BackgroundPlant nucleotide-binding site (NBS)-leucine-rich repeat (LRR) proteins encoded by resistance genes play an important role in the responses of plants to various pathogens, including viruses, bacteria, fungi, and nematodes. In this study, a comprehensive analysis of NBS-encoding genes within the whole cucumber genome was performed, and the phylogenetic relationships of NBS-encoding resistance gene homologues (RGHs) belonging to six species in five genera of Cucurbitaceae crops were compared.ResultsCucumber has relatively few NBS-encoding genes. Nevertheless, cucumber maintains genes belonging to both Toll/interleukine-1 receptor (TIR) and CC (coiled-coil) families. Eight commonly conserved motifs have been established in these two families which support the grouping into TIR and CC families. Moreover, three additional conserved motifs, namely, CNBS-1, CNBS-2 and TNBS-1, have been identified in sequences from CC and TIR families. Analyses of exon/intron configurations revealed that some intron loss or gain events occurred during the structural evolution between the two families. Phylogenetic analyses revealed that gene duplication, sequence divergence, and gene loss were proposed as the major modes of evolution of NBS-encoding genes in Cucurbitaceae species. Compared with NBS-encoding sequences from the Arabidopsis thaliana genome, the remaining seven TIR familes of NBS proteins and RGHs from Cucurbitaceae species have been shown to be phylogenetically distinct from the TIR family of NBS-encoding genes in Arabidopsis, except for two subfamilies (TIR4 and TIR9). On the other hand, in the CC-NBS family, they grouped closely with the CC family of NBS-encoding genes in Arabidopsis. Thus, the NBS-encoding genes in Cucurbitaceae crops are shown to be ancient, and NBS-encoding gene expansions (especially the TIR family) may have occurred before the divergence of Cucurbitaceae and Arabidopsis.ConclusionThe results of this paper will provide a genomic framework for the further isolation of candidate disease resistance NBS-encoding genes in cucumber, and contribute to the understanding of the evolutionary mode of NBS-encoding genes in Cucurbitaceae crops.

BackgroundTrichomes, developed from the protodermal cells (the outermost cell layer of the embryo), are hair-like structures covering the aerial parts of plants. The genetic network regulating trichome development has been extensively studied and well understood in the model species Arabidopsis thaliana, which bears unicellular, non-glandular and branched trichomes. However, little is known about the genetic and molecular basis of organogenesis of multi-cellular trichomes in plant species like cucumber (Cucumis sativus L.), which are likely different from Arabidopsis.ResultsWe identified a new trichome mutant in cucumber which exhibited a completely glabrous phenotype on all aerial organs. Genetic analysis indicated that the glabrous phenotype was inherited as a single recessive gene, csgl3. Fine genetic mapping delimited the csgl3 locus into a 68.4 kb region with 12 predicted genes. Genetic analysis, sequence alignment and allelic variation survey in natural populations identified Csa6G514870 encoding a class IV homeodomain-associated leucine zipper (HD-ZIP) transcription factor as the only candidate for CsGL3, which was 5188 bp in length with 10 predicted exons. Gene expression analysis revealed the loss-of-function of CsGL3 in the mutant due to the insertion of a 5-kb long terminal repeat (LTR) retrotransposon in the 4th exon of CsGL3. Linkage analysis in a segregating population and gene expression analysis of the CsGL1 and CsGL3 genes in csgl1, csgl3, and csgl1 + 3 genetic backgrounds uncovered interactions between the two genes. Phylogenetic analysis among 28 class IV HD-ZIP protein sequences from five species placed cucumber CsGL3 into the same clade with 7 other members that play important roles in trichome initiation.ConclusionsThe new glabrous mutation in cucumber was controlled by a single recessive locus csgl3, which was phenotypically and genetically distinct from two previously reported glabrous mutants csgl1 and csgl2. The glabrous phenotype in csgl3 was due to insertion of an autonomous, active, class I transposable element in CsGL3, a class IV HD-ZIP transcription factor. CsGL3 was epistatic to CsGL1. CsGL3 seemed to play important roles in cucumber trichome initiation whereas CsGL1 may act downstream in the trichome development pathway(s). Findings from the present study provide new insights into genetic control of trichome development in cucumber.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0693-0) contains supplementary material, which is available to authorized users.

Comparative genetic mapping revealed the origin of Xishuangbanna cucumber through diversification selection after domestication. QTL mapping provided insights into the genetic basis of traits under diversification selection during crop evolution. The Xishuangbanna cucumber, Cucumis sativus L. var. xishuangbannanesis Qi et Yuan (XIS), is a semi-wild landrace from the tropical southwest China with some unique traits that are very useful for cucumber breeding, such as tolerance to low light, large fruit size, heavy fruit weight, and orange flesh color in mature fruits. In this study, using 124 recombinant inbred lines (RILs) derived from the cross of the XIS cucumber with a cultivated cucumber inbred line, we developed a linkage map with 269 microsatellite (or simple sequence repeat) markers which covered 705.9 cM in seven linkage groups. Comparative analysis of orders of common marker loci or marker-anchored draft genome scaffolds among the wild (C. sativus var. hardwickii), semi-wild, and cultivated cucumber genetic maps revealed that the XIS cucumber shares major chromosomal rearrangements in chromosomes 4, 5, and 7 between the wild and cultivated cucumbers suggesting that the XIS cucumber originated through diversifying selection after cucumber domestication. Several XIS-specific minor structural changes were identified in chromosomes 1 and 6. QTL mapping with the 124 RILs in four environments identified 13 QTLs for domestication and diversifying selection-related traits including 2 for first female flowering time (fft1.1, fft6.1), 5 for mature fruit length (fl1.1, fl3.1, fl4.1, fl6.1, and fl7.1), 3 for fruit diameter (fd1.1, fd4.1, and fd6.1), and 3 for fruit weight (fw2.1, fw4.1, and fw6.1). Six of the 12 QTLs were consistently detected in all four environments. Among the 13 QTLs, fft1.1, fl1.1, fl3.1, fl7.1, fd4.1, and fw6.1 were major-effect QTLs for respective traits with each explaining at least 10 % of the observed phenotypic variations. Results from this study provide insights into the cytological and genetic basis of crop evolution leading to the XIS cucumber. The molecular markers associated with the QTLs should be useful in exploring the XIS cucumber genetic resources for cucumber breeding.

Cucumber, Cucumis sativus L. (2n = 2x = 14), is an important vegetable crop worldwide. It was the first specialty crop with a publicly available draft genome. Its relatively small, diploid genome, short life cycle, and self-compatible mating system offers advantages for genetic studies. In recent years, significant progress has been made in molecular mapping, and identification of genes and QTL responsible for key phenotypic traits, but a systematic review of the work is lacking. Here, we conducted an extensive literature review on mutants, genes and QTL that have been molecularly mapped or characterized in cucumber. We documented 81 simply inherited trait genes or major-effect QTL that have been cloned or fine mapped. For each gene, detailed information was compiled including chromosome locations, allelic variants and associated polymorphisms, predicted functions, and diagnostic markers that could be used for marker-assisted selection in cucumber breeding. We also documented 322 QTL for 42 quantitative traits, including 109 for disease resistances against seven pathogens. By alignment of these QTL on the latest version of cucumber draft genomes, consensus QTL across multiple studies were inferred, which provided insights into heritable correlations among different traits. Through collaborative efforts among public and private cucumber researchers, we identified 130 quantitative traits and developed a set of recommendations for QTL nomenclature in cucumber. This is the first attempt to systematically summarize, analyze and inventory cucumber mutants, cloned or mapped genes and QTL, which should be a useful resource for the cucurbit research community.