INVESTIGATION OF MOLECULAR MECHANISMS OF FRUIT FLESHINESS DEVELOPMENT IN THE ROSACEAE FAMILY

Abstract

This dissertation investigates the molecular mechanisms underlying fruit fleshiness in the Rosaceae family through comparative developmental and transcriptomic analyses. Fruit fleshiness has evolved multiple times independently in Rosaceae, yet the developmental and molecular basis distinguishing fleshy and dry fruit remains incompletely understood. To address this question, this study focuses on comparing two closely related Potentilla species with contrasting fruit types, Potentilla indica (fleshy fruit) and Potentilla gracilis (dry fruit), and then extended the analysis further across multiple fleshy fruit-forming Rosaceae species and dry-fruited Arabidopsis thaliana. In Chapter 1, the biological and evolutionary context of fruit development in angiosperms is introduced, with particular emphasis on the diversity of fruit types in the Rosaceae family. The chapter highlights the distinction between fleshy and dry fruits and reviews current advances in understanding the developmental and molecular basis of fruit formation, including hormonal regulation and transcriptional control. It also summarizes available genomic and transcriptomic resources and discusses the evolutionary significance of repeated origins of fruit fleshiness. Together, this chapter establishes the conceptual framework and research rationale for the comparative and functional analyses presented in this dissertation. In Chapter 2, fruit development in P. indica and P. gracilis was characterized morphologically and transcriptomically across four developmental stages at 5, 10, 15, and 20 days post-anthesis (DPA). The fleshy fruited P. indica exhibited pronounced receptacle enlargement, visible anatomical remodeling, and dynamic transcriptomic reprogramming, particularly during the transition from 10 to 15 DPA. In contrast, the dry-fruited P. gracilis showed limited receptacle expansion, modest anatomical change, and a more gradual transcriptional trajectory. Gene Ontology enrichment analyses further indicated stronger enrichment of hormone-related and cell wall–associated pathways in P. indica, whereas P. gracilis displayed fewer and more heterogeneous enriched functional categories. These results suggest that fleshy fruit development is associated with extensive transcriptional activation, tissue remodeling, and coordinated developmental regulation, whereas dry fruit development follows a comparatively constrained program. In Chapter 3, comparative transcriptomic analyses were performed across four Rosaceae fleshy-fruited species and the dry-fruited model Arabidopsis thaliana to identify conserved regulatory factors associated with fleshy fruit development. Orthogroup-based analysis identified a subset of genes that are consistently and highly expressed in fleshy fruits and lowly expressed in Arabidopsis siliques. Among these, members of the LIGHT-DEPENDENT SHORT HYPOCOTYLS (LSH) family were identified as candidate transcriptional regulators. Functional analyses using CRISPR/Cas9 mutagenesis in Fragaria vesca and inducible overexpression assays in Arabidopsis support a role for LSH genes in developmental patterning relevant to fruit formation. Together, this dissertation supports a model in which fleshy fruit evolution in Rosaceae is associated not with the origin of entirely novel genes, but with regulatory rewiring and enhanced deployment of conserved developmental programs. These findings provide new insights into the molecular basis of fruit-type diversification and establish a comparative framework for studying the developmental evolution of fleshy and dry fruits.