Population genetic

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Diversification into the genus Badnavirus: phylogeny and population genetic variability

Diversification into the genus Badnavirus: phylogeny and population genetic variability

The family Caulimoviridae comprises viruses with semicircular double-stranded DNA genomes encapsulated into isometric or bacilliform particles, being divided into eight genera. The genus Badnavirus is the most important due to its high number of species reported infecting cultivated plants worldwide. The present study aimed to evaluate the phylogenetic positioning and population genetic variability into the genus Badnavirus. Data sets comprising badnavirus full-length genome and partial RT/RNaseH sequences were retrieved from the non-redundant GenBank database. Multiple nucleotide sequence alignments were obtained for the data sets: complete genome, ORFIII, full (1020pb) and partial (579pb) RT/RNaseH domains. A total of 127 genome sequences were obtained, representing 53 badnavirus species. Nucleotide pairwise comparisons for RT/RNaseH showed that only a few isolates reported as distinct Badnavirus species shared ≥80% identity, the current threshold used for species demarcation into this genus. Bayesian phylogenetic trees for the complete genome and ORFIII showed four well supported clusters (badnavirus groups 1-4), with clusters 1 and 3 being sister groups comprising predominantly species/isolates infecting sugarcane and banana. Non-tree-like evolution evidenced putative recombination events affecting the Badnavirus diversification, and at least 23 independent events were detected with recombination breakpoints occurring mostly in the ORFIII and intergenic region. High levels of nucleotide diversity were observed for the partial RT/RNaseH region in populations of 11 distinct badnaviruses. These results showed that mutation and recombination are important mechanisms acting on the evolution of badnaviruses, and that the partial RT/RNaseH sequences are sufficient for species demarcation of most viruses reported in this genus.
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Population Genetic Analysis Of Giardia Duodenalis: Genetic Diversity And Haplotype Sharing Between Clinical And Environmental Sources

Population Genetic Analysis Of Giardia Duodenalis: Genetic Diversity And Haplotype Sharing Between Clinical And Environmental Sources

Giardia duodenalis is a flagellated intestinal protozoan responsible for infections in vari- ous hosts including humans and several wild and domestic animals. Few studies have correlated environmental contamination and clinical infections in the same region. The aim of this study was to compare groups of Giardia duodenalis from clinical and environ- mental sources through population genetic analyses to verify haplotype sharing and the degree of genetic similarity among populations from clinical and environmental sources in the metropolitan region of Campinas. The results showed high diversity of haplotypes and substantial genetic similarity between clinical and environmental groups of G. duode- nalis. We demonstrated sharing of Giardia genotypes among the different populations studied. The comparison between veterinary and human sequences led us to identify new zoonotic genotypes, including human isolates from genetic assemblage C. The ap- plication of a population genetic analysis in epidemiological studies allows quantification of the degree of genetic similarity among populations of Giardia duodenalis from differ- ent sources of contamination. The genetic similarity of Giardia isolates among human, veterinary, and environmental groups reinforced the correlation between clinical and environmental isolates in this region, which is of great importance for public health. K E Y W O R D S
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Reconstructing the population genetic history of the Caribbean.

Reconstructing the population genetic history of the Caribbean.

The Caribbean basin is home to some of the most complex interactions in recent history among previously diverged human populations. Here, we investigate the population genetic history of this region by characterizing patterns of genome-wide variation among 330 individuals from three of the Greater Antilles (Cuba, Puerto Rico, Hispaniola), two mainland (Honduras, Colombia), and three Native South American (Yukpa, Bari, and Warao) populations. We combine these data with a unique database of genomic variation in over 3,000 individuals from diverse European, African, and Native American populations. We use local ancestry inference and tract length distributions to test different demographic scenarios for the pre- and post- colonial history of the region. We develop a novel ancestry-specific PCA (ASPCA) method to reconstruct the sub-continental origin of Native American, European, and African haplotypes from admixed genomes. We find that the most likely source of the indigenous ancestry in Caribbean islanders is a Native South American component shared among inland Amazonian tribes, Central America, and the Yucatan peninsula, suggesting extensive gene flow across the Caribbean in pre-Columbian times. We find evidence of two pulses of African migration. The first pulse—which today is reflected by shorter, older ancestry tracts—consists of a genetic component more similar to coastal West African regions involved in early stages of the trans-Atlantic slave trade. The second pulse—reflected by longer, younger tracts—is more similar to present-day West- Central African populations, supporting historical records of later transatlantic deportation. Surprisingly, we also identify a Latino-specific European component that has significantly diverged from its parental Iberian source populations, presumably as a result of small European founder population size. We demonstrate that the ancestral components in admixed genomes can be traced back to distinct sub-continental source populations with far greater resolution than previously thought, even when limited pre-Columbian Caribbean haplotypes have survived.
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Factorial analysis of bootstrap variances of population genetic parameter estimates

Factorial analysis of bootstrap variances of population genetic parameter estimates

Five real data sets, obtained by Ciampi (1999), Reis et al. (2000), Seoane et al. (2000), Auler et al. (2002), and Telles et al. (2003) were considered. These authors studied the population genetic structure and/or the predominant re- productive system of tropical tree species. All the data sets presented hierarchical structure, so that variation was split into sources of variation due to populations, individuals within populations and genes within individuals. Reis et al. (2000) studied eight Euterpe edulis (known as “palmi- teiro”) populations, with an average of 24.8 individuals sampled per population, and used seven isoenzyme loci. Seoane et al. (2000) studied four Esenbechia leiocarpa (known as “guarantã”) populations, with 22 individuals per population, and used five polymorphic loci. Four isoen- zyme loci were considered by Telles et al. (2003) for study- ing six Anonna crassiflora (known as “araticunzeiro”) populations, with 30 individuals sampled per population. Ciampi (1999) used eight microsatellite loci to evaluate four Copaifera langsdorffii (known as “copaíba”) popula- tions, with 24 individuals sampled per population. Auler et al. (2002) used twelve polymorphic isoenzyme loci to eval- uate nine Araucaria angustifolia (known as “pinheiro-do- Paraná) populations with an average of 36.1 individuals sampled per population.
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Disentangling landscape effects on population genetic structure of a Neotropical savanna tree

Disentangling landscape effects on population genetic structure of a Neotropical savanna tree

in Central Brazil that is endemic to the ª Cerradoº (savanna) biome, relating population genetic divergence with broad-scale landscape patterns. Genetic divergence among 25 populations, estimated based on eight microsatellite loci for a total of 644 individuals, was correlated with landscape features using several forms of Mantel tests (standard Mantel correlations, Mantel correlograms, partial correlations, and multiple regression). Patterns of genetic divergence are significantly correlated with human-driven landscape features of habitat loss and fragmentation, after taking into account isolation-by-distance and historical effects of range expansion after the last glacial maximum. Our findings present important implications for the conservation of this species, because interruption of gene flow by habitat loss and fragmentation jeopardize the persistence of population in the medium- and long term due to disruption of demographic patterns, increased endogamy, and recruitment problems.
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Evolving balanced decision trees with a multi-population genetic algorithm

Evolving balanced decision trees with a multi-population genetic algorithm

used with success for several multi-objective optimization problems. In this paper, we present a new general multi- population genetic algorithm for evolving decision trees. It was designed to improve the possibility of evolving balanced decision trees, simultaneously optimized for the predictions of each class. Single-population genetic algorithms namely tend to construct decision trees with great variance in single class accuracies. The proposed approach is tested over 10 UCI datasets, and it is compared with a single-population genetic algorithm as well as with traditional decision-tree induction algorithms. Results show that the designed multi-population approach provides classification results comparable to C4.5 and CART in terms of accuracy and tree size, while outperforming them regarding balanced solutions (in terms of average class accuracy and range of single-class accuracies).
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A program for representing and simulating population genetic phenomena

A program for representing and simulating population genetic phenomena

The paper describes a computer program for representing and simulating population genetic phenomena, such as the distribution of gene and genotype frequencies under different mating systems (panmixia, inbreeding and assortative mating systems) and under influence of evolution factors (mutation, selection, gene flow and genetic drift). The program was written in Visual Basic (Microsoft, Inc.) and is able to run in any IBM-PC compatible computer running Windows 3.1 or later versions.

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A MULTI-POPULATION GENETIC ALGORITHM FOR TREE-SHAPED NETWORK DESIGN PROBLEMS

A MULTI-POPULATION GENETIC ALGORITHM FOR TREE-SHAPED NETWORK DESIGN PROBLEMS

Abstract: In this work we propose a multi-population genetic algorithm for tree-shaped network design problems using random keys. Recent literature on finding optimal spanning trees suggests the use of genetic algorithms. Furthermore, random keys encoding has been proved efficient at dealing with problems where the relative order of tasks is important. Here we propose to use random keys for encoding trees. The topology of these trees is restricted, since no path from the root vertex to any other vertex may have more than a pre-defined number of arcs. In addition, the problems under consideration also exhibit the characteristic of flows. Therefore, we want to find a minimum cost tree satisfying all demand vertices and the pre-defined number of arcs. The contributions of this paper are twofold: on one hand we address a new problem, which is an extension of the well known NP-hard hop-constrained MST problem since we also consider determining arc flows such that vertices requirements are met at minimum cost and the cost functions considered include a fixed cost component and a nonlinear flow routing component; on the other hand, we propose a new genetic algorithm to efficiently find solutions to this problem.
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A new eigenfunction spatial analysis describing population genetic structure

A new eigenfunction spatial analysis describing population genetic structure

The SSR curve, as presented here, is essentially uni- variate (i.e., one allele frequency is analyzed at time), similarly to Moran’s I correlograms, allowing interesting evolutionary inferences. On the other hand, dealing simultaneously with many alleles, such as done with a Mantel test or Mantel correlogram based on genetic dis- tances or similarity, does not allow a detailed description of multiple potential evolutionary processes driving patterns in each loci or allele frequency (except if these distances are defined with clearly defined expectations based on evolutionary models—see Diniz-Filho et al. 2012d ). Even so, if the researcher is interested in a general description of several alleles and loci, the SSR curve can still be applied using a multivariate R 2 rather than the univariate R 2 . Also, one can simply use the scores derived from any ordination analysis as response variable in the multiple regression models needed to generate the SSR curve.
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Population genetic structure of Sisyrinchium micranthum Cav. (Iridaceae)

Population genetic structure of Sisyrinchium micranthum Cav. (Iridaceae)

As five specimens of ESC172 (with light-violet- colored flowers) presented the same band profile, four were excluded from statistical analyses. This pattern suggests that they are the result of self-fertilization or may even be clones. Thus, asexual reproduction may be contributing to the maintenance of this population. This is the first indica- tion that reproduction in this species may not be strictly sexual. Thus, if reproduction is also vegetative, how would this fit into the mating system? On studying the relationship between mating system and life history (annual/perennial) in Solanum L. (Solanaceae), Vallejo-Marín and O’Brien (2007) found self-incompatibility and clonality to be strongly correlated. In their study, all of the self-incom- patible plants were clonal and all strict annuals were self- compatible. Even so, in Decodon verticillatus (L.) Elliott (Lythraceae), clonality potentially furthers the increase of selfed offspring by way of geitonogamy (selfing through pollen transfer between flowers on the same plant; Eckert, 2000). Thus, the low genetic diversity in ESC172 individu- als may possibly arise from self-fertilization alone, or as a consequence of both clonality and selfing. The connection of life-history with these aspects is unclear, as S. micranthum is usually cited as annual (Johnston, 1938; Innes, 1985; Goldblatt, 2003). Nonetheless, Parent (1987) reported specimens in northwest Spain that lived for more than one year, or at least survived the winter.
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Population genetic analysis of Caiman crocodilus (Linnaeus, 1758) from South America

Population genetic analysis of Caiman crocodilus (Linnaeus, 1758) from South America

entiation of the Anavilhanas locality from all but the geographically closest Mamirauá Lake, Purus River and Ja- nauacá Lake localities. The locality from the Anavilhanas archipelago is the only one sampled from a black water sys- tem (Sioli, 1984). Black water systems are limnologically and ecologically differentiated from white water systems, often supporting different animal and plant communities (Sioli, 1984; Goulding et al., 2003). There are a number of black water systems in the Amazon basin, but the Negro River is the largest. The observed differentiation of the Anavilhanas locality corroborates, in principle, the findings of Farias et al. (2004). Although Farias et al. (2004) did not include C. crocodilus from Anavilhanas in their analyses, they observed weak genetic differentiation between black water (Anavilhanas) and white water (rest of the Amazon basin) sampling localities of Melanosuchus niger, the other large alligatorid crocodilian found in Amazônia. Ecologi- cal differences between caiman populations occupying black water and white water habitats were also observed by Da Silveira (2002). Together, these genetic and ecological findings suggest that the observed black water / white water differentiation might be a real geographic structuring factor in Amazônia that reduces genetic exchange between lim- nologically differentiated systems. The two other signifi- cant pair-wise F ST comparisons observed within Amazônia
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Pattern-oriented modelling of population genetic structure

Pattern-oriented modelling of population genetic structure

Although several statistical approaches can be used to describe patterns of genetic variation and infer stochastic differentiation, selective responses, or interruptions of gene flow due to physical or environmental barriers, it is worthwhile to note that similar processes, controlled by several parameters in theoretical models, frequently give rise to similar patterns. Here, we develop a Pattern-Oriented Modelling (POM) approach that allows us to determine how a complex set of parameters potentially driving empirical genetic differentiation among populations generate alternative scenarios that can be fitted to observed data. We generated 10 000 random combinations of parameters related to population size, gene flow and response to gradients (both driven by dispersal and selection) in a spatially explicit model, and analysed simulated patterns with F ST statistics and mean correlograms using Moran’s I spatial autocorrelation coefficients. These statistics were compared with observed patterns for a tree species endemic to the Brazilian Cerrado. For a best match with observed F ST (equal to 0.182), the important parameters driving simulated scenario are mainly related to population structure, including low population size with closed populations (low N m ), strong distance decay of gene flow, in addition to a strong effect of the initial variance of allele frequencies. These scenarios present a low autocorrelation of allele frequencies. Best matching of correlograms, on the other hand, appears in simulations with a large population size, high N m and low population differentiation and F ST (as well as more gene flow). Thus, targeting the two statistics (correlograms and F ST ) shows that best matches with empirical data with two distinct sets of parameters in the simulations, because observed patterns involve both a relatively high F ST and significant autocorrelation. This conflict can be resolved by assuming that initial variance in allele frequencies can be interpreted as reflecting deep-time historical variation and evolutionary dynamics of allele frequencies, creating a relatively high level of population differentiation, whereas current patterns in gene flow creates spatial autocorrelation. This make sense in terms of the previous knowledge on population differentiation in D. alata, especially if patterns are explained by a combination of isolation-by-distance and allelic surfing due to range expansion after the last glacial maximum. This reveals the potential for more complex applications of POM in population genetics. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 113, 1152–1161.
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Population genetic structure of Brazilian shrimp species( Farfantepenaeus sp.,F

Population genetic structure of Brazilian shrimp species( Farfantepenaeus sp.,F

F. paulensis ranges from Cabo Frio (Rio de Janeiro State - RJ), along the continental shelves of Brazil and Uru- guay, to northeast Argentina (Pérez Farfante, 1969; Holthuis, 1980). The main F. paulensis offshore fishing area is located between Santos (São Paulo State - SP) and Torres (Rio Grande do Sul State - RS) (Iwai, 1973), but there are two major adult congregation zones: one off Santa Catarina State (SC), and the second between Santos and São Sebastião Island (littoral North of SP; Figure 1) (Zenger and Agnes, 1977; Melquíades, 1997). Important juvenile shrimp populations can be found in the estuaries of Rio Grande do Sul, but no adult breeding grounds are found in the offshore waters of Rio Grande do Sul or Uruguay (Iwai, 1973; Zenger and Agnes, 1977). Data on coastal cur- rents, wind direction and velocity between Florianópolis (SC) and Laguna de Castillo (Uruguay) indicate that the post larvae that populate nursery areas of Lagoa dos Patos and Uruguay may originate in the breeding grounds off Santa Catarina State (D’Incao, 1991). This hypothesis ob- tained further support from an allozyme study that indi- cated a high level of genetic homogeneity between populations from both areas (Delevedove, 1996).
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Tabapuã breed in Northeastern Brazil: genetic progress and population structure

Tabapuã breed in Northeastern Brazil: genetic progress and population structure

Results indicate that few animals account for much of the genetic variability in the studied population. The values encountered by Vercesi Filho et al. (2002a) are in line with those obtained in this study. In the last study period (1994- 1998), these authors observed that 50 animals accounted for 42.6% of the genetic variability. In a study involving Indubrasil animals, Carneiro et al. (2009) identified a much higher value, in which 50% of the population variability resulted from 225 ancestors (founders or not). On the other hand, Malhado et al. (2008a) reported that 414 ancestors could explain the same variability, in a study involving Nellore cattle in the state of Bahia.
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Genetic Diversity and Population Structure of Theileria annulata in Oman.

Genetic Diversity and Population Structure of Theileria annulata in Oman.

denaturation at 95°C for 5 minutes, 32 cycles at 95°C for 30 seconds, 42–62°C for 30 seconds and 65°C for 30 seconds, followed by a final extension step of 5 minutes at 65°C. The amplified products were observed on 2% ethidium bromide pre-stained agarose gel to determine the effi- cacy of PCR amplification. PCR products were then denatured and subjected to capillary elec- trophoresis on an ABI3130 xl Genetic Analyser (Applied Biosystems, UK). DNA fragment sizes were analysed relative to ROX-labeled GS500 ROX size-standard (Applied Biosystems) using Genemapper software (Applied Biosystems). The use of this technology facilitated the discrimination of multiple amplicons in a single reaction with a resolution of 1 base pair (bp). Multiple products from a single PCR reaction indicated the presence of a mixture of genotypes. To determine the relative concentration of each allele/amplicon, the area under each peak was assessed. In this way, the predominant allele at each locus was identified for each sample and this data was combined to generate a multi-locus genotype (MLG) that represents an estimate of the most abundant genotype in each sample. As peak area is essentially a continuous vari- able, it was always possible to identify the most abundant allele in any sample.
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Genetic profile of the Iberian Peninsula population : contributions of AIMs

Genetic profile of the Iberian Peninsula population : contributions of AIMs

The Neolithic period began approximately 7,000 years ago and is characterized by the development of agriculture and livestock. In Europe the first societies appeared in the European south-east between 7,000 b.C and 5,000 b.C., in the central and west Mediterranean from before 6,000 b.C, in central Europe before 5500 b.C and finally in the north-west of Europe before 4,000 b.C. [Ammerman et al., 1984; Whittle, 1996; Chikhi et al., 1998]. To explain this transition, there are two hypotheses: first, called demic diffusion model, that involves the movement of a large human contingent that colonize Europe by displacing or absorbing the European Paleolithic inhabitants, which predicts a major effect on the European gene pool [Semino et al., 1996; Cavalli-Sforza et al., 1997; Quintana-Murci et al., 1999; Simoni et al., 2000; Chikhi et al., 2002; Richards et al., 1996] and the second, called cultural diffusion model, which argues that the transition to agriculture occurred without large movements of populations and without changes in the genetic makeup of the pre-existing populations [Whittle, 1996; Semino et al., 1996; Richards et al., 1996].
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Molecular Genetic Studies of Multiple Sclerosis in the Portuguese Population

Molecular Genetic Studies of Multiple Sclerosis in the Portuguese Population

Based on the existing studies, we may conclude that the genetic architecture of MS in the Portuguese population does not differ from that of other Europeans. The most relevant of our findings is a preferential association of HLA-DRB1*15 allele with benign form of MS and a suggested association with the PTPN22 1858T risk allele in the same subgroup of patients. These observations sustain the hypothesis that a different etiopathogenesis (or possibly a stronger autoim- mune genotype/phenotype) may be implicated specifically in this form of MS. From a clinical perspective, benign MS presents particular features (lower age at onset, higher fe- male prevalence and more sensorial symptoms as a first symptom), which also support this hypothesis. In fact, these observations are not the first indications of heterogeneity in the etiopathogenesis of MS, and, in our opinion, would warrant confirmation in other populations. If true, it may be a source of biological markers of putative importance in the prediction of disease features and outcome, which could greatly help the clinical and therapeutically management of MS patients.
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Population structure, fluctuating asymmetry and genetic variability in an endemic and highly isolated Astyanax fish population (Characidae)

Population structure, fluctuating asymmetry and genetic variability in an endemic and highly isolated Astyanax fish population (Characidae)

The sinkhole 2 Astyanax had a diploid chromosome number of 2n = 48, with a preferential distribution of the constitutive heterochromatin in the telomeric region of the acrocentric chromosomes (Figure 3c, d). This hetero- chromatin distribution seems to be quite common among the Astyanax populations which live in the different Vila Velha sinkholes, this same karyotypic pattern having been detected in sinkhole 1 (Matoso et al., 2002) and Tibagi river (Artoni and Almeida, 2001) Astyanax specimens. This karyotype homogeneity may indicate that the sinkhole and riverine populations became isolated only recently and that insufficient evolutionary time has elapsed for the fixation of chromosomal rearrangements. In addition, the genomic and mitochondrial DNA of these populations are very simi- lar with only a small divergence occurring in the sinkhole 2 Astyanax population, which also supports the recent coloni- zation hypothesis (Matoso, 2002).
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Genetic diversity and population structure of the Guinea pig ( Cavia porcellus

Genetic diversity and population structure of the Guinea pig ( Cavia porcellus

The aim was to establish the genetic diversity and population structure of three guinea pig lines, from seven produc- tion zones located in Nariño, southwest Colombia. A total of 384 individuals were genotyped with six microsatellite markers. The measurement of intrapopulation diversity revealed allelic richness ranging from 3.0 to 6.56, and ob- served heterozygosity (Ho) from 0.33 to 0.60, with a deficit in heterozygous individuals. Although statistically signifi- cant (p < 0.05), genetic differentiation between population pairs was found to be low. Genetic distance, as well as clustering of guinea-pig lines and populations, coincided with the historical and geographical distribution of the popu- lations. Likewise, high genetic identity between improved and native lines was established. An analysis of group probabilistic assignment revealed that each line should not be considered as a genetically homogeneous group. The findings corroborate the absorption of native genetic material into the improved line introduced into Colombia from Peru. It is necessary to establish conservation programs for native-line individuals in Nariño, and control genealogi- cal and production records in order to reduce the inbreeding values in the populations.
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GENETIC GAINS AND SELECTION ADVANCES OF THE UENF-14 POPCORN POPULATION

GENETIC GAINS AND SELECTION ADVANCES OF THE UENF-14 POPCORN POPULATION

The progressive evolution of satisfactory results obtained in this work and the predicted results for the other cycles confirm the efficiency of intra-population recurrent selection in gradually increase the concentration of favorable alleles for GY and PE (PEREIRA; AMARAL JÚNIOR, 2001; RIBEIRO et al., 2012; FREITAS et al., 2014). They also indicate the possibility of obtaining a new crop variety superior to that released in 2013, after five selective cycles, (UENF-14) and recommended for the producers of the North and Northwest regions of the state of Rio de Janeiro (AMARAL JÚNIOR et al., 2013).
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