Functional Copy Number Variation of CsSHINE1 is Associated with Fruit Skin Netting Intensity in Cucumber, Cucumis sativus

Authors: ZHANG, HUIJIUN - University Of Wisconsin; WANG, YUHUI - University Of Wisconsin; TAN, JUNYI - University Of Wisconsin; Weng, Yiqun

Submitted to: Journal of Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/11/2022
Publication Date: 5/7/2022
Citation: Zhang, H., Wang, Y., Tan, J., Weng, Y. 2022. Functional copy number variation of CsSHINE1 is associated with fruit skin netting intensity in cucumber, cucumis sativus. Journal of Theoretical and Applied Genetics. 135, pages2101–2119. https://doi.org/10.1007/s00122-022-04100-4.
DOI: https://doi.org/10.1007/s00122-022-04100-4

Interpretive Summary: Background: Fruit skin netting or reticulation in cucumber is associated with important fruit quality attributes. So far two genes, H for Heavy netting and Rs for Russet skin have been identified for skin netting, but how these genes control netting formation is unknown. Findings: Here we reported cloning and functional characterization of the candidate for the Rs gene. We found that the Rs gene encodes a protein called SHINE1 (CsSHN1)/Wax Inducer1 (CsWIN1), which is known to play important roles in shaping the epidermal features in the flesh fruit crops. Through marker assisted backcrossing, we developed near isogenic lines for the Rs gene which allowed comparative analysis of effects of the Rs gene. We found that fruit with netted skin had different epidermal structures from that with smooth skin including thicker cuticles, smaller, palisade shaped epidermal and sub-epidermal cells with significant more accumulation of lignin and lipids in cell walls, higher peroxidase activities. These observations suggest multiple functions of the CsSHN1 gene in both regulating fruit skin netting and the shape and size of epidermal cells. We found heavily netted cucumber line WI7102 had two tandemly arrayed functional copies of SSHN1, the lightly netted Gy14 cucumber had one functional copy, while the smooth skin cucumber line 9930 had a loo-of-function copy of CSSHN1. We also found that the expression level of CsSHN1 gene is positively correlated with the degrees of fruit skin netting in these lines. Comparative analysis between cucumber and melon revealed conserved and divergent genetic mechanisms underlying fruit skin netting/reticulation that may reflect the different selection histories in the two crops. Who cares: This work is of theoretical interest for cucumber researchers in understanding the molecular mechanisms of fruit skin netting. This work also provides insights into genetic control of fruit epidermal features in cucumber which is of importance in cucumber breeding for different market classes.

Technical Abstract: Fruit skin netting in cucumber (Cucumis sativus) is associated with important fruit quality attributes. Two simply inherited genes H (Heavy netting) and Rs (Russet skin) control skin netting, but their molecular basis is unknown. Here we reported map-based cloning and functional characterization of the candidate gene for the Rs locus that encodes CsSHINE1 (CsSHN1) an AP2-domain containing ethylene responsive transcription factor protein. Comparative phenotypic analysis in near isogenic lines revealed that fruit with netted skin had different epidermal structures from that with smooth skin including thicker cuticles, smaller, palisade shaped epidermal and sub-epidermal cells with heavily suberized and lignified cell walls, higher peroxidase activities, which suggests multiple functions of CsSHN1 in regulating fruit skin netting and epidermal cell patterning. Among three representative cucumber inbred lines, three haplotypes at three polymorphic sites were identified inside CsSHN1: a functional copy in Gy14 (wild type) with light fruit skin netting, a copy number variant with two tandemly arrayed functional copies in WI7120 with heavy skin netting, and a loss-of-function copy in 9930 with smooth skin. The expression level of CsSHN1 in fruit exocarp of three lines was positively correlated with the skin netting intensity. Comparative analysis between cucumber and melon revealed conserved and divergent genetic mechanisms underlying fruit skin netting/reticulation that may reflect the different selection histories in the two crops. A discussion was made on genetic basis of fruit skin netting in the context of natural and artificial selections of fruit quality-related epidermal features during cucumber breeding.