Assessing accuracy of genotype imputation in the Afrikaner and Brahman cattle breeds of South Africa.

Imputation may be used to rescue genomic data from animals that would otherwise be eliminated due to a lower than desired call rate. The aim of this study was to compare the accuracy of genotype imputation for Afrikaner, Brahman, and Brangus cattle of South Africa using within- and multiple-breed reference populations. A total of 373, 309, and 101 Afrikaner, Brahman, and Brangus cattle, respectively, were genotyped using the GeneSeek Genomic Profiler 150 K panel that contained 141,746 markers. Markers with MAF ≤ 0.02 and call rates ≤ 0.95 or that deviated from Hardy Weinberg Equilibrium frequency with a probability of ≤ 0.0001 were excluded from the data as were animals with a call rate ≤ 0.90. The remaining data included 99,086 SNPs and 360 Afrikaner, 75,291 SNPs and 288 animals Brahman, and 97,897 SNPs and 99 Brangus animals. A total of 7986, 7002, and 7000 SNP from 50 Afrikaner and Brahman and 30 Brangus cattle, respectively, were masked and then imputed using BEAGLE v3 and FImpute v2. The within-breed imputation yielded accuracies ranging from 89.9 to 96.6% for the three breeds. The multiple-breed imputation yielded corresponding accuracies from 69.21 to 88.35%. The results showed that population homogeneity and numerical representation for within and across breed strategies, respectively, are crucial components for improving imputation accuracies.

Genotype by environment interaction effects in genetic evaluation of preweaning gain for Line 1 Hereford cattle from Miles City, Montana.

It has long been recognized that genotype × environment interaction potentially influences genetic evaluation of beef cattle. However, this recognition has largely been ignored in systems for national cattle evaluation. The objective of this investigation was to determine if direct and maternal genetic effects on preweaning gain would be reranked depending on an environmental gradient as determined by year effects. Data used were from the 76-yr selection experiment with the Line 1 Hereford cattle raised at Miles City, MT. The data comprised recorded phenotypes from 7,566 animals and an additional 1,862 ancestral records included in the pedigree. The presence of genotype × environment interaction was examined using reaction norms wherein year effects on preweaning gain were hypothesized to linearly influence the EBV. Estimates of heritability for direct and maternal effects, given the average environment, were 10 ± 2 and 26 ± 3%, respectively. In an environment that is characterized by the 5th (95th) percentile of the distribution of year effects, the corresponding estimates of heritability were 18 ± 3 (22 ± 3%) and 30 ± 3% (30 ± 3%), respectively. Rank correlations of direct and maternal EBV appropriate to the 5th and 95th percentiles of the year effects were 0.67 and 0.92, respectively. In the average environment, the genetic trends were 255 ± 1 g/yr for direct effects and 557 ± 3 g/yr for maternal effects. In the fifth percentile environment, the corresponding estimates of genetic trend were 271 ± 1 and 540 ± 3 g/yr, respectively, and in the 95th percentile environment, they were 236 ± 1 and 578 ± 3 g/yr, respectively. Linear genetic trends in environmental sensitivity were observed for both the direct (-8.06 × 10 ± 0.49 × 10) and maternal (8.72 × 10 ± 0.43 × 10) effects. Therefore, changing systems of national cattle evaluation to more fully account for potential genotype × environment interaction would improve the assessment of breeding stock, particularly for direct effects. Estimates of environmental sensitivity parameters could also facilitate identification of genetic limitations to production.

Genetic parameters for tick counts across months for different tick species and anatomical locations in South African Nguni cattle.

The objective of the study was to characterise genetic parameters across months for different tick species and anatomical locations in South African Nguni cattle. Tick counts were conducted monthly, over a 2-year period, on 586 Nguni cattle under natural infestation, from four herds located in different provinces of South Africa. The counts were recorded for six species of ticks (Amblyomma hebraeum, Rhipicephalus evertsi evertsi, Rhipicephalus decoleratus and microplus (Boofilids), Rhipicephalus appendiculatus, Rhipicephalus simus and Hyalomma marginatum) attached on eight anatomical locations on the animals and were summed by species and anatomical location. Heritability estimates, phenotypic and genetic correlations were estimated on a monthly basis using mixed linear models, fitting univariate and bivariate sire models. Fixed effects considered were location, sex, year and age as a covariate. Tick counts were higher in the hot months, and A. hebraeum was the most dominant tick species. Heritability estimates for tick count varied by month and trait and ranged from 0 to 0.89. Genetic correlations were mostly positive, and low to high, with some negative correlations with high standard error. Phenotypic correlations were low to moderate. In general, high genetic correlations were observed between whole body count and the anatomical location counts, suggesting that it may not be necessary to conduct whole body counts. Counts from the belly and perineum appeared to be the most suitable surrogate traits for whole body count. These findings provide useful information for developing strategies for the practical implementation of genetic selection, as a supplement to the traditional tick control measures.

Economic selection index development for Beefmaster cattle II: General-purpose breeding objective.

An economic selection index was developed for Beefmaster cattle in a general-purpose production system in which bulls are mated to a combination of heifers and mature cows, with resulting progeny retained as replacements or sold at weaning. National average prices from 2010 to 2014 were used to establish income and expenses for the system. Genetic parameters were obtained from the literature. Economic values were estimated by simulating 100,000 animals and approximating the partial derivatives of the profit function by perturbing traits 1 at a time, by 1 unit, while holding the other traits constant at their respective means. Relative economic values for the objective traits calving difficultly direct (CDd), calving difficulty maternal (CDm), weaning weight direct (WWd), weaning weight maternal (WWm), mature cow weight (MW), and heifer pregnancy (HP) were -2.11, -1.53, 18.49, 11.28, -33.46, and 1.19, respectively. Consequently, under the scenario assumed herein, the greatest improvements in profitability could be made by decreasing maintenance energy costs associated with MW followed by improvements in weaning weight. The accuracy of the index lies between 0.218 (phenotypic-based index selection) and 0.428 (breeding values known without error). Implementation of this index would facilitate genetic improvement and increase profitability of Beefmaster cattle operations with a general-purpose breeding objective when replacement females are retained and with weaned calves as the sale end point.

Genetic variance and covariance and breed differences for feed intake and average daily gain to improve feed efficiency in growing cattle.

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.

Potential emigration of Siberian cattle germplasm on Chirikof Island, Alaska.

Feral cattle residing in Chirikof Island, Alaska, are relatively distinct from breeds used in commercial production in North America. However, preliminary evidence suggested that they exhibit substantial genetic relationship with cattle from Yakutian region of Siberia. Thus, our objective was to further elucidate quantify the origins, admixture and divergence of the Chirikof Island cattle relative to cattle from Siberia and USA. Subject animals were genotyped at 15 microsatellite loci. Compared with Turano-Mongolian and North American cattle, Chirikof Island cattle had similar variation, with slightly less observed heterozygosity, fewer alleles per locus and a positive fixation index. Analysis of the genetic distances revealed two primary clusters; one that contained the North American breeds and the Kazakh White head, and a second that contained the Yakutian and Kalmyk breeds, and the Chirikof population. Thus, it is suggested that Chirikof Island cattle may be a composite of British breeds emanating from North America and Turano-Mongolian cattle. A potential founder effect, consistent with historical records of the Russian-American period, may contribute to the adaptation of the Chirikof Island cattle to their harsh high-latitude environment. Further study of adaptive mechanisms manifest by these cattle is warranted.

Economic selection index development for Beefmaster cattle I: Terminal breeding objective.

The objective of this study was to develop an economic selection index for Beefmaster cattle in a terminal production system where bulls are mated to mature cows with all resulting progeny harvested. National average prices from 2010 to 2014 were used to establish income and expenses for the system. Phenotypic and genetic parameter values among the selection criteria and goal traits were obtained from literature. Economic values were estimated by simulating 100,000 animals and approximating the partial derivatives of the profit function by perturbing traits one at a time, by 1 unit, while holding the other traits constant at their respective means. Relative economic values (REV) for the terminal objective traits HCW, marbling score (MS), ribeye area (REA), 12th-rib fat (FAT), and feed intake (FI) were 91.29, 17.01, 8.38, -7.07, and -29.66, respectively. Consequently, improving the efficiency of beef production is expected to impact profitability greater than improving carcass merit alone. The accuracy of the index lies between 0.338 (phenotypic selection) and 0.503 (breeding values known without error). The application of this index would aid Beefmaster breeders in their sire selection decisions, facilitating genetic improvement for a terminal breeding objective.

Effects of reduced in utero and post-weaning nutrition on milk yield and composition in primiparous beef cows.

Development and long-term retention of replacement beef females in a semi-arid environment are of a major concern for extensive livestock producers. Furthermore, the demand of not only producing a thriving, healthy calf, but having sufficient milk to support that first calf is essential. To address this issue, we conducted a 3-year study measuring milk production and milk constituent yields in primiparous beef heifers (n=48; 16/year reared under two different feeding regimens) raising steer calves. Cows received 1.8 or 1.2 kg/day winter supplementation for ~80 day before parturition and their heifer calves were then randomly assigned to heifer development treatments that provided ad libitum (AL) or 80% (less than ad libitum (LAL)) of ad libitum feed post weaning. Heifers developed on the AL treatment also received 1.8 kg/day winter supplementation for life, whereas heifers developed on the LAL treatment received 1.2 kg/day winter supplementation for life. Milk production of primiparous cows was measured with a portable milking machine every other week from days 27 to 125 postpartum. Milk yield for the 125-day lactation period was calculated from area under the lactation curve approximated by trapezoidal summation. The ANOVA model included in utero winter nutrition, post-weaning heifer development treatment, year and their interaction. Heifers subjected to the AL treatment reached peak milk yield ~12.3 day later (P=0.02) than heifers receiving LAL treatment. In addition, an in utero nutrition×post-weaning heifer treatment×year interaction existed (P⩽0.04) for milk peak yield, average daily milk yield (kg/day) and nutrient composition (protein, lactose, fat, solids non-fat, g/day). These interactions manifest as changes in magnitude and rank across the 3 years of the study. Livestock production in extensive environments is subject to variations in seasonal precipitation patterns and quality and quantity of grazeable forage and these fluctuations have a large impact on milk yield. In summary, the gestational nutritional environment of a heifer's mother may interact with the heifer's nutrient consumption during post-weaning growth and the current year to trigger variation in year-to-year milk production.

Genome-wide association study of tick resistance in South African Nguni cattle.

Ticks and tick-borne diseases are among the main causes of economic loss in the South African cattle industry through high morbidity and mortality rates. Concerns of the general public regarding chemical residues may tarnish their perceptions of food safety and environmental health when the husbandry of cattle includes frequent use of acaricides to manage ticks. The primary objective of this study was to identify single nucleotide polymorphism (SNP) markers associated with host resistance to ticks in South African Nguni cattle. Tick count data were collected monthly from 586 Nguni cattle reared in four herds under natural grazing conditions over a period of two years. The counts were recorded for six species of ticks attached in eight anatomical locations on the animals and were summed by species and anatomical location. This gave rise to 63 measured phenotypes or traits, with results for 12 of these traits being reported here. Tick count (x) data were transformed using log10(x+1) and the resulting values were examined for normality. DNA was extracted from hair and blood samples and was genotyped using the Illumina BovineSNP50 assay. After quality control (call rate >90%, minor allele frequency >0.02), 40,436 SNPs were retained for analysis. Genetic parameters were estimated and association analysis for tick resistance was carried out using two approaches: a genome-wide association (GWA) analysis using the GenABEL package and a regional heritability mapping (RHM) analysis. The Bonferroni genome-wide (P<0.05) corrected significance threshold was 1.24×10(-6), with 2.47×10(-5) as the suggestive significance threshold (P<0.10) (i.e., one false positive per genome scan) in the GWA analysis. Likelihood ratio test (LRT) thresholds for genome-wide and suggestive significance were 13.5 and 9.15 for the RHM analysis. Six ixodid tick species were identified, with Amblyomma hebraeum (the vector for Heartwater disease) being the dominant species. Heritability estimates (h(2)) from the fitted animal and sire models ranged from 0.02±0.00 to 0.17±0.04 for the transformed tick count data. Several genomic regions harbouring quantitative trait loci (QTL) were identified for different tick count traits by both the GWA and RHM approaches. Three genome-wide significant regions on chromosomes 7, 10 and 19 were identified for total tick count on the head, total body A. hebraeum tick count and total A. hebraeum on the perineum region, respectively. Additional regions significant at the suggestive level were identified on chromosomes 1, 3, 6, 7, 8, 10, 11, 12, 14, 15, 17, 19 and 26 for several of the traits. The GWA approach identified more genomic regions than did the RHM approach. The chromosomal regions identified here as harbouring QTL underlying variation in tick burden form the basis for further analyses to identify specific candidate genes and polymorphisms related to cattle tick resistance and provide the potential for marker-assisted selection in Nguni cattle.

Origins of cattle on Chirikof Island, Alaska, elucidated from genome-wide SNP genotypes.

Feral livestock may harbor genetic variation of commercial, scientific, historical or esthetic value. The origins and uniqueness of feral cattle on Chirikof Island, Alaska, are uncertain. The island is now part of the Alaska Maritime Wildlife Refuge and Federal wildlife managers want grazing to cease, presumably leading to demise of the cattle. Here we characterize the cattle of Chirikof Island relative to extant breeds and discern their origins. Our analyses support the inference that Yakut cattle from Russia arrived first on Chirikof Island, then ~120 years ago the first European taurine cattle were introduced to the island, and finally a large wave of Hereford cattle were introduced on average 40 years ago. In addition, this mixture of European and East-Asian cattle is unique compared with other North American breeds and we find evidence that natural selection in the relatively harsh environment of Chirikof Island has further impacted their genetic architecture. These results provide an objective basis for decisions regarding conservation of the Chirikof Island cattle.

Rapid Communication: Variance component estimates for Charolais-sired fed cattle and relative economic impact of bovine respiratory disease.

Variance components were estimated and relative economic importance of bovine respiratory disease (BRD) was derived from 3 yr of performance, morbidity, and mortality data collected from a single beef cattle finishing operation. One thousand one hundred eighty nine of 12,812 Charolais-sired calves were treated for BRD during the finishing period. Weaning weight (WW), DMI, days to harvest (D2H), HCW, yield grade (YG), and marbling score determined by image analysis (MARB) were collected to quantify the economic impact associated with treatment for BRD. Observed means and (co)variances for carcass and production traits were used to simulate populations of 10,000 healthy and 10,000 BRD treated calves. A bio-economic model was developed to derive the economic value associated with the incidence and number of treatments for BRD during the finishing period. Carcasses from healthy calves were worth $58.28 more on average compared to calves treated at least once for BRD. Heritability estimates for BRD were 0.15 when the trait was measured as number of treatments (0 to 4), and 0.14 when measured as incidence (0 or 1). The model indicated that D2H had the lowest relative economic importance in this system, with a cost of $1.91 per head for each additional day on feed. Furthermore, the relative economic value of BRD morbidity was approximately 10.65 greater than D2H when recording the BRD phenotype as the number of BRD treatments. The economic values of HCW, WW, and DMI were 11.47, 5.15, and 3.61 times more important than D2H, respectively. This indicates BRD morbidity has the second greatest relative economic value in this system, with a one percent increase in morbidity associated with an average loss of $2.08 per head. These results indicate that BRD morbidity can have an equal or greater economic importance when compared to carcass and production traits during the finishing period. Further, this indicates the opportunity exists to increase the genetic merit for profitability during the finishing period by incorporating BRD incidence into terminal-sire selection indexes.

Genetic gain and economic values of selection strategies including semen traits in three- and four-way crossbreeding systems for swine production.

Four semen traits: volume (VOL), concentration (CON), progressive motility of spermatozoa (MOT), and abnormal spermatozoa (ABN) provide complementary information on boar fertility. Assessment of the impact of selection for semen traits is hindered by limited information on economic parameters. Objectives of this study were to estimate economic values for semen traits and to evaluate the genetic gain when these traits are incorporated into traditional selection strategies in a 3-tier system of swine production. Three-way (maternal nucleus lines A and B and paternal nucleus line C) and 4-way (additional paternal nucleus line D) crossbreeding schemes were compared. A novel population structure that accommodated selection for semen traits was developed. Three selection strategies were simulated. Selection Strategy I (baseline) encompassed selection for maternal traits: number of pigs born alive (NBA), litter birth weight (LBW), adjusted 21-d litter weight (A21), and number of pigs at 21 d (N21); and paternal traits: number of days to 113.5 kg (D113), backfat (BF), ADG, feed efficiency (FE), and carcass lean % (LEAN). Selection Strategy II included Strategy I and the number of usable semen doses per collection (DOSES), a function of the 4 semen traits. Selection Strategy III included Strategy I and the 4 semen traits individually. The estimated economic values of VOL, CON, MOT, ABN, and DOSES for 7 to 1 collections/wk ranged from $0.21 to $1.44/mL, $0.12 to $0.83/10 spermatozoa/mm, $0.61 to $12.66/%, -$0.53 to -$10.88/%, and $2.01 to $41.43/%, respectively. The decrease in the relative economic values of semen traits and DOSES with higher number of collections per wk was sharper between 1 and 2.33 collections/wk than between 2.33 and 7 collections/wk. The higher economic value of MOT and ABN relative to VOL and CON could be linked to the genetic variances and covariances of these traits. Average genetic gains for the maternal traits were comparable across strategies. Genetic gains for paternal traits, excluding semen traits, were greater in selection Strategy I than Strategies III and II. Genetic gains for paternal and maternal traits were greater in the 4- and 3-way schemes, respectively. The selection strategy including the 4 semen traits is recommended because this approach enables genetic gains for these traits without compromising the genetic gains for maternal traits and with minimal losses in genetic gains for paternal traits.

Influence of Miles City Line 1 on the United States Hereford population.

The goal of this research was to document the influence of Line 1 (L1) Hereford cattle, developed by the USDA at its research facility in Miles City, MT, on the U.S. Hereford population. The L1 Hereford population originated in 1934 and has been thereafter maintained as a closed herd at that location. Dissemination of germplasm began in 1948. Pedigree data for approximately 14 million cattle recorded by the American Hereford Association (AHA) were used. A preliminary experiment was conducted to establish sample size necessary to estimate the pedigree relationship between L1 and the recorded Hereford population. Five random samples of 100, 400, 500, and 3,000 calves were drawn from the sets of calves born in 1980, 1990, and 2000. Sampled calves were pseudo mated to L1 sires from the decades 1968 to 1978, 1978 to 1988, and 1988 to 1998, respectively. Inbreeding coefficients were calculated for the resulting "offspring" and the relationship of each sampled animal to L1 was taken to be twice the maximum inbreeding coefficient for the set of L1 sires used in the pseudo matings. Based on the results of this experiment, it was decided that a sample size of 400 animals per replicate was sufficient to estimate the relationship between L1 and the general Hereford population recorded by the AHA. In a second experiment, 5 sets of 400 animals were drawn from the AHA herdbook representing each year from 1980 to 2008 and pseudo mated to L1 sires and their relationship to L1 calculated as described above. Over the period, the number of animals recorded by the AHA that were related to L1 increased by 1.69 ± 0.07% per year. The L1 Hereford population was ancestral to 79% of Hereford cattle recorded in 2006 through 2008. The greatest concentration of animals related to L1 was in the Great Plains and eastern Corn Belt of the United States, but animals related to L1 were found in 48 states. In a third experiment, 240 L1 Hereford cattle and 311 sires representative of the Hereford breed in the United States were genotyped using the Illumina BovineSNP50 BeadChip. Resulting genotypes were used to assess the probability that the animals sampled from the U.S. population were members of L1. The average probability of membership in L1 was 0.20 and the regression of genomic probability of membership on pedigree relationship was 1.73 ± 0.11 (r = 0.65). These results document the far-reaching and profound impact of a long-term research program.

Circulating bovine pregnancy associated glycoproteins are associated with late embryonic/fetal survival but not ovulatory follicle size in suckled beef cows.

The objective was to examine the relationship between ovulatory follicle size and embryo and fetal survival by using circulating concentrations of bovine pregnancy associated glycoproteins (bPAG) to detect the presence of an embryo or fetus and monitor placental function. Before examining the relationship between bPAG, ovulatory follicle size, and embryo and fetal survival, the half-life of bPAG was determined in Exp. 1. The half-life of bPAG after PGF2α-induced abortion on d 32 to 36 postinsemination was 35.8 ± 21.9 h (mean ± SD; range 7.1 to 78.5 h). In Exp. 2, suckled beef cows (n = 91) were treated with the CO-Synch protocol (GnRH on d -9, PGF2α on d -2, and GnRH and AI 48 h later [d 0]) and classified into 1 of 2 ovulatory follicle size groups: 1) small follicle (<12.5 mm; n = 25) or 2) large follicle (≥ 12.5 mm; n = 66). The first increase (P < 0.0001) in serum bPAG occurred in pregnant cows on d 24 after insemination and circulating bPAG decreased before a decrease in progesterone in 3 of 4 cows that lost an embryo or fetus. Pattern of secretion of bPAG in serum from d 24 to 60 after insemination (d 0) was affected by day (P < 0.0001), but not ovulatory follicle size. In Exp. 3, suckled beef cows (n = 1164) were administered the CO-Synch protocol either with (donor cows; n = 810) or without (recipient cows; n = 354) AI on d 0. Single embryos (n = 394) or oocytes (n = 45) were recovered from the donor cows [d 7; embryo transfer (ET)] and all live embryos were transferred into recipients the same day. Cows were classified on d 0 as having a small (<12.5 mm) or large (≥ 12.5 mm) ovulatory follicle, and randomly chosen as donors or recipients to remove confounding effects of ovulatory follicle size on fertility. Serum concentration of bPAG at d 28 was not affected by ovulatory follicle size (P = 0.85), embryo stage at ET (P = 0.75), embryo quality at ET (P = 0.64), estradiol at GnRH2 (P = 0.62) or serum progesterone at ET (d7; P = 0.14). Compared with cows that maintained pregnancy (n = 176), cows that exhibited late embryonic or fetal mortality (n = 19) after d 28 had decreased (P < 0.05) concentrations of bPAG on d 28. In summary, there was no relationship between serum bPAG and ovulatory follicle size or embryo stage or quality at ET; however, cows that lost an embryo after d 28 had reduced concentrations of bPAG on d 28 compared with cows that maintained pregnancy.

Preovulatory estradiol and the establishment and maintenance of pregnancy in suckled beef cows.

In postpartum beef cows, GnRH-induced ovulation of small dominant follicles decreased pregnancy rates and increased late embryonic/fetal mortality. In Exp. 1, single ovulation reciprocal embryo transfer (ET) was used to examine the relationship between preovulatory serum concentrations of estradiol at GnRH-induced ovulation in donor and recipient cows and establishment and maintenance of pregnancy. Suckled beef cows (n = 1,164) were administered GnRH (GnRH1, 100 µg) on d -9 (GnRH1), PGF(2α) on d -2, and GnRH2 (GnRH2, 100 µg) on d 0 (CO-Synch protocol) either with (donors; n = 810) or without (recipients; n = 354) AI. Single embryos (n = 394) or oocytes (n = 45) were recovered from the donor cows (d 7; ET) and all live embryos were transferred into recipients. Serum concentration of estradiol at GnRH2 was positively correlated with follicle size at GnRH2 (r = 0.45, P < 0.01) and progesterone at ET (r =0.34, P < 0.01). Donor cows with greater estradiol at GnRH2 were more likely to yield an embryo than an unfertilized oocyte (P < 0.01). Donor and recipient cows were retrospectively divided into 4 groups [low estradiol (<8.4 pg/mL) or high estradiol (≥8.4 pg/mL)] based on serum concentration of estradiol at GnRH2. Pregnancy rate at d 27 for low-low (n = 78), low-high (n = 80), high-low (n = 91), and high-high (n = 101) groups (donor-recipient, respectively) was 45, 65, 43, and 61% respectively (P < 0.02). Because recipient cows with greater estradiol concentration at GnRH2 had greater pregnancy rates in Exp. 1, the objective of Exp. 2 was to evaluate the effect of estradiol supplementation on pregnancy rate. Ovulation was synchronized in suckled beef cows (n = 600) using the CO-Synch protocol with the insertion of a controlled internal drug release (CIDR; intravaginal progesterone supplement) from d -9 until d -2. Approximately one-half of the cows (n = 297) received an injection of estradiol cypionate (ECP; 0.5 mg intramuscularly) 24 h before AI. Compared with the no treatment (Control) cows, ECP treatment increased (P < 0.01) pregnancy rates of cows induced to ovulate smaller dominant follicles (<12.2 mm). In conclusion, GnRH-induced ovulation of small dominant follicles was associated with reduced serum estradiol, fertilization rate (donor cows), and pregnancy establishment (recipient cows). Furthermore, ECP supplementation during the preovulatory period increased pregnancy rates in cows induced to ovulate smaller dominant follicles.

Triennial Reproduction Symposium: influence of follicular characteristics at ovulation on early embryonic survival.

Reproductive failure in livestock can result from failure to fertilize the oocyte or embryonic loss during gestation. Although fertilization failure occurs, embryonic mortality represents a greater contribution to reproductive failure. Reproductive success varies among species and production goals but is measured as a binomial trait (i.e., pregnancy), derived by the success or failure of multiple biological steps. This review focuses primarily on follicular characteristics affecting oocyte quality, fertilization, and embryonic health that lead to pregnancy establishment in beef cattle. When estrous cycles are manipulated with assisted reproductive technologies and ovulation is induced, duration of proestrus (i.e., interval from induced luteolysis to induced ovulation), ovulatory follicle growth rate, and ovulatory follicle size are factors that affect the maturation of the follicle and oocyte at induced ovulation. The most critical maturational component of the ovulatory follicle is the production of sufficient estradiol to prepare follicular cells for luteinization and progesterone synthesis and prepare the uterus for pregnancy. The exact roles of estradiol in oocyte maturation remain unclear, but cows that have lesser serum concentrations of estradiol have decreased fertilization rates and decreased embryo survival on d 7 after induced ovulation. When length of proestrus is held constant, perhaps the most practical follicular measure of fertility is ovulatory follicle size because it is an easily measured attribute of the follicle that is highly associated with its ability to produce estradiol.

Pregnancy establishment and maintenance in cattle.

A single ovulation, reciprocal embryo transfer study was used to investigate effects of oocyte competence and maternal environment on pregnancy establishment and maintenance in beef cows. Estrous cycles were synchronized in suckled beef cows and embryo donors were inseminated on d 0 (n = 810). Cows were classified on d 0 as having a small (<12.5 mm) or large (≥12.5 mm) ovulatory follicle and randomly chosen as donors or recipients to remove confounding effects of ovulatory follicle size on fertility. Embryos (n = 393) or oocytes (n = 44) were recovered on d 7, and all viable embryos were transferred into recipients (n = 354). All statistical analyses were conducted using the GLM procedure of SAS. Path analysis (with significance set at P < 0.10) was used to examine potential cause-effect relationships among the measured variables. Greater donor cow BW, circulating estradiol concentration at insemination, postpartum interval, and ovulatory follicle size directly increased (P < 0.10) fertilization success. Greater donor cow age was the only factor that directly decreased (P < 0.10) fertilization success. Viability of d-7 embryos was directly inhibited (P < 0.10) by rapid follicular growth rate from d -2 to 0 and heavier BW. Direct beneficial effects to embryo viability were increased serum progesterone concentration on d -2 and ovulatory follicle size. Pregnancy maintenance from d 7 to 27 was enhanced (P < 0.10) by increased serum estradiol concentration on d 0 and progesterone concentration on d 7 in the recipient cow. Increased follicular diameter in the recipient cow on d 0 was detrimental to pregnancy maintenance from d 7 to 27. This manuscript defines the complex interplay and relative contributions of endocrine and physical factors both prior and subsequent to fertilization that influence both oocyte competence and maternal environment and their roles in establishment and maintenance of pregnancy.

Effects of reduced panel, reference origin, and genetic relationship on imputation of genotypes in Hereford cattle.

The objective of this study was to investigate alternative methods of designing and using reduced SNP panels for imputing SNP genotypes. Two purebred Hereford populations, an experimental population known as Line 1 Hereford (L1, n = 240) and registered Hereford with American Hereford Association (AHA, n = 311), were used. Using different reference samples of 62 to 311 animals with 39,497 SNP on 29 autosomes and study samples of 57 or 62 animals for which genotypes were available for ~2,600 SNP (reduced panels), imputations were performed to predict the other ~36,900 loci that had been masked. An imputation package, including LinkPHASE and DAGPHASE, was used for imputation. Four reduced panels differing in minor allele frequency (MAF) and marker spacing were evaluated. Reduced panels included every 15th SNP across the genome (SNP_space), commercial Illumina Bovine3K Beadchip (SNP_3K), SNP with the highest MAF (SNP_MAF), and SNP with high MAF that were also evenly spaced across the genome (SNP_MS). Imputation accuracy was defined as the correlation of imputed genotypes and real genotypes. Reference samples were either from L1 or AHA. Among animals with genotypes, genetic relationships were estimated based on molecular marker genotypes or pedigree. Reduced panel design, number of animals in the reference sample, reference origin and genetic relationship between animals in the reference, and study samples all affected imputation accuracy (P < 0.001). Across genotyping schemes, imputed genotypes from SNP_MS had the greatest accuracy. A 0.1 increase in average pedigree relationship or average molecular relationship between reference and study samples increased imputation accuracy 10 to 20%. Using reference samples from the L1 population resulted in lower imputation accuracy than using reference samples from the admixed population AHA (P < 0.001). Increasing the number of animals in the reference panel by 100 individuals increased imputation accuracy by 8% when pedigree relationship was used as a covariate and 6% when molecular relationship was used as a covariate. We concluded that imputation accuracy would be increased through optimization of reduced panel design and genotyping strategy.

Using 50 k single nucleotide polymorphisms to elucidate genomic architecture of line 1 hereford cattle.

Hereford is a major beef breed in the USA, and a sub-population, known as Line 1 (L1), was established in 1934 using two paternal half-sib bulls and 50 unrelated females. L1 has since been maintained as a closed population and selected for growth to 1 year of age. Objectives were to characterize the molecular genetic architecture of L1 (n = 240) by comparing a cross-section of L1 with the general US. Hereford population (AHA, n = 311), estimating effects of imposed selection within L1 based on allele frequencies at 50 K SNP loci, and examining loci-specific effects of heterozygosity on the selection criterion. Animals were genotyped using the Illumina BovineSNP50 Beadchip, and SNP were mapped to UMD3.0 assembly of the bovine genome sequence. Average linkage disequilibrium (LD), measured by square of Pearson correlation, of adjacent SNP was 0.36 and 0.16 in L1 and AHA, respectively. Difference in LD between L1 and AHA decreased as SNP spacing increased. Persistence of phase between L1 and AHA decreased from 0.45 to 0.14 as SNP spacing increased from 50 to 5,000 kb. Extended haplotype homozygosity was greater in L1 than in AHA for 95.6% of the SNP. Knowledge of selection applied to L1 facilitated a novel approach to QTL discovery. Minor allele frequency was (FDR < 0.01) affected by cumulative selection differential at 191 out of 25,901 SNP. With the FDR relaxed to 0.05, 13 regions on BTA2, 5, 6, 9, 11, 14, 15, 18, 23, and 26 are co-located with previously identified QTL for growth. After adjustment of postweaning gain phenotypes for fixed effects and direct additive genetic effects, regression of residuals on genome-wide heterozygosity was -235.3 ± 91.6 kg. However, no SNP-specific loci where heterozygotes were significantly superior to the average of homozygotes were revealed (FDR ≥ 0.17). In conclusion, genome-wide SNP genotypes clarified effects of selection and inbreeding within L1 and differences in genomic architecture between the population segment L1 and the AHA population.

A prototype national cattle evaluation for feed intake and efficiency of Angus cattle.

Recent improvement in technologies for measuring individual feed intake has made possible the collection of data suitable for breed-wide genetic evaluation. The goals of this research were to estimate genetic parameters for components of feed efficiency and develop a prototype system for conducting a genetic evaluation of Angus cattle for feed intake. Weaning weight (WWT), postweaning BW gain (PGN), subcutaneous fat depth (SQF), and feed intake data were accumulated by the American Angus Association from a variety of cooperators and augmented with data collected for routine genetic evaluation of Angus cattle. The feed intake data were standardized (SFI, mean 0 and variance 1) within contemporary groups. Numbers of animals with observed phenotypes were 18,169, 7,107, 4,976, and 4,215 for WWT, PGN, SQF, and SFI, respectively. The 4-generation pedigree for animals with records contained 45,120 individuals. (Co)variance components were estimated with ASREML, fitting a 4-trait animal model with fixed contemporary groups for WWT, PGN, SQF, and SFI. Heritability estimates were 0.33 ± 0.03, 0.31 ± 0.04, 0.26 ± 0.04, and 0.42 ± 0.05 for direct genetic effects on WWT, PGN, SQF, and SFI, respectively. Genetic correlations of WWT and PGN with SFI were 0.40 ± 0.07 and 0.55 ± 0.10, respectively, and indicate their value as indicator traits in predicting EPD for feed intake. The genetic correlation of SQF and SFI was not different from 0. For all animals with a recorded feed intake phenotype, accuracy of their EPD for feed intake ranged from 0.16 to 0.64 with a mean of 0.26. However, 9,075 animals had an accuracy that was equal to or exceeded 0.2 for their feed intake EPD. Postanalysis calculation of measures of efficiency EPD was pursued. This work demonstrates the feasibility of conducting a national cattle evaluation for feed intake using indicator traits to reduce opportunity for selection bias, increase accuracy of the evaluation for a substantial number of animals, and ultimately facilitate calculation of selection indexes including feed intake.