A genome-wide association study to detect QTL for commercially important traits in Swiss Large White boars

The improvement of meat quality and production traits has high priority in the pork industry. Many of these traits show a low to moderate heritability and are difficult and expensive to measure. Their improvement by targeted breeding programs is challenging and requires knowledge of the genetic and molecular background. For this study we genotyped 192 artificial insemination boars of a commercial line derived from the Swiss Large White breed using the PorcineSNP60 BeadChip with 62,163 evenly spaced SNPs across the pig genome. We obtained 26 estimated breeding values (EBVs) for various traits including exterior, meat quality, reproduction, and production. The subsequent genome-wide association analysis allowed us to identify four QTL with suggestive significance for three of these traits (p-values ranging from 4.99×10⁻⁶ to 2.73×10⁻⁵). Single QTL for the EBVs pH one hour post mortem (pH1) and carcass length were on pig chromosome (SSC) 14 and SSC 2, respectively. Two QTL for the EBV rear view hind legs were on SSC 10 and SSC 16.

Is the American Zebu really Bos indicus?

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

A radiation hybrid map of river buffalo (Bubalus bubalis) chromosome 7 and comparative mapping to the cattle and human genomes

A preliminary radiation hybrid (RH) map containing 50 loci on chromosome 7 of the domestic river buffalo Bubalus bubalis (BBU; 2n = 50) was constructed based on a comparative mapping approach. The RH map of BBU7 includes thirty-seven gene markers and thirteen microsatellites. All loci have been previously assigned to Bos taurus (BTA) chromosome BTA6, which is known for its association with several economically important milk production traits in cattle. The map consists of two linkage groups spanning a total length of 627.9 cR(5,000). Comparative analysis of the BBU7 RH 5,000 map with BTA6 in cattle gave new evidence for strong similarity between the two chromosomes over their entire length and exposed minor differences in locus order. Comparison of the BBU7 RH 5,000 map with the Homo sapiens (HSA) genome revealed similarity with a large chromosome segment of HSA4. Comparative analysis of loci in both species revealed more variability than previously known in gene order and several chromosome rearrangements including centromere relocation. The data obtained in our study define the evolutionarily conserved segment on BBU7 and HSA4 to be between 3.5 megabases (Mb) and 115.8 Mb in the HSA4 (genome build 36) DNA sequence. Copyright (c) 2008 S. Karger AG, Basel.

Capacidade de combinação de características de produção de ovos de linhagens de matrizes de frango de corte, usando análise de componentes principais

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Estimativas de parâmetros genéticos para características de crescimento e produtividade em vacas da raça Canchim, utilizando-se inferência bayesiana

The objective of this study was to estimate genetic parameters for body weights at weaning (PD), 12 months old (P12) and adult age (PAD), culling age (TPR, days in herd), number (ND10) and kilograms (QD10) of calves weaned up to ten years of age, total number (NDT) and total kilograms (QDT) of calves weaned during herd life, and kilograms of calves weaned per year in herd (QTPR) of Canchim (5/8 Charolais + 3/8 Zebu) females from one herd. Data consisted of 3,249, 3.111, 1,138, 1,340, 1,362, 1,362, 1,340, 1,340 and 1,340 records of PD, P12, PAD, TPR, ND10, QD10, NDT, QDT and QTPR. respectively. Variance and covariance components were estimated by bivariate analyses between PD, P12 and PAD and other production traits using Bayesian inference. The models included the additive direct, permanent environmental and residual random effects and the fixed effects year and month of birth or calving, calving age and age of the animal, depending on the trait. QD10, QDT and QTPR of each female were obtained by adjusting the weaning weights of calves for year and month of birth, sex and age of cow. Average of heritability estimates were 0.38 (PD), 0.40 (P12), 0.54 (PAD), 0.22 (TPR), 0.22 (ND10), 0.24 (QD10), 0.23 (NDT), 0.23 (QDT) and 0.32 (QTPR), indicating genetic variability to obtain response by selection. Genetic correlations between TPR (-0.02, 0.26 and -0.12), ND10 (0.04, 0.10 and -0.29), QD10 (0.37, 0.39 and -0.13), NDT (-0.03, 0.14 and -0.25), QDT (0.20, 0.33 and -0.16), QTPR (0.21, 0.28 and -0.19) and body weights (PD, P12 and PAD) suggest that selection of females based on weaning and 12-month body weights will not affect productivity. However, it may be decreased by increasing female adult body weight.

Copy number variation of individual cattle genomes using next-generation sequencing

Copy number variations (CNVs) affect a wide range of phenotypic traits; however, CNVs in or near segmental duplication regions are often intractable. Using a read depth approach based on next-generation sequencing, we examined genome-wide copy number differences among five taurine (three Angus, one Holstein, and one Hereford) and one indicine (Nelore) cattle. Within mapped chromosomal sequence, we identified 1265 CNV regions comprising similar to 55.6-Mbp sequence-476 of which (similar to 38%) have not previously been reported. We validated this sequence-based CNV call set with array comparative genomic hybridization (aCGH), quantitative PCR (qPCR), and fluorescent in situ hybridization (FISH), achieving a validation rate of 82% and a false positive rate of 8%. We further estimated absolute copy numbers for genomic segments and annotated genes in each individual. Surveys of the top 25 most variable genes revealed that the Nelore individual had the lowest copy numbers in 13 cases (similar to 52%, chi(2) test; P-value <0.05). In contrast, genes related to pathogen- and parasite-resistance, such as CATHL4 and ULBP17, were highly duplicated in the Nelore individual relative to the taurine cattle, while genes involved in lipid transport and metabolism, including APOL3 and FABP2, were highly duplicated in the beef breeds. These CNV regions also harbor genes like BPIFA2A (BSP30A) and WC1, suggesting that some CNVs may be associated with breed-specific differences in adaptation, health, and production traits. By providing the first individualized cattle CNV and segmental duplication maps and genome-wide gene copy number estimates, we enable future CNV studies into highly duplicated regions in the cattle genome.

Torta de dendê em dieta para a tilápia-do-nilo: Desempenho produtivo

To evaluate the nutritional value of African palm kernel meal (Elaeis guineensis) on the performance of Nile tilapia (Oseochromis niloticus), five isonitrogenous (30% crude protein), isoenergetic (2,800 Kcal/kg of digestible energy), and isofibrous (10% crude fiber) diets, with increasing levels of African palm kernel meal (0, 7, 14, 21, 28 and 35%) were fed ad libitum for 18 weeks to Nile tilapia (Oreochromis niloticus) fingerlings, averaging 1.52 ± 0.04 g of body weight, housed for 120 days in 60 liter aquaria with six fingerlings. To determine the production traits, weight gain, apparent food conversion, specific growth rate, protein efficiency ratio, weight gain percentage, net protein utilization, and body composition, fish were weighted at six-week intervals. Statistical analysis of recorded data were performed through multivariate profile analysis and polynomial regression models. Results showed that feeding fingerling Nile tilapia with ratios containing up to 35% of African palm kernel meal does not affect production performance.

Polimorfismo nos genes da leptina e do receptor de melatonina em búfalas (Bubalus bubalis)

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Critérios de seleção para incremento de uniformidade de produção em bovinos de corte

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Métodos alternativos de muda forçada para poedeiras comerciais

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Polimorfismo no gene do hormônio Grelina em búfalas (Bubalus bubalis) e sua associação com produção e qualidade do leite

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Construção de uma biblioteca BAC e avaliação de marcadores para caracterização de regiões alvo do genoma do búfalo

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Identificação de genótipos superiores para crescimento e qualidade de carcaça em bovinos de corte submetidos ao modelo biológico superprecose

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Produtividade de vacas mestiças leiteiras em sistema semi-intensivo nos municípios de Irituia e Mãe do rio do nordeste paraense

Verificar a influência de fatores do meio ambiente sobre características de produção e reprodução em grupos genéticos de bovinos leiteiros explorados em algumas fazendas nos municípios de Irituia e Mãe do rio no Nordeste Paraense. Foi utilizada uma média de 454 animais em lactação mestiças de Holandês, Pardo-Suíça e Girolando pertencentes a duas fazendas com sistema de criação semi-intensivo na época menos chuvosa. As médias e desvio-padrão para produção de leite total foram iguais a 1097,36 ± 330,47 Kg, com coeficiente de variação igual a 25,64% sendo que o grupo genético Holandesa, a época de parto menos chuvosa e o ano de 2007 apresentaram maior produção. O período de lactação apresentou efeito linear e crescente sobre a produção de leite total. O período de lactação apresentou média e desvio-padrão iguais a 218,17 ± 43,17 dias, a maior média para o período de lactação foi observada na época mais chuvosa e a média do período de lactação diminuiu no decorrer dos anos 2007 e 2008. A média e desvio padrão de intervalo entre partos encontrado no rebanho foi igual a 398,975 ± 60,85 dias. A época menos chuvosa apresentou uma média de intervalo entre partos menor que época mais chuvosa e a média de intervalo entre partos foi reduzindo a partir de 2006. A média de idade ao primeiro parto encontrado foi de 38,57 ± 5,81 meses. Os coeficientes de determinação foram maiores que 0,85 (R²a > 0,85), sendo que para o grupo genético Holandesa, os ajustes foram melhores em relação aos ajustes dos outros dois grupos genéticos. Para o grupo genético Girolando, o formato da curva de lactação diferiu dos outros dois grupos genéticos dificultando o ajuste pelas funções Gama Incompleta, Linear Hiperbólica e Polinomial Inversa. Os ajustes promovidos pela função polinomial inversa apresentaram ligeiro desvio em relação às outras duas funções. O grupo genético Holandesa apresentou produção ao pico e persistência um pouco mais elevados em relação aos outros grupos genéticos.

Genome-wide association study for feedlot average daily gain in Nellore cattle (Bos indicus)

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)