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1.
BMC Genomics ; 23(1): 74, 2022 Jan 23.
Article in English | MEDLINE | ID: mdl-35065600

ABSTRACT

BACKGROUND: Cattle production is dependent upon fertility because it results in producing offspring to offset production costs. A number of semen attributes are believed to affect fertility and are frequently measured as part of routine breeding soundness exams or semen collection procedures. The objective of this study was to perform a single-step genome-wide association study (ssGWAS) for beef bull semen attributes. Beef bull fertility phenotypes including volume (VOL), concentration (CONC), number of spermatozoa (NSP), initial motility (IMot), post-thaw motility (PTMot), three-hour post-thaw motility (3HRPTMot), percentage of normal spermatozoa (%NORM), primary abnormalities (PRIM), and secondary abnormalities (SEC) were obtained from two artificial insemination (AI) centers. A total of 1819 Angus bulls with 50,624 collection records were used for ssGWAS. A five-generation pedigree was obtained from the American Angus Association and consisted of 6521 sires and 17,136 dams. Genotypes on 1163 bulls were also obtained from the American Angus Association and utilized in ssGWAS. RESULTS: A multi-trait animal model was used for the estimation of single nucleotide polymorphism (SNP) effects. Significant SNP were those with a -log10 P-value threshold greater than 4.0. Volume, CONC, NSP, IMot, PTMot, 3HRPTMot, %NORM, PRIM, and SEC have five, three, six, seven, two, six, six, and two genome-wide significant SNP, respectively. CONCLUSIONS: Several significant SNP were determined to be near or within quantitative trait loci (QTL) associated with beef bull semen attributes. In addition, genes associated with fertility were found to contain or be near the significant SNP found in the study. The results indicate there are regions of the genome that impact fertility, proving inclusion of genomic information into genetic evaluation should be advantageous for genetic improvement of male fertility traits.


Subject(s)
Genome-Wide Association Study , Semen , Animals , Cattle , Fertility/genetics , Insemination, Artificial , Male , Semen Analysis , Sperm Motility/genetics , Spermatozoa
2.
J Anim Sci ; 95(4): 1444-1450, 2017 Apr.
Article in English | MEDLINE | ID: mdl-28464090

ABSTRACT

Feed costs are a major economic expense in finishing and developing cattle; however, collection of feed intake data is costly. Examining relationships among measures of growth and intake, including breed differences, could facilitate selection for efficient cattle. Objectives of this study were to estimate genetic parameters for growth and intake traits and compare indices for feed efficiency to accelerate selection response. On-test ADFI and on-test ADG (TESTADG) and postweaning ADG (PWADG) records for 5,606 finishing steers and growing heifers were collected at the U.S. Meat Animal Research Center in Clay Center, NE. On-test ADFI and ADG data were recorded over testing periods that ranged from 62 to 148 d. Individual quadratic regressions were fitted for BW on time, and TESTADG was predicted from the resulting equations. We included PWADG in the model to improve estimates of growth and intake parameters; PWADG was derived by dividing gain from weaning weight to yearling weight by the number of days between the weights. Genetic parameters were estimated using multiple-trait REML animal models with TESTADG, ADFI, and PWADG for both sexes as dependent variables. Fixed contemporary groups were cohorts of calves simultaneously tested, and covariates included age on test, age of dam, direct and maternal heterosis, and breed composition. Genetic correlations (SE) between steer TESTADG and ADFI, PWADG and ADFI, and TESTADG and PWADG were 0.33 (0.10), 0.59 (0.06), and 0.50 (0.09), respectively, and corresponding estimates for heifers were 0.66 (0.073), 0.77 (0.05), and 0.88 (0.05), respectively. Indices combining EBV for ADFI with EBV for ADG were developed and evaluated. Greater improvement in feed efficiency can be expected using an unrestricted index versus a restricted index. Heterosis significantly affected each trait contributing to greater ADFI and TESTADG. Breed additive effects were estimated for ADFI, TESTADG, and the efficiency indices.


Subject(s)
Cattle/genetics , Eating/genetics , Genetic Variation , Hybrid Vigor/genetics , Weight Gain/genetics , Animal Feed/analysis , Animals , Body Weight/genetics , Breeding , Cattle/growth & development , Female , Male , Phenotype , Weaning
3.
J Anim Sci ; 95(2): 538-544, 2017 Feb.
Article in English | MEDLINE | ID: mdl-28380620

ABSTRACT

Accuracy of sire selection is limited by how well animals are characterized for their environment. The objective of this study was to evaluate the presence of genotype × environment interactions (G×E) for birth weight (BiW) and weaning weight (WW) for Red Angus in the United States. Adjusted weights were provided by the Red Angus Association of America. Environments were defined as 9 regions within the continental United States with similar temperature-humidity indices. Mean weights of calves were determined for each region and for each sire's progeny within each region. A reaction norm (RN) for each bull was estimated by regressing the sire means on the region means weighted for the number of progeny of each sire. The range for BiW and WW RN was -1.3 to 4.0 and -1.7 to 2.8, respectively. The heritabilities of BiW and WW RN were 0.40 and 0.39, respectively. Phenotypic and genetic correlations between BiW and WW RN were 0.19 and 0.54, respectively. The phenotypic correlation of the progeny mean to the RN was -0.20 ( <0.05) and suggests that sires with higher means are more stable in progeny performance across environments. Weights in different regions were considered separate traits and genetic correlations were estimated between all pairs of regions as another method to determine G×E. Genetic correlations < 0.80 indicate G×E at a level for concern, but existed for only 2 of 36 estimates for BiW and 12 of 36 estimates for WW. Genetic correlations between different regions ranged from 0.74 to 0.96 for BiW and 0.62 to 0.99 for WW and indicate that sires tend to rank similarly across environments for these traits.


Subject(s)
Birth Weight/genetics , Cattle/physiology , Gene-Environment Interaction , Animals , Breeding , Cattle/genetics , Cattle/growth & development , Environment , Female , Genotype , Male , United States , Weaning
4.
J Anim Sci ; 94(7): 2770-8, 2016 Jul.
Article in English | MEDLINE | ID: mdl-27482664

ABSTRACT

Bovine respiratory disease complex (i.e., shipping fever and bacterial bronchopneumonia) is a multifaceted respiratory illness influenced by numerous environmental factors and microorganisms. Bovine respiratory disease (BRD) is just one component of BRD complex. Because BRD is moderately heritable, it may be possible to reduce the incidence of BRD through genetic selection. The objectives of this study were to determine the heritability and associative genetic relationships among immune system traits (i.e., cortisol, total IgG, IgG isotypes, and IL-8) in cattle monitored for BRD incidence. At an average of 83 d after weaning (219 d age and mean = 221.7 kg [SD 4.34]), crossbred steer calves ( = 2,869) were received at a commercial feedlot in southeastern Colorado over a 2-yr period. At receiving, jugular blood samples were collected at 212 (yr 1) and 226 d (yr 2) of age for immune trait analyses. The BRD phenotype was defined as a binomial variable (0 = no and 1 = yes) and compared with immune system traits measured at receiving (prior to illness onset). An animal identified as BRD positive exhibited ≥ 2 clinical signs (i.e., eye or nasal discharge, cough, lethargy, rapid breathing, acute interstitial pneumonia, or acute upper respiratory syndrome and/or a rectal temperature > 39.7°C). Heritability and genetic correlation estimates for categorical variable BRD, cortisol, IgG, IgG1, IgG2, and IL-8 were estimated from a sire model using ASREML. Heritability estimates were low to moderate for BRD (0.17 ± 0.08), cortisol (0.13 ± 0.05), IgG (0.15 ± 0.05), IgG1 (0.11 ± 0.05), IgG2 (0.24 ± 0.06), and IL-8 (0.30 ± 0.06). A moderate negative genetic correlation was determined between BRD and cortisol ( = -0.19 ± 0.32). Moderate positive correlations were found between BRD with IgG (0.42 ± 0.28), IgG1 (0.36 ± 0.32), and IL-8 ( = 0.26 ± 0.26). Variation in the BRD phenotype and immune system traits suggested herd health improvement may be achieved through genetic selection.


Subject(s)
Bovine Respiratory Disease Complex/epidemiology , Hydrocortisone/blood , Immunoglobulin G/blood , Interleukin-8/blood , Animals , Body Temperature , Bovine Respiratory Disease Complex/blood , Cattle , Colorado , Gene Expression Regulation/immunology , Hydrocortisone/genetics , Immunoglobulin G/genetics , Incidence , Interleukin-8/genetics , Phenotype
5.
J Anim Sci ; 94(2): 483-9, 2016 Feb.
Article in English | MEDLINE | ID: mdl-27065118

ABSTRACT

The objective of this study was to elucidate the phenotypic relationships between docility and first-service AI conception rate in heifers. Data ( = 337) collected from 3 cooperator herds in Kansas at the start of synchronization protocol included exit velocity (EV), chute score (CS), fecal cortisol (FC), and blood serum cortisol (BC). Data were analyzed using logistic regression with 30-d pregnancy rate as the dependent variable. The model included the fixed effect of contemporary group and the covariates FC, BC, EV, CS, BW, and age. Correlation coefficients were calculated between all continuous traits. Pregnancy rate ranged from 34% to 60% between herds. Blood cortisol positively correlated with EV ( = 0.22, < 0.01), negatively correlated with age ( = -0.12, < 0.03), and tended to be negatively correlated with BW ( = -0.10, = 0.09). Exit velocity was positively correlated with CS ( = 0.24, < 0.01) and negatively correlated with BW ( = -0.15, < 0.01) and age ( = -0.12, < 0.03). Chute score negatively correlated with age ( = -0.14, < 0.01), and age and BW were moderately positively correlated ( = 0.42, < 0.01), as expected. Older, heavier animals generally had better temperament, as indicated by lower BC, EV, and CS. The power of our test could detect no significant predictors of 30-d pregnancy for the combined data from all ranches. When the data were divided by ranch, CS ( < 0.03) and BW ( < 0.01) were both significant predictors for 30-d pregnancy for ranch 1. The odds ratio estimate for CS has an inverse relationship with pregnancy, meaning that a 1-unit increase in average CS will reduce the probability of pregnancy at ranch 1 by 48.1%. Weight also has a negative impact on pregnancy because a 1-kg increase in BW will decrease the probability of pregnancy by 2.2%. Fertility is a complex trait that depends on many factors; our data suggest that docility is 1 factor that warrants further investigation.


Subject(s)
Cattle/psychology , Reproduction/physiology , Temperament , Animals , Behavior, Animal , Body Weight , Cattle/physiology , Female , Hydrocortisone/blood , Insemination, Artificial/veterinary , Pregnancy , Pregnancy Rate
6.
J Anim Sci ; 93(6): 2663-8, 2015 Jun.
Article in English | MEDLINE | ID: mdl-26115254

ABSTRACT

The objective was to estimate genetic parameters for udder traits in Hereford cattle. American Hereford Association (AHA) members initially recorded an overall score based on all udder characteristics. In 2008, the Beef Improvement Federation established guidelines, which were subsequently adopted by the AHA, for evaluating udder suspension and teat size. Therefore, a female was scored for either overall score or udder suspension and teat size for a single lactation, and females may be evaluated for overall score for a parity and then for udder suspension and teat size at a later parity. In all cases, subjective scores were assigned at parturition and ranged from 1 to 9, with a score of 9 considered ideal. Records on 48,191 animals and a 3-generation pedigree with 126,814 animals were obtained from the AHA, Kansas City, MO. These records contained repeated observations for overall score (n = 73,469), suspension (n = 38,412), and teat size (n = 38,412). Because the distribution of scores for all traits peaked at 7, a linear approximation was used in the analysis. Data were modeled using a multiple-trait animal model with random effects of additive genetic and permanent environment, fixed effect of contemporary group (herd-year-season), and a linear covariate for age in days. Heritability estimates (SE) for overall score, suspension, and teat size were 0.32 (0.01), 0.32 (0.01), and 0.28 (0.01), respectively. Through genetic selection for these traits, beef producers could improve udder traits. Repeatability estimates (SE) for overall score, suspension, and teat size were 0.45 (0.005), 0.47 (0.01), and 0.44 (0.01), respectively. Producers should continue evaluating udder traits repeatedly throughout a cow's lifetime. The phenotypic correlation (SE) between suspension and teat size was 0.64 (0.004) with 57% of records for suspension and teat size having the same score for both traits. The genetic correlations (SE) between teat size and suspension, overall score and teat size, and overall score and suspension were 0.81 (0.01), 0.71 (0.03), and 0.69 (0.03), respectively, and selection for one trait should result in correlated responses in the other traits. In conclusion, traits were moderately repeatable with scores from a parity being informative for subsequent parities. Because overall score, udder suspension, and teat size were moderately heritable with strong, positive genetic correlations, genetic improvement for these traits can be achieved through selection.


Subject(s)
Cattle/genetics , Cattle/physiology , Mammary Glands, Animal/physiology , Animals , Breeding , Female , Lactation/genetics , Models, Genetic , Parity , Parturition , Pedigree , Phenotype , Pregnancy
7.
J Anim Sci ; 91(2): 605-12, 2013 Feb.
Article in English | MEDLINE | ID: mdl-23148252

ABSTRACT

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.


Subject(s)
Cattle/genetics , Cattle/physiology , Genome-Wide Association Study/veterinary , Pregnancy, Animal , Animals , Bayes Theorem , Crosses, Genetic , Female , Fertility/genetics , Genotype , Models, Genetic , Pregnancy , Pregnancy, Animal/genetics
8.
J Anim Sci ; 90(10): 3398-409, 2012 Oct.
Article in English | MEDLINE | ID: mdl-23038745

ABSTRACT

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.


Subject(s)
Adipose Tissue/anatomy & histology , Cattle/growth & development , Cattle/physiology , Genome-Wide Association Study , Muscle, Skeletal/anatomy & histology , Polymorphism, Single Nucleotide , Adipose Tissue/diagnostic imaging , Animals , Bayes Theorem , Body Weight , Cattle/genetics , Female , Genotype , Models, Genetic , Muscle, Skeletal/diagnostic imaging , Quantitative Trait Loci , Ultrasonography
9.
Anim Genet ; 43(6): 662-73, 2012 Dec.
Article in English | MEDLINE | ID: mdl-22497286

ABSTRACT

We performed a genome-wide association study for Warner-Bratzler shear force (WBSF), a measure of meat tenderness, by genotyping 3360 animals from five breeds with 54 790 BovineSNP50 and 96 putative single-nucleotide polymorphisms (SNPs) within µ-calpain [HUGO nomenclature calpain 1, (mu/I) large subunit; CAPN1] and calpastatin (CAST). Within- and across-breed analyses estimated SNP allele substitution effects (ASEs) by genomic best linear unbiased prediction (GBLUP) and variance components by restricted maximum likelihood under an animal model incorporating a genomic relationship matrix. GBLUP estimates of ASEs from the across-breed analysis were moderately correlated (0.31-0.66) with those from the individual within-breed analyses, indicating that prediction equations for molecular estimates of breeding value developed from across-breed analyses should be effective for genomic selection within breeds. We identified 79 genomic regions associated with WBSF in at least three breeds, but only eight were detected in all five breeds, suggesting that the within-breed analyses were underpowered, that different quantitative trait loci (QTL) underlie variation between breeds or that the BovineSNP50 SNP density is insufficient to detect common QTL among breeds. In the across-breed analysis, CAPN1 was followed by CAST as the most strongly associated WBSF QTL genome-wide, and associations with both were detected in all five breeds. We show that none of the four commercialized CAST and CAPN1 SNP diagnostics are causal for associations with WBSF, and we putatively fine-map the CAPN1 causal mutation to a 4581-bp region. We estimate that variation in CAST and CAPN1 explains 1.02 and 1.85% of the phenotypic variation in WBSF respectively.


Subject(s)
Calcium-Binding Proteins/genetics , Calpain/genetics , Cattle/genetics , Genome-Wide Association Study/veterinary , Meat , Quantitative Trait Loci , Animals , Genetic Variation , Genotype , Polymorphism, Single Nucleotide
10.
Anim Genet ; 43(4): 367-74, 2012 Aug.
Article in English | MEDLINE | ID: mdl-22497295

ABSTRACT

Estimated breeding values for average daily feed intake (AFI; kg/day), residual feed intake (RFI; kg/day) and average daily gain (ADG; kg/day) were generated using a mixed linear model incorporating genomic relationships for 698 Angus steers genotyped with the Illumina BovineSNP50 assay. Association analyses of estimated breeding values (EBVs) were performed for 41,028 single nucleotide polymorphisms (SNPs), and permutation analysis was used to empirically establish the genome-wide significance threshold (P < 0.05) for each trait. SNPs significantly associated with each trait were used in a forward selection algorithm to identify genomic regions putatively harbouring genes with effects on each trait. A total of 53, 66 and 68 SNPs explained 54.12% (24.10%), 62.69% (29.85%) and 55.13% (26.54%) of the additive genetic variation (when accounting for the genomic relationships) in steer breeding values for AFI, RFI and ADG, respectively, within this population. Evaluation by pathway analysis revealed that many of these SNPs are in genomic regions that harbour genes with metabolic functions. The presence of genetic correlations between traits resulted in 13.2% of SNPs selected for AFI and 4.5% of SNPs selected for RFI also being selected for ADG in the analysis of breeding values. While our study identifies panels of SNPs significant for efficiency traits in our population, validation of all SNPs in independent populations will be necessary before commercialization.


Subject(s)
Animal Feed , Cattle/genetics , Genetic Association Studies/methods , Polymorphism, Single Nucleotide , Animals , Breeding , Genotype , Male , Phenotype
11.
J Anim Sci ; 88(7): 2321-36, 2010 Jul.
Article in English | MEDLINE | ID: mdl-20190161

ABSTRACT

A study was performed to evaluate differences in thermoregulatory ability of 2 Bos taurus breeds with known differences in heat tolerance. Nine Angus (AG; 304 +/- 7 kg of BW) and 9 Romosinuano (RO; 285 +/- 7.5 kg of BW) steers were transported to the Brody Environmental Center at the University of Missouri. Steers were housed for 18 d at thermoneutrality (TN; 21 degrees C) before initiation of heat stress (HS), which consisted of daily cyclic air temperature (26 degrees C, night; 36 degrees C, day) for 14 d. Rectal temperature and respiration rate were measured 6 times daily throughout the study. Sweat rates at shaved skin sites were recorded on specific days. Blood samples were taken once per week. Angus steers maintained rectal temperature 0.5 degrees C greater than RO at TN (P < 0.001). Likewise, respiration and sweat rates were greater (P < 0.001) in AG than RO at TN (P < 0.05). Rectal temperature increased during HS for both breeds with AG maintaining greater temperatures (P < 0.001). Both breeds increased respiration rate during HS, with AG steers exhibiting the greater rate (P < 0.001). Sweat rate increased more than 4-fold during HS (P < 0.001), followed by reduction after 7 d. Even after HS acclimation, AG exhibited the greater sweat rate (P < 0.001). Breed differences for serum leptin, creatinine, and cholesterol were found throughout the study with AG being greater than RO. Although there were no breed differences (P = 0.21) at TN, only AG steers exhibited a HS-induced increase (P < 0.05) in prolactin, creatinine, and cholesterol concentrations to suggest that an increase in rectal temperature is required for this effect. Use of rectal temperature along with endocrine markers, such as prolactin, may aid in the identification of B. taurus sensitivity to heat.


Subject(s)
Cattle/physiology , Animals , Body Temperature/physiology , Body Temperature Regulation/physiology , Cattle/blood , Cholesterol/blood , Creatinine/blood , Hot Temperature , Leptin/blood , Male , Prolactin/blood , Respiratory Rate/physiology , Species Specificity , Stress, Physiological/physiology , Sweating/physiology
12.
J Anim Sci ; 85(12): 3159-69, 2007 Dec.
Article in English | MEDLINE | ID: mdl-17878282

ABSTRACT

Deoxyribonucleic acid-based tests were used to assign paternity to 625 calves from a multiple-sire breeding pasture. There was a large variability in calf output and a large proportion of young bulls that did not sire any offspring. Five of 27 herd sires produced over 50% of the calves, whereas 10 sires produced no progeny and 9 of these were yearling bulls. A comparison was made between the paternity results obtained when using a DNA marker panel with a high (0.999), cumulative parentage exclusion probability (P(E)) and those obtained when using a marker panel with a lower P(E) (0.956). A large percentage (67%) of the calves had multiple qualifying sires when using the lower resolution panel. Assignment of the most probable sire using a likelihood-based method based on genotypic information resolved this problem in approximately 80% of the cases, resulting in 75% agreement between the 2 marker panels. The correlation between weaning weight, on-farm EPD based on pedigrees inferred from the 2 marker panels was 0.94 for the 24 bulls that sired progeny. Partial progeny assignments inferred from the lower resolution panel resulted in the generation of EPD for bulls that actually sired no progeny according to the high-P(E) panel, although the Beef Improvement Federation accuracies of EPD for these bulls were never greater than 0.14. Simulations were performed to model the effect of loci number, minor allele frequency, and the number of offspring per bull on the accuracy of genetic evaluations based on parentage determinations derived from SNP marker panels. The SNP marker panels of 36 and 40 loci produced EPD with accuracies nearly identical to those EPD resulting from use of the true pedigree. However, in field situations where factors including variable calf output per sire, large sire cohorts, relatedness among sires, low minor allele frequencies, and missing data can occur concurrently, the use of marker panels with a larger number of SNP loci will be required to obtain accurate on-farm EPD.


Subject(s)
Breeding/methods , Cattle/genetics , Pedigree , Polymorphism, Single Nucleotide , Quantitative Trait Loci , Animals , Female , Gene Frequency , Genetic Markers , Likelihood Functions , Male , Models, Genetic , Paternity , Probability , Weight Gain/genetics
13.
J Anim Sci ; 84(1): 32-40, 2006 Jan.
Article in English | MEDLINE | ID: mdl-16361489

ABSTRACT

Data obtained during 4 generations of divergent selection for placental efficiency were used to determine factors influencing survival at farrowing and weaning in litters produced by first-parity females. Data were collected from 193 litters and included records on 2,053 individuals. Farrowing survival (FS) and weaning survival (WS) were considered traits of the piglet and were scored 1 if the individual was alive at a time point or 0 if dead. Estimates of (co)variance components for direct and maternal additive genetic effects for FS and WS were obtained using an animal model and computed with the MTDFREML program. Estimates of direct heritability were 0.16 for FS and 0.18 for WS. Estimates of maternal heritability were 0.14 for FS and 0.10 for WS. Genetic correlation estimates between direct and maternal effects were high and negative for both traits. The direct genetic correlation between FS and WS was 0.92. Variables associated with FS and WS were determined using logistic regression procedures. Birth weight (BRW), placental weight, their interaction, and total born can be used as predictors of survival at farrowing in the absence of estimates of genetic merit for survival. The same model, excluding total number born, was the best model for predicting WS. In the presence of BRW information, placental efficiency did not improve the prediction of survival. While it was clearly disadvantageous for a piglet to be below the litter mean in BRW, being above the mean did not provide a substantial advantage in survival. Results from this analysis suggest that it is possible to select for increased survival at farrowing and at weaning. Information on a piglet's BRW, placental weight, litter average BRW, and deviation from litter average BRW can be used to optimize those values at levels resulting in high survival probability.


Subject(s)
Birth Weight/genetics , Birth Weight/physiology , Placenta/physiology , Swine/growth & development , Swine/genetics , Weaning , Animals , Female , Genotype , Longevity , Male , Organ Size , Parturition/genetics , Parturition/physiology , Phenotype , Pregnancy , Software , Survival Rate
14.
J Anim Sci ; 81(6): 1427-33, 2003 Jun.
Article in English | MEDLINE | ID: mdl-12817489

ABSTRACT

The objective of this study was to estimate parameters required for genetic evaluation of Simmental carcass merit using carcass and live animal data. Carcass weight, fat thickness, longissimus muscle area, and marbling score were available from 5,750 steers and 1,504 heifers sired by Simmental bulls. Additionally, yearling ultrasound measurements of fat thickness, longissimus muscle area, and estimated percentage of intramuscular fat were available on Simmental bulls (n = 3,409) and heifers (n = 1,503). An extended pedigree was used to construct the relationship matrix (n = 23,968) linking bulls and heifers with ultrasound data to steers and heifers with carcass data. All data were obtained from the American Simmental Association. No animal had both ultrasound and carcass data. Using an animal model and treating corresponding ultrasound and carcass traits separately, genetic parameters were estimated using restricted maximum likelihood. Heritability estimates for carcass traits were 0.48 +/- 0.06, 0.35 +/- 0.05, 0.46 +/- 0.05, and 0.54 +/- 0.05 for carcass weight, fat thickness, longissimus muscle area, and marbling score, respectively. Heritability estimates for bull (heifer) ultrasound traits were 0.53 +/- 0.07 (0.69 +/- 0.09), 0.37 +/- 0.06 (0.51 +/- 0.09), and 0.47 +/- 0.06 (0.52 +/- 0.09) for fat thickness, longissimus muscle area, and intramuscular fat percentage, respectively. Heritability of weight at scan was 0.47 +/- 0.05. Using a bivariate weight model including scan weight of bulls and heifers with carcass weight of slaughter animals, a genetic correlation of 0.77 +/- 0.10 was obtained. Models for fat thickness, longissimus muscle area, and marbling score were each trivariate, including ultrasound measurements on yearling bulls and heifers, and corresponding carcass traits of slaughter animals. Genetic correlations of carcass fat thickness with bull and heifer ultrasound fat were 0.79 +/- 0.13 and 0.83 +/- 0.12, respectively. Genetic correlations of carcass longissimus muscle area with bull and heifer ultrasound longissimus muscle area were 0.80 +/- 0.11 and 0.54 +/- 0.12, respectively. Genetic correlations of carcass marbling score with bull and heifer ultrasound intramuscular fat percentage were 0.74 +/- 0.11 and 0.69 +/- 0.13, respectively. These results provide the parameter estimates necessary for genetic evaluation of Simmental carcass merit using both data from steer and heifer carcasses, and their ultrasound indicators on yearling bulls and heifers.


Subject(s)
Adipose Tissue/diagnostic imaging , Body Composition/genetics , Cattle/genetics , Muscle, Skeletal/diagnostic imaging , Adipose Tissue/anatomy & histology , Age Factors , Animals , Body Composition/physiology , Breeding , Cattle/growth & development , Female , Likelihood Functions , Male , Meat/standards , Models, Biological , Models, Genetic , Muscle, Skeletal/anatomy & histology , Ultrasonography
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