Background A decline in the level of genetic diversity in livestock can result in reduced response to selection, greater incidence of genetic defects, and inbreeding depression. In this context, various metrics have been proposed to assess the level of genetic diversity in selected populations. Therefore, the main goals of this study were to: 1) investigate the population structure of 16 cattle populations from 15 different pure breeds or composite populations, which have been selected for different breeds goals; and, 2) identify and compare runs of homozygosity (ROH) and heterozygosity-enriched regions (HER) based on different single nucleotide polymorphism (SNP) panels and whole-genome sequence data (WGS), followed by functional genomic analyses. Results A total of 24,187 ROH were found across all cattle populations, with 55% classified in the 2-4 Mb size group. Fourteen homozygosity islands were found in five populations, where four ROH islands located on BTA1, BTA5, BTA16, and BTA19 overlapped between the Brahman (BRM) and Gyr (GIR) breeds. A functional analysis of the genes found in these islands revealed candidate genes known to play a role in the melanogenesis, prolactin signaling, and calcium signaling pathways. The correlations between inbreeding metrics ranged from 0.02 to 0.95, where the methods based on homozygous genotypes (FHOM), uniting of gametes (FUNI), and genotype additive variance (FGRM) showed strong correlations among them. All methods yielded low to moderate correlations with the inbreeding coefficients based on runs of homozygosity (FROH). For the HER, 3576 runs and 26 islands, distributed across all autosomal chromosomes, were found in regions containing genes mainly related to the immune system, indicating potential balancing selection. Although the analyses with WGS did not enable detection of the same island patterns, it unraveled novel regions not captured when using SNP panel data. Conclusions The cattle populations that showed the largest amount of ROH and HER were Senepol (SEN) and Montana (MON), respectively. Overlapping ROH islands were identified between GIR and BRM breeds, indicating a possible historical connection between the populations. The distribution and pattern of ROH and HER are population specific, indicating that different breeds have experienced divergent selection processes or different genetic processes.

Background: A decline in the level of genetic diversity can result in reduced response to selection, greater incidence of genetic defects, and inbreeding depression. In this context, some metrics have been proposed to assess the levels of populational genetic diversity in selected populations. The main goals of this study were to: 1) investigate the population structure of 16 cattle populations from 15 different pure breeds or composite populations, which have been selected for different breeds goals; and, 2) identify and compare runs of homozygosity (ROH) and heterozygosity-enriched regions (HER) based on different single nucleotide polymorphism (SNP) panels and whole-genome sequence data (WGS), followed by functional genomic analyses. Results: A total of 24,187 ROH were found across all cattle populations, with 55% classified in the 2-4 Mb size group. Fourteen homozygosity islands were found in five populations, where four islands located on BTA1, BTA5, BTA16, and BTA19 overlapped between the Brahman (BRM) and Gyr (GIR) breeds. A functional analysis of the genes found in these islands revealed candidate genes known to play a role in the melanogenesis, prolactin signaling, and calcium signaling pathways. The correlations between inbreeding metrics ranged from 0.02 to 0.95, where the methods based on homozygous genotypes (FHOM), uniting of gametes (FUNI), and genotype additive variance (FGRM) showed strong correlations among them. All methods yielded low to moderate correlations with the inbreeding coefficients based on runs of homozygosity (FROH). For the HER, 3,576 runs and 26 islands, distributed across all autosomal chromosomes, were found in regions containing genes mainly related to the immune system. Although the analyses with WGS did not enable detection of the same island patterns, it unraveled novel regions not captured when using SNP panel data.Conclusions: The cattle populations that showed the largest amount of ROH and HER were Senepol (SEN) and Montana (MON), respectively. Overlapping ROH islands were identified between GIR and BRM breeds, indicating a possible historical connection between the populations. The distribution and pattern of ROH and HER are population specific, indicating that different breeds have experienced divergent selection processes or different genetic processes.

Objective: The objective of this study was to evaluate the genetic behavior of a population of Holstein cattle in response to the variation of environmental temperature by analyzing the effects of genotype by environment interaction (GEI) through reaction norms for the somatic cell score (SCS).Methods: Data was collected for 67,206 primiparous cows from the database of the Paraná Holstein Breeders Association in Brazil, with the aim of evaluating the temperature effect, considered as an environmental variable, distinguished under six gradients, with the variation range found being 17°C to 19.5°C, over the region. A reaction norm model was adopted utilizing the fourth order under the Legendre polynomials, using the mixed models of analysis by the restricted maximum likelihood method by the WOMBAT software. Additionally, the genetic behavior of the 15 most representative bulls was assessed, in response to the changes in the temperature gradient.Results: A mean score of 2.66 and a heritability variation from 0.17 to 0.23 was found in the regional temperature increase. The correlation between the environmental gradients proved to be higher than 0.80. Distinctive genetic behaviors were observed according to the increase in regional temperature, with an observed increase of up to 0.258 in the breeding values of some animals, as well as a reduction in the breeding of up to 0.793, with occasional reclassifications being observed as the temperature increased.Conclusion: Non-relevant GEI for SCS were observed in Holstein cattle herds of southern Brazil. Thus, the inclusion of the temperature effect in the model of genetic evaluation of SCS for the southern Brazilian Holstein breed is not required.

Breeding and genetics Full-length research article Population structure and inbreeding of Holstein cattle in southern Brazil ABSTRACT-The present investigation aimed to evaluate the population structure and inbreeding of Holstein herds in southern Brazil. To carry out the analysis, the Associação Paranaense de Criadores de Bovinos da Raça Holandesa (APCBRH) in Brazil provided the data, which consisted of a pedigree file of 206,796 animals born between 1970 and 2014. Results regarding the following parameters were determined: pedigree integrity, effective number of founders, effective number of ancestors, generation interval, inbreeding coefficient, realized effective population size, and average relatedness coefficient. POPREP and ENDOG v.4.5 software packages were employed to estimate these parameters. Based on the data set, the mean generation interval was found to be 6.3 years, and the average inbreeding coefficient, related to inbred animals, was 4.99%. Furthermore, the realized effective population size varied throughout the time period, ranging from 22 to 114, whereas the rate of inbreeding in this same period showed a decreasing trend towards the later years in the period until 2014. Upon evaluation, average relatedness coefficient was estimated to be 0.71%. Moreover, the effective number of founders and ancestors were estimated as 418 and 400 animals, respectively. According to the level of inbreeding observed, it could be noticed that genetic diversity remains elevated, which will be important to the genetic progress in the Holstein breeding program in Southern Brazil.

Our objective was to evaluate the genetic merit of Holstein cattle population in southern Brazil in response to variations in the regional temperature by analyzing the genotype by environment interaction using reaction norms. Fat yield (FY) and protein yield (PY) data of 67 360 primiparous cows were obtained from the database of the Paraná Holstein Breeders Association, Brazil (APCBRH). The regional average annual temperature was used as the environmental variable. A random regression model was adopted applying mixed models with Restricted Maximum Likelihood (REML) algorithm using WOMBAT software. The genetic merit of the 15 most representative bulls, depending on the temperature gradient, was evaluated. Heritability ranged from 0.21 to 0.27 for FY and from 0.14 to 0.20 for PY. The genetic correlation observed among the environmental gradients proved to be higher than 0.80 for both traits. Slight reranking of bulls for both traits was detected, demonstrating that non-relevant genotype by environment interaction for FY and PY were observed. Consequently, no inclusion of the temperature effect in the model of genetic evaluation in southern Brazilian Holstein breed is required.

Purunã is a composite beef cattle breed, developed in Southern Brazil by crossing the Angus, Charolais, Canchim, and Caracu breeds. The goal of this study was to perform the first genetic characterization of the Purunã breed, based on both pedigree and genomic information. For this, 100 randomly selected animals were genotyped, and 11,205 animals born from 1997 to 2019 had pedigree information. The genetic analyses performed were principal component analysis, admixture, phylogenic tree, pedigree and genomic inbreeding, linkage disequilibrium (LD), effective population size (Ne), consistency of the gametic phase, runs of homozygosity (ROH), heterozygosity-enriched regions (HERs), and functional analyses of the ROH and HER regions identified. Our findings indicate that Purunã is more genetically related to the Charolais, Canchim, and Angus breeds than Caracu or Nellore. The levels of inbreeding were shown to be small based on all the metrics evaluated and ranged from −0.009 to 0.029. A low (−0.12–0.31) correlation of the pedigree-based inbreeding compared to all the genomic inbreeding coefficients evaluated was observed. The LD average was 0.031 (±0.0517), and the consistency of the gametic phase was shown to be low for all the breed pairs, ranging from 0.42 to 0.27 to the distance of 20 Mb. The Ne values based on pedigree and genomic information were 158 and 115, respectively. A total of 1,839 ROHs were found, and the majority of them are of small length (<4 Mb). An important homozygous region was identified on BTA5 with pathways related to behavioral traits (sensory perception, detection of stimulus, and others), as well as candidate genes related to heat tolerance (MY O 1A), feed conversion rate (RDH5), and reproduction (AMDHD1). A total of 1,799 HERs were identified in the Purunã breed with 92.3% of them classified within the 0.5–1 Mb length group, and 19 HER islands were identified in the autosomal genome. These HER islands harbor genes involved in growth pathways, carcass weight (SDCBP), meat and carcass quality (MT2A), and marbling deposition (CISH). Despite the genetic relationship between Purunã and the founder breeds, a multi-breed genomic evaluation is likely not feasible due to their population structure and low consistency of the gametic phase among them.

Background Given the economic relevance of fertility and reproductive traits for the beef cattle industry, investigating their genetic background and developing effective breeding strategies are paramount. Considering their late and sex-dependent phenotypic expression, genomic information can contribute to speed up the rates of genetic progress per year. In this context, the main objectives of this study were to estimate variance components and genetic parameters, including heritability and genetic correlations, for fertility, female precocity, and semen production and quality (andrological attributes) traits in Nellore cattle incorporating genomic information. Results The heritability estimates of semen quality traits were low-to-moderate, while moderate-to-high estimates were observed for semen morphological traits. The heritability of semen defects ranged from low (0.04 for minor semen defects) to moderate (0.30 for total semen defects). For seminal aspect (SMN_ASPC) and bull reproductive fitness (BULL_FIT), low (0.19) and high (0.69) heritabilities were observed, respectively. The heritability estimates for female reproductive traits ranged from 0.16 to 0.39 for rebreeding of precocious females (REBA) and probability of pregnancy at 14 months (PP14), respectively. Semen quality traits were highly genetically correlated among themselves. Moderate-to-high genetic correlations were observed between the ability to remain productive in the herd until four years of age (stayability; STAY) and the other reproductive traits, indicating that selection for female reproductive performance will indirectly contribute to increasing fertility rates. High genetic correlations between BULL_FIT and female reproductive traits related to precocity (REBA and PP14) and STAY were observed. The genetic correlations between semen quality and spermatic morphology with female reproductive traits ranged from -0.22 (REBA and scrotal circumference) to 0.48 (REBA and sperm vigor). In addition, the genetic correlations between REBA with semen quality traits ranged from -0.23 to 0.48, and with the spermatic morphology traits it ranged from -0.22 to 0.19. Conclusions All male and female fertility and reproduction traits evaluated are heritable and can be improved through direct genetic or genomic selection. Selection for better sperm quality will positively influence the fertility and precocity of Nellore females. The findings of this study will serve as background information for designing breeding programs for genetically improving semen production and quality and reproductive performance in Nellore cattle.

AbstractThe experiments reported in this research paper were aimed at assessing the genetic responses of a Holstein cow population, as a response to the variations in environmental temperature, through the analysis of the effects resulting from the genotype by environment interaction (GEI), based on reaction norms. Therefore, milk production data was collected from the database of the Paraná Holstein Breeders Association in Brazil for 67,360 primiparous cows born between 1990 and 2015, with the purpose of evaluating the temperature effect, considered as an environmental variable, distinguished under six gradients (17 ºC to 19.5 ºC) over the region. A random regression model was adopted, utilizing the fourth order under the Legendre polynomials, applying the mixed models of analysis by the REML method, and using the WOMBAT software. Additionally, the breeding value of the 15 most representative bulls was assessed, in response to the changes in the temperature gradient. The total milk production on average was estimated at 8,412.83 ± 2,012.08 kg. The heritabilities estimates were found in the low to moderate range, from 0.18 to 0.23, displaying a decline with a rise in the temperature, highlighting the influence it exerted on the heritabilities. Variations in the genetic expression of some bulls were noted to show differences of up to 289 kg of milk in response to the increase in the temperature from 17 ºC to 19.5 ºC. However, all the genetic correlations between the gradients for milk yield were above 0.80, in the range of 0.873 to 0.998, revealing no remarkable interaction between the genotype and environment. This result indicates that the application of the temperature variable in the models of genetic analysis in southern Brazil is not required.