Use of robust multivariate linear mixed models for estimation of genetic parameters for carcass traits in beef cattle.

Assumptions of normality of residuals for carcass evaluation may make inferences vulnerable to the presence of outliers, but heavy-tail densities are viable alternatives to normal distributions and provide robustness against unusual or outlying observations when used to model the densities of residual effects. We compare estimates of genetic parameters by fitting multivariate Normal (MN) or heavy-tail distributions (multivariate Student's t and multivariate Slash, MSt and MS) for residuals in data of hot carcass weight (HCW), longissimus muscle area (REA) and 12th to 13th rib fat (FAT) traits in beef cattle using 2475 records from 2007 to 2008 from a large commercial operation in Nebraska. Model comparisons using deviance information criteria (DIC) favoured MSt over MS and MN models, respectively. The posterior means (and 95% posterior probability intervals, PPI) of v for the MSt and MS models were 5.89 ± 0.90 (4.35, 7.86) and 2.04 ± 0.18 (1.70, 2.41), respectively. Smaller values of posterior densities of v for MSt and MS models confirm that the assumption of normally distributed residuals is not adequate for the analysis of the data set. Posterior mean (PM) and posterior median (PD) estimates of direct genetic variances were variable with MSt having the highest mean value followed by MS and MN, respectively. Posterior inferences on genetic variance were, however, comparable among the models for FAT. Posterior inference on additive heritabilities for HCW, REA and FAT using MN, MSt and MS models indicated similar and moderate heritability comparable with the literature. Posterior means of genetic correlations for carcass traits were variable but positive except for between REA and FAT, which showed an antagonistic relationship. We have demonstrated that genetic evaluation and selection strategies will be sensitive to the assumed model for residuals.

Application of multivariate heavy-tailed distributions to residuals in the estimation of genetic parameters of growth traits in beef cattle.

Assumptions of normality in most animal breeding applications may make inferences vulnerable to the presence of outliers. Heavy-tail densities are viable alternatives to normal distributions and provide robustness against unusual or outlying observations when used to model the densities of residual effects. Our objective is to compare estimates of genetic parameters by fitting multivariate normal (MN) or heavy-tail distributions [multivariate Student's t (MSt) and multivariate slash (MS)] for residuals in data of body birth weight (BBW), weaning (WW), and yearling (YW) weight traits in beef cattle. A total of 17,019 weight records for BBW, WW, and YW from 1998 through 2010 from a large commercial cow/calf operation in the sand hills of Nebraska were analyzed. Models included fixed effects of contemporary group and sire breed whereas animal and maternal effects were random and the degrees of freedom (v) was treated as unknown for MSt and MS. Model comparisons using deviance information criteria (DIC) favored MSt over MS and MN models, respectively. The posterior means [and 95% posterior probability intervals (PPI)] of v for the MSt and MS models were 5.28 (4.80, 5.85) and 1.88 (1.76, 2.00), respectively. Smaller values of posterior densities of v for MSt and MS models confirm that the assumption of normally distributed residuals is not adequate for the analysis of BBW, WW, and YW datasets. Posterior mean (PM) and posterior median (PD) estimates of direct and maternal genetic variances were the same and posterior densities of these parameters were found to be symmetric. The 95% PPI estimates from MN and MSt models for BBW did not overlap, which indicates significant difference between PM estimates from MN or MSt models. The observed antagonistic relationship between additive direct and additive maternal effects indicated that genetic evaluation and selection strategies will be sensitive to the assumed model for residuals.

Heritability and Bayesian genome-wide association study of first service conception and pregnancy in Brangus heifers.

Brangus [3/8 Brahman (Bos indicus) × 5/8 Angus (Bos taurus); n ≈ 800] heifers from 67 sires were used to estimate heritability and conduct a genome-wide association study (GWAS) for 2 binary fertility traits: first service conception (FSC) and heifer pregnancy (HPG). Genotypes were from 53,692 loci on the BovineSNP50 (Infinium Bead Chips, Illumina, San Diego, CA). Yearling heifers were estrous synchronized, bred by AI, and then exposed to natural service breeding. Reproductive ultrasound and DNA-based parentage testing were used to determine if the heifer conceived by AI or natural service, and code for FSC and HPG traits. Success rates for FSC and HPG were 53.3% and 78.0% ± 0.01%, and corresponding heritability estimates were 0.18 ± 0.07 and 0.10 ± 0.06, respectively. The models used in obtaining these heritability estimates and GWAS included fixed effects of year (i.e., 2005 to 2007), birth location, calving season, age of dam, and contemporary group. In GWAS, simultaneous associations of 1 Mb SNP windows with phenotype were undertaken with Bayes C analyses using GenSel software. The 1 Mb windows contained 21.3 ± 1.1 SNP. Analyses fitted a mixture model that treated SNP effects as random, with an assumed fraction pi = 0.9995 having no effect on phenotype. The windows that accounted for 1.0% of genetic variance were considered as QTL associated with FSC or HPG. Eighteen QTL existed on 15 chromosomes for the 2 traits. On average, each QTL accounted for 2.43% ± 0.2% of the genetic variance. Chromosome 8 harbored 2 QTL for FSC and 1 for HPG; however, these regions did not overlap. Chromosomes 3, 15, 16, 19, 24, 26, 27, 29, and X included QTL only for FSC, whereas chromosomes 2, 4, 10, 13, and 20 contained QTL only for HPG. The multitude of QTL detected for FSC and HPG in this GWAS involving Brangus heifers exemplifies the complex regulation of variation in heifer fertility traits of low heritability.

Bayesian genome-wide association analysis of growth and yearling ultrasound measures of carcass traits in Brangus heifers.

Data from developing Brangus heifers (3/8 Brahman-Bos indicus × 5/8 Angus-Bos taurus; n ≈ 802 from 67 sires) registered with International Brangus Breeders Association were analyzed to detect QTL associated with growth traits and ultrasound measures of carcass traits. Genotypes were from BovineSNP50 (Infinium BeadChip, Illumina, San Diego, CA; 53,692 SNP). Phenotypes included BW collected at birth and ∼205 and 365 d of age, and yearling ultrasound assessment of LM area, percent intramuscular fat, and depth of rib fat. Simultaneous association of SNP windows with phenotype were undertaken with Bayes C analyses, using GenSel software. The SNP windows were ≈ 5 SNP in length. Analyses fitted a mixture model that treated SNP effects as random, with an assumed fraction pi = 0.999 having no effect on phenotype. Bootstrap analyses were used to obtain significance values for the SNP windows with the greatest contribution to observed variation. The SNP windows with P < 0.01 were considered as QTL associated with a trait in which case their location was queried from dbSNP and the presence of a previously reported QTL in that location was checked in CattleQTLdb. For 9 traits, QTL were mapped to 139 regions on 25 chromosomes. Forty-one of these QTL were already described in CattleQTLdb, so 98 are new additions. The SNP windows on chromosomes 1, 3, and 6 were associated with multiple traits (i.e., 205- and 365- d BW, and ADG from birth to 205 and 365 d of age). Several chromosomes harbored regions associated with multiple traits; however, the SNP that comprised the window often varied among traits (i.e., chromosomes 1, 3, 4, 5, 6, 7, 9, 10, 11, 13, 14, 15, 16, 20, 21, 22, 24, 28, and 29). Results from whole genome association of SNP with growth and ultrasound carcass traits in developing Brangus heifers confirmed several published QTL and detected several new QTL.

Genomic prediction of simulated multibreed and purebred performance using observed fifty thousand single nucleotide polymorphism genotypes.

Genomic prediction involves characterization of chromosome fragments in a training population to predict merit. Confidence in the predictions relies on their evaluation in a validation population. Many commercial animals are multibreed (MB) or crossbred, but seedstock populations tend to be purebred (PB). Training in MB allows selection of PB for crossbred performance. Training in PB to predict MB performance quantifies the potential for across-breed genomic prediction. Efficiency of genomic selection was evaluated for a trait with heritability 0.5 simulated using actual SNP genotypes. The PB population had 1,086 Angus animals, and the MB population had 924 individuals from 8 sire breeds. Phenotypic values were simulated for scenarios including 50, 100, 250, or 500 additive QTL randomly selected from 50K SNP panels. Panels containing various numbers of SNP, including or excluding the QTL, were used in the analysis. A Bayesian model averaging method was used to simultaneously estimate the effects of all markers on the panels in MB (or PB) training populations. Estimated effects were utilized to predict genomic merit of animals in PB (or MB) validation populations. Correlations between predicted and simulated genomic merit in the validation population was used to reflect predictive ability. Panels that included QTL were able to account for 50% or more of the within-breed genetic variance when the trait was influenced by 50 QTL. The predictive power eroded as the number of QTL increased. Panels that composed the QTL and no other markers were able to account for 50% or more genetic variance even with 500 QTL. Panels that included genomic markers as well as QTL had less predictive power as the number of markers on the panel was increased. Panels that excluded the QTL and relied on markers in linkage disequilibrium (LD) to predict QTL effects performed more poorly than marker panels with QTL. Real-life situations with 50K panels that excluded the QTL could account for no more than 20% genetic variation for 50 QTL and less than 10% for 500 QTL. The difference between panels that included and excluded QTL indicates that the predictive ability of existing panels is limited by their LD. Training in PB to predict MB tended to be more predictive than training in MB to predict PB due to greater average levels of LD in PB than in MB populations. Improved across breed prediction of genomic merit will require panels with more than 50,000 markers.

Hyperimmunization of steers with J5 Escherichia coli bacterin: effects on isotype-specific serum antibody responses and cross reactivity with heterogeneous gram-negative bacteria.

Isotype-specific antibody responses and cross reactivity were profiled following hyperimmunization of steers with J5 Escherichia coli bacterin. The vaccine was administered at time 0, 30 d later, and every 2 wk for 10 subsequent immunizations. Blood was collected preimmunization and multiple times following each immunization. Isotype-specific anti-J5 Escherichia coli antibody response profiles in diluted sera harvested from each sample were assayed by ELISA and recorded as optical density. Selected sera were assayed for anti-J5 Escherichia coli antibody titers and used to determine cross reactivity against a variety of gram-negative bacteria. Immunization number and day postimmunization influenced response profiles for anti-J5 E. coli IgM, IgG(1)and IgG(2) antibodies. Two immunizations increased mean serum IgM and the IgG(1)antibody profiles above preimmunization levels, but 5 immunizations were required to detect significant IgG(2) antibody responses that were above preimmunization levels. Isotype-specific cross reactivity of the serum antibodies with a variety of heterologous gram-negative bacteria was also increased by hyperimmunization. However, no cross reactivity was observed for Staphylococcus aureus, purified lipopolysaccharide, or lipid A. Our results indicate that multiple booster doses of J5 E. coli bacterin may be required to elicit high levels of cross-reactive serum IgG(2) antibodies.

Reproductive toxicity of ergot alkaloids in mink.

Ergot alkaloids are-synthesized by fungi of the Claviceps family that infect rye as well as other cereals and grains. Since a portion of the ranch mink diet is cereal, mink are at a risk of being exposed to ergot alkaloids. This study was performed to determine the reproductive toxicity of ergot alkaloids derived from ergot-contaminated oats in mink. Four groups of 12 female mink each were fed diets containing 0, 3, 6 or 12 ppm ergot alkaloids from 2w prior to the breeding season until the kits were approximately 33-d old (133 d). Females were mated with untreated males. Ergo talkaloids caused a transient decrease in feed consumption, but body weights were unaffected. The gestation period of the mink in the 6 ppm group was longer compared to controls. The number of mink whelping varied significantly with 9 mink whelping each in the control and 3 ppm groups compared to 4 mink in the 6 ppm group and 1 in the 12 ppm group. Ergot alkaloids had a significant effect on kit survivabilitywith no kits surviving in the 12 ppm group. Serum prolactin was significantly depressed in the 3 ergot alkaloid groups compared to the control group. This study indicated that ingestion of ergot alkaloids at 3 ppm or higher resulted in reproductive toxicity in mink.

Use of Fungicides and Biological Controls in the Suppression of Fusarium Crown and Root Rot of Asparagus Under Greenhouse and Growth Chamber Conditions.

Growth chamber, greenhouse, and field experiments were conducted with fungicides and biological control agents, including nonpathogenic isolates of Fusarium oxysporum, to test their ability to control disease caused by F. oxysporum f. sp. asparagi and F. proliferatum. In greenhouse studies with asparagus seedlings in soil, Trichoderma harzianum strain T-22, benomyl, and fludioxonil treatments increased root weight and decreased root disease compared with the infested control when a low level of F. oxysporum f. sp. asparagi and F. proliferatum was used. The fungicide fludioxonil limited plant death caused by Fusarium spp. at high inoculum levels, whereas T. harzianum strain T-22 was not effective. Nonpathogenic isolates of F. oxysporum were effective in limiting Fusarium disease on asparagus seedlings in culture tubes, although isolates differed in their ability to control disease caused by F. oxysporum f. sp. asparagi and F. proliferatum. In greenhouse studies, no significant differences in plant death were found between asparagus plants growing in media infested with F. oxysporum f. sp. asparagi and F. proliferatum and left untreated, and those treated with nonpathogenic F. oxysporum. The efficacy of fungicides and biological control products to control Fusarium crown and root rot under commercial field conditions could not be evaluated due to low disease pressure.

Effects of Sodium Chloride on Commercial Asparagus and of Alternative Forms of Chloride Salt on Fusarium Crown and Root Rot.

Experiments with applications of NaCl (560 and 1,120 kg/ha) and lime (6,719 kg/ha) were conducted in asparagus fields in commercial production (one healthy and one exhibiting symptoms of early decline), and an experiment with NaCl (1,120 kg/ha) was conducted in a badly declined research field at Michigan State University from 1998 to 2000 to determine whether these treatments control Fusarium crown and root rot of asparagus. Growth chamber and greenhouse studies were conducted to test the ability of alternative forms (CaCl2, NH4Cl, and MnCl2) of chloride salt to reduce disease caused by F. oxysporum f. sp. asparagi and F. proliferatum. NaCl applications increased yield and fern health in the research plot, but not in commercial fields. Soil tests in these fields indicated that NaCl did not decrease levels of calcium, magnesium, or potassium, and did not affect pH. In growth chamber studies with asparagus seedlings in Hoagland's agar test tubes, and in greenhouse studies with asparagus seedlings in soil, none of the alternative forms of chloride salt tested were more effective than NaCl in controlling Fusarium crown and root rot.