Publications of NIPGR Scientists

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A 1000-loci transcript map of the barley genome: new anchoring points for integrative grass genomics
(Springer, 2007) Stein, Nils; Prasad, Manoj; Scholz, Uwe; Thiel, Thomas; Zhang, Hangning; Wolf, Markus; Kota, Raja; Varshney, Rajeev K.; Perovic, Dragan; Grosse, Ivo; Graner, Andreas
An integrated barley transcript map (consensus map) comprising 1,032 expressed sequence tag (EST)-based markers (total 1,055 loci: 607 RFLP, 190 SSR, and 258 SNP), and 200 anchor markers from previously published data, has been generated by mapping in three doubled haploid (DH) populations. Between 107 and 179 EST-based markers were allocated to the seven individual barley linkage groups. The map covers 1118.3 cM with individual linkage groups ranging from 130 cM (chromosome 4H) to 199 cM (chromosome 3H), yielding an average marker interval distance of 0.9 cM. 475 EST-based markers showed a syntenic organisation to known colinear linkage groups of the rice genome, providing an extended insight into the status of barley/rice genome colinearity as well as ancient genome duplications predating the divergence of rice and barley. The presented barley transcript map is a valuable resource for targeted marker saturation and identiWcation of candidate genes at agronomically important loci. It provides new anchor points for detailed studies in comparative grass genomics and will support future attempts towards the integration of genetic and physical mapping information.
2-Hydroxyacetophenone, the main component of the essential oil of the roots of Carissa opaca Stapf ex Haines
(Taylor & Francis Group, 2009) Mallavarupu, Gopal R.; Mishra, Raghvendra K.; Chaudhary, Swati; Pandey, Richa; Gupta, Sarika; Kumar, Sushil
The volatile oil obtained by hydrodistillation of the roots of Carissa opaca was analyzed by GC and GC/MS to study its composition. Thirty-five compounds representing 98.3% of the oil were identified. Si-gel chromatography of the oil yielded 2-hydroxyacetophenone, which was characterized by spectral methods (1H-, 13C-NMR and mass), as the main component, amounting to 89.5% of the oil.
A 286 bp upstream regulatory region of a rice anther-specific gene, OSIPP3, confers pollen-specific expression in Arabidopsis
(Springer, 2013) Khurana, Reema; Kathuria, Hitesh; Mukhopadhyay, Arnab; Kapoor, Sanjay; Tyagi, Akhilesh K.
OSIPP3 gene (coding for pectin methylesterase inhibitor protein) was isolated from a pre-pollinated inflorescence-specific cDNA library by differential screening of stage-specific libraries from Oryza sativa. OSIPP3 is present in the genome of rice as a single copy gene. OSIPP3 gene was expressed exclusively in the pre-pollinated spikelets of rice. Upstream regulatory region (URR) of OSIPP3 was isolated and a series of 5'-deletions were cloned upstream of GUS reporter gene and were used to transform Arabidopsis. OSIPP3_del1 and del2 transgenic plants showed GUS expression in root, anther and silique, while OSIPP3_del3 showed GUS activity only in anthers and siliques. Pollen-specific expression was observed in case of plants harboring OSIPP3_del4 construct. It can, therefore, be concluded that the OSIPP3 URR between -178 and +108 bp is necessary for conferring pollen-specific expression in Arabidopsis.
5M approach to decipher starch-lipid interaction in minor millets
(Springer Nature Publishing AG, 2023) Ramesh, Palakurthi; Singh, Roshan Kumar; Panchal, Anurag; Prasad, Manoj
The 5M approach can be applied to understand genetic complexity underlying nutritional traits of minor millets. It will help to systematically identify genomic regions/candidate genes imprinting metabolite profiles. Author’s work in this area is supported by research grants from Ministry of Science and Technology, Gov. of India [GrantCRG/2020/000488 and BT/Ag/Network/Wheat/2019–20].
9th Solanaceae Conference 2012
(National Academy of Sciences, India/ Springer, 2013) Prasad, Manoj
Solanaceae genome community holds annual meeting every year to discuss the updates on current research in field of genetics, genomics and evolutionary biology of Solanaceous crops. The 9th Solanaceae genome conference held at University of Neuchatel, Switzerland on 26th–30th August, 2012, on the theme “SOL2012 Conference from Bench to Innovative Applications”. The salient features of the conference are presented in short in this report.
A cytokinin-auxin antagonistic module participates in nitrogen-triggered tiller outgrowth in rice
(Oxford University Press, 2026) Chatterjee, Sourav; Dwivedi, Aditi; Sarkar, Ananda K; Ranjan, Aashish
Tillering is a key trait that shapes rice (Oryza sativa L.) shoot architecture and directly influences yield. While tiller bud formation is largely genetically determined, bud outgrowth into functional tillers is highly responsive to environmental cues. However, integration of environmental signals with genetic regulators to determine tiller bud fate remains poorly understood. Here, we investigated the effects of nitrogen on early stages of tiller bud outgrowth. Comprehensive phenotyping and temporal transcriptomic analyses demonstrated that both nitrate and ammonium promote bud outgrowth and elicit overlapping transcriptional responses, with nitrate acting more slowly. Gene regulatory network analysis identified phytohormone signaling as a key interface for nitrogen- triggered tiller outgrowth. Pharmacological and molecular experiments demonstrated the involvement of cytokinin–auxin antagonism in nitrogen-mediated tillering. Cytokinin promoted bud activation by repressing the critical bud dormancy regulators rice TEOSINTE BRANCHED 1 (OsTB1) and a homolog of PIN-FORMED 1 (OsPIN1a) through the Cytokinin Response Factors OsERF53/54. In contrast, auxin maintained dormancy by inducing OsTB1 and OsPIN1a expression through Auxin Response Factors OsARF11/16. Consistently, OsTB1 overexpression lines showed reduced responsiveness to nitrogen and hormone treatments, placing OsTB1 downstream of these convergent inputs. Sequence and gene expression differences in OsERF53/54, along with phenotypic variations across contrasting rice accessions, further substantiated the crucial roles of OsERF53/54 in nitrogen-mediated tillering. Together, we identify a key regulatory role of the cytokinin-auxin antagonistic module for integrating nitrogen signals to determine tiller bud fate. Adequate nitrogen promotes cytokinin signaling while attenuating auxin signaling and transport in tiller buds, thereby releasing dormancy and initiating bud outgrowth.
ABC transporter-mediated transport of glutathione conjugates enhances seed yield and quality in chickpea
(American Society of Plant Biologists, 2019) Basu, Udita; Upadhyaya, Hari D.; Srivastava, Rishi; Daware, Anurag; Malik, Naveen; Sharma, Akash; Bajaj, Deepak; Narnoliya, Laxmi; Thakro, Virevol; Kujur, Alice; Tripathi, Shailesh; Bharadwaj, Chellapilla; Hegde, V. S.; Pandey, Ajay K.; Singh, Ashok K.; Tyagi, Akhilesh K.; Parida, Swarup K.
The identification of functionally relevant molecular tags is vital for genomics-assisted crop improvement and enhancing the seed yield, quality and productivity in chickpea. The simultaneous improvement of yield/productivity as well as quality traits often requires pyramiding of multiple genes, which remains a major hurdle given various associated epistatic and pleotropic effects. Unfortunately, no single gene that can improve yield/productivity along with quality and other desirable agromorphological traits is known, hampering the genetic enhancement of chickpea. Using a combinatorial genomics-assisted breeding and functional genomics strategy, this study identified natural alleles and haplotypes of an ABCC3-type transporter gene that regulates seed weight, an important domestication trait, by transcriptional regulation and modulating the transport of glutathione conjugates in seeds of desi and kabuli chickpea. The superior allele/haplotype of this gene introgressed in desi and kabuli near-isogenic lines enhances the seed weight, yield, productivity and multiple desirable plant architecture and seed-quality traits without compromising the agronomic performance. These salient findings can expedite crop improvement endeavors and the development of nutritionally enriched high-yielding cultivars in chickpea.
ABI transcription factors and PROTEIN L-ISOASPARTYL METHYLTRANSFERASE module mediate seed desiccation tolerance and longevity in Oryza sativa
(The Company of Biologists, 2022) Kamble, Nitin Uttam; Majee, Manoj
In contrast to desiccation-tolerant orthodox seeds, recalcitrant seeds are desiccation sensitive and are unable to survive for a prolonged time. Here, our analyses of Oryza species with contrasting seed desiccation tolerance reveals that PROTEIN L-ISOASPARTYL METHYLTRANSFERASE (PIMT), an enzyme that repairs abnormal isoaspartyl (isoAsp) residues in proteins, acts as a key player that governs seed desiccation tolerance to orthodox seeds but is ineffective in recalcitrant seeds. We observe that, unlike the orthodox seed of Oryza sativa, desiccation intolerance of the recalcitrant seeds of Oryza coarctata are linked to reduced PIMT activity and increased isoAsp accumulation due to the lack of coordinated action of ABA and ABI transcription factors to upregulate PIMT during maturation. We show that suppression of PIMT reduces, and its overexpression increases, seed desiccation tolerance and seed longevity in O. sativa. Our analyses further reveal that the ABI transcription factors undergo isoAsp formation that affect their functional competence; however, PIMT interacts with and repairs isoAsp residues and facilitates their functions. Our results thus illustrate a new insight into the mechanisms of acquisition of seed desiccation tolerance and longevity by ABI transcription factors and the PIMT module.
Abiotic stress impact on the interaction between Macrophomina phaseolina and crop plants
(Springer Nature Publishing AG, 2024) Ranjan, Shubhashish; Mirchandani, Rishabh; Senthil-Kumar, Muthappa
Macrophomina phaseolina (Tassi.) Goid is an emerging pathogen that causes diseases like dry root rot and charcoal rot in more than 100 plant families. Abiotic stresses such as drought, salinity, and heat exacerbate this fungal effect and predispose crops to pathogen attacks. Importantly, these combined stresses lead to significant crop yield losses under field conditions. In this, we review the interaction between the devastating pathogen M. phaseolina and several abiotic stresses that are more likely to occur in scenarios of climate change. Drought, heat, and salinity are the major stresses that interact with M. phaseolina in the field. We discuss several field studies, unique physiological and molecular responses, and their mechanisms of control in response to combined stress. The net effect of these interactions depends on a multitude of factors; thus, these interactions modify the impact of biotic stresses on plants by altering their susceptibility. The aim of this review is to provide an overview of what is currently known about M. phaseolina and abiotic stress interactions, as well as several other edaphic factors that interact with plants. We briefly discuss the role of drought, salinity, heat stress, and edaphic factors (such as pH, N, P, K, etc.) that influence pathogen infection in plants. Furthermore, we discuss possible management strategies to combat crop loss due to combined stress. Thus, we suggest the future aspect of combined stress breeding, along with the use of multi-omics techniques and genome editing approaches, to develop cultivars that exhibit stability in a combined stress environment.
Abiotic stress tolerance in plants: Brassinosteroids navigate competently
(MDPI AG, 2022) Chaudhuri, Abira; Halder, Koushik; Abdin, Malik Z; Majee, Manoj; Datta, Asis
Brassinosteroid hormones (BRs) multitask to smoothly regulate a broad spectrum of vital physiological processes in plants, such as cell division, cell expansion, differentiation, seed germination, xylem differentiation, reproductive development and light responses (photomorphogenesis and skotomorphogenesis). Their importance is inferred when visible abnormalities arise in plant phenotypes due to suboptimal or supraoptimal hormone levels. This group of steroidal hormones are major growth regulators, having pleiotropic effects and conferring abiotic stress resistance to plants. Numerous abiotic stresses are the cause of significant loss in agricultural yield globally. However, plants are well equipped with efficient stress combat machinery. Scavenging reactive oxygen species (ROS) is a unique mechanism to combat the deleterious effects of abiotic stresses. In light of numerous reports in the past two decades, the complex BR signaling under different stress conditions (drought, salinity, extreme temperatures and heavy metals/metalloids) that drastically hinders the normal metabolism of plants is gradually being untangled and revealed. Thus, crop improvement has substantial potential by tailoring either the brassinosteroid signaling, biosynthesis pathway or perception. This review aims to explore and dissect the actual mission of BRs in signaling cascades and summarize their positive role with respect to abiotic stress tolerance.
Abiotic stress-responsive expression of wali1 and wali5 genes from wheat
(Landes Bioscience, 2012) Garg, Bharti; Puranik, Swati; Tuteja, Narendra; Prasad, Manoj
Two cDNA clones, encoding Aluminum-responsive wali1 and wali5, were identified in dehydration stress-specific cDNA library from wheat. Their sequence variations and structural dissimilarities indicated them to be non-homologous genes. Expression of both genes was induced by various abiotic stresses as well as in response to plant hormones and oxidative molecules. Further, they were expressed differentially in shoot and root tissues of wheat seedlings, their transcripts being specifically abundant in roots. Previously characterized as being only Aluminum treatment induced, this report proposes them as novel candidates for stress-responsive studies.
Abnormal Leaf morphologies associated with primary and secondary vein patterning defects in Catharanthus roseus: mid-vein defect converts simple leaf into binate compound leaf
(Springer, 2013) Kumar, Sushil; Sharma, Vishakha
Simple petiolated leaves are formed on the wild type plants of apocynaceous medicinal-cum-floricultural species Catharanthus roseus. A C. roseus variant line homozygous for two loss-of-function mutations, an induced leafless inflorescence (lli) mutations and a natural bisected leaf (bil) mutation, was isolated on account of its unique leaf bisection phenotype which was characterized. The lli bil phenotype was highly penetrant but poorly expressed. Only about one-fourth of leaves of lli bil plants were bisected. Leaf bisection was correlated with premature termination of midvein. Degree of bisection varied from a nick at the apex of lamina to formation of two complete leaflets. The notch in 43 % of the bisected leaves bore a pin-like apical adventitious growth. The features of bisected leaves showed that midvein was essential for symmetrical development of smooth lamina spans on its either side; although the development of spans was independent. Several lateral veins emerged from proximal midvein and grew acropetally. Lamina development in the proximal region failed in the absence of local lateral veins. Bisected leaves were also formed as bi-lobed simple leaves, each lobe having its own primary (mid) vein arising from proximally bifurcated midvein. Also formed were completely bisected leaves. In these binately compound leaves, each leaflet had its own petiolule attached to the leaf petiole. The lli bil genotype of C. roseus perhaps provides the only example of a compound leaved variant evolving from a simple leaved species. This phenotype of lli bil leaves supports the suggestion that simple leaf form was ancestral in angiosperms.
Abscisic acid, a principal regulator of plant abiotic stress responses
(Elsevier B.V., 2019) Sagar, Sushma; Singh, Amarjeet
Plants are routinely troubled by various abiotic stresses such as high salinity, dehydration, and low temperature during their life span. These abiotic stresses have detrimental effect on plant development, longevity, and productivity. Plants have evolved with a sessile nature, and unlike animals, they cannot move away from adverse growth conditions. Rather, they are destined to combat these stress conditions in their stationary habitat. Therefore, plants have devised an adaptive mechanism that entails the activation of several signal transduction pathways, leading to diverse molecular, cellular, and physiological changes (Singh et al., 2016, 2018). Most signal transduction pathways triggered in response to biotic or abiotic stresses are mediated by one or more plant hormones. Therefore, plant hormones are a crucial player in regulating plants’ response to various environmental cues (Iqbal et al., 2017; Khan et al., 2015a,b; Khan and Khan, 2014; Kazan, 2015; Per et al., 2018). Generally, phytohormones like salicylic acid (SA), jasmonic acid (JAs), and ethylene (ET) are implicated in plant response to pathogens, wounding, and other biotic stresses, whereas gibberellins (GAs), auxins (IAAs), brassinosteroids (BRs), and cytokinins are known to regulate plant development. However, recent advancements in plant stress related research have shown that all plant hormones could control multiple plant processes and are involved in crosstalk of signaling pathways. For example, SA, JA, and ET, apart from biotic stresses, are also involved in plant development and responses to abiotic stresses. Similarly, auxins and GA are crucial in abiotic and biotic stress responses (Colebrook et al., 2014; Kazan, 2013; Khan and Khan, 2013; Santino et al., 2013). Abscisic acid (ABA) is the key hormone that primarily regulates plants’ responses to various abiotic stresses; however, like other phytohormones ABA is also known to regulate plants’ response to biotic stress and development (Singh et al., 2016). The discovery of the vital phytohormone ABA dates way back to the 1960s. Several independent and convergent experiments carried out by various research groups led to the discovery of ABA (Cracker and Abeles, 1969). However, the earliest and most convincing was the discovery of ABA in cotton, where it was involved in fruit abscission and dormancy (Li et al., 2017). As time and research progressed, newer functions of ABA were unveiled, including adaptation to various stresses, stomatal closure, sugar accumulation, seed development, etc. Due to its crucial role in abiotic and biotic stresses, ABA is known as a “stress hormone”. Plenty of research on ABA accumulated ample information on its biosynthesis, storage, catabolism, site of action, and its possible targets. During the last decade, the ABA receptors and their crystal structures have been elucidated (Ma et al., 2009; Park et al., 2009). This information has provided a clear cut paradigm of the ABA signal transduction pathway. Moreover, recruiting the combinations of different key players such as PP2C phosphatase and SnRK2 kinases has helped to understand the signal transduction pathway. Recent studies have provided newer insights into the functional roles of the ABA signaling cascade in various aspects of plant growth and development. In this chapter, we discuss different facets of ABA in plants, including its biosynthesis, catabolism, ABA signaling pathway and various signaling components, and the role of ABA in abiotic stresses and plant development.
Absence of correlation between chimeric RNA and aging
(MDPI AG, 2017) Huang, Reyna; Kumar, Shailesh; Li, Hui
Chimeric RNAs have been recognized as a phenomenon not unique to cancer cells. They also exist in normal physiology. Aging is often characterized by deregulation of molecular and cellular mechanisms, including loss of heterochromatin, increased transcriptional noise, less tight control on alternative splicing, and more stress-induced changes. It is thus assumed that chimeric RNAs are more abundant in older people. In this study, we conducted a preliminary investigation to identify any chimeric RNAs with age-based trends in their expression levels in blood samples. A chimeric RNA candidate list generated by bioinformatic analysis indicated the possibility of both negative and positive trends in the expression of chimeric RNAs. Out of this candidate list, five novel chimeric RNAs were successfully amplified in multiple blood samples and then sequenced. Although primary smaller sample sizes displayed some weak trends with respect to age, analysis of quantitative PCR data from larger sample sizes showed essentially no relationship between expression levels and age. Altogether, these results indicate that, contradictory to the common assumption, chimeric RNAs as a group are not all higher in older individuals and that placing chimeric RNAs in the context of aging will be a much more complex task than initially anticipated.
Active site geometry of oxalate decarboxylase from Flammulina velutipes: Role of histidine coordinated manganese in substrate recognition
(Cold Spring Harbor Laboratory Press, 2002) Chakraborty, Subhra; Chakraborty, Niranjan; Jain, Deepti; Salunke, Dinakara M; Datta, Asis
Oxalate decarboxylase (OXDC) from the wood-rotting fungus Flammulina velutipes, which catalyzes the conversion of oxalate to formic acid and CO2 in a single-step reaction, is a duplicated double-domain germin family enzyme. It has agricultural as well as therapeutic importance. We reported earlier the purification and molecular cloning of OXDC. Knowledge-based modeling of the enzyme reveals a ␤-barrel core in each of the two domains organized in the hexameric state. A cluster of three histidines suitably juxtaposed to coordinate a divalent metal ion exists in both the domains. Involvement of the two histidine clusters in the catalytic mechanism of the enzyme, possibly through coordination of a metal cofactor, has been hypoth- esized because all histidine knockout mutants showed total loss of decarboxylase activity. The atomic absorption spectroscopy analysis showed that OXDC contains Mn2+ at up to 2.5 atoms per subunit. Docking of the oxalate in the active site indicates a similar electrostatic environment around the substrate-binding site in the two domains. We suggest that the histidine coordinated manganese is critical for substrate recognition and is directly involved in the catalysis of the enzyme.
Adaptation of plants to salt stress: the role of the ion transporters
(Springer Nature Publishing AG, 2021) Malakar, Paheli; Chattopadhyay, Debasis
Adaptation to high salinity is achieved by cellular ion homeostasis which involves regulation of toxic sodium ion (Na+) and Chloride ion (Cl−) uptake, preventing the transport of these ions to the aerial parts of the plants and vacuolar sequestration of these toxic ions. Ion transporters have long been known to play roles in maintaining ion homeostasis. Na+ enters the cell through various voltage dependent selective and non-selective ion channels. High Na+ concentration in the plasma membrane is balanced either by uptake of potassium ion (K+) by various potassium importing channels, by salt exclusion mechanism or by sequestration of Na+ in the vacuoles. Therefore, the role of high-affinity potassium transporter, the salt overly sensitive pathway, the most well-defined Na+ exclusion pathway that exports Na+ from cell into xylem and tonoplast localized cation transporters that compartmentalizes Na+ in vacuoles need to be studied in detail and applied to make the plant adaptable to saline soil. Knowledge on the regulation of expression of these transporters by the hormones, microRNAs and other non-coding RNAs can be utilized to manipulate the ion transport. Here, we reviewed paradigm of the ion transporters in salt stress signalling pathways from the recent and past studies aiding transformation of basic knowledge into biotechnological applications to generate engineered salt stress tolerant crops.
Adaptive reprogramming during early seed germination requires temporarily enhanced fermentation-A critical role for alternative oxidase regulation that concerns also microbiota effectiveness
(Frontiers Media S.A., 2021) Bharadwaj, Revuru; Noceda, Carlos; Mohanapriya, Gunasekharan; Kumar, Sarma Rajeev; Thiers, Karine Leitão Lima; Costa, José Hélio; Macedo, Elisete Santos; Kumari, Aprajita; Gupta, Kapuganti Jagadis; Srivastava, Shivani; Adholeya, Alok; Oliveira, Manuela; Velada, Isabel; Sircar, Debabrata; Sathishkumar, Ramalingam; Arnholdt-Schmitt, Birgit
Plants respond to environmental cues via adaptive cell reprogramming that can affect whole plant and ecosystem functionality. Microbiota constitutes part of the inner and outer environment of the plant. This Umwelt underlies steady dynamics, due to complex local and global biotic and abiotic changes. Hence, adaptive plant holobiont responses are crucial for continuous metabolic adjustment at the systems level. Plants require oxygen-dependent respiration for energy-dependent adaptive morphology, such as germination, root and shoot growth, and formation of adventitious, clonal, and reproductive organs, fruits, and seeds. Fermentative paths can help in acclimation and, to our view, the role of alternative oxidase (AOX) in coordinating complex metabolic and physiological adjustments is underestimated. Cellular levels of sucrose are an important sensor of environmental stress. We explored the role of exogenous sucrose and its interplay with AOX during early seed germination. We found that sucrose-dependent initiation of fermentation during the first 12 h after imbibition (HAI) was beneficial to germination. However, parallel upregulated AOX expression was essential to control negative effects by prolonged sucrose treatment. Early downregulated AOX activity until 12 HAI improved germination efficiency in the absence of sucrose but suppressed early germination in its presence. The results also suggest that seeds inoculated with arbuscular mycorrhizal fungi (AMF) can buffer sucrose stress during germination to restore normal respiration more efficiently. Following this approach, we propose a simple method to identify organic seeds and low-cost on-farm perspectives for early identifying disease tolerance, predicting plant holobiont behavior, and improving germination. Furthermore, the research strengthens the view that AOX can serve as a powerful functional marker source for seed hologenomes.
An advanced draft genome assembly of a desi type chickpea (Cicer arietinum L.)
(Nature Publishing Group, 2015) Parween, Sabiha; Nawaz, Kashif; Roy, Riti; Pole, Anil K.; Venkata Suresh, B.; Misra, Gopal; Jain, Mukesh; Yadav, Gitanjali; Parida, Swarup K.; Tyagi, Akhilesh K.; Bhatia, Sabhyata; Chattopadhyay, Debasis
Chickpea (Cicer arietinum L.) is an important pulse legume crop. We previously reported a draft genome assembly of the desi chickpea cultivar ICC 4958. Here we report an advanced version of the ICC 4958 genome assembly (version 2.0) generated using additional sequence data and an improved genetic map. This resulted in 2.7-fold increase in the length of the pseudomolecules and substantial reduction of sequence gaps. The genome assembly covered more than 94% of the estimated gene space and predicted the presence of 30,257 protein-coding genes including 2230 and 133 genes encoding potential transcription factors (TF) and resistance gene homologs, respectively. Gene expression analysis identified several TF and chickpea-specific genes with tissue-specific expression and displayed functional diversification of the paralogous genes. Pairwise comparison of pseudomolecules in the desi (ICC 4958) and the earlier reported kabuli (CDC Frontier) chickpea assemblies showed an extensive local collinearity with incongruity in the placement of large sequence blocks along the linkage groups, apparently due to use of different genetic maps. Single nucleotide polymorphism (SNP)-based mining of intra-specific polymorphism identified more than four thousand SNPs differentiating a desi group and a kabuli group of chickpea genotypes.
Advances in Agrobacterium tumefaciens-mediated genetic transformation of graminaceous crops
(Springer, 2016) Singh, Roshan Kumar; Prasad, Manoj
Steady increase in global population poses several challenges to plant science research, including demand for increased crop productivity, grain yield, nutritional quality and improved tolerance to different environmental factors. Transgene-based approaches are promising to address these challenges by transferring potential candidate genes to host organisms through different strategies. Agrobacterium-mediated gene transfer is one such strategy which is well known for enabling efficient gene transfer in both monocot and dicots. Due to its versatility, this technique underwent several advancements including development of improved in vitro plant regeneration system, co-cultivation and selection methods, and use of hyper-virulent strains of Agrobacterium tumefaciens harbouring super-binary vectors. The efficiency of this method has also been enhanced by the use of acetosyringone to induce the activity of vir genes, silver nitrate to reduce the Agrobacterium-induced necrosis and cysteine to avoid callus browning during co-cultivation. In the last two decades, extensive efforts have been invested towards achieving efficient Agrobacterium-mediated transformation in cereals. Though high-efficiency transformation systems have been developed for rice and maize, comparatively lesser progress has been reported in other graminaceous crops. In this context, the present review discusses the progress made in Agrobacterium-mediated transformation system in rice, maize, wheat, barley, sorghum, sugarcane, Brachypodium, millets, bioenergy and forage and turf grasses. In addition, it also provides an overview of the genes that have been recently transferred to these graminaceous crops using Agrobacterium, bottlenecks in this technique and future possibilities for crop improvement.
Advances in biotechnological applications in three important food legumes
(Springer, 2014) Das, Alok; Parida, Swarup K.
Legumes are the third largest family of flowering plants, known for their unique capacity of symbiotic nitrogen fixation. The draft genome sequences of three important food legumes [soybean (Glycine max), pigeonpea (Cajanus cajan) and chickpea (Cicer arietinum)] have been completed. Coupled with a deluge of information on transcriptomics, proteomics and metabolomics, they present a huge amount of genomic resources for the genetic improvement of legume crops. Developed molecular markers, structurally and functionally annotated genes/quantitative trait loci/alleles and regulatory sequences can be utilized in improvement breeding programmes. Further, the genetic transformation of two valuable pulses (chickpea and pigeonpea) has now taken centre stage, realizing the potential of genetically modified soybean, for enhanced prospects of food production. Together, the advances in biotechnological tools and the research community’s capacity to develop imaginative strategies will help in framing a legume development programme for ensuring the nutritional security of the world.