12.4Genomic Approaches to Identify

12.4Genomic Approaches to Identify Regulators of RSA Associatedwith Abiotic Stress ToleranceGenomics plays an important role in genome-wide identification of genes that areresponsible for conferring variation in traits (such as RSA) and tolerance to abioticstresses between two or more species. Genome-wide analysis of the availablegenome sequence data has helped in locating root development-related QTLs inrice [37]. Suryapriya et al. have developed a Web tool “rootbrowse” that has beenused to locate 861 QTLs related to root development using information gatheredfrom several QTL studies on populations derived from crosses between variousupland and lowland rice cultivars (indica and japonica) [37]. Using this tool,valuable information such as simple sequence repeat markers, protein-codinggenes, and functional annotation of the genes are also displayed along with theQTLs, and thus it would be helpful in predicting the genes related to RSA traits[37]. Both genetic and genomic approaches have been used to understand andimprove drought tolerance-related RSA traits in pearl millet [49]. Recently, NGS?based whole genome resequencing of DNA (QTL-seq) has been used to identifyQTL in rice [50]. It is worth mentioning that the use of association mapping touncover complex traits has been boosted by advance genomics tools that help in therapid identification and scoring of genetic markers (using sequence informationwhen comparing plants) [46]. Thus, the use of association mapping to study RSAtraits and stress tolerance offers tremendous opportunities. However, combiningrecently developed high-throughput phenotyping technology with associationmapping studies would be of great advantage to score huge number of RSA traitsand correlate them with genetic markers or genes.Recent advances in high-throughput sequencing or “next-generation sequen?cing” (NGS) are capable of producing huge amounts of sequence information in avery short period of time. This has accelerated genome-wide identification ofmarkers, differentially expressed transcriptomes, and small RNAs betweendifferent genotypes with contrasting traits. Microarray analysis is another popularapproach for genome-wide comparative transcriptome analysis. Arsenic toxicitystress has been shown to affect RSA traits by altering the expression of key signalingcomponents such as receptor-like cytoplasmic protein kinase, AP2 (APETALA2)/ERF (ethylene response factor), heat shock factor, MYB (myeloblastosis), zinc finger proteins, and so on, as observed by root-specific transcriptional profiling [51]. Usinga microarray-based functional genomics approach, the rice JAmyb was found tobe differentially expressed in roots under salinity stress, and its functionalanalysis has revealed the role in seed germination, seedling growth, and rootelongation [52]. In wheat, expression of TdAtg8 was highly upregulated in rootunder drought stress. Through functional analysis, it has been shown to affectroot architecture and regulate drought and osmotic stress responses in bothArabidopsis and wheat [53]. Using SAGE (serial analysis of gene expression)-based analysis, root-specific transcriptome data of maize has been shown tohave multiple stress-responsive factors, which might regulate RSA traits [54].ZmMKK4, a novel group C mitogen-activated protein kinase kinase (MAPKK)of maize, was shown to be involved in providing salt and cold tolerance. Usinga functional genomics approach, this gene was shown to affect the develop?mental process of the plant, including the root architecture [55]. Microarrayand subtractive hybridization approaches have identified and validated theexpression of WRKY transcription factors, zinc finger proteins, and NACdomain protein in tomato root under salinity stress [56,57]. Nutrient stress(e.g., excess nitrogen)-responsive genes have been identified and validated intomato roots using a microarray-based functional genomics approach [58]. Ironand potassium deficiency and salinity stresses have been shown to alter theexpression pattern of the 14-3-3 gene family in tomato root, indicating a cross?talk between these stresses to regulate RSA and stress tolerance [59]. Salinitystress was shown to affect RSA traits and root proteome of the tomato plant byaltering the fate of the various genes necessary for regulating the physiologicalphenomenon of tomato plant [60]. It has been shown that salt stress leads tothe accumulation of ABA, which influences the physiological response of theplant and therefore affects its proteome [61].Using a deep sequencing approach, transcripts differentially expressed inmaize root under low and high water potential have been identified, and theirpotential role in regulating the RSA has been indicated [62]. In addition toprotein-coding genes, many microRNAs (miRNAs) have been shown to bedifferentially expressed under abiotic stresses [63].