Phenotypic Traits and Genome-Wide Association Study of Camellia sinensis Flowers

YANG Hong; SHAO Chenyu; YAO Lin; RAO Jiayi; PENG L&#x000fc;wen; HUANG Feiyi; DUAN Jihua; XIE Nianci; CHEN Yuhong; LI Saijun; LIU Shuoqian; LEI Yu

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Journal of Tea Science ›› 2026, Vol. 46 ›› Issue (3) : 435-448.

Research Paper

Phenotypic Traits and Genome-Wide Association Study of Camellia sinensis Flowers

YANG Hong^1,2,3, SHAO Chenyu¹, YAO Lin^1,2,3, RAO Jiayi^1,2,3, PENG Lüwen^1,2,3, HUANG Feiyi^2,3, DUAN Jihua^2,3, XIE Nianci^2,3, CHEN Yuhong^2,3, LI Saijun^2,3, LIU Shuoqian^1,2,*, LEI Yu^1,2,*

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Abstract

As the primary reproductive organ of the tea plant (Camellia sinensis), the flower exhibits rich phenotypic diversity, which holds significant importance for the genetic improvement of tea plants. In this study, 64 tea germplasm accessions were used to systematically investigate the phenotypic diversity of nine qualitative traits and twelve quantitative traits related to floral morphology. Based on 47 111 high-quality SNP markers, population genetic structure analysis and genome-wide association study (GWAS) were performed. The results reveal abundant genetic diversity in floral traits among the tested materials, with ovary villi, weight per 100 flowers, and the proportion of the bifurcation to the columella showing relatively large variation, which could serve as core evaluation indicators. Population structure analysis divided the materials into three genetic subgroups, which were highly consistent with the phenotypic clustering results. Through GWAS, 245 SNP loci significantly associated with 10 important floral traits were identified. Furthermore, five core candidate genes (GWHTASIV003067, GWHTASIV018433, GWHTASIV032688, GWHTASIV001183, GWHTASIV044042) were identified, which are involved in key biological processes such as growth regulation, RNA editing, cell cycle control, chromatin remodeling and transcriptional regulation. This study provided a systematic multidimensional analysis of the genetic basis of floral traits in tea plants for the first time, offering important gene resources and a theoretical foundation for research into the molecular mechanisms of floral traits and for molecular marker-assisted breeding in tea plants.

Key words

Camellia sinensis / flower / genetic diversity / genome-wide association study (GWAS) / candidate gene

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YANG Hong, SHAO Chenyu, YAO Lin, RAO Jiayi, PENG Lüwen, HUANG Feiyi, DUAN Jihua, XIE Nianci, CHEN Yuhong, LI Saijun, LIU Shuoqian, LEI Yu. Phenotypic Traits and Genome-Wide Association Study of Camellia sinensis Flowers[J]. Journal of Tea Science. 2026, 46(3): 435-448

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