Evolutionary Patterns Of Stress-Related Genes And Analysis Of LncRNA Under The Low-Temperature Vernalization In Brassiaca Rapa

During the process of plant growth and development,various abiotic stressors are faced at any time,which have a serious impact on plant growth and development.Therefore,the study of plant stress-related genes and the molecular mechanism of adversity signal transduction has important theoretical and practical value.Brassica rapa crops mainly contain Chinese cabbage?B.rapa ssp.pekinensis?,Non-heading Chinese cabbage?B.rapa ssp.chinensis?and turnip?B.rapa ssp.rapa?,which belong to the cruciferae family of Brassica plants.B.rapa is one of the most important vegetable crops in China,which has a long history of cultivation and emerges rich germplasm resources after the long-term artificial domestication.At present,the main use of advanced proteomics technology combined with protein function research methods,comprehensive utilization of genomics,proteomics and metabolomics,systematically study the various plant stress signal pairs which influence and regulation of plant growth and development.From the molecular level,the level of evolution and the level of protein reveals its intrinsic laws and resolves its metabolic regulation and signal transduction network.In the model plant Arabidopsis thaliana stress-related genes have been studied more thoroughly,and there are relatively few studies on B.rapa.Therefore,research on the adversity-related gene system of B.rapa provides an important theoretical basis for cultivation and breeding.In this study,we identified stress-related genes?MAPK cascade gene,CDPK-SnRK,TIFY,BES1?and low-temperature vernalization-associated LncRNA in Non-heading Chinese cabbage,and revealed the expansion of related genes,retention patterns,evolutionary rules,replication differentiation and mining key genes for stress resistance using comparative genomics,molecular evolution,and gene expression analysis.At the same time,a large number of LncRNAs related to low temperature vernalization were obtained through transcriptome sequencing of Non-heading Chinese cabbage low-temperature vernalization materials.The results are as follows:1.Divergent evolutionary patterns of the MAPK cascade genes in Brassica rapa and plant phylogeneticsMitogen-activated protein kinase?MAPK?cascade signal transduction modules play crucial roles in regulating many biological processes in plants.These cascades are composed of three classes of hierarchically organized protein kinases,MAPKKKs,MAPKKs,and MAPKs.We finally identified 34 BrMAPK,14 BrMAPKK,and 112 BrMAPKKK genes in Brassica rapa.Here,we analyzed gene retention,phylogenetic,evolution and expression patterns of MAPK cascade genes in Brassica rapa.We further found that the MAPK branches,classes ? and ?,appeared after the split of bryophytes and green algae after analyzing the MAPK cascade genes in 8 species,and their rapid expansion led to the great size of the families of MAPKs.In contrast,the ancestral class ?subfamily of MAPKK gene families have been highly conserved from algae to angiosperms.For the MAPKKK family,the MEKK and Raf subfamily share a common evolutionary origin,and Raf plays a major role in the expansion of the MAPKKK gene family.The cis-elements and interaction network analyses showed the important function of MAPK cascade genes in development and stress responses in B.rapa.This study provides a solid foundation for molecular evolution analyses of MAPK cascade genes.2.Comprehensive analysis of the CDPK-SnRK superfamily genes in Chinese cabbage and its evolutionary implications in plantsCDPK-SnRK?Calcium-dependent protein kinases-Snfl-related protein kinases?gene family plays important roles in signaling pathways for disease resistance and various stress responses as indicated by emerging evidences.A total of 49 BrCPKs,14BrCRKs,3BrPPCKs,5BrPEPRKs,56BrSnRKs were identified in B.rapa.All BrCDPK-SnRK proteins had highly conserved kinase domains.By statistics of the number of CDPK-SnRK genes in each species,we found that the expansion of the CDPK-SnRK gene family started from angiosperm.The segmental duplication played a predominant role in CDPK-SnRK genes expansion.The analysis showed PPERK was more preferentially retained than other subfamilies and CPK was similarly retained to SnRK.Among the CPK and SnRK,CPKIII and SnRK1 genes were more preferentially retained than other groups.The CRK closest to CPK,which may share a common evolutionary origin.In addition,we identified 196 CPK genes and 252 SnRK genes in the 6 species and their different expansion and evolution types were discovered.Furthermore,the expressions of BrCDPK-SnRK genes are dynamic in different tissues as well as in response to abiotic stresses,demonstrating their important roles in development in B.rapa.3.Genome-wide analysis TIFY gene family and expression patterns of under stresses in Chinese CabbageThe TIFY gene family plays important roles in plant developmental processes and stress responses.In this study,35 TIFY genes were identified in Chinese cabbage.We constructed comparative analyses of gene structure,retention expansion,whole-genome duplication and expression patterns of TIFY genes in Brassica rapa and their evolution in 8 other plant species.By analyses of TIFY genes in 8 species,we found that JAZ has a closer relationship with PPD and JAZ appeared most recently and expanded most rapidly,which led to the rapid expansion of TIFYs in the Brassicaceae.In addition,their different evolution types were discovered.Finally,quantitative real-time polymerase chain reaction analysis showed the JAZ genes responded to different abiotic and biotic stress treatments.Such as BraTIFY014 and BraTIFY015 were both high expressed in the four abiotic treatments.4.Genome-wide analysis of the BES1 transcription factor family in Chinese cabbageThe BES1 transcription factor family is one of the most important families involved in growth and development,hormone responses,and abiotic or biotic stress responses in plants.In this study,15 BrBES1 genes were identified in Chinese cabbage,which could be classified into two groups according to their gene structural characteristics and motif compositions obtained.Fifteen BrBES1 genes mapped on chromosomes were further assigned to three subgenomes and eight ancestral karyotypes.Distribution mapping shows that BES1 proteins are non-randomly localized in 8 chromosomes.Fourteen orthologous gene pairs are shared by Brassica rapa and Arabidopsis.The expansion of BES1 genes in Brassica rapa results from genome triplication.Quantitative RT-PCR analysis showed that expressions of BrBES1 genes varied widely under different abiotic stress treatments for different times.5.The mechanism of long noncoding RNAs during vernalization in Non-heading Chinese cabbageFlowering time is an important agronomic trait in Brassica rapa?B.rapa?.Here,we used comparative transcriptome analysis between control and vernalized B.rapa to identify differentially expressed genes?DEGs?and LncRNAs?DELs?.A total of 300 DEGs and 254 DELs were identified.Co-localization networks consisting of 128 DEGs and 127 DELs were established,followed by analyses of hierarchical categories,functional annotations,and correlation from mRNA-to-LncRNA.We found that the BraZF-HD21?Bra026812?gene which responds to photoperiods and vernalization is correlated with LncRNA TCONS₀0035129.The correlated genes that were mapped to the plant hormone signal transduction pathway and increased gibberellin A3?GA3?content demonstrated that vernalization associates with plant hormone.