Genetic parameters for oocytes and embryo production and their association with linear type traits in dairy Gyr Cattle.

In vitro embryo production is one of the main reproductive techniques used in dairy Gyr cattle. In addition, linear type measures are well characterized and have been used in dairy Gyr breed selection for the last 4 decades. The estimation of genetic parameters for the number of aspirated oocytes and in vitro-produced embryos associated with the linear type measures would support genetic progress for animal breeding programs toward embryo production. This study aimed to estimate genetic parameters for aspirated oocytes, embryo in vitro production, and linear type traits, exploring the association between them. The repeatability model was applied to 14,251 ovum pick-up events from 1,916 Gyr donors. A subset of 604 donors from the same group had their body measurements taken. Single- and 2-trait analyses were carried out using the BLUPF90 family programs. Heritability estimates of 0.38, 0.34, and 0.20 were obtained for total oocytes, viable oocytes, and embryos, respectively,-and the heritability of the linear type traits ranged from 0.22 to 0.40. High genetic correlations between total oocytes and viable oocytes (0.99), and between oocytes (total and viable) and embryos (0.83) were obtained. Low to high genetic (-0.07 to 0.92) and phenotypic (0.32 to 0.86) correlations were obtained between the linear type traits. Moreover, low phenotypic correlations (0.01 to 0.13) were observed for oocytes (total and viable) and embryos with the linear type traits, whereas low to moderate genetic correlations (0.07 to 0.42) were observed between the same traits, especially for ilium width (0.42), rump area (0.38), and hip height (0.33). Thus, selection for in vitro production is achievable in Gyr dairy cattle, and superior genetic progress is associated with the selection of oocytes (total and viable). Furthermore, the moderate genetic association between oocytes and embryos with linear type traits, especially ilium width suggests that progress on in vitro embryo production may be achieved by accessing these measurements.

Candidate genes for longitudinal traits under sequential sampling in beef cattle.

Both the measurement age of a longitudinal trait and the common pre-sampling procedures used in beef cattle herds may affect the identification of a functional candidate gene (FCG) that is potentially associated with a trait. To identify the FCG that takes part in the genetic control of body weight at five different ages in a beef cattle population with and without sequential sampling, the animals were weighed at different measurement events, around 330, 385, 440, 495 and 550 days old. Genetic parameters were estimated for body weight at each age using a single trait (STM) and a random regression model (RRM). In addition, two different databases were used to estimate the genetic parameters: the first (DB100) was formed by all animals that were weighed in the five measurement events, and the second (DB70) has records of the same population, considering that 70% of the heaviest animals were selected after each measurement event. For DB100, genome-wide association studies (GWAS) were performed with 21,667 SNP markers to identify genomic windows that explained at least 1% of the genetic variance. Additionally, prioritization analyses were performed and FCGs were selected. We associated seven different FCGs with body weight at different ages. Among them, the gene DUSP10 was suggested as FCG in all five ages evaluated. Genetic parameters estimated for body weight using DB100 were similar when STM and RRM were applied. However, when DB70 was used as phenotypic data, there were differences between the two models. When the STM was applied, there were differences between the genetic parameters estimated for body weight when DB100 or DB70 were used as sources of phenotypes, but not for the estimates obtained with RRM. The importance of each gene for animal growth can change at different ages, and different genes may be more relevant to body weight at each different growth stage for beef cattle. Besides, sequential sampling can affect the GWAS results of a longitudinal trait. The age of the animal when a longitudinal trait is measured and pre-sampling can also contribute to inconsistencies in GWAS results for body weight in beef cattle, depending on the time when that data were collected, and consequently on the identification of FCG between studies, even when models that consider a covariance structure are used.

Multivariate analysis of herd structure and genetic resource indicators in seedstock beef cattle herds.

Genetic, environmental, technological and financial resources are used differently in cattle herds that participate in the same breeding programme. The percentages of calves sired by sires within their own herd or from external herds vary across herds, as do the intensities of use of reproductive biotechnologies. These divergences may be related to differences in the indicators of genetic performance for economic traits. The aim of this study was to determine the factors related to herd structure and genetic resource utilization that exert the greatest influence on the genetic merit of seedstock herds within a Nellore breeding programme. The database comprised 21 factors, along with genomic-enhanced expected progeny differences (GE-EPDs) for growth, reproductive and carcass traits, as well as a selection index of animals from 128 herds. By combining principal component analysis and cluster analysis, we were able to group the herds. We identified statistically significant differences (p < 0.05) in the mean values of the factors, GE-EPDs and genetic trends among the groups of herds. Differences in the percentage of sires from external herds and in sire age between the groups of herds were the factors most associated with differences in mean GE-EPDs and genetic trends. Using young sires from other herds or lineages is an effective strategy in animal breeding. By enhancing genetic variability, this approach does not only improve the genetic quality of herds but also accelerates genetic progress in desired traits over time. Therefore, to ensure the success of this strategy, it is crucial that seedstock herds undergo a thorough selection process aimed at maximizing the genetic potential of future generations of beef cattle.

Unravelling the genetic variability of host resilience to endo- and ectoparasites in Nellore commercial herds.

BACKGROUND: Host resilience (HR) to parasites can affect the performance of animals. Therefore, the aim of this study was to present a detailed investigation of the genetic mechanisms of HR to ticks (TICK), gastrointestinal nematodes (GIN), and Eimeria spp. (EIM) in Nellore cattle that were raised under natural infestation and a prophylactic parasite control strategy. In our study, HR was defined as the slope coefficient of body weight (BW) when TICK, GIN, and EIM burdens were used as environmental gradients in random regression models. In total, 1712 animals were evaluated at five measurement events (ME) at an average age of 331, 385, 443, 498, and 555 days, which generated 7307 body weight (BW) records. Of the 1712 animals, 1075 genotyped animals were used in genome-wide association studies to identify genomic regions associated with HR. RESULTS: Posterior means of the heritability estimates for BW ranged from 0.09 to 0.54 across parasites and ME. The single nucleotide polymorphism (SNP)-derived heritability for BW at each ME ranged from a low (0.09 at ME.331) to a moderate value (0.23 at ME.555). Those estimates show that genetic progress can be achieved for BW through selection. Both genetic and genomic associations between BW and HR to TICK, GIN, and EIM confirmed that parasite infestation impacted the performance of animals. Selection for BW under an environment with a controlled parasite burden is an alternative to improve both, BW and HR. There was no impact of age of measurement on the estimates of genetic variance for HR. Five quantitative trait loci (QTL) were associated with HR to EIM but none with HR to TICK and to GIN. These QTL contain genes that were previously shown to be associated with the production of antibody modulators and chemokines that are released in the intestinal epithelium. CONCLUSIONS: Selection for BW under natural infestation and controlled parasite burden, via prophylactic parasite control, contributes to the identification of animals that are resilient to nematodes and Eimeria ssp. Although we verified that sufficient genetic variation existed for HR, we did not find any genes associated with mechanisms that could justify the expression of HR to TICK and GIN.

Benchmarking in a beef cattle breeding program: Lessons from the best breeders.

Beef cattle breeding programs offer genetic evaluations and consulting services on animal breeding practices to help breeders improve the genetic merit of their herds. Some breeders are more willing to apply best practices and technologies than others. Consequently, the average genetic merit and genetic trends differ across herds. We benchmarked some parameters of an average herd (AVE) and the corresponding parameters of herds with higher genetic merit (TOP), both participating in a commercial Nellore breeding program. Expected progeny differences (EPD) for growth, reproductive and carcass traits and a selection index (SI) of animals born from 2005 to 2019 on 128 farms located in Brazil, Bolivia and Paraguay were used to compute the AVE parameters. The 20 herds with higher mean SI of animals born in the last five birth seasons were classified as TOP herds. The mean SI and EPD of animals born in the last five seasons in the TOP herds were, respectively, 89% and 79% to 206% higher (p ≤ 0.001) than those of animals from the AVE herd. Genetic trends over the entire period were also higher (50% for SI and 31% to 88% separately for each trait, p ≤ 0.006) in the TOP herds compared to the AVE herd. Although the difference in the numbers of cows, bulls and calves between the TOP and AVE herds did not reach statistical significance (p = 0.175, p = 0.273 and p = 0.061, respectively), the numbers of progeny per cow and per bull were 21% (p = 0.012) and 26% (p = 0.047) higher in the TOP herds, respectively. Multiple ovulation and embryo transfer and in vitro fertilization and embryo transfer (MOET/IVF) accounted for a higher percentage of births in the TOP herds compared to AVE (24.6% vs. 12.5%, p = 0.002). The generation interval was 17% shorter (p < 0.001) in the TOP herds compared to AVE. The average inbreeding coefficient of animals from the TOP herds (1.08 ± 0.52%) did not differ (p = 0.78) from that of AVE animals (1.26 ± 0.96%). In general, AVE herds are evolving in the desirable direction but differences in genetic merit between AVE and TOP herds are increasing over time. The more frequent use of MOET/IVF, a lower cow-to-bull ratio, and a larger family size (progeny per cow or per bull) can help achieve larger selection differentials and increase genetic trends and average genetic merits of TOP herds compared to AVE herds.

Selection for feed efficiency does not change the selection for growth and carcass traits in Nellore cattle.

The objectives were to conduct a genetic evaluation of residual feed intake (RFI) and residual feed intake adjusted for fat (RFIFat) and to analyse the effect of selection for these traits on growth, carcass and reproductive traits. Data from 945 Nellore bulls in seven feed efficiency tests in a feedlot were analysed. Genetic evaluation was performed using an animal model in which the feed efficiency test and age of the animal at the beginning of the test were considered as a systematic effect. Direct additive genetic and residual effects were considered as random effects. Correlations and genetic gains were estimated by two-trait analysis between feed efficiency measures (RFI and RFIFat) and other traits. Feed conversion showed low heritability (0.06), but dry matter intake (DMI), average daily gain, RFI, RFIFat, metabolic body weight and scrotal circumference measured at 450 days of age (SC450) showed moderate to high heritability (0.49, 0.28, 0.33, 0.36, 0.38 and 0.80, respectively). Similarly, ribeye area, backfat thickness, rump cap fat thickness, marbling score and subcutaneous fat thickness also had high heritability values (0.46, 0.37, 0.57, 0.51 and 0.47, respectively). Genetic correlations between RFI and SC450 were null, and between RFIFat and SC450 were strongly positive. Genetic and phenotypic correlations of RFI and RFIFat with carcass traits were not different from zero, as correlated responses for carcass traits were also not different from zero. The Nellore selection for feed efficiency by RFI or RFIFat allows the recognition of feed efficient animals, with DMI reduction and without significant changes in growth and carcass traits. However, because of the observed results between RFIFat and SC450, selection of animals should be analysed with caution and a preselection for reproductive traits is necessary to avoid reproductive impairments in the herd.

Genetic and phenotypic parameters for sexual precocity and parasite resistance traits in Nellore cattle.

Indicator traits of sexual precocity are widely used as selection criteria for the genetic improvement of beef cattle; however, the impact of selection for these traits on resistance to endoparasites and ectoparasites is unknown. Therefore, this study aimed to estimate the genetic and phenotypic parameters for indicator traits of sexual precocity and parasite resistance in Nellore cattle. The sexual precocity traits evaluated were probability of first calving (PFC) and scrotal circumference at 12 and 18 months of age (SC12 and SC18). The resistance-related traits included tick (TC), gastrointestinal nematode egg (NEC), and Eimeria spp. oocyst (EOC) counts. (Co)variance components were estimated by Bayesian inference using multitrait animal models. The mean heritabilities for PFC, SC12, SC18, TC, NEC, and EOC were 0.23, 0.38, 0.42, 0.14, 0.16, and 0.06, respectively, and suggest that selection will change the mean values of these traits over time. The genetic and phenotypic correlations for most pairs formed by a precocity and a resistance trait were not different from zero, suggesting that selection for sexual precocity traits will not result in changes in resistance traits. Thus, selection for indicator traits of sexual precocity does not elicit unfavorable correlated responses in resistance to endoparasites and ectoparasites, and joint selection aimed at improving these traits can be performed using multitrait selection methods, when necessary.

Genetic trends and trade-offs between growth and reproductive traits in a Nellore herd.

The knowledge of genetic trends and trade-offs between growth and reproductive traits might be useful to understand the evolution of these traits in livestock and natural populations of animals. We estimated the genetic trends and trade-offs between pre-weaning growth and calving intervals of Nellore animals from a commercial farm. Two-trait animal models were used to estimate covariance components and breeding values (EBV) for direct and maternal genetic effects of pre-weaning growth and direct genetic effects of calving intervals. Regression analyses were performed to examine the relationship between direct and maternal EBV of pre-weaning growth and direct EBV of calving intervals (dependent variables) and the coefficient of generation of each animal (independent variable). We also performed regression analyses to examine the relationship between direct EBV of calving intervals (dependent variables) and direct and maternal EBV of pre-weaning growth (independent variables). The genetic trends for direct and maternal genetic effect for pre-weaning growth were significant and presented genetic evolution in the studied Nellore herd. The genetic trends for the reproductive traits were also significant but indicated genetic changes in an unfavorable way. The genetic correlations between direct effects of pre-weaning growth and calving intervals traits and the genetic correlations between maternal effects of pre-weaning growth traits and direct effects of calving interval traits were not different from zero. The presence of trade-offs between the direct effects of growth and reproductive traits were confirmed through regression from direct EBV of calving intervals over EBV of pre-weaning growth traits. In addition, regression analyses showed that selection to increase pre-weaning growth also increased calving intervals. Our results showed that pre-weaning growth and calving intervals are increasing over generations and that trade-offs occurred between those traits in the studied Nellore herd.

Genetic analysis of resistance to ticks, gastrointestinal nematodes and Eimeria spp. in Nellore cattle.

The aim of the present study was to obtain genetic parameters for resistance to ticks, gastrointestinal nematodes (worms) and Eimeria spp. in Nellore cattle, analyze the inclusion of resistance traits in Nellore breeding programs and evaluate genetic selection as a complementary tool in parasite control programs. Counting of ticks, gastrointestinal nematode eggs and Eimeria spp. oocysts per gram of feces totaling 4270; 3872 and 3872 records from 1188; 1142 and 1142 animals, respectively, aged 146 to 597 days were used. The animals were classified as resistant (counts equal to zero) or susceptible (counts above zero) to each parasite. The statistical models included systematics effects of contemporary groups and the mean trajectory. The random effects included additive genetic effects, direct permanent environmental effects and residual. The mean trajectory and random effects were modeled with linear Legendre polynomials for all traits except for the mean trajectory of resistance to Eimeria spp., which employed the cubic polynomial. Heritability estimates were of low to moderate magnitude and ranged from 0.06 to 0.30, 0.06 to 0.33 and 0.04 to 0.33 for resistance to ticks, gastrointestinal nematodes and Eimeria spp., respectively. The posterior mean of genetic and environmental correlations for the same trait at different ages (205, 365, 450 and 550 days) were favorable at adjacent ages and unfavorable at distant ages. In general, the posterior mean of the genetic and environmental correlations between traits of resistance were low and high-density intervals were large and included zero in many cases. The heritability estimates support the inclusion of resistance to ticks, gastrointestinal nematodes and Eimeria spp. in Nellore breeding programs. Genetic selection can increase the frequency of resistant animals and be used as a complementary tool in parasite control programs.