Isolation and characterization of nine polymorphic microsatellite loci in Piper solmsianum (piperaceae).

PREMISE OF THE STUDY: Nine microsatellite (simple sequence repeat [SSR]) loci were characterized for natural populations of Piper solmsianum, a potential source of bioactive secondary metabolites, and analyzed to assess the levels of genetic diversity in this species. • METHODS AND RESULTS: Based on an enriched library using the oligonucleotides (CT)8 and (GT)8, a total of 19 pairs of SSR primers were designed and nine of them were highly polymorphic after screening of 37 specimens from two populations. The number of alleles per locus ranged from one to six while the observed heterozygosity for polymorphic loci ranged from 0.000 to 0.875. • CONCLUSIONS: The SSR regions characterized were informative, and the genetic markers will be useful to assess the genetic diversity and gene flow in populations of P. solmsianum.

Isolation and characteristics of eight novel polymorphic microsatellite loci in Lippia alba (Verbenaceae).

PREMISE OF THE STUDY: A set of eight microsatellite (simple sequence repeat [SSR]) markers for Lippia alba, an important medicinal and cosmetic plant, was developed to aid studies of genetic diversity and to define efficient strategies for breeding programs. METHODS AND RESULTS: Using a (CT)(8)- and (GT)(8)-enriched library, a total of 11 SSR loci were developed and optimized in L. alba. Of the 11 loci, eight were found to be polymorphic after screening 61 accessions from two populations. The parameters used to characterize loci were expected heterozygosity (H(e)) and number of alleles. A total of 44 alleles were identified, with an average of 5.5 alleles per loci, which were moderately to highly informative according to H(e). CONCLUSIONS: These new SSR markers have potential for informing genetic diversity, allele mining, and mapping studies and will be used to generate information for breeding programs of L. alba.

An EST-based analysis identifies new genes and reveals distinctive gene expression features of Coffea arabica and Coffea canephora.

BACKGROUND: Coffee is one of the world's most important crops; it is consumed worldwide and plays a significant role in the economy of producing countries. Coffea arabica and C. canephora are responsible for 70 and 30% of commercial production, respectively. C. arabica is an allotetraploid from a recent hybridization of the diploid species, C. canephora and C. eugenioides. C. arabica has lower genetic diversity and results in a higher quality beverage than C. canephora. Research initiatives have been launched to produce genomic and transcriptomic data about Coffea spp. as a strategy to improve breeding efficiency. RESULTS: Assembling the expressed sequence tags (ESTs) of C. arabica and C. canephora produced by the Brazilian Coffee Genome Project and the Nestlé-Cornell Consortium revealed 32,007 clusters of C. arabica and 16,665 clusters of C. canephora. We detected different GC3 profiles between these species that are related to their genome structure and mating system. BLAST analysis revealed similarities between coffee and grape (Vitis vinifera) genes. Using KA/KS analysis, we identified coffee genes under purifying and positive selection. Protein domain and gene ontology analyses suggested differences between Coffea spp. data, mainly in relation to complex sugar synthases and nucleotide binding proteins. OrthoMCL was used to identify specific and prevalent coffee protein families when compared to five other plant species. Among the interesting families annotated are new cystatins, glycine-rich proteins and RALF-like peptides. Hierarchical clustering was used to independently group C. arabica and C. canephora expression clusters according to expression data extracted from EST libraries, resulting in the identification of differentially expressed genes. Based on these results, we emphasize gene annotation and discuss plant defenses, abiotic stress and cup quality-related functional categories. CONCLUSION: We present the first comprehensive genome-wide transcript profile study of C. arabica and C. canephora, which can be freely assessed by the scientific community at http://www.lge.ibi.unicamp.br/coffea. Our data reveal the presence of species-specific/prevalent genes in coffee that may help to explain particular characteristics of these two crops. The identification of differentially expressed transcripts offers a starting point for the correlation between gene expression profiles and Coffea spp. developmental traits, providing valuable insights for coffee breeding and biotechnology, especially concerning sugar metabolism and stress tolerance.

[Molecular characterization and genetic divergence of Bemisia tabaci (Genn.) (Hemiptera: Aleyrodidae) on different crops and growing areas]. / Caracterização molecular e divergência genética de Bemisia tabaci (Genn.) (Hemiptera: Aleyrodidae) em diferentes culturas e locais de cultivo.

Knowledge on the genetic variation of populations of Bemisia tabaci (Genn.) can improve the understanding of genetic diversity found in their biotypes and, consequently, offer guidelines for its management. In this study, the molecular characterization was performed and genetic diversity data were obtained for this insect from three regions of Brazil on different crops [cotton and soybean (Mato Grosso - MT); cabbage (Distrito Federal - DF); soybean and potato (São Paulo - SP)], using RAPD markers. RAPD analysis indicated 80.6% polymorphic loci and the average genetic similarity obtained by the Jaccard coefficient was 0.67. The whitefly populations collected on potato (SP) and soybean (MT) had higher genetic diversity values (0.75 and 0.72, respectively). Shannon's index (Ho) showed higher values for potato and soybean (SP e MT), and a smaller value for cabbage (DF). A high genetic divergence within and among the collected populations occurred, structured according to the regions of collection. Moreover, the great genetic similarity observed between potato (SP) and soybean (SP) populations suggested that both belong to the same biotype B and reinforces the polyphagous behavior of the species.

Caracterização molecular e divergência genética de Bemisia tabaci (Genn. ) (Hemiptera: Aleyrodidae) em diferentes culturas e locais de cultivo / Molecular characterization and genetic divergence of Bemisia tabaci (Genn. ) (Hemiptera: Aleyrodidae) on different crops and growing areas

Knowledge on the genetic variation of populations of Bemisia tabaci (Genn.) can improve the understanding of genetic diversity found in their biotypes and, consequently, offer guidelines for its management. In this study, the molecular characterization was performed and genetic diversity data were obtained for this insect from three regions of Brazil on different crops [cotton and soybean (Mato Grosso - MT); cabbage (Distrito Federal - DF); soybean and potato (São Paulo - SP)], using RAPD markers. RAPD analysis indicated 80.6 percent polymorphic loci and the average genetic similarity obtained by the Jaccard coefficient was 0.67. The whitefly populations collected on potato (SP) and soybean (MT) had higher genetic diversity values (0.75 and 0.72, respectively). Shannon's index (Ho) showed higher values for potato and soybean (SP e MT), and a smaller value for cabbage (DF). A high genetic divergence within and among the collected populations occurred, structured according to the regions of collection. Moreover, the great genetic similarity observed between potato (SP) and soybean (SP) populations suggested that both belong to the same biotype B and reinforces the polyphagous behavior of the species.

Transcriptional profile of genes involved in the biosynthesis of phytate and ferritin in Coffea.

The present work aimed to study the control of the biosynthesis of the antinutritional factor phytate and its associated Fe-rich protein family, ferritin, in coffee. Phytate has the ability to chelate Fe, making it unavailable to human absorption. The Coffea genome databases were queried for genes associated with phytate metabolism and ferritin genes. The genetic framework for phytate biosynthesis and its reverse pathway was identified in silico analyses and indicate that Coffea phosphatidyl inositol kinase and monophosphatase families play nonredundant roles in phytate metabolism. The transcriptional profiles of phytate biosynthesis key-genes MYO-INOSITOL(3)P1 SYNTHASE, two genes coding for PHOSPHATIDYL INOSITOL KINASE, and three FERRITIN genes were temporally evaluated by qPCR in coffee seeds from two crop locations, Adamantina-SP and Ouro-Fino-MG, the last one traditionally associated with high-quality coffee beverage grain. A targeted metabolome profile of phytic acid contents throughout three fruit maturation stages in association with the transcriptional analysis was also obtained. Taken together, our data indicate that the investigated local conditions did not cause significant alterations in phytate biosynthesis. Futhermore, the temporal transcriptional profiling revealed that candidate gene expression is regulated independently of phytate accumulation. In contrast, the expression profile of ferritin-unit genes is affected by environmental conditions and genetic background. The roles of the investigated genes are discussed concerning the quality of coffee beverage.

Caffeine inheritance in interspecific hybrids of Coffea arabica x Coffea canephora (Gentianales, Rubiaceae)

Caffeine inheritance was investigated in F2 and BC1F1 generations between Coffea arabica var. Bourbon Vermelho (BV) and Coffea canephora var. Robusta 4x (R4x). The caffeine content of seeds and leaves was determined during 2004 and 2005. Microsatellite loci-markers were used to deduce the meiotic pattern of chromosome pairing of tetraploid interspecific hybrids. Genetic analysis indicated that caffeine content in seeds was quantitatively inherited and controlled by genes with additive effects. The estimates of broad-sense heritability of caffeine content in seeds were high for both generations. In coffee leaves, the caffeine content (BSH) from the same populations showed transgressive segregants with enhanced levels and high BSH. Segregation of loci-markers in BC1F1 populations showed that the ratios of the gametes genotype did not differ significantly from those expected assuming random associations and tetrasomic inheritance. The results confirm the existence of distinct mechanisms controlling the caffeine content in seeds and leaves, the gene exchange between the C. arabica BV and C. canephora R4x genomes and favorable conditions for improving caffeine content in this coffee population.

Analysis and functional annotation of an expressed sequence tag collection for tropical crop sugarcane.

To contribute to our understanding of the genome complexity of sugarcane, we undertook a large-scale expressed sequence tag (EST) program. More than 260,000 cDNA clones were partially sequenced from 26 standard cDNA libraries generated from different sugarcane tissues. After the processing of the sequences, 237,954 high-quality ESTs were identified. These ESTs were assembled into 43,141 putative transcripts. Of the assembled sequences, 35.6% presented no matches with existing sequences in public databases. A global analysis of the whole SUCEST data set indicated that 14,409 assembled sequences (33% of the total) contained at least one cDNA clone with a full-length insert. Annotation of the 43,141 assembled sequences associated almost 50% of the putative identified sugarcane genes with protein metabolism, cellular communication/signal transduction, bioenergetics, and stress responses. Inspection of the translated assembled sequences for conserved protein domains revealed 40,821 amino acid sequences with 1415 Pfam domains. Reassembling the consensus sequences of the 43,141 transcripts revealed a 22% redundancy in the first assembling. This indicated that possibly 33,620 unique genes had been identified and indicated that >90% of the sugarcane expressed genes were tagged.