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

Author
item YANG, LUMING - University Of Wisconsin
item LI, DAWEI - University Of Wisconsin
item LI, YUHONG - University Of Wisconsin
item GU, XINGFANG - Chinese Academy Of Agricultural Sciences
item HUANG, SANWEN - Chinese Academy Of Agricultural Sciences
item GARCIA-MAS, JORDI - Autonomous University Of Barcelona
item Weng, Yiqun

Submitted to: BMC Plant Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/11/2013
Publication Date: 3/25/2013
Citation: Yang, L., Li, D., Li, Y., Gu, X., Huang, S., Garcia-Mas, J., Weng, Y. 2013. A 1,681-locus consensus genetic map of cultivated cucumber including 67 NB-LRR resistance gene homolog and ten gene loci. Biomed Central (BMC) Plant Biology. 13(53):1-14.

Interpretive Summary: Most disease resistance (R) genes cloned so far in plants encode proteins with the nucleotide binding and leucine-rich repeat (NB-LRR) domains. Cucumber is an important vegetable crop that is susceptible to many pathogens, but very few R genes have been cloned. The availability of draft genome sequences provides an excellent opportunity for genome wide identification and characterization of the NB-LRR type R gene homolog (RGH) sequences in cucumber. Genetic and physical mapping of these RGHs will facilitate map-based cloning or association mapping of disease resistance genes. However, cultivated cucumber has a very narrow genetic base making it difficult to develop high-density genetic maps. Development of a consensus map is a method of choice to increase marker density. In this study, we identified, characterize and genetically mapped NB-LRR type RGHs and developed a high-density consensus genetic map for cultivated cucumber. From the Gy14 cucumber draft genome, 70 NB-containing RGHs were identified and characterized for R gene domain features (LRR, and TIR/CC). Fifty-two of the 70 RGHs were in clusters and their distribution across seven cucumber chromosomes was highly uneven. In silico analysis indicated that all 70 RGHs had EST support for gene expression. Comparative analysis unveiled high-degree homology in sequences and synteny in chromosomal locations of these RGH members between the cucumber and melon genomes. All 70 RGH loci were placed onto a high-density genetic map through linkage analysis. A 1,681-locus consensus map of cultivated cucumber was developed by integrating three component maps through a bin-mapping strategy. This integrated genetic map consisted of 1,641 marker, 70 RGH and 10 gene loci spanning 730.0 cM in seven linkage groups. Physically, 308 scaffolds with a total 193.2 Mbp DNA sequences were anchored onto this consensus genetic map that covered 52.6% of the 367 Mbp cucumber genome. Results from this study should be valuable genomics resources for the cucurbit research community which will provide a genomic framework for quantitative trait loci identification, map-based gene cloning, assessment of genetic diversity, association mapping, as well as marker-assisted selection in molecular breeding in cucumber.

Technical Abstract: The two objectives of the present study were to identify, characterize and map NB-LRR type resistance gene homologs (RGHs) in the cucumber genome, and to develop a high-density consensus genetic map for cultivated cucumber integrating all RGH loci identified herein. From the Gy14 cucumber draft genome, 70 NB-containing RGHs were identified and characterized for R gene domain features (LRR, and TIR/CC). Fifty-two of the 70 RGHs were in clusters and their distribution across seven cucumber chromosomes was highly uneven. In silico analysis indicated that all 70 RGHs had EST support for gene expression. Comparative analysis unveiled high-degree homology in sequences and synteny in chromosomal locations of these RGH members between the cucumber and melon genomes. All 70 RGH loci were placed onto a high-density genetic map through linkage analysis. A 1,681-locus consensus map of cultivated cucumber was developed by integrating three component maps through a bin-mapping strategy. This integrated genetic map consisted of 1,641 marker, 70 RGH and 10 gene loci spanning 730.0 cM in seven linkage groups. Physically, 308 scaffolds with a total 193.2 Mbp DNA sequences were anchored onto this consensus genetic map that covered 52.6% of the 367 Mbp cucumber genome. Results from this study should be valuable genomics resources for the cucurbit research community which will provide a genomic framework for quantitative trait loci identification, map-based gene cloning, assessment of genetic diversity, association mapping, as well as marker-assisted selection in molecular breeding in cucumber.