Sajad Ali

Genomic Selection in the Era of Next Generation Sequencing for Complex Traits in Plant Breeding

Genomic selection (GS) is a promising approach exploiting molecular genetic markers to design novel breeding programs and to develop new markers-based models for genetic evaluation. In plant breeding, it provides opportunities to increase genetic gain of complex traits per unit time and cost. The cost-benefit balance was an important consideration for GS to work in crop plants. Availability of genome-wide high-throughput, cost-effective and flexible markers, having low ascertainment bias, suitable for large population size as well for both model and non-model crop species with or without the reference genome sequence was the most important factor for its successful and effective implementation in crop species. These factors were the major limitations to earlier marker systems viz., SSR and array-based, and was unimaginable before the availability of next-generation sequencing (NGS) technologies which have provided novel SNP genotyping platforms especially the genotyping by sequencing. These marker technologies have changed the entire scenario of marker applications and made the use of GS a routine work for crop improvement in both model and non-model crop species. The NGS-based genotyping have increased genomic-estimated breeding value prediction accuracies over other established marker platform in cereals and other crop species, and made the dream of GS true in crop breeding. But to harness the true benefits from GS, these marker technologies will be combined with high-throughput phenotyping for achieving the valuable genetic gain from complex traits. Moreover, the continuous decline in sequencing cost will make the WGS feasible and cost effective for GS in near future. Till that time matures the targeted sequencing seems to be more cost-effective option for large scale marker discovery and GS, particularly in case of large and un-decoded genomes.

A review on heme oxygenase-1 induction: is it a necessary evil

Heme oxygenase-1 (HO-1) is considered to be the main protein in diseases arising as a result of oxidative and inflammatory insults. Tremendous research has been carried out on HO-1 since years, pertaining its cytoprotective effect against oxidative injury and other cellular stresses. HO-1, by regulating intracellular levels of pro-oxidant heme, or by other benefits of its by-products such as carbon monoxide (CO) and biliverdin (BV) had become an important candidate protein to be up-regulated to combat diverse stressful events. Although the beneficial effects of HO-1 induction have been reported in a number of cells and tissues, a growing body of evidence indicates that this increased HO-1 expression may lead to the progression of several diseases such as neurodegeneration, carcinogenesis. But it is not clear, what accounts for the increased expression of HO-1 in cells and tissues. The observed friendly role of HO-1 in a wide range of stress conditions since times is now doubtful. Therefore, more studies are needed to elucidate the exact role of HO-1 in various stressful events. Being more concise, elucidating the effect of HO-1 up-regulation on critical genes involved in particular diseases such as cancer will help to a larger extent to comprehend the exact role of HO-1. This review will assist in understanding the dual role (protective and detrimental) of HO-1 and the signaling pathway involved and will help in unraveling the doubtful role of HO-1 induction.

Overexpression of NPR1 in Brassica juncea Confers Broad Spectrum Resistance to Fungal Pathogens

Brassica juncea (Indian mustard) is a commercially important oil seed crop, which is highly affected by many biotic stresses. Among them, Alternaria leaf blight and powdery mildew are the most devastating diseases leading to huge yield losses in B. juncea around the world. In this regard, genetic engineering is a promising tool that may possibly allow us to enhance the B. juncea disease resistance against these pathogens. NPR1 (non-expressor of pathogen-related gene 1) is a bonafide receptor of salicylic acid (SA) which modulates multiple immune responses in plants especially activation of induced and systemic acquired resistance (SAR). Here, we report the isolation and characterization of new NPR1 homolog (BjNPR1) from B. juncea. The phylogenetic tree constructed based on the deduced sequence of BjNPR1 with homologs from other species revealed that BjNPR1 grouped together with other known NPR1 proteins of Cruciferae family, and was nearest to B. napus. Furthermore, expression analysis showed that BjNPR1 was upregulated after SA treatment and fungal infection but not by jasmonic acid or abscisic acid. To understand the defensive role of this gene, we generated B. juncea transgenic lines overexpressing BjNPR1, and further confirmed by PCR and Southern blotting. The transgenic lines showed no phenotypic abnormalities, and constitutive expression of BjNPR1 activates defense signaling pathways by priming the expression of antifungal PR genes. Moreover, BjNPR1 transgenic lines showed enhanced resistance to Alternaria brassicae and Erysiphe cruciferarum as there was delay in symptoms and reduced disease severity than non-transgenic plants. In addition, the rate of disease spreading to uninfected or distal parts was also delayed in transgenic plants thus suggesting the activation of SAR. Altogether, the present study suggests that BjNPR1 is involved in broad spectrum of disease resistance against fungal pathogens.

Expression analysis of chitinase upon challenge inoculation to Alternaria wounding and defense inducers in Brassica juncea

Highlights • Expression of chitinase gene was studied by RT-PCR in response to Alternaria brassicae.• Chitinase gene is induced by Alternaria, wounding and by JA and not by SA. It shows the tissue specificity of the gene.• Pathogen-inducible 2.5 kb chitinase class IV promoter was isolated from B. juncea by Genome Walking.• Induction pattern of chitinase gene is also reflected in promoter validation studied in transgenic Arabidopsis leaf.• This will help in using this promoter discretely in developing fungus resistant transgenic plants.

Fish antimicrobial peptides (AMP's) as essential and promising molecular therapeutic agents: A review

Antimicrobial peptides (AMPs) are generally considered as an essential component of innate immunity, thereby providing the first line of defense against wide range of pathogens. In addition, they can also kill the pathogens which are generally resistant to number of antibiotics, thereby providing the avenues for the development of future therapeutic agents. Fishes are constantly challenged by variety of pathogens which not only shows detrimental effect on their health but also increases risk of becoming resistant to conventional antibiotics. As fishes rely more on innate immunity, AMPs can serve as a potential defensive weapons in fishes for combating emerging devastating diseases. Generally, AMPs show multidimensional properties like rapid diffusion to the site of infection, recruitment of other immune cells to infected tissues and vigorous potential to rapidly neutralize broad range of pathogens (bacterial, fungal and viral). AMPs also exhibit diverse biological effect like endotoxin neutralization, immunomodulation and induction of angiogenesis in mammals. Due to these properties AMPs have become one of the most promising therapeutic agents to be studied. Till date, many AMPs have been isolated from the fishes but not fully characterized at molecular level. This review provides an overview of the structures, functions, and putative mechanisms of major families of fish AMPs. Further, we also highlighted how fish AMPs can be used as a novel therapeutic tool which is the theme of future research in drug development.

Plant-Bacterial Partnership: A Major Pollutants Remediation Approach

Environmental pollution due to global industrialization and urbanization has become a serious matter of concern for human inhabitants throughout the world. As safety point of human health and environmental issues, it required an efficient removal for the sake of minimized inlet of these hazard materials into the food chain generated by organic and inorganic pollutants. The physical and chemical means need specialized equipment, labor intensive and highly costs inputs which make less familiar to remove the pollutants, but it seems biological methods especially phytoremediation, gaining comprehensive remedial measure approach. The green technology based Phytoremediation carried out the process with the help of altogether action of plants and their specific attached microbial communities to remove, transform, degrade or immobilize various toxic organic and inorganic contaminants deposits in soil and polluted water and air pollutants could be treated well with this approach which is nowadays publicly high acclaimed, less disturbance to the environment remediate various form of pollutants and lower cost investment input. The symbiotic nature of plants combination with related beneficial bacteria (rhizobacteria or endophytic) offers tremendous potential as bacteria possess set of catabolic genes which produce catabolic enzymes to decontaminate complex organic compounds and inorganic pollutants with an effective way and in return of these bacteria increase plant growth promoting activities and gain more biomass in the plants. This chapter highlighted the remediation approach of major pollutants by phytoremediation with the main focal point on rhizoremediation and plant-bacterial partnerships and discuss how to improve the efficiency of phytoremediation by various approaches.

Genetic Engineering and Environmental Risk

Genetic engineering in today’s world is gaining much importance. It provides plant varieties with good agronomic characteristics, superior quality values and expressing traits of agricultural interest such as insect resistance and herbicide tolerance. The production and use of genetically modified organisms (GMO’s) is increasing steadily. There are various techniques by which genetic modified crops can be developed. But the issue still remains; whether altering genetic structure of any organism is ethical, will it create any problem to the people who consume it. Therefore, it is important to examine both pros and cons of genetic engineering and to determine whether this technology have place in a future. There are lots of controversies regarding the safety issue of GM crops and labeling of GMO products. Environmental risk assessment is a structural approach use to analyze the risk associated with GM crops. The goal of the risk assessment is to identify, characterize and evaluate risks by considering a wide range of potential pathways through which harm might occur. The assessment evaluates any risks posed by the genetic engineered (GE) plant in comparison to the risks posed by non-GE plant.

Pathogenesis-related proteins and peptides as promising tools for engineering plants with multiple stress tolerance

Pathogenesis-related (PR) proteins and antimicrobial peptides (AMPs) are a group of diverse molecules that are induced by phytopathogens as well as defense related signaling molecules. They are the key components of plant innate immune system especially systemic acquired resistance (SAR), and are widely used as diagnostic molecular markers of defense signaling pathways. Although, PR proteins and peptides have been isolated much before but their biological function remains largely enigmatic despite the availability of new scientific tools. The earlier studies have demonstrated that PR genes provide enhanced resistance against both biotic and abiotic stresses, which make them one of the most promising candidates for developing multiple stress tolerant crop varieties. In this regard, plant genetic engineering technology is widely accepted as one of the most fascinating approach to develop the disease resistant transgenic crops using different antimicrobial genes like PR genes. Overexpression of PR genes (chitinase, glucanase, thaumatin, defensin and thionin) individually or in combination have greatly uplifted the level of defense response in plants against a wide range of pathogens. However, the detailed knowledge of signaling pathways that regulates the expression of these versatile proteins is critical for improving crop plants to multiple stresses, which is the future theme of plant stress biology. Hence, this review provides an overall overview on the PR proteins like their classification, role in multiple stresses (biotic and abiotic) as well as in various plant defense signaling cascades. We also highlight the success and snags of transgenic plants expressing PR proteins and peptides.

CRISPR/Cas approach: A new way of looking at plant-abiotic interactions

It is not the most grounded of the species that survive, nor the most shrewd, however one most receptive to change. Crop plants being sessile are subjected to various abiotic stresses resulting significant yield losses about an average of more than 50 percent, thus greatly threatening the global crop production. In this regard, plant breeding innovations and genetic engineering approaches have been used in the past for generating stress tolerant crop genotypes, but due to complex inheritance of abiotic stress tolerance these approaches are not enough to bring significant trait improvement and to guarantee worlds future sustenance security. Although, RNA interference (RNAi) technology has been utilized amid the most recent decades to produce plants tolerant to environmental stress. But this technique ordinarily prompts to down-regulate as opposed to complete inhibition of target genes. Therefore, scientist/researchers were looking for techniques that should be efficient, precise and reliable as well as have potential to solve the issues experienced by previous approaches, and hence the CRISPR/Cas system came into spotlight. Although, only few studies using CRISPR/Cas approach for targeting abiotic stress tolerance related genes have been reported, but suggested its effective role for future applications in molecular breeding to improve abiotic stress tolerance. Hence, genome engineering via CRISPR-Cas system for targeted mutagenesis promise its immense potential in generating elite cultivars of crop plants with enhanced and durable climate resilience. Lastly, CRISPR-Cas will be future of crop breeding as well as to target minor gene variation of complex quantitative traits, and thus will be the key approach to release global hunger and maintain food security.

Genetic Testing of Maturity-Onset Diabetes of the Young Current Status and Future Perspectives

Diabetes is a global epidemic problem growing exponentially in Asian countries posing a serious threat. Among diabetes, maturity-onset diabetes of the young (MODY) is a heterogeneous group of monogenic disorders that occurs due to β cell dysfunction. Genetic defects in the pancreatic β-cells result in the decrease of insulin production required for glucose utilization thereby lead to early-onset diabetes (often <25 years). It is generally considered as non-insulin dependent form of diabetes and comprises of 1–5% of total diabetes. Till date, 14 genes have been identified and mutation in them may lead to MODY. Different genetic testing methodologies like linkage analysis, restriction fragment length polymorphism, and DNA sequencing are used for the accurate and correct investigation of gene mutations associated with MODY. The next-generation sequencing has emerged as one of the most promising and effective tools to identify novel mutated genes related to MODY. Diagnosis of MODY is mainly relying on the sequential screening of the three marker genes like hepatocyte nuclear factor 1 alpha (HNF1α), hepatocyte nuclear factor 4 alpha (HNF4α), and glucokinase (GCK). Interestingly, MODY patients can be managed by diet alone for many years and may also require minimal doses of sulfonylureas. The primary objective of this article is to provide a review on current status of MODY, its prevalence, genetic testing/diagnosis, possible treatment, and future perspective.