Transcriptomic profiling reveals candidate allelopathic genes in rice responsible for interactions with barnyardgrass

Abstract

Echinochloa crus-galli (barnyardgrass) is one of the most damaging weeds in rice fields worldwide. Allelopathy has been considered a possible application for weed management. Thus understanding its molecular mechanisms is important for rice production. This study generated transcriptomes from rice under mono- and co-culture with barnyardgrass at two-time points to identify the candidate genes controlling allelopathic interactions between rice and barnyardgrass. A total of 5,684 differentially expressed genes (DEGs) were detected, amongst which 388 genes were transcription factors. These DEGs include genes associated with momilactone and phenolic acid biosynthesis, which play critical roles in allelopathy. Additionally, we found significantly more DEGs at 3 hours than at 3 days, suggesting a quick allelopathic response in rice. Up-regulated DEGs involve diverse biological processes, such as response to stimulus and pathways related to phenylpropanoid and secondary metabolites biosynthesis. Down-regulated DEGs were involved in developmental processes, indicating a balance between growth and stress response to allelopathy from barnyardgrass. Comparison of DEGs between rice and barnyardgrass shows few common genes, suggesting different mechanisms underlying allelopathic interaction in these two species. Our results offer an important basis for identifying of candidate genes responsible for rice and barnyardgrass interactions and contribute valuable resources for revealing its molecular mechanisms.

Deciphering the Genetic Basis of Allelopathy in japonica Rice Cultivated in Temperate Regions Using a Genome-Wide Association Study

“…Lecithin:cholesterol acyltransferases, also named as phospholipid:diacylglycerol acyltransferases, are involved in the synthesis of triacylglycerol (Dahlqvist et al 2000 ). The up-regulation of this gene has been observed in previous allelopathic assays (Sultana et al 2023 ). Four additional genes coding for proteins of the lecithin:cholesterol acyltransferases family were localised in the vicinity in qAll-2.…”

“…Next to qAll-2b SNP peak, G1L3 is also localised. The up-regulation of G1 LIKE PROTEIN 3 ( G1L3 ) has been reported previously in transcriptomic analysis of rice in the interaction with barnyardgrass (Fang et al 2009 ; Sultana et al 2023 ).…”

“…Four genes coding for PAL could be found in qAll-2b. One of these genes Os02g0626600 , coding for PAL3, was previously found to be up-regulated in response to the presence of barnyard grass (Song et al 2008 ; Sultana et al 2023 ).…”

“…Earlier studies have also highlighted the positive regulatory role of PAL in rice's allelopathic potential (Fang et al 2013 ; Zhang et al 2019b ). PAL exhibits up-regulation in hydroponic systems in response to barnyard grass roots (Zhang et al 2019b ; Sultana et al 2023 ). Additionally, when the expression of OsPAL is silenced, it results in reduced allelopathic activity from donor rice to barnyard grass (Fang et al 2020 ).…”

“…Most reported allelochemicals in rice are secondary plant metabolites, including fatty acids, indoles, momilactones, phenolics and terpenes (Seal et al 2004 ; Khanh et al 2007 ; Kato-Noguchi and Peters 2013 ). Transcriptomic studies have also been conducted in the interaction of rice with barnyardgrass and differential expressed genes associated with momilactone and phenolic acid biosynthesis were found to be up-regulated in a quick allelopathic response (Song et al 2008 ; Sultana et al 2023 ). But no candidate genes have already been reported.…”