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Transcriptome landscape reveals the molecular mechanisms involved in the improvement of fruit traits by the grafting of watermelon and bottle gourd. Grafting has been used as a sustainable alternative for watermelon breeding to control soil-borne pathogens and to increase tolerance to various abiotic stresses. However, some reports have shown that grafting can negatively affect the quality of fruits. Despite several field studies on the effects of grafting on fruit quality, the regulation of this process at the molecular level has not been revealed. The aim of this study was to elucidate various molecular mechanisms involved in different tissues of heterografted watermelon and bottle gourd plants. Grafting with bottle gourd rootstock increased the size and rind thickness of watermelon fruits, whereas that with watermelon rootstock produced bottle gourd fruits with higher total soluble solid content and thinner rinds. Correspondingly, genes related to ripening, softening, cell wall strengthening, stress response and disease resistance were differentially expressed in watermelon fruits. Moreover, genes associated mainly with sugar metabolism were differentially expressed in bottle gourd fruits. RNA-seq revealed more than 400 mobile transcripts across the heterografted sets. More than half of these were validated from PlaMoM, a database for plant mobile macromolecules. In addition, some of these mobile transcripts contained a transfer RNA-like structure. Other RNA motifs were also enriched in these transcripts, most with a biological role based on GO analysis. This transcriptome study provided a comprehensive understanding of various molecular mechanisms underlying grafted tissues in watermelon.

Watermelon (Citrullus lanatus var. lanatus) is one of the most important vegetable crops in the world. Molecular markers have become the tools of choice for resolving watermelon taxonomic relationships and evolution. Increased numbers of single nucleotide polymorphism (SNP) markers together with simple sequence repeat (SSR) markers would be useful for phylogenetic analyses of germplasm accessions and for linkage mapping for marker-assisted breeding with quantitative trait loci and single genes. We aimed to construct a genetic map based on SNPs (generated by Illumina Veracode multiplex assays for genotyping) and SSR markers and evaluate relationships inferred from SNP genotypes between 130 watermelon accessions collected throughout the world. We incorporated 282 markers (232 SNPs and 50 SSRs) into the linkage map. The genetic map consisted of 11 linkage groups spanning 924.72 cM with an average distance of 3.28 cM between markers. Because all of the SNP-containing sequences were assembled with the whole-genome sequence draft for watermelon, chromosome numbers could be readily assigned for all the linkage groups. We found that 134 SNPs were polymorphic in 130 watermelon accessions chosen for diversity studies. The current 384-plex SNP set is a powerful tool for characterizing genetic relatedness and for developing medium-resolution genetic maps.

The 18S–28S and 5S rDNA sites are useful chromosome landmarks and provide valuable evidence about genome organization and evolution. This investigation was the first attempt to study the dynamics, distribution and directionality of rDNA gains and losses, as well as to understand the contribution of site number variation in the speciation of the genus Citrullus. In this study, we employed fluorescent in situ hybridization (FISH), using the18S–28S and 5S rDNA gene loci, to evaluate the differences between the (1) cultivated type watermelon C. lanatus var. lanatus (sweet watermelon), (2) the “bitter” desert watermelon C. colocynthis (colocynth) that is indigenous to the deserts of northern Africa, the Middle East and Asia, (3) the C. lanatus var. citroides (citron) “Tsamma” or “cow watermelon” that is known as and is indigenous to southern Africa, (4) and C. rehmii that thrive in the Namibian Desert. The FISH analyses showed that the sweet watermelon and colocynth have similar rDNA configuration. The sweet watermelon and colocynth genomes contain two 18S–28S rDNA gene loci, each located on a different chromosome, and one 5S rDNA locus which is co-localized with one of the 18S–28S rDNA gene loci. On the other hand, the C. rehmii has one 18S–28S rDNA locus and one 5S rDNA locus positioned on different chromosomes, while the citron has one18S–28S rDNA and two 5S rDNA loci, each located on a different chromosome. A FISH analysis of F1 (citron × sweet watermelon) chromosome spreads revealed uniparental homeologous rDNA gene copies pertaining to the sweet watermelon versus the citron chromosomes, with the sweet watermelon chromosome containing the 18S–28S and 5S rDNA locus versus the citron homologue chromosome that has the 5S rDNA locus, but not the 18S–28S rDNA locus. Genomic in situ hybridization (GISH) analysis, using the entire citron genome as a probe to be differentially hybridized on sweet watermelon chromosome spreads, revealed that the citron genomic probes mainly hybridize to subtelomeric and pericentromeric regions of the sweet watermelon chromosomes, suggesting extensive divergence between the citron and sweet watermelon genomes. The FISH and GISH cytogenetic analysis here indicate major differences in genome organization between the cultivated watermelon type sweet watermelon and its counterpart citron that thrive in southern Africa and considered a useful germplasm source for enhancing disease and pest resistance in watermelon cultivars.

Melon has tremendous fruit diversity, the product of complex interactions of consumer preferences in different countries and a wide range of agro-climatic zones. Understanding footprints of divergence underlying formation of various morphotypes is important for developing sustainable and high-quality melons. Basic understanding of population structure and linkage disequilibrium (LD) is limited in melon and has lagged behind other crops. Characterization of population structure and LD are essential for carrying out association mapping of quantitative trait loci (QTL) underlying various complex traits. Mapped single-locus microsatellite markers are known to be very valuable for resolving the population structure and 268 such markers were used in the current study to resolve population structure and LD pattern using 87 accessions of melons belonging to Eastern European, Euro-North American and Asian types. A mixed linear model was implemented to detect QTL for various fruit traits. Various levels of QTL with high to moderate stringency were detected for fruit shape, fruit weight, soluble solids, and rind pressure and a majority of them was found to be in agreement with the previously published data, indicating that association mapping can be very useful for melon molecular breeding. Minor discrepancies in the position, strength and the variation explained by the QTL present between the methods of association and recombinant mapping approaches can be bridged if more melon groups and larger sets of accessions are involved in future studies, combined with high-throughput marker panels.

Thirty-one accessions ofCitrullusspp. belonging toCitrullus lanatusvar.lanatus,C. lanatusvar.citroidesandCitrullus colocynthiswere subjected to phylogenetic analysis using combined datasets of amplified fragment length polymorphisms (AFLPs) and simple sequence repeats (SSRs). Tree topologies inferred by neighbour-joining analysis have resolved the phylogenic relationships among the species with special reference to established taxonomic classification. In this study, we have clearly resolved species boundaries of various taxa ofcitroides,lanatusandcolocynthisinto three well-supported clusters. Clustering pattern of principal component analysis with the shared polymorphisms using the subsets of data between any two taxon combinations helped to elucidate the introgression and interrelationships among the species. We report two major groups ofC. lanatustaxa, one of which has undergone wide introgressions with the taxa ofC. lanatusvar.citroidesandC. colocynthis. In this paper, we identified 583 AFLP bands that are polymorphic within the var.lanatusofC. lanatus, which is the largest set ever reported. The species-specific diagnostic SSRs and polymorphic AFLPs that are informative within and between the taxa reported in this paper would be immensely useful for future studies of these economically important genera.

Thirty-eight melon accessions, which are of primary breeding importance in the Ukraine, were analysed for diversity. These collections represent a major non-US and non-western Europe source of melon germplasm that have not yet been subjected to molecular characterization. Molecular diversity was estimated based on a robust set of 465 polymorphisms gathered by amplified fragment length polymorphisms and simple sequence repeats (SSR). In this paper, we report 12 newly developed polymorphic SSR primer pairs, and their use for molecular characterization in the Ukrainian melon collections. Based on these polymorphisms, we estimated similarity indices that ranged from 0.70 to 1.00 among various accessions. The phylogenetic tree based on the similarity indices and a three-dimensional plot of the first three vectors of the principal component analysis corresponded fairly well with the existing three classical morphotypes namelyaestivalis,europeusandhiemalis, under theconvarEuropeus, which is also known asadana. The polymorphisms generated in the current study, which are specific to the grouping of fruit types and days to maturity will be very useful for further genetic studies and marker-assisted selections.