Livestock is an integral part of societies worldwide and contributes to a host of human activities beyond food production, including income, heritage, insurance, labor, and culture. Livestock’s positive contributions to society are contrasted by environmental impacts, which include greenhouse gas (GHG) emissions, biodiversity loss, and natural resource depletion, among others. Though environmental impacts of ruminant livestock production extend beyond GHG emissions ( Rotz, 2020), considerable effort has been dedicated specifically to quantifying and mitigating enteric methane (CH₄) emissions from beef and dairy cattle, which is the focus of this review.

Background: In cattle, base color is assumed to depend on the enzymatic activity specified by the MC1R locus, i.e. the extension locus, with alleles coding for black ( E ^D ), red ( e ), and wild-type ( E ⁺ ). In most mammals, these alleles are presumed to follow the dominance model of E ^D > E ⁺ > e , although exceptions are found. In Bos indicus x Bos taurus F ₂ cattle, some E ^D E ⁺ heterozygotes are discordant with the dominance series for MC1R and display various degrees of red pigmentation on an otherwise predicted black background. The objective of this study was to identify loci that modify black coat color in these individuals. Results: Reddening was classified with a subjective scoring system. Interval analyses identified chromosome-wide suggestive ( P < 0.05) and significant ( P < 0.01) QTL on bovine chromosomes (BTA) 4 and 5, although these were not confirmed using single-marker association or Bayesian methods. Evidence of a major locus ( F = 114.61) that affects reddening was detected between 60 and 73 Mb on BTA 6 (Btau4.0 build), and at 72 Mb by single-marker association and Bayesian methods. The posterior mean of the genetic variance for this region accounted for 43.75% of the genetic variation in reddening. This region coincided with a cluster of tyrosine kinase receptor genes ( PDGFRA , KIT and KDR ). Fitting SNP haplotypes for a 1 Mb interval that contained all three genes and centered on KIT accounted for the majority of the variation attributed to this major locus, which suggests that one of these genes or associated regulatory elements, is responsible for the majority of variation in degree of reddening. Conclusions: Recombinants in a 5 Mb region surrounding the cluster of tyrosine kinase receptor genes implicated PDGFRA as the strongest positional candidate gene. A higher density marker panel and functional analyses will be required to validate the role of PDGFRA or other regulatory variants and their interaction with MC1R for the modification of black coat color in Bos indicus influenced cattle.

The size, support, and health of udders limit the productive life of beef cows, especially those with Bos indicus background, because, in general, such cows have a reputation for problems with udders. Genomic association studies of bovine udder traits have been conducted in dairy cattle and recently in Continental European beef breeds but not in cows with B. indicus background. The objective of this study was to determine associations of SNP and udder support scores, teat length, and teat diameter in half B. indicus (Nellore), half Bos taurus (Angus) cows. Udders of cows (n = 295) born from 2003 to 2007 were evaluated for udder support and teat length and diameter (n = 1,746 records) from 2005 through 2014. These included a subjective score representing udder support (values of 1 indicated poorly supported, pendulous udders and values of 9 indicated very well-supported udders) and lengths and diameters of individual teats in the 4 udder quarters as well as the average. Cows were in full-sibling or half-sibling families. Residuals for each trait were produced from repeated records models with cow age category nested within birth year of cows. Those residuals were averaged to become the dependent variables for genomewide association analyses. Regression analyses of those dependent variables included genotypic values as explanatory variables for 34,980 SNP from a commercially available array and included the genomic relationship matrix. Fifteen SNP loci on BTA 5 were associated (false discovery rate controlled at 0.05) with udder support score. One of those was also detected as associated with average teat diameter. Three of those 15 SNP were located within genes, including one each in vitamin D (1,25-dihydroxyvitamin D₃) receptor (VDR), protein tyrosine phosphatase, receptor type, R (PTPRR), and interleukin 22 (IL22). These are notable for their functional role in some aspect of mammary gland formation or health. Other candidate genes for these traits in the vicinity of the SNP loci include signal peptidase complex subunit 3 homolog (SPCS3) and dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 2 (DYRK2). Because these were detected in Nellore–Angus crossbred cows, which typically have very well-formed udders with excellent support across their productive lives, similar efforts in other B. indicus breeds should be completed, because that may facilitate further refinement of genomic regions responsible for variation in udder traits important in multiple breeds.

The use of Brahman in cow–calf production offers some adaptation to the harsh characteristics of endophyte-infected tall fescue. Criollo breeds, such as the Romosinuano, may have similar adaptation. The objectives were to estimate genetic effects in Romosinuano, Angus, and crossbred cows for their weights, weights of their calves, and ratios (calf weight:cow weight and cow weight change:calf weight gain) across lactation and to assess the influence of forage on traits and estimates. Cows (n = 91) were bred to Charolais bulls after their second parity. Calves (n = 214) were born from 2006 to 2009. Cows and calves were weighed in early (April and June), mid- (July), and late lactation (August and October). Animal was a random effect in analyses of calf data; sire was random in analyses of cow records and ratios. Fixed effects investigated included calf age, calf sex, cow age–year combinations, sire breed of cow, dam breed of cow, and interactions. Subsequent analyses evaluated the effect of forage grazed: endophyte-free or endophyte-infected tall fescue. Estimates of maternal heterosis for calf weight ranged from 9.3 ± 4.3 to 15.4 ± 5.7 kg from mid-lactation through weaning (P < 0.05). Romosinuano direct effects (of the cow) were –6.8 ± 3.0 and –8.9 ± 4.2 kg for weights recorded in April and June. Calf weights and weight gains from birth were greater (P < 0.05) for calves of cows grazing endophyte-free tall fescue except in mid-summer. Cow weight change from April to each time was negative for Angus cows and lower (P < 0.05) than other groups. Cows grazing endophyte-free tall fescue were heavier (P < 0.05) at all times but had more weight loss in late lactation. Angus cows had the lowest (P < 0.05) ratios (negative) of cow weight change:calf weight gain, indicating an energy-deficit condition. Cows grazing endophyte-free tall fescue had more negative (P < 0.05) values for this trait but not in early lactation (P < 0.05). Estimates of heterosis ranged from 12.8 ± 9.5 to 28.6 ± 9.4 kg for cow weight, 7.9 ± 3.0 to 15.8 ± 5.0 kg for cow weight change, and 0.07 ± 0.03 to 0.27 ± 0.1 for cow weight change:calf weight gain. Direct Romosinuano effects ranged from 14.8 ± 4.2 to 49.8 ± 7.7 kg for cow weight change and 0.2 ± 0.04 to 0.51 ± 0.14 for cow weight change:calf weight gain. The adaptive ability of Romosinuano in temperate fescue regions may be favorable with respect to relative cow and calf weight but may be a consequence of lower milk-producing ability. Copyright © 2016. American Society of Animal Science .

The objective of this work was to estimate heritability of each of 5 subjectively measured aspects of temperament of cattle and the genetic correlations of pairs of those traits. From 2003 to 2013, Nellore–Angus F₂ and F₃ calves (n = 1,816) were evaluated for aspects of temperament at an average 259 d of age, which was approximately 2 mo after weaning. Calves were separated from a group and subjectively scored from 1 (calm, good temperament) to 9 (wild, poor temperament) for aggressiveness (willingness to hit an evaluator), nervousness, flightiness, gregariousness (willingness to separate from the group), and a distinct overall score by 4 evaluators. Data were analyzed using threshold and linear models with additive genetic random effects. Two-trait animal models (nonthreshold) included the additive genetic covariance for pairs of traits and were used to estimate additive genetic correlations. Contemporary groups (n = 104) represented calves penned together for evaluation on given evaluation days. Heifers had greater (worse) means for all traits than steers (P < 0.05). The regression of score on age in days was included in final models for flightiness (P = 0.05; –0.006 ± 0.003) and gregariousness (P = 0.025; –0.007 ± 0.003). Estimates of heritability were large (0.51, 0.4, 0.45, 0.49, and 0.47 for aggressiveness, nervousness, flightiness, gregariousness, and overall temperament, respectively; SE = 0.07 for each). The ability to use this methodology to distinctly separate different aspects of calf temperament appeared to be limited, as estimates of additive genetic correlations were near unity for all pairs of traits; estimates of phenotypic correlation ranged from 0.88 ± 0.01 to 0.99 ± 0.002 for pairs of traits. Distinct subsequent analyses indicated a significant negative relationship of 4 of the various temperament scores with weight at weaning (regression coefficients ranged from –0.008 ± 0.002 for nervousness, flightiness, and gregariousness to –0.003 ± 0.002 for aggressiveness). In subsequent analyses, the regression of temperament trait on sequence of evaluation within a pen was highly significant and solutions ranged from 0.05 ± 0.007 for aggressiveness to 0.08 ± 0.007 for all other traits. The apparent large additive genetic variance for any one of these traits may be useful in identification of genes responsible for differences in cattle temperament. Copyright © 2014. American Society of Animal Science .

Bos indicus cattle often have the reputation for a poor or dangerous temperament. Identification of genomic regions that associate with temperament of such cattle may be useful for genetic improvement strategies. The objectives of this study were to evaluate subjective temperament scores (1 to 9; higher scores indicated more unfavorable temperament) for aggressiveness, nervousness, flightiness, gregariousness, and overall temperament of one-half Bos indicus steers in feedlot conditions at 1 yr of age and compare those scores of those steers when evaluated approximately 1 mo postweaning, and conduct whole genome association analyses using SNP markers and the temperament traits of those steers at 1 yr of age and for temperament traits of all calves at weaning. Contemporary groups (P < 0.001) were steers born in the same year and season, and fed in the same feedlot pen. Aggressiveness of steers at 1 yr of age was not associated with aggressiveness at weaning (linear regression coefficient did not differ from 0; P = 0.96), but regressions of all other yearling scores of steers on the scores at weaning were positive (coefficients ranged from 0.26 ± 0.04 to 0.32 ± 0.04; P < 0.001). Estimates of Pearson correlation coefficients (using unadjusted values and residual values) of the different traits measured at 1 yr of age were large (r > 0.63; P < 0.008) except for aggressiveness with nervousness, flightiness, or gregariousness, which did not differ from 0 (P > 0.1). Five SNP on BTA 1, 24, and 29 had suggestive associations (0.17 < P [adjusted for FDR] < 0.24) with aggressiveness, nervousness, or flightiness at evaluation postweaning and 13 SNP on 11 chromosomes had suggestive associations (0.07 < P [adjusted for FDR] < 0.24) with aggressiveness, nervousness, flightiness, or overall temperament score of steers at 1 yr of age. Genes close to these loci with roles in neural systems of various organisms included synaptotagmin 4 (BTA 24), FAT atypical cadhedrin 3 (BTA 29), tubulin tyrosine ligase-like 1 (BTA 5), spermatogenesis associated 17 (BTA 16), stanniocalcin 2 (BTA 20), and GABA_A receptor γ 3 (BTA 21).