Rajeev K Varshney

Murdoch University · Centre for Crop & Food Innovation

Background Microbial community played an essential role in ecosystem processes, be it mangrove wetland or other intertidal ecologies. Several enzymatic activities like hydrolases are effective ecological indicators of soil microbial function. So far, little is known on halophilic bacterial contribution and function on a genomic viewpoint of Indian...

Wheat is one of the most important cereal crops in the world. Cold stress is a major constraint in production of wheat grown in cold climate regions. In this study, we conducted a comprehensive assessment of cold stress tolerance in wheat genotypes through field screening, cell membrane stability through electrolyte leakage assay and biochemical pr...

The plant genome and its microbiome act together to enhance survival and promote host growth under various stresses. Plant microbiome plays an important role in plant productivity via a multitude of mechanisms including provision of nutrients and resistance against different biotic and abiotic factors. However, the molecular mechanisms responsible...

Trehalose (Tre) is a non-reducing disaccharide found in many species, including bacteria, fungi, invertebrates, yeast, and even plants, where it acts as an osmoprotectant, energy source, or protein/membrane protector. Despite relatively small amounts in plants, Tre concentrations increase following exposure to abiotic stressors. Trehalose-6-phospha...

Identifying a congenially targeted production environment and understanding the effects of genotype by environmental interactions on the adaption of chickpea genotypes is essential for achieving an optimal yield stability. Different models like additive main effect and multiplicative interactions (AMMI 1, AMM2), weighted average absolute scores of...

Contamination of arsenic in drinking water and foods is a threat for human beings. To achieve the goal for the reduction of arsenic availability, besides conventional technologies, arsenic bioremediation by using some potent bacteria is one of the hot topics for researchers. In this context, bacterium, AKS4c was isolated from arsenic contaminated w...

The rising global temperatures seriously threaten sustainable crop production, particularly the productivity and production of heat-sensitive crops like chickpeas. Multiple QTLs have been identified to enhance the heat stress tolerance in chickpeas, but their successful use in breeding programs remains limited. Towards this direction, we constructe...

The peanut is an important worldwide cash‐crop for edible oil and protein. However, the kinetic mechanisms that determine gene expression and chromatin accessibility during leaf development in peanut represented allotetraploid leguminous crops are poorly understood at single‐cell resolution. Here, a single‐nucleus atlas of peanut leaves is develope...

Resistance two foliar fungal diseases (rust and late leaf spot) are farmers preferred traits because of their devastating nature, while high oleic acid content has immerged as one of the important industry and consumer preferred traits due to increased shelf life and health benefits. With an objective to increase the frequency of the favorable alle...

The pear (Pyrus spp.) is a remarkable fruit, well known for its diverse flavors, textures, culinary versatility, and global horticultural importance. However, the genetic diversity responsible for its extensive phenotypic variations remains largely unexplored. Here, we de novo assembled and annotated the genomes of the maternal (PsbM) and paternal...

Complete, gapless telomere-to-telomere chromosome assemblies are a prerequisite for comprehensively investigating the architecture of complex regions, like centromeres or telomeres and removing uncertainties in the order, spacing, and orientation of genes. Using complementary genomics technologies and assembly algorithms, we developed highly contig...

Papaya (Carica Papaya) is one of the world’s most widely cultivated tropical horticulture crops. In 2022, the wholesale value of Australian papaya was $41.6 million (16,772 tonnes), most of which came from retail supply and less than $1 million (2 tonnes) of which came from export. In 2023, the potential export market for Australian papaya is estim...

Fatty Acid Desaturase 2 (FAD2) controls the conversion of oleic acids into linoleic acids. Mutations in FAD2 not only increase the high-oleic content, but also repress the leaf growth. However, the mechanism by which FAD2 regulates the growth pathway has not been elucidated in peanut leaves with single-cell resolution. In this study, we isolated fa...

High-quality reference genome assemblies, representative of global heterotic patterns, offer an ideal platform to accurately characterize and utilize genetic variation in the primary gene pool of hybrid crops. Here we report three platinum grade de-novo, near gap-free, chromosome-level reference genome assemblies from the active breeding germplasm...

Abiotic stresses incur severe yield losses in crop production. Several approaches can be used to develop crop cultivars that better tolerate stressful environments. To celebrate the 10th anniversary of The Crop Journal, this special issue focuses on the topic “Abiotic stress tolerance: genetics, genomics, and breeding” to address abiotic stresses...

In this study, arsenic tolerating bacteria Bacillus pacificus(AKS1a) was isolated from arsenic contaminated groundwater of Purbasthali, Purba Bardhaman, West Bengal, India and its bioremediation potential was preliminary screened. This multimetal resistant strain was able to grow against more than 20 mM arsenate and 10 mM arsenite salts. The genome...

In addition to the challenge of meeting global demand for food production, there are increasing concerns about food safety and the need to protect consumer health from the negative effects of foodborne allergies. Certain bio-molecules (usually proteins) present in food can act as allergens that trigger unusual immunological reactions, with potentia...

Many genome annotations include false-positive gene models, leading to errors in phylogenetic and comparative studies. Here, we propose a method to support gene model prediction based on evolutionary conservation and use it to identify potentially erroneous annotations. Using this method, we developed a set of 15,345 representative gene models from...

The global mean temperature is increasing at a rapid pace due to the rapid emission of greenhouse gases majorly from anthropogenic practices and is predicted to rise up to 1.5˚C above the pre-industrial level by the year 2050. The warming climate is affecting global crop production by altering biochemical, physiological, and metabolic processes res...

Crop wild relatives (CWRs) deliver untapped genetic diversity as they contain valuable breeding traits absent in the cultivated pool, e.g., traits imparting climate resilience. Facilitating genetic material from CWRs to breeding programs can advance effective traits and broaden the genetic base of cultivated crops (Bohra et al., 2022). The availabi...

Professor Andreas Graner stands as a towering figure in international crop plant genomics research, leaving an indelible imprint on the field over the past four decades. As we commemorate the 80th anniversary of Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany and Professor Graner's retirement in September 202...

Phytohormone signaling regulates plant growth and development. Single cell RNA sequencing (scRNA-seq) provides unprecedented opportunities to decipher hormone-mediated spatiotemporal gene regulatory networks. In a recent study, Nolan et al. used time-series scRNA-seq to identify the cortex as a key site for brassinosteroid (BR)-mediated gene expres...

Background The persistent high prevalence of anaemia among Indian women of reproductive age (WRA) despite aggressive long-term iron supplementation could be related to over-diagnosis from an inappropriately high haemoglobin (Hb) diagnostic cut-off. To develop an appropriate cut-off for Indian WRA, we hypothesized that during iron-folic acid (IFA) s...

Millets are a class of nutrient-rich coarse cereals with high resistance to abiotic stress; thus, they guarantee food security for people living in areas with extreme climatic conditions and provide stress-related genetic resources for other crops. However, no platform is available to provide a comprehensive and systematic multi-omics analysis for...

Peanut (Arachis) is a key oil and protein crop worldwide with large genome. The genomes of diploid and tetraploid peanuts have been sequenced, which were compared to decipher their genome structures, evolutionary, and life secrets. Genome sequencing efforts showed that different cultivars, although Bt homeologs being more privileged in gene retenti...

Crops expanding from their centres of domestication towards a wide range of agroclimatic regions has led to significant phenotypic and genetic divergence between cultivated forms. Since its domestication in the Fertile Crescent about 10 000 years ago, barley accompanied the spread of agriculture into Europe during the 5th and 6th millennia BC. It w...

Background: Approximately 90% of the world's chickpea is grown under rainfed conditions where terminal drought is one of the major constraints limiting productivity. The need of short-duration, Fusarium wilt tolerant cultivars/elite lines and able to escape drought due to early maturity were required. Methods: The present investigation was carried...

Salinity and drought stress substantially decrease crop yield and superiority, directly threatening the food supply needed to meet the rising food needs of the growing total population. Nanotechnology is a step towards improving agricultural output and stress tolerance by improving the efficacy of inputs in agriculture via targeted delivery, contro...

Malnutrition is a major challenge globally, and groundnut is a highly nutritious self-pollinated legume crop blessed with ample genomic resources, including the routine deployment of genomic-assisted breeding. This study aimed to identify genomic regions and candidate genes for high iron (Fe) and zinc (Zn) content, utilizing a biparental mapping po...

Plant diseases threaten global food security by reducing the production and quality of produce. Identification of disease resistance sources and their utilization in crop improvement is of paramount significance. However, constant evolution and occurrence of new, more aggressive and highly virulent pathotypes disintegrates the resistance of cultiva...

Climate change significantly impacts crop production by inducing several abiotic and biotic stresses. The increasing world population, and their food and industrial demands require focused efforts to improve crop plants to ensure sustainable food production. Among various modern biotechnological tools, microRNAs (miRNAs) are one of the fascinating...

The J-protein family comprises molecular chaperones involved in plant growth, development, and stress responses. Li le is known about this gene family in soybean. Hence, we characterized J-protein genes in soybean, with the most highly expressed and responsive during flower and seed development. We also revealed their phylogeny, structure, motif an...

Climate change is varying the availability of resources, soil physicochemical properties, and rainfall events, which collectively determines soil physical and chemical properties. Soil constraints-acidity (pH < 6), salinity (pH ≤ 8.5), sodicity, and dispersion (pH > 8.5)-are major causes of wheat yield loss in arid and semiarid cropping systems. To...

CRISPR/Cas9 gene technology is transported as RNA from transgenic roots to distal parts of unmodified grafted scion, where it is translated into proteins to induce heritable mutagenesis at desired loci. This technique has the potential to produce transgene-free and genetically stable plants in difficult-to-propagate and near-extinct species.

Key message The vacuolar processing enzyme gene TaVPE3cB is identified as a candidate gene for a QTL of wheat pith-thickness on chromosome 3B by BSR-seq and differential expression analyses. Abstract The high pith-thickness (PT) of the wheat stem could greatly enhance stem mechanical strength, especially the basal internodes which support the heav...

Groundnut productivity and quality have been impeded by rising temperatures in semi-arid environments. Hence, understanding the effects and molecular mechanisms of heat stress tolerance will aid in tackling yield losses. In this context, a recombinant inbred line (RIL) population was developed and phenotyped for eight seasons at three locations for...

Fusarium wilt (FW) is one of the most significant biotic stresses limiting chickpea production worldwide. To dissect the molecular mechanism of FW resistance in chickpea, comparative transcriptome analyses of contrasting resistance sources of chickpea genotypes under control and Fusarium oxysporum f. sp. ciceris (Foc) inoculated conditions were per...

Heterosis refers to the better performance of cross progeny compared with inbred parents, and its utilization contributes greatly to agricultural production. Several hypotheses have been proposed to explain heterosis mainly including dominance, over-dominance (or pseudo-overdominance) and epistasis. However, systematic dissection and verification o...

A better understanding of crop genomes reveals that structural variations (SVs) are crucial for genetic improvement. A graph-based pan-genome by Yan et al. uncovered 424 085 genomic SVs and provided novel insights into heat tolerance of pearl millet. We discuss how these SVs can fast-track pearl millet breeding under harsh environments.

Drought is one of the major constraints limiting chickpea productivity. To unravel complex mechanisms regulating drought response in chickpea, we generated transcriptomics, proteomics, and metabolomics datasets from root tissues of four contrasting drought-responsive chickpea genotypes: ICC 4958, JG 11, and JG 11+ (drought-tolerant), and ICC 1882 (...

Papain-like cysteine proteases (PLCPs) play essential roles in plant growth, senescence, and stress responses. However, researches on the PLCP genes are limited in cultivated peanut (Arachis hypogaea L.). Here, we identified and analyzed AhPLCP genes in cultivated peanut using bioinformatic approaches and verified the involvement of AhRD21B in resp...

A better understanding of crop genomes reveals that structural variations (SVs) are crucial for genetic improvement. A graph-based pan-genome by Yan et al. uncovered 424 085 genomic SVs and provided novel insights into heat tolerance of pearl millet. We discuss how these SVs can fast-track pearl millet breeding under harsh environments.

Terminal drought is one of the major constraints to crop production in chickpea (Cicer arietinum L.). In order to map drought tolerance related traits at high resolution, we sequenced multi-parent advanced generation intercross (MAGIC) population using whole genome resequencing approach and phenotyped it under drought stress environments for two co...

Abiotic stresses, including drought, salinity, cold, heat, and heavy metals, extensively reducing global agricultural production. Traditional breeding approaches and transgenic technology have been widely used to mitigate the risks of these environmental stresses. The discovery of engineered nucleases as genetic scissors to carry out precise manipu...

Wild emmer, the direct progenitor of modern durum and bread wheat, has mostly been studied for grain quality, biotic, and abiotic stress-related traits. Accordingly, it should also have a certain amount of diversity for morphological and agronomic traits. Despite having a high chance of huge diversity, it has not been deeply explored. In the curren...

Pratylenchus thornei is an economically important species of root-lesion nematode adversely affecting chickpea (Cicer arietinum) yields globally. Integration of resistant crops in farming systems is recognised as the most effective and sustainable management strategy for plant-parasitic nematodes. However, breeding for P. thornei resistance in chic...

Seed size is not only a yield-related trait but also an important measure to determine the commercial value of groundnut in the international market. For instance, small size is preferred in oil production, whereas large-sized seeds are preferred in confectioneries. In order to identify the genomic regions associated with 100-seed weight (HSW) and...

Context Chickpea (Cicer arietinum L.) are highly sensitive to elevated salinity, particularly at initial seedling establishment stage. Seedling screening would be an effective means to identify novel sources of donors for salt tolerance. Aim This study aimed to identify salt stress tolerant genotypes at seedling stage from 50 chickpea accessions. M...

The oral cavity of human contains bacteria that are critical for maintaining the homeostasis of the body. External stressors such as high altitude (HA) and low oxygen affect the human gut, skin and oral microbiome. However, compared to the human gut and skin microbiome, studies demonstrating the impact of altitude on human oral microbiota are curre...

Peanut ( Arachis hypogaea L.), one of the leading oilseed crops worldwide, is an important source of vegetable oil, protein, minerals and vitamins. Peanut is widely cultivated in Asia, Africa and America, and China is the largest producer and consumer of peanut. Genetic engineering has shown great potential to alter the DNA makeup of an organism wh...

Fluoride (F-) contamination of groundwater is a silent killer of human health that has now become a global problem. In the present study, we sought to isolate fluoride-resistant, urease producing bacteria from F- contaminated groundwater to evaluate their potential F- biomineralization. Strain MLN9, isolated from the fluoride-contaminated village o...

Abstract: Peanut (Arachis hypogaea L.) is an important food and feed crop worldwide and is affected by various biotic and abiotic stresses. The cellular ATP levels decrease significantly during stress as ATP molecules move to extracellular spaces, resulting in increased ROS production and cell apoptosis. Apyrases (APYs) are the nucleoside phosphata...

The severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2) caused global pandemic and drastically affected the humankind. Mitochondrial mutations have been found to be associated with several respiratory diseases. Missense mutation and pathogenic mitochondrial variants might unveil the potential involvement of the mitochondrial genome in coro...

Climate change and abiotic stress factors are key players in crop losses worldwide. Among which, extreme temperatures (heat and cold) disturb plant growth and development, reduce productivity and, in severe cases, lead to plant death. Plants have developed numerous strategies to mitigate the detrimental impact of temperature stress. Exposure to str...

The grain-filling stage in Triticum aestivum (wheat) is highly vulnerable to increasing temperature as terminal heat stress diminishes grain quality and yield. To examine the mechanism of terminal heat tolerance, we performed the biochemical and gene expression analyses using two heat-tolerant (WH730 and WH1218) and two heat-sensitive (WH711 and WH...

Heavy metal pollution in mining areas is a serious environmental concern. The exploration of mine-inhabiting microbes, especially bacteria may use as an effective alternative for the remediation of mining hazards. A highly copper-tolerant strain GKSM13 was isolated from the soil of the Singhbhum copper mining area and characterized for significant...

Fusarium wilt (FW) caused by the Fusarium oxysporum f. sp. ciceri is a devastating disease of chickpea (Cicer arietinum L.). To identify promising resistant genotypes and genomic loci for FW resistance, a core set of 179 genotypes of chickpea was tested for FW reactions at seedling and reproductive stages under field as well as controlled condition...

Outbreak of COVID-19 pandemic in December 2019 affected millions of people globally. After substantial research, several biomarkers for COVID-19 have been validated however no specific and reliable biomarker for the prognosis of patients with COVID-19 infection exists. Present study was designed to identify specific biomarkers to predict COVID-19 s...