Antonio Policarpo Souza Carneiro

The Indubrasil breed in the Brazilian Northeast: breeding and population structure

In order to provide knowledge for breeding, conservation programs and expansion policies of the Indubrasil breed from northeastern Brazil, the evolutionary history, estimates of genetic parameters and the populational structure of the breed were studied. Pedigree information was used from animals born from 1964 to 2006 and the adjusted weights at 205, 365 and 550 days of age of bovines born from 1976 onwards. The heritability coefficient estimates were lower than those reported in the literature for the adjusted weights at the three ages (P205: direct 0.11 ± 0,03 and maternal 0.01 ± 0.03; P365: direct 0.16 ± 0.04 and P550: direct 0.15 ± 0.05) and the genetic gains for the evaluated traits decreased in the sampled period (P205: -0.028 kg/year; P365: -0.030 kg/year and P550: -0.025 kg/year). The low genetic variability and the reduced genetic gains were probably due to a reduction in the effective size and increasing inbreeding within the period. Furthermore, the drastic reduction in the number of births per year and the low use of unrelated sires within the herds make the Indubrasil breed a genetic group potentially threatened by extinction, so that conservationist and expansion programmes should be set up.

Identidade de modelos não lineares para comparar curvas de crescimento de bovinos da raça Tabapuã

The objective of this work was to evaluate the use of identity of nonlinear models to compare growth curves of the cattle breed Tabapua, between five production regions from Northeast Brazil. Weight data of 3,695 males and 4,236 females from Maranhao, Gado Algodao, Mata Agreste, Sertao, and Itapetinga-Valadares regions were analyzed. After adjusting the Brody model, the likelihood ratio test was applied, with a chi-square approximation, to evaluate the equality of parameters of growth curves between those regions. The reduced model with equal rate of maturity for some regions, with 14 parameters, was the most appropriate for describing animal growth. Curves of male growth showed maturity rates in common in the following regions of production: Gado Algodao and Mata Agreste, Maranhao and Itapetinga-Valadares, and Sertao. For females, regions with maturity rates in common were: Mata Agreste and Sertao, Maranhao and Itapetinga-Valadares, and Gado Algodao. The use of a single curve is not appropriate to describe the growth of the cattle breed Tabapua in the studied regions.

Oscilação genética em populações submetidas a métodos de seleção tradicionais e associados a marcadores moleculares

The effect of genetic drift in populations under selection with different effective sizes was evaluated using data simulated by the GENESYS program. Selection was applied during 20 generations based on Individual selection (IS) using breeding values predicted by classical best linear unbiased prediction (BLUP) and BLUP associated with molecular markers (BLUPM). The similarity matrix used in BLUPM was obtained by simulation of 100 micro-satellites markers (simple sequence repeats) using a similarity coefficient corresponding to the mean Euclidean distance for quantitative data. Six populations of selection were simulated corresponding to two effective sizes (18.18 and 66.66), and three mating systems of selected sires (random mating, exclusion of half sibs and exclusion of half as well as full sibs). The average phenotypic value was the parameter of evaluation. Large variation on average phenotypic values was due to genetic drift, mainly for BLUP and BLUPM methods and also for populations with small effective sizes. The results indicate genetic drift may cause large variation in genetic gains by selection in breeding programs designed for small populations.

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.

Endogamia, fixação de alelos e limite de seleção em populações selecionadas por métodos tradicionais e associados a marcadores moleculares

This study aimed to evaluate the inbreeding coefficient, alleles fixation and selection limit in a population selected during 20 generations. Selection was based on breeding values predicted by classical best linear unbiased prediction (BLUP), BLUP associated with molecular markers (BLUPM) and individual selection (IS) using different mating designs. The genetic similarity matrix used in BLUPM was obtained by simulating 100 micro satellite markers (simple sequence repeats) using a similarity coefficient corresponding to the mean Euclidean distance between quantitative data. The selection methods were compared using populations with an effective size of 66.66 and a mean of 30 repetitions. The largest increase in inbreeding was observed for BLUPM, followed by BLUP and SI. The methods based on BLUP provided the higher fixation of favorable and unfavorable alleles. The BLUPM method provided the higher reduction in the selection limit during the twenty generations. Systems excluding between sibs mating resulted in lower increases in inbreeding rates, fewer losses due to unfavorable allele fixation and smaller decreases in selection limit.

Erros na classificação de touros, vacas e touros jovens geneticamente superiores avaliados na presença de heterogeneidade

Foram simuladas quatro estruturas de dados com diferentes padroes de heterogeneidade entre rebanhos e com diferentes graus de conexidade genetica. As estruturas simuladas diferiam quanto aos parâmetros heterogeneos entre rebanhos: 1) heterogeneidade para todos os parâmetros; 2) medias geneticas homogeneas e demais parâmetros heterogeneos; 3) heterogeneidade para parâmetros fenotipicos; e 4) rebanhos sem heterogeneidade. Apos a predicao dos valores geneticos, calculou-se a porcentagem de animais comuns entre dois grupos de classificacao para os animais geneticamente superiores: grupo 1 - classificacao com base nos valores geneticos verdadeiros e grupo 2 - classificacao com base nos valores geneticos preditos. Para dados com heterogeneidade para todos os parâmetros e 0% de conexidade genetica, a porcentagem de touros comuns aos dois grupos de classificacao foi baixa e houve grandes erros na classificacao dos touros geneticamente superiores. Quando os rebanhos possuiam 100% de conexidade genetica, esta porcentagem foi superior a 73% e os erros na classificacao dos touros foram menores. Para vacas e touros jovens, mesmo para dados com 100% de conexidade genetica entre rebanhos, a predicao dos valores geneticos foi muito afetada pela presenca da heterogeneidade para todos os parâmetros. Para as estruturas sem heterogeneidade para media genetica, as porcentagens de animais comuns entre os grupos de classificacao foram altas e os erros na classificacao dos animais geneticamente superiores foram pequenos, mesmo havendo heterogeneidade para outros parâmetros. Esses resultados sugerem que a heterogeneidade entre rebanhos para medias geneticas teve grande efeito sobre a acuracia da predicao dos valores geneticos dos animais. Contudo, quando a heterogeneidade entre os rebanhos ocorreu para outros parâmetros como variância genetica, media fenotipica e variância fenotipica, os resultados das avaliacoes geneticas dos animais foram proximos aos obtidos para dados sem heterogeneidade entre rebanhos.

Efeito da conexidade de dados sobre o valor fenotípico médio e a variância genética aditiva

Simulated data were used to verify the effect of the connectedness on the average phenotypic value and the additive genetic variance. The simulated genome was formed from a quantitative trait governed by 500 loci. Significance herd effect (9 herds) by 5% probability F test was simulated. Data sets with 0, 15, 30, 60, 90 and 100% of connectedness for heritabilities 0.10, 0.30 and 0.60 and for different progeny sizes (9, 54 and 90 progenies/sire) were simulated. In each generation nine males were selected and the number of selected females shifted according to the number of progenies considering in each data arrange. The selection was accomplished in ten generations, where the process was repeated 30 times. Data with smaller connectedness reduced the average phenotypic value, and the largest effect of the connectedness was for small heritability and small progeny size. The connectedness effect on the additive genetic variance was small.Simulated data were used to verify the effect of the connectedness on the average phenotypic value and the additive genetic variance. The simulated genome was formed from a quantitative trait governed by 500 loci. Significance herd effect (9 herds) by 5% probability F test was simulated. Data sets with 0, 15, 30, 60, 90 and 100% of connectedness for heritabilities 0.10, 0.30 and 0.60 and for different progeny sizes (9, 54 and 90 progenies/sire) were simulated. In each generation nine males were selected and the number of selected females shifted according to the number of progenies considering in each data arrange. The selection was accomplished in ten generations, where the process was repeated 30 times. Data with smaller connectedness reduced the average phenotypic value, and the largest effect of the connectedness was for small heritability and small progeny size. The connectedness effect on the additive genetic

Efeito da conexidade de dados sobre a acurácia dos testes de progênie e performance

Simulated data were used to verify the effect of the connectedness on the accuracy of progeny and performance tests. The simulated genome was formed from a quantitative trait governed by 500 loci. Significance herd effect (9 herds) by 5% probability F test was simulated. Data sets with 0, 15, 30, 60, 90 and 100% of connectedness for heritabilities 0.10, 0.30 and 0.60 and for different progeny sizes (9, 54 and 90 progenies/sire) were simulated. In each generation nine males were selected and the number of selected females shifted according to the number of progenies considering in each data arrange. The selection was accomplished in ten generations, where the process was repeated 30 times. Data with smaller connectedness reduced the accuracy of both tests and the connectedness was more important for small heritability and small progeny size. The heritability and the progeny size had larger influence in the genetic evaluation than the effect of connectedness.

Morphological phenotypic dispersion of garlic cultivars by cluster analysis and multidimensional scaling

Multivariate techniques have become a useful tool for studying the phenotypic diversity of Germplasm Bank accessions, since they make it possible to combine a variety of different information from these accessions. This study aimed to characterize the phenotypic dispersion of garlic (Allium sativum L.) using two multivariate techniques with different objective functions. Twenty accessions were morphologically characterized for bulb diameter, length, and weight; number of cloves per bulb; number of leaves per plant; and leaf area. Techniques based on generalized quadratic distance of Mahalanobis, UPGMA (Unweighted Pair Group Method with Arithmetic Mean) clustering, and nMDS (nonmetrric MultiDimensional Scaling) were applied and the relative importance of variables quantified. The two multivariate techniques were capable of identifying cultivars with different characteristics, mainly regarding their classification in subgroups of common garlic or noble garlic, according to the number of cloves per bulb. The representation of the phenotypic distance of cultivars by multidimensional scaling was slightly more effective than that with UPGMA clustering.

Impacts of ignoring the non-additive genetic effects of dominance on animal genetic evaluation

The objective of this study was to evaluate impacts of ignoring the dominance effects on the estimation of genetic parameters and prediction of genetic values by the restricted maximum likelihood method, under the additive animal model, using MTDFREML. Two gene action models were simulated for the same genomic architecture: one model that included only additive effects of the genes and the other with additive effects and positive and complete dominance into 100% of the loci. Under each genetic model, three base populations were generated corresponding to the characteristics with heritabilities of 0.15 (low), 0.30 (average) and 0.60 (high). Starting from the base populations the initial populations were generated which by selection and mating at random, for six consecutive and discrete generations, each one produced 18,000 animals with record. The estimates of the components of variance and heritability obtained in the model with additive gene action were similar to the actual values for all traits, while under dominance gene action, every component was overestimated, especially the additive genetic variance. The non-estimated dominance variance by the animal model adopted was redistributed between the additive genetic and residual components estimated. Accuracy was lost in the genetic evaluation, under the genetic model with dominance, that resulted in smaller correlations between the actual and predicted breeding values of the animals. Additional studies are needed since the simulated genome might not correspond to the true biological systems.