Cucurbita pepo is a highly polymorphic species. The cultivars can be grouped into eight morphotypes in two subspecies, ssp. pepo and ssp. ovifera. A collection of 69 accessions representative of the morphotypes and some unclassified types was used for analysing the morphological and molecular diversity of this species. This collection includes commercial cultivars and Spanish landraces, which represent the great diversification of types that have arisen in Europe after this species arrived from America. For the molecular variability studies, two PCR-based systems were employed, AFLP and SRAP, which preferentially amplify ORFs. Principal coordinates analysis and cluster analysis using the UPGMA method clearly separate the accessions into the two subspecies through the use of both markers. However, the gene diversity and the genetic identity values among morphotypes and subspecies varied between the two marker systems. The information given by SRAP markers was more concordant to the morphological variability and to the evolutionary history of the morphotypes than that of AFLP markers. In ssp. ovifera, the accessions of the different morphotypes were basically grouped according to the fruit colour. This may indicate different times of development and also the extent of breeding in the accessions used. This study has allowed identification of new types that can be employed for the development of new cultivars. The landraces of the spp. ovifera, used as ornamental in Europe, have proved to be of great interest for preserving the diversity of C. pepo.

SummaryThe Cucurbita genus (squashes, pumpkins and gourds) includes important domesticated species such as C. pepo, C. maxima and C. moschata. In this study, we present a high‐quality draft of the zucchini (C. pepo) genome. The assembly has a size of 263 Mb, a scaffold N50 of 1.8 Mb and 34 240 gene models. It includes 92% of the conserved BUSCO core gene set, and it is estimated to cover 93.0% of the genome. The genome is organized in 20 pseudomolecules that represent 81.4% of the assembly, and it is integrated with a genetic map of 7718 SNPs. Despite the small genome size, three independent lines of evidence support that the C. pepo genome is the result of a whole‐genome duplication: the topology of the gene family phylogenies, the karyotype organization and the distribution of 4DTv distances. Additionally, 40 transcriptomes of 12 species of the genus were assembled and analysed together with all the other published genomes of the Cucurbitaceae family. The duplication was detected in all the Cucurbita species analysed, including C. maxima and C. moschata, but not in the more distant cucurbits belonging to the Cucumis and Citrullus genera, and it is likely to have occurred 30 ± 4 Mya in the ancestral species that gave rise to the genus.

Cucurbits are major crop species, including fruits and vegetables cultivated worldwide that supply essential vitamins and minerals to current diets in developed and developing countries. Viral diseases are main factors affecting cucurbits cultivation. The most widespread and damaging have been aphidborne viruses belonging to the Potyviridae family. Whitefly-transmitted begomoviruses (Geminiviridae) have been identified more recently in different cucurbit species. A severe outbreak of Tomato leaf curl New Delhi virus (ToLCNDV) occurred in pumpkins and melons in the main production area of Southern Spain in 2012-2014. We developed a mechanical inoculation method to facilitate the screening of germplasm against this virus. Mechanical transmission with this method was confirmed in 4 genera and 13 species of the family, including the main crops, cucumber, melon, watermelon and pumpkins, and also croprelated exotic germplasm (landraces and wild species) used for cucurbits breeding. Diversity in the response was observed within and among species. Tolerance to mechanical transmission of ToLCNDV was identified in melon, within Cucumis melo subsp. agrestis var. momordica and in wild agrestis accessions. All the tolerant accessions came from India, the country in which this virus was firstly reported. Some of these accessions have been previously reported to be tolerant or resistant to other viruses and as they are fully crossable to commercial melons, they are good sources to develop new melon varieties with tolerance to ToLCNDV.

to this area as a probable center of domestication for this species (Nee, 1990;Sanjur et al., 2002; Wessel-Beaver, Cucurbita moschata (Duchesne ex Lam.) Duchesne ex Poir. is an 2000). Two independent domestication events in Mexico important crop in tropical areas. In Spain, the cultivation of this species is mainly based on landraces maintained for centuries. The Center and northern South America have also been proposed for Conservation and Breeding of Agricultural Diversity (COMAV) (Decker-Walters and Walters, 2000; Robinson and maintains a germplasm collection with about 250 C. moschata land-Decker-Walters, 1997). Furthermore, the absence of races, primarily from the Canary Islands and the Spanish peninsula, known wild species closely related to C. moschata inincluding some accessions from Central and South America. The creases the confusion concerning the site of domesticamorphological characterization of 47 accessions showed considerable tion. The wild species C. lundelliana L.H. Bailey, convariability, comparable to that found in different C. moschata centers fined to the Yucatan peninsula, and initially considered of diversity. Molecular analysis using AFLP (amplified fragment as the ancestor of C. moschata, does not seem to be so length polymorphism) markers, which analyze neutral genetic diverclosely related to the cultivated species according to sity, and SRAP (sequence-related amplified polymorphism) markers, morphological, isozymatic, and crossability studies (Merwhich preferentially amplify gene regions, showed a genetic diversity concordant with the morphological variability. With both markers, rick, 1990). It is currently thought that the wild progenithe accessions clustered according to geographical origin: Central tor of C. moschata was derived from a wild taxon closely America, South America, and Spain, suggesting the existence of two related to C. argyrosperma ssp. sororia (L.H. Bailey) independent domestications in both American areas, and/or intro-Merrick & Bates. However, these two species show difgressions from related species. In the principal coordinate analysis ferent isozyme patterns and reproductive barriers (Sanjur (PCoA), the Central and South American accessions grouped toet al., 2002). Decker-Walters and Walters (2000) suggest gether by AFLPs, separately from the Spanish ones, while with SRAP that the analysis of some wild squashes in Bolivia could the South American accessions grouped separately from the other shed some light on the study of the origin of C. moschata. accessions. This could be due to the different information providedThe cultivation of C. moschata soon spread to northby each marker system. The SRAP results agree with the more primieastern Mexico (ෂ3400 BP) and to southwestern USA tive traits showed by the South American landraces. In addition, the accessions from the Canary Islands grouped separately from those Center for Conservation and Breeding of the Agricultural DiversityCanary Islands, where this species is highly appreciated

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Tomato leaf curl New Delhi virus (ToLCNDV) is a bipartite begomovirus (family Geminiviridae) first reported in India and its neighbouring countries. ToLCNDV severely affects zucchini crop (Cucurbita pepo) in the main production areas of Southern Spain since 2012. This emerging begomovirus is a serious threat to this and other cucurbit crops. Breeding resistant cultivars is the most promising method for disease control, but requires the identification of sources of resistance in the Cucurbita genus. In this work, we screened for ToLCNDV resistance a large collection of Cucurbita spp. accessions, including landraces and commercial cultivars of the main cultivated species, C. pepo, Cucurbita moschata and Cucurbita maxima and wild species. The screening was performed using mechanical and whitefly inoculation. The level of resistance was assessed by scoring symptom severity and by measuring the virus content with quantitative polymerase chain reaction in selected genotypes. Diversity in the response was observed within and among species. Severe symptoms and high viral amounts were found at 30 days after mechanical and whitefly inoculation in C. pepo, in all accessions belonging to the Zucchini morphotype and to other morphotypes of both subspecies, pepo and ovifera, and even in the wild relative Cucurbita fraterna. C. maxima was also highly susceptible. This species showed characteristic symptoms of leaf decay and intense yellowing, different from those of mosaic, curling and internode shortening found in C. pepo. The only species showing resistance was C. moschata. Four accessions were symptomless or had some plants with only mild symptoms after three independent rounds of mechanical inoculation with different inoculum sources. Two of them also remained symptomless after virus inoculation with viruliferous whiteflies. ToLCNDV was detected in these asymptomatic accessions at 15 and 30 days post inoculation, but viral amounts were much lower than those found in susceptible genotypes, suggesting a high level of resistance. The symptoms in the susceptible accessions of this species were also different, with a characteristic leaf mottling, evolving to a severe mosaic. The newly identified C. moschata resistant accessions are good candidates for breeding programmes to avoid the damage caused by ToLCNDV.

Identification of three genomic regions and underlying candidate genes controlling the high level of resistance to ToLCNDV derived from a wild melon. SNP markers appropriated for MAS management of resistance. Tomato leaf curl New Delhi virus (ToLCNDV) is a bipartite begomovirus that severely affects melon crop (Cucumis melo) in the main production areas of Spain since 2012. In this work, we evaluated the degree of resistance of four accessions (two belonging to the subsp. agrestis var. momordica and two to the wild agrestis group) and their corresponding hybrids with a susceptible commercial melon belonging to the subsp. melo (Piel de Sapo, PS). The analysis using quantitative PCR (qPCR) allowed us to select one wild agrestis genotype (WM-7) with a high level of resistance and use it to construct segregating populations (F and backcrosses). These populations were phenotyped for symptom severity and virus content using qPCR, and genotyped with different sets of SNP markers. Phenotyping and genotyping results in the F and BC1s populations derived from the WM-7 × PS cross were used for QTL analysis. Three genomic regions controlling resistance to ToLCNDV were found, one major locus in chromosome 11 and two additional regions in chromosomes 12 and 2. The highest level of resistance (no or mild symptoms and very low viral titer) was obtained with the homozygous WM-7WM-7 genotype at the major QTL in chromosome 11, even with PSPS genotypes at the other two loci. The resistance derived from WM-7 is useful to develop new melon cultivars and the linked SNPs selected in this paper will be highly useful in marker-assisted breeding for ToLCNDV resistance in melon.

The Cucurbita genus (squashes, pumpkins, gourds) includes important domesticated species such as C. pepo, C. maxima and C. moschata . In this study, we present a high-quality draft of the zucchini ( C. pepo ) genome. The assembly has a size of 263 Mb, a scaffold N50 of 1.8 Mb, 34,240 gene models, includes 92% of the conserved BUSCO core gene set, and it is estimated to cover 93.0% of the genome. The genome is organized in 20 pseudomolecules, that represent 81.4% of the assembly, and it is integrated with a genetic map of 7,718 SNPs. Despite its small genome size three independent evidences support that the C. pepo genome is the result of a Whole Genome Duplication: the topology of the gene family phylogenies, the karyotype organization, and the distribution of 4DTv distances. Additionally, 40 transcriptomes of 12 species of the genus were assembled and analyzed together with all the other published genomes of the Cucurbitaceae family. The duplication was detected in all the Cucurbita species analyzed, including C. maxima and C. moschata , but not in the more distant cucurbits belonging to the Cucumis and Citrullus genera, and it is likely to have happened 30 ± 4 Mya in the ancestral species that gave rise to the genus.All rights reserved. No reuse allowed without permission.(which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.