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. 2013 Mar 25;13:53.
doi: 10.1186/1471-2229-13-53.

A 1,681-locus Consensus Genetic Map of Cultivated Cucumber Including 67 NB-LRR Resistance Gene Homolog and Ten Gene Loci

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Free PMC article

A 1,681-locus Consensus Genetic Map of Cultivated Cucumber Including 67 NB-LRR Resistance Gene Homolog and Ten Gene Loci

Luming Yang et al. BMC Plant Biol. .
Free PMC article

Abstract

Background: Cucumber is an important vegetable crop that is susceptible to many pathogens, but no disease resistance (R) genes have been cloned. The availability of whole genome sequences provides an excellent opportunity for systematic identification and characterization of the nucleotide binding and leucine-rich repeat (NB-LRR) type R gene homolog (RGH) sequences in the genome. Cucumber has a very narrow genetic base making it difficult to construct high-density genetic maps. Development of a consensus map by synthesizing information from multiple segregating populations is a method of choice to increase marker density. As such, the objectives of the present study were to identify and characterize NB-LRR type RGHs, and to develop a high-density, integrated cucumber genetic-physical map anchored with RGH loci.

Results: From the Gy14 draft genome, 70 NB-containing RGHs were identified and characterized. Most RGHs were in clusters with uneven distribution across seven chromosomes. In silico analysis indicated that all 70 RGHs had EST support for gene expression. Phylogenetic analysis classified 58 RGHs into two clades: CNL and TNL. Comparative analysis revealed high-degree sequence homology and synteny in chromosomal locations of these RGH members between the cucumber and melon genomes. Fifty-four molecular markers were developed to delimit 67 of the 70 RGHs, which were integrated into a genetic map through linkage analysis. A 1,681-locus cucumber consensus map including 10 gene loci and spanning 730.0 cM in seven linkage groups was developed by integrating three component maps with a bin-mapping strategy. Physically, 308 scaffolds with 193.2 Mbp total DNA sequences were anchored onto this consensus map that covered 52.6% of the 367 Mbp cucumber genome.

Conclusions: Cucumber contains relatively few NB-LRR RGHs that are clustered and unevenly distributed in the genome. All RGHs seem to be transcribed and shared significant sequence homology and synteny with the melon genome suggesting conservation of these RGHs in the Cucumis lineage. The 1,681-locus consensus genetic-physical map developed and the RGHs identified and characterized herein are valuable genomics resources that may have many applications such as quantitative trait loci identification, map-based gene cloning, association mapping, marker-assisted selection, as well as assembly of a more complete cucumber genome.

Figures

Figure 1
Figure 1
Phylogram of the NB-LRR proteins in the Gy14 cucumber genome. The neighbor-joining tree was constructed with 58 NB-containing protein sequences using MEGA5 software. Sequences were trimmed to extract just the NB domain. One thousand bootstrap repetitions were used, and support value (in percentages) for each node is indicated on the branch.
Figure 2
Figure 2
Graphic view of high-density genetic map of cultivated cucumber developed with the Gy14 × 9930 F2 mapping population showing locations of 67 RGHs and molecular tags on the map. 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. RGH loci are in red. Markers in green are molecular tags for corresponding RGHs.

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