A new set of differentially expressed signaling genes is early expressed in coffee leaf rust race II incompatible interaction

New races of coffee rust are overcoming resistance genes available in germplasm and cultivated cultivars and bringing recently some coffee-producing countries in severe economic challenge. The objective of this study was to identify the genes that are linked to host resistance to the major coffee rust race II. In our study, we have identified and studied a segregating population that has a single monogenic resistant gene to coffee rust. Coffee leaves of parents, resistant, and susceptible genotypes of the F2 generation plants were inoculated with pathogen spores. A differential analysis was performed by combined cDNA-AFLP and bulk segregant analysis (BSA) in pooled samples collected 48 and 72 h postinoculation, increasing the selectiveness for differential gene expression. Of 108 differential expressed genes, between 33,000 gene fragments analyzed, 108 differential expressed genes were identified in resistant plants. About 20 and 22 % of these resistant-correlated genes are related to signaling and defense genes, respectively. Between signaling genes, the major subclass corresponds to receptor and resistant homolog genes, like nucleotide-binding site leucine-rich repeat (NBS-LRR), Pto-like, RLKs, Bger, and RGH1A, all not previously described in coffee rust responses. The second major subclass included kinases, where two mitogen-activated kinases (MAPK) are identified. Further gene expression analysis was performed for 21 selected genes by real-time PCR gene expression analysis at 0, 12, 24, 48, and 72 h postinoculation. The expression of genes involved in signaling and defense was higher at 24 and 72 h after inoculation, respectively. The NBS-LRR was the more differentially expressed gene between the signaling genes (four times more expressed in the resistant genotype), and thraumatin (PR5) was the more expressed between all genes (six times more expressed). Multivariate analysis reinforces the significance of the temporal separation of identified signaling and defense genes: early expression of signaling genes support the hypothesis that higher expression of the signaling components up regulates the defense genes identified. Additionally the increased gene expression of these two gene sets is associated with a single monogenic resistance trait to to leaf coffee rust in the interaction characterized here

Data from: Mating system and genetic composition of the macaw palm (Acrocomia aculeata): implications for breeding and genetic conservation programs

Acrocomia aculeata (Arecaceae), a palm endemic to South and Central America, is a potential oil crop. Knowledge of the mating system of this species is limited to its reproductive biology and to studies using molecular markers. The present study analyzed genetic diversity between its developmental stages and determined its prevailing mating system in order to support genetic conservation and breeding programs. We tested nine microsatellite markers in 27 mother trees (adult plants) and 157 offspring (juvenile plants) from the southeastern region of Brazil. Heterozygosity levels differed between the two studied life stages, as indicated by the fixation index of adult and juvenile trees, suggesting that selection against homozygotes occurs during the plant life cycle. The mating system parameters analyzed indicate that A. aculeata is predominantly outcrossing (allogamous). However, its low levels of selfing suggest that there is individual variation with regard to self-incompatibility, which can be a survival strategy in isolated or fragmented habitats. Deviations in variance effective size were detected because of high mating rates among relatives and correlated matings. These findings indicate that the main source of inbreeding results from biparental inbreeding in the population and that the progenies are predominantly composed of full-sibs. The information provided by this study on the ecology and reproduction dynamics of A. aculeata should be useful to both breeding and genetic conservation programs, allowing the development of more precise mathematical models and the estimation of the appropriate number of mother trees for seed collection

Lanes et al 2016 Macaw palm genetic data

Excel file containing microsatellite genotypes of A. aculeata adult plants and their offspring, collected from the southeastern region of Brazil. Genetic data of nine microsatellite for 27 mother trees (adult plants) and 157 offspring (juvenile plants). The locus names are listed in the first line. The offspring are identified by alphanumeric code of genebank listed in the first column of the sheet.The genotypes of each accession are from columns 3 to 20. The allelic description of each offspring was determined by informative numerical codes. Missing genetic data are coded as "0"

The effects of encoding data in diversity studies and the applicability of the weighting index approach for data analysis from different molecular markers.

The use of molecular markers to study genetic diversity represents a breakthrough in this area, because of the increase in polymorphism levels and phenotypic neutrality. Codominant markers, such as microsatellites (SSR), are sensitive enough to distinguish the heterozygotes in genetic studies. Despite this advantage, there are some studies that ignore this feature and work with encoded data because of the simplicity of the evaluation, existence of polyploids and need for the combined analysis of different types of molecular markers. Thus, our study aims to investigate the consequences of these encodings on simulated and real data. In addition, we suggest an alternative analysis for genetic evaluations using different molecular markers. For the simulated data, we proposed the following two scenarios: the first uses SNP markers, and the second SSR markers. For real data, we used the SSR genotyping data from Coffea canephora accessions maintained in the Embrapa Germplasm Collection. The genetic diversity was studied using cluster analysis, the dissimilarity index, and the Bayesian approach implemented in the STRUCTURE software. For the simulated data, we observed a loss of genetic information to the encoded data in both scenarios. The same result was observed in the coffee studies. This loss of information was discussed in the context of a plantbreeding program, and the consequences were weighted to germplasm evaluations and the selection of parents for hybridization. In the studies that involved different types of markers, an alternative to the combined analysis is discussed, where the informativeness, coverage and quality of markers are weighted in the genetic diversity studies