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The present experiment was conducted during 2020–21 and 2021–22 at ICAR-Indian Agricultural Research Institute, New Delhi to study the impact of open-, self-, and cross-pollination on metaxenic traits (berries) and the incidence of cleistogamy in grapes (Vitis vinifera L.). Seven different cross-combinations were used on the grape variety Pusa Navrang, which were planted at 3 m × 3 m spacing and trained on the Y-trellis training system. The experiment was laid out in a randomized block design (RBD) with four replications. The incidence of cleistogamy, berry set, retention percentage, and the metaxenia effect of pollen grains in different grapevine varieties, namely, Pusa Navrang (PN), Black Muscat (BM), Pusa Swarnika (PS), Beauty Seedless (BS), Perlette (PER), Male Hybrid (MH), were studied. Also, pollen quantity and viability were determined for the different grapevine varieties under study. Depending on the genotypes and whether the fruit set is obtained inside the covered flowers, cleistogamy was confirmed. A significantly higher berry set (40–85%) and retention (32–77%) were recorded in open- and self-pollinated flowers. The total number of pollens/anther in six grape genotypes ranged from 7916.62–23832.02, whereas the maximum active pollen rates were noted in the Male Hybrid (70.01%) and Black Muscat (66.80%). The pollens from the Beauty Seedless genotype exhibited significant enhancement of metaxenic traits such as berry set, retention, and size in Pusa Navrang. Therefore, utilizing Beauty Seedless as a pollen parent in grape breeding programmes holds promise for enhancing berry set and overall berry quality, thus enhancing the hybridization efficiency.

The Cu2ZnSnS4 (CZTS) thin film is newly emerging semiconductor material in thin film solar cell industry. The CZTS composed of economical, common earth abundant elements. It has advantageous properties like high absorption coefficient and best band gap. Here we have applied low cost chemical bath deposition technique for synthesis of CZTS at low temperature, acidic medium and it’s characterization. The films were characterized by different techaniques like X-Ray diffraction, Raman, SEM, Optical absorbance, electrical conductivity and PEC study. The X-Ray diffraction, Raman scattering techniques utilized for structural study. The XRD revels kasterite phase and nanocrystalline nature of CZTS thin films. These results and its purity confirmed further by advanced Raman spectroscopy with 335 cm-1 major peak. The crystallite size which was found to be 50.19 nm. The optical absorbance study carried by use of UV-Visible spectroscopy analyses its band gap near about 1.5 eV and its direct type of absorption. The electrical conductivity technique gives p-type of conductivity. The scanning electron microscopy (SEM) study finds it’s rock like unique morphology. The EDS technique confirms its elemental composition and it’s fair stoichiometry. The analysis of PEC data revealed power conversion efficiency-PCE to 0.90%. The Cu2ZnSnS4 (CZTS) thin film is newly emerging semiconductor material in thin film solar cell industry. The CZTS composed of economical, common earth abundant elements. It has advantageous properties like high absorption coefficient and best band gap. Here we have applied low cost chemical bath deposition technique for synthesis of CZTS at low temperature, acidic medium and it’s characterization. The films were characterized by different techaniques like X-Ray diffraction, Raman, SEM, Optical absorbance, electrical conductivity and PEC study. The X-Ray diffraction, Raman scattering techniques utilized for structural study. The XRD revels kasterite phase and nanocrystalline nature of CZTS thin films. These results and its purity confirmed further by advanced Raman spectroscopy with 335 cm-1 major peak. The crystallite size which was found to be 50.19 nm. The optical absorbance study carried by use of UV-Visible spectroscopy analyses its band gap near about 1.5 eV and its direct type of absorption. The electrical conductivity technique gives p-type of conductivity. The scanning electron microscopy (SEM) study finds it’s rock like unique morphology. The EDS technique confirms its elemental composition and it’s fair stoichiometry. The analysis of PEC data revealed power conversion efficiency-PCE to 0.90%.

Abstract To combat drought stress in rice, a major threat to global food security, three major quantitative trait loci for ‘yield under drought stress’ (qDTYs) were successfully exploited in the last decade. However, their molecular basis still remains unknown. To understand the role of secondary regulation by miRNA in drought stress response and their relation, if any, with the three qDTYs, the miRNA dynamics under drought stress was studied at booting stage in two drought tolerant (Sahbaghi Dhan and Vandana) and one drought sensitive (IR 20) cultivars. In total, 53 known and 40 novel differentially expressed (DE) miRNAs were identified. The primary drought responsive miRNAs were Osa-MIR2919, Osa-MIR3979, Osa-MIR159f, Osa-MIR156k, Osa-MIR528, Osa-MIR530, Osa-MIR2091, Osa-MIR531a, Osa-MIR531b as well as three novel ones. Sixty-one target genes that corresponded to 11 known and 4 novel DE miRNAs were found to be co-localized with the three qDTYs, out of the 1746 target genes identified. We could validate miRNA-mRNA expression under drought for nine known and three novel miRNAs in eight different rice genotypes showing varying degree of tolerance. From our study, Osa-MIR2919, Osa-MIR3979, Osa-MIR528, Osa-MIR2091-5p and Chr01_11911S14Astr and their target genes LOC_Os01g72000, LOC_Os01g66890, LOC_Os01g57990, LOC_Os01g56780, LOC_Os01g72834, LOC_Os01g61880 and LOC_Os01g72780 were identified as the most promising candidates for drought tolerance at booting stage. Of these, Osa-MIR2919 with 19 target genes in the qDTYs is being reported for the first time. It acts as a negative regulator of drought stress tolerance by modulating the cytokinin and brassinosteroid signalling pathway.

Abstract Cluster bean (Cyamopsis tetragonoloba (L.) Taub 2n = 14, is commonly known as Guar. Apart from being a vegetable crop, it is an abundant source of a natural hetero-polysaccharide called guar gum or galactomannan. Here, we are reporting a chromosome-scale reference genome assembly of a popular cluster bean cultivar RGC-936, by combining sequencing data from Illumina, 10X Genomics, Oxford Nanopore technologies. An initial assembly of 1580 scaffolds with an N50 value of 7.12 Mb was generated and these scaffolds were anchored to a high density SNP linkage map. Finally, a genome assembly of 550.31 Mb (94% of the estimated genome size of ~ 580 Mb (through flow cytometry) with 58 scaffolds was obtained, including 7 super scaffolds with a very high N50 value of 78.27 Mb. Phylogenetic analysis using single copy orthologs among 12 angiosperms showed that cluster bean shared a common ancestor with other legumes 80.6 MYA. No evidence of recent whole genome duplication event in cluster bean was found in our analysis. Further comparative transcriptomics analyses revealed pod-specific up-regulation of genes encoding enzymes involved in galactomannan biosynthesis. The high-quality chromosome-scale cluster bean genome assembly will facilitate understanding of the molecular basis of galactomannan biosynthesis and aid in genomics-assisted improvement of cluster bean.

The SGNH hydrolase superfamily's GDSL-type esterase/lipase proteins (GELPs) play a crucial role in plant growth and stress tolerance. However, limited knowledge exists regarding the molecular role of GELP genes under drought conditions, especially in pigeon pea. In this study, 112 GDSL genes were found, distributed over the 11 pigeon pea chromosomes, and classified into 5 clades based on the phylogenetic analysis. The pigeon pea GDSL gene family seems to have grown significantly as a result of tandem duplications (48 %). Five exons and four introns represent the coding areas of more than 71.4 % of the CcGDSL genes, according to our analysis. According to the cis-elements study, CcGDSL gene expression was observed to be mostly influenced by fluctuating stressful situations and also by light and plant hormones. We could narrow down to 14 stress-responsive CcGDSL genes in order to assess their expression levels under seedling-stage drought stress conditions. Our data indicates that among these 112 genes, CcGDSL21, CcGDSL63, CcGDSL64 and CcGDSL92 could be involved in regulating the primary response under drought stress. This preliminary study will add to our understanding of GDSL genes in pigeon pea and help in elucidating their role in drought tolerance in pigeon pea.

Abstract 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.

von Willebrand factor A (vWA) genes are well characterized in humans except for few BONZAI genes, but the vWA genes are least explored in plants. Considering the novelty and vital role of vWA genes, this study aimed at characterization of vWA superfamily in rice. Rice genome was found to have 40 vWA genes distributed across all the 12 chromosomes, and 20 of the 40 vWA genes were unique while the remaining shared large fragment similarities with each other, indicating gene duplication. In addition to vWA domain, vWA proteins possess other different motifs or domains, such as ubiquitin interacting motif in protein degradation pathway, and RING finger in protein-protein interaction. Expression analysis of vWA genes in available expression data suggested that they probably function in biotic and abiotic stress responses including hormonal response and signaling. The frequency of transposon elements in the entire 3K rice germplasm was negligible except for 9 vWA genes, indicating the importance of these genes in rice. Structural and functional diversities showed that the vWA genes in a blast-resistant rice variety Tetep had huge variations compared to blast-susceptible rice varieties HP2216 and Nipponbare. qRT-PCR analysis of vWA genes in Magnaporthe oryzae infected rice tissues indicated OsvWA9, OsvWA36, OsvWA37 and OsvWA18 as the optimal candidate genes for disease resistance. This is the first attempt to characterize vWA gene family in plant species.

Abstract Pigeonpea, a tropical photosensitive crop, harbors significant diversity for days to flowering, but little is known about the genes that govern these differences. Our goal in the current study was to use genome wide association strategy to discover the loci that regulate days to flowering in pigeonpea. A single trait as well as a principal component based association study was conducted on a diverse collection of 142 pigeonpea lines for days to first and fifty percent of flowering over 3 years, besides plant height and number of seeds per pod. The analysis used seven association mapping models (GLM, MLM, MLMM, CMLM, EMLM, FarmCPU and SUPER) and further comparison revealed that FarmCPU is more robust in controlling both false positives and negatives as it incorporates multiple markers as covariates to eliminate confounding between testing marker and kinship. Cumulatively, a set of 22 SNPs were found to be associated with either days to first flowering (DOF), days to fifty percent flowering (DFF) or both, of which 15 were unique to trait based, 4 to PC based GWAS while 3 were shared by both. Because PC1 represents DOF, DFF and plant height (PH), four SNPs found associated to PC1 can be inferred as pleiotropic. A window of ± 2 kb of associated SNPs was aligned with available transcriptome data generated for transition from vegetative to reproductive phase in pigeonpea. Annotation analysis of these regions revealed presence of genes which might be involved in floral induction like Cytochrome p450 like Tata box binding protein, Auxin response factors, Pin like genes, F box protein, U box domain protein, chromatin remodelling complex protein, RNA methyltransferase. In summary, it appears that auxin responsive genes could be involved in regulating DOF and DFF as majority of the associated loci contained genes which are component of auxin signaling pathways in their vicinity. Overall, our findings indicates that the use of principal component analysis in GWAS is statistically more robust in terms of identifying genes and FarmCPU is a better choice compared to the other aforementioned models in dealing with both false positive and negative associations and thus can be used for traits with complex inheritance.

Abstract The RNA helicases are an important class of enzymes which are known to influence almost every aspect of RNA metabolism. The majority of RNA helicases belong to the SF2 (superfamily 2) superfamily, members of which are further categorized into three separate subfamilies i.e., the DEAD, DEAH and DExD/H-box subfamilies. In chickpea, these RNA helicases have not been characterized until now. A genome-wide analysis across the chickpea genome led to the identification of a total of 150 RNA helicase genes which included 50 DEAD, 33 DEAH and 67 DExD/H-box genes. These were distributed across all the eight chromosomes, with highest number on chromosome 4 (26) and least on chromosome 8 (8). Gene duplication analysis resulted in identification of 15 paralogous gene pairs with Ka/Ks values

Abstract 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.

Seed size and shape are important traits determining yield and quality in soybean. Seed size and shape are also desirable for specialty soy foods like tofu, natto, miso, and edamame. In order to find stable quantitative trait loci (QTLs) and candidate genes for seed shape and 100-seed weight, the current study used vegetable type and seed soybean-derived F2 and F2:3 mapping populations. A total of 42 QTLs were mapped, which were dispersed across 13 chromosomes. Of these, seven were determined to be stable QTLs and five of them were major QTLs, namely qSL-10-1, qSW-4-1, qSV-4-1, qSLW-10-1, and qSLH-10-1. Thirteen of the 42 QTLs detected in the current study were found at known loci, while the remaining 29 were discovered for the first time. Out of these 29 novel QTLs, 17 were major QTLs. Based on Protein Analysis Through Evolutionary Relationships (PANTHER), gene annotation information, and literature search, 66 genes within seven stable QTLs were predicted to be possible candidate genes that might regulate seed shape and seed weight in soybean. The current study identified the key candidate genes and quantitative trait loci (QTLs) controlling soybean seed shape and weight, and these results will be very helpful in marker-assisted breeding for developing soybean varieties with improved seed weight and desired seed shape.

Wild progenitor species of rice (Oryza rufipogon Griff./ Oryza nivara Sharma et. Shastry) are rich source of genes for both the biotic as well as abiotic stress tolerance. Wild rice accession NKSWR 173 has been identified as highly tolerant to salinity stress at seedling stage and moderately tolerant at reproductive stage after evaluation of more than two hundred wild rice accessions from across India. In a bid to introgress the salt tolerance trait from NKSWR 173 to a high-yielding mega variety of rice IR 64, we screened a segregating BC1 population for identification of suitable lines for making the second backcross using both controlled phenotyping and QTL flanking DNA markers. Four lines, namely SN 32, SN 33, SN 39 and SN 45 were found highly tolerant to salinity at both seedling and reproductive stage and were backcrossed to IR 64 to generate BC2F1 seeds for development of advance introgressed lines. Introgression of novel salinity tolerance genes for both the seedling and reproductive stages in mega variety of rice will be useful in achieving high productivity in salt affected rice areas.

Cytokinins constitutes a vital group of plant hormones regulating several developmental processes, including growth and cell division, and have a strong influence on grain yield. Chemically, they are the derivatives of adenine and are the most complex and diverse group of hormones affecting plant physiology. In this review, we have provided a molecular understanding of the role of cytokinins in developing seeds, with special emphasis on pulses and oilseed crops. The importance of cytokinin-responsive genes including cytokinin oxidases and dehydrogenases (CKX), isopentenyl transferase (IPT), and cytokinin-mediated genetic regulation of seed size are described in detail. In addition, cytokinin expression in germinating seeds, its biosynthesis, source-sink dynamics, cytokinin signaling, and spatial expression of cytokinin family genes in oilseeds and pulses have been discussed in context to its impact on increasing economy yields. Recently, it has been shown that manipulation of the cytokinin-responsive genes by mutation, RNA interference, or genome editing has a significant effect on seed number and/or weight in several crops. Nevertheless, the usage of cytokinins in improving crop quality and yield remains significantly underutilized. This is primarily due to the multigene control of cytokinin expression. The information summarized in this review will help the researchers in innovating newer and more efficient ways of manipulating cytokinin expression including CKX genes with the aim to improve crop production, specifically of pulses and oilseed crops.

Abstract Pigeonpea (Cajanus cajan L. Huth) is an agronomically important legume cultivated worldwide. In this study, we extensively analyzed gene‐body methylation (GbM) patterns in pigeonpea. We found a bimodal distribution of CG and CHG methylation patterns. GbM features‐ slow evolution rate and increased length remained conserved. Genes with moderate CG body methylation showed highest expression where as highly‐methylated genes showed lowest expression. Transposable element (TE)‐related genes were methylated in multiple contexts and hence classified as C‐methylated genes. A low expression among C‐methylated genes was associated with transposons insertion in gene‐body and upstream regulatory regions. The CG methylation patterns were found to be conserved in orthologs compared with non‐CG methylation. By comparing methylation patterns between differentially methylated regions (DMRs) of the three genotypes, we found that variably methylated marks are less likely to target evolutionary conserved sequences. Finally, our analysis showed enrichment of nitrogen‐related genes in GbM orthologs of legumes, which could be promising candidates for generating epialleles for crop improvement.

Pennisetum glaucum (L.) R. Br., being widely grown in dry and hot weather, frequently encounters heat stress at various stages of growth. The crop, due to its inherent capacity, efficiently overcomes such stress during vegetative stages. However, the same is not always the case with the terminal (flowering through grain filling) stages of growth, where recovery from stress is more challenging. However, certain pearl millet genotypes such as 841-B are known to overcome heat stress even at the terminal growth stages. Therefore, we performed RNA sequencing of two contrasting genotypes of pearl millet (841-B and PPMI-69) subjected to heat stress (42°C for 6 h) at flowering stages. Over 274 million high quality reads with an average length of 150 nt were generated, which were assembled into 47,310 unigenes having an average length of 1,254 nucleotides, N50 length of 1853 nucleotides, and GC content of 53.11%. Blastx resulted in the annotation of 35,628 unigenes, and functional classification showed 15,950 unigenes designated to 51 Gene Ontology terms. A total of 13,786 unigenes were allocated to 23 Clusters of Orthologous Groups, and 4,255 unigenes were distributed to 132 functional Kyoto Encyclopedia of Genes and Genomes database pathways. A total of 12,976 simple sequence repeats and 305,759 SNPs were identified in the transcriptome data. Out of 2,301 differentially expressed genes, 10 potential candidate genes were selected based on log2 fold change and adjusted p value parameters for their differential gene expression by qRT-PCR. We were able to identify differentially expressed genes unique to either of the two genotypes, and also, some DEGs common to both the genotypes were enriched. The differential expression patterns suggested that 841-B 6 h has better ability to maintain homeostasis during heat stress as compared to PPMI-69 6 h. The sequencing data generated in this study, like the SSRs and SNPs, shall serve as an important resource for the development of genetic markers, and the differentially expressed heat responsive genes shall be used for the development of transgenic crops.

Abstract Galactomannan is a polymer of high economic importance and is extracted from the seed endosperm of clusterbean (C. tetragonoloba). In the present study, we worked to reveal the stage-specific galactomannan biosynthesis and its regulation in clusterbean. Combined electron microscopy and biochemical analysis revealed high protein and gum content in RGC-936, while high oil bodies and low gum content in M-83. A comparative transcriptome study was performed between RGC-936 (high gum) and M-83 (low gum) varieties at three developmental stages viz. 25, 39, and 50 days after flowering (DAF). Total 209,525, 375,595 and 255,401 unigenes were found at 25, 39 and 50 DAF respectively. Differentially expressed genes (DEGs) analysis indicated a total of 5147 shared unigenes between the two genotypes. Overall expression levels of transcripts at 39DAF were higher than 50DAF and 25DAF. Besides, 691 (RGC-936) and 188 (M-83) candidate unigenes that encode for enzymes involved in the biosynthesis of galactomannan were identified and analyzed, and 15 key enzyme genes were experimentally validated by quantitative Real-Time PCR. Transcription factor (TF) WRKY was observed to be co-expressed with key genes of galactomannan biosynthesis at 39DAF. We conclude that WRKY might be a potential biotechnological target (subject to functional validation) for developing high gum content varieties.

Abstract Background Pigeon pea (Cajanus cajan L.) is the sixth major legume crop widely cultivated in the Indian sub-continent, Africa, and South-east Asia. Cytoplasmic male-sterility (CMS) is the incompetence of flowering plants to produce viable pollens during anther development. CMS has been extensively utilized for commercial hybrid seeds production in pigeon pea. However, the molecular basis governing CMS in pigeon pea remains unclear and undetermined. In this study transcriptome analysis for exploring differentially expressed genes (DEGs) between cytoplasmic male-sterile line (AKCMS11) and its fertility restorer line (AKPR303) was performed using Illumina paired-end sequencing. Results A total of 3167 DEGs were identified, of which 1432 were up-regulated and 1390 were down-regulated in AKCMS11 in comparison to AKPR303. By querying, all the 3167 DEGs against TAIR database, 34 pigeon pea homologous genes were identified, few involved in pollen development (EMS1, MS1, ARF17) and encoding MYB and bHLH transcription factors with lower expression in the sterile buds, implying their possible role in pollen sterility. Many of these DEGs implicated in carbon metabolism, tricarboxylic acid cycle (TCA), oxidative phosphorylation and elimination of reactive oxygen species (ROS) showed reduced expression in the AKCMS11 (sterile) buds. Conclusion The comparative transcriptome findings suggest the potential role of these DEGs in pollen development or abortion, pointing towards their involvement in cytoplasmic male-sterility in pigeon pea. The candidate DEGs identified in this investigation will be highly significant for further research, as they could lend a comprehensive basis in unravelling the molecular mechanism governing CMS in pigeon pea.

Cluster bean or guar [Cyamopsis tetragonoloba (L.) Taub] is a multipurpose legume crop of the arid regions of the Indian subcontinent. This industrially important crop is primarily used as a food and feed; and cultivated mainly for its galactomannan enriched seed. There is a lack of information on the genetics of important traits including flower colour and pubescence/hairiness and its correlation with the quantitative trait like yield and understanding the co-segregation of these traits may be helpful in yield improvement. Therefore, the current study was performed using 235 F2 segregating lines of guar generated from two diverse parents differing in many traits. Phenotyping of population was carried out for 13 agronomic traits, flower colour and hairiness. Results indicated that both parents of the population were diverse for both qualitative and quantitative traits except pods per plant. The heritability of various quantitative traits ranged from 32.68 % (seeds per pod) to 97.73 % (pods per plant). A significant positive correlation (0.40**) between days to maturity and plant height was observed. Yield demonstrated significant positive correlations with all traits except days to flowering. The path coefficient analysis showed that merely two characters, namely pods per plant (0.87) and pods per clusters (0.19) exerted a significant positive direct effect on seed yield per plant. The scrutiny of principal components revealed that the first four components described a cumulative variability of 73.4 %. The scattering of F2 plants in bi-plot confirmed our earlier observations that both parents were genetically dissimilar and quite diverse for the traits under study. A significant linkage of flower colour with pods per cluster, cluster on the main stem, pod length and seed per pod was observed. Likewise, hairiness displayed linkage with leaf area, plant height and days to flowering. The R2 value ranged from 1.7 % (seed per pod) to 3.8 % (days to flowering). The result suggested that subtle influence of hairiness and violet flower on yield and yield attributing traits have favoured their selection in the released varieties in the past. The future breeding strategies may emphasize combining pod length and leaf area with pods per plant in a smooth (hairless) genotype.

Ascorbate peroxidase (APX) is a member of the family of heme-containing peroxidases having a similar structure with Cytochrome c peroxidase (CCP) that effectively scavenge cytosolic and chloroplastic hydrogen peroxide (H2O2) under various stresses. In this study, computational characterization and homology analysis of APX protein from waterlogging tolerant (ICPL 84023) and sensitive (ICP 7035) pigeon pea genotypes were carried out resulting in 100% homology with Glycine max in case of former and 99% in later genotypes respectively with 97.39% alignment coverage among each other. The model structure was further refined by various tools like PROCHECK, ProSA, and Verify3D. The planned model of the APX enzyme was then tested to dock with H2O2along with molecular dynamics (MD) simulation analysis. The docked complex of ICPL 84023 showed the best G-score (23.39 kcal/mol) in comparison to ICP 7035 (16.74 kcal/mol) depicting the higher production of APX for scavenging reactive oxygen species (ROS) production making this genotype more tolerant. The important binding residues in the ICPL 84023-H2O2complex (SER1, THR4, GLU23, and GLY13) have shown less fluctuation than the ICP 7035-H2O2 complex (SER1, THR4, and GLU23). Overall, our results showed that amino acid residue glycine in ICPL 84023 APX gene has a high binding affinity with H2O2 which could be a key factor associated with waterlogging stress tolerance in pigeon pea.

Abstract Background Water permeability governed by seed coat is a major facet of seed crops, especially soybean, whose seeds lack physiological dormancy and experience rapid deterioration in seed viability under prolonged storage. Moreover, the physiological and chemical characteristics of soybean seeds are known to vary with seed coat color. Thus, to underpin the genes controlling water permeability in soybean seeds, we carried out an in-depth characterization of the associated genomic variation. Results In the present study, we have analyzed genomic variation between cultivated soybean and its wild progenitor with implications on seed permeability, a trait related to seed storability. Whole genome resequencing of G.max and G. soja, identified SNPs and InDels which were further characterized on the basis of their genomic location and impact on gene expression. Chromosomal density distribution of the variation was assessed across the genome and genes carrying SNPs and InDels were characterized into different metabolic pathways. Seed hardiness is a complex trait that is affected by the allelic constitution of a genetic locus as well as by a tricky web of plant hormone interactions. Seven genes that hold a probable role in the determination of seed permeability were selected and their expression differences at different stages of water imbibition were analyzed. Variant interaction network derived 205 downstream interacting partners of 7 genes confirmed their role in seed related traits. Interestingly, genes encoding for Type I- Inositol polyphosphate 5 phosphatase1 and E3 Ubiquitin ligase could differentiate parental genotypes, revealed protein conformational deformations and were found to segregate among RILs in coherence with their permeability scores. The 2 identified genes, thus showed a preliminary association with the desirable permeability characteristics. Conclusion In the light of above outcomes, 2 genes were identified that revealed preliminary, but a relevant association with soybean seed permeability trait and hence could serve as a primary material for understanding the molecular pathways controlling seed permeability traits in soybean.

Yellow stem borer (YSB), Scirpophaga incertulas (Walker) (Lepidoptera: Crambidae), a major monophagous insect pest of rice, causes significant yield losses. The rice–YSB interaction is very dynamic, making it difficult for management. The development of resistant lines has been unsuccessful as there are no effective resistant sources in the germplasm. Genome information is necessary for a better understanding of interaction with rice in terms of its recognition, response, and infestation mechanism. The draft genome of YSB is predicted to have 46,057 genes with an estimated size of 308 Mb, being correlated with the flow cytometry analysis. The existence of complex metabolic mechanisms and genes related to specific behavior was identified, being conditioned by a higher level of regulation. We deciphered the possible visual, olfactory, and gustatory mechanisms responsible for its evolution as a monophagous pest. Comparative genomic analysis revealed that YSB is unique in the way it has evolved. The obvious presence of high-immunity-related genes, well-developed RNAi machinery, and diverse effectors provides a means for developing genomic tools for its management. The identified 21,696 SSR markers can be utilized for diversity analysis of populations across the rice-growing regions. We present the first draft genome of YSB. The information emanated paves a way for biologists to design novel pest management strategies as well as for the industry to design new classes of safer and specific insecticide molecules.

To generate a genetic resource of heat stress responsive genes/ESTs, suppression subtractive hybridization (SSH) library was constructed in a heat and drought stress tolerant Indian bread wheat cultivar C306. Ninety three days old plants during grain filling stage were subjected to heat stress at an elevated temperature of 37°C and 42°C for different time intervals (30 min, 1h, 2h, 4h, and 6h). Two subtractive cDNA libraries were prepared with RNA isolated from leaf samples at 37°C and 42°C heat stress. The ESTs obtained were reconfirmed by reverse northern dot blot hybridization. A total of 175 contigs and 403 singlets were obtained from 1728 ESTs by gene ontology analysis. Differential expression under heat stress was validated for a few selected genes (10) by qRT-PCR. A transcript showing homology to Hsp90 was observed to be upregulated (7.6 fold) under heat stress in cv. C306. CDS of TaHsp90 (Accession no. MF383197) was isolated from cv. C306 and characterized. Heterologous expression of TaHsp90 was validated in E. coli BL21 and confirmed by protein gel blot and MALDI-TOF analysis. Computational based analysis was carried out to understand the molecular functioning of TaHsp90. The heat stress responsive SSH library developed led to identification of a number of heat responsive genes/ESTs, which can be utilized for unravelling the heat tolerance mechanism in wheat. Gene TaHsp90 isolated and characterized in the present study can be utilized for developing heat tolerant transgenic crops.

Oryza coarctata plant, collected from Sundarban delta of West Bengal, India, has been used in the present study to generate draft genome sequences, employing the hybrid genome assembly with Illumina reads and third generation Oxford Nanopore sequencing technology. We report for the first time the draft genome with the coverage of 85.71 % and deposited the raw data in NCBI SRA, with BioProject ID PRJNA396417.

Exome sequencing represents targeted capture and sequencing of 1–2% of ‘high-value genomic regions’ (subset of the genome) which are enriched for functional variants and harbors low level of repetitive regions. We discuss here an overview of exome sequencing, ways to approach plant exomes, and advantages and applicability of this powerful approach in deciphering functional regions of genomes. Though initially this approach was developed as an alternative to whole genome sequencing (WGS), but the multitude of benefits conferred by sequence capture via hybridization approaches created a niche for itself to solve many of biological riddles, particularly for resolving phylogenetic distances. The technique has also proved to be successful in understanding the basis of natural and induced molecular variation, marker development and developing genomic resources for complex, wild and non-model species, which are still intractable for WGS efforts. Thus, with profound applications of this powerful sequencing strategy, near future is expected to witness a collective expansion of both techniques, i.e., sequence capture via hybridization for evolutionary and ecological research and WGS approaches for its universal accessibility.

Oryza coarctata plants, collected from Sundarban delta of West Bengal, India, have been used in the present study to generate draft genome sequences, employing the hybrid genome assembly with Illumina reads and third generation Oxford Nanopore sequencing technology. We report for the first time that more than 85.71 % of the genome coverage and the data have been deposited in NCBI SRA, with BioProject ID PRJNA396417.

Pigeonpea [Cajanus cajan (L.) Millsp.] is a heat and drought resilient legume crop grown mostly in Asia and Africa. Pigeonpea is affected by various biotic (diseases and insect pests) and abiotic stresses (salinity and water logging) which limit the yield potential of this crop. However, resistance to all these constraints is not readily available in the cultivated genotypes and some of the wild relatives have been found to withstand these resistances. Thus, the utilization of crop wild relatives (CWR) in pigeonpea breeding has been effective in conferring resistance, quality and breeding efficiency traits to this crop. Bud and leaf tissue of Cajanus scarabaeoides, a wild relative of pigeon pea were used for transcriptome profiling. Approximately 30 million clean reads filtered from raw reads by removal of adaptors, ambiguous reads and low-quality reads (3.02 gigabase pairs) were generated by Illumina paired-end RNA-seq technology. All of these clean reads were pooled and assembled de novo into 1,17,007 transcripts using the Trinity. Finally, a total of 98,664 unigenes were derived with mean length of 396 bp and N50 values of 1393. The assembly produced significant mapping results (73.68%) in BLASTN searches of the Glycine max CDS sequence database (Ensembl). Further, uniprot database of Viridiplantae was used for unigene annotation; 81,799 of 98,664 (82.90%) unigenes were finally annotated with gene descriptions or conserved protein domains. Further, a total of 23,475 SSRs were identified in 27,321 unigenes. This data will provide useful information for mining of functionally important genes and SSR markers for pigeonpea improvement.

Pigeonpea (Cajanus cajan (L.) Millspaugh), a diploid (2n = 22) legume crop with a genome size of 852 Mbp, serves as an important source of human dietary protein especially in South East Asian and African regions. In this study, the draft chloroplast genomes of Cajanus cajan and Cajanus scarabaeoides were sequenced. Cajanus scarabaeoides is an important species of the Cajanus gene pool and has also been used for developing promising CMS system by different groups. A male sterile genotype harbouring the Cajanus scarabaeoides cytoplasm was used for sequencing the plastid genome. The cp genome of Cajanus cajan is 152,242bp long, having a quadripartite structure with LSC of 83,455 bp and SSC of 17,871 bp separated by IRs of 25,398 bp. Similarly, the cp genome of Cajanus scarabaeoides is 152,201bp long, having a quadripartite structure in which IRs of 25,402 bp length separates 83,423 bp of LSC and 17,854 bp of SSC. The pigeonpea cp genome contains 116 unique genes, including 30 tRNA, 4 rRNA, 78 predicted protein coding genes and 5 pseudogenes. A 50kb inversion was observed in the LSC region of pigeonpea cp genome, consistent with other legumes. Comparison of cp genome with other legumes revealed the contraction of IR boundaries due to the absence of rps19 gene in the IR region. Chloroplast SSRs were mined and a total of 280 and 292 cpSSRs were identified in Cajanus scarabaeoides and Cajanus cajan respectively. RNA editing was observed at 37 sites in both Cajanus scarabaeoides and Cajanus cajan, with maximum occurrence in the ndh genes. The pigeonpea cp genome sequence would be beneficial in providing informative molecular markers which can be utilized for genetic diversity analysis and aid in understanding the plant systematics studies among major grain legumes.

Three Ethyl methansulphonate (EMS)-induced stay-green mutants (SGM-1, SGM-2 and SGM-3) and their wild-type (WT), were tested for their Stay-Green (SG) and drought tolerance nature as the relation between these two attributes is not yet established in rice. In the dark induced senescence assay, SGM-3 showed delayed senescence while SGM-1 and SGM-2 showed complete lack of senescence. Mutants showed stable transcript abundance over time, for 15 candidate genes (CGs) associated with senescence, compared to the WT. SGM-3 however showed moderately increasing transcript abundance over time for ATG6a, ATG4a, NYC1, NOL and NYC3. Only SGM-3 performed better than the WT for yield and harvest index under well irrigated as well as drought conditions, though all the mutants showed better performance for other agronomic traits under both the conditions and ascorbate peroxidase activity under drought. Thus, SG trait showed positive correlation with drought tolerance though only SGM-3 could convert this into higher harvest index. Sequence analysis of 80 senescence-associated genes including the 15 CGs showed non-synonymous mutations in four and six genes in SGM-1 and SGM-2 respectively, while no SNPs were found in SGM-3. Analysis of the earlier reported Quantitative Trait Loci (QTL) regions in SGM-3 revealed negligible variations from WT, suggesting it to be a novel SG mutant.

A number of factors were responsible in the evolution of the first state craft in deccan locale. There were bound to be, several regional power centers beyond the main arena of Satvahna power. Their negotiation, complementing and supplementing each others need as well as with limited autonomy, enjoying their peripheral important status. Kanheri caves, specially the epigraphic evidences during Satvahna times, could be the best marker of variety of power specificities within deccan. These inscriptions made references to casts, gotras, communities, gahapaties as well as garini and kutumbini etc. These were all local social cultural forces were playing imperative roles in the larger eco-political ambiance of deccan. It's a kind of multidimensional relationship of mainstream political and cultural process, specially seprated to ecological setting. Surprisingly from these plaethora of inscriptions guilds and Satvahna royal house hold didn't carve out their space. Kanheri caves laid phenomenal role in trade and cultural interactions. The present paper as an attempt to explore socio cultural role of Kanheri caves in these interactions.

The genome of tomato ( L.) is being sequenced by an international consortium of 10 countries (Korea, China, the United Kingdom, India, the Netherlands, France, Japan, Spain, Italy, and the United States) as part of the larger “International Solanaceae Genome Project (SOL): Systems Approach to Diversity and Adaptation” initiative. The tomato genome sequencing project uses an ordered bacterial artificial chromosome (BAC) approach to generate a high-quality tomato euchromatic genome sequence for use as a reference genome for the Solanaceae and euasterids. Sequence is deposited at GenBank and at the SOL Genomics Network (SGN). Currently, there are around 1000 BACs finished or in progress, representing more than a third of the projected euchromatic portion of the genome. An annotation effort is also underway by the International Tomato Annotation Group. The expected number of genes in the euchromatin is ∼40,000, based on an estimate from a preliminary annotation of 11% of finished sequence. Here, we present this first snapshot of the emerging tomato genome and its annotation, a short comparison with potato ( L.) sequence data, and the tools available for the researchers to exploit this new resource are also presented. In the future, whole-genome shotgun techniques will be combined with the BAC-by-BAC approach to cover the entire tomato genome. The high-quality reference euchromatic tomato sequence is expected to be near completion by 2010.

Oryza coarctata plant, collected from Sundarban delta of West Bengal, India, has been used in the present study to generate draft genome sequences, employing the hybrid genome assembly with Illumina reads and third generation Oxford Nanopore sequencing technology. We report for the first time the draft genome with the coverage of 85.71 % and deposited the raw data in NCBI SRA, with BioProject ID PRJNA396417.