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

BMC Plant Biology

Research Article

Luming Yang¹  Yuhong Li²  Dawei Li²  Yiqun Weng³  Jordi Garcia-Mas⁴  Xingfang Gu⁵  Sanwen Huang⁵ 

[1] Horticulture Department, University of Wisconsin, 53706, Madison, WI, USA;Horticulture Department, University of Wisconsin, 53706, Madison, WI, USA;Horticulture College, Northwest A&F University, 712100, Yangling, China;Horticulture Department, University of Wisconsin, 53706, Madison, WI, USA;USDA-ARS Vegetable Crops Research Unit, Horticulture Department, University of Wisconsin, 53706, Madison, WI, USA;IRTA, Center for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, 08193, Bellaterra, Barcelona, Spain;Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100018, Beijing, China;

关键词: Cucumber;    Cucumis sativus;    NB-LRR;    Resistance gene homolog;    Genetic mapping;    Comparative mapping;    Map integration;   

DOI  :  10.1186/1471-2229-13-53

 received in 2012-06-17, accepted in 2013-03-11,  发布年份 2013

来源: Springer

【 摘 要 】

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.

【 授权许可】

Unknown   
© Yang et al.; licensee BioMed Central Ltd. 2013. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.