Cold stress (frost and chilling) decreases crop yields worldwide through tissue degradation and delayed growth. Most temperate plants have evolved cold resistance through cold-acclimatization [112]. Signaling pathways were being used in response to winter stress. The functional genes transform reactions, and reposts suggest that the signaling pathways for leaf senescence and plant defense responses may overlap [113]. The most characteristic region of cold-stress responsive genes includes transcription factors, such as CBF/DREB and stress-inducible candidate genes, identified as KIN (cold-induced), COR (cold-regulated), and LTI genes (induced by low temperature) or RD (dehydration) [114]. Several HSPs (heat shock proteins) are also reported for their functions against cold stress. HSPs, which perform as molecular chaperons, play an important regulatory function in protecting from stress by restoring normal protein conformation and thus maintaining cellular homeostasis in plants [115]. The number of the miRNA target genes in expression is intricate during stress and plant growth. These miRNAs are co-regulated by both developmental signals and ecological factors (Table 3). The cold-responsive miRNAs were detected by microarray analysis in Arabidopsis thaliana (miR165, miR31, miR156, miR168, miR171, miR396) and recommended by identifying their expression patterns in their promoter sequences and evaluating the cis-components (Table 3, Figure 1) [116,117]. Furthermore, high-intensity light (HL) responsive genes were assessed with the drought-inducible genes reported with a similar microarray system, which exposed an impenetrable intersection between drought and HL-induced genes. Moreover, 10 genes were identified as being involved in the regulation by HL, drought, salinity, and cold stress (Table 1 and Table 2). These genes are comprised of ERD10, RD29A, KIN1, LEA14, COR15a, and ERD7, and most of them are considered to be concerned in the defense of cellular components [78,118,119]. Along with the HL-inducible genes, some are also identified and encouraged by other stresses (heat, drought, and cold), including AtGolS, LEA, RAB, RD, COR, ERD, HSP, KIN, lipid-transfer proteins, and fibrillins [76,120,121].

Stress Condition	Plant Species	Inducible Genes	Known Responsive miRNAs	Functions	References
Drought stress	Arabidopsis thaliana	Rd29A (At5g52310) CCAAT-binding transcription factors	miR164, miR169, miR389, miR393, miR396, miR397, miR402	Pathogen immune response Drought tolerance Oxidative stress tolerance Pathogen immunity response Syncytium formation response to parasitic nematodes	[16,17,18,19]
	Medicago truncatula	CCAAT Binding Factor (CBF) Growth Regulating Factor (GRF) Cu/Zn superoxide dismutases (CSD1, CSD2) TIR-NBS-LRR domain protein	miR169, miR396 miR398, miR2118	Drought tolerance Syncytium formation response to parasitic nematodes Oxidative stress tolerance Photoperiod-sensitive male sterility	[16,20]
	Oryza sativa	SalT (LOC_Os01g24710) TIR1 OsLEA3 (LOC_Os05g46480)	miR393 miR402	Salt/cold tolerance	[6,17,18,21]
Cold stress	Arabidopsis thaliana	Rd29A (At5g52310) CBF3 (At4g25480)	miR165, miR172, miR169, miR396, miR397, miR402	Drought/cold tolerance Drought tolerance Heat stress tolerance	[16,17]
	Oryza Sativa	OsWRKY71 (LOC_Os02g08440) OsMAPK2(LOC_Os03g17700) Os05g47550, Os03g42280 Os01g73250, Os12g16350 Os03g19380	miR319, miR389, miR393, miR1320, miR1435 miR1884b, CHY1 CP12-2	Drought/salt tolerance Cold tolerance Pathogen immunity response	[17,21,22,23]
Salinity stress	Arabidopsis thaliana	Rd29A (At5g52310) COR15A (At2g42540)	miR389, miR393,	Oxidative stress tolerance Heat stress tolerance	[24]
	Populus trichocarpa	Dihydropyrimidinase	miR162, miR164, miR166, miR167, miR168, miR172, miR395, miR396	Pathogen immune response Drought tolerance Drought/cold tolerance Sulfate-deficiency response	[25,26,27]
	Glycine max		miR1507a, miR395	Sulfate-deficiency response	[28]
	Oryza sativa	SalT (LOC_Os01g24710) OsLEA3 (LOC_Os05g46480)	miR156, miR158, miR159, miR397, miR398, miR482.2, miR530a, miR1445	Drought tolerance Pathogen immune response Heat stress tolerance	[22,29,30,31]
	Zea mays		miR402	Seed germination and seedling growth of Arabidopsis under stress	[18]

Phenotype of Mutants	Genes	Function	AGI Code	Coded Proteins	Microarrays
Increased tolerance to drought	AtPARP2	DNA repair	At2g31320	Poly (ADPribose) polymerase	24K Affymetrix	[32,33,34]
Hypersensitive to drought stress	AHK1/ ATHK1	positive regulator of drought and salt stress responses	At2g17820	Histidine kinase	22K Agilent	[32,35,36]
Increased tolerance to drought stress	AREB1/ ABF2	regulate the ABRE-dependent expression	At1g45249	bZIP TF	22K Agilent	[33,37,38]
Increased tolerance to salt stress	AtbZIP60	encodes a predicted protein of 295 aa	At1g42990	bZIP TF	44K Agilent	[37,39]
Increased tolerance to drought stress	AtMYB60	regulates stomatal movements and plant drought tolerance	At1g08810	MYB TF	7K cDNA	[40]
Increased sensitivity to drought stress	AtMYB41	control of primary metabolism and negative regulation	At4g28110	MYB TF	24K Affymetrix	[41,42]
Increased tolerance to drought and salt stress	AHK2	positive regulators for cytokinin signaling	At5g35750	Histidine kinase	Agilent	[35,36]
Increased tolerance to drought and salt stress	AHK3	perception of cytokinin, downstream signal transduction	At1g27320	Histidine kinase	22K Agilent	[35,36]
Increased tolerance to drought and freezing stress	DREB1A/ CBF3	stress-inducible transcription factor	ERF/AP2 TF	ERF/AP2 TF	1.3K cDNA	[43]
Increased tolerance to drought stress	DREB2A	heat shock-stress responses.	At5g05410	ERF/AP2 TF	22K Agilent 7K cDNA	[44]
Hypersensitive to salt	HOS10	coordinating factor for responses to abiotic stress and for growth and development.	At1g35515	MYB TF	24K Affymetrix	[32,45]
Increased tolerance to drought stress	ZFHD1	mediates all the protein-protein interactions	At1g69600	Zinc finger HD TF	22K Agilent	[36,39]

 

DNA microarrays almost in all genes of the unicellular Synechocystis sp PCC6803 were used to investigate the gene expression sequential software [122]. A cDNA-microarray was used to test the profile expression in cold stress, and 328 temperature-regulated transcripts were reported. OsMYB3R-2 was studied further and was shown to be a dominant regulator against stress [123]. In this study, there was an attempt to use a 3.1K cDNA-microarray to express the cold-regulated transcripts in the Capsicum annuum. Several TFs, including the EREBP (CaEREBP-C1 to C4) family of four genes, a protein of the ring domain, a bZIP protein (CaBZ1), RVA1, a WRKY (CaWRKY1), and HSF1 protein have been observed among the cold stress-regulated genes. These genes included CaBZ1, CaEREBP-C3, NtPRp27, the SAR8.2 protein precursor, putative trans-activator factor, malate hydrogenase, putative protein of auxin-repressed, xyloglu-canendo-1, 4-D-gucanase precursor, LEA protein 5 (LEA5), homologous DNAJ protein, PR10 and Stns LTP [124,125]. cDNA microarray z1300 full-length cDNAs were used in Arabidopsis to identify cold stress-inducing genes and target genes of DREB1A/CBF3. Six genes were documented based on microarray and, in RNA gel blot analyses, it was observed that a novel DREB1A controls cold- and drought-inducible genes [43,126]. Furthermore, microarray with full-length cDNA was performed by 1300 full-length cDNAs and cDNA microarray to discover cold-induced genes. Previous reposts exhibited the target genes of DREB1A/CBF3 and stress-inducible gene expressions were controlled by transcription factors [76]; in contrast, stress-sensitive genes’ expressions were reported as specific to the growth stage [42]. Full-length cDNA microarray is convenient for analyzing the Arabidopsis gene expression patterns under cold stress, and can also be used to identify the functional genes of stress-related TFs that are likely to act as DNA elements by merging the genomic sequence data with the expression data [76,127]. Additionally, cold stress is also induced by the increase in the proline content in plants (osmoprotectant). Microarray and RNA gel blot research found that the proline can induce the expression of several genes with the proline-responsive elements in their promoters (PRE, ACTCAT) [120,127,128]. Microarray analysis was carried out to detect the cold-inducible AP2 gene family transcription factor RAV1 [129], which could control plant growth under stress. RAV1 is down-regulated by epibrassinolide, and transgenic Arabidopsis overexpressing RAV1 exhibits a rosette leaf and adjacent root growth retardation, although the early-flowering phenotype showed antisense to RAV1 plants [130,131].

Salt intrusion from saline soils and irrigation water is one of the most severe and harmful risks to reduce agricultural production and adverse effects on cultivated land and the geographical distribution of plant species [70,132,133], coupled with oxidative stress [134]. The most imperative cations in saline soils are calcium, potassium, magnesium, and sodium, and the main anions in saline soils are chloride, bicarbonate, sulfate, nitrate, and carbonates. Other electrolytes causative to salinity are borane, molybdenum, strontium, silicon dioxide, aluminum cation, and barium ion [135,136]. Higher concentrations of sodium chloride (NaCl) typically affect plant development, metabolism, and physiology at various metabolic phases (ion toxicity, nutrient imbalance, and oxidative stress) [70,137]. Despite such advances in scientific research, it remains unclear about the underlying molecular mechanism of salinity responses in plants. However, based on the combination of microarray and inhibition subtractive hybridization (SSH), changes in the transcriptome profile caused by salt induction were studied and evaluated [138]. Investigation of complete transcriptomics suggests that these processes, such as the synthesis of osmolytes and ion carriers and the regulation of transcription and translation mechanisms, have distinctive reactions under salinity stress. In particular, the introduction of transcripts of specific TFs, ribosomal genes, RNA-binding proteins, and translation initiation and elongation factors has been testified [139,140].

Using cDNA microarray in Synechocystis, 19 genes were reported to be instantaneously regulated under salinity stress. The salt- and osmo-regulated genes, and some putative sensor molecules, have been implicated during salinity stress signaling [35]. Several differentially regulated miRNAs have been reported against salinity stress. In A. thaliana, several microRNAs are regulated against salinity stress, such as miR156, miR158, miR159, miR165, miR167, miR168, miR169, miR171, miR319, miR393, miR394, miR396, and miR397 (Table 3, Figure 2) [84]. In Populus trichocarpa, miR1445, miR1447, miR1446a-e, miR530a, and miR171l-n were down-regulated (Table 3) [141]. Arenas-Huertero et al. [31] reported, in Proteus vulgaris, the production of miRS1 and miR159.2 expression in response to salinity. Furthermore, miR169g and family members of miR169n were induced in saline-rich conditions [142]. However, there is a need to discover and annotate novel functional genes which have a probable function against salinity stress. Subsequently, a large number of genes in plants still have unknown functions [143]. Recent studies revealed that specific down-regulation of the bacterial-type phosphoenolpyruvate carboxylase (PEPC) gene Atppc4 by artificial microRNA enhanced the salinity tolerance in A. thaliana. The increased salinity tolerance might be linked to enhanced PEPC activity [10,144]. Transcript control for salinity-tolerant rice with microarrays, like 1728 cDNAs from salinity-stressed roots libraries, was studied in response to high salinity (Table 3) [144,145,146].

Stress Condition	Plant Species	miRNA	Key Functions	Response	References
Drought stress	Medicago truncatula	miR398a,b miR408 miR399k miR2089 miR2111a-f,h-s miR2111g miR4414a	Oxidative stress tolerance Salt/drought/cold/oxidative osmotic-stress responses Phosphate-deficiency response	Up-regulated	[20,77,78,79,80]
		miR398b,c miR2111u,v miR5274b miR1510a-3p, 5p miR1510a	Heat stress tolerance Drought responsive Oxidative-stress tolerance triggering phasiRNA production from numerous NB-LRRs	Down-regulated	[77,79,80]
	Glycine max	miR5554a-c	Drought responsive		[79]
Salinity stress	Glycine max	miR169d miR395a miR395b,c miR1510a-5p miR1520d,e,l,n,q	Drought tolerance Sulfate-deficiency response triggering phasiRNA production from numerous NB-LRRs	Up-regulated	[20,81,82]
		gma-miR159b,c gma-miR169b,c gma-miR1520c	Pathogen immune response Drought/Salt tolerance	Down-regulated	[82]
	Phaseolus vulgaris	pvu-miR159.2	Plant–nematode interaction		[31]
Cold stress	Phaseolus vulgaris	pvu-miR2118	regulate the expression of genes encoding the TIR-NBS-LRR resistance protein	Up-regulated

 

A tiling path microarray was used to examine the high-throughput expression profiling patterns under various environmental stresses for all of the known miRNAs [16,70] (Table 1 and Table 4). The analysis revealed that the effects of miRNAs under low-temperature, drought, and high salinity with miRNA chips represent, approximately, all of the reported miRNAs cloned or recognized in A. thaliana (L.). High salinity stress agitates homeostasis in water potential. Extreme changes in water homeostasis and ions lead to molecular breakdown, stunted growth, and even the death of cells or whole plants [16,147].

Oligo-DNA microarrays were developed in common wheat, and these microarrays were designed to include approximately 32,000 distinctive genes characterized by several expressed sequence tags (ESTs). To classify the salinity-stress responsive genes, the expression profiles of transcripts that responded to stress were examined using microarrays. It was concluded that 5996 genes were verified by more than a 2-fold change in expression. These genes were categorized into twelve groups based on gene expression patterns [165]. Transcription-regulator activity, DNA binding, and the genes’ assigned transcription factor functions were preferentially classified as immediate response genes. In wheat, candidate genes were identified as involved in salinity-stress tolerance [165,166]. These genes are active in the regulation of transcription [112,143] and the signal transduction that is engaged in metabolic pathways [167] or acting as ion transporters [168]. cDNA library in yeast (Saccharomyces cerevisiae) was examined using a synthetic medium augmented with excessive salt concentrations (900 mM). A few clones showed comparatively improved growth. The notorious clones bore the Guanyl transferase (OsMPG1) mannose-1-phosphate gene [133]. Extreme salinity stress was significantly linked with the transcription factors of four tomato genes from the family of zinc finger. There has been prior evidence of the relationship between zinc finger transcription factors and plant salinity tolerance [169,170]. Overexpression of OSISAP1 in transgenic tobacco resulted in tolerance to salinity, dehydration, and cold stress in the new sprouts [171].

A microarray containing 384 genes associated with stress responses was used in Medicago truncatula genotypes (Jemalong A17 and 108-R) to compare rooting gene expression during salt stress. The homolog of flora TFIIIA-related TF, MtZpt2-1, and COLD-REGULATEDA1 genes were known to regulate the previous genes and were acknowledged in Jemalong A17 stress-tolerant genotypes. Two MtZpt2 Transcription factors (MtZpt2-1 and MtZpt2-2) have shown increased expression in the roots compared to 108-R [172]. Salinity stress is attributed to diverse stresses that persuade overlapping patterns in gene expression. For example, in an investigation of 8100 A. thaliana genes, approximately 2400 genes were reported to have a widespread expression in exposure to salt, oxidative and cold stress [92]. In addition, 23 genes were reported against NaCl stress. This also accounted for a small percentage of DEGs, including encoding transcription factors WOX2 and BZIP3, calcium-binding protein CML42, ubiquitin-protein ligase UBC17, and IDA-like 5 protein [92]. Most prominently, synthesized isiA encoded a novel chlorophyll (Chl)-binding protein [173] (Table 3).