Abstract
BackgroundCucumber 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.ResultsFrom 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.ConclusionsCucumber 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.
Highlights
Cucumber is an important vegetable crop that is susceptible to many pathogens, but no disease resistance (R) genes have been cloned
The Basic local alignment search tool (BLAST) alignment result is summarized in Characterization of nucleotide binding (NB)-containing R gene sequences in Gy14 cucumber genome Seventy non-redundant NB-encoding R gene homolog (RGH) were identified in the cucumber Gy14 draft genome
It seems all RGHs presented in the cucumber genome as single copy because BLAST alignment against the Gy14 draft genome assembly didn’t find any paralogs for each RGH sequence
Summary
Cucumber is an important vegetable crop that is susceptible to many pathogens, but no disease resistance (R) genes have been cloned. 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. The largest class of known R genes encodes proteins with a central nucleotide binding (NB) domain and a C-terminal leucine-rich repeat (LRR) domain [1]. The LRR domain contains tandemly arrayed repeats that is involved in the specific recognition of pathogen effectors [3]. Both TIR and CC domains are assumed to be involved in protein-protein interactions and signal transduction [4,5]
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