Rajeev K Varshney FRS

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.

The utility and demand of legumes are increasing unremittingly every year within the ever-growing populations especially within the vegetarian people over the world owing to its richness in proteins. However, biotic stresses are major factors in limiting legumes productivity especially in the Indian subcontinent and African continent. Global distribution and occurrence of various biotic stresses in legumes are well-documented. Among them, 50% of the diseases are caused by fungal pathogens and 38% by viral pathogens. Under changing climate scenario, various minor diseases are becoming major barriers in way for achieving high yields. Furthermore, the pathogens are becoming more aggressive. Resistant cultivars are widely recognized as the most efficient, safe, and economical method for management, and in the past few decades, a considerable care is being taken in legume protection strategies, and the production of legumes has increased magnificently, and disease-resistant varieties play a major role in that. In this chapter, we tried to collate the information about major diseases in legume crops, their worldwide distribution, and economic losses due to them. Some emerging challenges under changing climate have also been described including use of new tools and technologies that can play a key role in transforming legume-farming system for narrowing the yield gaps.

Oilseed crops, such as soybean, groundnut, mustard, sunflower, and sesame, are important in global agriculture due to human consumption and industrial applications. Considering their importance in global agriculture, there has been significant attention given to improving both seed oil content and quality. Oil synthesis and accumulation are regulated by complex biochemical pathways and are typically classified as quantitative traits. Over the past few decades, the elucidation of regulatory pathways governing fatty acid synthesis, identification of target genes and advancements in metabolic engineering have made significant progress. Additionally, advancements in sequencing technologies and revolutionized bioinformatics have helped in a significant transformation in the field of genomic analysis. This transformation involves a shift from analyzing individual cultivars to encompassing studies of entire species at the genomic level. This paradigm shift is aimed at comprehensively capturing the full spectrum of diversity. This chapter explores the complexities of traits linked to oil content and recent advancements in mapping these traits to gain a deeper understanding of their complexity. Additionally, the concepts of the pan-genome and super pan-genome, along with the methods employed for their construction are discussed. We also discuss the current challenges faced in major oilseed crops and consider the future prospects for this ever-evolving field.

Breeding for high oleate oilseed crops for healthier and more stable oils has seen significant progress over the years. This review explores the fatty acid composition of plant oils, emphasizing the shift toward higher oleic acid content. It highlights various alternative oilseeds, including soybean, rapeseed, sunflower, peanut, etc., as promising candidates for breeding programs. Factors influencing fatty acid composition, such as environmental conditions and genetic factors, are examined in detail. Key enzymes and genes regulating fatty acid biosynthesis, particularly stearoyl-ACP desaturase (SAD) and fatty acid desaturase (FAD), are discussed for their pivotal roles in determining oleate levels. Advances in gene discovery have identified crucial genetic determinants that facilitate targeted breeding for high oleate traits. Traditional breeding techniques are complemented by marker-assisted breeding, enhancing the precision and efficiency of developing high oleate cultivars. Genetic engineering and gene editing technologies, such as CRISPR/Cas9, offer transformative prospects for modifying fatty acid biosynthesis pathways. These cutting-edge approaches enable the precise manipulation of SAD and FAD genes to achieve desired fatty acid profiles. This review underscores the successful development of several improved varieties across various crops, reflecting the tangible outcomes of these advancements.

Pulses are a powerhouse of protein and hold an immense potential for food security and sustainable agriculture. However, exploiting their full potential centers on harnessing genetic, genomic, and bioinformatics resources still needs a great fillip. Efforts have been made globally to collect, preserve, and characterize their germplasm, facilitating the identification of desirable traits for breeding programs. Such collections can serve as a rich reservoir for genetic studies, enabling the development of improved varieties with enhanced yield, nutritional content, and resistance to biotic and abiotic stresses. Pulse genome sequencing has accelerated during the last 10 years, and most pulse crops now have high-quality reference genomes, transcriptomes, and genetic maps accessible. Moreover, genomic tools enable the detection of key genes responsible for important agronomic traits, disease resistance, and stress tolerance, paving the way for precision breeding approaches. Dedicated databases to curate genetic and phenotypic information and tools utilized for genome assembly, annotation, and variation analysis are constantly evolving. Pulses could see a revolutionary leap in genetic improvement through the synergy of cutting-edge genomic and phenomic tools with accelerating techniques such as genomic selection and speed breeding. The fusion of artificial intelligence (AI) and machine learning (ML) technologies with genomic science heralds a new era in crop breeding and genetic harvest in pulses. These tools offer exciting possibilities for boosting productivity, enhancing nutritional quality, and ensuring resilience to environmental stresses. As these tools become increasingly accessible and their applications more widespread, the potential for transformative impacts on global pulse scenarios continues to grow.