Using triallelic SNPs for determining parentage in North American yak ( Bos grunniens) and estimating cattle ( B. taurus) introgression.

Background: Genetic testing for pedigree accuracy is critical for managing genetic diversity in North American (NA) yak ( Bos grunniens), a population expanded mostly from imported zoological park specimens.  DNA testing also enhances species conservation by identifying recent B. taurus F1 hybrid ancestors (within three generations).  Biallelic single nucleotide polymorphisms (SNPs) can accomplish either task, but increases the marker count and costs necessary to achieve both.  Our aim was to identify novel, multifunctional, triallelic yak SNPs (tySNPs), with each having two alleles for yak parentage testing, and a third allele for identifying recent cattle introgression.  Methods:  Genome sequences were aligned to the cattle UMD3.1 assembly and SNPs were screened for 1) heterozygosity in a NA and a Chinese yak, 2) a third allele at high frequency in cattle, and 3) flanking sequences conserved in both species.  Subsequently, tySNPs were filtered for unique alignment to the haplotype-resolved F1 yak assembly.  Allele frequencies were estimated in a subset of 87 tySNPs by genotyping 170 NA yak. Results:  We identified 610 autosomal tySNPs, distributed in 441 clusters with 5 Mb average genome spacing.  The average NA yak minor allele frequency was high (0.296), while average introgressed cattle alleles were low (0.004).  In simulations with tySNPs, 28 were sufficient for globally-unique animal identification (P I=5.81x10 -12), 87 were able to exclude 19 random bulls from parentage at the 99% level without using the dam's genotype (P E=5.3x10 -4), and 87 were able to detect F1 hybridization events after three generations of yak backcrosses (1/16th B. taurus germplasm). Conclusions:  Identifying animals, determining parentage and detecting recent hybridization events was efficient with as few as 87 tySNPs.  A similar triallelic approach could be used with other bottlenecked Bos species that hybridize with cattle, such as NA plains bison ( B. bison).

Genome-wide association study of milk production traits in a crossbred dairy sheep population using three statistical models.

Milk production is one of the most important characteristics of dairy sheep, and the identification of genes affecting milk production traits is critical to understanding the genetics and improve milk production in future generations. Three statistical techniques, namely GWAS, ridge-regression BLUP and BayesC π , were used to identify SNPs in significant association with three milk production traits (milk yield, fat yield and protein yield) in a crossbred dairy sheep population. The results suggested that chromosomes 1, 3, 4, 5, 7 and 11 were likely to harbor genes important to milk production because these chromosomes had the greatest top-100-SNP variance contributions on the three milk production traits. The GWAS analysis identified between 74 and 288 genome-wide significant SNP (P < 0.05) whereas the BayesCπ model revealed between six and 63 SNPs, each with >95% posterior probability of inclusion as having a non-zero association effect on at least one of the three milk production traits. Positional candidate genes for milk production in sheep were searched, based on the sheep genomic assembly OAR version 3.1, such as those which map position coincided with or was located within 0.1 Mbp of a genome-wide suggestive or significant SNP. These identified SNPs and candidate genes supported some previous findings and also added new information about genetic markers for genetic improvement of lactation in dairy sheep, but keeping in mind that the majority of these positional candidate genes are not necessarily true causative loci for these traits and future validations are thus necessary.

Estimation of genomic breed composition of individual animals in composite beef cattle.

Three statistical models (an admixture model, linear regression, and ridge-regression BLUP) and two strategies for selecting SNP panels (uniformly spaced vs. maximum Euclidean distance of SNP allele frequencies between ancestral breeds) were compared for estimating genomic-estimated breed composition (GBC) in Brangus and Santa Gertrudis cattle, respectively. Animals were genotyped with a GeneSeek Genomic Profiler bovine low-density version 4 SNP chip. The estimated GBC was consistent among the uniformly spaced SNP panels, and values were similar between the three models. However, estimated GBC varied considerably between the three methods when using fewer than 10 000 SNPs that maximized the Euclidean distance of allele frequencies between the ancestral breeds. The admixture model performed most consistently across various SNP panel sizes. For the other two models, stabilized estimates were obtained with an SNP panel size of 20 000 SNPs or more. Based on the uniformly spaced 20K SNP panel, the estimated GBC was 69.8-70.5% Angus and 29.5-30.2% Brahman for Brangus, and 63.9-65.3% Shorthorn and 34.7-36.1% Brahman in Santa Gertrudis. The estimated GBC of ancestries for Santa Gertrudis roughly agreed with the pedigree-expected values. However, the estimated GBC in Brangus showed a considerably larger Angus composition than the pedigree-expected value (62.5%). The elevated Angus composition in the Brangus could be due to the mixture of some 1/2 Ultrablack animals (Brangus × Angus). Another reason could be the consequences of selection in Brangus cattle for phenotypes where the Angus breed has advantages.

A unified local objective function for optimally selecting SNPs on arrays for agricultural genomics applications.

Over the years, ad-hoc procedures were used for designing SNP arrays, but the procedures and strategies varied considerably case by case. Recently, a multiple-objective, local optimization (MOLO) algorithm was proposed to select SNPs for SNP arrays, which maximizes the adjusted SNP information (E score) under multiple constraints, e.g. on MAF, uniformness of SNP locations (U score), the inclusion of obligatory SNPs and the number and size of gaps. In the MOLO, each chromosome is split into equally spaced segments and local optima are selected as the SNPs having the highest adjusted E score within each segment, conditional on the presence of obligatory SNPs. The computation of the adjusted E score, however, is empirical, and it does not scale well between the uniformness of SNP locations and SNP informativeness. In addition, the MOLO objective function does not accommodate the selection of uniformly distributed SNPs. In the present study, we proposed a unified local function for optimally selecting SNPs, as an amendment to the MOLO algorithm. This new local function takes scalable weights between the uniformness and informativeness of SNPs, which allows the selection of SNPs under varied scenarios. The results showed that the weighting between the U and the E scores led to a higher imputation concordance rate than the U score or E score alone. The results from the evaluation of six commercial bovine SNP chips further confirmed this conclusion.

Evaluation of genotyping concordance for commercial bovine SNP arrays using quality-assurance samples.

SNP arrays are widely used in genetic research and agricultural genomics applications, and the quality of SNP genotyping data is of paramount importance. In the present study, SNP genotyping concordance and discordance were evaluated for commercial bovine SNP arrays based on two types of quality assurance (QA) samples provided by Neogen GeneSeek. The genotyping discordance rates (GDRs) between chips were on average between 0.06% and 0.37% based on the QA type I data and between 0.05% and 0.15% based on the QA type II data. The average genotyping error rate (GER) pertaining to single SNP chips, based on the QA type II data, varied between 0.02% and 0.08% per SNP and between 0.01% and 0.06% per sample. These results indicate that genotyping concordance rate was high (i.e. from 99.63% to 99.99%). Nevertheless, mitochondrial and Y chromosome SNPs had considerably elevated GDRs and GERs compared to the SNPs on the 29 autosomes and X chromosome. The majority of genotyping errors resulted from single allotyping errors, which also included the opposite instances for allele 'dropout' (i.e. from AB to AA or BB). Simultaneous allotyping errors on both alleles (e.g. mistaking AA for BB or vice versa) were relatively rare. Finally, a list of SNPs with a GER greater than 1% is provided. Interpretation of association effects of these SNPs, for example in genome-wide association studies, needs to be taken with caution. The genotyping concordance information needs to be considered in the optimal design of future bovine SNP arrays.

Genome-wide association study for response to vaccination in Angus calves1.

BACKGROUND: Bovine respiratory disease complex (BRDC) is one of the most important sources of loss within the beef cattle industry in the USA. Steps have been taken to reduce the incidence of BRDC through vaccination. Despite the effectiveness of vaccines, large proportions of cattle still experience morbidity and mortality. Identification of genomic regions that are associated with variation in response to vaccination would allow for the selection of individuals genetically predisposed to respond to vaccination based on specific markers, while heritability and accuracy estimates would help facilitate genomic selection. This in turn may lead to selection for beef cattle herds that may have lower incidence rate of BRDC after vaccination. This study utilizes an Angus herd of more than 2000 head of cattle to identify these regions of association. RESULTS: Genome wide association studies were performed for viral neutralization antibody level and response to vaccination traits against four different viruses associated with BRDC: bovine viral diarrhea virus 1 and 2 (BVDV1 and BVDV2), bovine respiratory syncytial virus (BRSV), and bovine herpesvirus (BHV1). A total of six 1-Mb windows were associated with greater than 1% of the genetic variance for the analyzed vaccination response traits. Heritabilities ranged from 0.08 to 0.21 and prediction accuracy ranged from 0.01 to 0.33 across 7 different vaccination traits. CONCLUSIONS: Although six 1-Mb windows were identified as associated with 1% or greater genetic variance for viral neutralization antibody level and response to vaccination traits, few genes around these windows could readily be considered candidates. This indicates the need for further functional genomic annotation, as these regions appear to be gene deserts. Traits ranged from lowly to moderately heritable, which indicated the potential for selection of individuals that are genetically pre-disposed to respond to vaccination. The relatively low amount of genetic variance accounted for by any 1-Mb window indicated that viral neutralization antibody level and response to vaccination traits are polygenic in nature. Selection for these traits is possible, but likely to be slow due to the low heritabilities and absence of markers with high genetic variation associated with them.

Improving accuracy of genomic prediction in Brangus cattle by adding animals with imputed low-density SNP genotypes.

Reliable genomic prediction of breeding values for quantitative traits requires the availability of sufficient number of animals with genotypes and phenotypes in the training set. As of 31 October 2016, there were 3,797 Brangus animals with genotypes and phenotypes. These Brangus animals were genotyped using different commercial SNP chips. Of them, the largest group consisted of 1,535 animals genotyped by the GGP-LDV4 SNP chip. The remaining 2,262 genotypes were imputed to the SNP content of the GGP-LDV4 chip, so that the number of animals available for training the genomic prediction models was more than doubled. The present study showed that the pooling of animals with both original or imputed 40K SNP genotypes substantially increased genomic prediction accuracies on the ten traits. By supplementing imputed genotypes, the relative gains in genomic prediction accuracies on estimated breeding values (EBV) were from 12.60% to 31.27%, and the relative gain in genomic prediction accuracies on de-regressed EBV was slightly small (i.e. 0.87%-18.75%). The present study also compared the performance of five genomic prediction models and two cross-validation methods. The five genomic models predicted EBV and de-regressed EBV of the ten traits similarly well. Of the two cross-validation methods, leave-one-out cross-validation maximized the number of animals at the stage of training for genomic prediction. Genomic prediction accuracy (GPA) on the ten quantitative traits was validated in 1,106 newly genotyped Brangus animals based on the SNP effects estimated in the previous set of 3,797 Brangus animals, and they were slightly lower than GPA in the original data. The present study was the first to leverage currently available genotype and phenotype resources in order to harness genomic prediction in Brangus beef cattle.

Endocannabinoid concentrations in plasma during the finishing period are associated with feed efficiency and carcass composition of beef cattle.

We previously have shown that plasma concentrations of endocannabinoids (EC) are positively correlated with feed efficiency and leaner carcasses in finishing steers. However, whether the animal growth during the finishing period affects the concentration of EC is unknown. The objective of this study was to quantify anandamide (AEA) and 2-arachidonyl glycerol (2-AG) in plasma during different stages of the finishing period and identify possible associations with production traits and carcass composition in beef calves. Individual DMI and BW gain were measured on 236 calves ( = 127 steers and = 109 heifers) for 84 d on a finishing ration. Blood samples were collected on d 0 (early), 42 (mid), and 83 (late) of days on study (DOS). Cattle were slaughtered 44 d after the feeding study. Plasma concentration of AEA at 0 DOS was indirectly associated with the G:F ( < 0.01) and directly associated with residual feed intake (RFI; < 0.05) in steers. In contrast, plasma concentration of AEA at 83 DOS was directly associated with the G:F and indirectly associated RFI in heifers and steers ( < 0.01). In addition, AEA concentration at 42 and 83 DOS was positively associated with ADG and DMI ( < 0.01) in heifers and steers. Furthermore, 2-AG concentration at 42 DOS was positively associated with ADG in steers ( < 0.01) and heifers ( < 0.10). Plasma concentration of AEA was positively associated ( < 0.05) with HCW, USDA-calculated yield grade, and 12th-rib fat thickness in heifers, whereas no associations were found in steers. In contrast, 2-AG concentration was not associated with any carcass traits. These results provide evidence that circulating EC change during animal growth and that AEA concentration may be a useful predictor of growth and feed efficiency and, in females, of carcass attributes.

Evaluation of responses to vaccination of Angus cattle for four viruses that contribute to bovine respiratory disease complex.

Although vaccination is an effective measure in reducing the risk of bovine respiratory disease complex (BRDC) in cattle, BRDC losses remain significant. Increasing the efficacy of vaccination depends on elucidating the protective immune response to different antigens included in vaccines, determining the best timing for vaccination, and understanding the impact of the age of the calf on vaccination. This study measured the serum antibodies present in calves following vaccination against 4 viruses commonly associated with BRDC: bovine viral diarrhea virus type 1 and 2 (BVDV1 and BVDV2), bovine respiratory syncytial virus (BRSV), and bovine herpesvirus 1 (BHV1). Serum antibody titers were measured in more than 1,600 calves at 3-wk intervals starting at the time of the first vaccination. This first vaccination occurred at weaning for approximately half of the individuals and 3 wk before weaning for the other half. Dam age (years), time of weaning (initial vaccination or booster vaccination), and age of calf within year-season (days within year-season) classification all were found to have a significant effect on measured traits such as the initial titer and overall response. An increased initial titer was negatively correlated with each response trait (initial, booster, and overall response). Calves that were weaned at initial vaccination had greater overall antibody response to BVDV1 and BVDV2 compared with calves weaned 3 wk before initial vaccination. In contrast, calves given their initial vaccination 3 wk before weaning had greater overall antibody response to BRSV and BHV1 compared with calves that were vaccinated at weaning. Furthermore, the circulating antibody titer at which each virus needed to be below for an individual calf to positively respond to vaccination was determined (log titer of 0.38 for BVDV1, 1.5 for BVDV2, 3.88 for BRSV, and 1.5 for BHV1). This information can be used to improve vaccination protocols to allow for a greater response rate of individuals to vaccination and, hopefully, improved protection.

Genomewide association study of liver abscess in beef cattle.

Fourteen percent of U.S. cattle slaughtered in 2011 had liver abscesses, resulting in reduced carcass weight, quality, and value. Liver abscesses can result from a common bacterial cause, , which inhabits rumen lesions caused by acidosis and subsequently escapes into the blood stream, is filtered by the liver, and causes abscesses in the liver. Our aim was to identify SNP associated with liver abscesses in beef cattle. We used lung samples as a DNA source because they have low economic value, they have abundant DNA, and we had unrestricted access to sample them. We collected 2,304 lung samples from a beef processing plant: 1,152 from animals with liver abscess and 1,152 from animals without liver abscess. Lung tissue from pairs of animals, 1 with abscesses and another without, were collected from near one another on the viscera table to ensure that pairs of phenotypically extreme animals came from the same lot. Within each phenotype (abscess or no abscess), cattle were pooled by slaughter sequence into 12 pools of 96 cattle for each phenotype for a total of 24 pools. The pools were constructed by equal volume of frozen lung tissue from each animal. The DNA needed to allelotype each pool was then extracted from pooled lung tissue and the BovineHD Bead Array (777,962 SNP) was run on all 24 pools. Total intensity (TI), an indicator of copy number variants, was the sum of intensities from red and green dyes. Pooling allele frequency (PAF) was red dye intensity divided TI. Total intensity and PAF were weighted by the inverse of their respective genomic covariance matrices computed over all SNP across the genome. A false discovery rate ≤ 5% was achieved for 15 SNP for PAF and 20 SNP for TI. Genes within 50 kbp from significant SNP were in diverse pathways including maintenance of pH homeostasis in the gastrointestinal tract, maintain immune defenses in the liver, migration of leukocytes from the blood into infected tissues, transport of glutamine into the kidney in response to acidosis to facilitate production of bicarbonate to increase pH, aggregate platelets to liver injury to facilitate liver repair, and facilitate axon guidance. Evidence from the 35 detected SNP associations combined with evidence of polygenic variation indicate that there is adequate genetic variation in incidence rate of liver abscesses, which could be exploited to select sires for reduced susceptibility to subacute acidosis and associated liver abscess.

Estimates of epistatic and pleiotropic effects of () and () genetic markers on beef heifer performance traits enhanced by selection.

Genetic marker effects and type of inheritance are estimated with poor precision when minor marker allele frequencies are low. A stable composite population (MARC II) was subjected to marker assisted selection for 2 yr to equalize and genetic marker frequencies to evaluate the epistatic and pleiotropic effects of these markers on BW, reproduction, and first calf performance traits in replacement beef females ( = 171) managed under 2 postweaning development protocols. Traits evaluated on the heifers were birth BW, weaning BW, 11-mo BW, 12-mo BW, 13-mo BW, first breeding season pregnancy evaluation BW, first calving season BW, 11-mo puberty, 12-mo puberty, 13-mo puberty, first breeding season pregnancy, and first calf weaning rate. Additionally, heifer's first calf performance traits of ordinal calving date, first calf birth BW, and first calf weaning BW (with and without age adjustment) were analyzed. Selection to increase minor allele frequencies and balanced sampling across genotype classes enhanced the ability to detect all genetic effects except dominance × dominance epistasis. The × genotype effect was significant ( < 0.05) for 11-mo BW and 12-mo BW and tended to be significant ( = 0.08) for 13-mo BW. Consistently, for all 3 traits, the most significant effect among epistatic × genotype effects was the additive effect, with the G allele decreasing BW. There were no associations between × genotype and fertility related traits ( ≥ 0.46) in this study. Additionally, there were no × genotype associations with first progeny performance traits ( ≥ 0.14). The large effect of the additive × additive interaction on first calf weaning BW was imprecisely estimated, which may warrant further investigation.

Leptin concentrations in finishing beef steers and heifers and their association with dry matter intake, average daily gain, feed efficiency, and body composition.

The objective of this experiment was to determine the association of circulating plasma leptin concentrations with production and body composition measures of finishing beef steers and heifers and to determine if multiple sampling time points improve the associations of plasma leptin concentrations with production and body composition traits. Individual dry matter intake (DMI) and ADG were determined for 84 d using steers and heifers (n = 127 steers and n = 109 heifers). Blood was collected on day 0, day 42, and day 83 for determination of plasma leptin concentrations. Leptin concentrations were greater in heifers than those in steers on day 0 (P < 0.001 for sex by day interaction), and leptin concentrations increased in both sexes but were not different from each other on day 83. Leptin concentrations at all 3 time points and the mean were shown to be positively associated with DMI (P ≤ 0.006), whereas the mean leptin concentration explaining 8.3% of the variance of DMI. Concentrations of leptin at day 42, day 83, and the mean of all 3 time points were positively associated with ADG (P ≤ 0.011). Mean leptin concentration was negatively associated with gain:feed ratio and positively associated with residual feed intake (RFI), indicating that more efficient cattle had lower leptin concentrations. However, leptin concentrations explained very little of the variation in residual feed intake (≤ 3.2% of the variance). Leptin concentrations were positively associated with body fat measured by ultrasonography at the 12th rib and over the rump (P < 0.001), with the mean leptin concentration explaining 21.9% and 12.7% of the variance in 12th rib and rump fat thickness, respectively. The same trend was observed with carcass composition where leptin concentrations were positively associated with 12th rib fat thickness, USDA-calculated yield grade (YG), and marbling score (P ≤ 0.006) and mean leptin concentration explained 16.8, 18.2, and 4.6% of the variance for 12th rib fat thickness, yield grade, and marbling score, respectively. Given these and previous results, it appears that leptin physiology could be a candidate for mechanisms that contribute to feed intake and feed efficiency variation in beef cattle.

Relationship of glucocorticoids and hematological measures with feed intake, growth, and efficiency of finishing beef cattle.

The objective of this experiment was to determine the association of glucocorticoids and markers for immune status in finishing beef steers and heifers with DMI, growth, and efficiency. Steers ( = 127) and heifers ( = 109) were individually fed a finishing ration for 84 d with BW measured every 21 d. Blood samples were collected via jugular venipuncture for metabolite (glucose and lactate) and cortisol analysis and rectal grab samples of feces were collected for corticosterone analysis on d 83 of the experiment. Plasma cortisol was not correlated to DMI ( = -0.08, > 0.05) or fractional DMI (g DMI/kg BW; = -0.03, > 0.05) but was negatively correlated with ADG ( = -0.17, < 0.01) and G:F ( = -0.20, < 0.01) and positively correlated to residual feed intake (RFI; = 0.14, < 0.05). Fecal corticosterone was positively correlated to fractional DMI ( = 0.15, < 0.05) and RFI ( = 0.23, < 0.01) and negatively correlated to G:F ( = -0.18, < 0.01). Using a mixed model analysis, none of the metabolites or hormones were associated with DMI ( > 0.05) but fecal corticosterone was positively associated with fractional DMI only in heifers ( = 0.04). Plasma lactate ( < 0.01) was and plasma cortisol ( < 0.10) tended to be negatively associated with ADG. Plasma cortisol ( < 0.05) and fecal corticosterone tended ( < 0.10) to be negatively associated with G:F. Fecal corticosterone was positively associated with RFI in heifers ( < 0.04). In a mixed model analysis, total leukocyte count was positively associated with ADG ( < 0.04) and tended to be positively associated with G:F ( < 0.06). Among leukocyte subtypes, neutrophil count was positively associated with ADG in steers ( < 0.02) and monocytes were positively associated with ADG in heifers ( < 0.03). Lymphocyte counts (LY) in steers were negatively associated with DMI ( = 0.03) and fractional DMI ( < 0.03). In heifers, LY tended to be positively associated with DMI ( < 0.09) and fractional DMI ( < 0.06). Lymphocyte count was also positively associated with ADG ( < 0.01) and G:F ( = 0.05) in heifers. The association of production traits with immune status seems to be different between steers and heifers. There was a stronger relationship of cortisol than fecal corticosterone to feed efficiency measures, suggesting that cortisol concentrations could be a better marker for feed efficiency traits than fecal corticosterone concentrations.

Genomewide association study of lung lesions in cattle using sample pooling.

Bovine respiratory disease complex (BRDC) is the most expensive disease in beef cattle in the United States costing the industry at least US$1 billion annually. Bovine respiratory disease complex causes damage to lung tissue resulting in persistent lung lesions observable at slaughter. Severe lung lesions at harvest have been associated with decreased preharvest ADG and increased clinical BRDC in the feedlot. Our objective was to identify SNP that are associated with severe lung lesions observed at harvest in feedlot cattle. We conducted a genomewide association study (GWAS) using a case-control design for severe lung lesions in fed cattle at slaughter using the Illumina Bovine HD array (approximately 770,000 SNP) and sample pooling. Lung samples were collected from 11,520 young cattle, a portion of which had not been treated with antibiotics (participating in a "natural" marketing program), at a large, commercial beef processing plant in central Nebraska. Lung samples with lesions (cases) and healthy lungs (controls) were collected when both phenotypes were in close proximity on the viscera (offal) table. We constructed 60 case and 60 control pools with 96 animals per pool. Pools were constructed by sampling sequence to ensure that case and control pool pairs were matched by proximity on the processing line. The Bovine HD array (770,000 SNP) was run on all pools. Fourteen SNP on BTA 2, 3, 4, 9, 11, 14, 15, 22, 24, and 25 were significant at the genomewide experiment-wise error rate of 5% ( ≤ 1.49 × 10). Eighty-five SNP on 28 chromosomes achieved a false discovery rate of 5% ( ≤ 5.38 × 10). Significant SNP were near (±100 kb) genes involved in tissue repair and regeneration, tumor suppression, cell proliferation, apoptosis, control of organ size, and immunity. Based on 85 significantly associated SNP in or near a collection of genes with diverse function on 28 chromosomes, we conclude that the genomic footprint of lung lesions is complex. A complex genomic footprint (genes and regulatory elements that affect the trait) is consistent with what is known about the cause of the disease: complex interactions among multiple viral and bacterial pathogens along with several environmental factors including dust, commingling, transportation, and stress. Characterization of sequence variation near significant SNP will enable accurate and cost effective genome-enhanced genetic evaluations for BRDC resistance in AI bulls and seed stock populations.

Sire breed effect on beef longissimus mineral concentrations and their relationships with carcass and palatability traits.

The objective of this study was to evaluate sire breed effect on mineral concentration in beef longissimus thoracis (LT) and investigate the correlations between beef mineral concentrations and carcass and palatability traits. Steer progeny (N=246) from the Germplasm Evaluation project-Cycle VIII were used in this study. In addition to carcass traits, LT was evaluated for mineral concentrations, Warner-Bratzler shear force, and palatability traits. A mixed linear model estimated breed effects on mineral concentrations. No significant sire breed (P≥0.43) or dam breed (P≥0.20) effects were identified for mineral concentrations. Pearson correlation coefficients were calculated among mineral concentrations, carcass, and sensory traits. Zinc concentration was positively correlated (P≤0.05) with total iron (r=0.14), heme iron (r=0.13), and magnesium (r=0.19). Significant (P<0.05) correlations were identified between non-heme or heme iron and most traits in this study. Magnesium concentration was correlated with all carcass and palatability traits.

A polymorphism in myostatin influences puberty but not fertility in beef heifers, whereas µ-calpain affects first calf birth weight.

The use of genetic markers to aid in selection decisions to improve carcass and growth characteristics is of great interest to the beef industry. However, it is important to examine potential antagonistic interactions with fertility in cows before widespread application of marker-assisted selection. The objective of the current experiment was to examine the influence of 2 commercially available markers currently in use for improving carcass traits, the myostatin (MSTN) F94L and µ-calpain (CAPN1) 316 and 4751 polymorphisms, on heifer development and reproductive performance. In Exp. 1, beef heifers (n = 146) were evaluated for growth and reproductive traits over a 3-yr period to determine if these polymorphisms influenced reproductive performance. In Exp. 2, heifers representing the 2 homozygous genotypes for the MSTN F94L polymorphism were slaughtered on d 4 of the estrous cycle and reproductive tracts were collected for morphological examination. In Exp. 1, there was a tendency (P = 0.06) for birth BW to be affected by MSTN with the Leu allele increasing birth BW in an additive fashion. Additionally, MSTN significantly affected the proportion of pubertal heifers by the start of the breeding season (P < 0.05) with the Leu allele additively decreasing the proportion pubertal; however, this did not result in a delay in conception or a decrease in pregnancy rates during the first breeding season (P > 0.15). The GT haplotype of CAPN1, which was previously associated with decreased meat tenderness, was associated with an additive decrease in birth BW of the first calf born to these heifers (P < 0.05). In Exp. 2, there were no differences between the MSTN genotypes for gross or histological morphology of the anterior pituitary, uterus, or ovaries (P > 0.05). From these results, we concluded that the MSTN F94L and CAPN1 polymorphisms can be used to improve carcass traits without compromising fertility in beef heifers. The influence of these markers on cow performance and herd life remains to be determined. While the delay in puberty associated with the MSTN F94L polymorphism did not negatively impact reproductive performance in heifers, caution should be used when combining this marker with other markers for growth or carcass traits until the potential interactions are more clearly understood.

CAPN1, CAST, and DGAT1 genetic effects on preweaning performance, carcass quality traits, and residual variance of tenderness in a beef cattle population selected for haplotype and allele equalization.

Genetic marker effects and type of inheritance are estimated with poor precision when minor marker allele frequencies are low. A stable composite population (MARC III) was subjected to marker-assisted selection for multiple years to equalize specific marker frequencies to 1) estimate effect size and mode of inheritance for previously reported SNP on targeted beef carcass quality traits (n=254), 2) estimate pleiotropic effects of previously reported SNP on nontarget performance traits (n=542 or 254), and 3) evaluate tenderness SNP specific residual variance for LM tenderness. Three haplotypes within µ-calpain (CAPN1), a SNP in calpastatin (CAST), and a dinucleotide substitution in diacylglycerol O-acyltransferase 1 (DGAT1) were successfully selected to equalize their frequencies. Traits evaluated were birth BW, weaning BW, yearling BW, final BW, dressing percent, HCW, fat thickness, LM area, USDA marbling score, yield grade, LM slice shear force (SSF), and visible and near-infrared (VISNIR)-predicted SSF. While the CAPN1 genotype effect on SSF was not significant (P=0.12), the direction and size of CAPN1 contrasts were consistent with previous research. Effects on SSF between divergent CAPN1 haplotypes (1.153 kg) and the additive effect of CAST (0.902 kg) were large, and animals homozygous for tender alleles at both CAPN1 and CAST would have 4.11 kg lower SSF (27.5% of the mean) than animals homozygous tough for both markers. Furthermore, the interaction between CAPN1 and CAST for SSF was not significant (P=0.40). There were significant effects for DGAT1 on adjusted fat thickness (P=0.02) and VISNIR-predicted SSF (P<0.001) with additive and dominance modes of inheritance (P<0.05) for both traits. Furthermore, CAST genotype specific residual variance models fit significantly better (P<0.001) than single residual variance models for SSF, with the tougher genotypes having progressively larger residual (and hence phenotypic) variances. Therefore, risk of a tough steak from the undesired CAST genotype is increased through both an increase in mean and an increase in variation. This work is supportive of the importance of CAPN1 and CAST for mean tenderness in beef, confirms an effect of CAST on beef LM tenderness variation, and identifies an effect of DGAT1 on subcutaneous fat thickness.

Use of ultrasound scanning and body condition score to evaluate composition traits in mature beef cows.

The experiment was designed to validate the use of ultrasound to evaluate body composition in mature beef cows. Both precision and accuracy of measurement were assessed. Cull cows (n = 87) selected for highly variable fatness were used. Two experienced ultrasound technicians scanned and assigned BCS to each cow on 2 consecutive days. Ultrasound traits were backfat thickness (UBFT), LM area (ULMA), body wall thickness (UBWT), rump fat depth (URFD), rump muscle depth (URMD), and intramuscular fat (UIMF; %). Cows were then harvested. Carcass traits were HCW, backfat thickness (CBFT), LM area (CLMA), body wall thickness (CBWT), and marbling score (CMS). Correlations between consecutive live measurements were greatest for subcutaneous fat (r > 0.94) and lower for BCS (r > 0.74) and URMD (r > 0.66). Repeatability bias differed from 0 for only 1 technician for URMD and UIMF (P < 0.01). Technicians differed in repeatability SE for only ULMA (P < 0.05). Correlations between live and carcass measurements were high for backfat and body wall thickness (r > 0.90) and slightly less for intramuscular fat and LM area (r = 0.74 to 0.79). Both technicians underestimated all carcass traits with ultrasound, but only CBFT and CBWT prediction bias differed from 0 (P < 0.05). Technicians had similar prediction SE for all traits (P > 0.05). Technician effects generally explained <1% of the total variation in precision. After accounting for technician, animal effects explained 50.4% of remaining variation in differences between repeated BCS (P < 0.0001) but were minimal for scan differences. When cows with mean BCS <4 or >7 were removed, the portion of remaining variation between repeated measurements defined by animal effects increased for most traits and was significant for UBFT and URFD (P = 0.03). Technician effects explained trivial variation in accuracy (P > 0.24). Animal effects explained 87.2, 75.2, and 81.7% (P < 0.0001) of variation remaining for CBFT, CLMA, and CBWT prediction error, respectively, and remained large and highly important (P < 0.0001) when only considering cows with BCS from 4 to 7. We conclude that experienced ultrasound technicians can precisely and accurately measure traits indicative of composition in mature beef cows. However, animal differences define substantial variation in scan differences and, especially, prediction errors. Implications for technician certification, carcass pricing, and genetic evaluation are discussed.

µ-Calpain, calpastatin, and growth hormone receptor genetic effects on preweaning performance, carcass quality traits, and residual variance of tenderness in Angus cattle selected to increase minor haplotype and allele frequencies.

Genetic marker effects and interactions are estimated with poor precision when minor marker allele frequencies are low. An Angus population was subjected to marker assisted selection for multiple years to increase divergent haplotype and minor marker allele frequencies to 1) estimate effect size and mode of inheritance for previously reported SNP on targeted beef carcass quality traits; 2) estimate effects of previously reported SNP on nontarget performance traits; and 3) evaluate tenderness SNP specific residual variance models compared to a single residual variance model for tenderness. Divergent haplotypes within µ-calpain (CAPN1), and SNP within calpastatin (CAST) and growth hormone receptor (GHR) were successfully selected to increase their frequencies. Traits evaluated were birth BW, weaning BW, final BW, fat thickness, LM area, USDA marbling score, yield grade, slice shear force (SSF), and visible and near infrared predicted slice shear force. Both CAPN1 and CAST exhibited additive (P < 0.001) modes of inheritance for SSF and neither exhibited dominance (P ≥ 0.19). Furthermore, the interaction between CAPN1 and CAST for SSF was not significant (P = 0.55). Estimated additive effects of CAPN1 (1.049 kg) and CAST (1.257 kg) on SSF were large in this study. Animals homozygous for tender alleles at both CAPN1 and CAST would have 4.61 kg lower SSF (38.6% of the mean) than animals homozygous tough for both markers. There was also an effect of CAST on yield grade (P < 0.02). The tender CAST allele was associated with more red meat yield and less trimmable fat. There were no significant effects (P ≥ 0.23) for GHR on any of the traits evaluated in this study. Furthermore, CAST specific residual variance models were found to fit significantly better (P < 0.001) than single residual variance models for SSF, with the tougher genotypes having larger residual variance. Thus, the risk of a tough steak from the undesired CAST genotype is increased through both an increase in mean and an increase in variation. This work confirms the importance of CAPN1 and CAST for tenderness in beef, provides a new effect of CAST on beef tenderness, and questions the utility of GHR as a selection marker for beef quality.

Evaluation of response to bovine viral diarrhea virus type 2 vaccination and timing of weaning on yearling ultrasound body composition, performance, and carcass quality traits in Angus calves.

There are concerns about antagonisms between immunity and animal productivity in livestock production. The objective of this study was to evaluate the effect of antibody levels through a response to vaccination protocol, weaning timing, and their interaction on performance and carcass quality traits in Angus beef cattle. Final antibody level and response to vaccination were based on neutralizing serum antibodies against bovine viral diarrhea virus type 2 (BVDV2). Calves were followed through development and the feedlot phase, with collection of yearling ultrasound (n=957), preharvest (n=762), and carcass (n=673) data. In this study, 48% of the animals were observed to have positively responded to the vaccine, as evidenced by higher final antibody levels compared to prevaccination antibody levels. Increased final antibody levels were significantly (P<0.05) associated with increased yearling weight and increased subcutaneous fat over the rump. An interaction between final antibody level and weaning time also was associated (P<0.05) with Warner-Bratzler shear force (WBSF) and meat pH, with a favorable, negative relationship between final antibody and WBSF in calves weaned at initial vaccination. Overall antibody response by wean time interaction had a significant (P<0.05) association with ADG and meat pH, with calves weaned at initial vaccination having a favorable, positive relationship between overall antibody response and ADG. Under both the final antibody and overall antibody response models, animals weaned at initial vaccination had significantly (P<0.05) lower intramuscular fat at yearling time and conversely higher harvest weight than animals weaned at the booster vaccination. When antibody response was grouped (none, low, high), a significant interaction (P<0.05) between antibody response group and weaning time was identified for ADG, harvest weight, and HCW. Animals weaned at the initial vaccination in the high antibody response group had the advantage for ADG, harvest weight, and HCW compared to animals in the high-response group that were weaned at booster vaccination. Linear increases in antibody response generally did not have negative effects on performance or carcass quality traits in finished cattle (P>0.05). Therefore, producers should not be concerned about decreased production or quality attributes as a result of developing a robust antibody response to vaccination for BVDV2 in beef cattle.