Characterization of lodging variation of weedy rice

Weedy rice (Oryza spp.), one of the most notorious weeds of cultivated rice, evades eradication through stem lodging and seed shattering. Many studies have focused on seed shattering, whereas variations in lodging have received less attention and the underlying mechanisms that cause the differences in lodging between weedy and cultivated rice have not been studied in detail. Here, we compared lodging variation among diverse Chinese weedy rice strains and between weedy rice and co-occurring cultivated rice. The chemical composition of basal stems was determined, and transcriptome and methylome sequencing were used to assess the variation in expression of lodging-related genes. The results showed that the degree of lodging varied between indica-derived weed strains with high lodging levels, which occurred predominantly in southern China, and japonica-derived strains with lower lodging levels, which were found primarily in the north. The more lodging-prone indica weedy rice had a smaller bending stress and lower lignin content than non-lodging accessions. In comparison to co-occurring cultivated rice, there was a lower ratio of cellulose to lignin content in the lodging-prone weedy rice. Variation in DNA methylation of lignin synthesis-related OsSWN1, OsMYBX9, OsPAL1, and Os4CL3 mediated the differences in their expression levels and affected the ratio of cellulose to lignin content. Taken together, our results show that DNA methylation in lignin-related genes regulates variations in stem strength and lodging in weedy rice, and between weed strains and co-occurring cultivated rice.