Transgenic tobacco plants overexpressing a wheat salt stress root protein (TaSSRP) exhibit enhanced tolerance to heat stress.

BACKGROUND: Heat stress is a detrimental abiotic stress that limits the development of many plant species and is linked to a variety of cellular and physiological problems. Heat stress affects membrane fluidity, which leads to negative effects on cell permeability and ion transport. Research reveals that heat stress causes severe damage to cells and leads to rapid accumulation of reactive oxygen species (ROS), which could cause programmed cell death. METHODS AND RESULTS: This current study aimed to validate the role of Triticum aestivum Salt Stress Root Protein (TaSSRP) in plants' tolerance to heat stress by modulating its expression in tobacco plants. The Relative Water Content (RWC), total chlorophyll content, and Membrane Stability Index (MSI) of the seven distinct transgenic lines (T0 - 2, T0 - 3, T0 - 6, T0 - 8, T0 - 9, T0 - 11, and T0 - 13), increased in response to heat stress. Despite the fact that the same tendency was detected in wild-type (WT) plants, changes in physio-biochemical parameters were greater in transgenic lines than in WT plants. The expression analysis revealed that the transgene TaSSRP expressed from 1.00 to 1.809 folds in different lines in the transgenic tobacco plants. The gene TaSSRP offered resistance to heat stress in Nicotiana tabacum, according to the results of the study. CONCLUSION: These findings could help to improve our knowledge and understanding of the mechanism underlying thermotolerance in wheat, and the novel identified gene TaSSRP could be used in generating wheat varieties with enhanced tolerance to heat stress.

Reactive oxygen species in plants: an invincible fulcrum for biotic stress mitigation.

Climate change-associated environmental vagaries have amplified the incidence of pests and pathogens on plants, thus imparting the increased quest for management strategies. Plants respond to stresses through intricate signaling networks that regulate diverse cellular mechanisms. Reactive oxygen species (ROS) are cardinal towards the maintenance of normal plant activities as well as improving stress management. Plants that exhibit a fine balance between ROS levels and its management apparently mitigate stresses better. There have been very many compendiums on signaling and management of ROS during several abiotic stresses. However, expansion of knowledge related to ROS induction and homeostasis during biotic stresses is pertinent. Hence, considering its importance, we provide insights in this review on how plants signal and manage ROS upon an oxidative burst during their interaction with pathogens and herbivores. Substantial degree of molecular changes and pivotal roles of ROS have been detected during phyto-pathogen/herbivore interactions, opening novel platforms to understand signaling/management of events under varied biotic stresses. It is interesting to know that, though plants react to biotic stresses through oxidative burst, receptors and elicitors involved in the signal transduction differ across stresses. The review provides explicit details about the specific signaling of ROS production in plants under pathogen and herbivore attack. Furthermore, we also provide an update about tackling the accumulated ROS under biotic stresses as another pivotal step. ROS signaling and homeostasis can be exploited as critical players and a fulcrum to tackle biotic stresses, thus paving the way for futuristic combinatorial stress management strategies. KEY POINTS: • The review is a comprehension of redox signaling and management in plants during herbivory and pathogen infection • Reactive oxygen species (ROS) is an important factor during normal plant activities as well as in their response to stresses. Diverse modes of ROS signaling and management have been observed during both biotic stresses independently • Exploration of plant biology in multi-stress resistant plants like the crop wild relatives could pave the way for combinatorial management of stress for a better tomorrow.

The potential application of genome editing by using CRISPR/Cas9, and its engineered and ortholog variants for studying the transcription factors involved in the maintenance of phosphate homeostasis in model plants.

Phosphorus (P), an essential macronutrient, is pivotal for growth and development of plants. Availability of phosphate (Pi), the only assimilable P, is often suboptimal in rhizospheres. Pi deficiency triggers an array of spatiotemporal adaptive responses including the differential regulation of several transcription factors (TFs). Studies on MYB TF PHR1 in Arabidopsis thaliana (Arabidopsis) and its orthologs OsPHRs in Oryza sativa (rice) have provided empirical evidence of their significant roles in the maintenance of Pi homeostasis. Since the functional characterization of PHR1 in 2001, several other TFs have now been identified in these model plants. This raised a pertinent question whether there are any likely interactions across these TFs. Clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) system has provided an attractive paradigm for editing genome in plants. Here, we review the applications and challenges of this technique for genome editing of the TFs for deciphering the function and plausible interactions across them. This technology could thus provide a much-needed fillip towards engineering TFs for generating Pi use efficient plants for sustainable agriculture. Furthermore, we contemplate whether this technology could be a viable alternative to the controversial genetically modified (GM) rice or it may also eventually embroil into a limbo.

CRISPR-Cas9 directed genome engineering for enhancing salt stress tolerance in rice.

Crop productivity in rice is harshly limited due to high concentration of salt in the soil. To understand the intricacies of the mechanism it is important to unravel the key pathways operating inside the plant cell. Emerging state-of-the art technologies have provided the tools to discover the key components inside the plant cell for salt tolerance. Among the molecular entities, transcription factors and/or other important components of sensing and signaling cascades have been the attractive targets and the role of NHX and SOS1 transporters amply described. Not only marker assisted programs but also transgenic approaches by using reverse genetic strategies (knockout or knockdown) or overexpression have been extensively used to engineer rice crop. CRISPR/Cas is an attractive paradigm and provides the feasibility for manipulating several genes simultaneously. Here, in this review we highlight some of the molecular entities that could be potentially targeted for generating rice amenable to sustain growth under high salinity conditions by employing CRISPR/Cas. We also try to address key questions for rice salt stress tolerance other than what is already known.

A comprehensive review on the influence of light on signaling cross-talk and molecular communication against phyto-microbiome interactions.

Generally, plant growth, development, and their productivity are mainly affected by their growth rate and also depend on environmental factors such as temperature, pH, humidity, and light. The interaction between plants and pathogens are highly specific. Such specificity is well characterized by plants and pathogenic microbes in the form of a molecular signature such as pattern-recognition receptors (PRRs) and microbes-associated molecular patterns (MAMPs), which in turn trigger systemic acquired immunity in plants. A number of Arabidopsis mutant collections are available to investigate molecular and physiological changes in plants under the presence of different light conditions. Over the past decade(s), several studies have been performed by selecting Arabidopsis thaliana under the influence of red, green, blue, far/far-red, and white light. However, only few phenotypic and molecular based studies represent the modulatory effects in plants under the influence of green and blue lights. Apart from this, red light (RL) actively participates in defense mechanisms against several pathogenic infections. This evolutionary pattern of light sensitizes the pathologist to analyze a series of events in plants during various stress conditions of the natural and/or the artificial environment. This review scrutinizes the literature where red, blue, white, and green light (GL) act as sensory systems that affects physiological parameters in plants. Generally, white and RL are responsible for regulating various defense mechanisms, but, GL also participates in this process with a robust impact! In addition to this, we also focus on the activation of signaling pathways (salicylic acid and jasmonic acid) and their influence on plant immune systems against phytopathogen(s).

Alteration of proteome in germinating seedlings of piegonpea (Cajanus cajan) after salt stress.

Pigeonpea (Cajanus cajan) is an important crop in semi-arid regions and a significant source of dietary proteins in India. The plant is sensitive to salinity stress, which adversely affects its productivity. Based on the dosage-dependent influence of salinity stress on the growth and ion contents in the young seedlings of pigeonpea, a comparative proteome analysis of control and salt stressed (150 mM NaCl) plants was conducted using 7 days-old seedlings. Among various amino acids, serine, aspartate and asparagine were the amino acids that showed increment in the root, whereas serine, aspartate and phenylalanine showed an upward trend in shoots under salt stress. Furthermore, a label-free and gel-free comparative Q-Tof, Liquid Chromatography-Mass spectrometry (LC-MS) revealed total of 118 differentially abundant proteins in roots and shoots with and without salt stress conditions. Proteins related to DNA-binding with one finger (Dof) transcription factor family and glycine betaine (GB) biosynthesis were differentially expressed in the shoot and root of the salinity-stressed seedlings. Exogenous application of choline on GB accumulation under salt stress showed the increase of GB pathway in C. cajan. Gene expression analysis for differentially abundant proteins revealed the higher induction of ethanolamine kinase (CcEthKin), choline-phosphate cytidylyltransferase 1-like (CcChoPh), serine hydroxymethyltransferase (CcSHMT) and Dof protein (CcDof29). The results indicate the importance of, choline precursor, serine biosynthetic pathways and glycine betaine synthesis in salinity stress tolerance. The glycine betaine protects plant from cellular damages and acts as osmoticum under stress condition. Protein interaction network (PIN) analysis demonstrated that 61% of the differentially expressed proteins exhibited positive interactions and 10% of them formed the center of the PIN. Further, The PIN analysis also highlighted the potential roles of the cytochrome c oxidases in sensing and signaling cascades governing salinity stress responses in pigeonpea. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12298-021-01116-w.

Genetics, Physiological Mechanisms and Breeding of Flood-Tolerant Rice (Oryza sativa L.).

Flooding of rice fields is a serious problem in the river basins of South and South-East Asia where about 15 Mha of lowland rice cultivation is regularly affected. Flooding creates hypoxic conditions resulting in poor germination and seedling establishment. Flash flooding, where rice plants are completely submerged for 10-15 d during their vegetative stage, causes huge losses. Water stagnation for weeks to months also leads to substantial yield losses when large parts of rice aerial tissues are inundated. The low-yielding traditional varieties and landraces of rice adapted to these flooding conditions have been replaced by flood-sensitive high-yielding rice varieties. The 'FR13A' rice variety and the Submergence 1A (SUB1A) gene were identified for flash flooding and subsequently introgressed to high-yielding rice varieties. The challenge is to find superior alleles of the SUB1A gene, or even new genes that may confer greater tolerance to submergence. Similarly, genes have been identified in tolerant landraces of rice for their ability to survive by rapid stem elongation (SNORKEL1 and SNORKEL2) during deep-water flooding, and for anaerobic germination ability (TPP7). Research on rice genotypes and novel genes that are tolerant to prolonged water stagnation is in progress. These studies will greatly assist in devising more efficient and precise molecular breeding strategies for developing climate-resilient high-yielding rice varieties for flood-prone regions. Here we review the state of our knowledge of flooding tolerance in rice and its application in varietal improvement.

Elucidation of salt-tolerance metabolic pathways in contrasting rice genotypes and their segregating progenies.

KEY MESSAGE: Differentially expressed antioxidant enzymes, amino acids and proteins in contrasting rice genotypes, and co-location of their genes in the QTLs mapped using bi-parental population, indicated their role in salt tolerance. Soil salinity is a major environmental constraint limiting rice productivity. Salt-tolerant 'CSR27', salt-sensitive 'MI48'and their extreme tolerant and sensitive recombinant inbred line (RIL) progenies were used for the elucidation of salt stress tolerance metabolic pathways. Salt stress-mediated biochemical and molecular changes were analyzed in the two parents along with bulked-tolerant (BT) and bulked-sensitive (BS) extreme RILs. The tolerant parent and BT RILs suffered much lower reduction in the chlorophyll as compared to their sensitive counterparts. Activities of antioxidant enzymes superoxide dismutase (SOD) and peroxidase (POD) and non-enzymatic antioxidant ascorbic acid were much higher in salt-stressed CSR27 and BT RILs than MI48 and BS RILs. Further, the tolerant lines showed significant enhancement in the levels of amino acids methionine and proline in response to salt stress in comparison to the sensitive lines. Similarly, the tolerant genotypes showed minimal reduction in cysteine content whereas sensitive genotypes showed a sharp reduction. Real time PCR analysis confirmed the induction of methionine biosynthetic pathway (MBP) enzymes cystathionine-ß synthase (CbS), S-adenosyl methionine synthase (SAMS), S-adenosyl methionine decarboxylase (SAMDC) and serine hydroxymethyl transferase (SHMT) genes in tolerant lines, suggesting potential role of the MBP in conferring salt tolerance in rice variety CSR27. Proteome profiling also confirmed higher expression of SOD, POD and plastidic CbS and other proteins in the tolerant lines, whose genes were co-located in the QTL intervals for salt tolerance mapped in the RIL population. The study signifies integrated biochemical-molecular approach for identifying salt tolerance genes for genetic improvement for stress tolerant rice varieties.

Haplotype distribution and association of candidate genes with salt tolerance in Indian wild rice germplasm.

KEY MESSAGE: The association of natural genetic variations of salt-responsive candidate genes belonging to different gene families with salt-tolerance phenotype and their haplotype variation in different geographic regions. Soil salinity covers a large part of the arable land of the world and is a major factor for yield losses in salt-sensitive crops, such as rice. Different gene families that respond to salinity have been identified in rice, but limited success has been achieved in developing salt-tolerant cultivars. Therefore, 21 salt stress-responsive candidate genes belonging to different gene families were re-sequenced to analyse their genetic variation and association with salt tolerance. The average single nucleotide polymorphism (SNP) density was 16 SNPs per kbp amongst these genes. The identified nucleotide and haplotype diversity showed comparatively higher genetic variation in the transporter family genes. Linkage disequilibrium (LD) analysis showed significant associations of SNPs in BADH2, HsfC1B, MIPS1, MIPS2, MYB2, NHX1, NHX2, NHX3, P5CS1, P5CS2, PIP1, SIK1, SOS1, and SOS2 genes with the salt-tolerant phenotype. A combined analysis of SNPs in the 21 candidate genes and eight other HKT transporter genes produced two separate clusters of tolerant genotypes, carrying unique SNPs in the ion transporter and osmoticum-related genes. Haplotype network analysis showed all the major and few minor alleles distributed over distant geographic regions. Minor haplotypes may be recently evolved alleles which migrated to distant geographic regions and may represent recent expansion of Indian wild rice. The analysis of genetic variation in different gene families identified the relationship between adaptive variations and functional significance of the genes. Introgression of the identified alleles from wild relatives may enhance the salt tolerance and consequently rice production in the salinity-affected areas.

Iron Availability Affects Phosphate Deficiency-Mediated Responses, and Evidence of Cross-Talk with Auxin and Zinc in Arabidopsis.

Phosphate (Pi) is pivotal for plant growth and development. Pi deficiency triggers local and systemically regulated adaptive responses in Arabidopsis thaliana. Inhibition of primary root growth (PRG) and retarded development of lateral roots (LRs) are typical local Pi deficiency-mediated responses of the root system. Expression of Pi starvation-responsive (PSR) genes is regulated systemically. Here, we report the differential influence of iron (Fe) availability on local and systemic sensing of Pi by Arabidopsis. P-Fe- condition disrupted local Pi sensing, resulting in an elongated primary root (PR). Altered Fe homeostasis in the lpsi mutant with aberration in local Pi sensing provided circumstantial evidence towards the role of Fe in the maintenance of Pi homeostasis. Reporter gene assays, expression analysis of auxin-responsive genes (ARGs) and root phenotyping of the arf7arf19 mutant demonstrated the role of Fe availability on local Pi deficiency-mediated LR development. In addition, Fe availability also exerted a significant influence on PSR genes belonging to different functional categories. Together, these results demonstrated a substantial influence of Fe availability on Pi deficiency-mediated responses of ontogenetically distinct traits of the root system and PSR genes. The study also provided evidence of cross-talk between Pi, Fe and Zn, highlighting a complex tripartite interaction amongst them for maintaining Pi homeostasis.

QTLs and Genes for Salt Stress Tolerance: A Journey from Seed to Seed Continued.

Rice (Oryza sativa L.) is a crucial crop contributing to global food security; however, its production is susceptible to salinity, a significant abiotic stressor that negatively impacts plant germination, vigour, and yield, degrading crop production. Due to the presence of exchangeable sodium ions (Na+), the affected plants sustain two-way damage resulting in initial osmotic stress and subsequent ion toxicity in the plants, which alters the cell's ionic homeostasis and physiological status. To adapt to salt stress, plants sense and transfer osmotic and ionic signals into their respective cells, which results in alterations of their cellular properties. No specific Na+ sensor or receptor has been identified in plants for salt stress other than the SOS pathway. Increasing productivity under salt-affected soils necessitates conventional breeding supplemented with biotechnological interventions. However, knowledge of the genetic basis of salinity stress tolerance in the breeding pool is somewhat limited because of the complicated architecture of salinity stress tolerance, which needs to be expanded to create salt-tolerant variants with better adaptability. A comprehensive study that emphasizes the QTLs, genes and governing mechanisms for salt stress tolerance is discussed in the present study for future research in crop improvement.

Low cellular P-quota and poor metabolic adaptations of the freshwater cyanobacterium Anabaena fertilissima Rao during Pi-limitation.

Anabaena fertilissima is a filamentous freshwater N(2)-fixing cyanobacterium, isolated from a paddy field. Growth of the cyanobacterium was limited by the non-availability of inorganic phosphate (Pi) in the growth medium and was found to be directly related to the cellular P quota, which declined rapidly in Pi-deficient cells. To overcome Pi-deficiency, cells induced both cell-bound and cell-free alkaline phosphatase activities (APase). The activity of cell-bound APase was rapid and 5-6 times higher than that of the cell-free APase activity. Native gel electrophoresis revealed the presence of two APase activity bands for both the cell bound and cell-free APase (Mr ≈42 and 34 kDa). For Pi-deficient cells, APase activity was inversely related to cellular P-quota. In A. fertilissima phosphate uptake was facilitated by single high-affinity phosphate transporter (K ( s ), 4.54 µM; V(max), 4.84 µmol mg protein(-1) min(-1)). Pi-deficiency severely reduced the photosynthetic rate, respiration rate and nitrate uptake, as well as the activities of nitrate reductase, nitrite reductase and nitrogenase enzymes. In photosynthesis, PSII activity was maximally inhibited, followed by PSI and whole chain activities. Transcript levels of five key glycolytic enzymes showed the poor adaptability of the cyanobacterium to switch its metabolic activity to PPi-dependent enzyme variants, which has rather constant cellular concentrations.

Transcriptome profiling reveals the genes and pathways involved in thermo-tolerance in wheat (Triticum aestivum L.) genotype Raj 3765.

Wheat, one of the most widely consumed staple food crops globally, is relatively vulnerable to high temperature-induced heat stress. It is therefore essential to gain more insight into the comprehensive mechanism of thermotolerance of wheat in order to safeguard its production. In view of this, we analysed heat stress responsive transcriptome data of wheat to determine its gene expression level under heat stress. A total of 7990 DEGs, including 4483 up-regulated and 3507 down regulated genes were identified. Gene Ontology (GO) analysis categorized 3910 DEGs into different ontology families. 146 pathways involving 814 DEGs were enriched during KEGG analysis. Metabolic pathways and biosynthesis of secondary metabolites were the major pathways enriched. MYB (myeloblastosis) transcription factors (TFs) and many other TFs as bHLH, WRKY, NAC, ERF, were determined to be quite abundant in the DEGs. Since various reports indicate that these TFs play important role in plants abiotic stress, it is an indication that our DEGs are functional in heat stress tolerance. Verification of few selected DEGs using RT-qPCR produced expression levels similar to the transcriptome data. This indicates that the transcriptome data is reliable. These results could be helpful in enhancing our understanding of the mechanism underlying thermotolerance in wheat.

Molecular docking used as an advanced tool to determine novel compounds on emerging infectious diseases: A systematic review.

Emerging infectious diseases (EID) as well as reappearing irresistible infections are expanding worldwide. Utmost of similar cases, it was seen that the EIDs have long been perceived as a predominant conclusion of host-pathogen adaption. Here, one should get to analyze their host-pathogen interlink and their by needs to look ways, as an example, by exploitation process methodology particularly molecular docking and molecular dynamics simulation, have been utilized in recent time as the most outstanding tools. Hence, we have overviewed some of important factors that influences on EIDs especially HIV/AIDs, H1N1 and coronavirus. Moreover, here we specified the importance of molecular docking applications especially molecular dynamics simulations approach to determine novel compounds on the emerging infectious diseases. Additionally, in vivo and in vitro studies approach to determine novel compounds on the emerging infectious diseases that has implemented to evaluate the limiting affinities between small particles as well as macromolecule that can further, used as a target of HIV/AIDs, H1N1, and coronavirus were also discussed. These novel drug molecules approved in vivo and in vitro studies with reaffirm results and hence, it is clear that the computational methods (mainly molecular docking and molecular dynamics) are found to be more effective technique for drug discovery and medical practitioners.

Current Research Trends and Prospects for Yield and Quality Improvement in Sesame, an Important Oilseed Crop.

Climate change is shifting agricultural production, which could impact the economic and cultural contexts of the oilseed industry, including sesame. Environmental threats (biotic and abiotic stresses) affect sesame production and thus yield (especially oil content). However, few studies have investigated the genetic enhancement, quality improvement, or the underlying mechanisms of stress tolerance in sesame. This study reveals the challenges faced by farmers/researchers growing sesame crops and the potential genetic and genomic resources for addressing the threats, including: (1) developing sesame varieties that tolerate phyllody, root rot disease, and waterlogging; (2) investigating beneficial agro-morphological traits, such as determinate growth, prostrate habit, and delayed response to seed shattering; (3) using wild relatives of sesame for wide hybridization; and (4) advancing existing strategies to maintain sesame production under changing climatic conditions. Future research programs need to add technologies and develop the best research strategies for economic and sustainable development.

Combining QTL mapping and transcriptome profiling of bulked RILs for identification of functional polymorphism for salt tolerance genes in rice (Oryza sativa L.).

Identification of genes for quantitative traits is difficult using any single approach due to complex inheritance of the traits and limited resolving power of the individual techniques. Here a combination of genetic mapping and bulked transcriptome profiling was used to narrow down the number of differentially expressed salt-responsive genes in rice in order to identify functional polymorphism of genes underlying the quantitative trait loci (QTL). A population of recombinant inbred lines (RILs) derived from cross between salt-tolerant variety CSR 27 and salt-sensitive variety MI 48 was used to map QTL for salt ion concentrations in different tissues and salt stress susceptibility index (SSI) for spikelet fertility, grain weight, and grain yield. Eight significant QTL intervals were mapped on chromosomes 1, 8, and 12 for the salt ion concentrations and a QTL controlling SSI for spikelet fertility was co-located in one of these intervals on chromosome 8. However, there were total 2,681 genes in these QTL intervals, making it difficult to pinpoint the genes responsible for the functional differences for the traits. Similarly, transcriptome profiling of the seedlings of tolerant and sensitive parents grown under control and salt-stress conditions showed 798 and 2,407 differentially expressed gene probes, respectively. By analyzing pools of RNA extracted from ten each of extremely tolerant and extremely sensitive RILs to normalize the background noise, the number of differentially expressed genes under salt stress was drastically reduced to 30 only. Two of these genes, an integral transmembrane protein DUF6 and a cation chloride cotransporter, were not only co-located in the QTL intervals but also showed the expected distortion of allele frequencies in the extreme tolerant and sensitive RILs, and therefore are suitable for future validation studies and development of functional markers for salt tolerance in rice to facilitate marker-assisted breeding.

A genome-wide association study in Indian wild rice accessions for resistance to the root-knot nematode Meloidogyne graminicola.

Rice root-knot nematode (RRKN), Meloidogyne graminicola is one of the major biotic constraints in rice-growing countries of Southeast Asia. Host plant resistance is an environmentally-friendly and cost-effective mean to mitigate RRKN damage to rice. Considering the limited availability of genetic resources in the Asian rice (Oryza sativa) cultivars, exploration of novel sources and genetic basis of RRKN resistance is necessary. We screened 272 diverse wild rice accessions (O. nivara, O. rufipogon, O. sativa f. spontanea) to identify genotypes resistant to RRKN. We dissected the genetic basis of RRKN resistance using a genome-wide association study with SNPs (single nucleotide polymorphism) genotyped by 50K "OsSNPnks" genic Affymetrix chip. Population structure analysis revealed that these accessions were stratified into three major sub-populations. Overall, 40 resistant accessions (nematode gall number and multiplication factor/MF < 2) were identified, with 17 novel SNPs being significantly associated with phenotypic traits such as number of galls, egg masses, eggs/egg mass and MF per plant. SNPs were localized to the quantitative trait loci (QTL) on chromosome 1, 2, 3, 4, 6, 10 and 11 harboring the candidate genes including NBS-LRR, Cf2/Cf5 resistance protein, MYB, bZIP, ARF, SCARECROW and WRKY transcription factors. Expression of these identified genes was significantly (P < 0.01) upregulated in RRKN-infected plants compared to mock-inoculated plants at 7 days after inoculation. The identified SNPs enrich the repository of candidate genes for future marker-assisted breeding program to alleviate the damage of RRKN in rice.

A 62K genic-SNP chip array for genetic studies and breeding applications in pigeonpea (Cajanus cajan L. Millsp.).

Pigeonpea is the second most important pulse legume crop for food and nutritional security of South Asia that requires accelerated breeding using high throughput genomic tools. Single nucleotide polymorphisms (SNPs) are highly suitable markers for this purpose because of their bi-allelic nature, reproducibility and high abundance in the genome. Here we report on development and use of a pigeonpea 62 K SNP chip array 'CcSNPnks' for Affymetrix GeneTitan® platform. The array was designed after filtering 645,662 genic-SNPs identified by re-sequencing of 45 diverse genotypes and has 62,053 SNPs from 9629 genes belonging to five different categories, including 4314 single-copy genes unique to pigeonpea, 4328 single-copy genes conserved between soybean and pigeonpea, 156 homologs of agronomically important cloned genes, 746 disease resistance and defense response genes and 85 multi-copy genes of pigeonpea. This fully genic chip has 28.94% exonic, 33.04% intronic, 27.56% 5'UTR and 10.46% 3'UTR SNPs and incorporates multiple SNPs per gene allowing gene haplotype network analysis. It was used successfully for the analysis of genetic diversity and population structure of 95 pigeonpea varieties and high resolution mapping of 11 yield related QTLs for number of branches, pod bearing length and number of seeds per pod in a biparental RIL population. As an accurate high-density genotyping tool, 'CcSNPnks' chip array will be useful for high resolution fingerprinting, QTL mapping and genome wide as well as gene-based association studies in pigeonpea.

Allelic sequence variation in the Sub1A, Sub1B and Sub1C genes among diverse rice cultivars and its association with submergence tolerance.

Erratic rainfall leading to flash flooding causes huge yield losses in lowland rice. The traditional varieties and landraces of rice possess variable levels of tolerance to submergence stress, but gene discovery and utilization of these resources has been limited to the Sub1A-1 allele from variety FR13A. Therefore, we analysed the allelic sequence variation in three Sub1 genes in a panel of 179 rice genotypes and its association with submergence tolerance. Population structure and diversity analysis based on a 36-plex genome wide genic-SNP assay grouped these genotypes into two major categories representing Indica and Japonica cultivar groups with further sub-groupings into Indica, Aus, Deepwater and Aromatic-Japonica cultivars. Targetted re-sequencing of the Sub1A, Sub1B and Sub1C genes identfied 7, 7 and 38 SNPs making 8, 9 and 67 SNP haplotypes, respectively. Haplotype networks and phylogenic analysis revealed evolution of Sub1B and Sub1A genes by tandem duplication and divergence of the ancestral Sub1C gene in that order. The alleles of Sub1 genes in tolerant reference variety FR13A seem to have evolved most recently. However, no consistent association could be found between the Sub1 allelic variation and submergence tolerance probably due to low minor allele frequencies and presence of exceptions to the known Sub1A-1 association in the genotype panel. We identified 18 cultivars with non-Sub1A-1 source of submergence tolerance which after further mapping and validation in bi-parental populations will be useful for development of superior flood tolerant rice cultivars.

Molecular Interaction-Based Exploration of the Broad Spectrum Efficacy of a Bacillus thuringiensis Insecticidal Chimeric Protein, Cry1AcF.

Bacillus thuringiensis insecticidal proteins (Bt ICPs) are reliable and valuable options for pest management in crops. Protein engineering of Bt ICPs is a competitive alternative for resistance management in insects. The primary focus of the study was to reiterate the translational utility of a protein-engineered chimeric Cry toxin, Cry1AcF, for its broad spectrum insecticidal efficacy using molecular modeling and docking studies. In-depth bioinformatic analysis was undertaken for structure prediction of the Cry toxin as the ligand and aminopeptidase1 receptors (APN1) from Helicoverpa armigera (HaAPN1) and Spodoptera litura (SlAPN1) as receptors, followed by interaction studies using protein-protein docking tools. The study revealed feasible interactions between the toxin and the two receptors through H-bonding and hydrophobic interactions. Further, molecular dynamics simulations substantiated the stability of the interactions, proving the broad spectrum efficacy of Cry1AcF in controlling H. armigera and S. litura. These findings justify the utility of protein-engineered toxins in pest management.