Histological and transcriptomic analysis reveals the cell number and plant hormone related to fruit size in Litchi chinensis Sonn.

• Large-fruited cultivars had greater pericarp weight and thickness, aril weight, aril cell size, seed weight, and seed cell size compared to small-fruited cultivars. • During early developmental stage, the cell number in pericarp and seed exhibited significant differences between large- and small-fruited cultivars . • Pericarp is the main limiting factor for fruit size in litchi. • Numerous DEGs enriched in phytohormone biosynthesis or signal transduction pathways might play critical roles in determining litchi fruit size. Fruit size is an important quantitative trait that directly affects yield and quality. However, fruits are generally small in the current main litchi cultivars, which seriously influence yield. In this study, we characterized the fruit phenotype and histology of large-fruited cultivars ‘Ziniangxi’ (ZNX) and ‘Hehuadahongli’ (HHDHL) and small-fruited cultivars ‘Chenzi’ (CZ) and ‘Guiwei’ (GW) at different developmental stages. Large-fruited cultivars (ZNX and HHDHL) had greater pericarp weight and thickness, aril weight, aril cell size, seed weight, and seed cell size compared to small-fruited cultivars (CZ and GW). ZNX had the largest single fruit weight at maturity, while CZ had the smallest fruit size. Then, the pericarps, arils, seeds, and the early developing fruits of CZ and ZNX at different developmental stages were used for transcriptome sequencing to unravel the mechanism underlying fruit size in litchi. A total of 21,672 DEGs were identified by pairwise comparisons of young fruits, pericarp, aril, and seeds at each developmental stage between CZ and ZNX cultivars. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that numerous genes associated with cytokinin, auxin, gibberellin and brassinosteroid exhibited differential expression between large- and small-fruited litchi cultivars, such as LcBEH2, LcIPT, LcGH3.1, LcCYP72A219 . These results provide a theoretical basis for the regulation of fruit size in litchi breeding.