Analysis of Stress-Responsive Gene Expression in Cultivated and Weedy Rice Differing in Cold Stress Tolerance

Expressing banana transcription factor MaERFVII3 in Arabidopsis confers enhanced waterlogging tolerance and root growth

Background

Waterlogging poses a significant threat to plant growth and yield worldwide. Identifying the genes responsible for mitigating waterlogging stress is crucial. Ethylene-responsive factors (ERFs) are transcriptional regulators that respond to various biotic and abiotic stresses in plants. However, their roles and involvement in responding to waterlogging stress remain largely unexplored. Hence, this study aimed to elucidate the role of ERFs in enhancing banana plant resilience to waterlogging.

Methods

We hypothesized that introducing a group VII ERF transcription factor in Arabidopsis could enhance waterlogging stress tolerance. To test this hypothesis, we isolated MaERFVII3 from banana roots, where it exhibited a significant induction in response to waterlogging stress. The isolated MaERFVII3 was introduced into Arabidopsis plants for functional gene studies.

Results

Compared with wild-type plants, the MaERFVII3-expressing Arabidopsis showed increased survival and biomass under waterlogging stress. Furthermore, the abundance of transcripts related to waterlogging and hypoxia response showed an elevation in transgenic plants but a decrease in wild-type and empty vector plants when exposed to waterlogging stress. Our results demonstrate the significant contribution of MaERFVII3 to waterlogging tolerance in Arabidopsis, providing baseline data for further exploration and potentially contributing to crop improvement programs.

Harnessing weedy rice as functional food and source of novel traits for crop improvement

A relative of cultivated rice (Oryza sativa L.), weedy or red rice (Oryza spp.) is currently recognized as the dominant weed, leading to a drastic loss of yield of cultivated rice due to its highly competitive abilities like producing more tillers, panicles, and biomass with better nutrient uptake. Due to its high nutritional value, antioxidant properties (anthocyanin and proanthocyanin), and nutrient absorption ability, weedy rice is gaining immense research attentions to understand its genetic constitution to augment future breeding strategies and to develop nutrition-rich functional foods. Consequently, this review focuses on the unique gene source of weedy rice to enhance the cultivated rice for its crucial features like water use efficiency, abiotic and biotic stress tolerance, early flowering, and the red pericarp of the seed. It explores the debating issues on the origin and evolution of weedy rice, including its high diversity, signalling aspects, quantitative trait loci (QTL) mapping under stress conditions, the intricacy of the mechanism in the expression of the gene flow, and ecological challenges of nutrient removal by weedy rice. This review may create a foundation for future researchers to understand the gene flow between cultivated crops and weedy traits and support an improved approach for the applicability of several models in predicting multiomics variables.

QTLs and Candidate Loci Associated with Drought Tolerance Traits of Kaybonnet x ZHE733 Recombinant Inbred Lines Rice Population

Rice is the most important staple crop for the sustenance of the world's population, and drought is a major factor limiting rice production. Quantitative trait locus (QTL) analysis of drought-resistance-related traits was conducted on a recombinant inbred line (RIL) population derived from the self-fed progeny of a cross between the drought-resistant tropical japonica U.S. adapted cultivar Kaybonnet and the drought-sensitive indica cultivar ZHE733. K/Z RIL population of 198 lines was screened in the field at Fayetteville (AR) for three consecutive years under controlled drought stress (DS) and well-watered (WW) treatment during the reproductive stage. The effects of DS were quantified by measuring morphological traits, grain yield components, and root architectural traits. A QTL analysis using a set of 4133 single nucleotide polymorphism (SNP) markers and the QTL IciMapping identified 41 QTLs and 184 candidate genes for drought-related traits within the DR-QTL regions. RT-qPCR in parental lines was used to confirm the putative candidate genes. The comparison between the drought-resistant parent (Kaybonnet) and the drought-sensitive parent (ZHE733) under DS conditions revealed that the gene expression of 15 candidate DR genes with known annotations and two candidate DR genes with unknown annotations within the DR-QTL regions was up-regulated in the drought-resistant parent (Kaybonnet). The outcomes of this research provide essential information that can be utilized in developing drought-resistant rice cultivars that have higher productivity when DS conditions are prevalent.

Ornithine δ-aminotransferase OsOAT is critical for male fertility and cold tolerance during rice plant development

Cold stress is a major factor limiting the production and geographical distribution of rice (Oryza sativa) varieties. However, the molecular mechanisms underlying cold tolerance remain to be elucidated. Here, we report that ornithine δ-aminotransferase (OsOAT) contributes to cold tolerance during the vegetative and reproductive development of rice. osoat mutant was identified as a temperature-sensitive male sterile mutant with deformed floral organs and seedlings sensitive to cold stress. Comparative transcriptome analysis showed that OsOAT mutation and cold treatment of the wild-type plant led to similar changes in the global gene expression profiles in anthers. OsOAT genes in indica rice Huanghuazhan (HHZ) and japonica rice Wuyungeng (WYG) are different in gene structure and response to cold. OsOAT is cold-inducible in WYG but cold-irresponsive in HHZ. Further studies showed that indica varieties carry both WYG-type and HHZ-type OsOAT, whereas japonica varieties mostly carry WYG-type OsOAT. Cultivars carrying HHZ-type OsOAT are mainly distributed in low-latitude regions, whereas varieties carrying WYG-type OsOAT are distributed in both low- and high-latitude regions. Moreover, indica varieties carrying WYG-type OsOAT generally have higher seed-setting rates than those carrying HHZ-type OsOAT under cold stress at reproductive stage, highlighting the favorable selection for WYG-type OsOAT during domestication and breeding to cope with low temperatures.

Identification of F-box gene family in Brassica oleracea and expression analysis in response to low-temperature stress

Unfavorable climatic conditions, such as low temperatures, often hinder the growth and production of crops worldwide. The F-box protein-encoding gene family performs an essential role in plant stress resistance. However, a comprehensive analysis of the F-box gene family in cabbage (Brassica oleracea var capitata L.) has not been reported yet. In this study, genome-wide characterization of F-box proteins in cabbage yielded 303 BoFBX genes and 224 BoFBX genes unevenly distributed on 9 chromosomes of cabbage. Phylogenetic analysis of 303 BoFBX genes was classified into nine distinct subfamily groups (GI-GIX). Analysis of the gene structure of BoFBX genes indicated that most genes within the same clade are highly conserved. In addition, tissue-specific expression analysis revealed that six F-box genes in cabbage showed the highest expression in rosette leaves, followed by roots and stems and the lowest expression was observed in the BoFBX156 gene. In contrast, the expression of the other five genes, BoFBX100, BoFBX117, BoFBX136, BoFBX137 and BoFBX213 was observed to be upregulated in response to low-temperature stress. Moreover, we found that the expression level of the BoFBX gene in the cold-tolerant cultivar "ZG" was higher than that in cold-sensitive "YC" with the extension of stress duration, while expression levels of each gene in "ZG" were higher than "YC" at 24 h. Knowledge of the various functions provided by BoFBXs genes and their expression patterns provides a firm theoretical foundation for explaining the functions of BoFBXs, thereby contributing to the molecular breeding process of cabbage.

Chromosomal Location of Pm12-A Novel Powdery Mildew Resistance Gene from Avena sterilis

Identification of new, effective disease resistance genes is a very important aspect of plant breeding. Also important is the precise location of individual loci and tagging them with DNA markers for marker assisted selection. The aim of the present study was identification of the molecular markers linked with Pm12, a new effective resistance gene to powdery mildew, and their location in the oat genome. The analysis was performed on 167 F₂ individuals from a hybrid of Fuchs × CN67383, with the status of the locus in each individual verified by progeny test in F₃. Segregation ratios confirmed the monogenic nature of resistance. Making use of the sequence data of DNA markers and the oat OT3098 v2 genome reference assembly, Pm12 is located on chromosome 7C. A comparison was also made with the reference consensus map, to which there are more reports of mapped genes to date. The mapping results suggest that Pm12 is located in the interval 103.8-111.7 cM on this map. No powdery mildew resistance locus has been identified in this region so far, suggesting that Avena sterilis CN67383 carries a novel locus offering effective resistance in oat breeding. The information included in the oat genome annotation allowed for the identification of candidate genes in the close region of the marker cluster for Pm12. This information may provide an interesting source of further analysis of the pathways of various genes in response to the stress of powdery mildew infection.

Comparative transcriptome analysis of synthetic and common wheat in response to salt stress

Salt stress reduces wheat yield. Therefore, improvement for enhanced salt stress tolerance is necessary for stable production. To understand the molecular mechanism of salt tolerance in common wheat and synthetic hexaploid (SH) wheat, RNA sequencing was performed on the roots of three wheat lines salt-tolerant SH wheat, salt-tolerant common wheat, and salt-sensitive common wheat. Differentially expressed genes (DEGs) in response to salt stress were characterized using gene ontology enrichment analysis. Salt tolerance in common wheat has been suggested to be mainly regulated by the activation of transporters. In contrast, salt tolerance in SH wheat is enhanced through up-regulation of the reactive oxygen species signaling pathway, other unknown pathways, and different ERF transcription factors. These results indicate that salt tolerance is differentially controlled between common wheat and SH wheat. Furthermore, QTL analysis was performed using the F₂ population derived from SH and salt-sensitive wheat. No statistically significant QTL was detected, suggesting that numerous QTLs with negligible contributions are involved in salt tolerance in SH wheat. We also identified DEGs specific to each line near one probable QTL. These findings show that SH wheat possesses salt tolerance mechanisms lacking in common wheat and may be potential breeding material for salt tolerance.

Gene-coexpression network analysis identifies specific modules and hub genes related to cold stress in rice

Background

When plants are subjected to cold stress, they undergo a series of molecular and physiological changes to protect themselves from injury. Indica cultivars can usually withstand only mild cold stress in a relatively short period. Hormone-mediated defence response plays an important role in cold stress. Weighted gene co-expression network analysis (WGCNA) is a very useful tool for studying the correlation between genes, identifying modules with high phenotype correlation, and identifying Hub genes in different modules. Many studies have elucidated the molecular mechanisms of cold tolerance in different plants, but little information about the recovery process after cold stress is available.

Results

To understand the molecular mechanism of cold tolerance in rice, we performed comprehensive transcriptome analyses during cold treatment and recovery stage in two cultivars of near-isogenic lines (9311 and DC907). Twelve transcriptomes in two rice cultivars were determined. A total of 2509 new genes were predicted by fragment splicing and assembly, and 7506 differentially expressed genes were identified by pairwise comparison. A total of 26 modules were obtained by expression-network analysis, 12 of which were highly correlated with cold stress or recovery treatment. We further identified candidate Hub genes associated with specific modules and analysed their regulatory relationships based on coexpression data. Results showed that various plant-hormone regulatory genes acted together to protect plants from physiological damage under short-term low-temperature stress. We speculated that this may be common in rice. Under long-term cold stress, rice improved the tolerance to low-temperature stress by promoting autophagy, sugar synthesis, and metabolism.

Conclusion

Through WGCNA analysis at the transcriptome level, we provided a potential regulatory mechanism for the cold stress and recovery of rice cultivars and identified candidate central genes. Our findings provided an important reference for the future cultivation of rice strains with good tolerance.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08438-3.

Comparative transcriptomic and physiological analyses of weedy rice and cultivated rice to identify vital differentially expressed genes and pathways regulating the ABA response

Weedy rice is a valuable germplasm resource characterized by its high tolerance to both abiotic and biotic stresses. Abscisic acid (ABA) serves as a regulatory signal in plant cells as part of their adaptive response to stress. However, a global understanding of the response of weedy rice to ABA remains to be elucidated. In the present study, the sensitivity to ABA of weedy rice (WR04-6) was compared with that of temperate japonica Shennong9816 (SN9816) in terms of seed germination and post-germination growth via the application of exogenous ABA and diniconazole, an inhibitor of ABA catabolism. Physiological analysis and a transcriptomic comparison allowed elucidation of the molecular and physiological mechanisms associated with continuous ABA and diniconazole treatment. WR04-6 was found to display higher ABA sensitivity than SN9816, resulting in the rapid promotion of antioxidant enzyme activity. Comparative transcriptomic analyses indicated that the number of differentially expressed genes (DEGs) in WR04-6 seedlings treated with 2 μM ABA or 10 μM diniconazole was greater than that in SN9816 seedlings. Genes involved in stress defense, hormone signal transduction, and glycolytic and citrate cycle pathways were highly expressed in WR04-6 in response to ABA and diniconazole. These findings provide new insight into key processes mediating the ABA response between weedy and cultivated rice.

RNA-Seq transcriptome analysis to identify candidate genes involved in non-target site-based mesosulfuron-methyl resistance in Beckmannia syzigachne

American sloughgrass (Beckmannia syzigachne Steud.) has become a dominant weed in fields with rice-wheat rotation. Moreover, herbicide resistance has rendered weed control difficult. We identified a biotype showing resistance to ALS inhibitor mesosulfuron-methyl with a resistant index 3.3, but without any ALS mutation. This study aims to identify and confirm the factors associated with non-target site resistance of this biotype to mesosulfuron-methyl using RNA-Seq. 118,111 unigenes were assembled, and 50.9% of these were annotated across seven databases. Eleven contigs related to metabolic resistance were identified based on differential expression via RNA-Seq which include a novel resistance-related transcription factor (MYC3) and two disease resistance proteins were also identified (At1g58602 and At1g15890). Fold changes in expression of these genes in comparison M-R vs. M-S ranged from 3.9 to 11.6, as confirmed by qPCR. The expression of a contig annotated as cytochrome P450 (CYP86B1) in resistant individuals was over 3 times higher than that in sensitive individuals at 0-72 h after mesosulfuron-methyl treatment. A similar trend was noted for three other genes annotated as glutathione S-transferase (GST), namely GST-T3, GST-U6, and GST-U14; the expression of GST-U6 in resistant individuals was up to 142.3 times higher than that in sensitive individuals at 24 h after mesosulfuron-methyl treatment. In addition, GST activity in resistant individuals was 2.1 to 5.3 times higher than that in sensitive individuals. The GR₅₀ of resistant biotype decreased from 24.4 to 11.3 g a.i. ha^-1 after P450 inhibitor malathion treatment. This study identified a cytochrome P450 gene CYP86B1 and three GST genes GST-T3, GST-U6, and GST-U14 that have higher expression in mesosulfuron-methyl resistant B. syzigachne, suggesting that both P450- and GST-based activities could be involved in resistance.

The 21st Century Agriculture: When Rice Research Draws Attention to Climate Variability and How Weedy Rice and Underutilized Grains Come in Handy

Rice, the first crop to be fully sequenced and annotated in the mid-2000s, is an excellent model species for crop research due mainly to its relatively small genome and rich genetic diversity. The 130-million-year-old cereal came into the limelight in the 1960s when the semi-dwarfing gene sd-1, better known as the "green revolution" gene, resulted in the establishment of a high-yielding semi-dwarf variety IR8. Deemed as the miracle rice, IR8 saved millions of lives and revolutionized irrigated rice farming particularly in the tropics. The technology, however, spurred some unintended negative consequences, especially in prompting ubiquitous monoculture systems that increase agricultural vulnerability to extreme weather events and climate variability. One feasible way to incorporate resilience in modern rice varieties with narrow genetic backgrounds is by introgressing alleles from the germplasm of its weedy and wild relatives, or perhaps from the suitable underutilized species that harbor novel genes responsive to various biotic and abiotic stresses. This review reminisces the fascinating half-century journey of rice research and highlights the potential utilization of weedy rice and underutilized grains in modern breeding programs. Other possible alternatives to improve the sustainability of crop production systems in a changing climate are also discussed.

Overexpression of Rice Expansin7 (Osexpa7) Confers Enhanced Tolerance to Salt Stress in Rice

Expansins are key regulators of cell-wall extension and are also involved in the abiotic stress response. In this study, we evaluated the function of OsEXPA7 involved in salt stress tolerance. Phenotypic analysis showed that OsEXPA7 overexpression remarkably enhanced tolerance to salt stress. OsEXPA7 was highly expressed in the shoot apical meristem, root, and the leaf sheath. Promoter activity of OsEXPA7:GUS was mainly observed in vascular tissues of roots and leaves. Morphological analysis revealed structural alterations in the root and leaf vasculature of OsEXPA7 overexpressing (OX) lines. OsEXPA7 overexpression resulted in decreased sodium ion (Na⁺) and accumulated potassium ion (K⁺) in the leaves and roots. Under salt stress, higher antioxidant activity was also observed in the OsEXPA7-OX lines, as indicated by lower reactive oxygen species (ROS) accumulation and increased antioxidant activity, when compared with the wild-type (WT) plants. In addition, transcriptional analysis using RNA-seq and RT-PCR revealed that genes involved in cation exchange, auxin signaling, cell-wall modification, and transcription were differentially expressed between the OX and WT lines. Notably, salt overly sensitive 1, which is a sodium transporter, was highly upregulated in the OX lines. These results suggest that OsEXPA7 plays an important role in increasing salt stress tolerance by coordinating sodium transport, ROS scavenging, and cell-wall loosening.

Physiological and transcriptional responses to low-temperature stress in rice genotypes at the reproductive stage

Rice growth and productivity is adversely affected by low-temperature stress. From a previous screen of diverse rice genotypes for cold tolerance parameters at the vegetative stage, we selected the tolerant Nipponbare and M202 genotypes and sensitive Cypress and Secano do Brazil genotypes for further analysis at the reproductive stage for physiological and yield parameters. Cold stress severely affected grain yield as estimated by the number of grain per panicle, panicle length, and 100 seed weight. Analysis of gene expression of 21 genes involved in physiological responses to low temperature tested, in the flag leaf and inflorescence tissue of these genotypes, showed an increased expression of the Lipid Transfer Protein genes LTP7 and LTP10 in flag leaf tissue of the tolerant Nipponbare and M202, along with a significant increase in the relative expression of stress-responsive transcription factors (TFs) and cold-inducible genes. In flag leaf tissue OsNAC9, OsNAC10 and OsNAP genes showed high correlation with photosynthesis, stomatal conductance, transpiration and Quantum Efficiency of PSII. In consequence of the foregoing results, we conclude that Nipponbare and M202 are cold tolerant genotypes and that LTP7, LTP10, OsNAC9, OsNAC10 and OsNAP genes can be used as markers in screening for cold tolerance at the reproductive stage. Furthermore based on the results we propose a model of low-temperature tolerance mechanism of how stress is perceived, and how the signal cascade acts to promote tolerance at below-ideal temperatures.

Transcriptomics profiling in response to cold stress in cultivated rice and weedy rice

Weedy rice is an important germplasm resource for rice improvement because it has useful genes for many abiotic stresses including cold tolerance. We identified the cold tolerance and cold sensitivity of two weedy rice lines (WR 03-35 and WR 03-26) and two cultivated rice lines (Kongyu 131 and 9311). During the seedling stage of these lines, we used RNA-seq to measure changes in weedy rice and cultivated rice whole-genome transcriptome before and after cold treatment. We identified 14,213 and 14,730 differentially expressed genes (DEGs) in cold-tolerant genotypes (WR 03-35, Kongyu 131), and 9219 and 720 DEGs were observed in two cold-sensitive genotypes (WR 03-26, 9311). Many common and special DEGs were analyzed in cold-tolerant and cold-sensitive genotypes, respectively. Some typical genes related to cold stress such as the basic helix-loop-helix (bHLH) gene and leucine-rich repeat (LRR) domain gene etc. The number of these DEGs in cold-tolerant genotypes is more than those found in cold-sensitive genotypes. The gene ontology (GO) enrichment analyses showed significantly enriched terms for biological processes, cellular components and molecular functions. In addition, some genes related to several plant hormones such as abscisic acid (ABA), gibberellic acid (GA), auxin and ethylene were identified. To confirm the RNA-seq data, semi-quantitative RT-PCR and qRT-PCR were performed on 12 randomly selected DEGs. The expression patterns of RNA-seq on these genes corresponded with the semi-quantitative RT-PCR and qRT-PCR method. This study suggests the gene resources related to cold stress from weedy rice could be valuable for understanding the mechanisms involved in cold stress and rice breeding for improving cold tolerance.

Deep RNAseq indicates protective mechanisms of cold-tolerant indica rice plants during early vegetative stage

Cold-tolerance in rice may be related to increased cellulose deposition in the cell wall, membrane fatty acids unsaturation and differential expression of several newly identified genes. Low temperature exposure during early vegetative stages limits rice plant's growth and development. Most genes previously related to cold tolerance in rice are from the japonica subspecies. To help clarify the mechanisms that regulate cold tolerance in young indica rice plants, comparative transcriptome analysis of 6 h cold-treated (10 °C) leaves from two genotypes, cold-tolerant (CT) and cold-sensitive (CS), was performed. Differentially expressed genes were identified: 831 and 357 sequences more expressed in the tolerant and in the sensitive genotype, respectively. The genes with higher expression in the CT genotype were used in systems biology analyses to identify protein-protein interaction (PPI) networks and nodes (proteins) that are hubs and bottlenecks in the PPI. From the genes more expressed in the tolerant plants, 60% were reported as affected by cold in previous transcriptome experiments and 27% are located within QTLs related to cold tolerance during the vegetative stage. Novel cold-responsive genes were identified. Quantitative RT-PCR confirmed the high-quality of RNAseq libraries. Several genes related to cell wall assembly or reinforcement are cold-induced or constitutively highly expressed in the tolerant genotype. Cold-tolerant plants have increased cellulose deposition under cold. Genes related to lipid metabolism are more expressed in the tolerant genotype, which has higher membrane fatty acids unsaturation, with increasing levels of linoleic acid under cold. The CT genotype seems to have higher photosynthetic efficiency and antioxidant capacity, as well as more effective ethylene, Ca²⁺ and hormone signaling than the CS. These genes could be useful in future biotechnological approaches aiming to increase cold tolerance in rice.

Enhanced photosynthesis endows seedling growth vigour contributing to the competitive dominance of weedy rice over cultivated rice

BACKGROUND

Weedy rice, as one of the worst paddy field weeds worldwide, bears vigorous seedlings and dominantly competes with cultivated rice causing serious crop yield losses. To elucidate the causes of its stronger seedling vigour endowing its dominant competition with cultivated rice, comparative studies on seedling growth characteristics were conducted among six weedy rice biotypes and the two indica and japonica cultivars Shanyou-63 (SY-63) and Zhendao-8 (ZD-8), respectively, in the greenhouse.

RESULTS

Weedy rice emerged 2 to 3 days earlier, rapidly grew 1.3-1.7 cm taller daily, produced more secondary adventitious roots and greater aboveground fresh biomass than cultivated rice. Moreover, weedy rice exhibited greater photosynthetic pigment content, net photosynthetic rate, stomatal conductance, intercellular CO₂ concentration, transpiration rate, and chlorophyll fluorescence kinetic parameters. An enhanced overall photosynthetic activity in weedy rices was attributed to the combined action of a larger antenna, more active reaction centres and higher quantum yield for electron transfer beyond Q_A .

CONCLUSIONS

Enhanced photosynthesis of weedy rice at the seedling stage should be the main factor for leading to strong competitive dominance over cultivated rice. © 2016 Society of Chemical Industry.

Breeding approaches and genomics technologies to increase crop yield under low-temperature stress

Improved knowledge about plant cold stress tolerance offered by modern omics technologies will greatly inform future crop improvement strategies that aim to breed cultivars yielding substantially high under low-temperature conditions. Alarmingly rising temperature extremities present a substantial impediment to the projected target of 70% more food production by 2050. Low-temperature (LT) stress severely constrains crop production worldwide, thereby demanding an urgent yet sustainable solution. Considerable research progress has been achieved on this front. Here, we review the crucial cellular and metabolic alterations in plants that follow LT stress along with the signal transduction and the regulatory network describing the plant cold tolerance. The significance of plant genetic resources to expand the genetic base of breeding programmes with regard to cold tolerance is highlighted. Also, the genetic architecture of cold tolerance trait as elucidated by conventional QTL mapping and genome-wide association mapping is described. Further, global expression profiling techniques including RNA-Seq along with diverse omics platforms are briefly discussed to better understand the underlying mechanism and prioritize the candidate gene (s) for downstream applications. These latest additions to breeders' toolbox hold immense potential to support plant breeding schemes that seek development of LT-tolerant cultivars. High-yielding cultivars endowed with greater cold tolerance are urgently required to sustain the crop yield under conditions severely challenged by low-temperature.

Comparative analysis of gene expression in response to cold stress in diverse rice genotypes

Cold stress is a major factor affecting rice (Oryza sativa) growth and productivity, limiting its distribution worldwide. Rice production is affected primarily due to its vulnerability to cold stress at seedling stage, as well as reproductive stage leading to spikelet sterility. We report here the analysis of 21 diverse rice genotypes from the USDA mini-core collection for cold tolerance and categorized their tolerance levels on the basis of reduction in growth measured by root and shoot length. The screening identified 12 cold tolerant genotypes from which six tolerant genotypes were characterized at the vegetative stage for cold tolerance and gas-exchange parameters. Two tolerant and two sensitive genotypes were used further for gene expression analysis. Lipid Transfer Protein (LTP) genes showed a clear difference in expression between cold tolerant and sensitive genotypes suggesting that they are good candidates for engineering cold tolerance in rice. Nipponbare was identified as a cold tolerant genotype with stress tolerance mechanism potentially operating via both ABA dependent and independent pathways.