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.

A survey of polymorphisms detected from sequences of popular beef breeds.

The genome sequence was obtained from 270 sires used in the Germplasm Evaluation (GPE) project. These bulls included 154 purebred AI sires from GPE Cycle VII breeds (Hereford, Angus, Simmental, Limousin, Charolais, Gelbvieh, and Red Angus), 83 F crosses of those breeds, and 33 AI sires from 8 other breeds. The exome capture sequence targeting coding regions of the genome was obtained from 176 of these bulls. Sequence reads were mapped to the UMD 3.1 bovine genome assembly; a mean of 2.5-fold (x) coverage per bull was obtained from the genomic sequence, and the targeted exons were covered at a mean of 20.0x. Over 28.8 million biallelic sequence variants were detected where each allele was present in at least 3 different bulls. These included 22.0 million previously reported variants and 94.1% of the 774,660 autosomal and BTA X SNP on the BovineHD BeadChip assay (HD). More than 92% of the variants detected in targeted exons were also detected from the low-coverage genome sequence. Less than 1% of the variants detected from the combined genome and exome sequence occurred in annotated protein-coding sequences and 5' and 3' untranslated regions (UTR) surrounding the 19,994 annotated protein coding regions. Variation was detected in the coding sequence or UTR of 96.8% of the genes: loss-of-function variants were predicted for 3,298 genes, 14,973 contained nonsynonymous variants, 11,276 had variation in UTR, and 17,721 genes contained synonymous variants. Minor allele frequencies (MAF) were <0.05 for 47.8% of the coding sequence and UTR variants, and MAF distributions were skewed toward low MAF. In contrast, 11.1% of the HD SNP detected in these bulls had MAF < 0.05, and the distribution was skewed toward higher MAF. Genes involved in immune system processes and immune response were overrepresented among those genes containing high MAF loss-of-function and nonsynonymous polymorphisms. Detected variants were submitted to the National Center for Biotechnology Information genetic variation database (dbSNP) under the handle MARC, batch GPE_Bull_GenEx.

Variation in the volume of zebra finch song control nuclei is heritable: developmental and evolutionary implications.

In many songbird species, females prefer males that sing a larger repertoire of syllables. Males with more elaborate songs have a larger high vocal centre (HVC) nucleus, the highest structure in the song production pathway. HVC size is thus a potential target of sexual selection. Here we provide evidence that the size of the HVC and other song production nuclei are heritable across individual males within a species. In contrast, we find that heritabilities of other nuclei in a song-learning pathway are lower, suggesting that variation in the sizes of these structures is more closely tied to developmental and environmental differences between individuals. We find that evolvability, a statistical measure that predicts response to selection, is higher for the HVC and its target for song production, the robustus archistriatalis (RA), than for all other brain volumes measured. This suggests that selection based on the functions of these two structures would result in rapid major shifts in their anatomy. We also show that the size of each song control nucleus is significantly correlated with the song related nuclei to which it is monosynaptically connected. Finally, we find that the volume of the telencephalon is larger in males than in females. These findings begin to join theoretical analyses of the role of female choice in the evolution of bird song to neurobiological mechanisms by which the evolutionary changes in behaviour are expressed.

Influence of partitioning data by sex on genetic variance and covariance components for weaning weight in beef cattle.

Heterogeneity of (co)variance components (VC) by sex is currently accounted for in national genetic evaluations for Simmental cattle. Parameters used in the national evaluation program are estimated from data split into male, female, and steer populations. Analyzing only male data does not account for selection of females, and vice versa. To determine the impact of selection, a Monte Carlo simulation was used, and estimates of VC for weaning weight were obtained when data were partitioned by sex. Weaning weight data were simulated using homogeneous VC for males and females for random and selected populations. Restricted maximum likelihood estimates were obtained for direct and maternal genetic and permanent and temporary environmental variances and genetic covariance between direct and maternal effects by analyzing complete or split data. Estimates differed (P < .01) from input values in data from selected populations split by sex, yielding a spurious heterogeneity of VC for sex. The heterogeneity was reduced in models using genetic groups but not completely removed. Splitting data by sex also influenced VC estimates in data simulated with heterogeneous VC for males and females.

Relationship between sire x year interactions and direct-maternal genetic correlation for weaning weight of Simmental cattle.

The interrelation of sire x year interactions (SY) and direct-maternal genetic correlation (rdm) for weaning weight was examined for bias in estimating rdm. Weaning weight records were simulated using models containing SY (D1), rdm (D2), or both (D3). When D1 data were analyzed ignoring SY, a nonzero rdm was observed, and direct and maternal genetic variance estimates were inflated. Analysis of D2 data ignoring rdm did not reveal a spurious SY, and direct and maternal genetic variance estimates were deflated. On application to weaning weights of Simmental cattle, the model ignoring SY resulted in a direct-maternal genetic correlation estimate of -.29. The model using both SY and rdm fit the data better (P < .01). The SY variance represented only 3% of phenotypic variance but explained 62% of the covariance between direct and maternal genetic effects estimated ignoring SY. However, a negative estimate of the genetic correlation (-.14) was still obtained.

Influence of sire misidentification on sire x year interaction variance and direct-maternal genetic covariance for weaning weight in beef cattle.

Biased estimates of the genetic correlation between direct and maternal effects may occur when sire x year interaction (SY) effects are ignored in analytical models used to estimate (co)variance components for weaning weight in beef cattle. Using simulation, sire misidentification was explored as a source contributing to estimates of SY variance. Identifications were falsified for 20% of sires of nonparents only or for 20% of sires of all animals. Sire misidentification influenced estimates of genetic and environmental parameters. In populations in which misidentification occurred only in nonparents, heritability estimates for direct growth were reduced, and heritability estimates of maternal effects were inflated. Also, spurious SY variance and direct-maternal covariance were produced. Direct-maternal covariance was biased in a positive direction, and SY variance was on the order of 1 to 3% of the phenotypic variance.

Genetic antagonism between body weight and milk production in beef cattle.

Korean cattle have an unusually short suckling period (4 mo) due to poor milking ability, and this is a hindrance to growth of calves. Therefore, Korean cattle breeders have shown interest in genetic improvement of milking ability. In this study, body weight (birth weight, weaning weight, and yearling weight) and five daily milk yields by period in Korean cattle (Hanwoo) were analyzed using a two-trait sire and maternal grandsire mixed model. The milk yields used were actually measured at sequential intervals from 1 to 4 mo after calving. Posterior means of the parameters were estimated using Gibbs sampling. Heritability estimates (0.25 to 0.26) for daily milk yield at weaning were larger than those with other periods. Genetic impact on daily milk yield, especially at weaning, was emphasized in order to lengthen the suckling period of Korean cattle. Genetic correlation estimates between BW and daily milk yield were all negative (-0.08 to -0.16 for birth weight, -0.04 to -0.21 for weaning weight, and -0.12 to -0.19 for yearling weight), whereas environmental correlation estimates were all positive (0.20 to 0.39 for birth weight, 0.34 to 0.51 for weaning weight, and 0.30 to 0.45 for yearling weight). The negative estimates of genetic correlation between weight and milk yield implied genetic antagonism between direct and maternal effects for weaning weight of beef cattle.

Estimation of genetic trend in a selected population with and without the use of a control population.

Data from a selection experiment conducted with sheep at Massey University, New Zealand, were analyzed to obtain an evaluation of selection response. Selection was for heavy 14-mo greasy fleece weight. Approximately seven generations of selection were represented in the data. Three estimates of genetic superiority of the selected line to the control line were obtained. All three estimates were obtained from a mixed model evaluation using the individual animal model for predicting breeding values from own and relatives' records. The estimators were 1) deviation of selected line predicted yearly phenotypes from control line predicted yearly phenotypes, 2) deviation of the predicted yearly phenotype for the selected line from the year estimate in the control line and 3) the mean yearly breeding value from the analysis of the selected line only. The realized heritability using the first approach was .20. However, the control line was found to have a slight positive drift; hence, this estimate was biased downward. Using Approach 2, accounting for drift, the realized heritability was .23. The same realized heritability, .23, was obtained from an analysis of the selected line ignoring the control (Approach 3), when a prior heritability of .30 was assumed for the mixed model evaluation. The estimate of genetic trend from predicted breeding values in the latter approach is, however, quite dependent on the assumed heritability.

Describing interactions in dystocia scores with a threshold model.

Field data on calving difficulty scores provided by the American Simmental Association were subjected to two methods of analysis: ordinary least-squares analysis and maximum likelihood with an assumed threshold model. In each analysis, the model included the interaction of sex of calf X age of dam. This interaction was readily apparent in the data (observed scale): within the youngest dams 58% of the heifer calves and 37% of the bull calves were born unassisted vs 96% and 92%, respectively, in the oldest dams. The objective was to determine if this interaction would be greatly reduced or would disappear on the underlying scale of a threshold model. The least-squares estimate of the sex difference was greatest within the youngest age-of-dam group (18 to 24 mo) and steadily declined with increasing age of dam, approaching zero for dams 6 yr and older. In contrast, the estimates of the sex difference from the threshold analysis were remarkably similar across ages of dam. It was concluded that observed interactions in calving ease data could be adequately described by a threshold model in which the effects of age of dam and sex of calf act additively on the underlying variable.

Analysis of gestation length in American Simmental cattle.

Records of gestation length (71,461) for Simmental cattle were distributed with mean 284.3 d and standard deviation 5.52 d. Gestation length was found to increase with percent Simmental and was 1.9 d longer for calves born to mature dams than for those born to heifer dams. Bull calves experienced gestation lengths 1.5 d longer than heifer calves. Sire, maternal grandsire, residual and total variances were estimated to be 2.42, .58, 22.78 and 25.78 d2, respectively, by Henderson's Method III. Heritability of gestation length was calculated to be .374 from the sire variance and .09 from the maternal grandsire variance. Direct additive genetic variance was considered to be of greater importance than maternal additive genetic variance. Correlations between the evaluations of sires for gestation length and heifer calving ease, birth weight and weaning weight were .26, .26 and .13, respectively.

Estimation of variance and covariance components to determine heritabilities and repeatability of weaning weight in American Simmental cattle.

Components of (co)variance for weaning weight were estimated from field data provided by the American Simmental Association. These components were obtained for the observational components of variance corresponding to a sire, maternal grandsire, and dam within maternal grandsire model. From these estimates, direct additive genetic variance (Sigma2A), maternal additive genetic variance (Sigma2M), covariance between direct and maternal additive genetic effects (SigmaAM), variance of permanent environment(Sigma2pe) and temporary environment variance(Sigma2te) were determined. A procedure to approximate restricted maximum likelihood (REML) estimates of the observational components of variance based on the expectation-maximization (EM) algorithm is described. From these results, phenotypic variance ( ) of weaning weight was 667.88 kg2. Values forSigma2A, Sigma2M, Sigma2pe and Sigma2te were 79,30,58,38,49.45, and 469.97 kg2, respectively. Genetic correlation between direct and maternal additive genetic effects was .16.

Evaluation of Simmental carcass EPD estimated using live and carcass data.

This study was conducted to compare carcass EPD predicted using yearling live animal data and/or progeny carcass data, and to quantify the association between the carcass phenotype of progeny and the sire EPD. The live data model (L) included scan weight, ultrasound fat thickness, longissimus muscle area, and percentage of intramuscular fat from yearling (369 d of age) Simmental bulls and heifers. The carcass data model (C) included hot carcass weight, fat thickness, longissimus muscle area, and marbling score from Simmental-sired steers and cull heifers (453 d of age). The combined data model (F) included live animal and carcass data as separate but correlated traits. All data and pedigree information on 39,566 animals were obtained from the American Simmental Association, and all EPD were predicted using animal model procedures. The genetic model included fixed effects of contemporary group and a linear covariate for age at measurement, and a random animal genetic effect. The EPD from L had smaller variance and range than those from either C or F. Further, EPD from F had highest average accuracy. Correlations indicated that evaluations from C and F were most similar, and L would significantly (P < 0.05) re-rank sires compared with models including carcass data. Progeny (n = 824) with carcass data collected subsequent to evaluation were used to quantify the association between progeny phenotype and sire EPD using a model including contemporary group, and linear regressions for age at slaughter and the appropriate sire EPD. The regression coefficient was generally improved for sire EPD from L when genetic regression was used to scale EPD to the appropriate carcass trait basis. The EPD from C and F had similar linear associations with progeny phenotype, although EPD from F may be considered optimal because of increased accuracy. These data suggest that carcass EPD based on a combination of live and carcass data predict differences in progeny phenotype at or near theoretical expectation.

Parameter estimation for carcass traits including growth information of Simmental beef cattle using restricted maximum likelihood with a multiple-trait model.

(Co)variance component estimates were computed for retail cuts per day of age (kilograms per day), cutability (percentage of carcass weight), and marbling score (1 through 11) using a multiple-trait sire model. Restricted maximum likelihood estimates of (co)variance components were obtained via an expectation-maximization algorithm. Carcass data consisted of 8,265 progeny records collected by U.S. Simmental producers. Growth trait information (birth weight, weaning weight, and[or] postweaning gain) for those progeny with carcass data and an additional 5,405 contemporaries formed the complete data set for analysis. A total of 420 sires were represented. Three models differing in number of traits were investigated: 1) carcass traits with growth traits, 2) carcass traits only, and 3) single trait. The final models did not include postweaning gain because of convergence problems. Parameter estimates for all three models were essentially the same. Heritability estimates were .30, .18, and .23 for retail cuts per day, cutability, and marbling score, respectively. Correlations between growth and carcass traits were low except for those with retail cuts per day, which were moderate and positive. The additional information gained by adding growth traits to the carcass-traits-only evaluation lowered prediction error variances most for retail cuts per day. Little change in prediction error variances was found for cutability and marbling score. Inclusion of growth traits in future sire evaluations for carcass traits will benefit the evaluation of retail cuts per day but have considerably less effect on cutability and marbling score.

Estimation of genetic variance and covariance components for weaning weight in Simmental cattle.

The objectives of this study were to estimate genetic parameters for weaning weight of Simmental cattle from data without selective reporting and to examine heterogeneity of parameters with a multiple trait approach. Heterogeneity of (co)variance components (VC) by sex is accounted for in national genetic evaluations for Simmental cattle. Completely reported data were split into bull, heifer, and steer populations to obtain VC estimates. Estimates of direct-maternal genetic correlation were negative, which suggests that selective reporting was not a cause of a negative correlation in Simmental data. However, analyzing only data for males does not account for selection on females and vice versa. Heterogeneous VC for sex were evaluated by analyzing Simmental data using a multiple trait model where male and female data were treated as two traits. Estimates of heritability of direct (maternal) effects were .19 (.07) and .25 (.12) and estimates of the direct-maternal genetic correlation were -.05 and -.20 for males and females, respectively. The multiple trait model fit the data better (P < .01) than the model under the assumption of homogeneous VC.

Maternal influences on growth of twin and single calves.

Milk production was measured at 28-d intervals by the calf weight change method in 30 dams with twins and in 28 dams with single calves. Average adjusted 170-d weaning weights for twins were between 41 and 38 kg less than for singles (depending on linear contrast). Yet dams with twins weaned between 91 and 97 kg more calf and produced substantially more milk. Significant dam breed and parity differences in calf growth and weaning weight were observed among twins. Dam breeds ranked in the order of decreasing productivity were Hereford-Angus crossbred, Angus and Hereford. Cows outproduced heifers. Among singles, such differences were small. As indicated by linear contrasts, maternal effects were larger in twins than in singles; however, these differences were generally not significant. Only milk production in the first half of lactation by dams with twins was found to be a significant predictor of calf growth and weaning weight. For every 1-kg increase in 6-h milk production in early lactation, 170-d adjusted weaning weight of twins increased (P less than .01) by 18.8 kg. Among singles, regression estimates for growth on milk yield were small and nonsignificant.

Variance heterogeneity in direct and maternal weight traits by sex and percent purebred for Simmental-sired calves.

Phenotypic variances for linear and transformed weight traits were partitioned into residual, direct genetic (D) and maternal genetic (M) components using REML techniques with American Simmental Association data from calves born 1969 to 1985. Variance components were estimated separately from subclasses defined by sex (male, female) and percent Simmental (50, greater than or equal to 75). The model included fixed effects of contemporary group and age-of-dam (less than 3, 3 to 5, greater than 5 yr). Additive relationships among sires and maternal grandsires were included. Results follow for a sire-maternal grandsire model for greater than or equal to 75% Simmental untransformed data based on 143,280 male and 281,805 female weaning weights (WW) representing 4,763 and 7,406 sires, respectively. Female results are bracketed. For computational simplification, 47,650 [30,909] postweaning gain (PW) records were included in the analysis only for 114,404 [182,255] calves with birth weight (BW). Phenotypic standard deviations (kg) were: BW, 4.5 [4.1]; WW, 26.9 [23.2]; and PW, 25.9 [19.9]. Heritabilities were: BWD, .40 [.45]; WWD, .32 [.39]; PWD, .26 [.32]; BWM, .13 [.15]; WWM, .20 [.16]; and PWM, .01 [.01]. These heritabilities are higher than previously used for genetic evaluations in this breed. Moderate and positive correlations .26 to .50, existed between direct effects and were similar for both sexes. Direct and maternal effects on the same trait were correlated negatively: BW, -.45 [-.31]; and WW, -.27 [-.34]. Genetic correlation between BWM and WWM was .53 [.49]. First-cross progeny exhibited less genetic and residual variation and had lower heritabilities than Simmental calves of higher percent. Correlations between sire evaluations on the subsets were consistent with those expected given a perfect genetic correlation between traits for each sex and percent Simmental. Logarithmic transformed records were no more homogeneous than untransformed records.

Genetic parameters for carcass traits and their live animal indicators in Simmental cattle.

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.

Comparison of Landim and Africander cattle in southern Mozambique: I. Body weights and growth.

The growth performance of Landim and Africander breeds was compared using data collected from 1968 to 1981 at the Chobela Research Station in Mozambique. Animals from both breeds were managed together in groups by age and sex, except when separated for breeding. Growth traits were body weights at birth, weaning at 7 mo, 18 mo, and first calving, and pre- and postweaning daily growth rates. These traits were analyzed using a mixed-effects least squares model containing breed, year-season of birth, sex, the nested effect of parity within breed, a linear regression on dam's age, and the random effect of sire within breed. Africander calves were 16, 9, and 7% heavier (P < .01) than Landim calves at birth, weaning, and 18 mo (18 +/- 6 kg heavier than the 237-kg Landim average). However, there was no detectable difference for age-adjusted weight at first calving and postweaning daily growth rate. Diminishing weight and growth differences with advancing age may indicate adaptation by the Landim to the prevailing environmental limitations in southern Mozambique, especially through younger ages at puberty and at first calving.

Comparison of Landim and Africander cattle in southern Mozambique: II. Female fertility, reproduction, and beef offtake.

Fertility and reproductive performance of Landim and Africander females were compared using data collected from 1968 to 1981 at the Chobela Research Station in Mozambique. Breeds were managed together and grouped by age and sex, except when separated for breeding. Traits were relative fertility (probability of fertile females calving from the first breeding season), age at first calving, first calving interval, and subsequent calving intervals. calving rates were tested by x2 procedures with equal expected frequencies in each subclass. The statistical model included breed, the random effect of sire within breed, year-season of birth or calving, and calving group within breed. Landim survivors were more fertile (P < .05) than the Africander ones throughout their recorded lifetimes. Landim females were 1.32 +/- .21 mo (or 3%) younger at first calving and had a 48 +/- 12 d (or 11%) shorter interval between first and second calving than the Africander average of 473 d. When reproductive and growth information were combined to compute an annual index of beef offtake expressed as 18-mo calf yield per unit of dam's weight at first calving, Landim cows annually yielded 30% more calf weight (P < .001) than Africander cows per kilogram of their own body maintenance despite lighter body weights at 18 mo. Superior fertility of Landim females led to greater beef offtake from higher calving rates. Greater fertility and relatively less feed to maintain the reproducing herd are probable mechanisms for a population to adapt to nutrient-limiting environments such as the one in southern Mozambique.

Deletion on chromosome 5 associated with decreased reproductive efficiency in female cattle.

Reproductive efficiency is arguably the most economically important trait in commercial beef cattle production, as failure to achieve pregnancy reduces the number of calves marketed per cow exposed to breeding. Identification of variation in the genome with predictive merit for reproductive success would facilitate accurate prediction of daughter pregnancy rate in sires enabling effective selection of bulls producing daughters with improved fertility. Copy number variation (CNV) is one form of structural variation that results in abnormal copies of DNA in the genome. Our lab previously reported a region between 25 and 70 Mb on chromosome 5 associated with reproductive efficiency. To further evaluate this region for genomic variations such as CNV, we initially applied a genomewide association approach based on the >700,000 SNP marker assay and PennCNV analysis to 68 Bos indicus cross females from a large commercial ranch in central Florida. A genomic segment located on chromosome 5, spanning the region of approximately 58.37 to 58.44 Mb (Bovine UMD3.1 assembly) was identified as containing a deletion associated with decreased reproductive efficiency. To verify this deletion, a quantitative real-time PCR test was developed to evaluate additional females in the central Florida and U.S. Meat Animal Research Center (USMARC) populations. The frequency of the homozygous deletion was 7% (23/319) in the central Florida population (Bos indicus cross) for females with 2 consecutive failed breeding seasons and 0% in the USMARC population (predominantly Bos taurus) of low reproductive females. To date, we have not identified the deletion in Bos taurus cattle, suggesting that the deletion is specific to Bos indicus cattle. From these data, we have identified a deletion on chromosome 5 associated with reproductive efficiency in Bos indicus-influenced cattle.