Molecular markers (RAPD, AFLP and microsatellites) were used to generate a linkage map and to identify QTLs associated to witches' broom (Crinipellis perniciosa) resistance in cacao (Theobroma cacao), using 82 individuals of an F 2 population derived from the clones ICS-1 (susceptible) and Scavina-6 (resistant). Fifteen evaluations of the number of brooms have been carried out in six years (1997)(1998)(1999)(2000)(2001)(2002). In order to increase the precision and accuracy in the measures of resistance, each F 2 plant was cloned in three replications in a randomized block design with singletree plots and evaluated over 2 years. Three hundred and forty-two markers were obtained, being 33 microsatellites, 77 AFLPs and 232 RAPDs. The distribution of the number of brooms in the F 2 population was skewed to resistance, suggesting the involvement of major genes controlling resistance and the repeatability estimated for resistance was 44%. A strong putative QTL was detected as being related to witches' broom resistance. Associated to this QTL, the microsatellite mTcCIR35 explained 35.5% of the phenotypic variation in resistance. This marker is being used for marker-assisted selection in Scavina-6 progenies, including those selected in private plantations, as an auxiliary tool to the phenotypic selection.

BackgroundWitches’ broom disease (WBD) caused by the fungus Moniliophthora perniciosa is responsible for considerable economic losses for cacao producers. One of the ways to combat WBD is to plant resistant cultivars. Resistance may be governed by a few genetic factors, mainly found in wild germplasm.ResultsWe developed a dense genetic linkage map with a length of 852.8 cM that contains 3,526 SNPs and is based on the MP01 mapping population, which counts 459 trees from a cross between the resistant ‘TSH 1188’ and the tolerant ‘CCN 51’ at the Mars Center for Cocoa Science in Barro Preto, Bahia, Brazil. Seven quantitative trait loci (QTL) that are associated with WBD were identified on five different chromosomes using a multi-trait QTL analysis for outbreeders. Phasing of the haplotypes at the major QTL region on chromosome IX on a diversity panel of genotypes clearly indicates that the major resistance locus comes from a well-known source of WBD resistance, the clone ‘SCAVINA 6’. Various potential candidate genes identified within all QTL may be involved in different steps leading to disease resistance. Preliminary expression data indicate that at least three of these candidate genes may play a role during the first 12 h after infection, with clear differences between ‘CCN 51’ and ‘TSH 1188’.ConclusionsWe combined the information from a large mapping population with very distinct parents that segregate for WBD, a dense set of mapped markers, rigorous phenotyping capabilities and the availability of a sequenced genome to identify several genomic regions that are involved in WBD resistance. We also identified a novel source of resistance that most likely comes from the ‘CCN 51’ parent. Thanks to the large population size of the MP01 population, we were able to pick up QTL and markers with relatively small effects that can contribute to the creation and selection of more tolerant/resistant plant material.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2415-x) contains supplementary material, which is available to authorized users.

Three new varieties of Passiflora hybrids were developed from crosses between P. sublanceolata J. M. MacDougal (ex P. palmeri var. sublanceolata Killip) versus P. foetida var. foetida L. Twenty putative hybrids were analyzed. Hybridizations were confirmed by RAPD and SSR markers. The RAPD primer UBC11 (5 0 -CCGGCCTTAC-3 0 ) generated informative bands. The SSR primer A08FP1 amplified species-specific fragments and heterozygote status was observed with the two parent bands 240 and 280 bp. The molecular markers generated by primers were analyzed in terms of the presence or absence of specific informative bands. The morphological characterization of the hybrids enabled their differentiation into three groups, identified as: (1) Passiflora 'Alva', composed of five hybrid plants with white flowers, large corona, light purple filaments at base, white and purple/white banding to apex; (2) P. 'Aninha', composed of six hybrid plants with pale pink flowers, corona filaments reddish/purple at base, white, purple/ white banding to apex; (3) P. 'Priscilla', composed of nine hybrid plants with white flowers, small corona, filaments dark purple at base, white and purple to apex. The genomic homology of parent plants was verified by cytogenetic analysis. Both parents were 2n = 22. Meiosis was regular in genitors and hybrids. Aneuploidy was observed at hybrid groups P. 'Alva' and P. 'Priscilla' (2n = 20). Other authors had already observed the same number of chromosomes for some P. foetida genotypes. Obtaining valuable interspecific hybrids opens up new perspectives to offer opportunities in agribusiness for producers and to arouse the interest of consumers into using passion flowers in the Brazilian ornamental plant market.

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Morphological and molecular characteristics were studied in six wild species of Passiflora. There were statistically significant differences among these six species for all characteristics studied. Intra-specific variability was observed for number of flowers, number of fruits, number of seeds, fruit length, fruit width and leaf area. Cluster analysis using morphological data showed three groups: 1) P. palmeri var. sublanceolata, P. morifolia and P. foetida var. foetida, 2) P. coriacea and P. micropetala, and 3) P. suberosa. The dendrogram constructed using randomly amplified polymorphic DNA (RAPD) data showed six different groups for each species. The genetic distances among the 24 accessions ranged from 0.05 (between P. morifolia accessions P1 and P3) to 0.95 (P. coriacea accession 31 and P. palmeri var. sublanceolata accession 49). The species showed high morphological and molecular inter-and intraspecific variability.