Open Access Research article

A 1,681-locus consensus genetic map of cultivated cucumber including 67 NB-LRR resistance gene homolog and ten gene loci

Luming Yang1, Dawei Li12, Yuhong Li12, Xingfang Gu3, Sanwen Huang3, Jordi Garcia-Mas4 and Yiqun Weng15*

Author Affiliations

1 Horticulture Department, University of Wisconsin, Madison, WI 53706, USA

2 Horticulture College, Northwest A&F University, Yangling, 712100, China

3 Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100018, China

4 IRTA, Center for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Bellaterra, Barcelona, 08193, Spain

5 USDA-ARS Vegetable Crops Research Unit, Horticulture Department, University of Wisconsin, Madison, WI, 53706, USA

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BMC Plant Biology 2013, 13:53  doi:10.1186/1471-2229-13-53

Published: 25 March 2013

Additional files

Additional file 1:

DNA and peptide sequences of 70 NB-containing R gene homologs in the Gy14 genome (in fasta format).

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Additional file 2:

Including seven supplemental MS Excel tables (Table S1 to Table S7). Table S1. Information of 70 NB-containing RGH sequences in the Gy14 cucumber draft genome. Left and right markers are the closest flanking markers for each RGH. Map location indicates their positions on the high-density cucumber linkage map developed in the present study (Figure 2). Gy14V1.0 is the Gy14 draft genome assembly Version 1.0 [27]. Corresponding cucumber 9930 CDS data are from Li et al. (2011) [26]. Table S2. Expressed sequence tag (EST) representation of RGHs based on BLAST search of Gy14 leaf and root transcriptome assembly (//cucumber.vcru.wisc.edu/, Weng et al. unpublished data) and 9930 V2.0 transcript assembly derived from 10 tissues [26]. Table S3. BLAST alignment of cucumber RGH sequences and the melon draft genome showing sequence homology and syntenic blocks of RGH loci in the two genomes. Melon draft genome assembly and RGH annotation are from Garcia-Mas et al. (2012) [56]. Chr = chromosome. The melon scaffold positions of annotated RHG are approximations. Table S4. Information of 783 cucumber and melon markers placed on the high-resolution cultivated cucumber genetic map. Marker loci are arranged by increasing order of map locations in each linkage group (LG). The physical location of each marker in the new Gy14 draft genome assembly (Gy14_V1.0) [27], and the Gy14 scaffolds are also shown. The Gy14 V1.0 or Gy14 scaffold position is the first nucleotide-binding site of the left primer of each marker. Table S5. Markers with discrepancies in chromosomal locations between the Gy14 × 9930 F2 (CSS-F2) (Table S4), and the Gy14 × PI 183967 RIL (CSH-RIL) [42] or the 9110Gt × 9930 RIL (CSS-RIL) [45] maps. Table S6. Spearman’s rank of correlation (r) of marker orders among the three component maps and the final integrated map. Table S7. Information of 1,681 cucumber and melon markers on the consensus cucumber genetic map. Marker loci were arranged by increasing order of map locations in each chromosome (CHR). The physical location of each marker in the new Gy14 whole genome assembly (Gy14_Chr_V1.0), and their positions in the original 9930 and Gy14 scaffolds are also shown. Bins indicate marker loci that were selected from component maps for bin map construction prior to map integration. Chr_source, cM_source and Map_source were LG, map position (in cM) and reference of three component maps from which each marker was employed.

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Additional file 3:

Supplemental data file including three supplemental figures (Figure S1 to Figure S3). Figure S1. Distribution of 70 NB domain-containing RGHs across seven cucumber chromosomes in the Gy14 genome. Figure S2. Graphic view of colinearity of common markers among three cucumber linkages used for consensus map construction. MapA = Gy14 × PI 183967 RIL (CSH-RIL) [42]; MapB = Gy14 × 9930 F2 (CSS-F2 map) (Additional file 2: Table S4, this study); MapC = 9110Gt × 9930 RIL (CSS-RIL) [45]. The graphs were drawn with the Circos software package (http://circos.ca/) [70]. Figure S3. Graphic view of consensus bin map of cucumber, which was developed from integration of three individual maps of Gy14 × 9930 F2 (CSS-F2) (Additional file 2: Table S4, this study), Gy14 × PI 183967 RIL (CSH-RIL) [42] and 9110Gt × 9930 RIL (CSS-RIL) [45] with JoinMap 3.0. Numbers on top of the map are linkage groups (LG) (1 through 7) which also correspond to chromosomes numbers. Cumulative map distance (cM) is shown to the left of each linkage group and marker designation is on the right.

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