title: Integrated analysis in bi-parental and natural populations reveals CsCLAVATA3 (CsCLV3) underlying carpel number variations in cucumber.
abstract: Carpel number variation in cucumber was controlled by a single gene, Cn . Linkage and association analysis revealed CsCLV3 as the candidate gene of the Cn locus. Carpel number (CN) is an important fruit quality trait of cucumber, but the genetic basis of CN variations is largely unknown. In the present study, segregating analysis in multiple bi-parental mapping populations (F2, F3, and RILs) derived from WI2757 (CN = 3) × True Lemon (CN = 5) suggested that CN is controlled by a simply inherited gene, Cn, with CN = 3 being incompletely dominant to CN = 5. Initial linkage mapping located Cn in a 1.9-Mb region of cucumber chromosome 1. Exploration of DNA sequence variations in this region with in silico bulked segregant analysis among eight re-sequenced lines allowed delimiting the Cn locus to a 16-kb region with five predicted genes including CsCLV3, a homolog of the Arabidopsis gene CLAVATA3. Fine genetic mapping in F2 and RIL populations and association analysis in natural populations confirmed CsCLV3 as the candidate gene for Cn, which was further evidenced from gene expression analysis and microscopic examination of floral meristem size in the two parent lines. This study highlights the importance of integrated use of linkage and association analysis as well as next-gen high-throughput sequencing in mapping and cloning genes that are difficult in accurate genotyping. The results provide new insights into the genetic control of CN variations in cucumber, which were discussed in the context of the well-characterized CLAVATA pathway for stem cell homeostasis and regulation of meristem sizes in plants. The associations of carpel number with fruit shape, size, and weight in cucumber and melon are also discussed.
authors.affiliation: Horticulture College, Shanxi Agricultural University, Taigu, 030801, China.|Horticulture Department, University of Wisconsin, Madison, WI, 53706, USA.
authors.forename: Sen
authors.initials: S
authors.lastname: Li
authors.affiliation: Horticulture Department, University of Wisconsin, Madison, WI, 53706, USA.|Horticulture College, Northwest A&F University, Yangling, 712100, China.
authors.forename: Yupeng
authors.initials: Y
authors.lastname: Pan
authors.affiliation: Horticulture Department, University of Wisconsin, Madison, WI, 53706, USA.|Beijing Vegetable Research Center and National Engineering Research Center for Vegetables, Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, China.
authors.forename: Changlong
authors.initials: C
authors.lastname: Wen
authors.affiliation: Horticulture Department, University of Wisconsin, Madison, WI, 53706, USA.|Horticulture College, Northwest A&F University, Yangling, 712100, China.
authors.forename: Yuhong
authors.initials: Y
authors.lastname: Li
authors.affiliation: Department of Vegetable Sciences, China Agricultural University, Beijing, 100193, China.
authors.forename: Xiaofeng
authors.initials: X
authors.lastname: Liu
authors.affiliation: Department of Vegetable Sciences, China Agricultural University, Beijing, 100193, China.
authors.forename: Xiaolan
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Division of Vegetable Science, Indian Agricultural Research Institute, New Delhi, 10012, India.
authors.forename: Tusar K
authors.initials: TK
authors.lastname: Behera
authors.affiliation: Horticulture College, Shanxi Agricultural University, Taigu, 030801, China.
authors.forename: Guoming
authors.initials: G
authors.lastname: Xing
authors.affiliation: Horticulture Department, University of Wisconsin, Madison, WI, 53706, USA. weng4@wisc.edu.|USDA-ARS, Vegetable Crops Research Unit, 1575 Linden Drive, Madison, WI, 53706, USA. weng4@wisc.edu.
authors.forename: Yiqun
authors.initials: Y
authors.lastname: Weng
mesh_terms: D002874:Chromosome Mapping; D032461:Chromosomes, Plant; D003433:Crosses, Genetic; D018553:Cucumis sativus / Q000235:genetics*; D018744:DNA, Plant / Q000235:genetics; D005638:Fruit / Q000254:growth & development*; D017343:Genes, Plant; D008040:Genetic Linkage; D056426:Genetic Loci; D005819:Genetic Markers; D018895:Microsatellite Repeats; D010641:Phenotype; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide
chemical_list: D018744:DNA, Plant; D005819:Genetic Markers