Runs of homozygosity: current knowledge and applications in livestock

This review presents a broader approach to the implementation and study of runs of homozygosity (ROH) in animal populations, focusing on identifying and characterizing ROH and their practical implications. ROH are continuous homozygous segments that are common in individuals and populations. The ability of these homozygous segments to give insight into a population's genetic events makes them a useful tool that can provide information about the demographic evolution of a population over time. Furthermore, ROH provide useful information about the genetic relatedness among individuals, helping to minimize the inbreeding rate and also helping to expose deleterious variants in the genome. The frequency, size and distribution of ROH in the genome are influenced by factors such as natural and artificial selection, recombination, linkage disequilibrium, population structure, mutation rate and inbreeding level. Calculating the inbreeding coefficient from molecular information from ROH (F_ROH ) is more accurate for estimating autozygosity and for detecting both past and more recent inbreeding effects than are estimates from pedigree data (F_PED ). The better results of F_ROH suggest that F_ROH can be used to infer information about the history and inbreeding levels of a population in the absence of genealogical information. The selection of superior animals has produced large phenotypic changes and has reshaped the ROH patterns in various regions of the genome. Additionally, selection increases homozygosity around the target locus, and deleterious variants are seen to occur more frequently in ROH regions. Studies involving ROH are increasingly common and provide valuable information about how the genome's architecture can disclose a population's genetic background. By revealing the molecular changes in populations over time, genome-wide information is crucial to understanding antecedent genome architecture and, therefore, to maintaining diversity and fitness in endangered livestock breeds.

Inclusion of cytoplasmic lineage effect and direct-maternal genetic covariance for genetic evaluation of growth traits in Nellore cattle

We evaluated the impact of cytoplasmic lineage effects (Lc) for growth traits on genetic evaluation, including the genetic covariance between direct and maternal effects (σ_am). Pedigree data from 496,190 Nellore animals and observations on birth weight (BW, N = 243,391), weaning weight (WW, N = 431,681), and post-weaning weight gain adjusted to 345 days (PWG, N = 172,131) were analyzed. Four univariate models were used to obtain estimates of (co)variance components using the restricted maximum likelihood method in the BLUPF90 program. Model 1 included Lc and σ_am. Model 2 included Lc and σ_am was set to zero. Model 3 did not include Lc. Model 4 did not include Lc and σ_am was set to zero. These models considered the effects of the Lc as random. Phenotypic variance obtained through cytoplasmic lineage effects was determined for all traits, ranging from 0.07 to 0.15, 0.15 to 0.03, and 0.05 to 0.03% for BW, WW, and PWG, respectively, for models 1 and 2. Correlations between direct and maternal genetic components were positive for WW and negative for BW and PWG. No differences were observed for genetic parameter estimates or animal ranking with the inclusion of σ_am. For BW, the likelihood ratio suggested that model 1 best fits the data, while model 4 was the most appropriate for WW and PWG. Thus, these models are recommended for genetic evaluations. Despite the low magnitude of cytoplasmic lineages, this effect could predict breeding value and improve the selection of animals for BW in this Nellore population.

Cyclin T2A Gene Maps on Human Chromosome 2q21

Cyclin T2a was recently identified as one of the regulatory subunits of the cdk–cyclin complex P-TEFb, the most studied positive factor in the regulation of transcription elongation. By fluorescent in situ hybridization (FISH), the gene codifying for cyclin T2a has been mapped on human chromosome 2q21. This locus also has been linked to different forms of myopathy. By use of a new specific antiserum raised against cyclin T2a, the immunohistochemical pattern of expression of cyclin T2a in human tissues has been examined and compared to that of cyclin T1, described in the previous report. The observation that immunohistochemical expression of cyclin T2a was high in skeletal muscle cells, whereas it was undetectable in two cases of centronuclear myopathy, together with its chromosomal location, suggests an involvement of the cdk9–cyclin T2a complex in this disease.

Valores econômicos para sistemas de recria e engorda de bovinos Nelore e cruzado

Foi desenvolvido o modelo bioeconômico nominado de Beef Management System para a obtenção de valores econômicos em quatro sistemas de recria e engorda de bovinos. Dos modelos analisados, dois utilizaram machos inteiros da raça Nelore e os outros dois machos inteiros cruzados (½ sangue taurino; ½ sangue zebu). Para cada grupamento genético estipulou-se dois modelos de produção, um 100 % a pasto e o outro com recria em pastagem e posterior confinamento. O estudo foi conduzido por meio de simulações em planilhas eletrônicas interligadas do programa Microsoft Office Excel. Os valores econômicos foram estimados para as características de ganho médio diário (GMD), rendimento de carcaça (RC), consumo alimentar (CA) e energia de mantença (EM), para cada um dos modelos propostos. Para obtenção dos valores econômicos, estipulou-se um aumento de 1 % no GMD e RC, e diminuiu-se 1 % da EM e CA. Com o aumento de 1 % no RC e no GMD, o custo de produção diminuiu 14,69 kg de carne (1 unidade de arroba) em todos os modelos estudados. A redução de 1 % na EM dos animais resultou em uma diminuição de 0,45 % no custo de produção de 14,69 kg de carne em ambos os modelos a pasto com confinamento e 0,55 % em ambos os modelos 100 % a pasto. Com a redução de 1 % na CA, o custo de produção de 14,69 kg de carne diminuiu 0,83 e 0,84 % nos modelos a pasto com confinamento de animais Nelores e cruzados e 0,85 e 0,83 % nos modelos 100 % a pasto de animais Nelores e cruzados. Essas características possuem um grande impacto econômico nos sistemas de recria e engorda, com grande vantagem para a característica de RC, uma vez que esta proporcionou os maiores valores econômicos para todos os sistemas estudados. Por meio das variáveis que compuseram os modelos estudados tornou-se possível mensurar a real importância do impacto genético das características e seus respectivos valores econômicos.

Genetic correlations between visual slaughter conformation scores and growth and reproductive traits in Canchim cattle

We obtained heritability and (co)variance component estimates for slaughter conformation scores at 420 days of age (SCS420), age at calving (first, AFC; second, ASC), calving occurrence until 38 months of age (CP38), weight at 420 days of age (W420), and scrotal circumference at 420 days (SC420) in Canchim (5/8 Charolais + 3/8 Zebu) cattle. A total of 23,168 records of Canchim animals, including 12,493 females and 10,675 males, were analyzed. SCS420 indicated carcass structure, muscle development, and subcutaneous fat deposition. The slaughter conformation score of each animal was relative to the whole contemporary group; 1 corresponded to the lowest expression of the trait and 6 to the highest. Heritabilities, and genetic and residual correlation estimates between SCS420 and reproductive and weight traits, were estimated by multitrait analyses using an animal model with Bayesian inference, employing a linear model for AFC, ASC, SC420, and W420 and a threshold model for CP38 and SCS420. Heritability estimates for SCS420, AFC, ASC, CP38, W420, and SC420 were 0.11, 0.15, 0.15, 0.15, 0.30, and 0.30, respectively. Genetic correlation estimates between SCS420 and the other traits were 0.08 (AFC), 0.58 (ASC), 0.08 (CP38), 0.43 (W420), and 0.17 (SC420). Visual slaughter conformation scores respond to individual selection and can be used as selection criteria in Canchim cattle. Selection to improve sexual precocity would not be effective in improving carcass conformation and composition, and selection for animals with high breeding values for yearling weight may improve slaughter conformation at the yearling stage.

Genotype × environment interaction for age at first calving, scrotal circumference, and yearling weight in Nellore cattle using reaction norms in multitrait random regression models

The aim of this study was to evaluate the effect of genotype × environment interaction (G×E) on age at first calving (AFC), scrotal circumference (SC), and yearling weight (YW) and to estimate genetic correlations between these traits in Nellore cattle using reaction norms in multitrait random regression models. In this study, 28,871, 41,386, and 89,152 records of Nellore cattle for AFC, SC, and YW, respectively, were used. The data were obtained from farms located in the north, northeast, midwest, and southeast regions of Brazil that participate in the DeltaGen Breeding Program. Environmental levels were defined as a function of contemporary groups, that is, animals born in the same herd and year, from the same management group (from birth to yearling), and of the same sex. Postweaning weight gain was used as a criterion to evaluate the environmental conditions for all traits. For reaction norm analyses, residual variances were modeled with homogeneous and heterogeneous classes. The model for SC and YW included the fixed effects of contemporary group and age of the animal as a covariate as well as random direct additive genetic and residual effects. The same model, excluding the covariate age of the animal, was used for AFC. The heritability estimates were low to high for AFC (0.09 to 0.50), high for SC (0.51 to 0.67), and moderate to high for YW (0.33 to 0.71). The genetic correlations (within each trait) along the environmental levels varied from -0.27 to 1.0 for AFC, from 0.73 to 1.0 for SC, and from 0.26 to 1.0 for YW. The genetic correlations between different traits in different environments varied from -0.14 to -0.60 between AFC and SC, from -0.05 to -0.32 between AFC and YW, and from -0.05 to 0.72 between YW and SC. The genetic correlations have had different magnitudes for AFC, SC, and YW, which could indicate the presence of G×E. The present results should support researchers and farmers in defining selection criteria to improve growth traits and sexual precocity. Our results suggest that animals for breeding have to be selected in the same environment and management conditions as their progeny will be reared.

Genetic association of growth traits with carcass and meat traits in Nellore cattle

The aim of this study was to estimate genetic and phenotypic associations of growth traits with carcass and meat traits in Nellore cattle. Data from male and female animals were used for weaning weight (WW; N = 241,416), yearling weight (YW, N = 126,596), weight gain from weaning to yearling (GWY, N = 78,687), and yearling hip height (YHH, N = 90,720), respectively; 877 male animals were used for hot carcass weight (HCW) and 884 for longissimus muscle area (LMA), backfat thickness (BT), marbling score (MS), and shear force (SF). The variance components were estimated by the restricted maximum likelihood method using three-trait animal models that included WW. The model for WW included direct and maternal additive genetic, maternal permanent environmental, and residual effects as random effects; contemporary group as fixed effects; and age of dam at calving and age of animal as covariates (linear and quadratic effects). For the other traits, maternal effects and the effect of age of dam at calving were excluded from the model. Heritability ranged from 0.10 ± 0.12 (LMA) to 0.44 ± 0.007 (YW). Genetic correlations ranged from -0.40 ± 0.38 (WW x LMA) to 0.55 ± 0.10 (HCW x YW). Growth, carcass, and meat traits have sufficient genetic variability to be included as selection criteria in animal breeding programs.

Association between ACTA1 candidate gene and performance, organs and carcass traits in broilers

This study investigates the genetic association of the SNP present in the ACTA1 gene with performance traits, organs and carcass of broilers to help marker-assisted selection of a paternal broiler line (TT) from EMBRAPA Swine and Poultry, Brazil. Genetic and phenotypic data of 1,400 broilers for 68 traits related to body performance, organ weights, weight of carcass parts, and yields as a percentage of organs and carcass parts were used. The maximum likelihood method, considering 4 analytical models, was used to analyze the genetic association between the SNP and these important economic traits. The association analysis was performed using a mixed animal model including the random effect of the animal (polygenic), and the fixed effects of sex (2 levels), hatch (5 levels) and SNP (3 levels), besides the random error. The traits significantly associated (P<0.05) with the SNP were analyzed, along with body weight at 42 days of age (BW42), by the restricted maximum likelihood method using the multi-trait animal model to estimate genetic parameters. The analysis included the residual and additive genetic random effects and the sex-hatch fixed effect. The additive effects of the SNP were associated with breast meat (BMY), liver yield (LIVY), body weight at 35 days of age (BW35); drumstick skin (DSW), drumstick (DW) and breast (BW) weights. The heritability estimates for these traits, in addition to BW42, ranged from 0.24±0.06 to 0.45±0.08 for LIVY and BW35, respectively. The genetic correlation ranged from 0.02±0.18 for LIVY and BMY to 0.97±0.01 for BW35 and BW42. Based on the results of this study, it can be concluded that ACTA1 gene is associated with performance traits BW35, LIV and BMY, DW, BW and DW adjusted for body weight at 42 days of age. Therefore, the ACTA1 gene is an important molecular marker that could be used together with others already described to increase the economically important traits in broilers.

Associations between single nucleotide polymorphisms and carcass traits in Nellore cattle using high-density panels

The objective of this study was to evaluate associations between single nucleotide polymorphism (SNP) markers and carcass traits measured postmortem in Nellore cattle. Records of loin eye area (LEA) and backfat thickness (BF) from 740 males and records of hot carcass weight (HCW) from 726 males were analyzed. All of the animals were genotyped using the BovineHD BeadChip. Association analyses were performed by the restricted maximum likelihood method that considered one SNP at a time. Significant SNPs were identified on chromosomes 2 and 6 for LEA and on chromosomes 7, 1, and 2 for BF. For HCW, associations with SNPs were found on chromosomes 13, 14, and 28, in addition to genome regions that were directly related to this trait, such as the EFCAB8 and VSTM2L genes, and to bone development (RHOU). Some SNPs were located in very close proximity to genes involved in basal metabolism (BLCAP, NNAT, CTNNBL1, TGM2, and LOC100296770) and the immune system (BPI).

Reaction norms for the study of genotype-environment interaction for growth and indicator traits of sexual precocity in Nellore cattle

The objective of this study was to quantify the magnitude of genotype-environment interaction (GxE) effects on age at first calving (AFC), scrotal circumference (SC), and yearling weight (YW) in Nellore cattle using reaction norms. For the study, 89,152 weight records of female and male Nellore animals obtained at yearling age were used. Genetic parameters were estimated with a single-trait random-regression model using Legendre polynomials as base functions. The heritability estimates were of low to medium magnitude for AFC (0.05 to 0.47) and of medium to high magnitude for SC (0.32 to 0.51) and YW (0.13 to 0.72), and increased as the environmental gradient became more favorable. The genetic correlation estimates ranged from 0.25 to 1.0 for AFC, from 0.71 to 1.0 for SC, and from 0.42 to 1.0 for YW. High Spearman correlation coefficients were obtained for the three traits, ranging from 0.97 to 0.99. The reaction norms along the environmental gradient of 10 sires each with the highest or lowest breeding value for YW predicted by single-trait analysis demonstrated more plastic phenotypes for YW and more robust phenotypes for SC. The effect of GxE was most important for YW and AFC with respect to SC. When animals are selected for higher SC or YW or lower AFC, considering or not the GxE effect, it is expected that the same animals will be selected. The reaction norms obtained based on sire breeding values along the environmental gradient showed that animals with extreme breeding values respond differently as environmental conditions improve.

Sequenciamento parcial dos genes TOX e NCOA2 em bubalinos

Os bubalinos são animais com uma importância grande para a produção de alimentos, além da ação sócio-econômica na região tropical. A caracterização de genes possibilita o estudo de características próprias da espécie e o desenvolvimento de tecnologia para sua produção. Esse trabalho estudou parcialmente os genes thymus high mobility group box protein (TOX) e o Nuclear Receptor Coactivator 2 (NCOA2) em femêas bubalinas da raça Murrah pela técnica de PCR-sequenciamento. Seis SNPs foram identificados em cada gene. Dois SNPs adjacentes no gene TOX criaram/destruíram um sitio de produção de um miRNA e são bons candidatos para serem estudos no futuro. A homologia das regiões desses genes com as correspondentes em bovinos é muito alta (99 %).

Study of lipid metabolism-related genes as candidate genes of sexual precocity in Nellore cattle

The objective of this study was to identify associations between known polymorphisms in genes related to adipose tissue and sexual precocity in Nellore cattle. A total of 1689 precocious and non-precocious heifers belonging to farms participating in Conexão Delta G breeding program were studied. SNPs from the Illumina High-Density Bovine SNP BeadChip were used. This chip contains 777,000 SNPs located within the region of the candidate genes at a distance of up to 5 kb, considering that linkage disequilibrium (LD) exists at this distance. Linear models were used for statistical analysis. The fastPHASE and GenomeStudio programs were used for haplotype reconstruction and LD analysis based on r2 statistics. Fifty-seven candidate genes and 443 SNPs were analyzed: among the latter, 370 SNPs formed 83 haplotypes, while the remaining SNPs were studied separately. Statistical analysis showed that only three haplotypes, one haplotype consisting of two SNPs located in the FABP4 gene and two haplotypes consisting of four and two SNPs located in the PPP3CA gene, had a significant effect on sexual precocity at P < 0.05. It can be concluded that the FABP4 and PPP3CA genes influence sexual precocity and may therefore be used in selection programs designed to improve sexual precocity in Nellore cattle.

Growth performance, and carcass and meat quality traits in progeny of Poll Nellore, Angus and Brahman sires under tropical conditions

This study aimed to characterise progeny of sires representing major families in the Poll Nellore breed. Fourteen Poll Nellore sires, two Angus sires and one Brahman sire were mated by AI to ~400 multiparous Poll Nellore dams. Calves were raised and stocked on pasture in central Brazil until reaching ~18 months of age, then fed a sugarcane bagasse-based diet on an ad libitum basis until reaching market weight and finish (average 23 months). There were 236 Poll Nellore (N), 38 Angus × Poll Nellore (AN) and 31 Brahman × Poll Nellore (BN) calves born in total. The weaning and 423-day weight weights, and growth rates and pre- and post-weaning were greater (P < 0.05) in males than in female calves, and were influenced by breed and by sire within the N animals. The weaning weights were higher (P < 0.05) in AN and BN than in N calves. The 423-day weight weights were greater (P < 0.05) in AN calves, followed by BN, with straightbred N being lightest. Feedlot average daily gain was unaffected (P > 0.05) by sex or by sire within N, but was lowest (P < 0.05) in N cattle, and highest in AN and BN animals, which did not differ (P > 0.05). Heifers reached the end of the study with lower bodyweight (BW) and dressing percentage than steers, resulting in lower carcass weights, smaller longissimus muscle areas (LMA), but greater 12th to 13th rib backfat (BF) and similar marbling score and mean shear force. However, the proportion of carcasses grading Choice or Prime was numerically greater in heifers than in steers (23.6% vs 9.8%). AN cattle reached greater harvest weights than BN, and those were heavier than N cattle (P < 0.001). However, dressing percentages were lowest in AN animals, so that there was no significant difference in carcass weight between AN and BN cattle. AN carcasses also had greater LMA, BF and marbling scores than the N carcasses. The proportion of carcasses grading Choice or Prime was numerically greater in AN cattle than in the BN and N groups (25.9%, 11.8% and 15.9%, respectively). Steaks from AN calves were more tender than N steaks, with the BN steaks being intermediate. There was significant variation among N sires for final BW, dressing percentage, carcass weight, LMA and marbling score, but not for BF or mean shear force. The percentages of carcasses of N cattle grading Choice or Prime ranged from 0% to 61.5%. Three N sires produced progeny with greater than 40% of carcasses grading Choice or above (Berílio OB, Furador OB, and Litoral OB). Likewise, three N sires (Blitz OB, Furador OB and Sossego OB) had progeny with 67%, 62% and 75%, respectively, of steaks classified as tender. This study confirmed that Zebu cattle have inferior carcass and meat quality relative to AN crossbreds under tropical conditions, however there is substantial variation within the N breed for these traits, and several sires have a proportion of their progeny comparable in terms of meat tenderness to those of Angus sires.

Plane of nutrition of Corriedale ewe lambs from foetal life to the onset of breeding affects weight at service and reproductive outcome

The objective of this study was to identify periods in the life (foetal and postnatal) of Corriedale ewe lambs where different nutrition levels can affect bodyweight at breeding and pregnancy rate in their first year of life. The effect of three different phases of nutrition on the growth and pregnancy rate (n = 133) of Corriedale ewe lambs of 7 months of age were evaluated. Phase 1 included the last phase of gestation of their mothers (30 last days of gestation, Day –30; partum = Day 0) until marking (Day 24). Phase 2 was between marking and weaning (Day 114) and phase 3 between weaning to the onset of breeding (Day 207). For phase 1, 350 adult ewes had access to improved pastures (phase 1, H) or native pastures (phase 1, L). After lambing, all ewes and their lambs were offered native pastures. After marking only ewes bearing females lambs were kept. In phase 2, 67 lambs born to H and 66 lambs born to L ewes were sorted in two new treatments: access to native pastures supplemented with ~1% of their bodyweight with soybean meal (phase 2, H) or access to native pastures alone (phase 2, L). In phase 3, each of the lambs of the four treatments applied during phase 2 were sorted in two new treatments: access to improved pastures (phase 3, H) or native pastures supplemented with 0.7% of liveweight with soybean meal (phase 3, L). Breeding period lasted 41 days and pregnancy diagnosis was performed 86 days after the onset of breeding. The pregnancy rate varied from 0% to 47%. Phase 3 of nutrition was the only phase that affected pregnancy rate (28% vs. 10% for female lambs offered H and L plane of nutrition respectively; P = 0.005). A discriminative analysis demonstrated that the liveweight at breeding was the only variable that affected the success of pregnancy in ewe lambs (P = 0.0025). Moreover, the ewe lambs that were heavier at the onset of breeding (more than 35 kg or in average 38 kg) were the most successful to get pregnant (35% of pregnancy for lambs over 35 kg and 13% for lambs under 35 kg, P = 0.0044). In conclusion, under the conditions of this experiment, the most important parameters to explain successful pregnancy of ewe lambs were the growth rate after weaning, and the liveweight at the onset of breeding.

Association between single-nucleotide polymorphisms and milk production traits in buffalo

The aim of this study was to identify single-nucleotide polymorphisms (SNPs) in buffaloes associated with milk yield and content, in addition to somatic cell scores based on the cross-species transferability of SNPs from cattle to buffalo. A total of 15,745 SNPs were analyzed, of which 1562 showed 1% significance and 4742 with 5% significance, which were associated for all traits studied. After application of Bonferroni's correction for multiple tests of the traits analyzed, we found 2 significant SNPs placed on cattle chromosomes BTA15 and BTA20, which are homologous to buffalo chromosomes BBU16 and BBU19, respectively. In this genome association study, we found several significant SNPs affecting buffalo milk production and quality. Furthermore, the use of the high-density bovine BeadChip was suitable for genomic analysis in buffaloes. Although extensive chromosome arm homology was described between cattle and buffalo, the exact chromosomal position of SNP markers associated with these economically important traits in buffalo can be determined only through buffalo genome sequencing.

Genetic associations between temperament and performance traits in Nellore beef cattle

The aim of this study was to estimate genetic associations between temperament and performance traits. Temperament was evaluated in yearling male and female Nellore cattle, using four traits: temperament score (TS), for assessing animals' reactions in a corral pen (n = 25,691); movement score (MOV), for animals' movements recorded inside the crush; crush score (CS), for animal's general reactivity inside the crush; and flight speed (FS), for the speed (in m/s) at which the animals exited the crush (n = 11,697, for the last three methods); for all the temperament traits, lower scores indicate animals with calmer temperament. Performance traits were visual scores for conformation (C), finishing precocity (P) and muscling (M) evaluated at yearlings, and average daily gain (ADG) was estimated from weaning to yearling. Bayesian inference using Gibbs sampling was applied to estimate (co)variance components and genetic and phenotypic parameters. Heritability estimates for the temperament traits ranged from 0.07 (CS) to 0.28 (FS). Genetic correlations of the temperament traits with ADG and C, P and M were negative and ranged from -0.02 to -0.31. Phenotypic correlations were negative and consistently lower than the genetic, ranging from -0.08 to -0.02. It was concluded that the temperament traits assessed had favourable genetic correlation estimates with the performance traits studied. However, indirect responses in temperament when selecting for higher ADG and visual scoring system of C, P and M, will be low.