3Bs of CRISPR-Cas mediated genome editing in plants: exploring the basics, bioinformatics and biosafety landscape

The recent thrust in research has projected the type II clustered regularly interspaced short palindromic repeats and associated protein 9 (CRISPR-Cas9) system as an avant-garde plant genome editing tool. It facilitates the induction of site-specific double-stranded DNA cleavage by the RNA-guided DNA endonuclease (RGEN), Cas9. Elimination, addition, or alteration of sections in DNA sequence besides the creation of a knockout genotype (CRISPRko) is aided by the CRISPR-Cas9 system in its wild form (wtCas9). The inactivation of the nuclease domain generates a dead Cas9 (dCas9), which is capable of targeting genomic DNA without scissoring it. The dCas9 system can be engineered by fusing it with different effectors to facilitate transcriptional activation (CRISPRa) and transcriptional interference (CRISPRi). CRISPR-Cas thus holds tremendous prospects as a genome-manipulating stratagem for a wide gamut of crops. In this article, we present a brief on the fundamentals and the general workflow of the CRISPR-Cas system followed by an overview of the prospects of bioinformatics in propelling CRISPR-Cas research with a special thrust on the available databases and algorithms/web-accessible applications that have aided in increasing the usage and efficiency of editing. The article also provides an update on the current regulatory landscape in different countries on the CRISPR-Cas edited plants to emphasize the far-reaching impact of the genomic editing technology.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-023-01397-3.

Cajanus Scarabaeoides Yellow Mosaic Virus, a New Bipartite Begomovirus Causing Yellow Mosaic Disease in Cajanus scarabaeoides in India

Yellow mosaic disease of Cajanus scarabaeoides (L.) Thouars (CsYMD) was observed in up to 46% of C. scarabaeoides plants in the mungbean, urdbean, and pigeon pea fields from 22 districts of Chhattisgarh State, India, during 2017 to 2019. The symptoms were characterized by yellow mosaic on green leaves and yellow discoloration of leaves in advanced stages of the disease. Severely infected plants showed shortened internodal length and reduced leaf size. CsYMD was transmissible to healthy C. scarabaeoides and C. cajan by whitefly (Bemisia tabaci). The infected plants developed typical yellow mosaic symptoms on their leaves within 16 and 22 days of inoculation, respectively, suggesting a begomovirus etiology. Molecular analysis revealed that this begomovirus has a bipartite genome composed of DNA-A (2,729 nucleotides) and DNA-B (2,630 nucleotides). Sequence and phylogenetic analyses revealed that the nucleotide sequence of the DNA-A component had the highest identity of 81.1% with DNA-A of Rhynchosia yellow mosaic virus (RhYMV; NC_038885), followed by mungbean yellow mosaic virus (MN602427; 75.3%). DNA-B had the highest identity of 74.0% with DNA-B of RhYMV (NC_038886). As per ICTV guidelines, this isolate had <91% nucleotide identity with DNA-A of any of the begomoviruses reported; so, it is proposed as a new begomovirus species, tentatively named C. scarabaeoides yellow mosaic virus (CsYMV). After agroinoculation with DNA-A and DNA-B clones of CsYMV, all Nicotiana benthamiana plants developed leaf curl symptoms along with light yellowing symptoms 8 to 10 days after inoculation (DAI), while ∼60% of the C. scarabaeoides plants developed yellow mosaic symptoms similar to those observed in the field 18 DAI, thus fulfilling Koch's postulates. From these agro-infected C. scarabaeoides plants, CsYMV was transmissible to healthy C. scarabaeoides plants by B. tabaci. Apart from these hosts, CsYMV also infected and caused symptoms in mungbean and pigeon pea.

Enhancing biocontrol potential of Trichogramma chilonis against borer pests of wheat and chickpea

Communication between plants and herbivores occur mostly through chemicals. Plants emit volatiles in response to the attack of herbivores called herbivore-induced plant volatiles (HIPVs), which are employed by the plants to attract their herbivores' natural enemies. Promising HIPVs when used in the form of controlled release formulations under field conditions can act as arrestants of released or wild population of parasitoids to spend comparatively more time in searching of various stages of herbivores; thus management of crop pests is enhanced. Gel formulation of octadecane (Saturated hydrocarbon) when applied 24 h after release of Trichogramma chilonis in wheat and chickpea enhanced the foraging activity against pink stem borer (Sesamia inferens) and pod borer (Helicoverpa armigera), respectively resulting in reduced symptoms and increased grain yields. Controlled release formulations of promising plant volatile organic compounds (pVOCs) can be useful to augment and enhance foraging activity of natural enemies against crop herbivores.

Achieving maximum efficiency of Mungbean yellow mosaic India virus infection in mungbean by agroinoculation

Mungbean is one of the important food legumes in the Indian-sub-continent. Yellow mosaic disease, caused by Mungbean yellow mosaic virus and Mungbean yellow mosaic India virus (MYMIV) poses a severe threat to its production. Agroinoculation has been the most preferred way to test the function of genomic components of these viruses. However, the available inoculation methods are not as efficient as whitefly transmission, thereby limiting their usage for screening and biological studies. We hereby report an efficient and reproducible agroinoculation method for achieving maximum (100%) efficiency using tandem repeat infectious agro-constructs of DNA A and DNA B of MYMIV. The present study targeted wounding of various meristematic tissues of root, shoot, parts of germinating seeds and also non-meristematic tissue of stem to test the suitable tissue types for maximum infection. Among the various tissues selected for, the inoculation on the epicotyl region showed maximum infectivity. Further, to enhance the infectivity of MYMIV, different concentrations of acetosyringone, incubation time and Agrobacterium cell density were also standardized. The incubation of wounded sprouted seeds in 1.0 OD of agroculture containing repeat construct of MYMIV for 2-4 h without acetosyringone followed by sowing in soil showed maximum infection of MYMIV within 10-12 days on the first trifoliate leaf. This standardized method is reproducible and has potential to screen germplasm lines and will be useful in mungbean biological/virological studies and breeding programmes.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-03088-w.

Distinct morpho-physiological and biochemical features of arid and hyper-arid ecotypes of Ziziphus nummularia under drought suggest its higher tolerance compared with semi-arid ecotype

Tree species in the arid and semi-arid regions use various strategies to combat drought stress. Ziziphus nummularia (Burm. f.) Wight et Arn., native to the Thar Desert in India, is highly drought-tolerant. To identify the most drought-tolerant ecotype of Z. nummularia, one ecotype each from semi-arid (Godhra, annual rainfall >750 mm), arid (Bikaner, 250-350 mm) and hyper-arid (Jaisalmer, <150 mm) regions was selected along with two other Ziziphus species, Ziziphus mauritiana Lamk. and Ziziphus rotundifolia Lamk., and screened for parameters contributing to drought tolerance. Among these, Z. nummularia (Jaisalmer) (CIAHZN-J) was the most drought - tolerant. The tolerance nature of CIAHZN-J was associated with increased membrane stability, root length and number, length of hairs and thorns, root dry/fresh weight ratio, seed germination (at -0.5 MPa), proline content (31-fold), catalase and sugar content (two- to three-fold). Apart from these characteristics, it also exhibited the longest duration to reach highest cumulative drought stress rating, maintained higher relative water content for a longer period of time with reduced leaf size, leaf rolling and falling of older leaves, and displayed sustained shoot growth during drought stress. To determine drought tolerance in Ziziphus, we developed a morphological symptom-based screening technique in this study. Additionally, transcriptome profiling of CIAHZN-J in response to drought revealed the up-regulation of genes involved in sugar metabolism and transport, abscisic acid biosynthesis, osmoregulation, reactive oxygen species homeostasis and maintaining water potential. Expression profiles and semi-quantitative reverse transcription PCR results further correlated with the physiological and biochemical mechanisms. In conclusion, CIAHZN-J is an excellent genetic stock for the identification of drought-responsive genes and can also be deployed in crop improvement programs for drought tolerance.

Molecular analysis, infectivity and host range of Tomato leaf curl Karnataka virus associated with Corchorus yellow vein mosaic betasatellite

Severe leaf curl disease of tomato (ToLCD) was noticed recently in the central parts of India and is an emerging threat to the cultivation of tomato. The genomic components of the begomovirus isolate, DNA A and betasatellite associated with ToLCD were cloned by rolling circle amplification method and sequenced. The sequence analysis revealed that the DNA A (2766 nt) of this isolate had the nucleotide identity of >91% with other strains of Tomato leaf curl Karnataka virus (ToLCKV), hence this isolate is proposed as a strain of ToLCKV, named as ToLCKV-Raipur. Similarly, the betasatellite molecule (1355 nt) had the highest identity of 91.1% with Corchorus yellow vein mosaic betasatellite (CoYVMB) and named as CoYVMB-Raipur. The full-length dimerized clones of these two genomic components were agroinoculated on natural (tomato), experimental (Nicotiana benthamiana) hosts and other 20 plant species belong to six different families. The severe leaf curl symptoms appeared only in the hosts, N. benthamiana, and in tomato inoculated with ToLCKV-Raipur alone and ToLCKV-Raipur with CoYVMB-Raipur after 8 and 16-18 days inoculation, respectively. This isolate was also transmissible to healthy tomato plants by whitefly from the tomato plant agroinoculated with ToLCKV-Raipur alone and with CoYVMB-Raipur and produced symptoms within 14-16 days after inoculation. Interestingly, this isolate infects horse gram and chilli by whitefly transmission and both the hosts showed positive for DNA A alone but not for betasatellite. Quantification of the genomic components of this isolate with the agroinoculated N. benthamiana samples by qRT-PCR results showed that the quantity of ToLCKV-Raipur was enhanced by three-fold while inoculated with CoYVMB-Raipur compared to ToLCKV-Raipur alone inoculated plants. However, CoYVMB-Raipur did not enhance the levels of ToLCKV-Raipur in the agroinoculated tomato plants. This is the first evidence of the natural co-occurrence of ToLCKV with betasatellite, CoYVMB causing ToLCD.

Modeling Commodity Flow in the Context of Invasive Species Spread: Study of Tuta absoluta in Nepal

Trade and transport of goods is widely accepted as a primary pathway for the introduction and dispersal of invasive species. However, understanding commodity flows remains a challenge owing to its complex nature, unavailability of quality data, and lack of systematic modeling methods. A robust network-based approach is proposed to model seasonal flow of agricultural produce and examine its role in pest spread. It is applied to study the spread of Tuta absoluta, a devastating pest of tomato in Nepal. Further, the long-term establishment potential of the pest and its economic impact on the country are assessed. Our analysis indicates that regional trade plays an important role in the spread of T. absoluta. The economic impact of this invasion could range from USD 17-25 million. The proposed approach is generic and particularly suited for data-poor scenarios.

Expression profiling and in silico homology modeling of Inositol pentakisphosphate 2-kinase, a potential candidate gene for low phytate trait in soybean

Low phytate soybeans are desirable both from a nutritional and economic standpoint. Inositol 1, 3, 4, 5, 6-pentakisphosphate 2-kinase (IPK1), optimizes the metabolic flux of phytate generation in soybean and thus shows much promise as a likely candidate for pathway regulation. In the present study, the differential spatial and temporal expression profiling of GmIpk1 and its two homologs Glyma06g03310 and Glyma04g03310 were carried out in Glycine max L. var Pusa 9712 revealing the early stages of seed development to be the potential target for gene manipulation. NCBI databank was screened using BLASTp to retrieve 32 plant IPK1 sequences showing high homology to GmIPK1 and its homologs. Bio-computational tools were employed to predict the protein's properties, conserved domains, and secondary structures. Using state-of-the-art in silico physicochemical approach, the three-dimensional (3D) GmIPK1 protein model (PMD ID-PM0079931), was developed based on Arabidopsis thaliana (PDB ID: 4AQK). Superimposition of 4AQK and best model of GmIPK1 revealed that the GmIPK1 aligned well and shows a sequence identity score of 54.32% with 4AQK and a low RMSD of 0.163 nm and almost similar structural features. The modeled structure was further refined considering the stereochemical geometry, energy and packing environment between the model and the template along with validation of its intrinsic dynamics. Molecular dynamics simulation studies of GmIPK1 were carried out to obtain structural insights and to understand the interactive behavior of this enzyme with ligands ADP and IP₆. The results of this study provide some fundamental knowledge on the distinct mechanistic step performed by the key residues to elucidate the structure-function relationship of GmIPK1, as an initiative towards engineering "low phytate soybean".

Seed targeted RNAi-mediated silencing of GmMIPS1 limits phytate accumulation and improves mineral bioavailability in soybean

Phytic acid (PA), the major phosphorus reserve in soybean seeds (60-80%), is a potent ion chelator, causing deficiencies that leads to malnutrition. Several forward and reverse genetics approaches have ever since been explored to reduce its phytate levels to improve the micronutrient and phosphorous availability. Transgenic technology has met with success by suppressing the expression of the PA biosynthesis-related genes in several crops for manipulating their phytate content. In our study, we targeted the disruption of the expression of myo-inositol-3-phosphate synthase (MIPS1), the first and the rate limiting enzyme in PA biosynthesis in soybean seeds, by both antisense (AS) and RNAi approaches, using a seed specific promoter, vicilin. PCR and Southern analysis revealed stable integration of transgene in the advanced progenies. The transgenic seeds (T4) of AS (MS14-28-12-29-3-5) and RNAi (MI51-32-22-1-13-6) soybean lines showed 38.75% and 41.34% reduction in phytate levels respectively, compared to non-transgenic (NT) controls without compromised growth and seed development. The electron microscopic examination also revealed reduced globoid crystals in the Protein storage vacoules (PSVs) of mature T4 seeds compared to NT seed controls. A significant increase in the contents of Fe2+ (15.4%, 21.7%), Zn2+ (7.45%, 11.15%) and Ca2+ (10.4%, 15.35%) were observed in MS14-28-12-29-3-5 and MI51-32-22-1-13-6 transgenic lines, respectively, compared to NT implicating improved mineral bioavailability. This study signifies proof-of-concept demonstration of seed-specific PA reduction and paves the path towards low phytate soybean through pathway engineering using the new and precise editing tools.

Exploring the role of Inositol 1,3,4-trisphosphate 5/6 kinase-2 (GmITPK2) as a dehydration and salinity stress regulator in Glycine max (L.) Merr. through heterologous expression in E. coli

Phytic acid (PA) is implicative in a spectrum of biochemical and physiological processes involved in plant stress response. Inositol 1,3,4, Tris phosphate 5/6 kinase (ITPK), a polyphosphate kinase that converts Inositol 1,3,4 trisphosphate to Inositol 1,3,4,5/6 tetra phosphate, averting the inositol phosphate pool towards PA biosynthesis, is a key regulator that exists in four different isoforms in soybean. In the present study, in-silico analysis of the promoter region of ITPKs was done and among the four isoforms, promoter region of GmITPK2 showed the presence of two MYB binding elements for drought inducibility and one for ABA response. Expression profiling through qRT-PCR under drought and salinity stress showed higher expression of GmITPK2 isoform compared to the other members of the family. The study revealed GmITPK2 as an early dehydration responsive gene which is also induced by dehydration and exogenous treatment with ABA. To evaluate the osmo-protective role of GmITPK2, attempts were made to assess the bacterial growth on Luria Broth media containing 200 mM NaCl, 16% PEG and 100 μM ABA, individually. The transformed E. coli BL21 (DE3) cells harbouring the GmITPK2 gene depicted better growth on the media compared to the bacterial cells containing the vector alone. Similarly, the growth of the transformed cells in the liquid media containing 200 mM NaCl, 16% PEG and 100 μM ABA showed higher absorbance at 600 nm compared to control, at different time intervals. The GmITPK2 recombinant E. coli cells showing tolerance to drought and salinity thus demonstrated the functional redundancy of the gene across taxa. The purity and specificity of the recombinant protein was assessed and confirmed through PAGE showing a band of ∼35 kDa on western blotting using Anti- Penta His- HRP conjugate antibody. To the best of our knowledge, the present study is the first report exemplifying the role of GmITPK2 isoform in drought and salinity tolerance in soybean.

Molecular modeling and in silico characterization of GmABCC5: a phytate transporter and potential target for low-phytate crops

Designing low-phytate crops without affecting the developmental process in plants had led to the identification of ABCC5 gene in soybean. The GmABCC5 gene was identified and a partial gene sequence was cloned from popular Indian soybean genotype Pusa16. Conserved domains and motifs unique to ABC transporters were identified in the 30 homologous sequences retrieved by BLASTP analysis. The homologs were analyzed for their evolutionary relationship and physiochemical properties. Conserved domains, transmembrane architecture and secondary structure of GmABCC5 were predicted with the aid of computational tools. Analysis identified 53 alpha helices and 31 beta strands, predicting 60% residues in alpha conformation. A three-dimensional (3D) model for GmABCC5 was developed based on 5twv.1.B (Homo sapiens) template homology to gain better insight into its molecular mechanism of transport and sequestration. Spatio-temporal real-time PCR analysis identified mid-to-late seed developmental stages as the time window for the maximum GmABCC5 gene expression, a potential target stage for phytate reduction. Results of this study provide valuable insights into the structural and functional characteristics of GmABCC5, which may be further utilized for the development of nutritionally enriched low-phytate soybean with improved mineral bioavailability.

Refined glufosinate selection and its extent of exposure for improving the Agrobacterium-mediated transformation in Indian soybean (Glycine max) genotype JS-335

Soybean like many other crops, in this genomic era, has well-established genomic database which provides a wide range of opportunities for improvement through genetic manipulation. But the growing demand for soybean transgenics with increased production and improved quality has been handicapped due to inefficient transformation strategies and hence an efficient, stable and reliable transformation system is of prime requisite. In the present study, Agrobacterium-mediated transformation was standardized by refining the glufosinate selection system in terms of dosage (0-6 mg l^-1) and degree of exposure. The cotyledonary node explants (with and without wounding) initially cultured on a non-selective shoot induction medium for 10 days before transferring them to the selective SIM with an optimized concentration of 5.0 mg l^-1 ammonium glufosinate, showed least selection escape frequency. Wounded cotyledonary node explants infected with Agrobacterium tumefaciens harboring pBIN-bar construct, showed an improved regeneration efficiency of 55.10% and transformation efficiency of 12.6% using Southern blotting in T₁ plants. Southern analysis of T₁ plants confirmed the integration of bar gene into the genomic DNA and the bar positive T₁ plants segregated in 3 : 1 ratio. This is the first report, to our knowledge, of a high transformation efficiency using Agrobacterium-mediated cot node-glufosinate system in an Indian soybean genotype.

Severe diarrhoea due to Cystoisospora belli in renal transplant patient on immunosuppressive drugs

Cystoisospora belli, formerly known as Isospora belli, protozoal parasite endemic to many regions of the world including the Caribbean, Central and South America, Africa, and South-East Asia. It is frequently encountered in patients with acquired immunodeficiency syndrome (AIDS) and is considered to be an AIDS-defining illness. Chronic severe watery diarrhoea due to C. belli has also been reported in other immunodeficiency states. C. belli infection in immunosuppressed patients has rarely been described. We describe severe diarrhoea due to C. belli in a human immunodeficiency virus-negative renal transplant recipient on immunosuppressive drugs. Oocysts of C. belli were detected in direct smear preparation of the diarrheic stool sample of the patient. The patient responded to combination treatment with Bactrim-double-strength (trimethoprim-sulfamethoxazole) and Nitazoxanide.

Strongyloides stercoralis hyperinfection in an immunocompetent patient with extreme eosinophilia

This report examines an unusual case of Srongyloides stercoralis hyperinfection in a 63-yr-old man. The patient had a history of vitamin B deficiency, on and off diarrhea, and clinical pellagra for a decade and a half. There was also evidence of extreme eosinophilia. The patient did not have any associated illness suggestive of immunosuppression. Treatment with ivermectin resulted in remarkable clinical improvement and reversion of eosinophil count to normal.

Human babesiosis--a case report

Babesiosis is an emerging, tick-transmitted, zoonotic disease caused by hematotropic parasites of the genus Babesia. Most cases of Babesial infections in humans have been acquired in temperate regions of the United States, Europe, France and England. A few cases of Babesiosis have been described in other parts of the world, including China, Taiwan, Egypt, South Africa, and Mexico.1,2 We report the first case of human Babesiosis, in a normosplenic, previously healthy individual from India.

Early diagnosis of filarial pleural effusion

This paper describes a case of pleural effusion due to filariasis. Microfilaria of Wucheraria bancrofti were detected in the pleural fluid on cytological examination. Treatment with diethylcarbamazine cleared the pleural effusion.

On combinatorial DNA word design

We consider the problem of designing DNA codes, namely sets of equi-length words over the alphabet [A, C, G, T] that satisfy certain combinatorial constraints. This problem is motivated by the task of reliably storing and retrieving information in synthetic DNA strands for use in DNA computing or as molecular bar codes in chemical libraries. The primary constraints that we consider, defined with respect to a parameter d, are as follows: for every pair of words w, x in a code, there are at least d mismatches between w and x if w not equal x and also between the reverse of w and the Watson-Crick complement of x. Extending classical results from coding theory, we present several upper and lower bounds on the maximum size of such DNA codes and give methods for constructing such codes. An additional constraint that is relevant to the design of DNA codes is that the free energies and enthalpies of the code words, and thus the melting temperatures, be similar. We describe dynamic programming algorithms that can (a) calculate the total number of words of length n whose free energy value, as approximated by a formula of Breslauer et al. (1986) falls in a given range, and (b) output a random such word. These algorithms are intended for use in heuristic algorithms for constructing DNA codes.

Discovery of association rules in medical data

Data mining is a technique for discovering useful information from large databases. This technique is currently being profitably used by a number of industries. A common approach for information discovery is to identify association rules which reveal relationships among different items. In this paper, we use this approach to analyse a large database containing medical-record data. Our aim is to obtain association rules indicating relationships between procedures performed on a patient and the reported diagnoses. Random sampling was used to obtain these association rules. After reviewing the basic concepts associated with data mining, we discuss our approach for identifying association rules and report on the rules generated.