Lodging variation of weedy rice in China and its epigenetic influencing mechanisms


 Weedy rice (Oryza spp.), one of the most notorious weeds in rice fields, evades eradication through stem lodging and seed shattering. Many studies have focused on seed shattering in weedy rice. However, the lodging differentiation of weedy rice in different regions of China has not been characterized, and the underlying mechanisms of lodging difference between weedy rice and associated cultivated rice have not been studied in detail. Here, we compared the 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 expression variation of lodging-related genes. Results showed that the lodging degree varies between indica-derived weed strains with high lodging levels, which occurred predominantly in southern China, and japonica-derived strains with lower lodging levels 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, the ratio of cellulose to lignin content in lodging-prone weedy rice was lower. DNA methylation variation of lignin synthesis-related OsSWN1, OsMYBX9, OsPAL1 and Os4CL3 mediated their expression level differnece and affected the ratio of cellulose to lignin content. Together, DNA methylation in lignin-related genes regulates stem strength and lodging variations in weedy rice, and between weed strains and their co-occurring cultivated rice.