Comparing Transcriptome and Stem Anatomy Analysis Reveals That the Phenylpropanoid Pathway Is a Key Driving Factor for Lodging Resistance in Brassica rapa

Brassica rapa is widely cultivated in alpine and cold mountainous regions due to its strong cold tolerance. However, lodging severely limits its yield and quality. This study integrated agronomic traits, stem microstructure, and transcriptomic profiles to explore the mechanism of lodging resistance by comparing a resistant cultivar (Ganyou 3064, GY) and a susceptible cultivar (Tianyou 2022, TY) across four developmental stages (full flowering, final flowering, podding, and maturity). At the four growth stages, the stem breaking strength of GY was 1.71, 1.93, 1.88, and 1.88 times that of TY, respectively. Compared with TY, the gravity center height of GY was decreased by 25.04%, 16.6%, 11.18%, and 8.98% at these four stages, respectively. Similarly, the lodging index of GY was decreased by 65.94%, 55.08%, 56.06%, and 55.63% compared with TY, respectively. Biochemical and anatomical analyses revealed that compared with TY, the lignin content of GY increased by 1.93%, 2.7%, 3.05%, and 3.42% at the four stages, while the cellulose content increased by 92.75%, 45.32%, 44.4%, and 49.92%, respectively. Meanwhile, the epidermal thickness, cortical thickness, vascular bundle length, vascular bundle area, and vascular bundle density of GY were also significantly increased. Transcriptomic and KEGG pathway analyses revealed a predictive defense mechanism of GY. At the final flowering stage, GY showed pre-activation of hormone and MAPK signal transduction, as well as phenylpropanoid biosynthesis; it shifted to energy supply and sustained cell wall reinforcement at the podding stage. In addition, upregulated genes in phenylpropanoid biosynthesis (such as PAL3, CCoAOMT, and CAD9) indicated that enhanced stem lignification is a key molecular determinant of lodging resistance. In summary, GY enhances its lodging resistance through coordinated morphological and transcriptional regulation. This study is the first to integrate the lodging characteristics of Brassica rapa, offering valuable candidate genes and phenotypic markers for molecular breeding.