Analysis of Genetic Variation of Rice Straw Characteristics and Its Influence on Biomass

Rice straw is a key source of lignocellulosic biomass. GWAS can be used to identify genetic loci controlling stem morphological traits that influence biomass. This study aimed to investigate the genotypic diversity of rice straw internodes through GWAS, using 34,232 single-nucleotide polymorphic sites with a minor allelic frequency (MAF) greater than 0.05. Morphological traits (32) were evaluated in 149 rice accessions at the heading stage. Among the 32 measured traits, 26 were found to be significant. GWAS identified 173 significant SNPs located within 64 QTLs with a putative function in biomass production. Among all the putative genes identified, 21 were selected as candidate genes, including WAK 53a and DUF (248, 295, 309, 1740, 3444, 3464, 3475). In general, the identified candidate genes were grouped into five categories: cytoskeletal and transport of cell wall components, growth and development, cell wall biosynthesis, wall-modifying genes, and regulatory genes. The three major TF groups were WRKY, ERF, and MYB. Haplotype analysis identified seven haplogroups, with five being significant. Path analysis revealed that panicle dry weight (0.64) and internode 3 dry weight (0.57) had the highest positive correlation with biomass. Our findings can be implemented in genome editing methodologies for functional characterization of the candidate genes. This study represents the first comprehensive GWAS of various stem-related morphological traits in Oryza sativa, aiming to identify candidate genes involved in lignocellulosic biomass production and to inform targeted breeding approaches.