Associative effect gene in detection of major genes

Os efeitos associativos são gerados pela influência que o ambiente social tem sobre a expressão de genes em animais companheiros de grupo. Este ambiente social é definido em parte por genes responsáveis pelo comportamento dos animais que compõe o grupo, denominados de genes associativos. Estes genes podem estar diminuindo o poder de detecção de major genes de efeitos diretos, ou até mesmo estarem sendo identificados como se fossem genes de efeitos diretos. Este trabalho foi feito com o objetivo de verificar a influência que genes associativos possam ter em análises de identificação de major genes. Os dados foram gerados por meio de simulação. Foi simulado um genoma de 2471 cM e as freqüências alélicas e efeitos de 200 QTL (locos de característica quantitativa) distribuídos pelo genoma. Dois destes QTL foram transformados em major genes, um com efeito direto sobre o fenótipo do animal, major gene direto, e outro com efeito associativo sobre o fenótipo dos companheiros de grupo, major gene associativo. A população estudada foi formada pela escolha ao acaso de 3740 animais simulados, filhos de 20 pais e 337 fêmeas, formando 11 classes de grupos, com 10 animais em cada grupo e estabelecendo-se 34 repetições para cada classe. As classes foram determinadas pelo número de animais portadores do alelo dominante para o gene associativo em cada grupo, variando de zero indivíduo B_ a 10 indivíduos B_. O major gene associativo foi sumulado agindo de duas maneiras: influenciando na predisposição do animal a se envolver em disputas por uma melhor posição na ordem hierárquica, efeito associativo pré-hierárquico, tendo um efeito promovido pela agressividade entre os animais; e outra, o efeito associativo pós-hierárquico, promovido pelas vantagens que animais em posições mais elevadas na ordem hierárquica têm por terem acesso diferenciado aos recursos. Dois grandes conjuntos de simulações foram realizados, utilizando a mesma população simulada, um considerando o gene associativo com efeitos pré e pós-hierárquico e outro considerando o gene associativo apenas com efeito pós-hierárquico. Dentro desses dois grandes conjuntos de simulações foram simulados três níveis de efeitos para o major gene direto (1%, 3% e 5% da média fenotípica da população acrescentada ao valor do fenótipo dos animais). O efeito do major gene associativo foi simulado contendo apenas um nível de efeito para o efeito associativo pré-hierárquico (cada animal agressivo B_ causava uma diminuição de 8% da expressão do major gene direto em animais companheiros de grupos) e quatro níveis de efeitos para o efeito associativo pós-hierárquico (cada animal B_ no grupo causava uma diminuição de 5%, 10%, 20% e 30% de diminuição na expressão do major gene direto em animais companheiros de grupos). Com o objetivo de verificar a influência de genes associativos em analises de detecção de major genes, ambos os major genes foram avaliados como sendo major genes de efeito direto, por testes de média, na tentativa de identificar major genes com efeito direto sobre o fenótipo dos animais. Os resultados mostraram que, para os níveis dos efeitos dos genes simulados, o efeito associativo não foi capaz de mascarar a identificação de major genes com efeito direto (p < 0,01). A análise testando se o major gene associativo seria identificado como um gene de efeito direto mostrou que, para as simulações dos níveis de efeitos do gene direto contribuindo com mais de 3% da média fenotípica da população, o major gene associativo foi identificado como um major gene de efeito direto (p < 0,01).The Associative effects are produced by the influence that social environment has on gene expression in group companion animals. This social environment is defined in part by genes responsible for the behavior of the animals composing the group, called associative genes. These genes may be diminishing the power detection of major genes with direct effects, or even being identified as if they were genes with direct effects. This work was made aiming the evaluation of the influence of associative genes in identification analyses of major genes. The data were generated by simulation. A genome of 2471 cM, the allele frequencies and effects of 200 QTL (quantitative trait loci) were simulated. Two of these QTL were transformed in major genes, one with direct effects over the individual phenotype, the direct major gene, and another with associative effects over the phenotype of group companions, the associative major gene. The population in study was made by selecting randomly 3740 simulated animals, offspring of 20 males and 337 females, forming 11 group classes with 10 animals in each group and setting 34 repetitions for each class. The classes were determined by the number of animals with the dominant allele for the associative gene in each group, varying from zero to 10 individuals B_. The associative major gene was simulated acting in two ways: influencing the predisposition of the animal to be involved in disputes for a better position in the hierarchy, the pre-hierarchical associative effect, having effect promoted by the aggressiveness among the animals; and another, the post-hierarchical effect, promoted by the benefits that animals in a higher hierarchical position have for having differentiated access to the resources. Two major sets of simulations were performed, using the same simulated population, one considering the associative gene with pre and post- hierarchical effects and another considering the associative gene only with post-hierarchical effects. Within these two major sets of simulations, three levels of effects for the direct major gene were considered (adding 1%, 3% and 5% of the population phenotype mean to the phenotype of the animals). The associative major gene effect was simulated considering only one level of effect for the pre-hierarchical effect (each aggressive animal B_ caused a decrease of 8% in the expression of the direct major gene at group companions) and four level of effects for the post-hierarchical effect (each B_ animal caused a decrease of 5%, 10%, 20% and 30% in the expression of the direct major gene at group companions). In order to verify the influence of associative genes in analyses of major gene detection, both major genes were evaluated as direct major genes, by mean test, in an attempt to identify major genes with direct effect in the phenotype of animals. The results showed that, for the genes effect levels simulated, the associative effect could not mask the identification of major genes with direct effect (p < 0,01). The analysis testing whether the associative major gene would be identified as a gene with direct effect showed that, in simulations with direct effect gene levels contributing with more than 3% of the phenotypic mean of the population, the associative major gene was identified as a major gene of direct effect (p < 0,01).Coordenação de Aperfeiçoamento de Pessoal de Nível Superio

The myogenin gene: sequencing in swine and phylogenetic analysis

A capacidade de produção de carne está relacionada com o número de fibras musculares apresentadas pelos animais recém nascidos. As fibras musculares são formadas na miogênese que ocorre durante o desenvolvimento embrionário, evento que é em parte controlado pela família de genes MyoD. O gene da Miogenina é membro dessa família e regula a expressão de genes músculo específicos. Ele desempenha uma função importante porque quando é ativado, as células do tecido muscular param de se multiplicar e o tecido passa a crescer apenas em volume. É considerado então um gene candidato. Os objetivos desse trabalho foram investigar possíveis alterações nas seqüências de nucleotídeos no gene da Miogenina em suínos de raças divergentes, e comparar o sequenciamento obtido em suínos com outras espécies que possuem o gene depositado no Genbank, a fim de estudar a história evolutiva do gene nestas espécies. A estratégia usada foi a divisão do gene em sete fragmentos que continham os três exons, os dois introns e as regiões 3 e 5 do gene. Foram seqüenciados dois varrões da raça nativa Piau e 12 matrizes comerciais. Os resultados obtidos mostraram um gene altamente conservado, com nenhum polimorfismo nas regiões exônicas. O sequenciamento dos introns não apresentou resultados satisfatórios. Métodos de avaliação filogenética também comprovaram o estado conservado do gene. Foram comparadas seqüências das espécies Sus scrofa (suínos), Bos taurus (bovinos), Ovis áries (ovinos), Homo sapiens (humanos), Mus musculus (camundongos), Rattus norvegicus (ratos), Gallus gallus (galinhas) e Meleagris gallopavo (perus), verificando as taxas de substituição de nucleotídeos não sinônimas (Ka) pela taxa de substituições sinônimas (Ks) nos sítios. Os resultados indicaram que provavelmente o gene tenha sofrido uma evolução adaptativa nas espécies do grupo Ruminantia (B. taurus e O. aries) após as duas espécies terem divergido do seu ancestral comum. Nas outras espécies, o gene o gene parece estar evoluindo de maneira conservativa.Meat production capacity is related to muscle fibers number show in newborn animals. The muscle fibers are formed in the myogenesis that takes place during the embryonic development, an event that is controlled in part by the MyoD gene family. The Myogenin gene is a member of this family and rules the expression of muscle specific genes. It has an important because when it is activated, the cells from the muscle tissue stop to multiply and it will be growing only in volume. It is considered than a candidate gene. The objectives of this study were to verify possible alterations in the nucleotide sequences of the Myogenin gene in swine from divergent breeds, and compare the sequence obtained in swine with others species that have this data in the Genbank, to study the evolutionary story of the gene in these species. The strategy used was to divide the gene in seven fragments that contain the three exons, two introns and the 3 and 5 regions of the gene. Two boars of the native breed Piau and 12 commercial sows were sequenciated. The results showed a highly conserved gene, with no polymorphism in the exons regions. The introns sequencing did not shown satisfactory results. Phylogenetic evaluation methods also prove the conservatory state of the gene. It was compared sequences from the species Sus scrofa (swine), Bos Taurus (cows), Ovis aries (sheeps), Homo sapiens (humans), Mus musculus (mice), Rattus norvegicus (rats), Gallus gallus (chickens) and Meleagris gallopavo (turkeys), verifying the nonsynonymous nucleotide substitution rate by the synonymous substitution rate in the sites. The results point out that probably the gene suffered an adaptive evolution in the Ruminantia group (B. Taurus and O. aries) after these species diverged from their common ancestral. In the other species, the gene seems to be evolving in a conservative way.Coordenação de Aperfeiçoamento de Pessoal de Nível Superio

Buffalos milk yield analysis using random regression models

Data comprising 1,719 milk yield records from 357 females (predominantly Murrah breed), daughters of 110 sires, with births from 1974 to 2004, obtained from the Programa de Melhoramento Genetic de Bubalinos (PROMEBUL) and from records of EMBRAPA Amazonia Oriental - EAO herd, located in Belem, Para, Brazil, were used to compare random regression models for estimating variance components and predicting breeding values of the sires. The data were analyzed by different models using the Legendre's polynomial functions from second to fourth orders. The random regression models included the effects of herd-year, month of parity date of the control; regression coefficients for age of females (in order to describe the fixed part of the lactation curve) and random regression coefficients related to the direct genetic and permanent environment effects. The comparisons among the models were based on the Akaike Infromation Criterion. The random effects regression model using third order Legendre's polynomials with four classes of the environmental effect were the one that best described the additive genetic variation in milk yield. The heritability estimates varied from 0.08 to 0.40. The genetic correlation between milk yields in younger ages was close to the unit, but in older ages it was low

Association of MYF5 gene allelic variants with production traits in pigs

We studied the phenotypic effects of polymorphisms at the MYF5 gene in a divergent F2 swine population and found that one polymorphism was due to an insertion and another to a deletion. The genotypes of 359 F2 animals were obtained and the Normal/Normal (NN) and Normal/Insertion (NI) genotypes analyzed to determine associations with phenotypic data for performance, carcass and meat quality traits. Significant differences were observed (p < 0.05) between NN and NI animals for drip (NN = 3.14 &plusmn; 1.56; NI = 3.69 &plusmn; 2.78%), cooking (NN = 32.26 &plusmn; 2.41; NI = 33.21 &plusmn; 2.31%) and total loss (NN = 34.16 &plusmn; 2.63 and NI = 34.97 &plusmn; 2.08%). The Deletion marker was not statistically tested. The results indicate that the allelic variant Insertion is associated with a deleterious effect on meat quality traits and should be monitored in marker assisted selection programs

Relationship between the Porcine Stress Syndrome gene and pork quality traits of F2 pigs resulting from divergent crosses

The PSS genotypes of 596 F2 pigs produced by initial mating of Brazilian commercial sows and native boars were characterized by PCR-RFLP and the pork quality traits were evaluated. Among the 596 pigs studied, 493 (82.7%) were NN and 103 (17.3%) were Nn. There were no differences between NN and Nn pigs in the following pork qualities: pHu (5.71 ± 0.16 vs 5.70 ± 0.11), intramuscular fat (1.55 ± 0.64% vs 1.65 ± 0.67%), shear force (5552 ± 878 g/1.2 cm vs 5507 ± 826 g/1.2 cm), lightness (44.96 ± 2.05 vs 45.01 ± 1.92), redness (0.64 ± 0.60 vs 0.79 ± 0.55), yellowness (6.62 ± 0.56 vs 6.65 ± 0.48), hue (84.28 ± 5.53 vs 83.41 ± 4.85), or chroma (6.68 ± 0.52 vs 6.73 ± 0.52). However, pork from Nn pigs had a significantly (p < 0.05) lower pH45 (6.41 ± 0.27 vs 6.51 ± 0.26) and greater drip (3.92 ± 1.90% vs 3.06 ± 1.60%), cooking (33.29 ± 2.26% vs 32.50 ± 2.54%) and total (35.67 ± 2.48% vs 34.01 ± 2.58%) loss compared to that of NN pigs. These results indicate that, even in divergent crosses, PSS gene carriers produce pork of poorer quality