The Cucumber Genome PDF Download

Cucumis hystrix (2n = 2x = 24) is the only known species in the genus Cucumis that is cross-compatible with cucumber (C. sativus, 2n = 2x = 14) and has potentials for cucumber improvement. To facilitate introgression of C. hystrix chromatins into cucumber genetic background, we developed a draft genome assembly for C. hystrix (TH1 accession) which contained 16,865 scaffolds (~78x coverage) for a total of 226.0 Mb, representing ~51% of the estimated 447 Mb C. hystrix genome. Through genotyping-by-sequencing (GBS), a linkage map for C. hystrix was constructed with 1,692 SNP loci, which was then integrated with a previously developed genetic map with 410 SSR markers. The resulting consensus map consisted of 12 linkage groups spanning 1119 cM and anchor 1,321 scaffolds, accounting for 60.2 Mb or ~26.62% of C. hystrix draft genome assembly. A karyotype for the C. hystrix genome was developed with molecular cytogenetic landmarks which allowed for a better understanding of the syntenic relationships among C. hystrix, cucumber and melon (C. melo, 2n = 2x = 24) chromosomes as well as the mechanisms in which the seven cucumber chromosomes were evolved from an x=12 ancestor through dysploid chromosome reduction. C. hystrix introgression lines (IL) in elite cucumber backgrounds were developed through marker-assisted backcrossing. Overall, 334 ILs were identified by SSR markers to carry C. hystrix alleles. These ILs included different introgression segments that covered about 57.29% of C. hystrix map. With genotyping-by-sequencing (GBS), the introgressions in the 55 ILs included 44 syntenic blocks or about 74.57% coverage of C. hystrix genetic map. Each IL has an average 5.4 introgression segments, averaging 1.7 Mbp in size. Homoeologous recombination reduction was observed genome-wide but recombination hotspots in C. hystrix were also identified. Phenotypic characterization for resistance to angular leaf spot (ALS) and downy mildew (DM) pathogens was conducted in selected ILs. Both genotypic data and phenotypic data indicated that the intermediate resistance to ALS in nine ILs and the high resistance to DM in four ILs was of C. hystrix origin. These C. hystrix introgression lines, although time consuming in development, should be valuable resources for cucumber improvement.