Integrating SEM-based phenotyping with GWAS reveals the genetic architecture of rice straw secondary cell wall and internode cell features

Rice stem performs assimilate transport and promises sturdiness due to cell wall structure and composition. However, less is known about the genetic basis of its structural characteristics. In this study, for the first time, the scanning electron microscope (SEM) imaging technique was developed to capture digital phenotypes to assess 18 straw traits collected from the cross-sections of 147 rice accessions. Genome-wide association studies (GWAS) identified 54 significant single-nucleotide polymorphisms (SNPs; integrated into 28 quantitative trait loci) residing in the genic sequences of rice (promoter and coding DNA sequence), and classified into three groups: 1) cell wall-defining genes, 2) cell size-defining genes, and 3) transcription factors. DUF246 and DUF1218, galactose oxidase, mitochondrial Rho GTPase, WUSCHEL-related homeobox 5 and scarecrow-like 9 are the novel genes identified among the 21 candidate genes. These genes may play roles in stem development traits, specifically the distance from the vascular bundle to the end of the parenchymal cells (DVBEPC) and the thickness of the straw cell wall in the protruding part (TSCWP). Post-GWAS analyses showed one significant haplotype on chromosome 4 and 25 significant epistatic interactions. Most notably, nine TF families were repeatedly detected among the significant QTL. Os07g0644300 (XPA-binding protein 2), located in the q7–1 genomic segment and associated with DVBEPC, was found to have a missense mutation. Phenotyping via SEM imaging provides precise genome-phenome association in understanding rice stem cell size and cell wall architecture, which ultimately can define biomass and lodging resistance.