Genomics and molecular breeding in lesser explored pulse crops: current trends and future opportunities

A foundational large language model for edible plant genomes

Significant progress has been made in the field of plant genomics, as demonstrated by the increased use of high-throughput methodologies that enable the characterization of multiple genome-wide molecular phenotypes. These findings have provided valuable insights into plant traits and their underlying genetic mechanisms, particularly in model plant species. Nonetheless, effectively leveraging them to make accurate predictions represents a critical step in crop genomic improvement. We present AgroNT, a foundational large language model trained on genomes from 48 plant species with a predominant focus on crop species. We show that AgroNT can obtain state-of-the-art predictions for regulatory annotations, promoter/terminator strength, tissue-specific gene expression, and prioritize functional variants. We conduct a large-scale in silico saturation mutagenesis analysis on cassava to evaluate the regulatory impact of over 10 million mutations and provide their predicted effects as a resource for variant characterization. Finally, we propose the use of the diverse datasets compiled here as the Plants Genomic Benchmark (PGB), providing a comprehensive benchmark for deep learning-based methods in plant genomic research. The pre-trained AgroNT model is publicly available on HuggingFace at https://huggingface.co/InstaDeepAI/agro-nucleotide-transformer-1b  for future research purposes.

Fusarium wilt pandemic: current understanding and molecular perspectives

Plant diseases pose a severe threat to the food security of the global human population. One such disease is Fusarium wilt, which affects many plant species and causes up to 100% yield losses. Fusarium pathogen has high variability in its genetic constitution; therefore, it has evolved into different physiological races to infect different plant species spread across the different geographical regions of the world. The pathogen mainly affects plant roots, leading to colonizing and blocking vascular bundle cells, specifically xylem vessels. This blocking results in chlorosis, vascular discoloration, leaf wilting, shortening of plant, and, in severe cases, premature plant death. Due to the soil-borne nature of the wilt pathogen, neither agronomic nor plant protection measures effectively reduce the incidence of the disease. Therefore, the most cost-effective management strategy for Fusarium wilt is developing varieties resistant to a particular race of the fungus wilt prevalent in a given region. This strategy requires understanding the pathogen, its disease cycle, and epidemiology with climate-changing scenarios. Hence, in the review, we will discuss the pathogenic aspect and genetics of the Fusarium wilt, including molecular interventions for developing climate-smart wilt tolerant/resistant varieties of crops. Overall, this review will add to our knowledge for advancing the breeding of resistance against the wilt pandemic.

Chromosome-level genome assembly and population genomic resource to accelerate orphan crop lablab breeding

Under-utilised orphan crops hold the key to diversified and climate-resilient food systems. Here, we report on orphan crop genomics using the case of Lablab purpureus (L.) Sweet (lablab) - a legume native to Africa and cultivated throughout the tropics for food and forage. Our Africa-led plant genome collaboration produces a high-quality chromosome-scale assembly of the lablab genome. Our assembly highlights the genome organisation of the trypsin inhibitor genes - an important anti-nutritional factor in lablab. We also re-sequence cultivated and wild lablab accessions from Africa confirming two domestication events. Finally, we examine the genetic and phenotypic diversity in a comprehensive lablab germplasm collection and identify genomic loci underlying variation of important agronomic traits in lablab. The genomic data generated here provide a valuable resource for lablab improvement. Our inclusive collaborative approach also presents an example that can be explored by other researchers sequencing indigenous crops, particularly from low and middle-income countries (LMIC).

Breeding and Genomic Approaches towards Development of Fusarium Wilt Resistance in Chickpea

Chickpea is an important leguminous crop with potential to provide dietary proteins to both humans and animals. It also ameliorates soil nitrogen through biological nitrogen fixation. The crop is affected by an array of biotic and abiotic factors. Among different biotic stresses, a major fungal disease called Fusarium wilt, caused by Fusarium oxysporum f. sp. ciceris (FOC), is responsible for low productivity in chickpea. To date, eight pathogenic races of FOC (race 0, 1A, and 1B/C, 2-6) have been reported worldwide. The development of resistant cultivars using different conventional breeding methods is very time consuming and depends upon the environment. Modern technologies can improve conventional methods to solve these major constraints. Understanding the molecular response of chickpea to Fusarium wilt can help to provide effective management strategies. The identification of molecular markers closely linked to genes/QTLs has provided great potential for chickpea improvement programs. Moreover, omics approaches, including transcriptomics, metabolomics, and proteomics give scientists a vast viewpoint of functional genomics. In this review, we will discuss the integration of all available strategies and provide comprehensive knowledge about chickpea plant defense against Fusarium wilt.

Development and Complex Application of Methods for the Identification of Mutations in the FAD3A and FAD3B Genes Resulting in the Reduced Content of Linolenic Acid in Flax Oil

Flax is grown worldwide for seed and fiber production. Linseed varieties differ in their oil composition and are used in pharmaceutical, food, feed, and industrial production. The field of application primarily depends on the content of linolenic (LIN) and linoleic (LIO) fatty acids. Inactivating mutations in the FAD3A and FAD3B genes lead to a decrease in the LIN content and an increase in the LIO content. For the identification of the three most common low-LIN mutations in flax varieties (G-to-A in exon 1 of FAD3A substituting tryptophan with a stop codon, C-to-T in exon 5 of FAD3A leading to arginine to a stop codon substitution, and C-to-T in exon 2 of FAD3B resulting in histidine to tyrosine substitution), three approaches were proposed: (1) targeted deep sequencing, (2) high resolution melting (HRM) analysis, (3) cleaved amplified polymorphic sequences (CAPS) markers. They were tested on more than a thousand flax samples of various types and showed promising results. The proposed approaches can be used in marker-assisted selection to choose parent pairs for crosses, separate heterogeneous varieties into biotypes, and select genotypes with desired homozygous alleles of the FAD3A and FAD3B genes at the early stages of breeding for the effective development of varieties with a particular LIN and LIO content, as well as in basic studies of the molecular mechanisms of fatty acid synthesis in flax seeds to select genotypes adequate to the tasks.

Progress of Genomics-Driven Approaches for Sustaining Underutilized Legume Crops in the Post-Genomic Era

Legume crops, belonging to the Fabaceae family, are of immense importance for sustaining global food security. Many legumes are profitable crops for smallholder farmers due to their unique ability to fix atmospheric nitrogen and their intrinsic ability to thrive on marginal land with minimum inputs and low cultivation costs. Recent progress in genomics shows promise for future genetic gains in major grain legumes. Still it remains limited in minor legumes/underutilized legumes, including adzuki bean, cluster bean, horse gram, lathyrus, red clover, urd bean, and winged bean. In the last decade, unprecedented progress in completing genome assemblies of various legume crops and resequencing efforts of large germplasm collections has helped to identify the underlying gene(s) for various traits of breeding importance for enhancing genetic gain and contributing to developing climate-resilient cultivars. This review discusses the progress of genomic resource development, including genome-wide molecular markers, key breakthroughs in genome sequencing, genetic linkage maps, and trait mapping for facilitating yield improvement in underutilized legumes. We focus on 1) the progress in genomic-assisted breeding, 2) the role of whole-genome resequencing, pangenomes for underpinning the novel genomic variants underlying trait gene(s), 3) how adaptive traits of wild underutilized legumes could be harnessed to develop climate-resilient cultivars, 4) the progress and status of functional genomics resources, deciphering the underlying trait candidate genes with putative function in underutilized legumes 5) and prospects of novel breeding technologies, such as speed breeding, genomic selection, and genome editing. We conclude the review by discussing the scope for genomic resources developed in underutilized legumes to enhance their production and play a critical role in achieving the "zero hunger" sustainable development goal by 2030 set by the United Nations.

Omics-Facilitated Crop Improvement for Climate Resilience and Superior Nutritive Value

Novel crop improvement approaches, including those that facilitate for the exploitation of crop wild relatives and underutilized species harboring the much-needed natural allelic variation are indispensable if we are to develop climate-smart crops with enhanced abiotic and biotic stress tolerance, higher nutritive value, and superior traits of agronomic importance. Top among these approaches are the "omics" technologies, including genomics, transcriptomics, proteomics, metabolomics, phenomics, and their integration, whose deployment has been vital in revealing several key genes, proteins and metabolic pathways underlying numerous traits of agronomic importance, and aiding marker-assisted breeding in major crop species. Here, citing several relevant examples, we appraise our understanding on the recent developments in omics technologies and how they are driving our quest to breed climate resilient crops. Large-scale genome resequencing, pan-genomes and genome-wide association studies are aiding the identification and analysis of species-level genome variations, whilst RNA-sequencing driven transcriptomics has provided unprecedented opportunities for conducting crop abiotic and biotic stress response studies. Meanwhile, single cell transcriptomics is slowly becoming an indispensable tool for decoding cell-specific stress responses, although several technical and experimental design challenges still need to be resolved. Additionally, the refinement of the conventional techniques and advent of modern, high-resolution proteomics technologies necessitated a gradual shift from the general descriptive studies of plant protein abundances to large scale analysis of protein-metabolite interactions. Especially, metabolomics is currently receiving special attention, owing to the role metabolites play as metabolic intermediates and close links to the phenotypic expression. Further, high throughput phenomics applications are driving the targeting of new research domains such as root system architecture analysis, and exploration of plant root-associated microbes for improved crop health and climate resilience. Overall, coupling these multi-omics technologies to modern plant breeding and genetic engineering methods ensures an all-encompassing approach to developing nutritionally-rich and climate-smart crops whose productivity can sustainably and sufficiently meet the current and future food, nutrition and energy demands.

The impact of insecticides and plant extracts on the suppression of insect vector (Bemisia tabaci) of Mungbean yellow mosaic virus (MYMV)

Mungbean yellow mosaic virus (MYMV) is an important constraint in successful production of mungbean (Vigna radiata L.) in many countries, including Pakistan. The MYMV spreads by insect vector whitefly (Bemisia tabaci Gennadius). The use of resistant cultivars is the most effective management tactics for MYMV. Twenty mungbean varieties/lines were screened against insect vector of MYMV under field condition in the current study. Resistance levels for varieties/lines were assessed through visual scoring of typical disease symptoms. Furthermore, the impacts of two insecticides 'Imidacloprid' and 'Thiamethoxam' and two plant extracts, i.e., neem (Azadirachta indica), and Eucalyptus (Eucalyptus camaldulensis) were tested on the suppression of whitefly. Field screening indicated that none of the tested varieties/lines proved immune/highly resistant, while significant variations were recorded among varieties/lines for resistance level. All varieties/lines were systemically infected with MYMV. The varieties 'AARI-2006' and 'Mung-14043' were considered as resistant to MYMV based on visual symptoms and the lowest vector population. These varieties were followed by 'NM-2006' and 'NL-31', which proved as moderately resistant to MYMV. All remaining varieties/lines were grouped as moderately to highly susceptible to MYMV based on visual symptoms' scoring. These results revealed that existing mungbean germplasm do not possess high resistance level MYMV. However, the lines showing higher resistance in the current study must be exploited in breeding programs for the development of resistant mungbean varieties/lines against MYMV. Imidacloprid proved as the most effective insecticide at all concentrations to manage whitefly population. Therefore, use of the varieties with higher resistance level and spraying Imidacloprid could lower the incidence of MYMV.

Advances in Genomics Approaches Shed Light on Crop Domestication

Crop domestication occurred ~10,000–12,000 years ago when humans shifted from a hunter–gatherer to an agrarian society. Crops were domesticated by selecting the traits in wild plant species that were suitable for human use. Research is crucial to elucidate the mechanisms and processes involved in modern crop improvement and breeding. Recent advances in genomics have revolutionized our understanding of crop domestication. In this review, we summarized cutting-edge crop domestication research by presenting its (1) methodologies, (2) current status, (3) applications, and (4) perspectives. Advanced genomics approaches have clarified crop domestication processes and mechanisms, and supported crop improvement.

Genomic interventions for sustainable agriculture

Agricultural production faces a Herculean challenge to feed the increasing global population. Food production systems need to deliver more with finite land and water resources while exerting the least negative influence on the ecosystem. The unpredictability of climate change and consequent changes in pests/pathogens dynamics aggravate the enormity of the challenge. Crop improvement has made significant contributions towards food security, and breeding climate-smart cultivars are considered the most sustainable way to accelerate food production. However, a fundamental change is needed in the conventional breeding framework in order to respond adequately to the growing food demands. Progress in genomics has provided new concepts and tools that hold promise to make plant breeding procedures more precise and efficient. For instance, reference genome assemblies in combination with germplasm sequencing delineate breeding targets that could contribute to securing future food supply. In this review, we highlight key breakthroughs in plant genome sequencing and explain how the presence of these genome resources in combination with gene editing techniques has revolutionized the procedures of trait discovery and manipulation. Adoption of new approaches such as speed breeding, genomic selection and haplotype-based breeding could overcome several limitations of conventional breeding. We advocate that strengthening varietal release and seed distribution systems will play a more determining role in delivering genetic gains at farmer's field. A holistic approach outlined here would be crucial to deliver steady stream of climate-smart crop cultivars for sustainable agriculture.

Breeding, Genetics, and Genomics Approaches for Improving Fusarium Wilt Resistance in Major Grain Legumes

Fusarium wilt (FW) disease is the key constraint to grain legume production worldwide. The projected climate change is likely to exacerbate the current scenario. Of the various plant protection measures, genetic improvement of the disease resistance of crop cultivars remains the most economic, straightforward and environmental-friendly option to mitigate the risk. We begin with a brief recap of the classical genetic efforts that provided first insights into the genetic determinants controlling plant response to different races of FW pathogen in grain legumes. Subsequent technological breakthroughs like sequencing technologies have enhanced our understanding of the genetic basis of both plant resistance and pathogenicity. We present noteworthy examples of targeted improvement of plant resistance using genomics-assisted approaches. In parallel, modern functional genomic tools like RNA-seq are playing a greater role in illuminating the various aspects of plant-pathogen interaction. Further, proteomics and metabolomics have also been leveraged in recent years to reveal molecular players and various signaling pathways and complex networks participating in host-pathogen interaction. Finally, we present a perspective on the challenges and limitations of high-throughput phenotyping and emerging breeding approaches to expeditiously develop FW-resistant cultivars under the changing climate.

Mapping QTL for important seed traits in an interspecific F2 population of pigeonpea

Seed traits present important breeding targets for enhancing grain yield and quality in various grain legume crops including pigeonpea. The present study reports significant genetic variation for six seed traits including seed length (SL), seed width (SW), seed thickness (ST), seed weight (SWT), electrical conductivity (EC) and water uptake (WU) among Cajanus cajan (L.) Millspaugh acc. ICPL 20340 and Cajanus scarabaeoides (L.) Thouars acc. ICP 15739 and an F2 population derived from this interspecific cross. Maximum phenotypic values recorded for the F2 population were higher than observed in the parent ICPL 20340 [F2 max vs ICPL 20340: SW (7.05 vs 5.38), ST (4.63 vs 4.51), EC (65.17 vs 9.72), WU (213.17 vs 109.5)], which suggested contribution of positive alleles from the wild parent, ICP 15739. Concurrently, to identify the QTL controlling these seed traits, we assayed two parents and 94 F2 individuals with 113 polymorphic simple sequence repeat (SSR) markers. In the F2 population, 98 of the 113 SSRs showed Mendelian segregation ratio 1:2:1, whereas significant deviations were observed for 15 SSRs with their χ ² values ranging between 6.26 and 20.62. A partial genetic linkage map comprising 83 SSR loci was constructed. QTL analysis identified 15 marker-trait associations (MTAs) for seed traits on four linkage groups i.e. LG01, LG02, LG04 and LG05. Phenotypic variations (PVs) explained by these QTL ranged from 4.4 (WU) to 19.91% (EC). These genomic regions contributing significantly towards observed variability of seed traits would serve as potential candidates for future research that aims to improve seed traits in pigeonpea.

Grass pea (Lathyrus sativus L.): orphan crop, nutraceutical or just plain food?

Although grass pea is an environmentally successful robust legume with major traits of interest for food and nutrition security, the genetic potential of this orphan crop has long been neglected. Grass pea (Lathyrus sativus L.) is a Neolithic plant that has survived millennia of cultivation and has spread over three continents. It is a robust legume crop that is considered one of the most resilient to climate changes and to be survival food during drought-triggered famines. The hardy penetrating root system allows the cultivation of grass pea in various soil types, including marginal ones. As an efficient nitrogen fixer, it meets its own nitrogen requirements and positively benefits subsequent crops. However, already in ancient India and Greece, overconsumption of the seeds and a crippling neurological disorder, later coined neurolathyrism, had been linked. Overemphasis of their suspected toxic properties has led to disregard the plant's exceptionally positive agronomic properties and dietary advantages. In normal socio-economic and environmental situations, in which grass pea is part of a balanced diet, neurolathyrism is virtually non-existent. The etiology of neurolathyrism has been oversimplified and the deficiency in methionine in the diet has been overlooked. In view of the global climate change, this very adaptable and nutritious orphan crop deserves more attention. Grass pea can become a wonder crop if the double stigma on its reputation as a toxic plant and as food of the poor can be disregarded. Additionally, recent research has exposed the potential of grass pea as a health-promoting nutraceutical. Development of varieties with an improved balance in essential amino acids and diet may be relevant to enhance the nutritional value without jeopardizing the multiple stress tolerance of this promising crop.

Rapid improvement of domestication traits in an orphan crop by genome editing

Genome editing holds great promise for increasing crop productivity, and there is particular interest in advancing breeding in orphan crops, which are often burdened by undesirable characteristics resembling wild relatives. We developed genomic resources and efficient transformation in the orphan Solanaceae crop 'groundcherry' (Physalis pruinosa) and used clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein-9 nuclease (Cas9) (CRISPR-Cas9) to mutate orthologues of tomato domestication and improvement genes that control plant architecture, flower production and fruit size, thereby improving these major productivity traits. Thus, translating knowledge from model crops enables rapid creation of targeted allelic diversity and novel breeding germplasm in distantly related orphan crops.

Improving Salt Tolerance of Chickpea Using Modern Genomics Tools and Molecular Breeding

INTRODUCTION

The high protein value, essential minerals, dietary fibre and notable ability to fix atmospheric nitrogen make chickpea a highly remunerative crop, particularly in low-input food production systems. Of the variety of constraints challenging chickpea productivity worldwide, salinity remains of prime concern owing to the intrinsic sensitivity of the crop. In view of the projected expansion of chickpea into arable and salt-stressed land by 2050, increasing attention is being placed on improving the salt tolerance of this crop. Considerable effort is currently underway to address salinity stress and substantial breeding progress is being made despite the seemingly highly-complex and environment-dependent nature of the tolerance trait.

CONCLUSION

This review aims to provide a holistic view of recent advances in breeding chickpea for salt tolerance. Initially, we focus on the identification of novel genetic resources for salt tolerance via extensive germplasm screening. We then expand on the use of genome-wide and cost-effective techniques to gain new insights into the genetic control of salt tolerance, including the responsive genes/QTL(s), gene(s) networks/cross talk and intricate signalling cascades.

Whole genome sequences in pulse crops: a global community resource to expedite translational genomics and knowledge-based crop improvement

Unprecedented developments in legume genomics over the last decade have resulted in the acquisition of a wide range of modern genomic resources to underpin genetic improvement of grain legumes. The genome enabled insights direct investigators in various ways that primarily include unearthing novel structural variations, retrieving the lost genetic diversity, introducing novel/exotic alleles from wider gene pools, finely resolving the complex quantitative traits and so forth. To this end, ready availability of cost-efficient and high-density genotyping assays allows genome wide prediction to be increasingly recognized as the key selection criterion in crop breeding. Further, the high-dimensional measurements of agronomically significant phenotypes obtained by using new-generation screening techniques will empower reference based resequencing as well as allele mining and trait mapping methods to comprehensively associate genome diversity with the phenome scale variation. Besides stimulating the forward genetic systems, accessibility to precisely delineated genomic segments reveals novel candidates for reverse genetic techniques like targeted genome editing. The shifting paradigm in plant genomics in turn necessitates optimization of crop breeding strategies to enable the most efficient integration of advanced omics knowledge and tools. We anticipate that the crop improvement schemes will be bolstered remarkably with rational deployment of these genome-guided approaches, ultimately resulting in expanded plant breeding capacities and improved crop performance.

Genetics- and genomics-based interventions for nutritional enhancement of grain legume crops: status and outlook

Meeting the food demands and ensuring nutritional security of the ever increasing global population in the face of degrading natural resource base and impending climate change is the biggest challenge of the twenty first century. The consequences of mineral/micronutrient deficiencies or the hidden hunger in the developing world are indeed alarming and need urgent attention. In addressing the problems associated with mineral/micronutrient deficiency, grain legumes as an integral component of the farming systems in the developing world have to play a crucial role. For resource-poor populations, a strategy based on selecting and/or developing grain legume cultivars with grains denser in micronutrients, by biofortification, seems the most appropriate and attractive approach to address the problem. This is evident from the on-going global research efforts on biofortification to provide nutrient-dense grains for use by the poorest of the poor in the developing countries. Towards this end, rapidly growing genomics technologies hold promise to hasten the progress of breeding nutritious legume crops. In conjunction with the myriad of expansions in genomics, advances in other 'omics' technologies particularly plant ionomics or ionome profiling open up novel opportunities to comprehensively examine the elemental composition and mineral networks of an organism in a rapid and cost-effective manner. These emerging technologies would effectively guide the scientific community to enrich the edible parts of grain legumes with bio-available minerals and enhancers/promoters. We believe that the application of these new-generation tools in turn would provide crop-based solutions to hidden hunger worldwide for achieving global nutritional security.