Multiomics analysis reveals that VrKNAT6 regulates pod number through jasmonic acid synthesis

Highlights 1 1. Multiple GWAS methods were employed to identify the mung bean pod development-related gene VrKNAT6 . 2. Metabolomic analysis of VrKNAT6 H1 -overexpressing mung bean hairy roots and Arabidopsis thaliana demonstrated that VrKNAT6 regulates pod number per plant by participating in JA synthesis. 3. Bioluminescence and luciferase complementation analyses revealed that VrKNAT6 interacts with VrATH1, indicating its involvement in the JA synthesis pathway. The number of pods per plant (PP) is strongly correlated with seed yield, and identifying genes that regulate PP could enhance the yield of mung bean ( Vigna radiata (L.) Wilczek), providing valuable insights for molecular breeding. In this study, VrKNAT6 was identified through genome-wide association and multiomics analyses. Chr3-14344673 (P=3.02E-10~8.80E-07) was found to be significantly associated with PP using EMMAX, CMLM, GEMMA, GLM, and 3VmrMLM. Among the 12 genes located within a 100 kb region near Chr3-14344673 on chromosome 3, EVM0027029 ( VrKNAT6 ) is homologous to known PP development-related genes in Oryza sativa and Arabidopsis thaliana . Overexpression of VrKNAT6 H1 significantly increased rosette numbers, branch numbers, PP, and the 1,000-seed weight in transgenic Arabidopsis lines. Furthermore, when overexpressed in mung bean hairy roots and Arabidopsis , VrKNAT6 H1 was found to participate in jasmonic acid (JA) synthesis through physical interaction with VrATH1 . This interaction partly explains the differences in branch numbers between VrKNAT6 H1 -overexpressing Arabidopsis lines and the control. Additionally, the expression of JA synthetase-related genes was significantly elevated in the positive VrKNAT6 H1 lines. Based on the multiomics analysis results, we propose a molecular regulatory mechanism for VrKNAT6 H1 , suggesting that it is a JA synthesis-related gene that could be utilized in mung bean high-yield molecular breeding.