Integration of georeferenced and genetic data for the management of biodiversity in sheep genetic resources in Brazil.

There are few animal germplasm/gene bank collections in Brazil, and basic studies are needed to attend the future internal and external demands from international partners. The aim of this work was to validate a "proof of concept" that integrates spatial (georeferenced data) and genetic data regarding the local of origin from 3518 DNA samples from 17 different genetic groups or breeds of sheep in the Brazilian Germplasm bank. Spatialisation shows that not all genetic groups have samples in the bank, and collection is concentrated in the conservation nuclei spread nationwide. Only 21% of states with a specific breed have samples in the gene bank. The mean number of animals sampled per collection was 32, while the mean distance travelled to collect samples was 262 km from the conservation nuclei. For example, the Brazilian Somali were only collected in the conservation nucleus in Ceará State. No samples were collected to date for the Cariri breed, which is recognised by the Brazilian Ministry of Agriculture. Only two farms and one breed in the bank are from the northern region. Of the 27 states, there are samples in the gene bank of sheep from 13, so several states have no samples, requiring collection from herds outside the official system of conservation to make sure that studies using this germplasm realised are not biased. Significant genetic differences are seen above 332 km, which should guide future sampling efforts. Suggestions are given for improving the quantity, quality and diversity of samples in the gene bank.

New world goat populations are a genetically diverse reservoir for future use.

Western hemisphere goats have European, African and Central Asian origins, and some local or rare breeds are reported to be adapted to their environments and economically important. By-in-large these genetic resources have not been quantified. Using 50 K SNP genotypes of 244 animals from 12 goat populations in United States, Costa Rica, Brazil and Argentina, we evaluated the genetic diversity, population structure and selective sweeps documenting goat migration to the "New World". Our findings suggest the concept of breed, particularly among "locally adapted" breeds, is not a meaningful way to characterize goat populations. The USA Spanish goats were found to be an important genetic reservoir, sharing genomic composition with the wild ancestor and with specialized breeds (e.g. Angora, Lamancha and Saanen). Results suggest goats in the Americas have substantial genetic diversity to use in selection and promote environmental adaptation or product driven specialization. These findings highlight the importance of maintaining goat conservation programs and suggest an awaiting reservoir of genetic diversity for breeding and research while simultaneously discarding concerns about breed designations.

Reproductive features and use of an anti-inflammatory drug in estrus-induced dairy goats artificially inseminated in a standing position with cervix immobilization.

This study evaluated reproductive features and role of Flunixin-Meglumine at timed artificial insemination (AI), using a new technique of standing position with cervix immobilization. In Experiment 1, 10 goats (n=5 nulliparous [Null] and 5 pluriparous [Plu]) were evaluated after estrus induction by recorded reproductive parameters to define the ideal time for AI. In Experiment 2, goats were artificially inseminated 51-54h after sponge removal with frozen-thawed semen. At AI, 1mL saline (CONTROL; 18 Null and 14 Plu) or 50mg Flunixin-Meglumine (FLUNIXIN; 15 Null and 18 Plu) was administered i.m. Location of semen deposition was recorded for both groups. In Experiment 1, all sexual behavior and ovulatory parameters were similar between Null and Plu for estrus response and ovulation (100%), interval from sponge removal to ovulation (∼64.2h), largest ovulatory follicle diameter (∼6.6mm), and number of ovulations (∼2.0). In Experiment 2, pregnancy rate was superior (P<0.01) for CONTROL (62.5%; 10 Null and 10 Plu) than FLUNIXIN (30.3%; 3 Null and 7 Plu) goats. Regardless of the treatment, intrauterine AI was more frequent (P<0.01) in Plu (100.0%; 32/32) than in Null (69.7%; 23/33) goats. Moreover, AI was more time-consuming (P<0.01) in Null (44±37s; 4-139s) than in Plu (21±19s, 4-78s) goats. Therefore, administration of Flunixin-Meglumine at the time of AI adversely affected pregnancy rate. High rates of intrauterine cervical penetration were obtained, achieving good pregnancy rates in goats not receiving Flunixin-Meglumine.

Do traditional sheep breeders perform conscious selection? An example from a participatory breeding program of Morada Nova sheep.

The implementation of sustainable breeding programs requires genetic breeding strategies that are appropriate for the reality production systems. It is also essential that the choice of animal selection criteria be based on breeders' knowledge and objectives. This work is an ethno-zootechnical study of the Morada Nova sheep breed and its crossbreeds. The goals of this study were to register and analyze indigenous breeders' knowledge and practices regarding animal selection criteria and to generate technical information to support a participatory breeding program of the breed. This study was conducted in the Morada Nova municipality in the state of Ceará, Brazil. Semi-structured interviews were evaluated using two groups of individuals, purebred Morada Nova sheep breeders (RMN, n = 13) and breeders of Morada Nova crossbreeds (MMN, n = 48). Interview questions were used to identify local selection criteria adopted by each group in the choice of animals for breeding. Data from the interviews were submitted to frequency distribution analysis and the Shapiro-Wilk test to verify their distribution. Later, the Kruskal-Wallis test was used to compare the two groups of farmers based on that information, in addition to multivariate statistical analysis and evaluation of Smith salience index. Breeders in the RMN group used selection criteria related to breed standards, such as pelage color. In contrast, breeders of the MMN group used criteria related to productivity, such as body conformation and milk production. Breeders should be engaged in the development of breeding programs, and it is important to consider their preferences and objectives when evaluating breeding animals.

Distribution of goat breeds in brazil and their relationship with environmental controls / Distribuição de raças de caprinos no brasil e sua relação com controles ambientais

A localização de todos os rebanhos de cabras de raça pura no Brasil foi espacializada de acordo com os controles climáticos (Índice de Temperatura e Umidade, precipitação, topografia, umidade relativa do ar) e controles ambientais (altitude, tipo de pastagem). Os dados foram analisados através de uma análise de regressão, variância, logistica e cluster. Matrizes de distância foram construídas de acordo com a longitude/ latitude e os controles ambientais foram correlacionados por meio do teste de Mantel. O ponto médio para a maioria das raças foi encontrado no estado da Bahia, mas no estado de Pernambuco encontraram-se os pontos médias das raças localmente adaptadas. A Anglonubiana foi a raça comercial com o ponto médio mais ao norte, enquanto as raças Toggenburg, Saanen e Alpina tiveram o ponto médio de produção mais ao sul do país. Houve pouca diferença entre os controles ambientais para as raças localamente adaptadas e comerciais, mas raças dupla aptidão encontraram-se nas regiões com menor precipitação e Índice de Desenvolvimento Humano , mas com as temperaturas e área de mata mais elevadas . As raças comerciais são mais difundidas no Brasil do que raças locais, sendo que as últimas ocorrem um maior risco de extinção devido a doenças, seca ou cruzamento com outras raças.

The localization of all flocks of purebred goats in Brazil was spatialized in ARCGIS along with climatic (THI, precipitation, topography, relative humidity) and physical environmental controls (altitude, pasture type). Data were analysed using analysis of variance, logisitic regression and cluster analyses. Distance matrices were constructed using longitude/latitude and those from environmental controls and these were correlated using Mantel test. Midpoint for most breeds was in Bahia State, but in Pernambuco for locally adapted breeds. The Anglonubian was the commercial breed with the northernmost midpoint. Toggenburg, Saanen and Apline breeds had the southernmost midpoint. There was little difference between environmental controls for locally adapted and commercial breeds, but dual purpose breeds were in regions with lower rainfall and HDI but higher temperatures and shrubland. Commercial herds are more widespread in Brazil than local breeds putting the latter at higher risk of extinction through drought, disease or crossing with other breeds.

Validation of a microsatellite panel for parentage testing of locally adapted and commercial goats in Brazil.

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.

Estimativas de parâmetros genéticos para características de crescimento em ovinos da raça Somalis Brasileira / Genetic parameters estimates for growth traits in Somalis Brasileira hair sheep breed

Objetivou-se estimar parâmetros genéticos para características de crescimento em ovinos da raça Somalis Brasileira. Os dados utilizados neste estudo foram provenientes do rebanho da Embrapa Caprinos e Ovinos, localizado na cidade de Sobral - CE. Os dados continham registros de 1.120 animais no arquivo de pedigree. As características analisadas foram: peso ao nascer (PN), peso ao desmame (PD), ganho de peso do nascimento ao desmame (GND) e peso adulto (PA). As estimativas dos componentes de (co)variâncias e os parâmetros genéticos foram obtidos pelo método da Máxima Verossimilhança Restrita não Derivativa (DFREML), utilizando o programa MTDFREML. Nas análises unicaracterística, as herdabilidades foram de magnitude baixa a moderada. As magnitudes das herdabilidades maternas foram todas superiores às herdabilidades diretas. As herdabilidades das análises multicaracterísticas entre PN, PD e GND superaram as análises unicaracterísticas. As correlações genéticas apresentaram grande variação quanto aos seus valores.

The aim of this study was to estimate genetic parameters for growth traits in Somalis Brasileira hair sheep breed. The data used in this study were from the flock of Embrapa Caprinos and Ovinos, located in the city of Sobral - CE, Brazil. Data contained records of 1,120 animals in the pedigree file. The analyzed traits were birth weight (PN), weaning weight (PD), weight gain from birth to weaning (GND) and adult weight (PA). Estimates of (co)variances and genetic parameters were obtained by Derivative Free Restricted Maximum Likelihood Method (DFREML) using the MTDFREML software. The heritabilities were low to moderate in univariate analysis. The maternal heritabilities were higher than direct heritabilities. The heritabilities in multivariate analysis exceeded those in univariate analysis. The values of genetic correlations varied widely.

Spatialization of climate, physical and socioeconomic factors that affect the dairy goat production in Brazil and their impact on animal breeding decisions / Espacialização de fatores climáticos, físicos e socioeconômicos que afetam a produção de caprinos leiteiros no Brasil e seu impacto sobre as decisões em melhoramento animal

Brazil has high climate, soil and environmental diversity, as well as distinct socioeconomic and political realities, what results in differences among the political administrative regions of the country. The objective of this study was to determine spatial distribution of the physical, climatic and socioeconomic aspects that best characterize the production of dairy goats in Brazil. Production indices of milk per goat, goat production, milk production, as well as temperature range, mean temperature, precipitation, normalized difference vegetation index, relative humidity, altitude, agricultural farms; farms with native pasture, farms with good quality pasture, farms with water resources, farms that receive technical guidance, family farming properties, non-familiar farms and the human development index were evaluated. The multivariate analyses were carried out to spatialize climatic, physical and socioeconomic variables and so differenciate the Brazilian States and Regions. The highest yields of milk and goat production were observed in the Northeast. The Southeast Region had the second highest production of milk, followed by the South, Midwest and North. Multivariate analysis revealed distinctions between clusters of political-administrative regions of Brazil. The climatic variables were most important to discriminate between regions of Brazil. Therefore, it is necessary to implement animal breeding programs to meet the needs of each region.

O Brasil possui diversidade edafoclimática e realidades socioeconômicas e políticas distintas. Isto contribui para diferenciar as regiões político administrativas do país. Objetivou-se espacializar os fatores físicos, climáticos e socioeconômicos que melhor discriminam a produção de caprinos leiteiros no Brasil. Foram analisados índice de produção de leite por cabra; índice de produção de caprinos; índice de produção de leite, amplitude da temperatura; temperatura média; precipitação; índice normalizado de diferença vegetativa; umidade relativa do ar; altitude; estabelecimentos agropecuários; estabelecimentos com pastagem nativa; estabelecimentos com pastagens de boa qualidade; estabelecimentos com recursos hídricos; estabelecimentos que recebem orientação técnica; estabelecimentos de agricultura familiar; estabelecimentos de agricultura não familiar e índice de desenvolvimento humano. Foram realizadas análises multivariadas para espacializar as variáveis climáticas, físicas e socioeconômicas e, assim, discriminar os Estados e Regiões brasileiras. As maiores produções de caprinos e de leite foram observadas na região Nordeste. A região Sudeste apresentou segunda maior produção de leite, seguido pelo Sul, Centro-Oeste e Norte. As médias para produtividade mostraram que as regiões Centro-Oeste e Sudeste apresentaram animais mais especializados a produção de leite. As análises multivariadas evidenciaram distinções entre clusters das regiões político-administrativas do Brasil. As variáveis climáticas foram as mais importantes para discriminar entre as regiões brasileiras. A heterogeneidade dos componentes climáticos, físicos e socioeconômicos evidenciou peculiaridades em cada região. Portanto, é preciso implementar programas de melhoramento genético animal que atendam as necessidades de cada região.

Molecular and pedigree analysis applied to conservation of animal genetic resources: the case of Brazilian Somali hair sheep.

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.

Genetic parameters for growth, reproductive and maternal traits in a multibreed meat sheep population.

The genetic parameters for growth, reproductive and maternal traits in a multibreed meat sheep population were estimated by applying the Average Information Restricted Maximum Likelihood method to an animal model. Data from a flock supported by the Programa de Melhoramento Genético de Caprinos e Ovinos de Corte (GENECOC) were used. The traits studied included birth weight (BW), weaning weight (WW), slaughter weight (SW), yearling weight (YW), weight gain from birth to weaning (GBW), weight gain from weaning to slaughter (GWS), weight gain from weaning to yearling (GWY), age at first lambing (AFL), lambing interval (LI), gestation length (GL), lambing date (LD - number of days between the start of breeding season and lambing), litter weight at birth (LWB) and litter weight at weaning (LWW). The direct heritabilities were 0.35, 0.81, 0.65, 0.49, 0.20, 0.15 and 0.39 for BW, WW, SW, YW, GBW, GWS and GWY, respectively, and 0.04, 0.06, 0.10, 0.05, 0.15 and 0.11 for AFL, LI, GL, LD, LWB and LWW, respectively. Positive genetic correlations were observed among body weights. In contrast, there was a negative genetic correlation between GBW and GWS (-0.49) and GBW and GWY (-0.56). Positive genetic correlations were observed between AFL and LI, LI and GL, and LWB and LWW. These results indicate a strong maternal influence in this herd and the presence of sufficient genetic variation to allow mass selection for growth traits. Additive effects were of little importance for reproductive traits, and other strategies are necessary to improve the performance of these animals.

Genetic parameters for growth, reproductive and maternal traits in a multibreed meat sheep population

The genetic parameters for growth, reproductive and maternal traits in a multibreed meat sheep population were estimated by applying the Average Information Restricted Maximum Likelihood method to an animal model. Data from a flock supported by the Programa de Melhoramento Genético de Caprinos e Ovinos de Corte (GENECOC) were used. The traits studied included birth weight (BW), weaning weight (WW), slaughter weight (SW), yearling weight (YW), weight gain from birth to weaning (GBW), weight gain from weaning to slaughter (GWS), weight gain from weaning to yearling (GWY), age at first lambing (AFL), lambing interval (LI), gestation length (GL), lambing date (LD - number of days between the start of breeding season and lambing), litter weight at birth (LWB) and litter weight at weaning (LWW). The direct heritabilities were 0.35, 0.81, 0.65, 0.49, 0.20, 0.15 and 0.39 for BW, WW, SW, YW, GBW, GWS and GWY, respectively, and 0.04, 0.06, 0.10, 0.05, 0.15 and 0.11 for AFL, LI, GL, LD, LWB and LWW, respectively. Positive genetic correlations were observed among body weights. In contrast, there was a negative genetic correlation between GBW and GWS (-0.49) and GBW and GWY (-0.56). Positive genetic correlations were observed between AFL and LI, LI and GL, and LWB and LWW. These results indicate a strong maternal influence in this herd and the presence of sufficient genetic variation to allow mass selection for growth traits. Additive effects were of little importance for reproductive traits, and other strategies are necessary to improve the performance of these animals.

Efeito da incorporação da covariância entre os efeitos direto e materno sobre a análise para a característica dias para ganhar 160 Kg / Effect of the covariance between maternal and direct effects on the analyses for the traits days to gain 160 kg

O objetivo deste trabalho foi estudar o efeito da covariância entre os efeitos direto e materno sobre as estimativas dos parâmetros genéticos e nas predições dos valores genéticos, direto e materno, para a característica dias para ganhar 160 kg (D160) na fase pré-desmama. Os parâmetros e as predições dos valores genéticos foram estimados utilizando o aplicativo MTDFREML. O modelo 1 incluiu os efeitos genéticos direto e materno e de ambiente permanente, além do efeito fixo de grupo contemporâneo e da covariável idade da vaca ao parto, assumindo a covariância entre o efeito direto e materno (sigmaam 0); o modelo 2, considerou os mesmos efeitos do modelo 1, mas a covariância entre os efeitos direto e materno foi considerada nula (sigmaam=0). As estimativas de correlação de classificação dos animais pelos valores genético foram realizadas utilizando a correlação de Spearman. As estimativas de herdabilidade direta e materna para D160 foram respectivamente, 0,12 ± 0,01 e 0,09 ± 0,02, sob o modelo 1, e 0,12 ± 0,01 e 0,07 ± 0,02, sob o modelo 2. A correlação genética entre os efeitos direto e materno foi de -0,14 ± 0,12 (modelo 1). A inclusão da covariância entre os efeitos direto e materno nos modelos de análises não alterou a estimativa dos parâmetros genéticos e a classificação dos animais pela ordem dos valores genéticos estimados, quando se considerou toda a população. Entretanto, verificou-se que à medida que diminui a proporção de animais selecionados diminui a correspondência entre a classificação dos animais obtida pelos dois modelos.