Showing papers in "Genetics and Molecular Biology in 2006"
TL;DR: The genetic nature of microsatellites, the mechanisms and models of mutation that control their evolution and aspects related to their genesis, distribution and transferability between taxa are described.
Abstract: Microsatellites, or simple sequence repeats (SSRs), have been the most widely applied class of molecular markers used in genetic studies, with applications in many fields of genetics including genetic conservation, population genetics, molecular breeding, and paternity testing. This range of applications is due to the fact that microsatellite markers are co-dominant and multi-allelic, are highly reproducible, have high-resolution and are based on the polymerase chain reaction (PCR). When first introduced, the development of microsatellite markers was expensive but now new and efficient methods of repetitive sequence isolation have been reported, which have led to reduced costs and microsatellite-technology has been increasingly applied to several species, including non-model organisms. The advent of microsatellite markers revolutionized the use of molecular markers but the development of biometric methods for analyzing microsatellite data has not accompanied the progress in the application of these markers, with more effort being need to obtain information on the evolution of the repetitive sequences, which constitute microsatellites in order to formulate models that fit the characteristics of such markers. Our review describes the genetic nature of microsatellites, the mechanisms and models of mutation that control their evolution and aspects related to their genesis, distribution and transferability between taxa. The implications of the use of microsatellites as a tool for estimating genetic parameters are also discussed.
365 citations
TL;DR: Water samples from three sites in the Corrego dos Bagres stream in the Franca municipality of the Brazilian state of Sao Paulo were subjected to the comet assay and micronucleus test using erythrocytes from the fish Oreochromis niloticus, supporting the hypothesis that chromium residues can be genotoxic.
Abstract: Cytotoxicity of metals is important because some metals are potential mutagens able to induce tumors in humans and experimental animals. Chromium can damage DNA in several ways, including DNA double strand breaks (DSBs) which generate chromosomal aberrations, micronucleus formation, sister chromatid exchange, formation of DNA adducts and alterations in DNA replication and transcription. In our study, water samples from three sites in the Corrego dos Bagres stream in the Franca municipality of the Brazilian state of Sao Paulo were subjected to the comet assay and micronucleus test using erythrocytes from the fish Oreochromis niloticus. Nuclear abnormalities of the erythrocytes included blebbed, notched and lobed nuclei, probably due to genotoxic chromium compounds. The greatest comet assay damage occurred with water from a chromium-containing tannery effluent discharge site, supporting the hypothesis that chromium residues can be genotoxic. The mutagenicity of the water samples was assessed using the onion root-tip cell assay, the most frequent chromosomal abnormalities observed being: c-metaphases, stick chromosome, chromosome breaks and losses, bridged anaphases, multipolar anaphases, and micronucleated and binucleated cells. Onion root-tip cell mutagenicity was highest for water samples containing the highest levels of chromium.
358 citations
TL;DR: It was shown that the type and size of experimental populations can exert an influence on the accuracy of genetic maps and this approach is equally applicable to other organisms.
Abstract: Based on simulation studies, it was shown that the type and size of experimental populations can exert an influenceon the accuracy of genetic maps. A hypothetical genome map (one chromosome with nine equidistant molecularmarkers) was generated for the following population types: F 2 with dominant and co-dominant markers, backcross-ing, recombinant inbred lines (RIL) and double-haploid. The population sizes were 50, 100, 150, 200, 500 and 1000individuals and 100 simulations were made for each population. The inaccuracies of the populations with the lowestnumber of individuals were shown by inversions in the order of the markers and the establishment of more than onelinkage group in up to 38% of the simulations, depending on the population type. Stress and variance values of thedistancesbetweenadjacentmarkersweresignificantlyreducedwiththeincreasedsizeofthepopulation.Moreaccu-rate maps were obtained for the co-dominant F 2 and RIL whereas the maps for the dominant F 2 population were lessaccurate. The higher the number of individuals, the more precise was the map. In all populations, a total of 200 indi-viduals were considered as being sufficient for the construction of reasonably accurate genetic maps. Although thispaper deals with plant populations this approach is equally applicable to other organisms.
113 citations
TL;DR: Four microsatellite loci developed in this study were found to be useful for sweet orange DNA typing and will be useful as tools in the selection of zygotic and nucellar plants, identification of seedlings etc.
Abstract: The aims of this study were to develop simple sequence repeat markers (SSRs or microsatellite markers) in citrus and to evaluate the efficiency of these markers for characterization of sweet orange. We developed SSRs from a genomic library of 'Pera IAC' sweet orange enriched for AG/TC, GT/CA, TCA/AGT and AAC/TTG sequence repeats. We selected 279 sequences from which 171 primer pairs were designed of which 113 with the best banding patterns were selected. Characterization of sweet orange microsatellite loci revealed that AG/TC was the most abundant (69%) microsatellite class isolated, followed by GT/CA (15.9%), TCA/AGT (8%) and AAC/TTG (6.2%). The number of alleles ranged from 1 to 4, with a mean of 2 alleles per locus. Four microsatellite loci developed in this study were found to be useful for sweet orange DNA typing. The data obtained from microsatellites loci considered polymorphic will be useful as tools in the selection of zygotic and nucellar plants, identification of seedlings etc. for the cultivars Pera IAC, Lanceta, Pera GS 2000, Lamb Summer, Lima, Lima Tardia, Lima Verde, Mimo do Ceu, Valencia Folha Murcha, Valencia Folha Concha, Natal Murcha, Sanguinea and Baia Gigante.
106 citations
TL;DR: This study of the genetic diversity of cotton cultivars with SSR markers support the need to introduce new alleles into the gene pool of the breeding cultivars.
Abstract: Genetic diversity and the relationship between varieties are of great importance for cotton breeding. Our work was designed to estimate the informativeness of the cotton (Gossypium hirsutum L.) simple sequence repeat (SSR) microsatellite locus and to estimate the genetic distance between 53 cotton cultivars as well as to select a set of SSR primers able to differentiate between the 53 cotton cultivars studied. After extracting DNA from the 53 cultivars and characterized it using 31 pairs of SSR primers we obtained a total of 66 alleles with an average of 2.13 alleles per SSR locus and values of polymorphism information content (PIC) varying from 0.18 to 0.62, the dissimilarity coefficient varying from zero to 0.41. Statistical analysis using the unweighted pair-group method using arithmetic average (UPGMA) revealed seven subgroups which were consistent with the genealogical information available for some of the cultivars. The SSR genetic profile obtained for each of the cultivars made it possible to discriminate 52 of the 53 cultivars. This study of the genetic diversity of cotton cultivars with SSR markers support the need to introduce new alleles into the gene pool of the breeding cultivars.
96 citations
TL;DR: A phylogenetic analysis of the 5.8S rDNA and internal transcribed spacer sequences from some entomogenous Paecilomyces species supports the polyphyly of the genus and showed the existence of cryptic species.
Abstract: A phylogenetic analysis of the 5.8S rDNA and internal transcribed spacer (ITS1 and ITS2) sequences from some entomogenous Paecilomyces species supports the polyphyly of the genus and showed the existence of cryptic species. In the Eurotiales, anamorphs Paecilomyces variotii and Paecilomyces leycettanus were related to the teleomorphs Talaromyces and Thermoascus. In the Hypocreales, three major ITS subgroups were found, one of which included Paecilomyces viridis, Paecilomyces penicillatus, Paecilomyces carneus and isolates identified as Paecilomyces lilacinus and Paecilomyces marquandii. However, the majority of the P. lilacinus and P. marquandii isolates formed a distinct and distantly related subgroup, while the other major subgroup contained Paecilomyces farinosus, Paecilomyces amoeneroseus, Paecilomyces fumosoroseus and Paecilomyces tenuipes.
81 citations
TL;DR: A brief historic account of how ethylene became the focus of fruit ripening research as well as the development and the state-of- art of these studies at both biochemical and genetic levels is presented.
Abstract: The effects of ethylene on plants have been recognized since the Nineteenth Century and it is widely known as the phytohormone responsible for fruit ripening and for its involvement in a number of plant growth and development processes. Elucidating the mechanisms involved in the ripening of climacteric fruit and the role that ethylene plays in this process have been central to fruit production and the improvement of fruit quality. The biochemistry, genetics and physiology of ripening has been extensively studied in economically important fruit crops and a considerable amount of information is available which ranges from the ethylene biosynthesis pathway to the mechanisms of perception, signaling and control of gene expression. However, there is still much to be discovered about these processes and the objective of this review is to present a brief historic account of how ethylene became the focus of fruit ripening research as well as the development and the state-of- art of these studies at both biochemical and genetic levels.
78 citations
TL;DR: It is suggested that not all blocks of tandemly repetitive sequences, such as 5S rDNA sites, can be observed as heterochromatin blocks, including heteromorphism for CMA+ bands.
Abstract: We investigated four orchids of the genus Maxillaria (M. discolor, M. acicularis, M. notylioglossa and M. desvauxiana) in regard to the position of heterochromatin blocks as revealed using chromomycin A3 (CMA) and 4'-6-diamidino-2-phenylindole (DAPI) fluorochrome staining and 5S and 45S rDNA sites using fluorescence in situ hybridization (FISH). The species showed differences in chromosome number and a diversified pattern of CMA+ and DAPI+ bands, including heteromorphism for CMA+ bands. The 5S and 45S rDNA sites also varied in number and most of them were co-localized with CMA+ bands. The relationship between 5S rDNA sites and CMA+ bands was more evident in M. notylioglossa, in which the brighter CMA+ bands were associated with large 5S rDNA sites. However, not all 5S and 45S rDNA sites were co-localized with CMA+ bands, probably due to technical constraints. We compare these results to banding data from other species and suggest that not all blocks of tandemly repetitive sequences, such as 5S rDNA sites, can be observed as heterochromatin blocks.
67 citations
TL;DR: The objective of this study was to characterize the allelic diversity of 192 traditional varieties of Brazilian rice using 12 simple sequence repeat (SSR or microsatellite) markers, indicating that SSR markers are fundamental to determining the genetic relationship between landraces.
Abstract: The rice (Oryza sativa) breeding program of the Rice and Bean research center of the Brazilian agricultural company Empresa Brasileira de Pesquisa Agropecuaria (Embrapa) is well established and provides new cultivars every year to attend the demand for improved high yielding varieties with tolerance to biotic and abiotic stresses. However, the elite genitors used to compose new populations for selection are closely related, contributing to the yield plateau reached in the last 20 years. To overcome this limit, it is necessary to broaden the genetic basis of the cultivars using diverse germplasm such as wild relatives or traditional varieties, with the latter being more practical because they are more easily crossed with elite germplasm to accelerate the recovery of modern plant types in the breeding lines. The objective of our study was to characterize the allelic diversity of 192 traditional varieties of Brazilian rice using 12 simple sequence repeat (SSR or microsatellite) markers. The germplasm was divided into 39 groups by common name similarity. A total of 176 alleles were detected, 30 of which (from 23 accessions) were exclusive. The number of alleles per marker ranged from 6 to 22, with an average of 14.6 alleles per locus. We identified 16 accessions as a mixture of pure lines or heterozygous plants. Dendrogram analysis identified six clusters of identical accessions with different common names and just one cluster with identical accessions with the same common name, indicating that SSR markers are fundamental to determining the genetic relationship between landraces. A subset of 24 landraces, representatives of the 13 similarity groups plus the 11 accessions not grouped, was the most variable set of genotypes analyzed. These accessions can be used as genitors to increase the genetic variability available to rice breeding programs.
65 citations
TL;DR: The microsatellite-derived dendrogram faithfully reflected the phylogenetic relationships between Secale species but did not indicate a possible domestication process of the cultivated rye based on the geographical sources of the accessions.
Abstract: The genetic diversity and phylogenetic relationships in the genus Secale L. (rye) was evaluated using 24 Secale cereale microsatellite (SCM) markers. The average polymorphism information content (PIC) value of each microsatellite locus in 30 Secale accessions evaluated was higher than that in 47 cultivated ryes (Secale cereale ssp. cereale). The mean genetic similarity (GS) index in Secale was lower than that in cultivated rye. The highest within-species GS index was observed for S. sylvestre and the lowest for S. strictum, whereas the highest between-species GS index was found between S. cereale and S. vavilovii and the lowest between S. sylvestre and S. cereale. There was no obvious difference in GS levels in the cultivated rye accessions from Asia, Europe, North America or South America. Cluster analysis indicated that all the Secale accessions could be distinguished by the 24 microsatellite loci. We also found that the S. sylvestre accessions were obviously divergent from the accessions of other species and that the S. vavilovii accessions were closely related to the S. cereale accessions. Our results also showed that S. strictum was heterogeneous and showed great within-species differences. The microsatellite-derived dendrogram faithfully reflected the phylogenetic relationships between Secale species but did not indicate a possible domestication process of the cultivated rye based on the geographical sources of the accessions.
56 citations
TL;DR: Results indicate that P. polystachyum infusions present cytotoxic and anti-proliferative activity and therefore have therapeutic potential and are used to treat digestive problems in Brazil.
Abstract: In Brazil leaf infusions of the plant Pterocaulon polystachyum DC (Asteraceae) are used to treat digestive problems. We used plants from six P. polystachyum populations to prepare fresh aqueous leaf infusions at the concentration normally used in Brazil (2.5 g L-1) and at twice (5 g L-1) and four times (10 g L-1) this concentration. We rooted onion bulbs in a water control or one of the infusions for 24 h and used the in vivo onion (Allium cepa) root-tip cell test to investigate the potential mutagenicity of the infusions by calculating the mitotic index for the control and the experimental treatments and comparing them using the Chi-squared test (c2, p = 0.05). There was a highly significant decrease in the mitotic index of root-tip cells treated with infusion as compared to those exposed to water only. These results indicate that P. polystachyum infusions present cytotoxic and anti-proliferative activity and therefore have therapeutic potential.
TL;DR: The results suggest that karyotype differentiation can occur mainly due to changes in repetitive DNA, with little modification in the general composition of the conventionally stained karyotypes.
Abstract: We studied the karyotypes of four Brazilian Cestrum species (C. amictum, C. intermedium, C. sendtnerianum and C. strigilatum) using conventional Feulgen staining, C-Giemsa and C-CMA3/DAPI banding, induction of cold-sensitive regions (CSRs) and fluorescent in situ hybridization (FISH) with rDNA probes. We found that the karyotypes of all four species was 2n = 2x = 16, with, except for the eighth acrocentric pair, a predominance of meta- and submetacentric chromosomes and various heterochromatin classes. Heterochromatic types previously unreported in Cestrum as neutral C-CMA30/DAPI0 bands, CMA3+ bands not associated with NORs, and C-Giemsa/CSR/DAPI- bands were found. The heterochromatic blocks varied in size, number, position and composition. The 45S rDNA probe preferentially located in the terminal and subterminal regions of some chromosomes, while 5S rDNA appeared close to the centromere of the long arm of pair 8. These results suggest that karyotype differentiation can occur mainly due to changes in repetitive DNA, with little modification in the general composition of the conventionally stained karyotype.
TL;DR: The results show the efficiency of AFLP markers in large scale studies of genetic similarity and are discussed in relation to soybean breeding in Brazil.
Abstract: Genetic similarity among soybean genotypes was studied by applying the amplified fragment length polymorphism (AFLP) technique to 317 soybean cultivars released in Brazil from 1962 to 1998. Genetic similarity (GS) coefficients were estimated using the coefficient of Nei and Li (Nei and Li 1979), and the cultivars were clustered using the unweighted pair-group method with averages (UPGMA). The parentage coefficients of 100 cultivars released between 1984 and 1998 were calculated and correlated with the genetic similarity obtained by the markers. The genetic similarity coefficients varied from 0.17 to 0.97 (x = 0.61), with 56.8% of the coefficients being above 0.60 and only 9.7% equal to or less than 0.50. The similarity coefficients have remained constant during the last three decades. Dendrogram interpretation was hindered by the large number of cultivars used, but it was possible to detect groups of cultivars formed as expected from their genealogy. Another dendrogram, composed of 63 cultivars, allowed a better interpretation of the groups. Parentage coefficients among the 100 cultivars varied from zero to one (x = 0.21). However, no significant correlation (r = 0.12) was detected among the parentage coefficients and the AFLP genetic similarity. The results show the efficiency of AFLP markers in large scale studies of genetic similarity and are discussed in relation to soybean breeding in Brazil.
TL;DR: The exclusion probabilities and the polymorphism information content of some loci in Nellore cattle were lower than in Bos taurus breeds, and this multiplex analysis can contribute toward pedigree information, adequate genetic improvements and breeding programs.
Abstract: We assessed the polymorphism of 10 microsatellites in Brazilian Nellore cattle (Bos indicus) using a commercial multiplex system. Allele frequencies, polymorphism information content, heterozygosity and exclusion probability were calculated. Allele frequencies revealed that in the sample analyzed the markers were not equally polymorphic. The exclusion probabilities and the polymorphism information content of some loci in Nellore cattle were lower than in Bos taurus breeds. When all the microsatellites were considered the combined exclusion probability was 0.9989. This multiplex analysis can contribute toward pedigree information, adequate genetic improvements and breeding programs.
TL;DR: The objective of this study was to evaluate the transferability of microsatellite primers and the assay of genetic variability between and within the germplasm of some species of the Arachis section.
Abstract: The Arachis section is the most important of the nine sections of the genus Arachis because it includes the cultivated peanut, Arachis hypogaea. The genetic improvement of A. hypogaea using wild relatives is at an early stage of development in spite of their potential as sources of genes, including those for disease and pests resistance, that are not found in the A. hypogaea primary gene pool. Section Arachis species germplasm has been collected and maintained in gene banks and its use and effective conservation depends on our knowledge of the genetic variability contained in this material. Microsatellites are routinely used for the analysis of genetic variability because they are highly polymorphic and codominant. The objective of this study was to evaluate the transferability of microsatellite primers and the assay of genetic variability between and within the germplasm of some species of the Arachis section. Fourteen microsatellite loci developed for three different species of Arachis were analyzed and 11 (78%) were found to be polymorphic. All loci had transferability to all the species analyzed. The polymorphic loci were very informative, with expected heterozygosity per locus ranging from 0.70 to 0.94. In general, the germplasm analyzed showed wide genetic variation.
TL;DR: The genotyping of 292 goats from three herds found that the general heterozygosity was 0.6952 for Alpine, 0.7043 for Saanen and 0.4984 for Moxoto goats, indicating similarity between the imported breeds and the existence of crosses between them.
Abstract: Brazilian naturalized goat breeds are adapted to the semiarid conditions prevalent in the Northeast region of the country (which has the largest Brazilian goat heard) and represent an as yet uninvestigated source of genetic diversity. Currently, imported goat breeds are crossed with Brazilian naturalized goat breeds, endangering the genetic potential of the naturalized breeds. We used 11 microsatellite markers to determine the genetic diversity among imported (non-naturalized) dairy Alpine and Saanen goats and naturalized Brazilian Moxoto goats. We genotyped 292 goats from three herds (one private, one from the University of Minas Gerais and the Moxoto conservation herd from Embrapa Caprinos) and found that the general heterozygosity was 0.6952 for Alpine, 0.7043 for Saanen and 0.4984 for Moxoto goats. The number of alleles ranged from 5 (INRA005) to 11 (BM3205), with an average of 7 alleles per locus in the imported breeds and 3.5 alleles per locus in the Moxoto breed. Mean differentiation between populations was higher for herds (FSTS = 0.0768) than for breeds (FSTP = 0.0263), indicating similarity between the imported breeds and the existence of crosses between them. Nei's genetic distance was highest between the Moxoto breed and the imported breeds. These indicate that further studies using these molecular markers would be fruitful.
TL;DR: The results showed significant associations between the LL genotype of the GH1/Alu I polymorphism and higher weight gain and body weight at slaughter (p < 0.05) and the POU1F1/Hinf I polymorphisms did not have any effect on the growth and carcass traits analyzed.
Abstract: The objectives of the present study were to estimate the allele and genotype frequencies of the GH1/Alu I and POU1F1/Hinf I polymorphisms in beef cattle belonging to different genetic groups and to determine the effects of these polymorphisms on growth and carcass traits in cattle submitted to feedlot management, an intensive production model. Genotyping was performed on 384 animals, including 79 Nellore, 30 Canchim (5/8 Charolais + 3/8 Zebu), 30 Simmental x Nellore crossbred and 245 Angus x Nellore crossbred cattle. Body weight, weight gain, dressing percentage, Longissimus dorsi area and backfat thickness were fitted using the General Linear Model (GLM) procedure of the SAS program and the least square means of the genotypes were compared using the F test. The results showed significant associations between the LL genotype of the GH1/Alu I polymorphism and higher weight gain and body weight at slaughter (p < 0.05). The POU1F1/Hinf I polymorphism did not have any effect on the growth and carcass traits analyzed.
TL;DR: Regression analyses of geographic distances and pairwise FST values estimated from RAPD markers showed that there is a correlation between genetic structure and geographic localization.
Abstract: The tropical mosquito, Aedes aegypti is the most important domestic vector of urban yellow fever and dengue. Genetic population studies on this vector are important because they may lead to new tools for surveillance. An analysis of genetic structure was conducted among populations of A. aegypti from 11 localities in four demographic regions within six Brazilian federal states. Markers included 21 random amplified polymorphic DNA (RAPD) loci. RAPD markers were detected among populations and cluster analysis revealed two main groups. We found high genetic polymorphism (HS = 0.224) and high levels of genetic differentiation between populations from different states (GST = 0.430), as well as in populations from cities in the same state (GST = 0.410). These results indicate significant differentiation in A. aegypti populations in Brazil. Regression analyses of geographic distances and pairwise FST values estimated from RAPD markers showed that there is a correlation between genetic structure and geographic localization.
TL;DR: The results indicate that selection of maternal plants for high oil content would be more efficient than selection based on single seeds, and the estimate of narrow-sense heritability for oil content was 73.52% with the interaction heritability being larger than the general heritability, indicating that the early generations can be used for selection for highOil content.
Abstract: Analysis of genetic main effects and genotype x environment (GE) interaction effects on the oil content of oilseed rape (Brassica napus L.) was conducted by using a genetic model for the quantitative traits of seeds in diploid plants. The experiments were carried out over two years with 8 parents and a diallel mating design, which produced F1 and F2 generations. We found that the oil content of rape was simultaneously controlled by embryo genetic effect, cytoplasmic effects and maternal genetic effect as well as GE interaction effects, with the cytoplasmic and maternal effects playing the main role. The results indicate that selection of maternal plants for high oil content would be more efficient than selection based on single seeds. Since the GE interaction effects accounted for 73.69% of the total genetic effects and were more important than the genetic main effects it seems that selection might be influenced by environmental conditions. The estimate of narrow-sense heritability for oil content was 73.52% with the interaction heritability being larger than the general heritability, indicating that the early generations can be used for selection for high oil content. The prediction of genetic effects suggested that the parent cultivars Youcai 601 and Gaoyou 605 were better than the other cultivars for increasing oil content during the breeding of B. napus. The implications for the quantitative trait loci mapping of seed traits interfered by these three genetic systems is also discussed.
TL;DR: The relative importance of the non-additive effects of cold tolerance at the germination stage in rice suggests that selection should be applied in advanced generations of the breeding program.
Abstract: Cold tolerance during germination is important for ensuring fast and uniform establishment of a rice crop early in the season However, evaluation of this trait under field conditions is limited by environmental variation, which makes it difficult to identify genetically superior lines Evaluation of cold tolerance under controlled temperature conditions may be performed by assessing percentage of reduction in coleoptile length and coleoptile growth Our study determined the inheritance and heritability of cold tolerance at the germination stage in crosses between six rice genotypes Diallel analysis showed that while both additive and non-additive gene action were involved, the non-additive action was relatively more important for percentage of reduction in coleoptile length and coleoptile growth Our data shows that genotype Quilla 66304 would be the best parent in crosses aimed at increasing cold tolerance at the germination stage in rice due to its high general combining ability for both percentage of reduction in coleoptile length and coleoptile growth Generation mean analysis was also performed for coleoptile growth in six cold-sensitive x cold-tolerant crosses and proved that non-additive effects were due to dominance and epistatic interactions Though broad sense heritability values were high, the relative importance of the non-additive effects suggests that selection should be applied in advanced generations of the breeding program
TL;DR: The findings indicate that its long-lived planktotrophic larvae provides this species with considerable dispersal ability throughout its range which is favoured by the ocean currents along the chilean coast.
Abstract: Genetic differentiation in the Chilean blue mussel Mytilus chilensis (Hupe 1854) was investigated based on the variation in the allozyme frequencies of Pgm, Gpi, Icd, Me, Gsr, Lap and Pep in eight samples collected along 1800 km from Arauco (VIII Region) to Punta Arenas (XII Region). Despite the large geographic separations, values of Neis unbiased genetic distance, D (0.004-0.048) and standardised genetic variation among populations, Fst (0.011-0.055) were small. The levels of gene flow (Nm = 8) found in this study prevent the effect of differentiation among populations by genetic drift. This findings indicate that its long-lived planktotrophic larvae provides this species with considerable dispersal ability throughout its range which is favoured by the ocean currents along the chilean coast. In terms of management of the M. chilensis fishery, the results provide no evidence for discrete stocks, with the possible exception of the Punta Arenas population. Considering the intensive aquaculture activities with this species the present study provide preliminary data which can be used as a baseline for further characterization and /or monitoring these mussel populations.
TL;DR: The genetic structure of Caiman crocodilus was investigated using a 1085 bp mtDNA fragment of the cytochrome b gene and the observed genetic patterns are compatible with the ecology of C. crocodilus, and history of human exploitation.
Abstract: The genetic structure of Caiman crocodilus was investigated using a 1085 bp mtDNA fragment of the cytochrome b gene. Inferences were based on 125 individuals from nine localities in Peru, Brazil and French Guiana. With the exception of Mamiraua Lake, Anavilhanas Archipelago and the Tapara Community which show a signal of demographic expansion, the sampled localities are in a mutation-drift genetic equilibrium. Divergence between the Amazon basin and extra-Amazon basin localities is significant; however, inference from Nested Clade Analysis cannot distinguish between continuous range expansion, long distance colonization or past fragmentation; however, past fragmentation is unlikely due to low number of mutational steps separating these two regions. The divergence is probably maintained by the reduced ability of C. crocodilus to cross salt water barriers. Within the Amazon basin, continuous range expansion without isolation-by-distance is the most likely process causing genetic structuring. The observed genetic patterns are compatible with the ecology of C. crocodilus, and history of human exploitation. As commercial hunting depleted more valuable species, C. crocodilus expanded its range and ecological niche, prompting hunters to harvest it. Following a period of intense hunting, C. crocodilus is now experiencing recovery and a second population expansion especially in protected areas.
TL;DR: This study used inter-simple sequence repeats (ISSR) to assess levels of genetic variation in R. crenulata from nine diverse natural populations in eastern Tibet and northern Yunnan, the first time such a study has been carried out.
Abstract: The plant Rhodiola crenulata is a perennial herbaceous species distributed in the plateau region of southwestern China, especially the Hengduan Mountains region. It has been one of the most important traditional herbal remedies in Tibet for more than one thousand years, but the accelerated and uncontrolled collection of this plant since the 1980s has lead to deforestation. We used inter-simple sequence repeats (ISSR) to assess levels of genetic variation in R. crenulata from nine diverse natural populations in eastern Tibet and northern Yunnan, the first time such a study has been carried out. The 12 primers we used were able to detect 184 polymorphic loc. Analysis of molecular variance (AMOVA) indicated that species level genetic diversity was relatively high (p = 97.83%, and Ho = 0.464) and analysis using Shannons index showed that the within and between genetic diversity of R. crenulata are approximately equal. Neis genetic distance and unweighted pair-group method with arithmetic averages (UPGMA) cluster analysis showed that the three populations from Tibet and the six populations from Yunnan form two major clusters. The Yunnan populations from three locations were further divided into three corresponding groups, indicating that genetic differentiation was correlated to geographic distribution. Understanding the genetic structure of R. crenulata provides insight for the conservation and management of this endangered species.
TL;DR: A theoretical framework in which target persistence and genetic representation of targets defined using multiple genetic criteria can be explicitly incorporated into the broad-scale reserve network models used to optimize biodiversity conservation based on multiple species data is discussed.
Abstract: Conservation genetics has been focused on the ecological and evolutionary persistence of targets (species or other intraspecific units), especially when dealing with narrow-ranged species, and no generalized solution regarding the problem of where to concentrate conservation efforts for multiple genetic targets has yet been achieved. Broadly distributed and abundant species allow the identification of evolutionary significant units, management units, phylogeographical units or other spatial patterns in genetic variability, including those generated by effects of habitat fragmentation caused by human activities. However, these genetic units are rarely considered as priority conservation targets in regional conservation planning procedures. In this paper, we discuss a theoretical framework in which target persistence and genetic representation of targets defined using multiple genetic criteria can be explicitly incorporated into the broad-scale reserve network models used to optimize biodiversity conservation based on multiple species data. When genetic variation can be considered discrete in geographical space, the solution is straightforward, and each spatial unit must be considered as a distinct target. But methods for dealing with continuous genetic variation in space are not trivial and optimization procedures must still be developed. We present a simple heuristic and sequential algorithm to deal with this problem by combining multiple networks of local populations of multiple species in which minimum separation distance between conserved populations is a function of spatial autocorrelation patterns of genetic variability within each species.
TL;DR: The results suggest that Tibet might be a center of genetic diversity for cultivated barley, the cultivated six-rowed naked barley on the Qinghai-Tibet plateau of China may have evolved in Tibet and spread to Qinghai and then to Ganzi prefecture of Sichuan province.
Abstract: Cultivated six-rowed naked barley (Hordeum vulgare ssp. hexastichon var. nudum Hsu) is the oldest cultivated barley in China. We used 35 simple sequence repeat (SSR) markers selected from seven barley linkage groups to study the genetic diversity, geographical differentiation and evolutionary relationships among 65 H. vulgare ssp. hexastichon landrace accessions collected from the Qinghai-Tibet plateau of China, 25 accessions from Tibet (TB), 20 from Qinghai (QH) and 20 from Ganzi (GZ) prefecture in Sichuan province. At the 35 SSR loci we identified 248 alleles among the 65 accessions, 119 (47.98%) of the alleles being common alleles. We also found that the TB accessions possessed 47 private alleles, about 1.5 times more than the 31 private alleles found in the QH accessions and about 5 times more than 9 private alleles found in the GZ accessions. Generally, the TB accessions showed significantly higher genetic diversity than either the QH or GZ accessions whereas no significant difference in genetic diversity was found between the QH and GZ accessions. Partitioning analysis of genetic diversity showed that about 81% of the total variation was due to within-subgroup diversity and about 19% was clearly accounted for by geographical differentiation among the three subgroups. The distributions of alleles for most loci (71.4%) were significantly different among the three subgroups and geographical differentiation could be found according to the distribution of SSR alleles. Cluster analysis indicated that most of the accessions could be clustered into groups which basically coincided with their geographical distribution. These results suggest that Tibet might be a center of genetic diversity for cultivated barley, the cultivated six-rowed naked barley on the Qinghai-Tibet plateau of China may have evolved in Tibet and spread to Qinghai and then to Ganzi prefecture of Sichuan province.
TL;DR: In this paper, the authors describe meiosis in elephant grass x pearl millet hybrids and their progenitors and their three hybrid accessions presented a high frequency of abnormalities characterized by irregular chromosomal segregation which resulted in the formation of sterile pollen.
Abstract: The cultivated and sexually compatible species Pennisetum purpureum (elephant grass, 2n = 4x = 28) and Pennisetum glaucum (pearl millet, 2n = 2x = 14) can undergo hybridization which favors the amplification of their genetic background and the introgression of favorable alleles into breeding programs. The main problem with interspecific hybrids of these species is infertility due to triploidy (2n = 3x = 21). This study describes meiosis in elephant grass x pearl millet hybrids and their progenitors. Panicles were prepared according to the conventional protocol for meiotic studies and Alexanders stain was used for assessing pollen viability. Pearl millet accessions presented regular meiosis with seven bivalents and high pollen viability. For elephant grass, 14 bivalents in diakinesis and metaphase I were observed. The BAG 63 elephant grass accession, derived from tissue culture, presented a high frequency of meiotic abnormalities. The three hybrid accessions presented a high frequency of abnormalities characterized by irregular chromosomal segregation which resulted in the formation of sterile pollen.
TL;DR: The differential banding techniques and FISH revealed NOR size polymorphism due to structural events such as breaks and duplication of the larger rDNA site cluster and observed syntenic localization of the 5S ribosomal genes in the distal segment of the 45S cluster.
Abstract: We used differential staining techniques (BSG, GTG, AgNO3, DAPI and CMA3 banding) and fluorescent in situ hybridization (FISH) with 5S and 18S probes to investigated the karyotypic and cytogenetic chracteristics of Prochilodus lineatus specimens from a population in Vila Velha state park (Parque Estadual de Vila Velha, Ponta Grossa, Parana state, southern Brazil). The specimens studied showed the same karyotype as that found in other P. lineatus populations, i.e. 2n = 54 biarmed chromosomes (40m + 14 sm) and c-positive heterochromatin preferentially located pericentromerically in all chromosomes. The presence of partial or totally heterochromatic supernumerary chromosomes with numeric intra-individual variation was confirmed in the analyzed population. The nucleolar organizing regions (NORs) were interstitially situated on the long arm of chromosome pair 4 directly beneath the centromere. The differential banding techniques and FISH revealed NOR size polymorphism due to structural events such as breaks and duplication of the larger rDNA site cluster. We also observed syntenic localization of the 5S ribosomal genes in the distal segment of the 45S cluster.
TL;DR: The results suggest that genetic variability needs monitoring in order to avoid the compromise of genetic improvement in economically important traits in the breeding program.
Abstract: Parameters based on the probability of gene origin were used to describe the genetic variability in strains of Nellore and polled Nellore (Bos indicus) cattle that participated in the Program for Genetic Improvement of the Nellore Breed (Programa de Melhoramento Genetico da Raca Nelore). The effective number of founders was 87.2 for Nellore and 107.9 for polled Nellore, while the number of ancestors was 59.8 for Nellore and 61.5 for polled Nellore and the remaining genomes were 39.4 for Nellore and 34.5 for polled Nellore cattle. The results indicate an intense use (by artificial insemination) of some sires and the absence of subdivisions in the population. The family structure in the two breeds was mainly caused by the genetic contribution of the same sires and only mating preferences for descendants of some founders are recorded in either breed. The results suggest that genetic variability needs monitoring in order to avoid the compromise of genetic improvement in economically important traits in the breeding program.
TL;DR: According to the results, the populations from the East and West banks of the Tocantins river are more divergent than true species like S. mystax and S. imperator, and consequently these very divergent populations may represent distinct taxonomic entities (species?).
Abstract: The Saguinus represent the basal genus of the Callitrichinae subfamily. Traditionally this genus is divided into three groups: Hairy, Mottled and Bare-face, however, molecular data failed to validate these groups as monophyletic units, as well as raised some subspecies to the species status. This is the case of the former subspecies Saguinus midas midas and S. midas niger, which are now considered as different species. In the present study, we sequenced a portion of the D-loop mtDNA region in populations from the East bank of the Xingu and from both banks of the Tocantins river, in order to test the effectiveness of large rivers as barriers to the gene flow in Saguinus. According to our results, the populations from the East and West banks of the Tocantins river are more divergent than true species like S. mystax and S. imperator. The Tocantins river may be acting as a barrier to gene flow, and consequently these very divergent populations may represent distinct taxonomic entities (species?).
TL;DR: In contrast to the variable 18S rDNA distribution pattern, highly stable chromosomal positioning of the 5S r DNA sites was observed in the four A. altiparanae populations.
Abstract: Fluorescence in situ hybridization (FISH) was undertaken in order to determinate the chromosomal distribution pattern of 18S and 5S ribosomal DNAs (rDNA) in four populations of the characid fish Astyanax altiparanae from the upper Parana river basin, Brazil. The 18S rDNA probe FISH revealed numerical and positional variations among specimens from the Kecaba stream compared to specimens of the other populations studied. In contrast to the variable 18S rDNA distribution pattern, highly stable chromosomal positioning of the 5S rDNA sites was observed in the four A. altiparanae populations. Divergence in the distribution pattern of 18S and 5S rDNA sites is also discussed.