Resumo: O objetivo deste trabalho foi avaliar a utilidade de um subconjunto de 18 polimorfismos de nucleotídeo único (SNPs) para a certificação das raças de ovinos Crioula Brasileira, Morada Nova (MN) e Santa Inês (SI). Dados de 588 animais foram analisados com o programa Structure. Em 82% dos casos, observou-se designação racial correta com confiança acima de 90%. A maioria dos casos de designação incorreta de raça foi observada em MN e SI. Portanto, apesar de o subconjunto de 18 SNPs ter confiabilidade elevada, ele não é suficiente para a inequívoca certificação das raças estudadas, principalmente das deslanadas. É necessário o desenvolvimento de um painel mais preciso para uso amplo em certificação racial.

Abstract: The objective of this work was to evaluate the usefulness of a subset of 18 single nucleotide polymorphisms (SNPs) for breed identification of Brazilian Crioula, Morada Nova (MN), and Santa Inês (SI) sheep. Data of 588 animals were analyzed with the Structure software. Assignments higher than 90% confidence were observed in 82% of the studied samples. Most of the low-value assignments were observed in MN and SI breeds. Therefore, although there is a high reliability in this subset of 18 SNPs, it is not enough for an unequivocal assignment of the studied breeds, mainly of hair breeds. A more precise panel still needs to be developed for the widespread use in breed assignment.

Resumo: O recente desenvolvimento de painéis de “single nucleotide polymorphisms” (SNPs) distribuídos ao longo do genoma possibilitou a realização de diversos trabalhos com diferentes espécies. O processo seletivo promove o aumento ou a diminuição da frequência alélica (ou gênica) em loci específicos do genoma, além de promover o arrasto dos alelos próximos no cromossomo. Desta forma, são formadas regiões do genoma com o aumento na frequência de determinados alelos na população, o que caracteriza a assinatura de seleção. A detecção destas assinaturas é importante para a caracterização dos recursos genéticos, bem como a identificação de genes ou regiões envolvidos no controle e na expressão de características de importância produtiva e econômica. Os ovinos são uma importante espécie para estes estudos, uma vez que encontram-se amplamente dispersos em diferentes ambientes e apresentam grande diversidade fenotípica. Devido à grande quantidade de dados gerados nas análises genômicas, são necessários métodos estatísticos e programas específicos para a detecção de assinaturas de seleção. Assim, os objetivos deste artigo de revisão são apresentar os principais métodos estatísticos e os programas atualmente utilizados para análise de dados genômicos e a detecção de assinaturas de seleção; descrever os resultados dos recentes trabalhos publicados sobre assinaturas de seleção em ovinos; e discutir alguns desafios e oportunidades nesta área de pesquisa.

Abstract: The recent development of genome-wide single nucleotide polymorphism (SNP) arrays made it possible to carry out several studies with different species. The selection process can increase or reduce allelic (or genic) frequencies at specific loci in the genome, besides dragging neighboring alleles in the chromosome. This way, genomic regions with increased frequencies of specific alleles are formed, caracterizing selection signatures or selective sweeps. The detection of these signatures is important to characterize genetic resources, as well as to identify genes or regions involved in the control and expression of important production and economic traits. Sheep are an important species for theses studies as they are dispersed worldwide and have great phenotypic diversity. Due to the large amounts of genomic data generated, specific statistical methods and softwares are necessary for the detection of selection signatures. Therefore, the objectives of this review are to address the main statistical methods and softwares currently used for the analysis of genomic data and the identification of selection signatures; to describe the results of recent works published on selection signatures in sheep; and to discuss some challenges and opportunities in this research field.

Abstract The first horses were brought to Brazil by the colonizers after 1534. Over the centuries, these animals evolved and adapted to local environmental conditions usually unsuitable for exotic breeds, thereby originating locally adapted Brazilian breeds. The present work represents the first description of maternal genetic diversity in these horse breeds based on D-loop sequences. A D-Loop HSV-I fragment of 252 bp, from 141 horses belonging to ten Brazilian breeds / genetic groups (locally adapted and specialized breeds) were analysed. Thirty-five different haplotypes belonging to 18 haplogroups were identified with 33 polymorphic sites. Haplotype diversity (varying from 0.20 to 0.96) and nucleotide diversity (varying from 0.0039 to 0.0239) was lower for locally adapted than for specialized breeds, with the same pattern observed for FST values. Haplogroups identified in Brazilian breeds are in agreement with previous findings in South American samples. The low variability observed mainly in locally adapted breeds, indicates that, to ensure conservation of these breeds, careful reproductive management is needed. Additional genetic characterization studies are required to support accurate decision-making.

Resumo: O objetivo deste trabalho foi identificar polimorfismo de nucleotídeo único (SNPs) em dados de ressequenciamento dos genes MC1R, ASIP e TYRP1, obtidos de ovelhas Crioulas (Ovis aries) com cores de pelagem distintas. Polimorfismos nos genes ASIP (agouti-signaling protein), MC1R (melanocortin 1 receptor) e TYRP1 (tyrosinase-related protein 1) foram analisados em 115 ovinos, provenientes do núcleo de conservação da ovelha Crioula, da Embrapa. No total, 7.914 pb foram sequenciados por animal, e 14 SNPs foram identificados. Dois ensaios adicionais foram realizados para detectar duplicações e deleções no gene ASIP. Noventa e cinco por cento da variação de cor da pelagem foi explicada pelas interações epistáticas entre alelos específicos dos genes MC1R e ASIP. Evidências sugerem um importante papel das variantes TYRP1 para cor da lã, apesar das suas baixas frequências. O painel de marcadores usado foi eficiente em detectar alelos associados à coloração da pelagem nos animais estudados e, portanto, pode ser usado na implementação de um programa de seleção assistida por marcadores, no núcleo de conservação de ovinos da raça Crioula.

Abstract: The objective of this work was to identify single nucleotide polymorphisms (SNPs) in resequencing data from MC1R, ASIP, and TYRP1 genes derived from Crioula sheep (Ovis aris) with different coat colors. Polymorphisms in the ASIP (agouti-signaling protein), MC1R (melanocortin 1 receptor), and TRYP1 (tyrosinase-related protein 1) genes were analyzed in 115 sheep from Embrapa’s conservation nucleus of crioula sheep, in Brazil. A total of 7,914 bp were sequenced per animal, and 14 SNPs were identified. Two additional assays were performed to detect duplications and deletions in the ASIP gene. Ninety-five percent of the coat color variation was explained by epistatic interactions observed between specific alleles in the MC1R and ASIP genes. Evidence suggests an important role of TYRP1 variants for wool color, despite their low frequencies. The marker panel was efficient enough in predicting coat color in the studied animals and, therefore, can be used to implement a marker-assisted selection program in the conservation nucleus of sheep of the crioula breed.

A identificação de parâmetros/ métricas associados à adaptação ambiental é uma das principais tendências e desafios da pecuária mundial. Desta forma, o objetivo deste trabalho foi avaliar as características de tolerância ao calor de bovinos da raça Nelore e Pantaneiro no ecossistema do Pantanal matogrossense no pico de calor da região. Estes animais foram mantidos por duas horas à sombra (8:00h às 10:00h) e em seguida uma hora ao sol (10:00h às 11:00h). Após a exposição foram analisados parâmetros de frequência cardíaca (FC), frequência respiratória (FR), temperatura retal (TR), temperatura superficial da costela (TSC), temperatura superficial do pescoço (TSP) e temperatura superficial da garupa (TSG). Também foram avaliados a taxa de sudação (TXS), comprimento e densidade de pelos e calculados o índice de tolerância ao calor (ITC). No período estudado, a temperatura ambiental variou de 29,0 a 40,0ºC e a média para umidade relativa foi de 75%. O ambiente teve influência marcante sobre as variáveis fisiológicas, com exceção da FR. A TR e a TXS diferiram significativamente entre os grupos genéticos, sendo da raça Nelore mais elevada em relação à Pantaneira, mas todas dentro dos limites fisiológicos. A análise multivariada mostrou a importância de variáveis como taxa de sudação e comprimento de pelos para adaptação de bovinos na região. Apesar do Nelore vermelho estar separado dos outros dois grupos, foi possível concluir que ambas as raças analisadas apresentaram capacidade de adaptação e tolerância ao calor às condições climáticas do Pantanal e podem ser produzidas de modo sustentável na região.

Identification of parameters/metrics associated with environmental adaptation is one of the main trends and challenges for livestock worldwide. Thus, this study was conducted at Nhumirim Farm, in Nhecolândia, Pantanal, during the month of February, period with highest ambient temperatures. We used five cattle of each genetic group (White Nelore, Red Nelore and Pantaneira) to evaluate characteristics related to heat tolerance. Heart rate (HR), respiratory rate (RR), rectal temperature (RT), skin temperature (ST), sweating rate (SR), morphometric measurements, hair length (HL) and heat tolerance index (HTI) were evaluated. During the study the air temperature ranged from 29.0 to 40.0ºC and the average relative humidity was 75%. RT and ST were highest in White Nelore, followed by Red Nelore and Pantaneira. The average HTI value for the three groups was between 9 and 10, indicating high tolerance. The environment had considerable effect on physiological variables, except RR, RT and SR that significantly differed between genetic groups, with Nelore being higher than the Pantaneira, but all within physiological limits. Multivariate analysis showed the importance of variables such as sweating rate and hair length for the adaptation of cattle in the region. The red Nelore separated from the other two groups. We conclude, therefore, that both zebu (white and red Nelore) and European (Pantaneira) showed adaptability and heat tolerance to climatic conditions of the Pantanal.

The identification of regions that have undergone selection is one of the principal goals of theoretical and applied evolutionary genetics. Such studies can also provide information about the evolutionary processes involved in shaping genomes, as well as physical and functional information about genes/genomic regions. Domestication followed by breed formation and selection schemes has allowed the formation of very diverse livestock breeds adapted to a wide variety of environments and with special characteristics. The advances in genomics in the last five years have enabled the development of several methods to detect selection signatures and have resulted in the publication of a considerable number of studies involving livestock species. The aims of this review are to describe the principal effects of natural/artificial selection on livestock genomes, to present the main methods used to detect selection signatures and to discuss some recent results in this area. This review should be useful also to research scientists working with wild animals/non-domesticated species and plant biologists working with breeding and evolutionary biology.

Brazilian goats are generally kept in small herds and extensive rearing systems, mainly in the northeastern region of the country. Despite production improvement in recent years, the lack of pedigree control has affected genetic progress. This study aimed to validate a panel of 16 microsatellites for parentage testing in locally adapted and commercial goats breeds raised in Brazil, as well as to compare its efficiency with the panel recommended by the Brazilian Ministry of Agriculture, Livestock and Supplies (MAPA) in 2004. The number of alleles and expected heterozygosity (He) per marker ranged from four to 18, and from 0.051 to 0.831, respectively. Using all markers, 100% of parentage cases of the validation dataset were resolved with a strict confidence level of 95%. The 16 microsatellites panel showed adequate exclusion power (99.99%) and identity accuracy (99.99%). Suggestions for improvement of the marker panel endorsed by MAPA are provided.

A genealogical analysis of registered Pantaneiro horses was carried out with 3647 males and 6794 females. Of these animals, 50.66% had identified sires and 48.86% identified dams. The number of pedigrees increased over the generations, with higher registration of parents of sires than dams. Two municipalities are responsible for almost 70% of all registers: i) Poconé (Mato Grosso State), where the headquarters of the breeders association is located and ii) Corumbá (Mato Grosso do Sul State), where EMBRAPA Pantanal conducts its research. The mean inbreeding was 0.04% and average relatedness was 0.13%. Mean generation interval was 8.20 years. There is moderate to high genetic differentiation between farms (15% of total genetic variation) while between municipalities there is little differentiation. Wright's fixation statistics were calculated and F IS (inbreeding coefficient of individuals relative to the subpopulation) values indicate some heterozygosity between farms but not municipalities, with overall F IT (inbreeding coefficient of individuals relative to the total population) close to zero. The municipalities with the highest number of animals (Poconé and Corumbá) import relatively fewer sires (45 and 67% respectively). Genetic indices from genealogical data on the Pantaneiro horse population show that inbreeding is under control.Future breeding plans should include germplasm exchange between municipalities. The conservation program for the Pantaneiro horse has been shown to be successful but careful planning is needed in the future to avoid inbreeding and changes in important breed traits given the increasing interest in the use of the breed in sporting competitions.

Three production systems for sheep (Low - L, Medium - M and High - H technology), with increasing technological levels, were studied under conditions in the Center-west of Brazil, to determine economic weights and selection indices of important traits. Receipts and costs were simulated using an economic simulator to calculate the structure of the operational costs. Only characteristics that were responsible for more than 10% of the profit were studied, which included: number of weaned lambs, food consumption (ewe and lamb), weight of carcass and weight of female lambs sold for reproduction. Regardless of the index used (profitability or yield) or system (L, M or H), the economic weights are larger for the number of lambs weaned per ewe. With improvement in the technology used within the production system (H to L) the importance of this trait becomes less important. Lamb growth increased and weight of female for slaughter decreased in importance in higher technology systems. Changes in herd structure had little influence on economic values, whereas (co)variances were important sources of change in selection indices.

In this work, linear body measures were taken and production indices calculated for 100 Cuban Creole goats and 100 crossbred goats in order to aid in the characterization of animal genetic resources in Cuba. Low variation was found for all indices of the Creole goats, showing homogeneity between the groups of animals studied. Most of the functional indices are related to the milk biotype which is in agreement the possible origin of the breed from animals of the Iberian Peninsula and Canary Islands. The crossbreds were more varied, mostly due to undesigned disorganized crossing. These data may help in identifying a commercial niche for the breed and contribute to in situ conservation of the Cuban Creole goat.

Os objetivos neste estudo foram analisar modelos não-lineares para descrever o crescimento em ovinos da raça Morada Nova criados no estado da Bahia e, após a definição do modelo de melhor ajuste, calcular a taxa de crescimento absoluto e avaliar a influência de fatores ambientais (sexo e tipo de parto) sobre os parâmetros da curva. Utilizaram-se dados de pesagem de 40 ovinos, do nascimento aos 385 dias de idade. Os modelos não-lineares utilizados foram: Brody, Von Bertalanffy, Richards, Logístico e Gompertz. Os modelos Von Bertalanffy, Brody e Richards foram os que apresentaram os melhores ajustes e são equivalentes para explicar o crescimento dos animais. A taxa de crescimento absoluto teve acentuado decréscimo na fase pós-desmama, o que indica a necessidade de se adotar um regime alimentar adequado para acompanhar as exigências de nutrientes dos animais nessa fase. Os efeitos ambientais (sexo e tipo de parto) influenciaram significativamente a taxa a maturidade (k), mas apenas o sexo do animal afetou o peso à maturidade (A). Os animais que nasceram de parto simples tiveram peso maior que o daqueles de parto duplo, e estes apresentaram ganho compensatório. Os machos tiveram maior crescimento que as fêmeas, que, por sua vez, apresentaram maior precocidade. A correlação estimada entre os parâmetros A e k foi negativa (-0,65) para o modelo Von Bertalanffy e (-0,71) para os modelos Brody e Richards, e isso indica que os animais mais precoces possuem menor probabilidade de atingir pesos elevados à idade adulta.

The objective of the present study was to evaluate non-linear models to describe Morada Nova sheep herds raised in the State of Bahia and, after defining the best suiting model, calculate the rate of absolute growth and evaluate the influence of environmental factors (sex and type of parturition) on the curve parameters. Weighting data from 40 sheep from birth up to 385 days of age were used. The non-linear models used were: Brody, Von Bertalanffy, Richards, Logistic and Gompertz. Von Bertalanffy, Brody and Richards models presented the best adjustments and were equivalent to explain the growth of the analyzed animals. A remarkable drop in the absolute growth rate was observed after weaning, suggesting that a proper diet should be implemented to supply the nutritional demands of the animals at this stage. The environmental effects (sex and type of parturition) have significantly influenced the maturity rate (k), but only the sex of the lamb affected weight at maturity (A). Animals born from single parturition proved to be heavier than twins which, in turn, presented compensatory gain. The growth of males was higher than of females and the latter presented more precocity than males. Estimated correlation between parameters A and k was negative (-0.65) for the Von Bertalanffy model and for the Brody and Richards models (-0.71) indicating that the most precocious animals are less likely to reach elevated weights when adults.

This study estimated the genetic diversity and structure of 12 genetic groups (GG) of locally adapted and specialized pigs in the state of Pernambuco using 22 microsatellite markers. Nine locally adapted breeds (Baé, Caruncho, Canastra, Canastrão, Mamelado, Moura, Nilo, Piau and UDB (Undefined Breed)) and 3 specialized breeds (Duroc, Landrace and Large White), totaling 190 animals, were analyzed. The Analysis of Molecular Variance (AMOVA) showed that 3.2% of the total variation was due to differences between genetic groups, and 3.6% to differences between local and commercial pigs. One hundred and ninety eight alleles were identified and apart from the Large White breed, all GG presented Hardy-Weinberg Equilibrium deviations for some loci. The total and effective allele means were lower for Duroc (3.65 and 3.01) and higher for UDB (8.89 and 4.53) and Canastra (8.61 and 4.58). Using Nei's standard genetic distance and the UPGMA method, it was possible to observe that the Landrace breed was grouped with the local genetic groups Canastra, Moura, Canastrão, Baé and Caruncho. Due to the complex admixture pattern, the genetic variability of the 12 genetic groups can be analyzed by distributing the individuals into two populations as demonstrated by a Bayesian analysis, corroborating the results from AMOVA, which revealed a low level of genetic differentiation between the inferred populations.

Estudos em genética e melhoramento de ovinos no Brasil têm aumentado significativamente nos últimos anos. Estes envolvem pesquisa em caracterização, criação e cruzamento de ovinos utilizando as novas tecnologias disponíveis, incorporando tanto a genética quantitativa clássica e molecular. São abordadas sugestões para melhorias nas técnicas de estatística, nos recursos computacionais, bem como na análise de DNA e nas lacunas no conhecimento atual e possibilidades de possíveis investigações. Há uma necessidade de maior interação entre vários grupos de trabalho no país, bem como as interações com outras disciplinas, como Sistemas de Informação Geográfica, Estatística, Bioinformática, bem como estudos biológicos, como fisiologia e proteômica.

Studies in genetics and breeding of sheep in Brazil have increased significantly in recent years. These involve research in characterization, breeding and crossing sheep using new technologies available incorporating both classical quantitative and molecular genetics. Improvements in statistical techniques, computational resources as well as analysis of DNA and gaps in present knowledge and opportunities for possible research are pointed out. There is a need for greater interaction between various groups working in the country as well as interactions with other disciplines such as Geographical Information Systems, Statistics, Bioinformatics, as well as biological studies such as physiology and proteomics.

Foram colhidos dados morfométricos de 859 suínos naturalizados do Brasil (Piau, Tatu, Nilo, Caruncho, Casco de Burro, Moura, Monteiro e Rabo de Peixe), Colômbia (Criolla Zungo, Sanpedreño e Casco de Mula) e Uruguai (Mamellado) Dados sobre raça, sexo e idade foram coletados, assim como varias avaliações morfométricas. A análise de variância foi realizada utilizando-se o procedimento PROC GLM do SAS sobre os dados morfométricos. Os coeficientes de variância oscilaram de 11,50 a 83,81% e o coeficiente de determinação foi de moderado a alto. As fêmeas foram em geral menores na maioria das avaliações em relação aos machos, indicando dimorfismo sexual. A Moura foi a raça naturalizada mais próxima das raças comerciais, seguida da Piau, enquanto a Monteiro apresentou-se mais distante. O dendograma obtido a partir de informações morfológicas apresentou divisão dentro de três grupos. A caracterização foi possível utilizando-se dados morfológicos e morfométricos.

Morphometric data was collected on 859 naturalized swine in Brazil (Piau, Tatu, Nilo, Caruncho, Casco de Burro, Moura, Monteiro and Rabo de Peixe), Colombia (Criolla Zungo, Sanpedreño and Casco de Mula) and Uruguay (Mamellado), both on farm and in published material. Information was collected on breed, sex and age, as well as various morphometric measurements. Analysis of variance was carried out using PROC MIXED of SAS ® on phenotypic data. The coefficients of variance varied between 11.50 and 83.81%, and the coefficient of determination was medium to high. Females were in general smaller for most measurements than males, showing sexual dimorphism. The Moura was the closest naturalized breed to the commercial breeds, followed by the Piau, while the Monteiro was the furtherest. The dendrogram obtained from morphological information showed a division of the pigs into three groups. Characterization was possible using morphological and morphometric data.

Estudou-se a diversidade genética de pacas (Agouti paca) de três plantéis comerciais no Brasil. Como o genoma desta espécie é desconhecido, utilizaram-se o polimorfismo de DNA amplificado ao acaso e reação em cadeia da polimerase (RAPD-PCR). Dez primers selecionados geraram 60 bandas polimórficas. A variabilidade genética inter e intrapopulações estimada pela análise de variância molecular (AMOVA) foi de 12,55 e 87,45%, respectivamente. A menor distância de Nei encontrada foi de 11,76% entre as populações de Carangola (CG) e São Francisco do Glória (SF). Este valor pode ser explicado pelo intercâmbio de matrizes e reprodutores que já ocorre entre esses dois criatórios geograficamente próximos entre si. Na análise dos componentes principais, foram observados grupos bem estruturados e definidos, agregando indivíduos à sua população de origem, com algumas exceções. A diversidade foi menor na população São Francisco que em Carangola e Castelo (CS). Esse resultado sugere que, em criatórios com 5 a 6 dezenas de animais (CG e CS), a variabilidade se mantém melhor que naquele com cerca de uma dúzia de animais (SF). A técnica de RAPD-PCR mostrou-se informativa para quantificar a variabilidade genética entre e intrapopulações de pacas. O fenograma gerado pelo método UPGMA por meio do programa NTSYS-PC a partir da distância de Nei agrupou CG e SF num mesmo ramo e este ligado ao CS, com acurácia de 76 e 100%, respectivamente, ao bootstrap. Esse resultado condiz com as informações geográficas e o histórico dos rebanhos e mostra a necessidade de substituição periódica de machos reprodutores. Mais estudos devem ser desenvolvidos com marcadores codominantes e com pacas de localidades mais distintas.

The genetic diversity was analyzed among spotted paca (Agouti paca) from three commercial flocks located in Brazil. As the genome of this species is unknown, the RAPD-PCR technique was used. Ten primers generated sixty polymorphic bands. The among and within population genetic variability estimated by analysis of molecular variance (AMOVA) was 12.55 and 87.45%, respectively. The shortest Nei distance value was 11.76% among the Carangola (CG) and São Francisco do Glória (SF) populations. This value can be explained by the exchange of reproduction males and females between the two geographically close breeding sites. The analysis of principal components showed well defined and structured groups aggregating animals according their population of origin, with some exceptions. Lower diversity was found in the São Francisco population than in the Carangola and Castelo (CS) populations. This result suggested the variability is better conserved in breeding farms with fifty or sixty animals (CG and CS) than in the breeding farm with a dozen animals (SF). The RADP-PCR technique proved to be informative for the quantification of among and within population genetic variability of the spotted paca. The phenogram generated by UPGMA using the NTSYS-PC software from the Nei Distance, grouped CG and SF on a single branch connected to the CS, with 76 and 100% accuracy, respectively, to the bootstrap. This result was not only consistent with the historical and geographical information on flocks, but also shows the need for periodic reproductive male replacement. Future studies should be developed with co-dominant markers and include spotted paca from more distant places.