetic structure of a stud from Central Queensland. Animals on the study were bred using multi-sire mating in mobs of composite tropically adapted cattle of the Senepol, Belmont and Bonsmara breeds. Following genotyping using an array of 54 000 SNP, we were able to separate animals into breed groups using principal components and show that ~400 SNP were sufficient to separate animals into stable groups if the sample was genetically diverse. However, precise principal component values were only achieved when a few thousand SNP were used. We characterised the pedigree relationships between individuals using a genome relationship matrix. At least 3000 SNP were required to calculate accurate relationship coefficients between individuals. Around 19% of paired comparisons between animals showed similarity equivalent to sharing a great-grandparent or 1/64 shared ancestry. Approximately 8% of the individuals showed more than 10% inbreeding. To demonstrate the utility of calculating the relationship coefficients, we counted the tick burden on each animal at more than one time and then calculated the heritability of tick burden of h2 = 0.46 (±0.08). There was no significant genetic difference in tick burden between Belmont and Bonsmara cattle compared with Senepol on this property once a genetic relationship matrix was included to account for co-ancestry of individuals.

Background The goal of genome wide analyses of polymorphisms is to achieve a better understanding of the link between genotype and phenotype. Part of that goal is to understand the selective forces that have operated on a population. Results In this study we compared the signals of selection, identified through population divergence in the Bovine HapMap project, to those found in an independent sample of cattle from Australia. Evidence for population differentiation across the genome, as measured by FST, was highly correlated in the two data sets. Nevertheless, 40% of the variance in FST between the two studies was attributed to the differences in breed composition. Seventy six percent of the variance in FST was attributed to differences in SNP composition and density when the same breeds were compared. The difference between FST of adjacent loci increased rapidly with the increase in distance between SNP, reaching an asymptote after 20 kb. Using 129 SNP that have highly divergent FST values in both data sets, we identified 12 regions that had additive effects on the traits residual feed intake, beef yield or intramuscular fatness measured in the Australian sample. Four of these regions had effects on more than one trait. One of these regions includes the R3HDM1 gene, which is under selection in European humans. Conclusion Firstly, many different populations will be necessary for a full description of selective signatures across the genome, not just a small set of highly divergent populations. Secondly, it is necessary to use the same SNP when comparing the signatures of selection from one study to another. Thirdly, useful signatures of selection can be obtained where many of the groups have only minor genetic differences and may not be clearly separated in a principal component analysis. Fourthly, combining analyses of genome wide selection signatures and genome wide associations to traits helps to define the trait under selection or the population group in which the QTL is likely to be segregating. Finally, the FST difference between adjacent loci suggests that 150,000 evenly spaced SNP will be required to study selective signatures in all parts of the bovine genome.

From a study of 3 large half-sib families of cattle, we describe linkage between DNA polymorphisms on bovine chromosome 7 and meat tenderness. Quantitative trait loci (QTL) for Longissimus lumborum peak force (LLPF) and Semitendonosis adhesion (STADH) were located to this map of DNA markers, which includes the calpastatin (CAST) and lysyl oxidase (LOX) genes. The LLPF QTL has a maximum lodscore of 4.9 and allele substitution of approximately 0.80 of a phenotypic standard deviation, and the peak is located over the CAST gene. The STADH QTL has a maximum lodscore of 3.5 and an allele substitution of approximately 0.37 of a phenotypic standard deviation, and the peak is located over the LOX gene. This suggests 2 separate likelihood peaks on the chromosome. Further analyses of meat tenderness measures in the Longissimus lumborum, LLPF and LL compression (LLC), in which outlier individuals or kill groups are removed, demonstrate large shifts in the location of LLPF QTL, as well as confirming that there are indeed 2 QTL on bovine chromosome 7. We found that both QTL are reflected in both LLPF and LLC measurements, suggesting that both these components of tenderness, myofibrillar and connective tissue, are detected by both measurements in this muscle.

The imprints of domestication and breed development on the genomes of livestock likely differ from those of companion animals. A deep draft sequence assembly of shotgun reads from a single Hereford female and comparative sequences sampled from six additional breeds were used to develop probes to interrogate 37,470 single-nucleotide polymorphisms (SNPs) in 497 cattle from 19 geographically and biologically diverse breeds. These data show that cattle have undergone a rapid recent decrease in effective population size from a very large ancestral population, possibly due to bottlenecks associated with domestication, selection, and breed formation. Domestication and artificial selection appear to have left detectable signatures of selection within the cattle genome, yet the current levels of diversity within breeds are at least as great as exists within humans.