Genome-wide association study and pathway analysis for carcass fatness in Nellore cattle measured by ultrasound.

Identifying genes or genomic regions influencing carcass-quality traits such as fatness (FTN) is essential to optimize the genetic selection processes in beef cattle. The aim of this study was to identify genomic regions associated with FTN in Nellore cattle as well as to elucidate the metabolic pathways related to the phenotypic expression. Ultrasound-based measurements of FTN were collected in 11 750 animals, with 39 903 animals in the pedigree file. Additionally, 1440 animals were genotyped using the GGP-indicus 35K SNP panel, which contained 33 623 SNPs after quality control. Twenty genes related to FTN were found on 11 chromosomes, explaining 12.96% of the total additive genetic variance. Gene ontology revealed seven genes: NR1L2, PKD2, GSK3ß, EXT1, RAD51B, SORCS1 and DPH6, associated with important processes related to FTN. In addition, novel candidate genes (MAATS1, LYPD1, CDK5RAP2, RAD51B, c13H2Oorf96 and TRAPPC11) were detected and could provide further knowledge to uncover genetic regions associated to carcass fatness in beef cattle.

Flaxseed improves embryo production in Boer goats.

Flaxseed is a source of polyunsaturated fatty acids and could be used as a dietary ingredient to enhance reproductive performance of ruminants. The objectives of this study were to determine the effect of feeding diets with different levels of flaxseed on the nutrient intake, and quantity and quality of embryos in Boer goats. A total of 24 multiparous Boer goats were fed with a diet containing either 0, 4, 8 or 12% of flaxseed (n = 6 per group) and subjected to superovulation to determine the quantity and quality of embryos collected on 7 d after natural service. The nutrient intake was linearly associated with levels of flaxseed in the diet and, whereas while the fat (measured as ether extract) intake was positively associated, the non-fiber carbohydrate intake had a negative association with increasing levels of flaxseed in the diet. The quantity, quality and stage of embryonic development on 7 d after natural service were significantly different between levels of flaxseed in the diet. The number of viable embryos was greater in goats fed with a diet containing 4, 8, and 12% flaxseed (94, 84, and 87%, respectively) than those fed with a diet containing 0% flaxseed (65%). On the other hand, the number of degenerated embryos was greater for goats fed with a diet containing 0% flaxseed (35%) than those fed with a diet containing 4, 8, and 12% flaxseed (6, 16, and 13%, respectively). The proportion of grade 1 embryo collected was greater for goats fed with a diet containing 4 and 8% flaxseed (74 and 83%, respectively) than those fed with a diet containing 0 and 12% flaxseed (40 and 46%, respectively). In summary, our study demonstrated that feeding a diet with moderate levels of flaxseed could produce a greater number of better-quality embryos in Boer goats.

Quantitative trait loci for morphometric and mineral composition traits of the tibia bone in a broiler × layer cross.

Many economic losses occur in the poultry industry due to leg fragility. Knowing the genomic regions that influence traits associated with the growth and composition of the leg's bone can help to improve the selection process leading to increased leg resistance to fracture. The present study aimed to map quantitative trait loci (QTL) for mineral composition and morphometric traits of the tibia in 478 animals from an F2 broiler × layer cross. The measurement of weight, length and width of Tibia was carried out at 42 days of age. Ash, dry matter, levels of calcium (Ca), phosphorus (P), magnesium (Mg), Zinc (Zn) and Calcium:Phosphorus (Ca:P) ratio were also recorded. The population was genotyped for 128 microsatellite markers and one single nucleotide polymorphism, covering 2630 cM of the chicken genome. A likelihood ratio test was performed to find QTLs. Additive and dominance effects of the QTLs were included in the model. In the chromosomes 2 (GGA2), 6 (GGA6), 8 (GGA8), 24 (GGA24) and 26 (GGA26) some suggestive QTLs (P<0.00276) were mapped for tibia weight (GGA2 and GGA26), ash percentage (GGA2 and GGA6), dry matter percentage (GGA2), Ca (GGA8 and GGA24) and Ca:P ratio (GGA8), many of which are close to genes already identified as good candidates for those traits. The suggestive QTL on GGA2 has a pleiotropic effect on ash percentage, dry matter and bone weight, whereas in the GGA8 there seems to be two QTLs, one for Ca and another for Ca:P ratio. Thus, this study identified at least five genomic regions, in different chromosomes, that can be targeted for further research to identify potential mutations influencing the development and composition of leg bones in Gallus gallus.

Single nucleotide polymorphisms in the growth hormone and IGF type-1 (IGF1) genes associated with carcass traits in Santa Ines sheep.

Polymorphisms in the growth hormone (GH) and IGF type-1 (IGF1) genes have been associated with the economic traits in farm animals, including BW of some sheep breeds. However, it remains unknown if these polymorphisms also affect carcass traits in sheep. Thus, we aimed to identify polymorphisms in the GH and IGF1 genes in Santa Ines sheep in order to describe their allelic and genotypic frequencies as well as to test the hypotheses that they are associated with the carcass traits. Fragments of 4550 bp (IGF1) and 1194 bp (GH) were sequenced in up to 191 lambs. In all, 18 polymorphisms were identified in the IGF1 and 21 in the GH gene. The IGF1 polymorphisms rs430457475, rs412470350, rs409110739 and rs400113576 showed an additive effect on the internal carcass length (-0.9265±0.4223), rump girth (-2.9285±1.1473), rib yield (-1.0003±0.4588) and neck weight (-0.0567±0.0278), respectively. In addition, the polymorphisms rs58957314 in the GH affected the rib weight (-0.4380±0.1272) and rib yield (-2.2680±0.6970), loin weight (-0.1893±0.0516) and loin yield (-0.9423±0.3259), palette weight (-0.2265±0.0779) and palette yield (-0.9424±0.4184), leg weight (-0.3960±0.1375), neck weight (-0.0851±0.0394) and carcass finishing score (-0.1700±0.0839). These results allow us to conclude that there are polymorphisms in the IGF1 and GH genes associated with carcass traits in Santa Ines sheep, which can provide important information for marker-assisted selection.

Estimates of genomic heritability and genome-wide association study for fatty acids profile in Santa Inês sheep.

BACKGROUND: Despite the health concerns and nutritional importance of fatty acids, there is a relative paucity of studies in the literature that report genetic or genomic parameters, especially in the case of sheep populations. To investigate the genetic architecture of fatty acid composition of sheep, we conducted genome-wide association studies (GWAS) and estimated genomic heritabilities for fatty acid profile in Longissimus dorsi muscle of 216 male sheep. RESULTS: Genomic heritability estimates for fatty acid content ranged from 0.25 to 0.46, indicating that substantial genetic variation exists for the evaluated traits. Therefore, it is possible to alter fatty acid profiles through selection. Twenty-seven genomic regions of 10 adjacent SNPs associated with fatty acids composition were identified on chromosomes 1, 2, 3, 5, 8, 12, 14, 15, 16, 17, and 18, each explaining ≥0.30% of the additive genetic variance. Twenty-three genes supporting the understanding of genetic mechanisms of fat composition in sheep were identified in these regions, such as DGAT2, TRHDE, TPH2, ME1, C6, C7, UBE3D, PARP14, and MRPS30. CONCLUSIONS: Estimates of genomic heritabilities and elucidating important genomic regions can contribute to a better understanding of the genetic control of fatty acid deposition and improve the selection strategies to enhance meat quality and health attributes.

Parâmetros genéticos e efeitos de sexo e cruzamento recíproco sobre características de interesse econômico em aves F2 / Genetic parameters and effects of sex and reciprocal cross on economic traits in F2 broilers

Este estudo teve por objetivo estimar os parâmetros genéticos de características de interesse econômico, mensuradas em populações F2 desenvolvidas pela Embrapa Suínos e Aves utilizando cruzamento recíproco entre linhagens de corte e de postura. Ainda, foram avaliados os efeitos de sexo e de cruzamento recíproco sobre as características em estudo. Os pesos com um, 35 e 42 dias de idade; ganho de peso; consumo de ração e conversão alimentar entre 35 e 41 dias de idade; pesos dos pulmões, fígado, coração, moela, peito, pernas, carcaça, dorso, asas, cabeça, pés e gordura abdominal, além do comprimento do intestino, foram os fenótipos estudados. Foram estimados os componentes de variâncias genética aditiva e residual, além dos coeficientes de herdabilidade e das correlações genética e fenotípica. Os machos apresentaram maior peso para todas as características estudadas, nos dois cruzamentos recíprocos, exceto para gordura abdominal na população oriunda do cruzamento de machos de postura com fêmeas de corte. Os animais oriundos do cruzamento de machos de postura com fêmeas de corte foram mais pesados que os recíprocos, para todas as idades, além de apresentarem maior comprimento de intestino e maiores pesos de moela, carcaça, dorso, peito e cabeça. Os coeficientes de herdabilidade foram altos para consumo de ração e para os pesos ao nascimento, da moela e da gordura abdominal. As correlações fenotípicas estimadas foram, em sua maioria, baixas ou moderadas, contudo muitas correlações genéticas altas foram observadas. Ressalta-se que houve expressiva diferença nos coeficientes de herdabilidade de algumas características em função do cruzamento recíproco estudado, o que pode ser devido a efeitos materno, citoplasmático, ligados ao sexo ou imprinting.(AU)

This study aimed to estimate genetic parameters for several economic traits in F2 populations developed by Embrapa Swine and Poultry National Research Center, through reciprocal crosses of broilers and layer lines. Furthermore, sex and reciprocal cross effects were evaluated. Weights at 1, 35 and 42 days of age; weight gain, feed intake and feed conversion between 35 and 41 days of age; weights of the lungs, heart, liver, gizzard, breast, thighs, carcass, back, wings, head, legs and abdominal fat; and intestine length were studied. Residual and genetic additive variance components, heritability coefficients, and genetic and phenotypic correlations were estimated. Males were heavier than females for all studied traits in both reciprocal crosses, except for abdominal fat weight in chickens from the male layer x female broiler cross. Chickens from male layer x female broiler cross were heavier than those from its reciprocal cross, also having larger intestine length and gizzard, carcass, back, breast and head weights. The heritability coefficients were high for feed intake and body weight at birth, gizzard, and abdominal fat. The estimated phenotypic correlations were mostly lower or moderate, however, most high genetic correlations were observed. We found significant differences in heritability coefficients for some traits due to the reciprocal cross, which may be due maternal, cytoplasmic, sex-linked or imprinting effects.(AU)

Quantitative trait loci with sex-specific effects for internal organs weights and hematocrit value in a broiler-layer cross.

Rapid growth in broilers is associated with susceptibility to metabolic disorders such as pulmonary hypertension syndrome (ascites) and sudden death. This study describes a genome search for QTL associated with relative weight of cardio respiratory and metabolically important organs (heart, lungs, liver and gizzard), and hematocrit value in a Brazilian broiler-layer cross. QTL with similar or different effects across sexes were investigated. At 42 days of age after fasted for 6 h, the F2 chickens were weighed and slaughtered. Weights and percentages of the weight relative to BW42 of gizzard, heart, lungs, liver and hematocrit were used in the QTL search. Parental, F1 and F2 individuals were genotyped with 128 genetic markers (127 microsatellites and 1 SNP) covering 22 linkage groups. QTL mapping analyses were carried out using mixed models. A total of 11 genome-wide significant QTL and five suggestive linkages were mapped. Thus, genome-wide significant QTL with similar effects across sexes were mapped to GGA2, 4 and 14 for heart weight, and to GGA2, 8 and 12 for gizzard %. Additionally, five genome-wide significant QTL with different effects across sexes were mapped to GGA 8, 19 and 26 for heart weight; GGA26 for heart % and GGA3 for hematocrit value. Five QTL were detected in chromosomal regions where QTL for similar traits were previously mapped in other F2 chicken populations. Seven novel genome-wide significant QTL are reported here, and 21 positional candidate genes in QTL regions were identified.

Histomorfometria do epitélio ruminal de cabritos 1/2 sangue Boer submetidos a dietas com tortas oriundas da produção do biodiesel / Histomorphometrics of the ruminal epithelium of 1/2 blood Bôer goats submitted to diets with pies from the production of biodiesel

Objetivou-se determinar o melhor nível de inclusão e de substituição das tortas de dendê e amendoim, respectivamente, em dietas para cabritos 1/2 sangue Boer, por meio da avaliação histomorfométrica das papilas ruminais. Foram utilizados 40 cabritos 1/2 sangue Boer, para cada período experimental, machos, não castrados, com idade aproximada de três meses e com peso inicial de 15,01±1,76kg. Os períodos experimentais constaram de 75 dias e 72 dias. As dietas consistiram de volumoso feno de Tifton-85 e de ração em mistura completa, contendo níveis de inclusão da torta de dendê nas proporções de 0,0; 7,0; 14,0; e 21,0% com base na matéria seca; e de mistura completa, contendo níveis de substituição do farelo de soja pela torta de amendoim nas proporções de 0,0; 33,0; 66,0; e 100%, constituindo-se os tratamentos. No epitélio do rúmen, foram avaliadas altura e largura das papilas, assim como densidade papilar e espessura da parede muscular do rúmen. Entre estas, a altura das papilas, no experimento com torta de amendoim, foi a única a sofrer efeito linear decrescente (P<0,0014); as demais variáveis, tanto dos animais alimentados com torta de amendoim quanto daqueles alimentados com torta de dendê, não foram afetadas pela dieta. As médias de altura encontradas foram de 2,6 e 2,3mm para as tortas de amendoim e dendê, respectivamente. Portanto, a inclusão de até 21% de torta de dendê e a substituição de 100% de torta de amendoim no concentrado de cabritos não alteraram a morfometria das papilas ruminais.

The aim of this study was to determine the best level of pies and replacement of palm oil and peanut, respectively, in diets of 1/2 blood Bôer goats from the histomorphometry of the rumen papillae. A total of 40 1/2 blood male, unneutered, aged approximately three months and initial weight of 15.01±1.76kg Bôer goats were used in each experimental period. The experimental periods consisted of 75 days and 72 days. The diets consisted of roughage hay Tifton-85 and total mixed ration containing levels of inclusion of palm kernel cake in the proportions of 0.0, 7.0, 14.0 and 21.0% based on dry matter; and the second experiment consisted of a complete mixture containing substitution levels of soybean meal by groundnut cake in the proportions of 0.0, 33.0, 66.0 and 100%. Epithelial cells were evaluated in the rumen height and width of the papillae, and density and thickness of the papillary muscle of the rumen. Among these, the height of the papillae in the experiment with peanut butter pie was the only one to suffer a negative linear effect (P<0.0014), the other variables, both in animals fed groundnut cake and palm oil, were not affected by the diet. The average heights found were 2.6 and 2.3, for pies, peanut and palm oil, respectively. Therefore, the inclusion of up to 21% palm kernel cake and replacement of 100% peanut cake in the concentrate of kids did not alter the morphology of the rumen papillae.

Histomorfometria do epitélio ruminal de cabritos 1/2 sangue Boer submetidos a dietas com tortas oriundas da produção do biodiesel / Histomorphometrics of the ruminal epithelium of 1/2 blood Bôer goats submitted to diets with pies from the production of biodiesel

Objetivou-se determinar o melhor nível de inclusão e de substituição das tortas de dendê e amendoim, respectivamente, em dietas para cabritos 1/2 sangue Boer, por meio da avaliação histomorfométrica das papilas ruminais. Foram utilizados 40 cabritos 1/2 sangue Boer, para cada período experimental, machos, não castrados, com idade aproximada de três meses e com peso inicial de 15,01±1,76kg. Os períodos experimentais constaram de 75 dias e 72 dias. As dietas consistiram de volumoso feno de Tifton-85 e de ração em mistura completa, contendo níveis de inclusão da torta de dendê nas proporções de 0,0; 7,0; 14,0; e 21,0% com base na matéria seca; e de mistura completa, contendo níveis de substituição do farelo de soja pela torta de amendoim nas proporções de 0,0; 33,0; 66,0; e 100%, constituindo-se os tratamentos. No epitélio do rúmen, foram avaliadas altura e largura das papilas, assim como densidade papilar e espessura da parede muscular do rúmen. Entre estas, a altura das papilas, no experimento com torta de amendoim, foi a única a sofrer efeito linear decrescente (P<0,0014); as demais variáveis, tanto dos animais alimentados com torta de amendoim quanto daqueles alimentados com torta de dendê, não foram afetadas pela dieta. As médias de altura encontradas foram de 2,6 e 2,3mm para as tortas de amendoim e dendê, respectivamente. Portanto, a inclusão de até 21% de torta de dendê e a substituição de 100% de torta de amendoim no concentrado de cabritos não alteraram a morfometria das papilas ruminais.(AU)

The aim of this study was to determine the best level of pies and replacement of palm oil and peanut, respectively, in diets of 1/2 blood Bôer goats from the histomorphometry of the rumen papillae. A total of 40 1/2 blood male, unneutered, aged approximately three months and initial weight of 15.01±1.76kg Bôer goats were used in each experimental period. The experimental periods consisted of 75 days and 72 days. The diets consisted of roughage hay Tifton-85 and total mixed ration containing levels of inclusion of palm kernel cake in the proportions of 0.0, 7.0, 14.0 and 21.0% based on dry matter; and the second experiment consisted of a complete mixture containing substitution levels of soybean meal by groundnut cake in the proportions of 0.0, 33.0, 66.0 and 100%. Epithelial cells were evaluated in the rumen height and width of the papillae, and density and thickness of the papillary muscle of the rumen. Among these, the height of the papillae in the experiment with peanut butter pie was the only one to suffer a negative linear effect (P<0.0014), the other variables, both in animals fed groundnut cake and palm oil, were not affected by the diet. The average heights found were 2.6 and 2.3, for pies, peanut and palm oil, respectively. Therefore, the inclusion of up to 21% palm kernel cake and replacement of 100% peanut cake in the concentrate of kids did not alter the morphology of the rumen papillae.(AU)

Utilização de modelos unicaracterística e multicaracterística na estimação de parâmetros genéticos na raça Nelore / Utilization of single-trait and multi-trait models applied to genetic parameter estimation in Nellore Cattle

Estimativas dos parâmetros genéticos e dos componentes de covariância para peso ao nascimento (PN), peso à desmama (PD), circunferência escrotal (CE), ganho de peso pós-desmama (GP) e musculosidade (MUSC) foram obtidas com modelos unicaracterística, bicaracterística e multicaracterística, utilizando-se um banco de dados de 69.525 animais da raça Nelore. Os parâmetros foram estimados pelo método da máxima verossimilhança restrita, com modelos que incluíram o efeito genético aditivo direto e materno, além do grupo de manejo a desmama e de ambiente permanente da vaca, todos como aleatórios, e do efeito fixo de grupo de contemporâneo. Os coeficientes de herdabilidade estimados para as características pós-desmama com o modelo multicaracterística (0,45; 0,31 e 0,25, respectivamente, para CE, GP e MUSC) foram maiores que as estimativas obtidas com os modelos unicaracterística (0,42; 0,21 e 0,22) e bicaracterística (0,39; 0,25 e 0,24). Da mesma forma, as correlações genéticas estimadas foram, em grande parte, maiores para o modelo multicaracterística. Estes resultados indicam que a redução do viés, proporcionada pelo modelo multicaracterística, aumenta as estimativas dos parâmetros genéticos e demonstra que os resultados com análises unicaracterística e bicaracterística são subestimados. Os resultados da resposta à seleção demonstraram que a musculosidade apresentou grande potencial seletivo, e o cálculo das respostas correlacionadas de musculosidade e demais características estudadas demonstrou que sua utilização em programas de seleção pode ser vantajosa aos criadores...

Genetic parameters and components of (co)variance for birth weight (BW), weaning weight (WW), scrotal circumference (SC), weight gain at post-weaning (WG), and muscle score (MUSC) were obtained with univariate, bivariate and multivariate models, using a dataset of 69,525 Nellore cattle. The parameters were estimated by restricted maximum likelihood method. Direct and maternal additive genetic effects, group of management, and maternal permanent environmental effect were adjusted as random effects, while contemporary group was adjusted as fixed effect. Multivariate approach allowed higher estimate heritability for postweaning traits (0.45; 0.31 and 0.25, respectively for SC, WG and MUSC) than univariate (0,42; 0,21 and 0,22) and bivariate models (0,39; 0,25 and 0,24). Similarly, the genetic correlations were higher in the multivariate approach. These results indicate that reducing the bias provided by the mutivariate model improves the estimates of genetic parameters and shows that the results of bivariate and univarite models are underestimated. Selection for muscle score presented great potential for correlated response in other traits and its use in selection programs can be a useful tool for breeders...

Protein synthesis and degradation gene SNPs related to feed intake, feed efficiency, growth, and ultrasound carcass traits in Nellore cattle.

We looked for possible associations of SNPs in genes related to protein turnover, with growth, feed efficiency and carcass traits in feedlot Nellore cattle. Purebred Nellore bulls and steers (N = 290; 378 ± 42 kg body weight, 23 months ± 42 days old) were evaluated for daily feed intake, body weight gain (BWG), gross feed efficiency, feed conversion ratio, partial efficiency of growth, residual feed intake (RFI), ultrasound backfat, rump fat, and ribeye area. Genotypes were obtained for SNPs in the growth hormone receptor (GHR-1 and GHR-2); calpain (CAPN4751); calpastatin (UoGCAST); ubiquitin-conjugating enzyme 2I (UBE2I-1 and UBE2I-2); R3H domain containing 1 (R3HDM1-1, -2, -3, and -4), ring finger protein 19 (RNF19); proteasome 26S subunit, non-ATPase, 13 (PSMD13); ribosomal protein, large, P2 (RPLP2); and isoleucine-tRNA synthetase 2, mitochondrial (IARS2) genes. Allelic substitution, additive and dominant effects were tested and molecular breeding values were computed. CAPN4751, GHR-1 and -2, IARS2, R3HDM1-4, and UoGCAST were found to be normally segregating polymorphisms. Additive and dominance effects were observed on BWG, feed efficiency and carcass traits, although dominant effects predominated. Significant allelic substitution effects were observed for CAPN4751, GHR-1 and -2, and UoGCAST on BWG, gross feed efficiency, RFI, and carcass traits, under single- or multiple-marker analyses. Correlations between molecular breeding values and phenotypes were low, excepted for RFI, based on allelic substitution estimates obtained by stepwise linear regression. We conclude that SNPs in genes related to protein turnover are related to economically important traits in Nellore cattle.

Fracionamento de carboidratos e degradabilidade ruminal da cana-de-açúcar tratada com óxido de cálcio / Fractioning Fractioning of carbohydrates and rumen degradability of sugar cane treated with calcium oxide

Avaliaram-se o fracionamento de carboidratos e a degradabilidade in situ da matéria seca (MS) e da fibra em detergente neutro (FDN) da cana-de-açúcar tratada com óxido de cálcio (CaO). Foram testadas as porcentagens de 0; 0,75; 1,5; 2,25; 3,0; 3,75 e 4,5% de CaO, e o material testemunha (cana-de-açúcar in natura) para a avaliação do fracionamento de carboidratos, e as porcentagens de 0; 1,5; 3,0 e 4,5% de CaO para a avaliação da degradabilidade in situ da MS e da FDN. O CaO foi adicionado em pó na cana-de-açúcar, em porcentagem da matéria natural, por 24 horas. A porcentagem de inclusão de CaO na cana-de-açúcar proporcionou valores mais baixos para teores de carboidratos totais (CT) comparados aos valores da cana-de-açúcar in natura. Observou-se crescimento linear das frações A+B1 e B2, e redução na fração C da cana-de-açúcar em função da porcentagem de CaO. Os maiores valores de fração insolúvel potencialmente degradável da MS e menores de fração indigestível (Ip) da FDN foram observados na cana-de-açúcar com 3,0 e 4,5% de CaO. A adição de 3,0 e 4,5% de CaO na cana-de-açúcar promove diminuição da fração indigestível dos carboidratos e melhores taxas de degradação ruminal tanto da MS quanto da FDN.

Were evaluated the fractioning of carbohydrates and in situ dry matter (DM) and neutral detergent fiber (NDF) of sugarcane treated with calcium oxide (CaO). Levels 0, 0.75, 1.5, 2.25, 3.0, 3.75 and 4.5% CaO, and the material witness (sugarcane in nature) were tested for the assessment of fractioning of carbohydrates and levels 0, 1.5, 3.0 and 4.5% CaO for the evaluation of in situ DM and NDF. The levels of CaO were added in powder form, as a percentage of natural matter in sugarcane for 24 hours. The inclusion levels of CaO in sugarcane showed lower values for the total carbohydrates (TC) when compared with sugarcane in natura. A linear growth of the fractions A + B1 and B2 was observed, as well as a decrease in C fraction of sugarcane depending on the levels of CaO. The highest values of insoluble fraction potentially degradable in rumen and the lower values of NDF indigestible fraction (Ip) were observed in sugarcane with 3.0 and 4.5% CaO. The addition of 3.0 and 4.5% CaO to sugarcane decreased the indigestible carbohydrates fraction and promotes better rates of ruminal degradation of both DM and NDF.

Quantitative trait loci associated with chemical composition of the chicken carcass.

Major objectives of the poultry industry are to increase meat production and to reduce carcass fatness, mainly abdominal fat. Information on growth performance and carcass composition are important for the selection of leaner meat chickens. To enhance our understanding of the genetic architecture underlying the chemical composition of chicken carcasses, an F(2) population developed from a broiler × layer cross was used to map quantitative trait loci (QTL) affecting protein, fat, water and ash contents in chicken carcasses. Two genetic models were applied in the QTL analysis: the line-cross and the half-sib models, both using the regression interval mapping method. Six significant and five suggestive QTL were mapped in the line-cross analysis, and four significant and six suggestive QTL were mapped in the half-sib analysis. A total of eleven QTL were mapped for fat (ether extract), five for protein, four for ash and one for water contents in the carcass using both analyses. No study to date has reported QTL for carcass chemical composition in chickens. Some QTL mapped here for carcass fat content match, as expected, QTL regions previously associated with abdominal fat in the same or in different populations, and novel QTL for protein, ash and water contents in the carcass are presented here. The results described here also reinforce the need for fine mapping and to perform multi-trait analyses to better understand the genetic architecture of these traits.

Single nucleotide polymorphisms in CAPN and leptin genes associated with meat color and tenderness in Nellore cattle.

We analyzed single nucleotide polymorphisms in calpain, leptin, leptin receptor, and growth hormone receptor genes and their association with color, drip and cooking losses of longissimus muscle at 7, 14 and 21 days postmortem in 638 purebred Nellore bulls slaughtered between 22 and 26 months of age. Meat samples were vacuum-packed and aged at 4°C. The single nucleotide polymorphisms T945M, GHR2, E2FB, and CAPN4751 were evaluated. All genotypic classes were observed; however, the T/T genotype of T945M and E2FB was found at a low frequency. A significant association of E2FB with drip loss (a measure of water-holding capacity) was detected at seven days of meat aging. CAPN4751 had an additive effect on red and yellow color intensities. The T allele of CAPN4751 was found to be positively associated with improved meat color, but not with meat tenderness, differing from a previous report indicating that it is associated with meat tenderness. We conclude that the potential for use of CAPN4751 as a marker for these meat quality traits requires further research.

QTL for percentage of carcass and carcass parts in a broiler x layer cross.

An F2 experimental population, developed from a broiler layer cross, was used in a genome scan of QTL for percentage of carcass, carcass parts, shank and head. Up to 649 F2 chickens from four paternal half-sib families were genotyped with 128 genetic markers covering 22 linkage groups. Total map length was 2630 cM, covering approximately 63% of the genome. QTL interval mapping using regression methods was applied to line-cross and half-sib models. Under the line-cross model, 12 genome-wide significant QTL and 17 suggestive linkages for percentages of carcass parts, shank and head were mapped to 13 linkage groups (GGA1, 2, 3, 4, 5, 7, 8, 9, 11, 12, 14, 18 and 27). Under the paternal half-sib model, six genome-wide significant QTL and 18 suggestive linkages for percentages of carcass parts, shank and head were detected on nine chicken linkage groups (GGA1, 2, 3, 4, 5, 12, 14, 15 and 27), seven of which seemed to corroborate positions revealed by the previous model. Overall, three novel QTL of importance to the broiler industry were mapped (one significant for shank% on GGA3 and two suggestive for carcass and breast percentages on GGA14 and drums and thighs percentage on GGA15). One novel QTL for wings% was mapped to GGA3, six novel QTL (GGA1, 3, 7, 8, 9 and 27) and suggestive linkages (GGA2, 4, and 5) were mapped for head%, and suggestive linkages were identified for back% on GGA2, 11 and 12. In addition, many of the QTL mapped in this study confirmed QTL previously reported in other populations.

Association of SNPs on CAPN1 and CAST genes with tenderness in Nellore cattle.

We examined whether single-nucleotide polymorphisms (SNPs) in the calpain (CAPN) and calpastatin (CAST) genes, described from Bos primigenius taurus, are polymorphic in Nellore cattle. We also looked for a possible association of linkage disequilibrium of this polymorphism with tenderness of the longissimus dorsi muscle after 7, 14 and 21 days of postmortem aging in 638 purebred Nellore bulls. Meat tenderness was measured as Warner-Bratzler shear force. Additive and dominance effects were tested for SNPs of the three genotypic classes; the substitution effect was tested for SNPs with missing genotypic classes. Genotypic and gene frequencies were also calculated for the different SNPs. An increase in tenderness was observed from 7 to 21 days; the average values for shear force at 7, 14 and 21 days of aging were 5.92 +/- 0.06, 4.92 +/- 0.05, and 4.38 +/- 0.04 kg, respectively. All markers showed polymorphism, but there was no CC genotype for CAPN316, and few animals showed the AA genotype for CAPN530. The alleles CAPN4751, UOGCAST1, and WSUCAST were found to have additive and dominance effects for shear force at 7, 14 and 21 days, while CAPN316 showed a substitution effect for shear force at 7 and 21 days. An additive-by-additive epistatic interaction was observed between CAPN4751 and markers on the CAST gene. In conclusion, these markers should be considered for use in breeding programs.

Association of single nucleotide polymorphisms with carcass traits in Nellore cattle.

The association between two single nucleotide polymorphisms (SNPs), T945M and UCP1SNP1, with hot carcass weight (HCW, kg, N = 618), longissimus dorsi muscle area (REA, cm(2), N = 633), and backfat thickness (BF, mm, N = 625), measured in Nellore cattle in Brazil, was evaluated. Likelihood ratio tests were used to evaluate reduced (fixed effects of general mean, contemporary group, yearling weight, age at slaughter, and random effect of infinitesimal genetic value) and full model (reduced model effects plus quantitative trait locus effects). Additive and dominance effects were tested for each SNP. Genotypic and gene frequencies were also obtained for the SNPs and a descriptive phenotype analysis was made. Mean values for HCW, REA and BF were equal to 288.13 +/- 0.55 kg, 73.14 +/- 0.27 cm(2), and 4.28 +/- 0.07 mm, respectively; the coefficients of variation were 4.74, 9.24, and 42.43%, respectively. Gene frequencies for T945M and UCP1SNP1 were f(C) = 0.89, f(T) = 0.11, f(C) = 0.81, and f(G) = 0.19. The SNP T945M had a genotypic frequency of only three animals for TT genotype. Additive effects were observed for T945M on REA and BF, while UCP1SNP1 affected HCW and BF. Based on the significant additive effects of the SNPs and the gene frequencies that we found, we can expect genetic gains with marker assisted selection.

Quantitative trait loci associated with fatness in a broiler-layer cross.

An F(2) population established by crossing a broiler male line and a layer line was used to map quantitative trait loci (QTL) affecting abdominal fat weight, abdominal fat percentage and serum cholesterol and triglyceride concentrations. Two genetic models, the line-cross and the half-sib, were applied in the QTL analysis, both using the regression interval method. Three significant QTL and four suggestive QTL were mapped in the line-cross analysis and four significant and four suggestive QTL were mapped in the half-sib analysis. A total of five QTL were mapped for abdominal fat weight, six for abdominal fat percentage and four for triglyceride concentration in both analyses. New QTL associated with serum triglyceride concentration were mapped on GGA5, GGA23 and GG27. QTL mapped between markers LEI0029 and ADL0371 on GGA3 for abdominal fat percentage and abdominal fat weight and a suggestive QTL on GGA12 for abdominal fat percentage showed significant parent-of-origin effects. Some QTL mapped here match QTL regions mapped in previous studies using different populations, suggesting good candidate regions for fine-mapping and candidate gene searches.

Genetic parameters for pre-weaning traits in Braunvieh cattle.

The objective of this study was to estimate genetic parameters for pre-weaning traits of Braunvieh cattle raised under tropical conditions in Brazil. The weight and weight gain parameters were birth weight (BW, N = 9955), weight at 120 days of age (W120, N = 5901), weaning weight at 205 days (WW, N = 6970), weight gain from birth to 205 days (GAIN205, N = 6013), weight gain from birth to 120 days (GAIN120, N = 5135), and weight gain from 120 to 205 days (GAIN85, N = 4482). Variance components were estimated using the animal model with the MTDFREML software. The relationship matrix included 35,188 animals; phenotypic measures were available for 18,688. Direct and maternal heritability increased from birth to weaning, with estimates of 0.23 +/- 0.037, 0.25+/- 0.050, 0.41+/- 0.059 for direct heritability for BW, W120 and WW, respectively, 0.08 +/- 0.012, 0.15 +/- 0.032, 0.22 +/- 0.036 for maternal genetic effects, and 0.18, 0.14 and 0.16 for total heritability estimates. For pre-weaning gains, estimates of heritability were 0.36 +/- 0.059, 0.30+/- 0.059, 0.12 +/- 0.035 for direct genetic effects of the traits GAIN205, GAIN120 and GAIN85, respectively, 0.23 +/- 0.038, 0.17 +/- 0.037, 0.03 +/- 0.029 for estimates of maternal heritability, and 0.12, 0.13, 0.16 for total heritability, respectively. Genetic correlations between weights were greater between measures taken at shorter intervals. This information can be used to optimize the design of programs for genetic improvement of Braunvieh cattle raised under tropical conditions.

Quantitative trait loci for performance traits in a broiler x layer cross.

An F(2) resource population, derived from a broiler x layer cross, was used to map quantitative trait loci (QTL) for body weights at days 1, 35 and 41, weight gain, feed intake, feed efficiency from 35 to 41 days and intestinal length. Up to 577 F(2) chickens were genotyped with 103 genetic markers covering 21 linkage groups. A preliminary QTL mapping report using this same population focused exclusively on GGA1. Regression methods were applied to line-cross and half-sib models for QTL interval mapping. Under the line-cross model, eight QTL were detected for body weight at 35 days (GGA2, 3 and 4), body weight at 41 days (GGA2, 3, 4 and 10) and intestine length (GGA4). Under the half-sib model, using sire as common parent, five QTL were detected for body weight at day 1 (GGA3 and 18), body weight at 35 days (GGA2 and 3) and body weight at 41 days (GGA3). When dam was used as common parent, seven QTL were mapped for body weight at day 1 (GGA2), body weight at day 35 (GGA2, 3 and 4) and body weight at day 41 (GGA2, 3 and 4). Growth differences in chicken lines appear to be controlled by a chronological change in a limited number of chromosomal regions.