Genomic in situ hybridization (GISH), which is a modification of fluorescent in situ hybridization, has been widely used in the study of plants. It has become one of the most important techniques for molecular cytogenetics. GISH is a technique that allows distinguishing the genomes in a cell. With this technique, it is possible to differentiate the genomes in a hybrid; consequently, this tool has been applied to the study of hybrid lineages, genetic improvement programs, and studies of the evolution of polyploids. Moreover, GISH can be applied to the analysis of the meiotic behavior in hybrids and polyploids, providing information concerning the relationship between species. This review presents the wide application of this technique in plants.

A great interest exists in the production of hybrid plants of the genus Passiflora given the beauty and exotic features of its flowers which have ornamental value. Hybrid paternity confirmation is therefore important for assuring germplasm origin, and is typically carried out by molecular marker segregation. The aim of this study was to karyotypically characterize the chromosome heritance patterns of the progeny resultant from a cross of P. gardneri and P. gibertii using classical cytogenetics, chromosome banding, and molecular cytogenetics. All analyzed genotypes showed the same diploid chromosome number as the genitor species: 2n = 18. Classical and CMA3 and DAPI staining allowed for chromosome counting and satellite identification (secondary constrictions). Fluorescence in situ hybridization (FISH) and genomic in situ hybridization (GISH) were used to characterize subgenomes by either identifying rDNA-specific genome patterns or parental genomes, respectively. The heritance of chromosomal markers presenting rDNA sites from each parent for genome identification confirmed that all obtained plants were hybrids. These results will improve breeding programs involving the species of this genus. Apart from confirming hybridization, GISH allowed the visualization of recombination between the homeologous chromosome and the introgression of sequences of interest.

The cytogenomic study of repetitive regions is fundamental for the understanding of morphofunctional mechanisms and genome evolution. Passiflora edulis a species of relevant agronomic value, this work had its genome sequenced by next generation sequencing and bioinformatics analysis performed by RepeatExplorer pipeline. The clusters allowed the identification and characterization of repetitive elements (predominant contributors to most plant genomes). The aim of this study was to identify, characterize and map the repetitive DNA of P. edulis, providing important cytogenomic markers, especially sequences associated with the centromere. Three clusters of satellite DNAs (69, 118 and 207) and seven clusters of Long Terminal Repeat (LTR) retrotransposons of the superfamilies Ty1/Copy and Ty3/Gypsy and families Angela, Athila, Chromovirus and Maximus-Sire (6, 11, 36, 43, 86, 94 and 135) were characterized and analyzed. The chromosome mapping of satellite DNAs showed two hybridization sites co-located in the 5S rDNA region (PeSat_1), subterminal hybridizations (PeSat_3) and hybridization in four sites, co-located in the 45S rDNA region (PeSat_2). Most of the retroelements hybridizations showed signals scattered in the chromosomes, diverging in abundance, and only the cluster 6 presented pericentromeric regions marking. No satellite DNAs and retroelement associated with centromere was observed. P. edulis has a highly repetitive genome, with the predominance of Ty3/Gypsy LTR retrotransposon. The satellite DNAs and LTR retrotransposon characterized are promising markers for investigation of the evolutionary patterns and genetic distinction of species and hybrids of Passiflora.

The genomic in situ hybridization (GISH) technique was applied to Passiflora interspecific F1 HD13-133 hybrids (Passiflora sublanceolata x Passiflora foetida) and HD15-101 (Passiflora gardineri x Passiflora gibertii), and the backcrossed hybrids (BC1) HD18-106 and HD18-113 (Passiflora sublanceolata x HD13-133). GISH was performed using genomic probes prepared with the DNA from the paternal genitor, whereas the maternal DNA was used as blocking DNA and employed at various concentrations (20X, 40X, 60X, and 100X) in relation to the probe concentration. At the same time, GISH was applied with the use of simultaneous probes from both genomes, paternal and maternal, that were detected with avidin-FITC and anti-digoxigenin-rhodamine, respectively. Both methodologies allowed the distinguishing of the maternal and paternal genomes, thus confirming the hybrid nature of all the analyzed genotypes. Furthermore, the presence of recombinant chromosomes in BC1 hybrids revealed the occurrence of meiotic recombination in HD13 hybrids. This application of the GISH technique is an important step towards genomic analyses of Passiflora hybrids: it can broaden the phylogenetic and evolutionary studies of the genus and, at the same time, contribute to breeding programs.

In the Americas’ leading cocoa-producing countries, more productive clonal cultivars than traditional biclonal hybrids have been created. In Brazil, several disease-resistant and self-compatible clones such as PS 1319, FA 13, and SJ 02 have been selected on producer farms. The CCN 51 clone from Ecuador is also significant in Brazil. This study aimed to analyze these clones concerning their genetic structures using single-nucleotide polymorphisms, productive potential, disease resistance, and the physico-chemical and organoleptic characteristics of the beans. Clone SJ 02 has ancestry from Contamana (40.7%), Iquitos (34.5%), and Amelonado (23.5%). PS 1319 is primarily Amelonado (67.9%), with Criollo (15.7%) and Contamana (15.6%). FA 13 mainly consists of Amelonado (53.5%) and Iquitos (44.1%). Local cultivars of Bahia are mostly Amelonado, with 99.8% in Comum and Parazinho, 97.4% in Maranhão, and 95.5% in Pará. PS 1319, SJ 02, and FA 13 clones were significantly more productive than CCN 51 but did not differ in disease resistance levels. Significant differences were noted among the cultivars in physicochemical traits (fat, caffeine, and theobromine content). Sensorially, SJ 02 outperformed the other cultivars and was comparable to the reference clone BN 34. The findings indicate that Brazil’s elite clones, derived from complex crosses involving Amelonado, Contamana, Iquitos, and Criollo groups, are productive, resistant, and exhibit favorable physico-chemical and organoleptic qualities, making them valuable for future clonal breeding programs.