Integration of digital phenotyping, GWAS, and transcriptomic analysis revealed a key gene for bud size in tea plant (<i>Camellia sinensis</i>)

Tea plant (<i>Camellia sinensis</i>) is among the most significant beverage crops globally. The size of tea buds not only directly affects the yield and quality of fresh leaves, but also plays a key role in determining the suitability of different types of tea. Analyzing the genetic regulation mechanism of tea bud size is crucial for enhancing tea cultivars and boosting tea yield. In this study, a digital phenotyping technology was utilized to collected morphological characteristics of the apical buds of 280 tea accessions of representative germplasm at the 'two and a bud' stage. Genetic diversity analysis revealed that the length, width, perimeter, and area of tea buds followed a normal distribution and exhibited considerable variation across natural population of tea plants. Comparative transcriptomic analysis of phenotypic extreme materials revealed a strong negative correlation between the expression levels of four <i>KNOX</i> genes and tea bud size. A key candidate gene, <i>CsKNOX6</i>, was confirmed by further genome-wide association studies (GWAS). Its function was preliminarily characterized by heterologous transformation of <i>Arabidopsis thaliana</i>. Overexpression of <i>CsKNOX6</i> reduced the leaf area in transgenic plants, which initially determined that it is a key gene negatively regulating bud size. These findings enhance our understanding of the role of <i>KNOX</i> genes in tea plants and provide some references for uncovering the genetic regulatory mechanisms behind tea bud size.