Genetic diversity in wild (Sus scrofa scrofa) and domestic (Sus scrofa domestica) pigs and their hybrids based on polymorphism of a fragment of the D-loop region in the mitochondrial DNA

We examined the variation in mitochondrial DNA by sequencing the D-loop region in wild and domestic (large-white breed) pigs, in hybrids between domestic and wild pigs, and in Monteiro pigs. A D-loop fragment of approximately 330 bp was amplified by PCR. Sequencing of DNA amplicons identified haplotypes previously described as European and Asian types. Monteiro pigs and wild pigs had European haplotypes and domestic pigs had both European and Asian haplotypes. ©FUNPEC-RP.

Genetic diversity of microsatellite loci in Leopardus pardalis, Leopardus wiedii and Leopardus tigrinus

The microsatellite loci FCA045, FCA077, FCA008, and FCA096 are highly variable molecular markers which were used to determine the genetic diversity in 148 captive Leopardus sp. The PCR-amplified products of microsatellite loci were characterized in ABI Prism 310 Genetic Analyzer. Allele numbers, heterozygosity, polymorphism information content, exclusive allele number, and shared alleles were calculated. Sixty-five alleles were found and their sizes ranged from 116 to 216 bp in four microsatellite loci. The heterozygosity ranged from 0.36 to 0.81 in Leopardus pardalis, 0.57 to 0.67 in L. tigrinus and 0.80 to 0.92 in L. wiedii. The polymorphism information content was from 0.80 to 0.88 in L. pardalis, 0.76 to 0.88 in L. tigrinus and 0.77 to 0.90 in L. wiedii. The margay (L. wiedii) showed the highest index of polymorphism among the three species in this study. These results imply that microsatellite DNA markers can help in the study of the genetic diversity of Leopardus specimens. ©FUNPEC-RP.

Reconfiguration of distribution systems by a modified genetic algorithm

In this paper a genetic algorithm based reconfiguration method is proposed to minimize the real power losses of distribution systems. The main innovation of this research work is that new types of crossover and mutation operators are proposed, such that the best possible results are obtained, with an acceptable computational effort. The crossover and mutation operators were developed so as to take advantage of the particular characteristics of distribution systems (as the radial topology). Simulation results indicate that the proposed method is very efficient, being able to find excellent configurations, with low computational effort, especially for larger systems. ©2007 IEEE.

Assessing genetic variability in bat species of Emballonuridae, Phyllostomidae, Vespertilionidae and Molossidae families (Chiroptera) by RFLP-PCR

A PCR-RFLP analysis of the restriction pattern in nuclear (RAG2) and mitochondrial (12S/16S) gene sequences of bat species from the Molossidae, Phyllostomidae, Vespertilionidae, and Emballonuridae families produced a large number of fragments: 107 for RAG2 and 155 for 12S/16S combined in 139 and 402 haplotypes, respectively. The values detected for gene variation were low for both sequences (0.13 for RAG2 and 0.15 for 12S/16S) and reflected their conservative feature, reinforced by high values of inter- and intraspecies genetic identity (70-100%). The species with a high gene divergence were variable in the analyses of RAG2 (Eumops perotis, Artibeus lituratus, and Carollia perspicillata) and of 12S/16S (Nyctinomops laticaudatus, C. perspicillata, and Cynomops abrasus), and furthermore, one of them, C. perspicillata, also showed the highest intraspecific variation. The species that exhibited the lowest variation for both genes was Molossus rufus. In the families, the highest variation was observed in the Molossidae and this can be attributed to variation exhibited by Eumops and Nyctinomops species. The variations observed were interpreted as a natural variability within the species and genus that exhibited a conserved pattern in the two gene sequences in different species and family analyzed. Our data reinforce the idea that the analyses of mitochondrial and nuclear genes contribute to our knowledge of the diversity of New World bats. The genetic variability found in different taxa suggests that an additional diversity, unnoticed by other methods, can be revealed with the use of different molecular strategies. ©FUNPEC-RP.

Tracking the fin trade: Genetic stock identification in western Atlantic scalloped hammerhead sharks Sphyrna lewini

Location or stock-specific landing data are necessary to improve management of shark stocks, especially those imperiled by overexploitation as a result of the international shark fin trade. In the current absence of catch monitoring directly at extraction sites, genetic stock identification of fins collected from major market supply chain endpoints offers an overlooked but potentially useful approach for tracing the fins back to their geographical, or stock of, origin. To demonstrate the feasibility of this approach, we used mitochondrial control region (mtCR) sequences to trace the broad geographical origin of 62 Hong Kong market-derived Sphyrna lewini fins. Of these fins 21% were derived from the western Atlantic, where this species is listed as 'Endangered' by the International Union for the Conservation of Nature (IUCN). We also show that S. lewini mtCR sequences are geographically segregated in the western Atlantic (overall ΦST = 0.74, n = 177 sharks), indicating that breeding females either remain close to, or home back to, their natal region for parturition. Mixed stock analysis simulations showed that it is possible to estimate the relative contributions of these mitochondrial stocks to fin mixtures in globally sourced trade hubs. These findings underscore the feasibility of using genetic stock identification to source market-derived shark fins to obtain essential and otherwise unavailable data on exploitation levels, and thus to productively inform stock assessment and management of S. lewini and potentially also of other fished shark species. © Inter-Research 2009.

Genetic parameters for milk yield, age at first calving and interval between first and second calving in milk Murrah buffaloes

In the present study, data of 1,578 first lactation females, calving from 1985 to 2006 were analysed with the purpose of estimating genetic parameters for milk yield (MY), age at first calving (AFC) and interval between first and second calving (IBFSC) in dairy buffaloes of the Murrah breed in Brazil, Heritability estimates for MY, AFC and IBFSC traits were 0.20, 0.07 and 0.14, respectively. Genetic correlations between MY and AFC and IBFSC were -0.12 and 0.07, respectively, while the corresponding phenotypic correlations were -0.15 and 0.30, respectively. Genetic and phenotypic correlations between AFC and IBFSC were 0.35 and 0.37, respectively. Genetic correlation between MY and AFC showed desirable negative association, suggesting that daughters of the bulls with high breeding values for MY could reach physiological mature at a precocious age. Genetic correlation between MY and IBFSC, showed that the selection for milk production could result in the increase of calving intervals.

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.

Application of molecular markers on genetic improvement and reproduction in the post-genomic Era: Emerging biotechnologies and perspectives in livestock

Background: New challenges are rising in the animal protein market, and one of the main world challenges is to produce more in shorter time, with better quality and in a sustainable way. Brazil is the largest beef exporter in volume hence the factors affecting the beef meat chain are of major concern in countrýs economy. An emerging class of biotechnological approaches, the molecular markers, is bringing new perspectives to face these challenges, particularly after the publication of the first complete livestock genome (bovine), which has triggered a massive initiative to put in practice the benefits of the so called the Post-Genomic Era. Review: This article aimed at showing the directions and insights in the application of molecular markers on livestock genetic improvement and reproduction as well at organizing the progress so far, pointing some perspectives of these emerging technologies in Brazilian ruminant production context. An overview on the nature of the main molecular markers explored in ruminant production is provided, which describes the molecular bases and detection approaches available for microsatellites (STR) and single nucleotide polymorphisms (SNP). A topic is dedicated to review the history of association studies between markers and important trait variation in livestock, showing the timeline starting on quantitative trait loci (QTL) identification using STR markers and ending in high resolution SNP panels to proceed whole genome scans for phenotype/genotype association. Also the article organizes this information to reveal how QTL prospection using STR could open ground to the feasibility of marker-assisted selection and why this approach is quickly being replaced by studies involving the application of genome-wide association using SNP research in a new concept called genomic selection. Conclusion: The world's scientific community is dedicating effort and resources to apply SNP information in livestock selection through the development of high density panels for genomic association studies, connecting molecular genetic data with phenotypes of economic interest. Once generated, this information can be used to take decisions in genetic improvement programs by selecting animals with the assistance of molecular markers.

Characterization of the genetic diversity of Mycobacterium tuberculosis in São Paulo city, Brazil

Background: Tuberculosis is a major health problem in São Paulo, Brazil, which is the most populous and one of the most cosmopolitan cities in South America. To characterize the genetic diversity of Mycobacterium tuberculosis in the population of this city, the genotyping techniques of spoligotyping and MIRU were applied to 93 isolates collected in two consecutive years from 93 different tuberculosis patients residing in São Paulo city and attending the Clemente Ferreira Institute (the reference clinic for the treatment of tuberculosis). Findings. Spoligotyping generated 53 different spoligotype patterns. Fifty-one isolates (54.8%) were grouped into 13 spoligotyping clusters. Seventy- two strains (77.4%) showed spoligotypes described in the international databases (SpolDB4, SITVIT), and 21 (22.6%) showed unidentified patterns. The most frequent spoligotype families were Latin American Mediterranean (LAM) (26 isolates), followed by the T family (24 isolates) and Haarlem (H) (11 isolates), which together accounted for 65.4% of all the isolates. These three families represent the major genotypes found in Africa, Central America, South America and Europe. Six Spoligo-International- types (designated SITs by the database) comprised 51.8% (37/72) of all the identified spoligotypes (SIT53, SIT50, SIT42, SIT60, SIT17 and SIT1). Other SITs found in this study indicated the great genetic diversity of M. tuberculosis, reflecting the remarkable ethnic diversity of São Paulo city inhabitants. The MIRU technique was more discriminatory and did not identify any genetic clusters with 100% similarity among the 93 isolates. The allelic analysis showed that MIRU loci 26, 40, 23 and 10 were the most discriminatory. When MIRU and spoligotyping techniques were combined, all isolates grouped in the 13 spoligotyping clusters were separated. Conclusions: Our data indicated the genomic stability of over 50% of spoligotypes identified in São Paulo and the great genetic diversity of M. tuberculosis isolates in the remaining SITs, reflecting the large ethnic mix of the São Paulo city inhabitants. The results also indicated that in this city, M. tuberculosis isolates acquired drug resistance independently of genotype and that resistance was more dependent on the selective pressure of treatment failure and the environmental circumstances of patients. © 2011 Leite et al; licensee BioMed Central Ltd.

Characterization of the Genetic Variability of a Sugarcane Commercial Cross Through Yield Components and Quality Parameters

The phenotypic characterization as well as the knowledge of the correlation among traits, is the first step to quantify the potential of a cross for further QTL (quantitative trait loci) detection. The present work aimed to evaluate the yield components and quality parameters variability of a mapping population derived from a bi-parental cross between IACSP95-3018 and IACSP93-3046 at plant cane and ratoon cane as well as to estimate the heritabilities and pair-wise correlation among the traits evaluated. The progeny clones differed significantly for the traits measures indicating the existence of significant amount of variability among them as also as the presence of transgressive clones. Broad-sense heritabilities values were generally high for stalk diameter, stalk weight, stalk height, Brix and Pol%Cane in plant cane and ratoon cane. Tones of sugarcane per hectare (TCH) were significantly correlated with stalk weight and stalk number in both years. Regarding to all the yield components, stalk number together with stalk weight were the most important components in the determination of TCH. While fiber and Pol%Cane were negative correlated showing that they are inversely correlated traits. © 2012 Society for Sugar Research & Promotion.

A genetic algorithm for crop rotation

In the last few years, crop rotation has gained attention due to its economic, environmental and social importance which explains why it can be highly beneficial for farmers. This paper presents a mathematical model for the Crop Rotation Problem (CRP) that was adapted from literature for this highly complex combinatorial problem. The CRP is devised to find a vegetable planting program that takes into account green fertilization restrictions, the set-aside period, planting restrictions for neighboring lots and for crop sequencing, demand constraints, while, at the same time, maximizing the profitability of the planted area. The main aim of this study is to develop a genetic algorithm and test it in a real context. The genetic algorithm involves a constructive heuristic to build the initial population and the operators of crossover, mutation, migration and elitism. The computational experiment was performed for a medium dimension real planting area with 16 lots, considering 29 crops of 10 different botanical families and a two-year planting rotation. Results showed that the algorithm determined feasible solutions in a reasonable computational time, thus proving its efficacy for dealing with this practical application.

Genetic correlations between mature cow weight and productive and reproductive traits in Nellore cattle

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

Comparison of random regression models to estimate genetic parameters for milk production in Guzerat (Bos indicus) cows

Random regression models have been widely used to estimate genetic parameters that influence milk production in Bos taurus breeds, and more recently in B. indicus breeds. With the aim of finding appropriate random regression model to analyze milk yield, different parametric functions were compared, applied to 20,524 test-day milk yield records of 2816 first-lactation Guzerat (B. indicus) cows in Brazilian herds. The records were analyzed by random regression models whose random effects were additive genetic, permanent environmental and residual, and whose fixed effects were contemporary group, the covariable cow age at calving (linear and quadratic effects), and the herd lactation curve. The additive genetic and permanent environmental effects were modeled by the Wilmink function, a modified Wilmink function (with the second term divided by 100), a function that combined third-order Legendre polynomials with the last term of the Wilmink function, and the Ali and Schaeffer function. The residual variances were modeled by means of 1, 4, 6, or 10 heterogeneous classes, with the exception of the last term of the Wilmink function, for which there were 1, from 0.20 to 0.33. Genetic correlations between adjacent records were high values (0.83-0.99), but they declined when the interval between the test-day records increased, and were negative between the first and last records. The model employing the Ali and Schaeffer function with six residual variance classes was the most suitable for fitting the data. © FUNPEC-RP.

Genetic Diversity in the Modern Horse Illustrated from Genome-Wide SNP Data

Horses were domesticated from the Eurasian steppes 5,000-6,000 years ago. Since then, the use of horses for transportation, warfare, and agriculture, as well as selection for desired traits and fitness, has resulted in diverse populations distributed across the world, many of which have become or are in the process of becoming formally organized into closed, breeding populations (breeds). This report describes the use of a genome-wide set of autosomal SNPs and 814 horses from 36 breeds to provide the first detailed description of equine breed diversity. FST calculations, parsimony, and distance analysis demonstrated relationships among the breeds that largely reflect geographic origins and known breed histories. Low levels of population divergence were observed between breeds that are relatively early on in the process of breed development, and between those with high levels of within-breed diversity, whether due to large population size, ongoing outcrossing, or large within-breed phenotypic diversity. Populations with low within-breed diversity included those which have experienced population bottlenecks, have been under intense selective pressure, or are closed populations with long breed histories. These results provide new insights into the relationships among and the diversity within breeds of horses. In addition these results will facilitate future genome-wide association studies and investigations into genomic targets of selection. © 2013 Petersen et al.

A hybrid multi-population genetic algorithm applied to solve the multi-level capacitated lot sizing problem with backlogging

The present paper proposes a new hybrid multi-population genetic algorithm (HMPGA) as an approach to solve the multi-level capacitated lot sizing problem with backlogging. This method combines a multi-population based metaheuristic using fix-and-optimize heuristic and mathematical programming techniques. A total of four test sets from the MULTILSB (Multi-Item Lot-Sizing with Backlogging) library are solved and the results are compared with those reached by two other methods recently published. The results have shown that HMPGA had a better performance for most of the test sets solved, specially when longer computing time is given. © 2012 Elsevier Ltd.