Transcriptome Analysis Of Maize Inbred Lines In Response To Abiotic Stress

The world population is rising at an alarming rate and is likely to attain about 9.8 billion by the end of the year 2050.On the contrary,agricultural productivity is not increasing at a requisite rate to keep pace with growing food demand.Maize(Zea mays L.)is the primary food crop exceeding rice and wheat in importance since 2012.It is a versatile cereal crop that is highly sensitive to abiotic stress at all stages of development.Studies have shown that the decrease in maize yield varies by 10-76% depending on the type of abiotic stress intensity,the crop's sensitivity,and the growth stage.However,at the seedling stage,abiotic stresses hamper the early crop establishment as well as the entire growth cycle,thus influencing the adaptive ability of the plant at an early stage and limiting the yield potential.Therefore,elucidating the mechanism of how maize responds to abiotic stress at the seedling stage has tremendous significance for maize production as well as for the maize breeding programs.The development of stress-tolerant crops that mitigate the effects of abiotic stresses on crop productivity is crucially needed to sustain agricultural production.Despite exhaustive research in this field,a concise blueprint regarding the genetic regulation of abiotic stress tolerance in plants has not yet been fully explored due to the complex nature of these traits.Nevertheless,genetic engineering of crops with stress-tolerant characteristics is a promising approach for improving stress tolerance.Understanding the mechanisms by which tolerant plants perceive and transduce the stress signals to initiate adaptive responses is a prerequisite for engineering stress-tolerant crop plants.Molecular and genomic studies have shown that these abiotic stresses induce several genes with various functions and that different transcription factors are involved in the regulation of stress-inducible genes.Genetic engineering strategies rely on the transfer of one or several genes involved in signaling and regulatory pathways,encoding enzymes present in pathways leading to the synthesis of functional and structural protectants,or encoding stress-tolerance-conferring proteins.Naturally,tolerant plants have developed stress-specific adaptive responses and responses that protect them from more than one environmental stress.Thus,they represent an ideal starting point for the identification of genes encoding stress-tolerant traits.My Ph.D.research study focuses on the transcriptome profiling of tolerant and sensitive maize genotypes under abiotic stress conditions(drought and cold)at the seedling stage to identify significant genes and pathways essential for engineering tolerant maize.In the first chapter,i discuss the significance of my study and expound on the objectives i have addressed in this research.Chapter two,on the other hand,focuses on a systematic literature review of maize's origin and distribution,ecological requirements,maize production constraints,and the implications of these constraints,all of which are relevant to my research study.Also,i have highlighted the fundamentals of plant responses to abiotic stresses,as well as the most efficient method for identifying and profiling tolerant related genes,which can be used to decode selection footprints and critical adaptive variants in maize breeding.In chapter three,i conducted a comparative transcriptome and physiological analyses of droughttolerant(CML69)and susceptible(LX9801)inbred lines subjected to drought treatment at the seedling stage for three and five days.Resultantly,the drought tolerant-line had significantly(p < 0.05)higher leaf relative water content and lower electrolyte leakage and malondialdehyde content than the susceptible-line.Using RNA-seq based approach,i identified 10,084 differentially expressed genes(DEGs)with 6,906 and 3,178 DEGs been annotated and unannotated,respectively.Two critical sets of drought-responsive DEGs,including 4,687 genotype-specific and 2,219 common drought-responsive genes,were mined out of the annotated DEGs.Under drought stress,the tolerant-line DEGs were predominantly associated with the cytoskeleton,cell wall modification,glycolysis/gluconeogenesis,transport,osmotic regulation,drought avoidance,ROS scavengers,defense,and transcriptional factors.For the susceptible-line,the DEGs were highly enriched in the photosynthesis,histone,and carbon fixation pathways.The unannotated DEGs were implicated in lnc RNAs including TE-lnc RNAs,and transposable elements.The results of the physiological response were in agreement with RNA-seq results.My findings provide an invaluable foundational basis of the molecular networks mediating drought stress tolerance of maize at the seedling stage.In chapter 4,i conducted a comparative transcriptome profiling of 24 cold-tolerant and 22-sensitive inbred lines affected by cold stress at the seedling stage.Using the RNA-seq method,i identified 2,237 differentially expressed genes(DEGs),including 1,656 and 581 annotated and unannotated DEGs,respectively.Further analysis of the 1,656 annotated DEGs mined out two critical sets of coldresponsive DEGs,including 779 and 877 DEGs,which were significantly enhanced in the tolerant and sensitive lines,respectively.Functional analysis of 1,656 DEGs highlighted the enrichment of signaling,carotenoid,lipid metabolism,transcription factors(TFs),peroxisome,and amino acid metabolism.A total of 147 TFs belonging to 32 families,including MYB,ERF,NAC,WRKY,b HLH,MIKC MADS,and C2H2,were strongly altered by cold stress.Moreover,the 779 tolerant lines enhanced DEGs were predominantly associated with carotenoid,ABC transporter,glutathione,lipid metabolism,and amino acid metabolism.In comparison,the 877 cold-sensitive lines enhanced DEGs were significantly enriched to MAPK signaling,peroxisome,ribosome,and carbon metabolism pathways.The biggest proportion of the unannotated DEGs were implicated in the roles of long non-coding RNAs(lnc RNAs).Collectively,my findings provide valuable insights into a deeper understanding of the molecular mechanisms underlying maize response to cold stress at the seedling stage,thus opening up possibilities for the breeding program of maize tolerance to cold stress.Finally,my last chapter summarizes the significance of this Ph.D.study with more emphasis on the essential genes regulated by abiotic stress(drought and cold)in maize seedlings.The chapter has also pinpointed the scientific gaps and challenges that require further research to develop new,more robust,and abiotic stress tolerant ideotypes of maize and other crop plants.Overall,my study provides new insights into the gene regulatory networks regulating stress-relevant pathways,pinpointing candidate genes for future research.