Genetic variation within and among species of genus Arachis, section Rhizomatosae

The genus Arachis is endemic to South America and comprises 80 species, 69 of which have already been described and eleven not yet published. The genus includes the cultivated peanut ( A. hypogaea) and several forage species, the most important ones being A. glabrata and A. pintoi. Accessions of section Rhizomatosae, including three tetraploid species 2n = 4x = 40 (A. glabrata, A. pseudovillosa and A. nitida nom. nud.) and one diploid species 2n = 2x = 20 (A. burkartii), were evaluated using RAPD markers to assay genetic variability within and among species. The ten random primers used yielded a total of 113 polymorphic bands. The data were scored as the presence or absence of each band in each sample. A distance matrix and dendrogram were obtained using Link's coefficient and the neighbor-joining method. Most accessions analyzed grouped into two major clusters: the first comprised most accessions of A. glabrata and accessions of A. nitida, and the second cluster comprised accessions of A. burkartii. Arachis pseudovillosa and a few accessions of A. glabrata and A. nitida were placed between these major clusters. The diploid and tetraploid species were grouped quite separately, suggesting that the tetraploids did not originate from the diploid species analyzed.

Effects of broiler breeder genetic, diet type, and feeding program on maternal antibody transfer and development of lymphoid tissues in chicken progeny

Maternal antibody (MatAb) transfer is important for early chicken survivability. Diet composition and the amount of feed given to breeder pullets during rearing may affect the development of immunity and the transfer of MatAb to progeny, and could affect progeny performance and resistance to disease. The effects of broiler breeder nutrition and feeding management practices were evaluated for the transfer of MatAb to progeny and for spleen and bursa development at hatching in 2 genetic strains (A and B). In this experiment, the levels of MatAb against Newcastle disease virus were assessed by enzyme-linked immunosorbent assays in serum samples taken of pedigreed chicken progeny from hatching to 13 d of age. Chickens were fed corn-and wheat-based diets, as were their parents. The breeder feeding program and diet type altered the Newcastle disease virus MatAb found in progeny at hatching and affected how long these antibodies were maintained in circulation. Bursal follicle size at hatching was influenced by an interaction among all factors evaluated. Percentage of white pulp in the spleen was affected mainly by genetic strain and diet type, but responses varied according to the breeder feeding program. It was concluded that breeder feeding programs influence MatAb transfer and half-life, and may also affect the early development of lymphoid tissues.

Additive genetic relationship of longevity with fertility and production traits in Nellore cattle based on bivariate models

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

Epidemiology and genetics of endemic goiter. II. Genetic aspects

Complex genetic models and segregation analysis were applied to family data obtained in a hyperendemic goiter area in Brazil. The single locus and Falconer's models did not fit the data. Edward's model showed convergency, but statistical concordance has not been obtained. Although the genetic load model explains statistically the family data, it would be hard to imagine that endemic goiter could be explained by a model where synergism among genetic and environmental factors is not assumed.

Estimates of direct and maternal genetic effects for weights from birth to 600 days of age in Nelore cattle

Estimates of direct and maternal variance and heritability for weights at each week (up to 280 days of age) and month of age (up to 600 days of age) in Zebu cattle are presented. More than one million records on 200 000 animals, weighed every 90 days from birth to 2 years of age, were available. Data were split according to week (data sets 1) or month (data sets 2) of age at recording, creating 54 and 21 data sets, respectively. The model of analysis included contemporary groups as fixed effects, and age of dam (linear and quadratic) and age of calf (linear) effects as covariables. Random effects fitted were additive direct and maternal genetic effects, and maternal permanent environmental effect. Direct heritability estimates decreased from 0.28 at birth, to 0.12-0.13 at about 150 days of age, stayed more or less constant at 0.14-0.16 until 270 days of age and increased with age after that, up to 0.25-0.26. Maternal heritability estimates increased from birth (0.01) to a peak of 0.14 for data sets 1 and 0.07-0.08 for data sets 2 at about 180-210 days of age, before decreasing slowly to 0.07 and 0.05, respectively, at 300 days, and then rapidly diminished after 300 days of age. Permanent environmental effects were 1.5 to four times higher than genetic maternal effects and showed a similar trend.

Genetic variation within and among species of five sections of the genus Arachis L. (Leguminosae) using RAPDs

Some Arachis species are widely used as commercial plants, e.g. the groundnut A. hypogaea, an important source of good quality protein and oil, and A. pintoi and A. glabrata, that are utilized as forage species. Germplasm of most Arachis species is available in germplasm banks. However, little it is known about the genetic attributes of this germplasm, and mainly about its genetic variability, which is very important for its maintenance. In the present study RAPDs were used to assay the genetic variation within and among 48 accessions of five sections of the genus Arachis and to establish the genetic relationships among these accessions. Ten of 34 primers tested were selected for DNA amplification reactions since they yielded the largest numbers of polymorphic loci. A dendrogram was constructed based on data from the 10 primers selected. Eighty RAPD polymorphic bands were analyzed among the accessions studied. The relationships among species based on RAPDs were similar to those previously reported based on morphological, cytological and crossability data; demonstrating that RAPDs can be used to determine the genetic relationships among species of the different sections of the genus Arachis. In general, wide variation was found among accessions and low variation was found within the accessions that had two or more plants analyzed. However, higher polymorphism was found in the section Trierectoides and in one accession of A. major, indicating that generalizations should be avoided and each species should be analyzed in order to establish collection and maintenance strategies.

Atlantic forest fragmentation and genetic diversity of an isolated population of the Blue-manakin, Chiroxiphia caudata (Pipridae), assessed by microsatellite analyses

Habitat fragmentation is predicted to restrict gene flow, which can result in the loss of genetic variation and inbreeding depression. The Brazilian Atlantic forest has experienced extensive loss of habitats since European settlement five centuries ago, and many bird populations and species are vanishing. Genetic variability analysis in fragmented populations could be important in determining their long-term viability and for guiding management plans. Here we analyzed genetic diversity of a small understory bird, the Blue-manakins Chiroxiphia caudata (Pipridae), from an Atlantic forest fragment (112 ha) isolated 73 years ago, and from a 10,000 ha continuous forest tract (control), using orthologous microsatellite loci. Three of the nine loci tested were polymorphic. No statistically significant heterozygote loss was detected for the fragment population. Although genetic diversity, which was estimated by expected heterozygosity and allelic richness, has been lower in the fragment population in relation to the control, it was not statistically significant, suggesting that this 112 ha fragment can be sufficient to maintain a blue-manakin population large enough to avoid stochastic effects, such as inbreeding and/or genetic drift. Alternatively, it is possible that 73 years of isolation did not accumulate sufficient generations for these effects to be detected. However, some alleles have been likely lost, specially the rare ones, what is expected from genetic drift for such a small and isolated population. A high genetic differentiation was detected between populations by comparing both allelic and genotypic distributions. Only future studies in continuous areas are likely to answer if such a structure was caused by the isolation resulted from the forest fragmentation or by natural population structure.

Genetic effects on preweaning weight gain of Nelore-Hereford calves according to different models and estimation methods

Additive and nonadditive genetic effects on preweaning weight gain (PWG) of a commercial crossbred population were estimated using different genetic models and estimation methods. The data set consisted of 103,445 records on purebred and crossbred Nelore-Hereford calves raised under pasture conditions on farms located in south, southeast, and middle west Brazilian regions. In addition to breed additive and dominance effects, the models including different epistasis covariables were tested. Models considering joint additive and environment (latitude) by genetic effects interactions were also applied. In a first step, analyses were carried out under animal models. In a second step, preadjusted records were analyzed using ordinary least squares (OLS) and ridge regression (RR). The results reinforced evidence that breed additive and dominance effects are not sufficient to explain the observed variability in preweaning traits of Bos taurus x Bos indicus calves, and that genotype x environment interaction plays an important role in the evaluation of crossbred calves. Data were ill-conditioned to estimate the effects of genotype x environment interactions. Models including these effects presented multicolinearity problems. In this case, RR seemed to be a powerful tool for obtaining more plausible and stable estimates. Estimated prediction error variances and variance inflation factors were drastically reduced, and many effects that were not significant under ordinary least squares became significant under RR. Predictions of PWG based on RR estimates were more acceptable from a biological perspective. In temperate and subtropical regions, calves with intermediate genetic compositions (close to 1/2 Nelore) exhibited greater predicted PWG. In the tropics, predicted PWG increased linearly as genotype got closer to Nelore. ©2006 American Society of Animal Science. All rights reserved.

Genetic algorithm of chu and beasley for static and multistage transmission expansion planning

In this paper the genetic algorithm of Chu and Beasley (GACB) is applied to solve the static and multistage transmission expansion planning problem. The characteristics of the GACB, and some modifications that were done, to efficiently solve the problem described above are also presented. Results using some known systems show that the GACB is very efficient. To validate the GACB, we compare the results achieved using it with the results using other meta-heuristics like tabu-search, simulated annealing, extended genetic algorithm and hibrid algorithms. © 2006 IEEE.

Genetic polymorphism, molecular characterization and relatedness of Macrobrachium species (Palaemonidae) based on RAPD-PCR.

The prawn genus Macrobrachium belongs to the family Palaemonidae. Its species are widely distributed in lakes, reservoirs, floodplains, and rivers in tropical and subtropical regions of South America. Globally, the genus Macrobrachium includes nearly 210 known species, many of which have economic and ecological importance. We analyzed three species of this genus (M. jelskii, M. amazonicum and M. brasiliense) using RAPD-PCR to assess their genetic variability, genetic structure and the phylogenetic relationship between them and to look for molecular markers that enable separation of M. jelskii and M. amazonicum, which are closely related syntopic species. Ten different random decamer primers were used for DNA amplification, yielding 182 fragments. Three of these fragments were monomorphic and exclusive to M. amazonicum or M. jelskii and can be used as specific molecular markers to identify and separate these two species. Similarity indices and a phylogenetic tree showed that M. amazonicum and M. jelskii are closest to each other, while M. brasiliense was the most differentiated species among them; this may be attributed to the different habitat conditions to which these species have been submitted. This information will be useful for further studies on these important crustacean species.

An enhanced genetic algorithm to solve the static and multistage transmission network expansion planning

An enhanced genetic algorithm (EGA) is applied to solve the long-term transmission expansion planning (LTTEP) problem. The following characteristics of the proposed EGA to solve the static and multistage LTTEP problem are presented, (1) generation of an initial population using fast, efficient heuristic algorithms, (2) better implementation of the local improvement phase and (3) efficient solution of linear programming problems (LPs). Critical comparative analysis is made between the proposed genetic algorithm and traditional genetic algorithms. Results using some known systems show that the proposed EGA presented higher efficiency in solving the static and multistage LTTEP problem, solving a smaller number of linear programming problems to find the optimal solutions and thus finding a better solution to the multistage LTTEP problem. Copyright © 2012 Luis A. Gallego et al.

Linear and Poisson models for genetic evaluation of tick resistance in cross-bred Hereford x Nellore cattle

Cattle resistance to ticks is measured by the number of ticks infesting the animal. The model used for the genetic analysis of cattle resistance to ticks frequently requires logarithmic transformation of the observations. The objective of this study was to evaluate the predictive ability and goodness of fit of different models for the analysis of this trait in cross-bred Hereford x Nellore cattle. Three models were tested: a linear model using logarithmic transformation of the observations (MLOG); a linear model without transformation of the observations (MLIN); and a generalized linear Poisson model with residual term (MPOI). All models included the classificatory effects of contemporary group and genetic group and the covariates age of animal at the time of recording and individual heterozygosis, as well as additive genetic effects as random effects. Heritability estimates were 0.08 ± 0.02, 0.10 ± 0.02 and 0.14 ± 0.04 for MLIN, MLOG and MPOI models, respectively. The model fit quality, verified by deviance information criterion (DIC) and residual mean square, indicated fit superiority of MPOI model. The predictive ability of the models was compared by validation test in independent sample. The MPOI model was slightly superior in terms of goodness of fit and predictive ability, whereas the correlations between observed and predicted tick counts were practically the same for all models. A higher rank correlation between breeding values was observed between models MLOG and MPOI. Poisson model can be used for the selection of tick-resistant animals. © 2013 Blackwell Verlag GmbH.

Genetic and non-genetic effects on calf vigor at birth and preweaning mortality in nellore calves

The objective of the present study was to evaluate the genetic and non-genetic effects that influencevigor at birth and preweaning mortality in Nellore calves. A total of 11,727 records of births that occurred between 1978 and 2006, offspring of 363 sires, were analyzed. Poor calf vigor at birth (VB) and preweaning mortality divided into stillbirth (SB), early mortality (EM) and total mortality (TM) were analyzed as binary variables. Generalized linear models were used for the evaluation of non-genetic effects and generalized linear mixed models for genetic effects (sire and animal models). The incidences were 4.75% for VB, 2.66% for SB, 5.28% for EM, and 7.99% for TM. Birth weight was the effect that most influenced the traits studied. Calves weighing less than 22kg(females) and less than 24kg (males) were at a higher risk of low vigor and preweaning mortality. Preweaning mortality was higher among calves born from cows aged .3 and .11 years at calving compared with cows aged 7 to 10 years. Male calves presented less vigor and higher preweaning mortality than female calves. Selection for postweaning weight did not influence preweaning mortality. The heritability estimates ranged between 0.01 and 0.09 for VB, 0.00 and 0.27 for SB, 0.03 and 0.17 for EM and 0.02 and 0.10 for TM. Stillbirth should be included as a selection criterion in breeding programs of Nellore cattle, alone or as part of a selection index, aiming to reduce preweaning mortality. © 2013 Sociedade Brasileira de Zootecnia.

The roles of marginal lagoons in the maintenance of genetic diversity in the Brazilian migratory fishes Prochilodus argenteus and P. costatus

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

Genetic Correlation for Pre-Weaning and Post-Weaning Traits of Mediterranean Buffaloes from Brazil, Estimated By Bayesian Inference

The aim of this study was to estimate genetic, environmental and phenotypic correlation between birth weight (BW) and weight at 205 days age (W205), BW and weight at 365 days age (W365) and W205-W365, using Bayesian inference. The Brazilian Program for Genetic Improvement of Buffaloes provided the data that included 3,883 observations from Mediterranean breed buffaloes. With the purpose to estimate variance and covariance, bivariate analyses were performed using Gibbs sampler that is included in the MTGSAM software. The model for BW, W205 and W365 included additive direct and maternal genetic random effects, maternal environmental random effect and contemporary group as fixed effect. The convergence diagnosis was achieved using Geweke, a method that uses an algorithm implemented in R software through the package Bayesian Output Analysis. The calculated direct genetic correlations were 0.34 (BW-W205), 0.25 (BW-W365) and 0.74 (W205-W365). The environmental correlations were 0.12, 0.11 and 0.72 between BW-W205, BW-W365 and W205-W365, respectively. The phenotypic correlations were low for BW-W205 (0.01) and BW-W365 (0.04), differently than the obtained for W205-W365 with a value of 0.67. The results indicate that BW trait have low genetic, environmental and phenotypic association with the two others traits. The genetic correlation between W205 and W365 was high and suggests that the selection for weight at around 205 days could be beneficial to accelerate the genetic gain.