ORIGINAL PAPER Fine genetic mapping of cp: a recessive gene for compact (dwarf) plant architecture in cucumber, Cucumis sativus L. Yuhong Li • Luming Yang • Mamta Pathak • Dawei Li • Xiaoming He • Yiqun Weng Received: 10 April 2011 / Accepted: 13 June 2011 / Published online: 7 July 2011 Ó Springer-Verlag (outside the USA) 2011 Abstract The compact (dwarf) plant architecture is an important trait in cucumber (Cucumis sativus L.) breeding that has the potential to be used in once-over mechanical harvest of cucumber production. Compact growth habit is controlled by a simply inherited recessive gene cp. With 150 F 2:3 families derived from two inbred cucumber lines, PI 308915 (compact vining) and PI 249561 (regular vin- ing), we conducted genome-wide molecular mapping with microsatellite (simple sequence repeat, SSR) markers. A framework genetic map was constructed consisting of 187 SSR loci in seven linkage groups (chromosomes) covering 527.5 cM. Linkage analysis placed cp at the distal half of the long arm of cucumber Chromosome 4. Molecular markers cosegregating with the cp locus were identified through whole genome scaffold-based chromosome walking. Fine genetic mapping with 1,269 F 2 plants delimited the cp locus to a 220 kb genomic DNA region. Annotation and function pre- diction of genes in this region identified a homolog of the cytokinin oxidase (CKX) gene, which may be a potential candidate of compact gene. Alignment of the CKX gene homologs from both parental lines revealed a 3-bp deletion in the first exon of PI 308915, which can serve as a marker for marker-assisted selection of the compact phenotype. This work also provides a solid foundation for map-based cloning of the compact gene and understanding the molecular mech- anisms of the dwarfing in cucumber. Introduction Cucumber, Cucumis sativus L. (2n = 2x = 14) is an important specialty vegetable crop worldwide. In the United States, cucumber yield has been stagnant since the 1980s (Gusmini and Wehner 2008). With mixed results obtained when selecting directly for yield, it was proposed that the most effective approach to breeding for yield may be selecting for yield components with a higher heritability (Wehner 1989; Cramer and Wehner 2000). Such traits may include the number of harvests per plant, stem length, number of branches per plant, number of flowering nodes per branch, time to anthesis, percentage of pistillate flow- ers, and percentage of fruit set (Cramer and Wehner 2000). These traits can be manipulated to create various genotypes that possess an array of architectural habits. One such trait is the compact (dwarf) plant growth habit, which in cucumber generally refers to mutants with reduced vine length (or plant height). Several types of Communicated by Y. Xue. Electronic supplementary material The online version of this article (doi:10.1007/s00122-011-1640-6) contains supplementary material, which is available to authorized users. Y. Li Á D. Li Horticulture College, Northwest Agriculture & Forestry University, Yangling 712100, China Y. Li Á L. Yang Á M. Pathak Á D. Li Á X. He Á Y. Weng (&) Horticulture Department, University of Wisconsin, Madison, WI 53706, USA e-mail: weng4@wisc.edu; yiqun.weng@ars.usda.gov M. Pathak Department of Vegetable Crops, Punjab Agricultural University, Ludhiana 141 004, India X. He Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China Y. Weng USDA-ARS, Vegetable Crops Research Unit, 1575 Linden Drive, Madison, WI 53706, USA 123 Theor Appl Genet (2011) 123:973–983 DOI 10.1007/s00122-011-1640-6