Genomide wide association study of cuticle and lipid droplet properties of cucumber (Cucumis sativus L.) fruit

Authors: RETT-CADMAN, STEPHANIE - Michigan State University; Weng, Yiqun; ZHANGJUN, FEI - Boyce Thompson Institute; THOMPSON, ADDIE - Michigan State University; GRUMET, REBECCA - Michigan State University

Submitted to: International Journal of Molecular Sciences
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/25/2024
Publication Date: 8/25/2024
Citation: Rett-Cadman, S., Weng, Y., Zhangjun, F., Thompson, A., Grumet, R. 2024. Genomide wide association study of cuticle and lipid droplet properties of cucumber (Cucumis sativus L.) fruit. International Journal of Molecular Sciences. 25(17). https://doi.org/10.3390/ijms25179306.
DOI: https://doi.org/10.3390/ijms25179306

Interpretive Summary: The fruit surface is a critical first line of defense against environmental stresses. The fruit surface is covered with thin layer of cuticle that is comprised of a matrix of chemical compounds like cutin monomers and waxes. The cuticle layer not only protects the fruit, but also provides mechanical support throughout development. The epidermal layer of cucumber fruit contains prominent lipid droplets (LDs), which have been recognized as dynamic organelles involved in lipid storage and metabolism, stress response, and accumulation of specialized metabolites. However, the genetic basis of LD variation in cucumber fruit epidermis is largely unknown. The objective of this study is to genetically characterize natural variation for cuticle and LD associated traits in cucumber fruit. Phenotypic characterization and genome wide association studies (GWAS) were performed using a re-sequenced (30-40x coverage) cucumber core population that accounts for >96% of the allelic diversity present in the United States National Plant Germplasm System (NPGS) collection. The core collection was grown in the field and fruit were harvested at 16-20 days post-pollination, an age where cuticle and LD traits are stable. Fresh tissue sections were prepared from the mid-section of the fruit and stained with Sudan IV, a red lipid stain, to measure cuticle thickness, LD size and number. The cucumber core collection showed extensive variation for the measured traits. GWAS identified several QTL that correspond with prior candidate genes for cuticle or lipid biosynthesis as well as suggesting new candidate genes of interest. This work provides novel insights into the genetic control of LD size and number in cucumber fruit epidermis. The results are of interest to cucurbit geneticists to understand the genetic and molecular mechanisms on cuticle structure and development.

Technical Abstract: The fruit surface is a critical first line of defense against environmental stresses. Overlaying the fruit epidermis is the cuticle comprised of a matrix of cutin monomers and waxes, which in addition to protection, provides mechanical support throughout development. The epidermal layer of cucumber (Cucumis sativus L.) fruit also contains prominent lipid droplets (LDs). LDs have recently been recognized as dynamic organelles involved in lipid storage and metabolsim, stress response, and accumulation of specialized metabolites. The objective of this work was to genetically characterize natural variation for cuticle and LD associated traits in cucumber fruit. Phenotypic characterization and genome wide association studies (GWAS) were performed using a re-sequenced (30-40x coverage) cucumber core population that accounts for >96% of the allelic diversity present in the United States National Plant Germplasm System collection. The core collection was grown in the field and fruit were harvested at 16-20 days post-pollination (dpp), an age where cuticle and LD traits are stable. Fresh tissue sections were prepared from the mid-section of the fruit and stained with Sudan IV, a red lipid stain, to measure cuticle thickness, LD size and number. The cucumber core collection showed extensive variation for the measured traits. GWAS identified several QTL that correspond with prior candidate genes for cuticle or lipid biosynthesis as well as suggesting new candidate genes of interest.