Collinearity Prediction Of The AP2/ERF Gene Function Across Wheat (Triticum Aestivum L.) And Rice (Oryza Sativa L.) Genomes

Plants, in their growth and development process, encounter various natural confronts, frompests, diseases and ecological stern of temperature and water. To cope and adjust withthese environmental challenges, plants have developed a coalesced network of signallingat cellular, molecular and system level that leads to changes in their biochemical andphysiological processes. All this is achieved through a series of gene co-expression at thelevel of transcription. The transcription factors in a synchronized way control the feat ofmultiple stress response by activating or suppressing the expression of many coding genesand are described as attractive targets for application in plant biotechnology. Amongdifferent transcription factors, ethylene responsive transcription factors (ERF) family playsa vital role in plant growth and makes the plants able to fight against ambiance. Thereby; itis important to cram the role of these genes to ameliorate crop yield and make themappropriate to sundry environmental conditions.Wheat (Triticum aestivum L.) being hexaploid in nature is in its initial stage of genomesequencing. Although the genome size of rice (Oryza sativa L.) is40times smaller thanwheat but a remarkable degree of homology at gene level by comparative genetic mappingis found among these two species which help to predict the function of new genes in wheatgenome to ameliorate crop yield.To achieve the objectives, primarily170AP2/ERF family genes are keyed out byphylogenetic analysis in the rice genome (O. sativa L. subsp. Japonica). They are carvedup into four major groups (AP2, ERF, DREB and RAV), ten subgroups and two soloists.Gene’s structure analysis divulges that at position-6, amino acid threonine (Thr-6) isconserved in the double domain AP2proteins as compared to amino acid arginine (Arg-6)found preserved in the single domain ERF proteins. In addition, histidine (His) amino acidis found in both domains of double domain AP2protein, which is missing in the singledomain ERF proteins. Motif analysis displayed the conserved motifs in their respectiveclades in the phylogenetic tree outside the AP2/ERF domain that regulate plausiblefunctions. Expression analysis unwraps the distribution of rice AP2/ERF family genes indifferent plant tissues. In the vegetative organs, the transcript of these genes is found mostabundant in roots followed by leaf and stem, whereas in reproductive tissues, the gene’s expression is observed high in embryo and lemma. From chromosomal localization, itseems that repetition and tandem-duplication may contribute to the evolution of new genesin rice genome. Moreover, the interspecific comparison (rice-wheat) of116wheatAP2/ERF genes results in finding of36rice loci and unveils the extent of collinearitybetween the two genomes. Microsynteny analysis reveals26duplicate segments in rice.The phylogeny estimates of metameric duplicate indicates that three genes of AP2, eightgenes of CRT/DRE and eleven genes of ERF subfamilies exhibited homology with ricegenome. Chromosoal localization exhibited that chromosome (chr) chr-8and chr-9areshowing more orthologous loci for CRT/DRE genes whereas chr-2and chr-4exhibitsorthologes for ERF subfamily. Maximum conserved synteny is found in chr-3for AP2double domain subfamily genes. Only chr-7has AP2double domain subfamily genes.Macrosynteny between rice and Arabidopsis, the distant related genome, glimpses11homologs/orthologs loci in both genomes. The chromosomal distribution of AP2/ERFfamily genes displayed that chr-1in Arabidopsis has more paralogs followed by chr-5. InArabidopsis, ERF subfamily gene’s orthologs are found on chr-1, chr-3and chr-5whereasDRE subfamily genes are found out on chr-2and chr-5respectively. Orthologs for RAVand AP2with double domain in Arabidopsis are ascertained on chr-1and chr-3respectively. Translocation, deletion and ploidy level ensuant in rhythm of divergenceperplexes synteny among the genomes. The canvass also probes the prediction of genefunction in wheat by comparative mapping. One predicted transcription factorPTTa00075.1was found conserved orthologs on rice chr-1and chr-6respectively. TheDNA coding sequence comprised of765bp ORF length and encodes the protein sequenceof254amino acids. The conserved amino acid valine (V) at position14and glutamine (E)at position19was found preserved in the domain. The predicted gene designationTaDREB2was confirmed by the conserved motif SVAETIK and RKAPAKG present inthe N-terminal region and responded in ABA-independent manner. The gene wasamplified and cloned from the wheat (T. aestivum L. cv. Chinese spring) which is inducedby dehydration and salt. It expressed more in stem, leaf, head leaf and mild expression wasobserved in root and booting leaf and the least was found in the senescence leaf. The over expression vector was constructed to generate transgenic tobacco plants viaAgrobacterium-mediated transformation method.It was observed when grown on mannitol media plates,the germination%and rate ofgermination of transgenic plants was higher than that of the control. Root length waspronounced significant longer in the transgenic lines over the wild type. To depictingincrease tolerance of transgenic lines to dehydration stress, water loss assay exhibited thatafter six hours, wild type have lost67%whereas the transgenic lines retained more than56%water. Accumulation of significant more fresh weight in transgenic plantlets in stresscondition depends on the TaDREB2transcripts. Prolonged arrested irrigation resulted incurling and wilting of leaves in wild type after three to five days of drought stress whichwas delayed in all the transgenic lines. Regarding the salt affect, the leaves of overexpression lines were dark green in colour while the wild type exhibited yellow andstunted growth. Accumulation of proline and peroxidase (POD) activity increasedsignificantly in over expression lines as compared to wild type in salt and drought stressthat act as osmotic protection agent and scavenger of reactive oxygen species (ROS),respectively.The canvas also probes the difficulties using BLAST searches in identifying orthologsamong genomes who are in their infancy. It is concluded that both macrocollinearityexposed by comparative mapping and microcollinearity divulged by sequence homologyof wheat with rice help to predict the gene function and provides a strong platform thatrice genome has a substantial wallop on other grasses in terms of both genomic analysesand crop melioration. It is concluded that the data generated in this survey will be useful inconducting genomics research to construe AP2/ERF gene’s precise role during the stressresponse in crop improvement.