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Title: Integrated analysis in bi-parental and natural populations reveals CsCLAVATA3 (CsCLV3) underlying carpel number variations in cucumber

Author
item LI, SEN - Shanxi University
item PAN, YUPENG - University Of Wisconsin
item WEN, CHANGLONG - University Of Wisconsin
item LI, YUHONG - University Of Wisconsin
item LIU, XIAOFENG - Agricultural University Of China
item ZHANG, XIAOLAN - Agricultural University Of China
item BEHERA, TUSAR - Indian Agricultural Research Institute
item XING, GUOMING - Shanxi University
item Weng, Yiqun

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/23/2015
Publication Date: 2/16/2016
Publication URL: https://handle.nal.usda.gov/10113/62377
Citation: Li, S., Pan, Y., Wen, C., Li, Y., Liu, X., Zhang, X., Behera, T.K., Xing, G., Weng, Y. 2016. Integrated analysis in bi-parental and natural populations reveals CsCLAVATA3 (CsCLV3) underlying carpel number variations in cucumber. Theoretical and Applied Genetics. 129(5):1007-1022. doi: 10.1007/s00122-016-2679-1.

Interpretive Summary: 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 carpel number 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. We then explored DNA sequence variations of this region with in silico bulked segregant analysis in eight re-sequenced lines, which allowed delimiting the Cn locus to a 16 kb region with 5 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. The expression of CsCLV3 in different organs was higher in CN=3 than that in CN=5 lines. The results provided new insights into the genetic control of carpel number variations in cucumber. This study highlighted 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 for accurate genotyping. Results were discussed in the context of the well characterized CLAVATA pathway for stem cell homeostasis and regulation of meristem sizes in plants. We also discussed possible associations of carpel numbers with fruit shape, size and weight in cucumber and melon.

Technical Abstract: Carpel number (CN) is an important fruit quality trait of cucumber, but the genetic basis of this trait in cucumber 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 carpel number is controlled by a simply inherited gene, Cn, with CN=3 being incompletely dominant to CN=5. Initial framework mapping located the Cn gene in a 1.9 Mb region of cucumber chromosome 1. We then explored DNA sequence variations of this region with bioinformatic tools in eight re-sequenced lines, which allowed delimiting the Cn locus to a 16 kb region with 5 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. The expression of CsCLV3 in different organs was higher in CN=3 than that in CN=5 lines. The results provided new insights into the genetic control of carpel number variations in cucumber. This study highlighted 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 for accurate genotyping. Results were discussed in the context of the well characterized CLAVATA pathway for stem cell homeostasis and regulation of meristem sizes in plants. We also discussed possible associations of carpel numbers with fruit shape, size and weight in cucumber and melon.