Genome-wide identification of MATE and ALMT genes and their expression profiling in mungbean (Vigna radiata L.) under aluminium stress.

The Multidrug and toxic compound extrusion (MATE) and aluminium activated malate transporter (ALMT) gene families are involved in response to aluminium (Al) stress. In this study, we identified 48 MATE and 14 ALMT gene families in Vigna radiata genome and classified into 5 (MATE) and 3 (ALMT) clades by phylogenetic analysis. All the VrMATE and VrALMT genes were distributed across mungbean chromosomes. Tandem duplication was the main driving force for evolution and expansion of MATE gene family. Collinearity of mungbean with soybean indicated that MATE gene family is closely linked to Glycine max. Eight MATE transporters in clade 2 were found to be associated with previously characterized Al tolerance related MATEs in various plant species. Citrate exuding motif (CEM) was present in seven VrMATEs of clade 2. Promoter analysis revealed abundant plant hormone and stress responsive cis-elements. Results from quantitative real time-polymerase chain reaction (qRT-PCR) revealed that VrMATE19, VrMATE30 and VrALMT13 genes were markedly up-regulated at different time points under Al stress. Overall, this study offers a new direction for further molecular characterization of the MATE and ALMT genes in mungbean for Al tolerance.

Carbon dioxide responsiveness mitigates rice yield loss under high night temperature.

Increasing night-time temperatures are a major threat to sustaining global rice (Oryza sativa L.) production. A simultaneous increase in [CO2] will lead to an inevitable interaction between elevated [CO2] (e[CO2]) and high night temperature (HNT) under current and future climates. Here, we conducted field experiments to identify [CO2] responsiveness from a diverse indica panel comprising 194 genotypes under different planting geometries in 2016. Twenty-three different genotypes were tested under different planting geometries and e[CO2] using a free-air [CO2] enrichment facility in 2017. The most promising genotypes and positive and negative controls were tested under HNT and e[CO2] + HNT in 2018. [CO2] responsiveness, measured as a composite response index on different yield components, grain yield, and photosynthesis, revealed a strong relationship (R2 = 0.71) between low planting density and e[CO2]. The most promising genotypes revealed significantly lower (P < 0.001) impact of HNT in high [CO2] responsive (HCR) genotypes compared to the least [CO2] responsive genotype. [CO2] responsiveness was the major driver determining grain yield and related components in HCR genotypes with a negligible yield loss under HNT. A systematic investigation highlighted that active selection and breeding for [CO2] responsiveness can lead to maintained carbon balance and compensate for HNT-induced yield losses in rice and potentially other C3 crops under current and future warmer climates.

Targeting Induced Local Lesions in Genomes (TILLING): advances and opportunities for fast tracking crop breeding.

The intensification of food production via conventional crop breeding alone is inadequate to cater for global hunger. The development of precise and expeditious high throughput reverse genetics approaches has hugely benefited modern plant breeding programs. Targeting Induced Local Lesions in Genomes (TILLING) is one such reverse genetics approach which employs chemical/physical mutagenesis to create new genetic sources and identifies superior/novel alleles. Owing to technical limitations and sectional applicability of the original TILLING protocol, it has been timely modified. Successions include: EcoTILLING, Double stranded EcoTILLING (DEcoTILLING), Self-EcoTILLING, Individualized TILLING (iTILLING), Deletion-TILLING (De-TILLING), PolyTILLING, and VeggieTILLING. This has widened its application to a variety of crops and needs. They can characterize mutations in coding as well as non-coding regions and can overcome complexities associated with the large genomes. Combining next generation sequencing tools with the existing TILLING protocols has enabled screening of huge germplasm collections and mutant populations for the target genes. In silico TILLING platforms have transformed TILLING into an exciting breeding approach. The present review outlines these multifarious TILLING modifications for precise mutation detection and their application in advance breeding programmes together with relevant case studies. Appropriate use of these protocols will open up new avenues for crop improvement in the twenty first century.

Linking genome wide RNA sequencing with physio-biochemical and cytological responses to catalogue key genes and metabolic pathways for alkalinity stress tolerance in lentil (Lens culinaris Medikus).

BACKGROUND: Alkaline soils cause low productivity in crop plants including lentil. Alkalinity adaptation strategies in lentil were revealed when morpho-anatomical and physio-biochemical observations were correlated with transcriptomics analysis in tolerant (PDL-1) and sensitive (L-4076) cultivars at seedling stage. RESULTS: PDL-1 had lesser salt injury and performed better as compared to L-4076. Latter showed severe wilting symptoms and higher accumulation of Na+ and lower K+ in roots and shoots. PDL-1 performed better under high alkalinity stress which can be attributed to its higher mitotic index, more accumulation of K+ in roots and shoots and less aberrantly dividing cells. Also, antioxidant enzyme activities, osmolytes' accumulation, relative water content, membrane stability index and abscisic acid were higher in this cultivar. Differentially expressed genes (DEGs) related to these parameters were upregulated in tolerant genotypes compared to the sensitive one. Significantly up-regulated DEGs were found to be involved in abscisic acid (ABA) signalling and secondary metabolites synthesis. ABA responsive genes viz. dehydrin 1, 9-cis-epoxycarotenoid dioxygenase, ABA-responsive protein 18 and BEL1-like homeodomain protein 1 had log2fold change above 4.0. A total of 12,836 simple sequence repeats and 4,438 single nucleotide polymorphisms were identified which can be utilized in molecular studies. CONCLUSIONS: Phyto-hormones biosynthesis-predominantly through ABA signalling, and secondary metabolism are the most potent pathways for alkalinity stress tolerance in lentil. Cultivar PDL-1 exhibited high tolerance towards alkalinity stress and can be used in breeding programmes for improving lentil production under alkalinity stress conditions.

Walking through crossroads-rice responses to heat and biotic stress interactions.

Rice, the most important source of calories for humans is prone to severe yield loss due to changing climate including heat stress. Additionally, rice encounters biotic stresses in conjunction with heat stress, which exacerbates the adverse effects, and exponentially increase such losses. Several investigations have identified biotic and heat stress-related quantitative trait loci (QTLs) that may contribute to improved tolerance to these stresses. However, a significant knowledge gap exists in identifying the genomic regions imparting tolerance against combined biotic and heat stress. Hereby, we are presenting a conceptual meta-analysis identifying genomic regions that may be promising candidates for enhancing combined biotic and heat stress tolerance in rice. Fourteen common genomic regions were identified along chromosomes 1, 2, 3, 4, 6, 10 and 12, which harbored 1265 genes related to heat stress and defense responses in rice. Further, the meta expression analysis revealed 24 differentially expressed genes (DEGs) involved in calcium-mediated stress signaling including transcription factors Myb, bHLH, ROS signaling, molecular chaperones HSP110 and pathogenesis related proteins. Additionally, we also proposed a hypothetical model based on GO and MapMan analysis representing the pathways intersecting heat and biotic stresses. These DEGs can be potential candidate genes for improving tolerance to combined biotic and heat stress in rice. We present a framework highlighting plausible connecting links (QTLs/genes) between rice response to heat stress and different biotic factors associated with yield, that can be extended to other crops.

Transcriptome skimming of lentil (Lens culinaris Medikus) cultivars with contrast reaction to salt stress.

Extensive transcriptomic skimming was conducted to decipher molecular, morphological, physiological, and biochemical responses in salt-tolerant (PDL-1) and salt-sensitive (L-4076) cultivars under control (0 mM NaCl) and salinity stress (120 mM NaCl) conditions at seedling stage. Morphological, physiological, and biochemical studies revealed that PDL-1 exhibited no salt injury and had higher K+/Na+ ratio, relative water content (RWC), chlorophyll, glycine betaine, and soluble sugars in leaves while lower H2O2 induced fluorescence signals in roots as compared to L-4076. Transcriptomic profile revealed a total of 17,433 significant differentially expressed genes (DEGs) under different treatments and cultivar combinations that include 2557 upregulated and 1533 downregulated transcripts between contrasting cultivars under salt stress. Accuracy of transcriptomic analysis was validated through quantification of 10 DEGs via quantitative real-time polymerase chain reaction (qRT-PCR). DEGs were functionally characterized by Gene Ontology (GO) analysis and assigned to various metabolic pathways using MapMan. DEGs were found to be significantly associated with phytohormone-mediated signal transduction, cellular redox homoeostasis, secondary metabolism, nitrogen metabolism, and cellular stress signaling. The present study revealed putative molecular mechanism of salinity tolerance in lentil together with identification of 5643 simple sequence repeats (SSRs) and 176,433 single nucleotide polymorphisms (SNPs) which can be utilized to enhance linkage maps density along with detection of quantitative trait loci (QTLs) associated with traits of interests. Stress-related pathways identified in this study divulged plant functioning that can be targeted to improve salinity stress tolerance in crop species.

Plant epigenomics for extenuation of abiotic stresses: challenges and future perspectives.

Climate change has escalated abiotic stresses, leading to adverse effects on plant growth and development, eventually having deleterious consequences on crop productivity. Environmental stresses induce epigenetic changes, namely cytosine DNA methylation and histone post-translational modifications, thus altering chromatin structure and gene expression. Stable epigenetic changes are inheritable across generations and this enables plants to adapt to environmental changes (epipriming). Hence, epigenomes serve as a good source of additional tier of variability for development of climate-smart crops. Epigenetic resources such as epialleles, epigenetic recombinant inbred lines (epiRILs), epigenetic quantitative trait loci (epiQTLs), and epigenetic hybrids (epihybrids) can be utilized in epibreeding for improving stress tolerance of crops. Epigenome engineering is also gaining momentum for developing sustainable epimarks associated with important agronomic traits. Different epigenome editing tools are available for creating, erasing, and reading such epigenetic codes in plant genomes. However, epigenome editing is still understudied in plants due to its complex nature. Epigenetic interventions such as epi-fingerprinting can be exploited in the near future for health and quality assessment of crops under stress conditions. Keeping in view the challenges and opportunities associated with this important technology, the present review intends to enhance understanding of stress-induced epigenetic changes in plants and its prospects for development of climate-ready crops.

Fab Advances in Fabaceae for Abiotic Stress Resilience: From 'Omics' to Artificial Intelligence.

Legumes are a better source of proteins and are richer in diverse micronutrients over the nutritional profile of widely consumed cereals. However, when exposed to a diverse range of abiotic stresses, their overall productivity and quality are hugely impacted. Our limited understanding of genetic determinants and novel variants associated with the abiotic stress response in food legume crops restricts its amelioration. Therefore, it is imperative to understand different molecular approaches in food legume crops that can be utilized in crop improvement programs to minimize the economic loss. 'Omics'-based molecular breeding provides better opportunities over conventional breeding for diversifying the natural germplasm together with improving yield and quality parameters. Due to molecular advancements, the technique is now equipped with novel 'omics' approaches such as ionomics, epigenomics, fluxomics, RNomics, glycomics, glycoproteomics, phosphoproteomics, lipidomics, regulomics, and secretomics. Pan-omics-which utilizes the molecular bases of the stress response to identify genes (genomics), mRNAs (transcriptomics), proteins (proteomics), and biomolecules (metabolomics) associated with stress regulation-has been widely used for abiotic stress amelioration in food legume crops. Integration of pan-omics with novel omics approaches will fast-track legume breeding programs. Moreover, artificial intelligence (AI)-based algorithms can be utilized for simulating crop yield under changing environments, which can help in predicting the genetic gain beforehand. Application of machine learning (ML) in quantitative trait loci (QTL) mining will further help in determining the genetic determinants of abiotic stress tolerance in pulses.

Genome-wide identification and functional prediction of salt- stress related long non-coding RNAs (lncRNAs) in chickpea (Cicer arietinum L.).

LncRNAs (long noncoding RNAs) are 200 bp length crucial RNA molecules, lacking coding potential and having important roles in regulating gene expression, particularly in response to abiotic stresses. In this study, we identified salt stress-induced lncRNAs in chickpea roots and predicted their intricate regulatory roles. A total of 3452 novel lncRNAs were identified to be distributed across all 08 chickpea chromosomes. On comparing salt-tolerant (ICCV 10, JG 11) and salt-sensitive cultivars (DCP 92-3, Pusa 256), 4446 differentially expressed lncRNAs were detected under various salt  treatments. We predicted 3373 lncRNAs to be regulating their target genes in cis regulating manner and 80 unique lncRNAs were observed as interacting with 136 different miRNAs, as eTMs (endogenous target mimic) targets of miRNAs and implicated them in the regulatory network of salt stress response. Functional analysis of these lncRNA revealed their association in targeting salt stress response-related genes like potassium transporter, transporter family genes, serine/threonine-protein kinase, aquaporins like TIP1-2, PIP2-5 and transcription factors like, AP2, NAC, bZIP, ERF, MYB and WRKY. Furthermore, about 614 lncRNA-SSRs (simple sequence repeats) were identified as a new generation of molecular markers with higher efficiency and specificity in chickpea. Overall, these findings will pave the understanding of comprehensive functional role of potential lncRNAs, which can help in providing insight into the molecular mechanism of salt tolerance in chickpea. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12298-021-01093-0.

Genetic Dissection and Identification of Candidate Genes for Salinity Tolerance Using Axiom®CicerSNP Array in Chickpea.

Globally, chickpea production is severely affected by salinity stress. Understanding the genetic basis for salinity tolerance is important to develop salinity tolerant chickpeas. A recombinant inbred line (RIL) population developed using parental lines ICCV 10 (salt-tolerant) and DCP 92-3 (salt-sensitive) was screened under field conditions to collect information on agronomy, yield components, and stress tolerance indices. Genotyping data generated using Axiom®CicerSNP array was used to construct a linkage map comprising 1856 SNP markers spanning a distance of 1106.3 cM across eight chickpea chromosomes. Extensive analysis of the phenotyping and genotyping data identified 28 quantitative trait loci (QTLs) explaining up to 28.40% of the phenotypic variance in the population. We identified QTL clusters on CaLG03 and CaLG06, each harboring major QTLs for yield and yield component traits under salinity stress. The main-effect QTLs identified in these two clusters were associated with key genes such as calcium-dependent protein kinases, histidine kinases, cation proton antiporter, and WRKY and MYB transcription factors, which are known to impart salinity stress tolerance in crop plants. Molecular markers/genes associated with these major QTLs, after validation, will be useful to undertake marker-assisted breeding for developing better varieties with salinity tolerance.

Molecular mapping of aluminium resistance loci based on root re-growth and Al-induced fluorescent signals (callose accumulation) in lentil (Lens culinaris Medikus).

Development of aluminium (Al) resistant genotypes through molecular breeding is a major approach for increasing seed yield under acidic conditions. There are no available reports on mapping of Al resistance loci and molecular breeding for Al resistant varieties in lentil. The present study reports a major quantitative trait loci (QTL) for Al resistance using simple sequence repeat (SSR) markers in F2 and F3 mapping populations derived from contrasting parents. Phenotypic response to Al was measured on the bases of root re-growth (RRG), fluorescent signals (callose accumulation) and Al contents in hydroponic assay. After screening 495 SSR markers to search polymorphism between two contrasting parents, 73 polymorphic markers were used for bulk segregation analysis. Two major QTLs were identified using seven trait linked markers, one each for fluorescent signals and RRG mapped on linkage group (LG) 1 under Al stress conditions in F2 mapping population of cross BM-4 × L-4602. One major QTL (qAlt_fs) was localised between PLC_88 and PBA_LC_373, covering 25.9 cM with adjacent marker PLC_88 at a distance of 0.4 cM. Another major QTL (qAlt_rrg) for RRG was in the marker interval of PBA_LC_1247 and PLC_51, covering a distance of 45.7 cM with nearest marker PBA_LC_1247 at a distance of 21.2 cM. Similarly, in F3 families of BM-4 × L-4602 and BM-4 × L-7903, LG-1 was extended to 285.9 and 216.4 cM respectively, having four newly developed genic-SSR markers. These QTLs had a logarithm of odd (LOD) value of 140.5 and 28.8 along with phenotypic variation of 52% and 11% for fluorescent signals and RRG respectively, whereas, qAlt_rrg had LOD of 36 and phenotypic variance of 25% in F3 population of BM-4 × L-4602. Two major QTLs identified in the present study can be further dissected for candidate gene discovery and development of molecular markers for breeding improved varieties with high Al resistance.

Transcriptome analysis of lentil (Lens culinaris Medikus) in response to seedling drought stress.

BACKGROUND: Drought stress is one of the most harmful abiotic stresses in crop plants. As a moderately drought tolerant crop, lentil is a major crop in rainfed areas and a suitable candidate for drought stress tolerance research work. Screening for drought tolerance stress under hydroponic conditions at seedling stage with air exposure is an efficient technique to select genotypes with contrasting traits. Transcriptome analysis provides valuable resources, especially for lentil, as here the information on complete genome sequence is not available. Hence, the present studies were carried out. RESULTS: This study was undertaken to understand the biochemical mechanisms and transcriptome changes involved in imparting adaptation to drought stress at seedling stage in drought-tolerant (PDL-2) and drought-sensitive (JL-3) cultivars. Among different physiological and biochemical parameters, a significant increase was recorded in proline, glycine betaine contents and activities of SOD, APX and GPX in PDL-2 compared to JL-3while chlorophyll, RWC and catalase activity decreased significantly in JL-3. Transcriptome changes between the PDL-2 and JL-3 under drought stress were evaluated using Illumina HiSeq 2500 platform. Total number of bases ranged from 5.1 to 6.7 Gb. Sequence analysis of control and drought treated cDNA libraries of PDL-2 and JL-3 produced 74032, 75500, 78328 and 81523 contigs, respectively with respective N50 value of 2011, 2008, 2000 and 1991. Differential gene expression of drought treated genotypes along with their controls revealed a total of 11,435 upregulated and 6,934 downregulated transcripts. For functional classification of DEGs, KEGG pathway annotation analysis extracted a total of 413 GO annotation terms where 176 were within molecular process, 128 in cellular and 109 in biological process groups. CONCLUSION: The transcriptional profiles provide a foundation for deciphering the underlying mechanism for drought tolerance in lentil. Transcriptional regulation, signal transduction and secondary metabolism in two genotypes revealed significant differences at seedling stage under severe drought. Our finding suggests role of candidate genes for improving drought tolerance in lentil.

Physiological and biochemical characterization of NERICA-L-44: a novel source of heat tolerance at the vegetative and reproductive stages in rice.

The predicted increase in the frequency and magnitude of extreme heat spikes under future climate can reduce rice yields significantly. Rice sensitivity to high temperatures during the reproductive stage is well documented while the same during the vegetative stage is more speculative. Hence, to identify and characterize novel heat-tolerant donors for both the vegetative and reproductive stages, 71 rice accessions, including approximately 75% New Rice for Africa (NERICAs), were phenotyped across field experiments during summer seasons in Delhi, India, and in a controlled environment study at International Rice Research Institute, Philippines. NERICA-L-44 (NL-44) recorded high seedling survival (52%) and superior growth and greater reproductive success exposed to 42.2°C (sd ± 2.3) under field conditions. NL-44 and the heat-tolerant check N22 consistently displayed lower membrane damage and higher antioxidant enzymes activity across leaves and spikelets. NL-44 recorded 50-60% spikelet fertility, while N22 recorded 67-79% under controlled environment temperature of 38°C (sd±1.17), although both had about 87% fertility under extremely hot field conditions. N22 and NL-44, exposed to heat stress (38°C), had similar pollen germination percent and number of pollen tubes reaching the ovary. NL-44 maintained low hydrogen peroxide production and non-photochemical quenching (NPQ) with high photosynthesis while N22 avoided photosystem II damage through high NPQ under high-temperature stress. NL-44 with its reproductive stage resilience to extreme heat stress, better antioxidant scavenging ability in both vegetative tissue and spikelets and superior yield and grain quality is identified as a novel donor for increasing heat tolerance at both the vegetative and reproductive stages in rice.

Physiological and biochemical effects of 24-Epibrassinolide on drought stress adaptation in maize (Zea mays L.).

Maize production and productivity are affected by drought stress in tropical and subtropical ecologies, as the majority of the area under maize cultivation in these ecologies is rain-fed. The present investigation was conducted to study the physiological and biochemical effects of 24-Epibrassinolide (EBR) as a plant hormone on drought tolerance in maize. Two maize hybrids, Vivek hybrid 9 and Bio 9637, were grown under three different conditions: (i) irrigated, (ii) drought, and (iii) drought+EBR. A total of 2 weeks before the anthesis, irrigation was discontinued to produce a drought-like condition. In the drought+EBR treatment group, irrigation was also stopped, and in addition, EBR was applied as a foliar spray on the same day in the drought plots. It was observed that drought had a major influence on the photosynthesis rate, membrane stability index, leaf area index, relative water content, and leaf water potential; this effect was more pronounced in Bio 9637. Conversely, the activities of antioxidant enzymes such as catalase (CAT), ascorbate peroxidase (APX), and superoxide dismutase (SOD) increased in both hybrids under drought conditions. Specifically, Vivek hybrid 9 showed 74% higher CAT activity under drought conditions as compared to the control. Additionally, EBR application further enhanced the activity of this enzyme by 23% compared to plants under drought conditions. Both hybrids experienced a significant reduction in plant girth due to drought stress. However, it was found that exogenously applying EBR reduced the detrimental effects of drought stress on the plant, and this effect was more pronounced in Bio 9637. In fact, Bio 9637 treated with EBR showed an 86% increase in proline content and a 70% increase in glycine betaine content compared to untreated plants under drought conditions. Taken together, our results suggested EBR enhanced tolerance to drought in maize hybrids. Hence, pre-anthesis foliar application of EBR might partly overcome the adverse effects of flowering stage drought in maize.

Yield, growth and physiological responses of mung bean [Vigna radiata (L.) Wilczek] genotypes to waterlogging at vegetative stage.

A study was conducted to examine the physiological response of contrasting mung bean (Vigna radiata) genotypes viz., T 44 & MH-96-1 (tolerant) and Pusa Baisakhi & MH-1K-24 (sensitive) under waterlogging conditions. Plants were waterlogged at vegetative stage (30 days after sowing) for 3, 6 and 9 days. Waterlogging resulted in decreased leaf area, crop growth rate, root growth and nodules number, membrane stability index, photosynthesis rate, chlorophyll and carotenoid contents, flowering rate, pod setting, yield and altered dry matter partitioning. Sensitive genotypes showed large reductions in aforementioned physiological traits and slow recovery in photosynthesis rate. On the other hand, tolerant genotypes maintained higher photosynthetic rate, chlorophylls and carotenoids, growth rate, membrane stability and fast photosynthetic recovery under waterlogging. After 9 days of exposure to waterlogging, photosynthetic rate and yield losses in most sensitive genotype (MH-1K-24) were 83 and 85 %, respectively. On an average, photosynthetic loss at 3, 6 and 9 days of waterlogging was 43, 51, and 63 %, respectively, while grain yield loss was 20, 34 and 52 % respectively.

Elevated CO2 along with inoculation of cyanobacterial biofilm or its partners differentially modulates C-N metabolism and quality of tomato beneficially.

Diazotrophic cyanobacteria are known to influence nutrient availability in soil, however, their benefits under elevated CO2 environment, particularly on fruit quality attributes, is a less investigated aspect. Laboratory developed cyanobacterium-fungal biofilm (An-Tr), composed of Anabaena torulosa (An) as the matrix with the partner as Trichoderma viride (Tr), along with the individual partners were evaluated under ambient (aCO2-400 ± 50 ppm) and elevated (eCO2-700 ± 50 ppm) conditions, with and without tomato plants. An-Tr inoculation exhibited distinct and significantly higher values for most of the soil microbiological parameters, plant growth attributes and antioxidant/defense enzyme activities measured at 30 and 60 DAI (days after inoculation). Significant enhancement in soil nutrient availability, leaf chlorophyll, with 45-50% increase in the enzyme activities related to carbon and nitrogen assimilation, higher yields and better-quality parameters of tomato, with An-Tr biofilm or An inoculation, were recorded, particularly under eCO2 conditions. The fruits from An-Tr treatments under eCO2 exhibited a higher titrable acidity, along with more ascorbic acid, carotenoids and lycopene content, highlighting the superiority of this inoculant. Multivariate analyses revealed significant (p ≤ 0.05) interactions among cultures, DAI, and CO2 levels, illustrating that cyanobacterial inoculation can be advocated as a strategy to gainfully sequester eCO2. Significant improvement in yield and fruit quality along with 50% N savings, further attest to the promise of cyanobacterial inoculants for tomato crop in the climate change scenario.

Meta-Analysis of Microarray Data and Their Utility in Dissecting the Mapped QTLs for Heat Acclimation in Rice.

In the current global warming scenario, it is imperative to develop crops with improved heat tolerance or acclimation, for which knowledge of major heat stress-tolerant genes or genomic regions is a prerequisite. Though several quantitative trait loci (QTLs) for heat tolerance have been mapped in rice, candidate genes from these QTLs have not been reported yet. The meta-analysis of microarray datasets for heat stress in rice can give us a better genomic resource for the dissection of QTLs and the identification of major candidate genes for heat stress tolerance. In the present study, a database, RiceMetaSys-H, comprising 4227 heat stress-responsive genes (HRGs), was created using seven publicly available microarray datasets. This included in-house-generated microarray datasets of Nagina 22 (N22) and IR64 subjected to 8 days of heat stress. The database has provisions for searching the HRGs through genotypes, growth stages, tissues, and physical intervals in the genome, as well as Locus IDs, which provide complete information on the HRGs with their annotations and fold changes, along with the experimental material used for the analysis. The up-regulation of genes involved in hormone biosynthesis and signalling, sugar metabolism, carbon fixation, and the ROS pathway were found to be the key mechanisms of enhanced heat tolerance. Integrating variant and expression analysis, the database was used for the dissection of the major effect of QTLs on chromosomes 4, 5, and 9 from the IR64/N22 mapping population. Out of the 18, 54, and 62 genes in these three QTLs, 5, 15, and 12 genes harboured non-synonymous substitutions. Fifty-seven interacting genes of the selected QTLs were identified by a network analysis of the HRGs in the QTL regions. Variant analysis revealed that the proportion of unique amino acid substitutions (between N22/IR64) in the QTL-specific genes was much higher than the common substitutions, i.e., 2.58:0.88 (2.93-fold), compared to the network genes at a 0.88:0.67 (1.313-fold) ratio. An expression analysis of these 89 genes showed 43 DEGs between IR64/N22. By integrating the expression profiles, allelic variations, and the database, four robust candidates (LOC_Os05g43870, LOC_Os09g27830, LOC_Os09g27650, andLOC_Os09g28000) for enhanced heat stress tolerance were identified. The database thus developed in rice can be used in breeding to combat high-temperature stress.

Global gene expression profiling under nitrogen stress identifies key genes involved in nitrogen stress adaptation in maize (Zea mays L.).

Maize is a heavy consumer of fertilizer nitrogen (N) which not only results in the high cost of cultivation but may also lead to environmental pollution. Therefore, there is a need to develop N-use efficient genotypes, a prerequisite for which is a greater understanding of N-deficiency stress adaptation. In this study, comparative transcriptome analysis was performed using leaf and root tissues from contrasting inbred lines, viz., DMI 56 (tolerant to N stress) and DMI 81 (susceptible to N stress) to delineate the differentially expressed genes (DEGs) under low-N stress. The contrasting lines were grown hydroponically in modified Hoagland solution having either sufficient- or deficient-N, followed by high-throughput RNA-sequencing. A total of 8 sequencing libraries were prepared and 88-97% of the sequenced raw reads were mapped to the reference B73 maize genome. Genes with a p value ≤ 0.05 and fold change of ≥ 2.0 or ≤ - 2 were considered as DEGs in various combinations performed between susceptible and tolerant genotypes. DEGs were further classified into different functional categories and pathways according to their putative functions. Gene Ontology based annotation of these DEGs identified three different functional categories: biological processes, molecular function, and cellular component. The KEGG and Mapman based analysis revealed that most of the DEGs fall into various metabolic pathways, biosynthesis of secondary metabolites, signal transduction, amino acid metabolism, N-assimilation and metabolism, and starch metabolism. Some of the key genes involved in N uptake (high-affinity nitrate transporter 2.2 and 2.5), N assimilation and metabolism (glutamine synthetase, asparagine synthetase), redox homeostasis (SOD, POX), and transcription factors (MYB36, AP2-EREBP) were found to be highly expressed in the tolerant genotype compared to susceptible one. The candidate genes identified in the present study might be playing a pivotal role in low-N stress adaptation in maize and hence could be useful in augmenting further research on N metabolism and development of N-deficiency tolerant maize cultivars.

Spermidine exogenous application mollifies reproductive stage heat stress ramifications in rice.

Introduction: Rice productivity is severely hampered by heat stress (HS) which induces oxidative stress in this crop. This oxidative stress can be alleviated using various exogenous chemicals, including spermidine (Spd). Therefore, the present study was carried out to characterize HS components and to elucidate the role of exogenous Spd application in rice at the flowering stage. Methods: Two contrasting rice genotypes, i.e. Nagina22 (N22) and Pusa Basmati-1121 (PB-1121) were placed in temperature tunnels and exposed to HS (38-43°C) with and without Spd (1.5 mM) foliar application during the heading stage till the end of the anthesis stage. Result: Heat stress induced the production of H2O2 and thiobarbituric acid reactive substances, which resulted in lower photosynthesis, spikelet sterility, and reduced grain yield. Interestingly, foliar application of Spd induced antioxidant enzyme activities and thus increased total antioxidant capacity resulting in higher photosynthesis, spikelet fertility, and improved grain yield under HS in both genotypes. Under HS with Spd, higher sugar content was recorded as compared to HS alone, which maintained the osmotic equilibrium in leaf and spikelets. Spd application initiated in vivo polyamine biosynthesis, which increased endogenous polyamine levels. Discussion: This study corroborates that the exogenous application of Spd is promising in induction of antioxidant defence and ameliorating HS tolerance in rice via improved photosynthesis and transpiration. Thereby, the study proposes the potential application of Spd to reduce HS in rice under current global warming scenario.

Genome-Wide Association Mapping Reveals Novel Putative Gene Candidates Governing Reproductive Stage Heat Stress Tolerance in Rice.

Temperature rise predicted for the future will severely affect rice productivity because the crop is highly sensitive to heat stress at the reproductive stage. Breeding tolerant varieties is an economically viable option to combat heat stress, for which the knowledge of target genomic regions associated with the reproductive stage heat stress tolerance (RSHT) is essential. A set of 192 rice genotypes of diverse origins were evaluated under natural field conditions through staggered sowings for RSHT using two surrogate traits, spikelet fertility and grain yield, which showed significant reduction under heat stress. These genotypes were genotyped using a 50 k SNP array, and the association analysis identified 10 quantitative trait nucleotides (QTNs) for grain yield, of which one QTN (qHTGY8.1) was consistent across the different models used. Only two out of 10 MTAs coincided with the previously reported QTLs, making the remaing eight novel. A total of 22 QTNs were observed for spikelet fertility, among which qHTSF5.1 was consistently found across three models. Of the QTNs identified, seven coincided with previous reports, while the remaining QTNs were new. The genes near the QTNs were found associated with the protein-protein interaction, protein ubiquitination, stress signal transduction, and so forth, qualifying them to be putative for RSHT. An in silico expression analysis revealed the predominant expression of genes identified for spikelet fertility in reproductive organs. Further validation of the biological relevance of QTNs in conferring heat stress tolerance will enable their utilization in improving the reproductive stage heat stress tolerance in rice.