Rupesh Deshmukh

• Doctor of Philosophy
• Professor at Université Laval

The extensive generation of agricultural waste worldwide poses significant environmental challenges. Traditional disposal methods, such as crop burning, contribute to severe air pollution and ecological degradation. Current agricultural waste management strategies often fail to fully utilize the potential of these residues for conversion into valua...

Plants are an important source of essential bioactive compounds that not only have a beneficial role in human health and nutrition but also act as drivers for shaping gut microbiome. However, the mechanism of their functional attributes is not fully understood despite their significance. One such important plant is Crocus sativus, also known as saf...

Climate change biotic and abiotic stressors lead to unpredictable crop yield losses, threatening global food and nutritional security. In the past, traditional breeding has been instrumental in fulfilling food demand; however, owing to its low efficiency, dependence on environmental conditions, labor intensity, and time consumption, it fails to mai...

Prime editors are reverse transcriptase (RT)-based genome editing tools utilizing double strand break (DSB) free mechanisms to decrease off-target editing in genomes and enhance the efficiency of targeted insertions. Multiple prime editors developed within a short span of time are a testament to the potential of this technique for targeted insertio...

The Glycine max L. has been affected by more than 100 diseases, including Macrophomina phaseolina producing charcoal rot disease, which reduces production by 70%. In this investigation, RNA-Seq analysis is used for the first time to explore role of silicon in preventing soybean charcoal rot. The study explores the molecular mechanism underlying soy...

The global population is growing rapidly, and with it, the demand for food. In the coming decades, more and more people will be living in urban areas, where land for traditional agriculture is scarce. Urban agriculture can help to meet this growing demand for food in a sustainable way. Urban agriculture is the practice of growing food in urban area...

Sugar Efflux transporters (SWEET) are involved in diverse biological processes of plants. Pathogens have exploited them for nutritional gain and subsequently promote disease progression. Recent studies have implied the involvement of potato SWEET genes in the most devastating late blight disease caused by Phytophthora infestans. Here, we identified...

Flax (Linum usitatissimum L.) is a self-pollinating, annual, diploid crop grown for multi-utility purposes for its quality oil, shining bast fiber, and industrial solvent. Being a cool (Rabi) season crop, it is affected by unprecedented climatic changes such as high temperature, drought, and associated oxidative stress that, globally, impede its gr...

The book addresses recent advances in biofortification using different approaches like foliar fertilizer, plant breeding, and genetic engineering as well as its utilization for improvement of nutritional quality of cereals. The content compiled is contributed by the renowned scientists actively working in the area of the cereal biofortification. Th...

Plant omics, which includes genomics, transcriptomics, metabolomics and proteomics, has played a remarkable role in the discovery of new genes and biomolecules that can be deployed for crop improvement. In wheat, great insights have been gleaned from the utilization of diverse omics approaches for both qualitative and quantitative traits. Especiall...

Key message We summarise recent advancements to achieve higher homologous recombination based gene targeting efficiency in different animals and plants. Abstract The genome editing has revolutionized the agriculture and human therapeutic sectors by its ability to create precise, stable and predictable mutations in the genome. It depends upon targe...

Grain legumes are a rich source of dietary protein for millions of people globally and thus a key driver for securing global food security. Legume plant-based ‘dietary protein’ biofortification is an economic strategy for alleviating the menace of rising malnutrition-related problems and hidden hunger. Malnutrition from protein deficiency is predom...

In order to meet the growing human food and nutrition demand a perpetual process of crop improvement is idealized. It has seen changing trends and varying concepts throughout human history; from simple selection to complex gene-editing. Among these techniques, random mutagenesis has been shown to be a promising technology to achieve desirable genet...

Rice is a global food grain crop for more than one-third of the human population and a source for food and nutritional security. Rice production is subjected to various stresses; blast disease caused by Magnaporthe oryzae is one of the major biotic stresses that has the potential to destroy total crop under severe conditions. In the present review,...

Understanding the genetic basis of quantitative traits has been a major goal for plant breeders to use in breeding programs. However, the mapping of quantitative traits is time consuming and costly process. The advancements in molecular genetics and genomics have facilitated the dissection of quantitative trait loci (QTLs) underlying complex traits...

Although at the infancy stage, biomolecular network biology is a comprehensive approach to understand complex biological function in plants. Recent advancements in the accumulation of multi-omics data coupled with computational approach have accelerated our current understanding of the complexities of gene function at the system level. Biomolecular...

Economically, cotton ( Gossypium spp.) represents the most important family of the crop for the textile industry and a cornerstone of the rural economy. Domestication, agronomic practices, and breeding systems have made cotton the most cultivated and utilized fiber crop globally. Cotton breeders continuously adapt tools and technologies that encomp...

Sugars as photosynthates are well known as energy providers and as building blocks of various structural components of plant cells, tissues and organs. Additionally, as a part of various sugar signaling pathways, they interact with other cellular machinery and influence many important cellular decisions in plants. Sugar signaling is further reliant...

Exogenous addition of silicon alleviates metsulfuron methyl induced stress in wheat seedlings, Plant Physiology et Biochemistry (2021), doi: https://doi. Abstract 17 Uncontrolled application of herbicides in the agricultural field poses a severe risk to crops by 18 affecting their yields. Therefore, methods are required to reduce the toxic effects...

Aluminum (Al) precipitates in acidic soils having a pH < 5.5, in the form of conjugated organic and inorganic ions. Al-containing minerals solubilized in the soil solution cause several negative impacts in plants when taken up along with other nutrients. Moreover, a micromolar concentration of Al present in the soil is enough to induce several irre...

Exogenous applications of silicon (Si) can initiate cellular defence pathways to enhance plant resistance to abiotic and biotic stresses. Plant Si accumulation is regulated by several transporters of silicic acid (e.g. Lsi1, Lsi2, and Lsi6), but the precise mechanisms involved in overall Si transport and its beneficial effects remains unclear. In s...

Over the last decade, silicon (Si) has been widely accepted as a beneficial element for plant growth. The advantages plant derives from the Si are primarily based on the uptake and transport mechanisms. In the present study, the Si uptake regime was studied in finger millet (Eleusine coracana (L). Gaertn.) under controlled and stress conditions. Th...

Jujube (Ziziphus jujuba Mill.), a deciduous tree, is well known for its medicinal and nutritional values. Being an extremophile, it has an excellent capability to survive under arid conditions with limited water availability. In this regard, studying the role of water transport regulating proteins such as Aquaporins (AQPs) in jujube is of great imp...

Gene editing technologies have revolutionized the development of new and innovative bio-products in plants as well as animals in recent years. Of the different techniques available, CRISPR/Cas has been and will remain the basis of genome engineering for researchers across the world because of its easiness to use and specificity. There have been exc...

Silicon is widely recognized as a beneficial element for plant growth. Numerous studies have shown the beneficial effects of silicon, particularly under stress conditions. For the efficient exploration of silicon derived benefits, understanding silicon uptake mechanism, subsequent transport and accumulation in different tissues is essential. Here,...

Aquaporins (AQPs) play a pivotal role in the cellular transport of water and many other small solutes, influencing many physiological and developmental processes in plants. In the present study, extensive bioinformatics analysis of AQPs was performed in Aquilegia coerulea L., a model species belonging to basal eudicots, with a particular focus on u...

Over the past decades, numerous efforts were made towards the improvement of cereal crops mostly employing traditional or molecular breeding approaches. The current scenario made it possible to efficiently explore molecular understanding by targeting different genes to achieve desirable plants. To provide guaranteed food security for the rising wor...

Aquaporins are pore-forming transmembrane proteins that facilitate the movement of water and many other small neutral solutes across the cells and intracellular compartments. Plants exhibits high diversity in aquaporin isoforms and broadly classified into five different subfamilies on the basis of phylogenetic distribution and subcellular occurrenc...

Plant viruses infect various economically important crops and cause a serious threat to agriculture. As of now, conventional strategies employed are inadequate to circumvent the proliferation of rapidly evolving plant viruses. In this regard, recent advancement in genome-editing approach looks promising to produce plants resistant to DNA/RNA virus...

Transcription factors (TFs) are regulatory proteins that have the ability to alter targeted gene expression either solely by themselves or as a part of the protein complex. Many such TFs have significant regulatory role in plant defence. Being master switches for gene regulation, they become the unique candidate for targeting functional hub and dyn...

Gases such as ethylene, hydrogen peroxide (H2O2), nitric oxide (NO), carbon monoxide (CO) and hydrogen sulfide (H2S) have been recognized as vital signaling molecules in plants and animals. Of these gasotransmitters, NO and H2S have recently gained momentum mainly because of their involvement in numerous cellular processes. It is therefore importan...

Silicon (Si) is a beneficial substrate for many plants, conferring heightened resilience to environmental stress. A plant's ability to absorb Si is primarily dependent on the presence of a Si‐permeable Lsi1 (NIP2‐1) aquaporin in its roots. Structure‐function analyses of Lsi1 channels from higher plants have thus far revealed two key molecular deter...

Abiotic stress imposed by many factors such as: extreme water regimes, adverse temperatures, salinity, and heavy metal contamination result in severe crop yield losses worldwide. Plants must be able to quickly respond to these stresses in order to adapt to their growing conditions and minimize metabolic losses. In this context, transporter proteins...

Pigeonpea (Cajanus cajan L.), a protein-rich legume, is a major food component of the daily diet for residents in semi-arid tropical regions of the word. Pigeonpea is also known for its high level of tolerance against biotic and abiotic stresses. In this regard, understanding the genes involved in stress tolerance has great importance. In the prese...

Fast neutron (FN) radiation mediated mutagenesis is a unique approach among the several induced mutagenesis methods being used in plant science in terms of impacted mutations. The FN mutagenesis usually creates deletions from few bases to several million bases (Mb). A library of random deletion generated using FN mutagenesis lines can provide indis...

Cannabis sativa is an economically important crop providing bast fibres for the textile and biocomposite sector. Length is a fundamental characteristic determining the properties of bast fibres. Aquaporins, channel-forming proteins facilitating the passage of water, urea, as well as elements such as boron and silicon, are known to play a role in th...

Induced mutagenesis has been proven to be a successful strategy for the improvement of several crops including rice. In the present review, different induced mutagenesis approaches have been discussed concerning the efficient exploration for rice improvement. Significant efforts and the popular rice varieties developed through the mutagenesis appro...

Metal Tolerance Proteins (MTPs) are the class of membrane proteins involved in the transport of metals, mainly Zn, Mn, Fe, Cd, Co and Ni, and confer metal tolerance in plants. In the present study, a comprehensive molecular analysis of rice MTP genes was performed to understand the evolution, distribution and expression dynamics of MTP genes. Explo...

Induced mutagenesis is one of the most effective strategies for trait improvement without altering the well-optimized genetic background of the cultivars. In this review, several currently accessible methods such as physical, chemical and insertional mutagenesis have been discussed concerning their efficient exploration for the tomato crop improvem...

Fast neutron (FN) radiation mediated mutagenesis is a unique approach among the several induced mutagenesis methods being used in plant science in terms of impacted mutations. The FN mutagenesis usually creates deletions from a few bases to several million bases (Mb). A library of random deletion generated using FN mutagenesis lines can provide ind...

Over the past few decades, heavy metal contamination in soil and water has increased due to anthropogenic activities. The higher exposure of crop plants to heavy metal stress reduces growth and yield, and affect the sustainability of agricultural production. In this regard, the use of silicon (Si) supplementation offers a promising prospect since n...

Rice blast caused by Magnaporthe oryzae is one of the most destructive diseases of rice in the world. The blast fungus shows a high degree of variability in the field and limited information is available on its genetic diversity and population structure in India. Twenty five polymorphic SSR markers were used to investigate the genetic diversity and...

Silicon (Si) being considered as a non-essential element for plant growth and development finds its role in providing several benefits to the plant, especially under stress conditions. Thus, Si can be regarded as “multi-talented” quasi-essential element. It is the most abundant element present in the earth’s crust after oxygen predominantly as a si...

Rice blast caused by Magnaporthe oryzae is one of the most destructive diseases of rice in the world. The blast fungus shows a high degree of variability in the field and limited information is available on its genetic diversity and population structure in India. Twenty five polymorphic SSR markers were used to investigate the genetic diversity and...

Understanding of genetic diversity is important to explore existing gene in any crop breeding program. Most of the diversity preserved in the landraces which are well–known reservoirs of important traits for biotic and abiotic stresses. In the present study, the genetic diversity at twenty-four most significant blast resistance gene loci using twen...

Population assignment of landraces described by GenAlEx charts representing the log likelihood data of landrace using disease reaction: a) Moderately resistant and resistant and populations b) Susceptible and resistant populations c) Susceptible and moderately resistant populations. (TIF)

Details of landraces used in the current study. (XLSX)

Reaction of landraces to leaf blast disease in the uniform blast nursery. (TIF)

Genotyping of 161 landraces using markers associated with blast resistance genes, associated gene frequency and their phenotypic reaction to leaf blast in uniform blast nursery. (XLSX)

Population structure group of 161 landraces based on inferred ancestry values. (XLSX)

Metabolomics is one of the most emerging technologies being used for crop improvement. It allows a comprehensive understanding of complex networks of biological processes, which will certainly help to accelerate the sustainable crop production. In a short time, valuable efforts have been made in developing high-throughput instruments, online tools,...

Pulse crops being an excellent source of lysine-rich proteins, vitamins, several essential minerals, and secondary metabolites are of immense importance in human nutrition. Due to lack of adequate amount of protein and micronutrient in the diet, over a billion people are suffering from malnutrition around the world. In this regard, pulses play a cr...

Figure S3 Frequency histogram of the percentage of missing data points in WGRS of 91 RILs with 16 674 polymorphic SNPs in the population.

Figure S4 Distribution of markers on linkage groups.

Figure S6 Genetic and QTL map of major QTLs (>10% PVE) comprising SNP and SSR markers in Tifrunner × GT‐C20 population in peanut (Pandey et al., 2017a).

Figure S2 Percentage reads mapped to the diploid reference A‐ and B‐genome in each RIL and the two parents.

Figure S5 QTL maps showing the major QTL peaks at different LODs on vertical axis.

Table S1 Phenotypic variation of diseases (ELS, LLS and TSWV) in T‐population parents and RILs. Table S2 Overview of the WGRS data and alignment to the reference genome. Table S3 Summary of SNPs detected between Tifrunner and GT‐C20 and SNPs used in RIL population. Table S4 Number of homeologus and translocated markers. Table S5 Effect of major...

Figure S1 Phenotypic distribution of ELS, LLS and TSWV in T‐pop RILs during different seasons.

The Indian initiative, in creating mutant resources for the functional genomics in rice, has been instrumental in the development of 87,000 ethylmethanesulfonate (EMS)-induced mutants, of which 7,000 are in advanced generations. The mutants have been created in the background of Nagina 22, a popular drought- and heat-tolerant upland cultivar. As it...

Contents I. II. III. IV. V. VI. VII. References Silicon (Si) is not classified as an essential plant nutrient, and yet numerous reports have shown its beneficial effects in a variety of species and environmental circumstances. This has created much confusion in the scientific community with respect to its biological roles. Here, we link molecular a...

Whole genome re‐sequencing (WGRS) of mapping populations has facilitated development of high‐density genetic linkage maps essential for fine mapping and candidate gene discovery for traits of interest in crop species. Leaf spots, including early leaf spot (ELS) and late leaf spot (LLS), and Tomato spotted wilt virus (TSWV) are devastating diseases...

Aquaporins (AQPs) are a class of integral membrane proteins involved in the transport of water and many other small solutes. The AQPs have been extensively studied in many land species obtaining water and nutrients from the soil, but their distribution and evolution have never been investigated in aquatic plant species, where solute assimilation is...