Morphological Characteristics and Molecular Marker-Assisted Identification of Ovary Glabrous Phenotype in the Population of Nanchuan Dachashu (Camellia nanchuanica)

Nanchuan Dachashu (Camellia nanchuanica), an arboreal tea species from Chongqing, China, exhibits valuable germplasm characteristics and tea production quality. However, the morphological diversity and genetic basis of key traits, such as tree architecture, leaf anatomy, and ovary trichomes, within this natural population remain to be elucidated. In this study, we conducted a survey on 90 wild individuals from this population, with a special focus on ovary trichomes—an important taxonomic trait. Considerable variations were observed in tree architecture, leaf size and shape, and anatomical structures. Through association analysis, we identified the SNP locus Chr9_89939207 to be associated with the glabrous/hairy ovary trait. A KASP marker was subsequently developed based on this locus, which could accurately distinguish between glabrous and hairy ovary individuals of Nanchuan Dachashu, as well as differentiate this species from C. sinensis or other hairy ovary species. The SNP locus Chr9_89939207 resides in the exon of a predicted protein phosphatase 2C (PP2C) gene, CSS0003297, which potentially regulates ovary trichome development in tea plants. These results reveal extensive morphological variation within the Nanchuan Dachashu population, establish a molecular tool for the identification of valuable interspecific hybrids, and provide insights into the breeding and industrial applications of this germplasm.