Multiple Omics Analysis Of Rice Seedling In Response To Cadmium Stress

Cadmium(Cd)influence in rice is a growing global concern.Although many molecular mechanisms related to cadmium transportation,accumulation and resistance have been identified in rice exposure to Cd stress,no comprehensive study has been done comprising integrative analysis of small RNAs,degradome and transcriptome sequencing and analysis of phosphoproteome sequencing for rice seedling under different concentrations(0???10??and 100??)of Cd stress to identify Cd-regulated miRNAs/their targets and phosphoproteins under Cd stress.Our primary result is as following:(1)A total of 4,223 differentially expressed genes were identified by transcriptome analysis to response to cadmium stress,including 2,487 genes induced by cadmium and 1,736genes inhibited by cadmium stress.Functional analysis showed that these differentially expressed genes were mainly involved in photosynthesis(photoharvesting,photosystem I and II,photosynthesis,electron carrier activity and chlorophyll binding)and protein degradation metabolic pathways(naphthalene,anthracene,limonene,pinene degradation,and hexachlorobenzene degradation).(2)Through analysis of the miRNAome and the degradome,40 miRNAs including 38known miRNAs representing 22 miRNA families and 2 novel miRNAs were substantially altered in response to Cd stress.18 differentially altered target genes were inversely correlated with 18 Cd responsive miRNAs.Majority of these targeted genes are transcript factors such as Auxin response factor 13(ARF13),Scarecrow-like protein 6(SCL6),Squamosa promoter-binding-like proteins(SPLs),Nuclear transcription factor Y subunit A-6(NFYA6),Gibberellin-dependent avian myeloblastosis virus oncogene(GAMYB)and No apical meristem protein domain containing proteins(NACs),most of which were involved in signal transduction such as abscisic acid(ABA),Auxin,Gibberellin acid(GA)and MAPK(Mitogen-activated protein kinase).Functional analysis revealed that genes involved in photosynthesis pathway(osa00196,osa00195 and osa00710)and protein degradation pathway(osa04612)were identified to be participated in response to Cd stress in rice,including osa-mi R156I-5p_R-1/SPLs,osa-mi R171a₁ss12CT/DEGP10 and osa-mi R169r-5p_R/NFYA6 circuits,respectively.The present study would confer a useful approach to investigate miRNA-mediated molecular mechanisms underlying plant response to Cd stress.(3)An analysis of quantitative phosphoproteome of the seedlings hydroponically growed in solution containing different Cd concentrations(0???10??and 100??)identified2454 phosphosites,associated with 1244 proteins.A total of 482 of these proteins became differentially phosphorylated as a result of exposure to Cd stress;the number of proteins affected in this way was six times greater in the 100?M Cd ²⁺treatment than in the 10?M treatment.A functional analysis implied that a significant number of the differentially phosphorylated proteins were transcription factors involved in signaling,in stress tolerance and in the neutralization of reactive oxygen species.