Identification of Fruit-Associated QTLs in Winter Squash (Cucurbita maxima Duchesne) Using Recombinant Inbred Lines.

Cucurbita maxima Duchesne squash and pumpkins are cultivated world-wide. Cucurbita maxima fruits are produced for fresh market and are valuable for food processing. Therefore, fruit characteristics and yield are the traits of high economic importance for breeders. To date, the genetic basis of fruit-associated traits in C. maxima have been poorly understood. In the present study, we evaluated fruit-associated traits and conducted quantitative trait locus (QTL) analysis using recombinant inbred lines (RILs) derived from a cross of two inbred lines with different fruit morphotypes. Phenotypic data for nine fruit traits (earliness, weight, number per plant, yield per plant, length and diameter, shape index, flesh thickness, sucrose content and dry matter content) were collected for RILs in two open-field experiments. Pairwise analysis of the phenotypic data revealed correlations among the fruit and yield-associated traits. Using a previously developed genetic map, we identified 26 QTLs for eight traits. The QTLs were found in 10 locations on eight chromosomes of C. maxima. The QTLs were detected across experiments and explained up to 41.4% of the observed phenotypic variations. Major-effect QTLs for multiple fruit-associated traits were clustered on chromosome 4, suggesting that this genomic region has been under selection during diversification and/or domestication of C. maxima.

Genetic mapping of psl locus and quantitative trait loci for angular leaf spot resistance in cucumber (Cucumis sativus L.).

One of the most important cucumber diseases is bacterial angular leaf spot (ALS), whose increased occurrence in open-field production has been observed over the last years. To map ALS resistance genes, a recombinant inbred line (RIL) mapping population was developed from a narrow cross of cucumber line Gy14 carrying psl resistance gene and susceptible B10 line. Parental lines and RILs were tested under growth chamber conditions as well as in the field for angular leaf spot symptoms. Based on simple sequence repeat and DArTseq, genotyping a genetic map was constructed, which contained 717 loci in seven linkage groups, spanning 599.7 cM with 0.84 cM on average between markers. Monogenic inheritance of the lack of chlorotic halo around the lesions, which is typical for ALS resistance and related with the presence of recessive psl resistance gene, was confirmed. The psl locus was mapped on cucumber chromosome 5. Two major quantitative trait loci (QTL) psl5.1 and psl5.2 related to disease severity were found and located next to each other on chromosome 5; moreover, psl5.1 was co-located with psl locus. Identified QTL were validated in the field experiment. Constructed genetic map and markers linked to ALS resistance loci are novel resources that can contribute to cucumber breeding programs.

Genetic mapping of ovary colour and quantitative trait loci for carotenoid content in the fruit of Cucurbita maxima Duchesne.

The high content of carotenoids, sugars, dry matter, vitamins and minerals makes the fruit of winter squash (Cucurbita maxima Duchesne) a valuable fresh-market vegetable and an interesting material for the food industry. Due to their nutritional value, long shelf-life and health protective properties, winter squash fruits have gained increased interest from researchers in recent years. Despite these advantages, the genetic and genomic resources available for C. maxima are still limited. The aim of this study was to use the genetic mapping approach to map the ovary colour locus and to identify the quantitative trait loci (QTLs) for high carotenoid content and flesh colour. An F6 recombinant inbred line (RIL) mapping population was developed and used for evaluations of ovary colour, carotenoid content and fruit flesh colour. SSR markers and DArTseq genotyping-by-sequencing were used to construct an advanced genetic map that consisted of 1824 molecular markers distributed across linkage groups corresponding to 20 chromosomes of C. maxima. Total map length was 2208 cM and the average distance between markers was 1.21 cM. The locus affecting ovary colour was mapped at the end of chromosome 14. The identified QTLs for carotenoid content in the fruit and fruit flesh colour shared locations on chromosomes 2, 4 and 14. QTLs on chromosomes 2 and 4 were the most meaningful. A correlation was clearly confirmed between fruit flesh colour as described by the chroma value and carotenoid content in the fruit. A high-density genetic map of C. maxima with mapped loci for important fruit quality traits is a valuable resource for winter squash improvement programmes.

The genome sequence of the North-European cucumber (Cucumis sativus L.) unravels evolutionary adaptation mechanisms in plants.

Cucumber (Cucumis sativus L.), a widely cultivated crop, has originated from Eastern Himalayas and secondary domestication regions includes highly divergent climate conditions e.g. temperate and subtropical. We wanted to uncover adaptive genome differences between the cucumber cultivars and what sort of evolutionary molecular mechanisms regulate genetic adaptation of plants to different ecosystems and organism biodiversity. Here we present the draft genome sequence of the Cucumis sativus genome of the North-European Borszczagowski cultivar (line B10) and comparative genomics studies with the known genomes of: C. sativus (Chinese cultivar--Chinese Long (line 9930)), Arabidopsis thaliana, Populus trichocarpa and Oryza sativa. Cucumber genomes show extensive chromosomal rearrangements, distinct differences in quantity of the particular genes (e.g. involved in photosynthesis, respiration, sugar metabolism, chlorophyll degradation, regulation of gene expression, photooxidative stress tolerance, higher non-optimal temperatures tolerance and ammonium ion assimilation) as well as in distributions of abscisic acid-, dehydration- and ethylene-responsive cis-regulatory elements (CREs) in promoters of orthologous group of genes, which lead to the specific adaptation features. Abscisic acid treatment of non-acclimated Arabidopsis and C. sativus seedlings induced moderate freezing tolerance in Arabidopsis but not in C. sativus. This experiment together with analysis of abscisic acid-specific CRE distributions give a clue why C. sativus is much more susceptible to moderate freezing stresses than A. thaliana. Comparative analysis of all the five genomes showed that, each species and/or cultivars has a specific profile of CRE content in promoters of orthologous genes. Our results constitute the substantial and original resource for the basic and applied research on environmental adaptations of plants, which could facilitate creation of new crops with improved growth and yield in divergent conditions.

The genetic basis of resistance to downy mildew in Cucumis spp.--latest developments and prospects.

Downy mildew, caused by the Oomycete pathogen Pseudoperonospora cubensis, is one of the most destructive diseases of cucumber (Cucumis sativus L.) and muskmelon (C. melo L.). Although the process of pathogenesis is well understood, there are few disease control options available. The development and deployment of resistant cultivars is generally considered to be the best approach to control downy mildew. The recently completed sequencing of the cucumber genome provides a great opportunity for reliable and thorough study of the sequence and function of resistance genes in the Cucurbitaceae, which will help us to understand the resistance mechanisms and metabolic pathways activated by these genes. It can be anticipated that, in the near future, we will have more information about the genetic bases of resistance to downy mildew in Cucumis, which will facilitate efforts to breed for resistance to this pathogen.