Analysis of genetic variability of commercial melon cultivars using SSR molecular markers

Taking into account the scenario of melon production (Cucumis melo L.) in Brazil, it is notable the importance of the culture in the fruit market. The preference of the national market is concentrated in the fruits of the yellow type. Therefore, it is possible that the genetic base of the commercial cultivars is relatively narrow due to the loss of important genes in the breeding process, and it is possible to introgress external genes for increasing recombination possibilities that generate sources of resistance to the main diseases and superior genotypes. This study evaluated the genetic variability of 87 melon accessions composed of 72 commercial cultivars belonging to the Inodorus and Cantaloupensis groups and 15 plant introductions (PIs). Forty-four polymorphic SSR primers were used to amplify a total of 202 alleles. The expected heterozygosity presented an average of 0.519 and the PIC index of 0.458, being moderately informative. The dendrogram generated for the 72 cultivars grouped the genotypes into 2 main groups, and there was no association with the classification of groups of the genotypes in the grouping. The number of SSR markers was sufficient to predict wide genetic variability among the cultivars studied, with the similarity between 0.35 and 0.98. The dendrogram presented for the 72 cultivars and the 15 PI genotypes was not associated with the classification of the genotypes in the grouping, and the 15 PIs were well dispersed with similarity indexes that resemble the two groups studied. A set of 25 primers was identified that were useful in distinguishing the 72 cultivars. These primers can be used in later research with the cultivars, as well as in crop protection situations, being an important tool in the useful and rapid distinction of genotypes, and in commercial disputes regarding the certification of the main melon cultivars used in the country.

Variability among Capsicum baccatum accessions from Goiás, Brazil, assessed by morphological traits and molecular markers

Capsicum peppers are native to the Americas, with Brazil being a significant diversity center. Capsicum baccatum accessions at Instituto Federal (IF) Goiano represent a portion of the species genetic resources from central Brazil. We aimed to characterize a C. baccatum working collection comprising 27 accessions and 3 commercial cultivars using morphological traits and molecular markers to describe its genetic and morphological variability and verify the occurrence of duplicates. This set included 1 C. baccatum var. praetermissum and 29 C. baccatum var. pendulum with potential for use in breeding programs. Twenty-two morphological descriptors, 57 inter-simple sequence repeat, and 34 random amplified polymorphic DNA markers were used. Genetic distance was calculated through the Jaccard similarity index and genetic variability through cluster analysis using the unweighted pair group method with arithmetic mean, resulting in dendrograms for both morphological analysis and molecular analysis. Genetic variability was found among C. baccatum var. pendulum accessions, and the distinction between the two C. baccatum varieties was evident in both the morphological and molecular analyses. The 29 C. baccatum var. pendulum genotypes clustered in four groups according to fruit type in the morphological analysis. They formed seven groups in the molecular analysis, without a clear correspondence with morphology. No duplicates were found. The results describe the genetic and morphological variability, provide a detailed characterization of genotypes, and discard the possibility of duplicates within the IF Goiano C. baccatum L. collection. This study will foment the use of this germplasm collection in C. baccatum breeding programs.

Genetic variability of a Brazilian Capsicum frutescens germplasm collection using morphological characteristics and SSR markers

Characterization studies provide essential information for the conservation and use of germplasm in plant breeding programs. In this study, 103 Capsicum frutescens L. accessions from the Active Germplasm Bank of Embrapa Hortaliças, representative of all five Brazilian geographic regions, were characterized based on morphological characteristics and microsatellite (or simple sequence repeat - SSR) molecular markers. Morphological characterization was carried out using 57 descriptors, and molecular characterization was based on 239 alleles from 24 microsatellite loci. From the estimates of genetic distances among accessions, based on molecular characterization, a cluster analysis was carried out, and a dendrogram was established. Correlations between morphological and molecular variables were also estimated. Twelve morphological descriptors were monomorphic for the set of C. frutescens accessions, and those with the highest degree of polymorphism were stem length (14.0 to 62.0 cm), stem diameter (1.0 to 4.2 cm), days to flowering (90 to 129), days to fruiting (100 to 140), fruit weight (0.1 to 1.4 g), fruit length (0.6 to 4.6 cm), and fruit wall thickness (0.25 to 1.5 mm). The polymorphism information content for the SSR loci varied from 0.36 (EPMS 417) to 0.75 (CA49), with an overall mean of 0.57. The correlation value between morphological and molecular characterization data was 0.6604, which was statistically significant. Fourteen accessions were described as belonging to the morphological type tabasco, 85 were described as malagueta, and four were malaguetinha, a morphological type confirmed in this study. The typical morphological pattern of malagueta was described. Six similarity groups were established for C. frutescens based on the dendrogram and are discussed individually. The genetic variability analyzed in the study highlights the importance of characterizing genetic resources available for the development of new C. frutescens cultivars with the potential for various niche markets.

Novel and highly informative Capsicum SSR markers and their cross-species transferability

This study was undertaken primarily to develop new simple sequence repeat (SSR) markers for Capsicum. As part of this project aimed at broadening the use of molecular tools in Capsicum breeding, two genomic libraries enriched for AG/TC repeat sequences were constructed for Capsicum annuum. A total of 475 DNA clones were sequenced from both libraries and 144 SSR markers were tested on cultivated and wild species of Capsicum. Forty-five SSR markers were randomly selected to genotype a panel of 48 accessions of the Capsicum germplasm bank. The number of alleles per locus ranged from 2 to 11, with an average of 6 alleles. The polymorphism information content was on average 0.60, ranging from 0.20 to 0.83. The cross-species transferability to seven cultivated and wild Capsicum species was tested with a set of 91 SSR markers. We found that a high proportion of the loci produced amplicons in all species tested. C. frutescens had the highest number of transferable markers, whereas the wild species had the lowest. Our results indicate that the new markers can be readily used in genetic analyses of Capsicum.

Transferability of microsatellite markers of Capsicum annuum L. to C. frutescens L. and C. chinense Jacq

In order to support further genetic, diversity, and phylogeny studies of Capsicum species, the transferability of a Capsicum annuum L. simple sequence repeat (SSR) microsatellite set was analyzed for C. frutescens L. ("malagueta" and "tabasco" peppers) and C. chinense Jacq. (smell peppers, among other types). A total of 185 SSR primers were evaluated in 12 accessions from 115 C. frutescens L. and 480 C. chinense Jacq, representing different types within each species. Transferability to C. frutescens L. and C. chinense Jacq. occurred for 116 primers (62.7%). Nineteen (16.37%) were polymorphic in C. frutescens L. and 36 (31.03%) in C. chinense Jacq., 17 of which were coincident and could be used to analyze samples obtained for the 2 species. Among these primers, CA49 showed a different amplitude range of alleles between the 2 species (130-132 base pairs for C. frutescens L. and 120-128 base pairs for C. chinense Jacq.), and could differentiate the species. A total of 55 alleles were identified among the 19 polymorphic SSR loci among accessions of C. frutescens L., with the number of alleles per locus ranging from 2 to 5, a mean of 2.89, and the polymorphic information content ranging from 0.30 to 0.65. The number of alleles identified in C. chinense Jacq. was 119, ranging from 2 to 5 alleles per locus, an average of 3.30, and polymorphic information content from 0.19 to 0.68. The C. annuum L. SSR primers were most often transfer-able and polymorphic for C. frutescens L. and C. chinense Jacq., and we present a set of SSR for each species.

Morphological and genetic relationships between wild and domesticated forms of peppers (Capsicum frutescens L. and C. chinense Jacquin)

Capsicum chinense and C. frutescens peppers are part of the Brazilian biodiversity, and the Amazon basin is the area of greatest diversity for them, especially for that former species. Nevertheless, little is known about their evolutionary history. Aiming to identify genotypes with wild and domesticated characteristics, 30 accessions of the germplasm bank of Embrapa were characterized using morphological descriptors and ISSR molecular markers. Of the 72 primers tested, 42% showed amplification and produced 136 amplicons with some of the primers, namely i7Pv and i57Zm, allowing the identification of each species. ISSR also revealed polymorphisms within a species, especially between domesticated and wild forms. Four wild accessions collected in the Amazon region (CNPH 4315, CNPH 4372, CNPH 4337 and CNPH 4325B) popularly known as "olho-de-peixe" or "olho-de periquito" were molecularly classified as C. chinense and showed fruit with similar characteristics as the wild species: upright position, rounded to campanulate shape, small size (1.0 cm long and 0.8 cm wide), average weight of 0.2 g, dark-red color when ripe, easy detachment of calyx and presence of calyx annular constriction (discriminative of C. chinense). The wild form CNPH 4353 known as "malaguetinha" was morphologically and molecularly classified as C. frutescens, demonstrating a more preserved morphology in C. frutescens than in C. chinense. A significant correlation was found between morphological and molecular characterization, and the combination of the two analyses was effective in identifying and classifying the wild forms and contributing to evolutionary studies in the genus.

Genetic divergence among accessions of melon from traditional agriculture of the Brazilian Northeast

The genetic divergence of 38 melon accessions from traditional agriculture of the Brazilian Northeast and three commercial hybrids were evaluated using fruit descriptors and microsatellite markers. The melon germplasm belongs to the botanic varieties cantalupensis (19), momordica (7), conomon (4), and inodorus (3), and to eight genotypes that were identified only at the species level. The fruit descriptors evaluated were: number of fruits per plant (NPF), fruit mass (FM; kg), fruit longitudinal diameter (LD; cm), fruit transversal diameter (TD; cm), shape index based on the LD/TD ratio, flesh pulp thickness, cavity thickness (CT; cm), firmness fruit pulp (N), and soluble solids (SS; °Brix). The results showed high variability for all descriptors, especially for NPF, LD, and FM. The grouping analysis based on fruit descriptors produced eight groups without taxonomic criteria. The LD (22.52%), NPF (19.70%), CT (16.13%), and SS (9.57%) characteristics were the descriptors that contributed the most to genotype dissimilarity. The 17 simple sequence repeat polymorphic markers amplified 41 alleles with an average of 2.41 alleles and three genotypes per locus. Some markers presented a high frequency for the main allele. The genetic diversity ranged from 0.07 to 0.60, the observed heterozygosity had very low values, and the mean polymorphism information content was 0.32. Molecular genetic similarity analyses clustered the accessions in 13 groups, also not following taxonomic ranks. There was no association between morphoagronomic and molecular groupings. In conclusion, there was great variability among the accessions and among and within botanic groups.

Genetic relationships among Heliconia (Heliconiaceae) species based on RAPD markers

The family Heliconiaceae contains a single genus, Heliconia, with approximately 180 species of Neotropical origin. This genus was formerly allocated to the family Musaceae, but today forms its own family, in the order Zingiberales. The combination of inverted flowers, a single staminode and drupe fruits is an exclusive characteristic of Heliconia. Heliconias are cultivated as ornamental garden plants, and are of increasing importance as cut flowers. However, there are taxonomic confusions and uncertainties about the number of species and the relationships among them. Molecular studies are therefore necessary for better understanding of the species boundaries of these plants. We examined the genetic variability and the phylogenetic relationships of 124 accessions of the genus Heliconia based on RAPD markers. Phenetic and cladistic analyses, using 231 polymorphic RAPD markers, demonstrated that the genus Heliconia is monophyletic. Groupings corresponding to currently recognized species and some subgenera were found, and cultivars and hybrids were found to cluster with their parents. RAPD analysis generally agreed with morphological species classification, except for the position of the subgenus Stenochlamys, which was found to be polyphyletic.

Genetic diversity studies of Brazilian garlic cultivars and quality control of garlic-clover production

The garlic cultivars grown in Brazil evolved from somatic mutations and clone selection by breeding programs and by the introduction of germplasm from other countries. Morphological characters have been used to differentiate these cultivars. Two hundred and six random amplified polymorphic DNA markers were utilized for a diversity analysis of the 17 most planted garlic cultivars in Brazil. Bootstrap analysis showed that the number of markers was efficient and sufficient to obtain a coefficient of variation of 10%. Similarity varied between 16 and 98% and cluster analysis showed that, in general, genetic similarities correlate with morphological characters of the cultivars and production cycle variation. High bootstrap values at most of the nodes supported the dendrogram stability. The grouping of most varieties agreed well with previous reports based on morphological characters. As a vegetative-propagated species, viral diseases are a key problem regarding production and quality of the bulbs, causing gradual loss of yield and decrease in storage capacity. To improve the health quality of garlic seed, a virus-free stock of garlic cloves of the Amarante cultivar was obtained. The ability to distinguish garlic cultivars to detect varietal mixing after in vitro multiplication is extremely important, since correct identification is not possible until bulbs are produced. Random amplified polymorphic DNA markers were also used to differentiate cultivars while they are in vitro and not amenable to morphological discrimination. No difference was identified between the fingerprints of the virus-free or of the infected bulks of Amarante, showing that there was no clove mixing in the handling of material in the clonal multiplication phase.

Relationships in Ananas and other related genera using chloroplast DNA restriction site variation

Chloroplast DNA (cpDNA) diversity was examined using PCR-RFLP to study phylogenetic relationships in Ananas and related genera. One hundred fifteen accessions representing the seven Ananas species and seven other Bromelioideae including the neighboring monospecific genus Pseudananas, two Pitcairnioideae, and one Tillandsioideae were included in the study. Eight primers designed from cpDNA were used for generating fragments. Restriction by 18 endonucleases generated 255 variable fragments. Dissimilarities were calculated from the resulting matrix using the Sokal and Michener index and the neighbor-joining method was used to reconstruct the diversity tree. Phylogenetic reconstruction was attempted using Wagner parsimony. Phenetic and cladistic analyses gave consistent results. They confirm the basal position of Bromelia in the Bromelioideae. Ananas and Pseudananas form a monophyletic group, with three strongly supported sub-groups, two of which are geographically consistent. The majority of Ananas parguazensis accessions constitute a northern group restricted to the Rio Negro and Orinoco basins in Brazil. The tetraploid Pseudananas sagenarius joins the diploid Ananas fritzmuelleri to constitute a southern group. The third and largest group, which includes all remaining species plus some accessions of A. parguazensis and intermediate phenotypes, is the most widespread and its distribution overlaps those of the northern and southern groups. Ananas ananassoides is dominant in this sub-group and highly variable. Its close relationship to all cultivated species supports the hypothesis that this species is the wild ancestor of the domesticated pineapple. The data indicate that gene flow is common within this group and scarcer with both the first and second groups. Comparison of cpDNA data with published genomic DNA data point to the hybrid origin of Ananas bracteatus and support the autopolyploidy of Pseudananas. The Ananas-Pseudananas group structure and distribution are consistent and we propose a scenario based on the refugia hypothesis to explain our data. These results and hypotheses bring some interesting points to consider in the current discussion on Ananas taxonomy.