SNP- and haplotype-based single-step genomic predictions for body weight, wool, and reproductive traits in North American Rambouillet sheep.

Rambouillet sheep are commonly raised in extensive grazing systems in the US, mainly for wool and meat production. Genomic evaluations in US sheep breeds, including Rambouillet, are still incipient. Therefore, we aimed to evaluate the feasibility of performing genomic prediction of breeding values for various traits in Rambouillet sheep based on single nucleotide polymorphisms (SNP) or haplotypes (fitted as pseudo-SNP) under a single-step GBLUP approach. A total of 28,834 records for birth weight (BWT), 23,306 for postweaning weight (PWT), 5,832 for yearling weight (YWT), 9,880 for yearling fibre diameter (YFD), 11,872 for yearling greasy fleece weight (YGFW), and 15,984 for number of lambs born (NLB) were used in this study. Seven hundred forty-one individuals were genotyped using a moderate (50 K; n = 677) or high (600 K; n = 64) density SNP panel, in which 32 K SNP in common between the two SNP panels (after genotypic quality control) were used for further analyses. Single-step genomic predictions using SNP (H-BLUP) or haplotypes (HAP-BLUP) from blocks with different linkage disequilibrium (LD) thresholds (0.15, 0.35, 0.50, 0.65, and 0.80) were evaluated. We also considered different blending parameters when constructing the genomic relationship matrix used to predict the genomic-enhanced estimated breeding values (GEBV), with alpha equal to 0.95 or 0.50. The GEBV were compared to the estimated breeding values (EBV) obtained from traditional pedigree-based evaluations (A-BLUP). The mean theoretical accuracy ranged from 0.499 (A-BLUP for PWT) to 0.795 (HAP-BLUP using haplotypes from blocks with LD threshold of 0.35 and alpha equal to 0.95 for YFD). The prediction accuracies ranged from 0.143 (A-BLUP for PWT) to 0.330 (A-BLUP for YGFW) while the prediction bias ranged from -0.104 (H-BLUP for PWT) to 0.087 (HAP-BLUP using haplotypes from blocks with LD threshold of 0.15 and alpha equal to 0.95 for YGFW). The GEBV dispersion ranged from 0.428 (A-BLUP for PWT) to 1.035 (A-BLUP for YGFW). Similar results were observed for H-BLUP or HAP-BLUP, independently of the LD threshold to create the haplotypes, alpha value, or trait analysed. Using genomic information (fitting individual SNP or haplotypes) provided similar or higher prediction and theoretical accuracies and reduced the dispersion of the GEBV for body weight, wool, and reproductive traits in Rambouillet sheep. However, there were no clear improvements in the prediction bias when compared to pedigree-based predictions. The next step will be to enlarge the training populations for this breed to increase the benefits of genomic predictions.

Evaluation of the use of Leptodactylus ocellatus (Anura: Leptodactylidae) frog tissues as bioindicator of metal contamination in Contas River, Northeastern Brazil.

This paper presents a study on the viability of the use of tissues of the Leptodactylus ocellatus species (Anura Leptodactylidae) as a bioindicator of metal pollution. The study is based on the determination and correlation of the concentrations of manganese, chromium, zinc, nickel, copper and iron in sediments and tissues (skin, muscles and viscera) of the frog Leptodactylus ocellatus collected in the middle region of the Contas River in Bahia, Brazil. The highest levels of the metals studied were found in the viscera of this animal. In this tissue, a higher correlation of the concentration of these metals with those found in sediments was also observed. The concentrations of elements found in the skin and muscles of these amphibians have revealed no correlation with the sediment where they were collected. According to the results obtained, the viscera of the L. ocellatus species presents itself as a good bioindicator of contamination by the metals studied.

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.

A Comprehensive Comparison of Haplotype-Based Single-Step Genomic Predictions in Livestock Populations With Different Genetic Diversity Levels: A Simulation Study.

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.

Haplotype-Based Single-Step GWAS for Yearling Temperament in American Angus Cattle.

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 polymorphisms (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 quantitative trait loci (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 candidate genes.

Genotype by environment interactions for body weight in Mediterranean buffaloes using reaction norm models / Interacción genotipo × ambiente para peso corporal de búfalos Mediterráneos utilizando modelos de norma de reacción / Interação genótipo × ambiente para peso corporal de búfalos Mediterrâneos utilizando modelos de norma de reação

Abstract Background: Buffalo breeding has significantly increased in Brazil over recent years. However, few genetic evaluations have been conducted. Objective: To assess Genotype x Environment Interactions in the Mediterranean Water Buffalo in Brazil, for weight at 205 days of age, using reaction norm models via random regression. Methods: Data for buffaloes born between 1990 and 2014 were collected from five farms ascribed to the Brazilian Buffaloe Improvement Program, located in the North (1), Northeast (1), South (2) and Southeast (1) regions of Brazil. The initial database consisted of 5,280 observations at 205 days of age (W205). We assessed fit using two hierarchical reaction norm models: a two-step (HRNM2s) and a one-step (HRNM1s). Model fit was estimated using the Deviance Information Criterion, Deviance Based on Bayes Factors and Deviance based on Conditional Predictive Ordinate. The environmental descriptors were created to group individuals into common production environments based on year, season, herd and sex. Results: The best fit was obtained for the hierarchical reaction norm model with one-step (HRNM1s). Direct heritability estimates for this model ranged from 0.17 to 0.67 and the maternal heritability from 0.02 to 0.11 with increasing environmental gradient. Lower correlations among the sire classifications were obtained in comparison with HRNM1s in environments with low and high management, confirming the presence of genotype x environment interactions. Conclusion: We recommend a wider application of genetic evaluation in buffalo aimed at identifying optimal genotypes within specific environments.

Resumen Antecedentes: La cría de búfalos ha aumentado significativamente en Brasil en los últimos años. Sin embargo, se han realizado escasas evaluaciones genéticas. Objetivo: Evaluar las interacciones genotipo x ambiente en búfalos de agua Mediterráneos criados en Brasil, para peso a los 205 días de edad, utilizando modelos de reacción mediante regresión aleatoria. Métodos: Los datos de búfalos nacidos entre 1990 y 2014 se obtuvieron de cinco granjas situadas en el Norte (1), Nordeste (1), Sur (2) y del Sureste (1) de Brasil. Todas estas haciendas participan en el Programa Brasileño de Mejoramiento de Búfalos. Nuestra base de datos inicial consistió de 5.280 observaciones a los 205 días de edad (P205). Evaluamos el ajuste utilizando dos modelos de norma de reacción jerárquica: de dos pasos (HRNM2s) y un paso (HRNM1s). El ajuste del modelo se estimó usando el Criterio de información de la desviación, desviación basado en los factores de bayes y desviación basado en la ordenación predictiva condicional. Los descriptores ambientales fueron creados para agrupar individuos en ambientes de producción comunes basados en año, estación, rebaño y sexo. Resultados: El mejor ajuste se obtuvo para el modelo de norma de reacción jerárquica con un paso (HRNM1s). Las estimaciones de heredabilidad directa para este modelo variaron de 0,17 a 0,67 y la heredabilidad materna de 0,02 a 0,11 con gradiente ambiental creciente. Las correlaciones más bajas entre las clasificaciones de los reproductores se obtuvieron en comparación con las HRNM1s, en ambientes con bajo y alto manejo, confirmando la presencia de interacciones genotipo x ambiente. Conclusiones: Recomendamos la aplicación amplia de la evaluación genética en búfalos para identificar genotipos óptimos en ambientes específicos.

Resumo Antecedentes: A criação de búfalos aumentou significativamente no Brasil nos últimos anos. No entanto, eles raramente foram objeto de avaliações genéticas. Objetivo: Avaliar as interações genótipo x ambiente em búfalo Mediterrâneo criados no Brasil, para peso aos 205 dias de idade, utilizando modelos de reação por meio de regressão aleatória. Métodos: Os dados para búfalos de água do Mediterrâneo nascidos entre 1990 e 2014 foram coletados de cinco fazendas localizadas nas regiões Norte (1), Nordeste (1), Sul (2) e Sudeste (1) do Brasil. Todas essas fazendas participam do Programa Brasileiro de Melhoramento dos Búfalos. Nosso banco de dados inicial consistiu de 5.280 observações aos 205 dias de idade (P205). Nós avaliamos o ajuste usando dois modelos de norma de reação hierárquica: um de dois passos (HRNM2s) e um passo (HRNM1s). O ajuste do modelo foi estimado usando o Critério de informações do desvio, desvio baseado nos fatores de bayes e desvio baseado na ordenação preditiva condicional. Os descritores ambientais foram criados para agrupar indivíduos em ambientes de produção comuns baseados em ano, estação, rebanho e sexo. Resultados: O melhor ajuste foi obtido para o modelo de norma de reação hierárquica com um passo (HRNM1s). As estimativas de herdabilidade direta para este modelo variaram de 0,17 a 0,67 e a herdabilidade materna de 0,02 a 0,11 com gradiente ambiental crescente. As correlações mais baixas entre as classificações dos reprodutores foram obtidas em comparação com as HRNM1s, em ambientes com baixo e alto manejo, confirmando a presença de interações genótipo x ambiente. Conclusões: Recomendamos a aplicação mais ampla da avaliação genética em búfalos visando identificar genótipos ótimos em ambientes específicos.

Parameters and genetic trends for reproductive characteristics of a closed Angus herd / Parámetros y tendencias genéticas de características reprodutivas de um rebaño cerrado Angus / Parâmetros e tendências de carcaterísticas reprodutivas de um rebanho fechado Angus

Abstract Background: Closed breeding populations are useful to conduct basic and applied research. The Wye Angus herd is one of them. It was founded using only a few animals. The pedigree of the descendants of the original herd can be completely described by historical records resulting from strong selection. Wye Angus genetics has influenced that of Aberdeen Angus, Red Angus, and Brangus cattle worldwide. Objective: To evaluate parameters and genetic trends associated with the reproduction traits of the Wye Angus herd between the years 1937 and 2012. Methods: We used pedigree information of 11,692 individuals. The reproductive traits assessed were age at first calving (AFC), calving interval (CI), and scrotal circumference (SC). The covariance components were estimated by Bayesian inference. The genetic trends were obtained by linear regression of the genetic values over birth years of the animals. Results: The heritability estimates for AFC, and CI were negligible, although a small genetic gain was associated with CI. Because the AFC and CI values of the herd are small, past reproductive management has produced favourable results for the heifers. Conclusion: The Wye Angus herd has enough genetic variability for genetic gain through selection on SC.

Resumen Antecedentes: Las poblaciones reproductivas cerradas son útiles para realizar investigacion básica y aplicada. El hato Wye Angus es uno de ellos. Fue fundado utilizando sólo unos pocos animales. El pedigrí de los descendientes del hato original puede describirse completamente mediante registros históricos resultantes de una fuerte selección. La genética del Wye Angus ha influido en la del Aberdeen Angus, Red Angus y Brangus en todo el mundo. Objetivo: Evaluar los parámetros y las tendencias genéticas de características reproductivas del rebaño Wye Angus en el periodo entre 1937 y 2012. Métodos: Utilizamos información de pedigrí de 11.692 individuos. Las características evaluadas fueron circunferencia escrotal (SC), edad al primer parto (AFC) y el intervalo entre partos (CI). Los componentes de (co)variancia fueron obtenidos mediante metodología Bayesiana. Las tendencias genéticas fueron obtenidas por regresión lineal ponderada de los valores genéticos sobre el año de nacimiento del animal. Resultados: Las estimaciones de heredabilidad para AFC y CI fueron insignificantes, aunque se asoció un pequeño beneficio genético con CI. Sin embargo, la AFC y el CI del rebaño son bajos, indicando que el manejo reproductivo ha traído resultados favorables para las novillas. Conclusion: El rebaño Wye Angus posee suficiente variabilidad genética para la ganancia genética por medio de la selección para SC.

Resumo Antecedentes: O rebanho Wye Angus foi fundado a partir de poucos animais e destaca-se por ser um rebanho fechado, com informações completas de pedigree e forte seleção, oferecendo vantagens únicas em termos de realização de pesquisas em melhoramento genético animal. Além disso, a genética de Wye Angus tem influenciado os de Aberdeen Angus, Red Angus e Brangus em todo o mundo. Objetivo: Avaliar os parâmetros genéticos e tendências de características reprodutivas do rebanho Wye Angus no período entre 1937 e 2012. Métodos: Foram usadas informações do pedigree de 11.692 individuos. As características avaliadas foram: perímetro escrotal (SC), idade ao primeiro parto (AFC), e do intervalo entre partos (CI). Componentes de (co) variância foram obtidos por meio da metodologia Bayesiana. As tendências genéticas foram obtidas por regressão linear ponderada dos valores genéticos sobre o ano de nascimento do animal. Resultados: Hereditariedade para AFC e CI foram insignificantes, embora um pequeno ganho genético tenha sido associado a CI. No entanto, os valores para AFC e CI do rebanho são baixos, indicando que o manejo reprodutivo trouxe resultados favoráveis para as novilhas. Conclusão: O rebanho Wye Angus tem variabilidade genética suficiente para ganho genético através de seleção para SC.

A canonical correlation analysis of the association between carcass and ham traits in pigs used to produce dry-cured ham.

The association between carcass and ham traits in a pig population used to produce dry-cured ham was studied using canonical correlation analysis. The carcass traits examined were hot carcass weight (HCW), backfat thickness (BT) and loin depth (LD), and the ham traits studied were gross ham weight (GHW), trimmed ham weight (THW), ham inner layer fat thickness (HIFT), ham outer layer fat thickness (HOFT), pH (pH) and the Göfo value. Carcass and ham traits are not independent. The canonical correlations (r) between the carcass and ham traits at 130 kg were 0.77, 0.24 and 0.20 for the first, second and third canonical pair, respectively, and were all significant (p < 0.01) by the Wilks test. The corresponding canonical correlations between the three canonical variate pairs for the carcass and ham traits at 160 kg were 0.88, 0.42 and 0.14, respectively (p < 0.05 for all, except the third). The correlations between the traits and their canonical variate showed an association among HCW, GHW and THW, and between BT and HOFT. These results indicate that carcass traits should be used to cull pigs that are not suitable for dry-cured ham production.

A canonical correlation analysis of the association between carcass and ham traits in pigs used to produce dry-cured ham

The association between carcass and ham traits in a pig population used to produce dry-cured ham was studied using canonical correlation analysis. The carcass traits examined were hot carcass weight (HCW), backfat thickness (BT) and loin depth (LD), and the ham traits studied were gross ham weight (GHW), trimmed ham weight (THW), ham inner layer fat thickness (HIFT), ham outer layer fat thickness (HOFT), pH (pH) and the Göfo value. Carcass and ham traits are not independent. The canonical correlations (r) between the carcass and ham traits at 130 kg were 0.77, 0.24 and 0.20 for the first, second and third canonical pair, respectively, and were all significant (p < 0.01) by the Wilks test. The corresponding canonical correlations between the three canonical variate pairs for the carcass and ham traits at 160 kg were 0.88, 0.42 and 0.14, respectively (p < 0.05 for all, except the third). The correlations between the traits and their canonical variate showed an association among HCW, GHW and THW, and between BT and HOFT. These results indicate that carcass traits should be used to cull pigs that are not suitable for dry-cured ham production.