Accuracy of prediction of genomic breeding values for residual feed intake and carcass and meat quality traits in Bos taurus, Bos indicus, and composite beef cattle.

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 XKR4 gene was significantly associated with subcutaneous rump fat thickness in indicine and composite cattle.

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.

A genome-wide association study of meat and carcass traits in Australian cattle.

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 < 0.001) associated with the traits IMF, LLPF, and CHILLP8, respectively. A second, nonoverlapping sample of 1,338 taurine and indicine cattle from the same large progeny test experiment genotyped for 335 SNP, including as a positive control the calpastatin (CAST) c.2832A > 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.

DNA variation in the gene ELTD1 is associated with tick burden in cattle.

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.

The effect of variation at the retinoic acid receptor-related orphan receptor C gene on intramuscular fat percent and marbling score in Australian cattle.

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.

A splice site single nucleotide polymorphism of the fatty acid binding protein 4 gene appears to be associated with intramuscular fat deposition in longissimus muscle in Australian cattle.

Fatty acid binding protein 4 (FABP4) is a candidate gene affecting fatness traits of mammals. However, its association with fatness traits in cattle and other livestock species is not consistent from one study to another. Here, we sequenced the coding sequence of FABP4 looking for non-synonymous variants. We identified a splice site mutation between the third exon and the third intron of bovine FABP4. We genotyped this SNP, FABP4:g.2502C>G, in 1409 cattle with intramuscular fat measurements from seven breeds. The average allele frequency of the C allele was 0.66 with a range of 0.45 to 0.85. A regression on the number of G alleles shows a statistically significant effect of alpha = 0.11, P = 0.044. This appears to confirm an association between IMF and variation at FABP4, with an effect of 0.3% of the variation in our sample when using this SNP.

Epistasis between calpain 1 and its inhibitor calpastatin within breeds of cattle.

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 sigma(p) (P = 0.0003) and of the CAST:c.155C>T SNP was also 0.14 sigma(p) (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 x dominance components of epistasis than additive x additive and dominance x 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.

A validated whole-genome association study of efficient food conversion 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.

The effect of genetic variation of the retinoic acid receptor-related orphan receptor C gene on fatness in cattle.

Genotypes at the retinoic acid receptor-related orphan receptor C (RORC) gene were associated with fatness in 1750 cattle. Ten SNPs were genotyped in RORC and the adjacent gene leucine-rich repeat neuronal 6D (LRRN6D) to map the QTL, 7 of which are in a 4.2-kb sequence around the ligand-binding domain of the RORC gene. Of the 29 inferred haplotypes for these SNPs, 2 have a combined frequency of 54.6% while the top 5 haplotypes have a combined frequency of 85.3%. The average D' value of linkage disequilibrium was 0.92 although the average r2 was a low 0.18. The RORC:g.3290T>G SNP had the strongest association with marbling. The inferred haplotypes were significantly associated with marbling and the difference between the most divergent haplotypes was 0.35 sigma(p) of marbling and 0.28 sigma(p) of rump fat, explaining the previously reported QTL effect. cDNA for RORC were sequenced and 2 new alternative transcripts were found. Fetal tissue shows 40 times greater transcription of RORC than adult tissue. The highest expression in fetal tissue was found in liver and kidney, but in adults the longissimus muscle had the greatest expression of the tissues tested.

The growth hormone 1 GH1:c.457C>G mutation is associated with intramuscular and rump fat distribution in a large sample of Australian feedlot cattle.

The GH1:c.457C>G 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, P < 0.01) in this data set. This mutation had no significant effect on eye muscle area or hot dressed carcass weight (P > 0.1). Given these relationships, the differences between GH1 alleles could be the result of differential deposition of fat in fat depots.

Expression of a modified Neocallimastix patriciarum xylanase in Butyrivibrio fibrisolvens digests more fibre but cannot effectively compete with highly fibrolytic bacteria in the rumen.

AIMS: This study investigated the competitive abilities of two Neocallimastix patriciarum-derived xylanases constructs in Butyrivibrio fibrisolvens H17c (xynA and pUMSX) and their ability to compete in vivo. METHODS AND RESULTS: The digestibility of neutral detergent fibre (NDF) increased during co-culture of xynA or pUMSX and weakly cellulolytic, but not with highly cellulolytic, ruminococci. Competition studies among xynA, pUMSX and cellulolytic consortia demonstrated that xynA was the fittest. XynA did not persist at high levels in the rumen and was undetectable after 22 days. CONCLUSION: The construction of recombinant xylanolytic B. fibrisolvens does improve the digestibility of fibre above that of the native, but digestibility is still less than that of the most potent fibre digesters such as ruminococci. SIGNIFICANCE AND IMPACT OF THE STUDY: Fibre digestion may be improved by genetic manipulation of ruminal bacteria but ecological parameters, such as persistence in vivo and the niche of the organism, must be taken into account.

Isolation and characterization of a trypsin-like enzyme from the buffalo fly, Haematobia irritans exigua.

The incorporation of soybean trypsin inhibitor (SBTI) into the diet of the buffalo fly, Haematobia irritans exigua (De Meijere), results in increased mortality and reduced fecundity. A trypsin-like enzyme which binds to SBTI was isolated by affinity chromatography on a Sepharose-SBTI column followed by ion-exchange chromatography. The enzyme was inhibited by benzamidine, phenylmethylsulfonyl fluoride, ovomucoid, leupeptin and alpha-2 macroglobulin. The enzyme was not inhibited by EDTA or p-chloromecuribenzoic acid and had a broad pH optimum of pH 7-9. Vaccination of sheep produced antibodies specific for the trypsin-like enzyme which inhibited enzyme activity in vitro but did not affect the survival of flies maintained in in vitro culture.

Monoclonal antibody-based enzyme immunoassay for trypsinogen in neonatal screening for cystic fibrosis.

An enzyme immunoassay (EIA) with monoclonal antibodies against human trypsinogen in neonatal blood-spots has been evaluated for screening for neonatal cystic fibrosis (CF). In a retrospective study, 36 of 39 CF samples were distinguished from controls matched for age and storage time. 7 infants with CF were detected in 16,500 infants screened in a prospective study. The EIA is quicker and less labour intensive than conventional assays for the detection of immunoreactive trypsin and may have further advantages of specificity and sensitivity for monitoring the release of pancreatic zymogens in CF.