The first registers of Somali sheep in Brazil are from the beginning of the 1900s. This breed, adapted to the dry climate and scarce food supply, is restricted in the northeast region of the country. Molecular marker technologies, especially those based on genotyping microsatellite and mtDNA loci, can be used in conjunction with breeding (pedigree analysis) and consequently the maintenance of genetic variation in herds. Animals from the Brazilian Somali Conservation Nuclei from Embrapa Sheep and Goats in Ceará State were used to validate genetic monitoring by traditional pedigree methods and molecular markers. Nineteen microsatellite markers and 404 base pairs from the control region of mtDNA were used. For total herd diversity, an average 5.32 alleles were found, with expected heterozygosity of 0.5896, observed heterozygosity of 0.6451, 0.4126 for molecular coancestrality, and coefficient of inbreeding (F (IS)) was -0.095. Comparing molecular coancestrality means over the years, there was a consistent increase in this parameter within the herd, increasing from 0.4157 to 0.4769 in 2 years (approx. 12% variation). Sixteen mtDNA haplotypes were identified. Inbreeding and other estimates from genealogical analyses confirm the results from molecular markers. From these results, it is possible to state that microsatellites are useful tools in genetic management of herds, especially when routine herd recording is not carried out, or there were gaps in recent generations. As well as pedigree control, genetic diversity can be optimized. Based on the results, and despite herd recording in the herd of Brazilian Somali of Embrapa Sheep and Goats, additional management measures need to be carried out in this herd to reduce inbreeding and optimize genetic variation.

O objetivo deste trabalho foi estimar as correlações genéticas, fenotípicas e ambientais sobre os pesos ao nascimento (PN) e aos 205 (P205), 365 (P365) e 550 (P550) dias de idade, em animais da raça Nelore Mocha, criados no estado da Bahia. As análises bi-características foram realizadas através do programa MTDFREML. As correlações genéticas foram iguais a 0,08 (PN e P205), 0,00 (PN e P365), - 0,14 (PN e P550), 0,90 (P205 e P365), 0,81, (P205 e P550) e 0,97 (P365 e P550). As correlações ambientais foram 0,12 (PN e P205), 0,11 (PN e P365), 0,16 (PN e P550), 0,35 (P205 e P365), 0,13 (P205 e P550) e 0,54 (P365 e P550). Os valores obtidos para as correlações fenotípicas foram 0,09 (PN e P205), 0,05 (PN e P365), 0,00 (PN e P550), 0,75 (P205 e P365) 0,65 (P205 e P550) e 0,87 (P365 e P550). O peso ao nascimento apresentou ausência de associações genéticas, ambientais e fenotípicas com as demais pesagens. Por outro lado, os valores obtidos para as correlações genéticas entre as outras pesagens, indicam que a seleção para peso em idades jovens deverá promover mudanças nos pesos posteriores dos animais.

The level of genetic diversity in a population is inversely proportional to the linkage disequilibrium (LD) between individual single nucleotide polymorphisms (SNPs) and quantitative trait loci (QTLs), leading to lower predictive ability of genomic breeding values (GEBVs) in high genetically diverse populations. Haplotype-based predictions could outperform individual SNP predictions by better capturing the LD between SNP and QTL. Therefore, we aimed to evaluate the accuracy and bias of individual-SNP- and haplotype-based genomic predictions under the single-step-genomic best linear unbiased prediction (ssGBLUP) approach in genetically diverse populations. We simulated purebred and composite sheep populations using literature parameters for moderate and low heritability traits. The haplotypes were created based on LD thresholds of 0.1, 0.3, and 0.6. Pseudo-SNPs from unique haplotype alleles were used to create the genomic relationship matrix (G) in the ssGBLUP analyses. Alternative scenarios were compared in which the pseudo-SNPs were combined with non-LD clustered SNPs, only pseudo-SNPs, or haplotypes fitted in a second G (two relationship matrices). The GEBV accuracies for the moderate heritability-trait scenarios fitting individual SNPs ranged from 0.41 to 0.55 and with haplotypes from 0.17 to 0.54 in the most (Ne ≅ 450) and less (Ne < 200) genetically diverse populations, respectively, and the bias fitting individual SNPs or haplotypes ranged between −0.14 and −0.08 and from −0.62 to −0.08, respectively. For the low heritability-trait scenarios, the GEBV accuracies fitting individual SNPs ranged from 0.24 to 0.32, and for fitting haplotypes, it ranged from 0.11 to 0.32 in the more (Ne ≅ 250) and less (Ne ≅ 100) genetically diverse populations, respectively, and the bias ranged between −0.36 and −0.32 and from −0.78 to −0.33 fitting individual SNPs or haplotypes, respectively. The lowest accuracies and largest biases were observed fitting only pseudo-SNPs from blocks constructed with an LD threshold of 0.3 (p < 0.05), whereas the best results were obtained using only SNPs or the combination of independent SNPs and pseudo-SNPs in one or two G matrices, in both heritability levels and all populations regardless of the level of genetic diversity. In summary, haplotype-based models did not improve the performance of genomic predictions in genetically diverse populations.

Summary Brazilian hair sheep constitute a genetic diversity hotspot. These animals are found in the harsh environments of the Brazilian Northwest (semi‐arid) region. Genotypes (50K SNP chip) from seven Brazilian sheep breeds (five hair and two coarse wool types) and 87 worldwide breeds were used to test for population structure, admixture and genetic diversity. Moreover, phylogenetic trees evaluating migration events between genetic groups were built. Brazilian Somali, a fat‐tailed breed, had a close relationship with East African breeds and clustered distinctly from other Brazilian breeds. Brazilian Blackbelly and Barbados Blackbelly had a close relationship. The Morada Nova breed did not show close relationships with European or African breeds, revealing a single migration event from an Algerian hair breed. Brazilian Fat‐tail and Morada Nova share a common ancestor, but the former showed introgressions from Brazilian Somali and Afrikaner breeds, explaining the fat‐tail phenotype. The Santa Inês breed received a substantial contribution from Brazilian Bergamasca and showed an admixed origin with recent introgressions from other breeds, mainly from Suffolk. Furthermore, Brazilian Somali and Brazilian Fat‐tail are the most endangered sheep genetic resources in Brazil and should be the focus for ex situ conservation programs. In conclusion, Brazilian hair sheep show an African origin and are characterized by diverse genetic composition, reinforcing the need for conservation of these genetic resources, and at the same time, this highly diverse group has variability that can be used in breeding programs.

Behavior is a complex trait and, therefore, understanding its genetic architecture is paramount for the development of effective breeding strategies. The objective of this study was to perform traditional and weighted single-step genome-wide association studies (ssGWAS and WssGWAS, respectively) for yearling temperament (YT) in North American Angus cattle using haplotypes. Approximately 266 K YT records and 70 K animals genotyped using a 50 K single nucleotide polymorphism (SNP) panel were used. Linkage disequilibrium thresholds (LD) of 0.15, 0.50, and 0.80 were used to create the haploblocks, and the inclusion of non-LD-clustered SNPs (NCSNP) with the haplotypes in the genomic models was also evaluated. WssGWAS did not perform better than ssGWAS. Cattle YT was found to be a highly polygenic trait, with genes and QTL broadly distributed across the whole genome. Association studies using LD-based haplotypes should include NCSNPs and different LD thresholds to increase the likelihood of finding the relevant genomic regions affecting the trait of interest. The main candidate genes identified, i.e., ATXN10, ADAM10, VAX2, ATP6V1B1, CRISPLD1, CAPRIN1, FA2H, SPEF2, PLXNA1, and CACNA2D3, are involved in important biological processes and metabolic pathways related to behavioral traits, social interactions, and aggressiveness in cattle. Future studies should further investigate the role of these genes.

resUMoConhecer o progresso genético e fenotípico de uma população é importante para se avaliar o resultado dos programas de seleção adotados e como elementos norteadores de ações futuras. Assim, objetivou-se estimar parâmetros genéticos, tendências genéticas e fenotípicas dos pesos aos 205 (P205), 365 (P365) e 550 (P550) dias de idade, idade ao primeiro parto (IPP), circunferência escrotal (CE) e intervalos de partos (IDP) de 175.231 bovinos Nelore, nascidos no período de 1967 a 2011 na região Nordeste do Brasil. Os componentes de (co) variância e valores genéticos foram obtidos por meio da metodologia da máxima verossimilhança restrita. As estimativas dos coeficientes de herdabilidades para as características de crescimento foram de baixa a moderada magnitude. A seleção direta proporcionará maiores ganhos genéticos para P550. Para as características reprodutivas, a estimativa de herdabilidade foi baixa para IPP e próxima a zero para IDP. Contudo, para a CE a herdabilidade foi moderada, indicando seu uso como critério de seleção. As tendências genéticas diretas para P205, P365, P550 e IPP, indicam pequenos ganhos genéticos ao longo dos anos. Os progressos fenotípicos evidenciam que as características estão melhorando com o decorrer dos anos, principalmente em decorrên-cia da melhoria ambiental. Genetics parameters for growth and reproductive traits in Nellore Cattle from Brazil sUMMarYTo know the genetic and phenotypic progress of a population is important to evaluate the outcome of the adopted selection programmes and as guiding elements of future actions. The objective was to estimate genetic parameters, genetic and phenotypic trends of weights at 205 (W205) 365 (W365) 550 (W550) days of age, age at first calving (AFC), scrotal circumference (SC) and calving interval (CI) of 175.231 Nellore, born in the period 1967-2011 in the Northeast region of Brazil. The components of (co) variance and breeding values were obtained by restricted maximum likelihood methodology. Estimates of heritability coefficients for growth traits were of a low to moderate magnitude. Direct selection will provide greater genetic gains for W550. For reproductive traits, the heritability estimate was low for ACF and close to zero for CI. However, for the SC heritability was moderate, indicating its use as selection criteria. Direct genetic trends for W205, W365, W550 and ACF indicate small genetic gains over the years. Phenotypic progress shows that the features are improving with the years, mainly because of environmental improvements. additional keYwordsGenetic gain. Genetic trends.

Inbreeding depression is caused by breeding between closely related individuals and can have a significant negative impact on cattle production. It can be estimated at the population level using pedigree analysis or molecular markers. Such estimations can then be used to better manage the genetic resources of herds. The objective of this study was to evaluate genetic variability and the influence of inbreeding depression on productive traits in 45 785 animals Nellore cattle (polled variety) from Brazil. Inbreeding depression was determined by fitting four regression models (linear, quadratic, exponential and Michaelis-Menten) to the errors generated by the animal model. The traits studied were weight at 205 (W205), 365 (W365) and 550 (W550) days of age. The effective number of founders (fe) and ancestors (fa) was 288 and 283, respectively, with 173 ancestors explaining 50% of the genetic variability in the population. Inbreeding depression effects were identified on all growth traits (W205, W365, and W550), demonstrating significant losses in evaluated weight means. For each 1% increase in inbreeding there was a depression of about 0.14% or 0.24 kg (W205), 0.12% or 0.29 kg (W365) and 0.09% or 0.29 kg (W550). Exponential and Michaelis-Menten models were similarly efficient predictors for all the traits (P<0.01). We conclude that Nellore cattle in Northeastern Brazil presents low genetic variation and the relationship between inbreeding and depressed productivity in this breed is not linear, with the greatest effects occurring when endogamy is above 20%. To change this scenario, it is important to use a high number of male breeders, mainly young individuals of high breeding value, and improvement of reproductive indexes of females. To achieve this goal, a traditional mating system focused on the utilization of a few (and famous) male breeders should be avoided by both farmers and technicians.

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