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 CH_4res 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.

Genome-wide association studies (GWAS) are employed to identify genomic regions and candidate genes associated with several traits. The aim of this study was to perform a GWAS to identify causative variants and genes associated with milk yield, frame, and udder conformation traits in Gir dairy cattle. Body conformation traits were classified as "frame," and "udder" traits for this study. After genotyping imputation and quality control 42,105 polymorphisms were available for analyses and 24,489 cows with pedigree information had phenotypes. First, P-value was calculated based on the variance of the prediction error of the SNP-effects on the first iteration. After that, 2 more iterations were performed to carry out the weighted single-step genome-wide association methodology, performed using genomic moving windows defined based on linkage disequilibrium. The significant SNPs and top 10 windows explaining the highest percentage of additive genetic variance were selected and used for QTL and gene annotation. The variants identified in our work overlapped with QTLs from the animal QTL database on chromosomes 1 to 23, except for chromosome 4. The Gir breed is less studied than the Holstein breed and as such the animal QTL database is biased to Holstein results. Hence it is noteworthy that our GWAS had similarities with previously described QTLs. These previously known QTLs were related to milk yield, body height, rump angle, udder width, and udder depth. In total, 5 genes were annotated. Of these genes, FAM13A and CMSS1 had been previously related to bone and carcass weight in cattle.

This work aimed to evaluate the effects of sire's and dam's biological type, dam's age class at calving and individual heterozygosis, and to estimate variance components for weaning weight adjusted to 210 days (WW210) in beef cattle of different breed groups. Records of 13 687 animals, obtained from 2000 to 2007, were used. Bulls from the biological types Zebu (N), Adapted (A), British (B), Continental (C) and ¼N|¼A|¼B|¼C were mated with purebred zebu (N) and crossbred females (½C|½N and ½B|½N). Dam age at calving was 3–12 years. The influence of several effects on WW210 was tested using the least square method. Variance component analysis was performed using a Bayesian approach. The model included contemporary group, dam's age class at calving, sire's and dam's biological types as systematic effects, animal's age and individual heterozygosis as linear covariates, and direct and maternal additive genetic, maternal permanent environmental and residual effects as random effects. The progeny of bulls from biological type B and the crossbred cows showed higher WW210 means. Cows at 6–7 years old weaned heavier calves. Direct and maternal heritability estimates for WW210 were 0.5 ± 0.04 and 0.1 ± 0.02, respectively. Calves with 100% individual heterozygosis weighed on average 25.98 kg more at weaning compared to progenies from pure breeds. Sire's and dam's biological types influence the WW210 of the crossed progenies. Crossbred cows produce heavier calves compared to biological type N cows. These results and the obtained direct and maternal heritabilities suggest it is possible to choose the lines of sires and dams that could be used to make the crosses to obtain progenies with better performance for WW210.

Context: Gir is a tropically adapted breed of Bos taurus indicus cattle that has been intensively selected for milk production in Brazil. Selection programs also consider body-conformation traits because these have been associated with health, welfare, and cow longevity, thus affecting productivity. Aims: This study focused on Gir cattle to estimate genetic and phenotypic parameters for body-conformation traits, as well as their correlations with milk production traits. Methods: Body-conformation traits were classified as ‘frame’, ‘foot and leg’, or ‘mammary system’ traits. The dataset contained 1105 cows recorded with body-conformation traits and 38 996 records of 305-day cumulative milk yield, from 24 489 Gir cows. The pedigree file included 38 571 animals, of which 1593 were genotyped using six different single-nucleotide polymorphism panels. After genotyping imputation, and quality control, 42 105 polymorphisms were available for analyses. Univariate and bivariate animal models, using Bayesian approach via the Gibbs sampling algorithm, were used to estimate genetic parameters, benefiting from both genotypes and pedigree data. Key results: The heritabilities for body-conformation traits ranged from a low of 0.08 ± 0.04 to a medium value of 0.35 ± 0.07, and the heritability for milk production was 0.23 ± 0.01. We identified unfavourable genetic correlations between milk yield and udder depth (0.63 ± 0.11) as well as body height (0.31 ± 0.13). In contrast, there was a favourable genetic correlation between milk yield and rear udder width (0.61 ± 0.14). Conclusion: The heritability estimates confirmed the possibility of selecting animals for milk yield and body conformation traits related to the frame and mammary system categories. Based on the estimated genetic correlations, considerable importance should be given to the emphasis on selection for increased milk yield, because in the long term, this may promote undesirable changes in some type traits as body height and udder depth. Implications: This information is relevant to selective breeding of Gir to enhance tropical milk production.