Rajeev K Varshney FRS

Genomic prediction (GP) in mango breeding faces challenges due to the species’ complex biology, long cycles, and limited reference populations. To accelerate genetic improvement, this study integrated data from diverse global populations to increase the reference population size. It included three mango collections reserved in Australia (225), USA (161), and China (224), totalling 610 individuals. Fruit weight (FW) and total soluble solids (TSS) were measured in multiple datasets, while several other traits were measured in specific datasets. We evaluated genetic diversity, performed genome-wide association studies (GWAS), and assessed GP accuracy using standard, genotype-by-environment (GxE), and multi-trait models, both within and across collections. Findings revealed a highly admixed genetic structure, with faster linkage disequilibrium (LD) decay in the Chinese collection, indicating higher genetic diversity. Data integration significantly enhanced GWAS power, identifying 19 quantitative trait loci (QTL) for FW and 9 for TSS. GxE models consistently achieved higher or comparable prediction accuracies for FW and TSS compared to the non-GxE models, especially when combining Australian and USA collections. This was not the case when predicting into or from the Chinese collection, mostly due to differences in the phenotyping protocol. While single-trait models performed comparably to multi-trait models in predicting new individuals (Coss-Validation: CV1), multi-trait models significantly improved prediction accuracy in scenarios with incomplete phenotypic records (CV2). This study demonstrates that strategic global data integration significantly enhances GWAS power and GP accuracy in mango. This collaborative approach is crucial for developing more efficient and accelerated breeding programs for mango and other perennial trees.

Wheat production is increasingly threatened by biotic and abiotic stresses, with stripe rust, caused by Puccinia striiformis f. sp. tritici being among the most devastating diseases. To dissect stripe rust resistance mechanisms, 329 diverse wheat genotypes were evaluated across six distinct environments in India (three locations over two years). The panel exhibited wide variation for stripe rust resistance and was genotyped using a 35K SNP-array. Genome-wide association study (GWAS) revealed 49 significant marker-trait associations (MTAs), explaining 1.58% to 29.7% of phenotypic variation, with notable quantitative-trait locus (QTL) hotspots on chromosomes 2A, 3B and 4B. Several MTAs co-localized with known resistance loci, while AX-92621629 appeared novel, suggesting new genomic region contributing to adult plant resistance. Candidate genes near significant single-nucleotide polymorphisms (SNPs) were enriched for defense-related functions, including nucleotide-binding site leucine-rich repeat (NBS-LRR) proteins, receptor-like kinases and transcription factors involved in defense signaling. To further investigate resistance mechanisms, metabolomic profiling, phytohormone and flavonoid dynamics were conducted on two contrasting wheat genotypes (resistant SKUA_415; susceptible SKUA_246) using untargeted Gas Chromatography-Mass Spectrometry (GC‒MS) and Liquid Chromatography-Mass Spectrometry (LC‒MS) approaches. Key defense-related metabolites, including myo-inositol, ketoglutaric acid, rutin and schaftoside and kaempferol derivatives were identified. These metabolites were downregulated in SKUA_246 following infection, while SKUA_415 showed up-regulation of defense phytohormones, anthocyanins and flavonoids. The two contrasting genotypes also exhibited clear allelic differentiation at key resistance-linked SNP loci, consistent with their divergent metabolomic responses. This study highlights identification of promising genes/QTLs/MTAs and metabolic markers for breeding next-generation stripe rust resistant wheat cultivars.

This book addresses the need to develop future crops that are highly resilient and adaptable to fluctuating environmental conditions, in order to sustain global food security in the years ahead. Climate change is accelerating land degradation, disrupting global carbon and nitrogen cycles, intensifying pest and disease outbreaks, altering weather patterns and reducing crop productivity. To safeguard and sustain both food and ecosystem security, it is imperative to innovate and design future crops for agricultural sustainability. Emerging new breeding techniques (NBTs), including genomics-assisted breeding, genome editing and synthetic biology, are now being harnessed to create the crops of tomorrow. This book provides an outlook on 'crops for the future'. Chapters explore the complexity of the challenges, the demands of the evolving global scenario and the prerequisites for action that range from the domestication of forgotten orphan crops, to crops for extreme environments, bioenergy, nutritional security to the re-design of plants with desirable traits using advanced genomics tools.

This volume is intended for professionals, researchers, policymakers and commercial entrepreneurs concerned with plant genetic diversity and breeding, with the goal of enhancing agricultural productivity and ensuring the sustainability of global food resources.

This book explores the significance of Nutri dense crops traditionally consumed during fasting in India. It highlights their nutritional benefits and their role in sustainable agriculture. Covering a diverse range of crops such as barnyard millet, amaranth, buckwheat, makhana, and chia seeds, the book sheds light on their historical and cultural relevance, along with their modern-day importance.

The chapters provide detailed insights into each crop’s biology, cultivation practices, genetic resources, and potential for commercialization. Readers will find valuable information on their production, breeding techniques, and innovative value-addition methods that enhance their utility in today’s food systems.

This book serves as a comprehensive resource for researchers, students, agricultural professionals, and food industry stakeholders. It aims to raise awareness and encourage the cultivation and consumption of these nutrient-rich crops, supporting both health and sustainable farming practices.

The peanut or groundnut (Arachis hypogaea L.) is a tetraploid legume, which originated around 4,000-6,000 years ago through the hybridization event between A. duranensis (A-genome) and A. ipaensis (B-genome), resulting in AABB genomic composition. Limited genetic diversity stemming from a short evolutionary history and hybridization barriers has impeded the development of extensive marker resources. To enhance peanut adaptability and resilience, a solution involving integrating diverse germplasm, prebreeding, and genomics would be required. Germplasm, encompassing wild relatives and landraces, offers essential genetic diversity for enhancing disease resistance and environmental adaptability. The Peanut Genome Consortium (PGC) strives to create high-quality reference genomes, analyze transcriptomes, and identify correlations between traits and markers to aid molecular breeding. This integration facilitates the transfer of beneficial wild-relative traits into cultivated varieties by utilizing marker-assisted selection and advanced phenotyping techniques. The approach conserves local landraces and wild species and strengthens genetic diversity and resilience. Genome sequencing advances have propelled high-resolution trait mapping and candidate gene identification. Single nucleotide polymorphisms (SNPs) are favored markers due to their prevalence. The availability of reference genomes for A. duranensis and A. ipaensis have enabled next-generation sequencing, empowering diverse genetic and breeding applications. While simple sequence repeat (SSR) markers remain important, cost-effective SNP genotyping platforms are under development. Peanut breeding targets challenges like drought, aflatoxin contamination, and oil content. Integration of sequencing technologies, precise phenotyping, and trait-focused research is pivotal to carry out effective breeding programmes to address the challenges associated with peanuts. The future of peanut genomics and molecular tools holds potential for addressing varied production and quality constraints.

Peanuts are a vital oilseed and legume crop, playing a significant role in global food security. The genetic variability of peanuts is crucial for enhancing cultivars through genetic improvement. However, rapid advancements in genomics over the past decade have transformed the status of peanuts in agricultural research. As a result, peanut research groups worldwide now bear the responsibility to adopt a holistic and integrated approach, one that leverages genomics data alongside traditional crop breeding programs. Incorporating cutting-edge genomics and biotechnology tools is essential to complement conventional breeding strategies. Without these modern advancements, achieving future breeding objectives efficiently will be highly challenging. In this context, this book offers updated insights into the latest progress in peanut genomics and biotechnology, focusing on the developments of the last 5 years. Key topics include modern genome sequencing technologies, significant genomic discoveries, and advancements in biotechnology tools that are crucial for peanut breeding programs. Specifically, this chapter provides an overview of the book's content, offering a comprehensive analysis of the current state of peanut genomics and biotechnology. It highlights how these fields are being applied in both current and future innovative breeding programs, which are vital for meeting global agricultural and food demands.

Aflatoxin contamination in peanuts poses a significant challenge to global food safety and trade. Current strategies for managing aflatoxins for pre- and post-harvest aflatoxin contamination in peanuts include both conventional and advanced approaches. Traditional breeding efforts have identified several key genetic markers associated with resistance, and marker-assisted selection has been improving the efficiency of developing resistant peanut varieties. Biotechnological innovations, such as RNA interference (RNAi) and transgenic methods, have shown promising results in reducing aflatoxin production by Aspergillus species. In this chapter, we present in-depth analyses of peanut responses to aflatoxin contamination, incorporating insights from functional genomics studies. Molecular genetics tools for aflatoxin management, such as germplasm evaluation and the exploration of genetic factors influencing aflatoxin resistance, are highlighted. We present fundamental strategies for mitigating peanut aflatoxin contamination by integrating the application of omics tools, including functional genomics, to unravel molecular insights. Genomics-assisted breeding seems to be a very promising approach for developing aflatoxin-resistant peanut varieties. Finally, we propose future research directions, emphasizing addressing complex genetics factors regulating aflatoxin contamination, their underlying mechanisms, and the application of gene-editing technologies to develop peanut varieties with durable resistance.

Aflatoxin contamination continues to be a perennial issue resulting in significant economic losses to the peanut industry globally. It also poses a serious risk to human and animal health, making it a major focus of research into novel mitigation strategies. Over the last 63 years, much has been learned about the production and regulation of aflatoxin in Aspergillus fungi and the interactions of these organisms with host plants like maize and peanut, though there are many fundamental questions about the nature and purpose of aflatoxin production that remain unanswered. Aflatoxin contamination has been consistently connected to the occurrence of drought and heat stresses, which are of growing concern with ongoing climate change. The cause of this association has, however, remained elusive. Based on the observation that antioxidant mechanisms are consistently featured among host plant responses to both drought and heat stress and Aspergillus infection, we began an investigation into the potential role of reactive oxygen species (ROS) in drought-A. flavus interactions, the role of ROS in aflatoxin production regulation, how ROS may function in signaling between host plants and A. flavus during infections under drought conditions, and their effects on aflatoxin contamination. We also investigated the fundamental differences between isolates of A. flavus in aflatoxin production capability and how these may be linked to antioxidant protection for the fungus. Here, we review the history and current status of our ongoing research into the role of ROS in aflatoxin production using biotechnology and various omics technologies, including transcriptomics, proteomics, metabolomics, and comparative genomics. Resources and knowledge generated by these studies can inform future research directions into peanut-A. flavus interactions, evolution and gene functional studies in A. flavus, and the development and selection of new genetic and biological markers for plant breeding applications to reduce aflatoxin contamination in peanut and beyond.

Peanut (Arachis hypogaea) is an important legume crop worldwide, prized for its nutritional value and economic significance. However, its production faces challenges from biotic and abiotic stresses, including diseases, drought, salinity, and extreme temperatures. Understanding the molecular mechanisms behind peanut growth, development, and stress responses is essential for enhancing crop resilience and productivity. This chapter delves into key molecular pathways, highlighting the roles of hormones such as auxins, gibberellins, and abscisic acid (ABA) in regulating root architecture, flowering, and seed development. It also examines signal transduction pathways like the MAPK cascade and calcium-mediated signaling, which aid peanuts in adapting to environmental stress. Epigenetic regulation, involving DNA methylation, histone modifications, and non-coding RNAs, further modulates gene expression, allowing dynamic responses to developmental and environmental stimuli. Additionally, the chapter discusses disease resistance mechanisms, including the activation of pathogen recognition receptors and stress-responsive transcription factors, as well as strategies for abiotic stress tolerance involving drought and salinity signaling pathways. Advances in modern breeding techniques, such as marker-assisted selection (MAS) and CRISPR/Cas9 genome editing, are also highlighted as tools for developing high-yielding, stress-tolerant peanut varieties. By integrating molecular insights with advanced breeding technologies, this chapter offers a comprehensive framework for improving peanut production amidst global challenges.

In a world where food security and sustainable agriculture face unprecedented challenges, the cultivated peanut emerges as an important food crop. Representing an essential quality oil and food legume crop grown across over 100 countries, peanuts provide vital nutrition and economic stability. Peanut Genomics and Biotechnology: Status and Prospects for Sustainability delves into the fascinating journey of peanuts, from their evolutionary origins as a natural tetraploid hybrid to their critical roles in addressing global food and oil demands amidst changing climates.

Advances in peanut genomics and biotechnology have transformed the possibilities for sustainable production. This book is a comprehensive guide to these breakthroughs, offering insights into peanut genome sequencing, breeding programs, and the innovative biotechnological tools that are driving progress. From decoding the complexities of the peanut genome to addressing abiotic and biotic stresses, this resource provides actionable solutions to develop resilient cultivars with superior yields and nutritional content.

Peanut Genomics and Biotechnology: Status and Prospects for Sustainability is useful to students, researchers, and practitioners, bringing together knowledge on genome editing technologies, omics, and bioinformatics applications. By providing a single, consolidated source of systemic information, it empowers scientists and agricultural professionals to revolutionize peanut breeding programs and contribute to sustainable agriculture.