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Heifer early calving (HC) plays a key role in beef cattle herds' economic sustainability and profitability by reducing production costs and generation intervals. However, the genetic basis of HC in Nelore heifers at different ages remains to be well understood. In this study, we aimed to perform a multi-trait weighted single-step genome-wide association (MT w-ssGWAS) to uncover the genetic mechanism involved in HC at 24 (HC24), 26 (HC26), 28 (HC28), and 30 (HC30) months of age in Nelore heifers. The MT w-ssGWAS pointed out four shared windows regions for HC24, HC26, HC28, and HC30 on BTA 5, 6, 14, and 16, explaining a larger proportion of genetic variation from 9.2% for HC30 to 10.6% for HC28. The shared regions harbored candidate genes related with the major gatekeeper for early puberty onset by controlling metabolic aspects related to homeostasis, reproductive, and growth (IGF1, PARPBP, PMCH, GNRHR, LYN, TMEM68, PLAG1, CHCHD7, KISS1, GOLT1A, and PPP1R15B). The MT w-ssGWAS and pathway analysis highlighted differences in physiological processes that support complex interactions between the gonadotropic axes, growth aspects, and sexual precocity in Nelore heifers, providing useful information for genetic improvement and management strategies., (Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved.)

Analyses of livestock genomes have been used to detect selection signatures, which are genomic regions associated with traits under selection leading to a change in allele frequency. The objective of the present study was to characterize selection signatures in Canchim composite beef cattle using cross-population analyses with the founder Nelore and Charolais breeds. High-density single nucleotide polymorphism genotypes were available on 395 Canchim representing the target population, along with genotypes from 809 Nelore and 897 Charolais animals representing the reference populations. Most of the selection signatures were co-located with genes whose functions agree with the expectations of the breeding programs; these genes have previously been reported to associate with meat quality, as well as reproductive traits. Identified genes were related to immunity, adaptation, morphology, as well as behavior, could give new perspectives for understanding the genetic architecture of Canchim. Some selection signatures identified genes that were recently introduced in Canchim, such as the loci related to the polled trait., Competing Interests: The authors have declared that no competing interests exist.

Our objectives were to estimate genetic parameters for male and female reproductive traits and their genetic correlations with body weight and carcass traits, evaluate the genetic trends over the years, and verify the effect of inbreeding on the phenotypes of Brahman cattle. The traits evaluated were body weights at 120, 210, 365, and 450 days of age (W120, W210, W365, and W450); scrotal circumference at 365 and 450 days of age (SC365 and SC450), age at first calving (AFC), gestation length (GL), stayability (STAY), ribeye area (REA), backfat thickness (BFT), and rump fat thickness (RFT). Direct heritability estimates ranged from 0.10 ± 0.03 (AFC) to 0.43 ± 0.06 (GL). Maternal heritability estimates for body weights, scrotal circumferences, and GL ranged from 0.07 ± 0.02 to 0.15 ± 0.03. The proportion of the maternal permanent environment for W120 and W210 was equal to 0.11 ± 0.02. Genetic correlations varied between -0.60 ± 0.25 (STAY and BFT) to 0.97 ± 0.01 (W365 and W450). Except for AFC, all genetic trends were significant (p < 0.05) and presented favorable annual genetic gains. Unfavorable effects due to the increase of inbreeding coefficients were observed for body weights and AFC, suggesting greater attention be paid to the applied mating systems to control inbreeding. Reproductive traits, such as AFC and STAY, could be assisted indirectly by scrotal circumference selection. The emphasis applied to body weight selection, especially at W210, may assist REA. The BFT and RFT traits presented genetic variability and have responded to selection, although not included in the Brahman selection index., (Copyright © 2021 Elsevier Inc. All rights reserved.)

In this study, we chose 17 worldwide sheep populations of eight breeds, which were intensively selected for different purposes (meat, milk, or wool), or locally-adapted breeds, in order to identify and characterize factors impacting the detection of runs of homozygosity (ROH) and heterozygosity-rich regions (HRRs) in sheep. We also applied a business intelligence (BI) tool to integrate and visualize outputs from complementary analyses. We observed a prevalence of short ROH, and a clear distinction between the ROH profiles across populations. The visualizations showed a fragmentation of medium and long ROH segments. Furthermore, we tested different scenarios for the detection of HRR and evaluated the impact of the detection parameters used. Our findings suggest that HRRs are small and frequent in the sheep genome; however, further studies with higher density SNP chips and different detection methods are suggested for future research. We also defined ROH and HRR islands and identified common regions across the populations, where genes related to a variety of traits were reported, such as body size, muscle development, and brain functions. These results indicate that such regions are associated with many traits, and thus were under selective pressure in sheep breeds raised for different purposes. Interestingly, many candidate genes detected within the HRR islands were associated with brain integrity. We also observed a strong association of high linkage disequilibrium pattern with ROH compared with HRR, despite the fact that many regions in linkage disequilibrium were not located in ROH regions.

One of the most significant challenges in deer is the ability to maintain genetic diversity, avoiding inbreeding and sustaining population health and reproduction. Although our general knowledge of reproductive physiology is improving, it appears that the application of assisted reproductive technology (ART) will more efficiently advance wildlife conservation efforts and preserve genetic diversity. The purpose of this review is to present the most important results obtained with the use of ART in Neotropical deer. Thus, the state-of-the-art for estrus synchronization, semen technology, artificial insemination, and in vivo embryo production will be presented. In vitro embryo production (IVP) is also a biotechnology that is taking initial steps in deer. In this aspect, the approach with the proteomics of ovarian follicular fluid is being used as a tool for a better understanding of oocyte maturation. Finally, cell banks and the use of interspecific somatic cell nuclear transfer (iSCNT) as well as the use of stem cells for gametes differentiation are promising techniques.

The aim of this study was to analyze the genomic homology between cattle ( Bos taurus ) and buffaloes ( Bubalus bubalis ) and to propose a rearrangement of the buffalo genome through linkage disequilibrium analyses of buffalo SNP markers referenced in the cattle genome assembly and also compare it to the buffalo genome assembly. A panel of bovine SNPs (single nucleotide polymorphisms) was used for hierarchical, non-hierarchical and admixture cluster analyses. Thus, the linkage disequilibrium information between markers of a specific panel of buffalo was used to infer chromosomal rearrangement. Haplotype diversity and imputation accuracy of the submetacentric chromosomes were also analyzed. The genomic homology between the species enabled us to use the bovine genome assembly to recreate a buffalo genomic reference by rearranging the submetacentric chromosomes. The centromere of the submetacentric chromosomes exhibited high linkage disequilibrium and low haplotype diversity. It allowed hypothesizing about chromosome evolution. It indicated that buffalo submetacentric chromosomes are a centric fusion of ancestral acrocentric chromosomes. The chronology of fusions was also suggested. Moreover, a linear regression between buffalo and cattle rearranged assembly and the imputation accuracy indicated that the rearrangement of the chromosomes was adequate. When using the bovine reference genome assembly, the rearrangement of the buffalo submetacentric chromosomes could be done by SNP BTA (chromosome of Bos taurus ) calculations: shorter BTA (shorter arm of buffalo chromosome) was given as [(shorter BTA length - SNP position in shorter BTA)] and larger BTA length as [shorter BTA length + (larger BTA length - SNP position in larger BTA)]. Finally, the proposed linkage disequilibrium-based method can be applied to elucidate other chromosomal rearrangement events in other species with the possibility of better understanding the evolutionary relationship between their genomes., (Copyright © 2020 Jordan de Abreu Santos et al.)

This study compared imputation from lower-density commercial and customized panels to high-density panels and a combined panel (Illumina and Affymetrix) in Nelore beef cattle. Additionally, linkage disequilibrium and haplotype block conformation were estimated in individual high-density panels and compared with corresponding values in the combined panel after imputation. Overall, 814 animals were genotyped using BovineHD BeadChip (IllumHD), and 93 of these animals were also genotyped using the Axion Genome-Wide BOS 1 Array Plate (AffyHD). In general, customization considering linkage disequilibrium and minor allele frequency had the highest accuracies. The IllumHD panel had higher values of linkage disequilibrium for short distances between SNPs than AffyHD and the combined panel. The combined panel had an increased number of small haplotype blocks. The use of a combined panel is recommended due to its increased density and number of haplotype blocks, which in turn increase the probability of a marker being close to a quantitative trait locus of interest. Considering common SNPs between IllumHD and AffyHD for the customization of a low-density panel increases the imputation accuracy for IllumHD, AffyHD and the combined panel.

Single nucleotide polymorphism (SNP) markers are used to study population structure and conservation genetics, which permits assessing similarities regarding the linkage disequilibrium and information about the relationship among individuals. To investigate the population genomic structure of 300 females and 25 males from a commercial maternal pig line we analyzed linkage disequilibrium extent, inbreeding coefficients using genomic and conventional pedigree data, and population stratification. The average linkage disequilibrium (r2) was 0.291 ± 0.312 for all adjacent SNPs, distancing less than 100 Kb (kilobase) between markers. The average inbreeding coefficients obtained from runs of homozygosity (ROH) and pedigree analyses were 0.119 and 0.0001, respectively. Low correlation was observed between the inbreeding coefficients possibly as a result of genetic recombination effect accounted for the ROH estimates or caused by pedigree identification errors. A large number of long ROHs might indicate recent inbreeding events in the studied population. A total of 36 homozygous segments were found in more than 30% of the population and these ROH harbor genes associated with reproductive traits. The population stratification analysis indicated that this population was possibly originated from two distinct populations, which is a result from crossings between the eastern and western breeds used in the formation of the line. Our findings provide support to understand the genetic structure of swine populations and may assist breeding companies to avoid a high level of inbreeding coefficients to maintain genetic diversity, showing the effectiveness of using genome-wide SNP information for quantifying inbreeding when the pedigree was incomplete or incorrect., Competing Interests: The authors have declared that no competing interests exist.

Genomic regions under high selective pressure present specific runs of homozygosity (ROH), which provide valuable information on the genetic mechanisms underlying the adaptation to environment imposed challenges. In broiler chickens, the adaptation to conventional production systems in tropical environments lead the animals with favorable genotypes to be naturally selected, increasing the frequency of these alleles in the next generations. In this study, ~1400 chickens from a paternal broiler line were genotyped with the 600 K Affymetrix® Axiom® high-density (HD) genotyping array for estimation of linkage disequilibrium (LD), effective population size (N e ), inbreeding and ROH. The average LD between adjacent single nucleotide polymorphisms (SNPs) in all autosomes was 0.37, and the LD decay was higher in microchromosomes followed by intermediate and macrochromosomes. The N e of the ancestral population was high and declined over time maintaining a sufficient number of animals to keep the inbreeding coefficient of this population at low levels. The ROH analysis revealed genomic regions that harbor genes associated with homeostasis maintenance and immune system mechanisms, which may have been selected in response to heat stress. Our results give a comprehensive insight into the relationship between shared ROH regions and putative regions related to survival and production traits in a paternal broiler line selected for over 20 years. These findings contribute to the understanding of the effects of environmental and artificial selection in shaping the distribution of functional variants in the chicken genome.

Background: Beef cattle breeding programs in Brazil have placed greater emphasis on the genomic study of reproductive traits of males and females due to their economic importance. In this study, genome-wide associations were assessed for scrotal circumference at 210 d of age, scrotal circumference at 420 d of age, age at first calving, and age at second calving, in Canchim beef cattle. Data quality control was conducted resulting in 672,778 SNPs and 392 animals., Results: Associated SNPs were observed for scrotal circumference at 420 d of age (435 SNPs), followed by scrotal circumference at 210 d of age (12 SNPs), age at first calving (six SNPs), and age at second calving (four SNPs). We investigated whether significant SNPs were within genic or surrounding regions. Biological processes of genes were associated with immune system, multicellular organismal process, response to stimulus, apoptotic process, cellular component organization or biogenesis, biological adhesion, and reproduction., Conclusions: Few associations were observed for scrotal circumference at 210 d of age, age at first calving, and age at second calving, reinforcing their polygenic inheritance and the complexity of understanding the genetic architecture of reproductive traits. Finding many associations for scrotal circumference at 420 d of age in various regions of the Canchim genome also reveals the difficulty of targeting specific candidate genes that could act on fertility; nonetheless, the high linkage disequilibrium between loci herein estimated could aid to overcome this issue. Therefore, all relevant information about genomic regions influencing reproductive traits may contribute to target candidate genes for further investigation of causal mutations and aid in future genomic studies in Canchim cattle to improve the breeding program.

The aim of this study was to estimate genetic parameters for scrotal circumference at 365 (SC365) and 450 (SC450) days of age, age at first calving (AFC), ribeye area (REA), backfat (BF) thickness, and rump fat (RF) thickness, in order to provide information on potential traits for Nelore cattle breeding program. Genetic parameters were estimated using the Average Information Restricted Maximum Likelihood method in single- and multitrait analyses. Four different animal models were tested for SC365, SC450, REA, BF, and RF in single-trait analyses. For SC365 and SC450, the maternal genetic effect was statistically significant (P < 0.01) and was included for multitrait analyses. The direct heritability estimates for SC365, SC450, AFC, REA, BF, and RF were equal to 0.31, 0.38, 0.24, 0.32, 0.16, and 0.19, respectively. Maternal heritability for SC365 and SC450 was equal to 0.06 and 0.08, respectively. The highest genetic correlations were found among the scrotal circumferences. Testing for the inclusion of maternal effects in genetic parameters estimation for scrotal circumference should be evaluated in the Nelore breeding program, mostly for correctly ranking the animal's estimated breeding values. Similar heritability estimates were observed for scrotal circumference, as well as favorable genetic correlations of this trait with AFC and carcass traits. Thus, scrotal circumference measured at 365 days of age could be a target trait for consideration in the Nelore selection index in order to improve most of the traits herein analyzed., (Copyright © 2016. Published by Elsevier Inc.)

The aims of our study were to estimate genetic parameters for body weight and visual scores and to evaluate their inclusion as selection criteria in the Nelore breeding program in Brazil. The traits studied were the body weight adjusted to 210 (W210) and to 450 (W450) days of age and visual scores for body structure, finishing precocity, and muscling evaluated at weaning (BS W , FP W , and MS W ) and yearling (BS Y , FP Y , and MS Y ) ages. A total of 33,242, 26,259, 23,075, and 26,057 observations were considered to analyze W210, W450, and visual scores at weaning and yearling. The significant (P < 0.05) fixed effects for all traits were farm, birth season, birth year, sex, and management group. Single-trait analyses were performed to define the most fitting model to our data using the average information restricted maximum likelihood algorithm, for weaning traits. Subsequently, these models were used in single- and two-trait analyses considering the Bayesian inference algorithm. Two-trait Bayesian analyses resulted in average direct heritability estimates for BS W , FP W , MS W , W210, BS Y , FP Y , MS Y , and W450 of 0.28, 0.30, 0.27, 0.28, 0.40, 0.44, 0.39, and 0.50, respectively. Genetic correlations varied from 0.40 to 0.96. Benefits to animal performance can best be achieved by considering body structure, finishing precocity, and muscling as selection criteria in the Nelore breeding programs. The decision to use visual scores measured at weaning should be considered in order to decrease generation interval and assist pre-selecting individuals, expecting carcass improvements in the future progeny.

The aim of this study was to evaluate the level of introgression of breeds in the Canchim (CA: 62.5% Charolais-37.5% Zebu) and MA genetic group (MA: 65.6% Charolais-34.4% Zebu) cattle using genomic information on Charolais (CH), Nelore (NE), and Indubrasil (IB) breeds. The number of animals used was 395 (CA and MA), 763 (NE), 338 (CH), and 37 (IB). The Bovine50SNP BeadChip from Illumina panel was used to estimate the levels of introgression of breeds considering the Maximum likelihood, Bayesian, and Single Regression method. After genotype quality control, 32,308 SNPs were considered in the analysis. Furthermore, three thresholds to prune out SNPs in linkage disequilibrium higher than 0.10, 0.05, and 0.01 were considered, resulting in 15,286, 7,652, and 1,582 SNPs, respectively. For k = 2, the proportion of taurine and indicine varied from the expected proportion based on pedigree for all methods studied. For k = 3, the Regression method was able to differentiate the animals in three main clusters assigned to each purebred breed, showing more reasonable according to its biological viewpoint. Analyzing the data considering k = 2 seems to be more appropriate for Canchim-MA animals due to its biological interpretation. The usage of 32,308 SNPs in the analyses resulted in similar findings between the estimated and expected breed proportions. Using the Regression approach, a contribution of Indubrasil was observed in Canchim-MA when k = 3 was considered. Genetic parameter estimation could account for this breed composition information as a source of variation in order to improve the accuracy of genetic models. Our findings may help assemble appropriate reference populations for genomic prediction for Canchim-MA in order to improve prediction accuracy. Using the information on the level of introgression in each individual could also be useful in breeding or crossing design to improve individual heterosis in crossbred cattle., Competing Interests: Ricardo Vieira Ventura is an employee of Beef Improvement Opportunities (BIO). This does not alter our adherence to PLOS ONE policies on sharing data and materials. There is no other competing interest to be declared according to the policy of PLOS ONE.

Background: Knowledge on the levels of linkage disequilibrium (LD) across the genome, persistence of gametic phase between breed pairs, genetic diversity and population structure are important parameters for the successful implementation of genomic selection. Therefore, the objectives of this study were to investigate these parameters in order to assess the feasibility of a multi-herd and multi-breed training population for genomic selection in important purebred and crossbred pig populations in Canada. A total of 3,057 animals, representative of the national populations, were genotyped with the Illumina Porcine SNP60 BeadChip (62,163 markers)., Results: The overall LD (r 2 ) between adjacent SNPs was 0.49, 0.38, 0.40 and 0.31 for Duroc, Landrace, Yorkshire and Crossbred (Landrace x Yorkshire) populations, respectively. The highest correlation of phase (r) across breeds was observed between Crossbred animals and either Landrace or Yorkshire breeds, in which r was approximately 0.80 at 1 Mbp of distance. Landrace and Yorkshire breeds presented r ≥ 0.80 in distances up to 0.1 Mbp, while Duroc breed showed r ≥ 0.80 for distances up to 0.03 Mbp with all other populations. The persistence of phase across herds were strong for all breeds, with r ≥ 0.80 up to 1.81 Mbp for Yorkshire, 1.20 Mbp for Duroc, and 0.70 Mbp for Landrace. The first two principal components clearly discriminate all the breeds. Similar levels of genetic diversity were observed among all breed groups. The current effective population size was equal to 75 for Duroc and 92 for both Landrace and Yorkshire., Conclusions: An overview of population structure, LD decay, demographic history and inbreeding of important pig breeds in Canada was presented. The rate of LD decay for the three Canadian pig breeds indicates that genomic selection can be successfully implemented within breeds with the current 60 K SNP panel. The use of a multi-breed training population involving Landrace and Yorkshire to estimate the genomic breeding values of crossbred animals (Landrace × Yorkshire) should be further evaluated. The lower correlation of phase at short distances between Duroc and the other breeds indicates that a denser panel may be required for the use of a multi-breed training population including Duroc.

Background: Recent technological advances in genomics have allowed the genotyping of cattle through single nucleotide polymorphism (SNP) panels. High-density SNP panels possess greater genome coverage and are useful for the identification of conserved regions of the genome due to selection, known as selection signatures (SS). The SS are detectable by different methods, such as the extended haplotype homozygosity (EHH); and the integrated haplotype score (iHS), which is derived from the EHH. The aim of this study was to identify SS regions in Canchim cattle (composite breed), genotyped with high-density SNP panel., Results: A total of 687,655 SNP markers and 396 samples remained for SS analysis after the genotype quality control. The iHS statistic for each marker was transformed into piHS for better interpretation of the results. Chromosomes BTA5 and BTA14 showed piHS > 5, with 39 and nine statistically significant SNPs (P < 0.00001), respectively. For the candidate selection regions, iHS values were computed across the genome and averaged within non-overlapping windows of 500 Kb. We have identified genes that play an important role in metabolism, melanin biosynthesis (pigmentation), and embryonic and bone development., Conclusions: The observation of SS indicates that the selection processes performed in Canchim, as well as in the founder breeds (i.e. Charolais), are maintaining specific genomic regions, particularly on BTA5 and BTA14. These selection signatures regions could be associated with Canchim characterization.

The aim of this study was to estimate genetic parameters for accumulated productivity (ACP), first calving interval (CI1), second calving interval (CI2), and mean calving interval (MCI) in Nelore beef cattle. The ACP trait is a reproduction index and comprises the total number of calves born per dam, weight of weaned calves, and age of the dam at calving. Genetic parameters were estimated by the average information restricted maximum likelihood method in two-trait analyses. The average heritability estimate for ACP was 0.17 (0.03). For CI1, CI2, and MCI, the heritability estimates were 0.02, 0.02, and 0.06, respectively. Genetic correlations between ACP with CI1, CI2, and MCI were -0.16 ± 0.47, -0.29 ± 0.53, and -0.40 ± 0.27, respectively. Despite of the low heritability estimates obtained in our study, reproduction traits should be further studied and their inclusion in the selection criteria must be evaluated in order to improve the performance of females because these traits are of great economic importance in beef cattle. Accumulated productivity could contribute to decrease the mean calving interval in Nelore cattle.

The Tabapuã breed is a beef cattle Brazilian breed known for its sexual precocity and desirable characteristics for tropical conditions. However, this is a newly formed breed and few studies have been conducted regarding genetic parameters and genetic trends for its reproductive traits. The objective of the present study was to estimate the genetic parameters, genetic trends, and relative selection efficiency for weaning weight adjusted to 210 d of age (W210), age at first calving (AFC), average calving interval (ACI), first calving interval (CI1), and accumulated productivity (ACP) among Tabapuã beef cattle. Pedigree data on 15,241 Tabapuã animals born between 1958 and 2011 and phenotype records from 7,340 cows born between 1970 and 2011 were supplied by the National Association of Breeders and Researchers (Associação Nacional de Criadores e Pesquisadores). Analysis through the least squares method assisted in defining the fixed effects that were considered within the models. The estimates for the genetic parameters were obtained through the REML, using a multitrait animal model. The likelihood ratio test applied for W210 was significant ( < 0.05) for the inclusion of maternal additive genetic and permanent environmental effects in the model. Genetic trends were calculated through linear regression of the EBV of the animals, according to the year of birth. The heritability estimates obtained ranged from 0.04 ± 0.03 for CI1 to 0.25 ± 0.05 for W210. The genetic correlations ranged from 0.004 ± 0.19 for W210-AFC and 0.93 ± 0.12 for ACI-CI1. The genetic trend was significant ( < 0.05) and favorable for CI1 and the maternal genetic effect of W210 and was significant ( < 0.05) and unfavorable for AFC, ACI, and ACP. The ACP could be used in the selection index to assist the breeding goal of improved productive and reproductive performance. The genetic trends indicated small and unfavorable genetic changes for AFC, ACI, and ACP in light of the recent implementation of a genetic breeding program for this breed.

Background: Genotype imputation has been used to increase genomic information, allow more animals in genome-wide analyses, and reduce genotyping costs. In Brazilian beef cattle production, many animals are resulting from crossbreeding and such an event may alter linkage disequilibrium patterns. Thus, the challenge is to obtain accurately imputed genotypes in crossbred animals. The objective of this study was to evaluate the best fitting and most accurate imputation strategy on the MA genetic group (the progeny of a Charolais sire mated with crossbred Canchim X Zebu cows) and Canchim cattle. The data set contained 400 animals (born between 1999 and 2005) genotyped with the Illumina BovineHD panel. Imputation accuracy of genotypes from the Illumina-Bovine3K (3K), Illumina-BovineLD (6K), GeneSeek-Genomic-Profiler (GGP) BeefLD (GGP9K), GGP-IndicusLD (GGP20Ki), Illumina-BovineSNP50 (50K), GGP-IndicusHD (GGP75Ki), and GGP-BeefHD (GGP80K) to Illumina-BovineHD (HD) SNP panels were investigated. Seven scenarios for reference and target populations were tested; the animals were grouped according with birth year (S1), genetic groups (S2 and S3), genetic groups and birth year (S4 and S5), gender (S6), and gender and birth year (S7). Analyses were performed using FImpute and BEAGLE software and computation run-time was recorded. Genotype imputation accuracy was measured by concordance rate (CR) and allelic R square (R(2))., Results: The highest imputation accuracy scenario consisted of a reference population with males and females and a target population with young females. Among the SNP panels in the tested scenarios, from the 50K, GGP75Ki and GGP80K were the most adequate to impute to HD in Canchim cattle. FImpute reduced computation run-time to impute genotypes from 20 to 100 times when compared to BEAGLE., Conclusion: The genotyping panels possessing at least 50 thousands markers are suitable for genotype imputation to HD with acceptable accuracy. The FImpute algorithm demonstrated a higher efficiency of imputed markers, especially in lower density panels. These considerations may assist to increase genotypic information, reduce genotyping costs, and aid in genomic selection evaluations in crossbred animals.

A multitrait model (MC) and 5 reduced-rank models with principal component structure (components PC, PC, PC, PC, and PC) were compared. The objectives were to determine the most appropriate model for estimating genetic parameters and to evaluate the genetic progress of dual-purpose buffaloes in Colombia using that model. The traits evaluated were weaning weight (WW), yearling weight (W12), weight at 18 mo of age (W18), weight at 2 yr of age (W24), age at first calving (AFC), and milk yield at 270 d of first lactation (MY270). Genealogy and productive information from 34,326 buffaloes born in Colombia between 1997 and 2014 were used. Colombian Association of Buffalo Breeders (ACB) provided the data. Direct additive genetic and residual random effects were included for all the traits. In addition, the maternal additive genetic effect and permanent environmental random effect were included for WW, while a maternal additive genetic effect was included for W12. The fixed effects were contemporary group (farm, year, and calving season: January to April, May to August, or September to December; for all traits) and sex (for WW, W12, W18, and W24). Additionally, parity was included as a fixed effect for WW and W12. Age at weighing was used as a covariate for WW, W12, W18, and W24. Genetic progress of all traits was analyzed using a generalized smooth model (GAM). According to the Akaike information criteria (AIC), the best model was the one with reduced rank and first 3 principal components (PC). This model maintained 100% of the original variance. Genetic parameters estimated with this model were similar to those estimated by MC, but with smaller standard errors. Heritability for weight-related traits ranged between 0.23 and 0.44. Heritabilities for AFC and MY270 were 0.14 and 0.24, respectively. The genetic correlations obtained between all weights (WW, W12, W18, and W24) were positive and high. Correlations between all weights with AFC were negative and moderate. Correlations between all weights with MY270 were positive and moderate, and between MY270 with AFC were negative and low.

The availability of dense genomic information has increased genome-wide association studies for the bovine species; however research to assess the effect of single genes on production traits is still important to elucidate the genes functions. On this study the association of IGF1, GH, and PIT1 markers with growth and reproductive traits (birth weight, weaning weight, weight at 12 and 18 months of age, preweaning average daily weight gain, age and weight at first calving, and scrotal circumference at 12 and 18 months of age) were assessed by means of the variance component approach. The phenotypes were adjusted and then analyzed under two animal models, one which considered the polygenic and genotype (IGF1, GH or PIT1 markers) effects (Model 1), and the other which considers only the polygenic effect (Model 2). When the likelihood ratio test and the Bonferroni correction was applied at 5 % significance level, the genetic markers for the IGF1, GH, and PIT1 genes did not influence significantly the traits (p > 0.002). However, evidence of association of IGF1 with birth weight (p = 0.06) and GH with weight at first calving (p = 0.03) and with weight at 12 months of age (p = 0.08) was observed. In conclusion we could not confirm the associations between IGF1, GH, and PIT1 and growth traits that were previously reported in Canchim cattle, and no association was observed between these genes and reproductive traits. Future studies involving functional markers of IGF1, GH and PIT1 genes may help to clarify the role of these genes in growth and reproductive processes.

Beef cattle producers in Brazil use body weight traits as breeding program selection criteria due to their great economic importance. The objectives of this study were to evaluate different animal models, estimate genetic parameters, and define the most fitting model for Brahman cattle body weight standardized at 120 (BW120), 210 (BW210), 365 (BW365), 450 (BW450), and 550 (BW550) days of age. To estimate genetic parameters, single-, two-, and multi-trait analyses were performed using the animal model. The likelihood ratio test was verified between all models. For BW120 and BW210, additive direct genetic, maternal genetic, maternal permanent environment, and residual effects were considered, while for BW365 and BW450, additive direct genetic, maternal genetic, and residual effects were considered. Finally, for BW550, additive direct genetic and residual effects were considered. Estimates of direct heritability for BW120 were similar in all analyses; however, for the other traits, multi-trait analysis resulted in higher estimates. The maternal heritability and proportion of maternal permanent environmental variance to total variance were minimal in multi-trait analyses. Genetic, environmental, and phenotypic correlations were of high magnitude between all traits. Multi-trait analyses would aid in the parameter estimation for body weight at older ages because they are usually affected by a lower number of animals with phenotypic information due to culling and mortality.

Studies are being conducted on the applicability of genomic data to improve the accuracy of the selection process in livestock, and genome-wide association studies (GWAS) provide valuable information to enhance the understanding on the genetics of complex traits. The aim of this study was to identify genomic regions and genes that play roles in birth weight (BW), weaning weight adjusted for 210 days of age (WW), and long-yearling weight adjusted for 420 days of age (LYW) in Canchim cattle. GWAS were performed by means of the Generalized Quasi-Likelihood Score (GQLS) method using genotypes from the BovineHD BeadChip and estimated breeding values for BW, WW, and LYW. Data consisted of 285 animals from the Canchim breed and 114 from the MA genetic group (derived from crossings between Charolais sires and ½ Canchim + ½ Zebu dams). After applying a false discovery rate correction at a 10% significance level, a total of 4, 12, and 10 SNPs were significantly associated with BW, WW, and LYW, respectively. These SNPs were surveyed to their corresponding genes or to surrounding genes within a distance of 250 kb. The genes DPP6 (dipeptidyl-peptidase 6) and CLEC3B (C-type lectin domain family 3 member B) were highlighted, considering its functions on the development of the brain and skeletal system, respectively. The GQLS method identified regions on chromosome associated with birth weight, weaning weight, and long-yearling weight in Canchim and MA animals. New candidate regions for body weight traits were detected and some of them have interesting biological functions, of which most have not been previously reported. The observation of QTL reports for body weight traits, covering areas surrounding the genes (SNPs) herein identified provides more evidence for these associations. Future studies targeting these areas could provide further knowledge to uncover the genetic architecture underlying growth traits in Canchim cattle.

Background: The development of linkage disequilibrium (LD) maps and the characterization of haplotype block structure at the population level are useful parameters for guiding genome wide association (GWA) studies, and for understanding the nature of non-linear association between phenotypes and genes. The elucidation of haplotype block structure can reduce the information of several single nucleotide polymorphisms (SNP) into the information of a haplotype block, reducing the number of SNPs in a coherent way for consideration in GWA and genomic selection studies., Results: The maximum average LD, measured by r2 varied between 0.33 to 0.40 at a distance of < 2.5 kb, and the minimum average values of r2 varied between 0.05 to 0.07 at distances ranging from 400 to 500 kb, clearly showing that the average r2 reduced with the increase in SNP pair distances. The persistence of LD phase showed higher values at shorter genomic distances, decreasing with the increase in physical distance, varying from 0.96 at a distance of < 2.5 kb to 0.66 at a distance from 400 to 500 kb. A total of 78% of all SNPs were clustered into haplotype blocks, covering 1,57 Mb of the total autosomal genome size., Conclusions: This study presented the first high density linkage disequilibrium map and haplotype block structure for a composite beef cattle population, and indicates that the high density SNP panel over 700 k can be used for genomic selection implementation and GWA studies for Canchim beef cattle.

Phenotypic data from female Canchim beef cattle were used to obtain estimates of genetic parameters for reproduction and growth traits using a linear animal mixed model. In addition, relationships among animal estimated breeding values (EBVs) for these traits were explored using principal component analysis. The traits studied in female Canchim cattle were age at first calving (AFC), age at second calving (ASC), calving interval (CI), and bodyweight at 420 days of age (BW420). The heritability estimates for AFC, ASC, CI and BW420 were 0.03±0.01, 0.07±0.01, 0.06±0.02, and 0.24±0.02, respectively. The genetic correlations for AFC with ASC, AFC with CI, AFC with BW420, ASC with CI, ASC with BW420, and CI with BW420 were 0.87±0.07, 0.23±0.02, -0.15±0.01, 0.67±0.13, -0.07±0.13, and 0.02±0.14, respectively. Standardised EBVs for AFC, ASC and CI exhibited a high association with the first principal component, whereas the standardised EBV for BW420 was closely associated with the second principal component. The heritability estimates for AFC, ASC and CI suggest that these traits would respond slowly to selection. However, selection response could be enhanced by constructing selection indices based on the principal components.

Genetic parameters for weight at maturity (WM), maturation rate (MR), age and weight at first calving (AFC and WFC) and second calving (ASC and WSC) were estimated for females of the Canchim breed. The number of records per trait ranged from 1440 to 1923. The restricted maximum likelihood method was used and the statistical model included the fixed effect of contemporary group and the additive genetic and residual as random effects. The mean heritability estimate and respective standard errors were 0.34±0.05 (WM), 0.13±0.04 (MR), 0.14±0.04 (AFC), 0.44±0.06 (WFC), 0.16±0.06 (ASC) and 0.39±0.06 (WSC). The heritability estimate for WM and MR suggested that it would be possible to achieve changes in the animals' growth curve through selection, but the genetic correlation between these two traits suggested that there would be antagonism between them. Selection for WM would result in animals with later growth and would also affect individuals' sexual precocity. This was also seen from the genetic correlations between WM and the other traits, which ranged from 0.37 to 0.98; and between MR and the other traits, which ranged from -0.83 to -0.25. Selection to modify WM would be expected to result in correlated responses in AFC, WFC and WSC and a moderate response in ASC. Although the heritability estimate for MR was low, selection aimed for its increase might cause a large decrease in AFC, ASC and WFC and a moderate change in WSC, and this could be an alternative for improving the progeny's overall performance.

In this study, the objective was to estimate genetic parameters of body weight at 210 (BW210) and 365 (BW365) days of age in relation to rib eye area (REA), subcutaneous back fat thickness (BF) and rump fat (RF), and their respective genetic trends, in Nelore beef cattle. Estimates of genetic parameters and breeding values for the studied traits were obtained using the REML method. The direct and maternal heritability estimates were respectively: 0.25±0.02 and 0.21±0.01, for BW210, and 0.29±0.02 and 0.09±0.01, for BW365. The heritability estimates for transformed REA, BF and RF were 0.29±0.03, 0.21±0.02 and 0.23±0.03, respectively. There were genetic associations between BW210 and REA, BW365 and REA, and BF and RF, while the other correlations were low. The selection process that was conducted at the farms participating in the breeding program, taking the proposed selection index into consideration, caused genetic changes to these traits., (Copyright © 2012 Elsevier Ltd. All rights reserved.)

Animal temperament is a trait of economic relevance and its use as a selection criterion requires the identification of environmental factors that influence this trait, as well as the estimation of its genetic variability and interrelationship with other traits. The objectives of this study were to evaluate the effect of the covariates dam age at calving (ADC), long yearling age (YA) and long yearling weight (YW) on temperament score (T) and to estimate genetic parameters for T, scrotal circumference (SC) at long YA and age at first calving (AFC) in Nellore cattle participating in a selection program. The traits were analyzed by the restricted maximum likelihood method under a multiple-trait animal model. For all traits, contemporary group was included as a fixed effect and additive genetic and residual as random effects. In addition to these effects, YA, YW and ADC were considered for analyzing T. In the case of SC and AFC, the effect of long YW was included as a covariate. Genetic parameters were estimated for and between traits. The three covariates significantly influenced T. The heritability estimates for T, SC and AFC were 0.18 ± 0.02, 0.53 ± 0.04 and 0.23 ± 0.08, respectively. The genetic correlations between T and SC, and T and AFC were -0.07 ± 0.17 and -0.06 ± 0.19, respectively. The genetic correlation estimated between SC and AFC was -0.57 ± 0.16. In conclusion, a response to selection for T, SC and AFC is expected and selection for T does not imply correlated responses with the other traits.

Studies estimating genetic parameters for reproductive traits in chickens can be useful for understanding and improvement of their genetic architecture. A total of 1276 observations of fertility (FERT), hatchability of fertile eggs (HFE) and hatchability of total eggs (HTE) were used to estimate the genetic and phenotypic parameters of 467 females from an F2 population generated by reciprocal crossing between a broiler line and a layer line, which were developed through a poultry genetics breeding program, maintained by Embrapa Swine and Poultry, Concordia, Santa Catarina, Brazil. Estimates of heritability and genetic and phenotypic correlations were obtained using restricted maximum likelihood calculations under the two-trait animal model, including the fixed effect of group (hatching of birds from the same genetic group) and the random additive genetic and residual effects. The mean percentages for FERT, HFE and HTE were 87.91 ± 19.77, 80.07 ± 26.81 and 70.67 ± 28.55%, respectively. The highest heritability estimate (h(2)) was 0.28 ± 0.04 for HTE. Genetic correlations for FERT with HFE (0.43 ± 0.17), HFE with HTE (0.98 ± 0.02) and FERT with HTE (0.69 ± 0.10) were positive and significant. Individuals with high breeding value for HTE would have high breeding values for HFE and FERT because of the high genetic association between them. These results suggest that HTE should be included as a selection criterion in genetic breeding programs to improve the reproductive performance of chickens, because HTE had the highest heritability estimate and high genetic correlation with FERT and HFE, and it is the easiest to measure.

Heritability estimates and genetic correlations were obtained for body weight and scrotal circumference, adjusted, respectively, to 12 (BW12 and SC12) and 18 (BW18 and SC18) months of age, for 10 742 male Nellore cattle. The adjustments to SC12 and SC18 were made using a nonlinear logistic function, while BW12 and BW18 were obtained by linear adjustment. The contemporary groups (CGs) were defined from animals born on the same farm, in the same year and birth season. The mean heritability estimates obtained using the restricted maximum likelihood method in bi-trait analysis were 0.25, 0.25, 0.29 and 0.42 for BW12, BW18, SC12 and SC18, respectively. The genetic correlations were 0.30 ± 0.11, 0.21 ± 0.13, 0.21 ± 0.11, -0.08 ± 0.15, 0.16 ± 0.12 and 0.89 ± 0.04 between the traits BW12 and BW18; BW12 and SC12; BW12 and SC18; BW18 and SC12; BW18 and SC18; and SC12 and SC18. The heritability for SC18 was considerably greater than for SC12, suggesting that this should be included as a selection criterion. The genetic correlation between BW18 and SC12 was close to zero, indicating that these traits did not influence each other. The contrary occurred between SC12 and SC18, indicating that selection using one of these could alter the other. Because of the mean magnitudes of heritabilities in the various measurements of weight and scrotal perimeter, it is suggested that the practice of individual selection for these traits is possible.