Heritability estimates and genome-wide association study of methane emission traits in Nellore cattle.

The objectives of the present study were to estimate the heritability for daily methane emission (CH4) and residual daily methane emission (CH4res) in Nellore cattle, as well as to perform genome-wide association studies (GWAS) to identify genomic regions and candidate genes influencing the genetic variation of CH4 and CH4res. Methane emission phenotypes of 743 Nellore animals belonging to three breeding programs were evaluated. CH4 was measured using the sulfur hexafluoride (SF6) tracer technique (which involves an SF6 permeation tube introduced into the rumen, and an appropriate apparatus on each animal), and CH4res was obtained as the difference between observed CH4 and CH4 adjusted for dry matter intake. A total of 6,252 genotyped individuals were used for genomic analyses. Data were analyzed with a univariate animal model by the single-step GBLUP method using the average information restricted maximum likelihood (AIREML) algorithm. The effects of single nucleotide polymorphisms (SNPs) were obtained using a single-step GWAS approach. Candidate genes were identified based on genomic windows associated with quantitative trait loci (QTLs) related to the two traits. Annotation of QTLs and identification of candidate genes were based on the initial and final coordinates of each genomic window considering the bovine genome ARS-UCD1.2 assembly. Heritability estimates were of moderate to high magnitude, being 0.42 ± 0.09 for CH4 and 0.21 ± 0.09 for CH4res, indicating that these traits will respond rapidly to genetic selection. GWAS revealed 11 and 15 SNPs that were significantly associated (P < 10-6) with genetic variation of CH4 and CH4res, respectively. QTLs associated with feed efficiency, residual feed intake, body weight and height overlapped with significant markers for the traits evaluated. Ten candidate genes were present in the regions of significant SNPs; three were associated with CH4 and seven with CH4res. The identified genes are related to different functions such as modulation of the rumen microbiota, fatty acid production, and lipid metabolism. CH4 and CH4res presented sufficient genetic variation and may respond rapidly to selection. Therefore, these traits can be included in animal breeding programs aimed at reducing enteric methane emissions across generations.

An agent-based simulation model to compare different reproductive strategies in cow-calf operations: Economic performance.

In a companion paper, Ojeda-Rojas et al. (2021) [1] describe a stochastic agent-based simulation (ABS) model of a cow-calf operation on a commercial farm in São Paulo, Brazil. The model's parameterization was based on data collected from two sources: a real beef cattle herd and related scientific literature. Based on the mentioned simulation model, this study aims to assess the economic outcome of 10 different reproductive scenarios: Natural mating only (ONM); one timed artificial insemination (TAI) plus natural mating (NM) (1TAI + NM); two TAI plus NM, with 24, 32, and 40 days between TAI (2TAI/24 + NM, 2TAI/32 + NM, and 2TAI/40 + NM, respectively); three TAI without NM, with 24, 32, and 40 days between TAI (3TAI/24, 3TAI/32, and 3TAI/40, respectively); and three TAI plus NM, with an interval between TAI of 24 (3TAI/24 + NM) and 32 days (3TAI/32 + NM). The simulation was performed on an animal-by-animal basis over a time horizon of 5000 days. Each scenario had 32 farms, and each farm kept up to 400 adult females. According to the scenario, a bull population was composed of 0, 7, or 15 individuals. The outcomes, represented as means ± standard deviations, were assessed after reaching a steady-state (1825 days). The model outcomes showed that the 3TAI/24 + NM scenario resulted in higher incomes (US$ 96,479.19 ± 709.81), whereas the ONM scenario had the lowest incomes (US$ 79,753.37 ± 741.87). The 3TAI/24 + NM (US$ 101.720.63 ± 79.21) and ONM (US$ 90.898.58 ± 59.17) scenarios presented the highest and lowest total operating costs (TOC), respectively. However, when TOC was evaluated per kg of the weaned calf, the highest and lowest costs were associated with the ONM (US$ 2.81 ± 0.03/kg) and 2TAI/24 + NM (US$ 2.17 ± 0,04/kg) scenarios, respectively. Our model suggests that reproductive strategies that use TAI have a better economic performance than those under NM. However, when performing three TAI with an interval of 40 days, the benefit was lower; in some cases, it was even worse than the ONM. Combining TAI with early pregnancy diagnosis resulted in better economic performance than other TAI programs and NM. The 2TAI/24 + NM scenario outperformed the others due to the contrast between its high income and moderate costs. Beef cattle production is a highly complex system. Simulations models, specifically ABS models, could make the decision-making process on complex systems straightforward and effective. Furthermore, ABS models can overcome the limitations of conventional research approaches, such as high costs and long experimentation periods.

An agent-based simulation model to compare different reproductive strategies in cow-calf operations: Technical performance.

The objective of this study was to create a stochastic, agent-based simulation model of a synthetic population of beef cattle, and then use it to compare the technical performance of different reproductive strategies. The model was parameterized using data from a real beef cattle herd and from the peer-reviewed scientific literature to represent a Nelore cattle herd in the state of São Paulo, Brazil. Ten scenarios were evaluated: natural mating (NM) only (ONM); one timed artificial insemination (TAI) plus NM (1TAI + NM); two TAI plus NM, with 24, 32, and 40 days between inseminations (2TAI/24 + NM, 2TAI/32 + NM, and 2TAI/40 + NM, respectively); three TAI without NM, with 24, 32, and 40 days between TAI (3TAI/24, 3TAI/32, and 3TAI/40, respectively); and three TAI plus NM, with 24 and 32 days (3TAI/24 + NM and 3TAI/32 + NM, respectively). NM began 10 days after the last TAI and was performed until the end of the breeding season. The size of the female herd was set to contain up to 400 individuals. The bull population was established at 0, 7, or 15 bulls depending on the used scenario. Simulation was performed for 5000 days. The outcomes for each scenario are means ± S.E. assessed on 32 farms at 1-day time intervals and on an animal-by-animal basis after steady state was reached (1825 days). The 3TAI/24 + NM scenario resulted in a greater number of births (279.85 ± 0.47 births), while the ONM scenario had the least value (202.38 ± 0.43 births). The heaviest males and females at weaning belonged to 3TAI/24, with 190.85 ± 0.17 kg for males and 173.89 ± 0.13 kg for females. The ONM scenario had the lightest males (166.84 ± 0.18 kg) and females (151.75 ± 0.16 kg). The greatest and least total pregnancy rates were found in 3TAI/24 + NM (0.91 ± 0.00) and ONM (0.62 ± 0.00), respectively. The ONM scenario required 52.5 days more than scenarios that included TAI to reach 50% of pregnancy. The greatest ages at culling for cows was 3TAI/24 + NM (3658.88 ± 10.41 days). In contrast, the lowest age at culling was found in ONM (2823.93 ± 8.28 days). We concluded that the proposed model represents the main interactions of a real beef cattle herd. It has all the advantages of a physical experiment, but does not require incurring significant expenses nor altering the real system. This study offers evidence that the scenarios that present the best technical performance are those that used TAI with a 24-day interval between inseminations.

Association between residual feed intake, digestion, ingestive behavior, enteric methane emission and nitrogen metabolism in Nellore beef cattle.

This study aimed to evaluate nutrient intake and digestibility, enteric methane emission and nitrogen utilization efficiency in Nellore cattle ranked by residual feed intake (RFI). Twenty-four Nellore bulls at 466 ± 24 days of age and with 352 ± 14.6 kg of body weight, classified as low and high RFI, were evaluated. Animals were kept in individual pens for three periods of 28 days and variables were measured. Data were analyzed as repeated measures over time, considering as fixed effects RFI class, period and RFI class x period interaction, and linear (co)variate of age. No significant differences in dry matter or nutrient intake were detected between RFI classes, but total digestible nutrients intake tended to be lower in low RFI animals, and apparent nutrient digestibility was higher in high RFI animals. Partial efficiency of growth tended to be lower in high RFI animals. RFI class did not interfere with enteric methane production or microbial protein synthesis, but fecal nitrogen output was higher in low RFI animals. The greater efficiency of low RFI animals is consequence of lower maintenance requirements, since energy from higher nutrients digestibility in high RFI animals was spent on metabolic processes other than body tissue deposition.

Genome-wide identification of runs of homozygosity islands in the Gyr breed (Bos indicus).

Runs of homozygosity (ROH) are contiguous homozygous regions of the genome. These regions can be used to identify genes associated with traits of economic interest, as well as inbreeding levels. The aim of the present study was to analyse the length and distribution of ROH islands in Gyr cattle and to identify genes within these regions. A population of 173 animals selected for beef production and a population of 291 animals selected for dairy production were used. Differences in the number of short ROH (ROH1-2 Mb ) were observed between the two populations, while the number of long ROH (ROH>16 Mb ) was similar. ROH islands with the highest incidences (>0.50) overlapped in several segments of the genome in the two populations. The genes identified were associated with milk production, growth, reproduction, immune response and resistance traits. Our results contribute to the understanding of how selection can shape the distribution of ROH and ROH islands within the same breed when animals are selected for different purposes such as dairy or beef production.

Linkage disequilibrium and effective population size in Gir cattle selected for yearling weight.

Linkage disequilibrium (LD) plays an important role in genomic selection and mapping of quantitative trait loci (QTL). This study investigated the pattern of LD and effective population size (Ne ) in Gir cattle selected for yearling weight. For this purpose, 173 animals with imputed genotypes (from 18 animals genotyped with the Illumina BovineHD BeadChip and 155 animals genotyped with the Bovine LDv4 panel) were analysed. The LD was evaluated at distances of 25-50 kb, 50-100 kb, 100-500 kb and 0.5-1 Mb. The Ne was estimated based on 5 past generations. The r2 values (a measure of LD) were, respectively, .35, .29, .18 and .032 for the distances evaluated. The LD estimates decreased with increasing distance of SNP pairs and LD persisted up to a distance of 100 kb (r2  = .29). The Ne was greater in generations 4 and 5 (24 and 30 animals, respectively) and declined drastically after the last generation (12 animals). The results showed high levels of LD and low Ne , which were probably due to the loss of genetic variability as a consequence of the structure of the Gir population studied.

Sexual maturity and fertility-related measures in young Nellore bulls receiving long-term dietary supplementation with rumen-protected polyunsaturated fatty acids.

The objective of this study was to evaluate the effects of long-term supplementation with rumen-protected fatty acids (FA) on growth and reproductive parameters of young Nellore bulls in a grazing regime. Forty-eight young bulls were distributed into two groups: FA (supplemented with rumen-protected polyunsaturated FA); and control (control fat-free supplement). The animals were supplemented from 14.3 to 24.6 months of age and growth and reproductive parameters were evaluated at 28-day intervals. The semen was cryopreserved in the last collection and fresh and post-thaw semen samples were evaluated. Feeding FA did not affect (P > 0.05) growth, reproductive parameters (scrotal circumference, sperm concentration per mL of ejaculate, percentage of sperm defects, sperm quality and fertility in vitro), or testicular ultrasonographic characteristics. However, thawed semen from bulls fed FA exhibited better quality (P < 0.05) than control semen for the following parameters evaluated by computer-assisted sperm analysis: average path velocity [µm/s: 90.48 vs. 79.66 post-thaw and 74.81 vs. 72.80 post-rapid thermoresistance test (TRT)], straight-line velocity (µm/s: 72.37 vs. 65.20 post-thaw and 64.96 vs. 63.25 post-TRT), and curvilinear velocity (µm/s: 148.44 vs. 131.31 post-thaw and 115.68 vs. 113.35 post-TRT). In addition, feeding FA increased peripheral concentrations of testosterone, leptin, total cholesterol and high-density lipoprotein. In conclusion, the increase in testosterone concentrations in bulls fed FA was not related to variations in growth parameters and sexual maturity. In addition, post-thawing sperm velocities were enhanced by diet, however, such increases were not related to better in vitro embryo production rates.

Genome-Wide Association Study for Carcass Traits in an Experimental Nelore Cattle Population.

The purpose of this study was to identify genomic regions associated with carcass traits in an experimental Nelore cattle population. The studied data set contained 2,306 ultrasound records for longissimus muscle area (LMA), 1,832 for backfat thickness (BF), and 1,830 for rump fat thickness (RF). A high-density SNP panel (BovineHD BeadChip assay 700k, Illumina Inc., San Diego, CA) was used for genotyping. After genomic data quality control, 437,197 SNPs from 761 animals were available, of which 721 had phenotypes for LMA, 669 for BF, and 718 for RF. The SNP solutions were estimated using a single-step genomic BLUP approach (ssGWAS), which calculated the variance for windows of 50 consecutive SNPs and the regions that accounted for more than 0.5% of the additive genetic variance were used to search for candidate genes. The results indicated that 12, 18, and 15 different windows were associated to LMA, BF, and RF, respectively. Confirming the polygenic nature of the studied traits, 43, 65, and 53 genes were found in those associated windows, respectively for LMA, BF, and RF. Among the candidate genes, some of them, which already had their functions associated with the expression of energy metabolism, were found associated with fat deposition in this study. In addition, ALKBH3 and HSD17B12 genes, which are related in fibroblast death and metabolism of steroids, were found associated with LMA. The results presented here should help to better understand the genetic and physiologic mechanism regulating the muscle tissue deposition and subcutaneous fat cover expression of Zebu animals. The identification of candidate genes should contribute for Zebu breeding programs in order to consider carcass traits as selection criteria in their genetic evaluation.