Abhishek Bohra

Biotic stresses compromise grain legume production worldwide. Deployment of the resistant varieties of grain legume crops that can withstand high disease/pest pressures is the straightforward and sustainable approach for stress management. A high resistance level of crop plants not only reduces the overall production costs but also poses no or little risk to the environment. Modern genomic technologies have deepened our understanding of the genetic determinants governing a plant’s resistance to diseases and pests and plant–pathogen/pest interactions. In-depth knowledge of the plant stress response would help devise sustainable strategies for management of biotic stresses in legume crops. The growing DNA sequence information on large germplasm collections and experimental populations of legume crops expands our capacity to characterize and utilize the untapped diversity of plant traits that confer resistance to major biotic stresses. Advanced systems have helped relieve the long-standing “phenotyping bottleneck” through imparting precision, accuracy, high throughput, and cost-effectiveness to the plant phenotyping procedures. The wealth of genetic sequence information, large-scale screening data, and multi-omics datasets available opens new avenues for identification and validation of target genomic regions and associated superior haplotypes for introgression breeding and gene editing. Successful application of the clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas) system in model legumes (e.g., Medicago truncatula, Lotus japonicus, soybean) holds great promise for further extending the modern gene editing technology to other grain legume crops for improving stress responses, with emergence of new ways to overcome their transformation recalcitrance. The haplotype catalogues and trait packages for biotic stress tolerance derived from growing genetic sequence and plant phenotyping data, when integrated with refined introgression approaches, provide breeders with an unprecedented resource for rapidly modifying plant traits to overcome stressful conditions.

Climate change threatens our global crop production capacity and jeopardizes our ability to achieve the food security targets. To feed the global population in the next two decades, crop production needs to double in resource‐constrained agricultural settings amid growing climate uncertainties. Enhanced adoption of cutting‐edge genomic technologies and crop breeding strategies will be crucial to achieve sustainable stress management, besides non‐genetic means and optimized agronomic management practices. Also, diversification of farming systems, improved delivery systems, and reduced post‐harvest losses will contribute to realize the potential of new crop technologies in stressed environments. Forging international collaborations involving multidisciplinary research teams is imperative to bridge the crop performance gap between experimental settings and farmers’ fields.

Pigeonpea is an important food legume crop of semi-arid tropics. The ability to perform better in marginal environments renders this crop highly attractive for low-input farming systems. Pigeonpea has received limited attention with respect to the development of genomic resources. Nevertheless, the last decade has witnessed a remarkable rise in pigeonpea genomics, transforming pigeonpea from a “genomic orphan” to a crop that now enjoys availability of next generation genomic resources including reference genome sequence, whole-genome resequencing (WGRS) data sets and a pangenome. The availability of reference genome sequences in combination with NGS-based genotyping protocols and high-density SNP arrays has helped elucidate the genetic architectures of important agronomic traits in pigeonpea. High-resolution mapping of traits has been achieved following phenotyping of wider germplasm sets with sequenced genomes. In this context, more efficient designs such as MAGIC and NAM have been made available for trait discovery. Gene-level resolution of genetic architectures will be crucial to enable targeted manipulation. In parallel, efforts are underway to improve genetic gains in pigeonpea breeding programme through accelerating generation turnover. Growing WGRS data sets of comprehensive germplasm collections pave the way for deployment of new breeding approaches like haplotype-based breeding and genome-wide predictions to expeditiously breed modern pigeonpea cultivars to ensure nutritious food for burgeoning population worldwide.

Legume crops are important to global food security and sustainability of agricultural systems. However, low and unstable yield of grain legumes as compared to cereals has been a major bottleneck in the expansion of cultivation area in these crops. The past two decades have witnessed remarkable growth in genomics-derived improvement in most of the crop species including legumes. Genomics-assisted approaches have enabled the fast-track development of varieties with agriculturally important traits in these crops. Further the search of more efficient and accurate methods has opened avenues for genomic selection (GS) implementation in crop improvement programs. Initial reports on GS in legumes are encouraging, and these studies are guiding researchers for optimal resource utilization for enhancing prediction ability of line performance. Efforts to shorten long generation time through optimization of rapid generation technologies (RGT) in legumes have further enhanced the ability of genomics-based crop improvement. Legume crops such as pigeonpea and soybean are also exploiting heterosis to boost yield gains. In this regard, genomics advances have been made to support hybrid breeding efforts in these crops. Further, new strategies like sequence-based breeding have been proposed which efficiently combine population improvement with GS and genome-wide association (GWAS). In this chapter, we summarize the major breakthroughs in legume genomics and molecular breeding. This is accompanied by a brief discussion on recent cases that apply GS and speed breeding in grain legumes. We conclude this chapter by highlighting future scope and limitations of adopting new genomics and breeding tools for shaping legume improvement.

Increasing food demand, with the burgeoning population worldwide is reaching an alarming condition along with depleting resources and unpredictable climatic vagaries. Thus, twenty-first century agriculture is facing a daunting task of developing high-yielding and multiple stress tolerant plants to ensure food security. Thus, in-depth analysis of crop stress response is essentially required. Therefore, linking phenomics with crop breeding programs can fill the gap between complex targeted traits and genotypic responses. Phenotyping ensures reliable data for predicted trait, during identification and selection of improved varieties in conventional breeding programs. Besides this, high-throughput phenotyping helps in delineating phenotypic and genotypic associations along with characterization of potential genomic regions for forward genetics in molecular breeding. Recent advancements in high-throughput automated imaging techniques provide huge amount of data and high-resolution images. To make precise decisions, specific tools are required to disentangle this huge array of data. We uncovered here a comprehensive overview of (1) phenomic techniques for climate smart agriculture, (2) association between breeding and phenomics, and (3) strategies for big data analysis for crop improvement programs. To conclude, automated plant phenotyping techniques are precise tools for in-depth analysis and identification of traits responsible for crop improvement.

Grain legumes are a key source for human nutrition and animal feed in the world. Also, these crops are important to support sustainable, low-input, and diverse farming systems. Efforts to improve legume crop yields have delivered modest outcomes. Increasing the productivity of these crops in an increasingly challenging environment with dwindling natural resources such as land and water demands the immediate incorporation of breakthrough technologies in crop breeding programs. A variety of genomic technologies in combination with modern breeding designs are now in place to optimize strategies for accelerated legume crop improvement. The current genomic arsenal of these grain legume crops includes reference genome assemblies and resequenced genomes, high-density molecular markers and genome maps, and a variety of genes/QTLs controlling agriculturally important traits. Innovative breeding techniques such as genomic selection and speed breeding that significantly reduce the breeding cycle time have been optimized in legume crops to improve breeding outcomes. The continuous decline in sequencing costs has paved the way for adopting sequence-based breeding to improve the breeding populations and varietal development. In this chapter, we highlight the recent genomic advances made in three major semiarid tropic (SAT) grain legume crops, that is, chickpea, pigeonpea, and groundnut. We follow with a discussion on how these technological advances have been translated into molecular breeding products in these crops. The chapter also explores opportunities to adopt modern breeding techniques to hasten the rate of genetic gains in these crops.

Pigeonpea is an important food legume crop for rainfed agriculture in developing countries, particularly in India. Productivity gains in pigeonpea have remained static, and the challenge of improving pigeonpea yield is further aggravated by increasingly uncertain climatic conditions. Improved pigeonpea cultivars with favourable traits, allowing them to cope with climatic adversities, are urgently required. Modern genomic technologies have the potential to rapidly improve breeding traits that confer resistance to biotic and abiotic stresses. Recent advances in pigeonpea genomics have led to the development of large-scale genomic tools to accelerate breeding programs. Availability of high-density genotyping assays and high-throughput phenotyping platforms motivate researchers to adopt new breeding techniques like genomic selection (GS) for improving complex traits. Accurate GS predictions inferred from multilocation and multiyear data sets also open new avenues for ‘remote breeding’ which is very much required to achieve genotype selection for future climates. Speed breeding pigeonpea with deployment of rapid generation advancement (RGA) technologies will improve our capacity to breed cultivars endowed with resilient traits. Once such climate-resilient cultivars are in place, their rapid dissemination to farmer’s fields will be required to witness the real impact. Equally important will be the acceleration of varietal turnover to keep pace with the unpredictably changing climatic conditions so that cultivars are constantly optimized for the climatic conditions at any given time.

Micronutrient deficiencies are reported to affect more than two billion people worldwide. Importantly, people inhabiting rural and semi-urban areas are more vulnerable to these nutritional disorders. In view of the inadequacy of nutrition-specific approaches that rely on changing the food-consumption behaviour, nutrition-sensitive interventions like crop biofortification offer sustainable means to address the problem of malnutrition worldwide. Biofortification enhances nutrient density in crop plants during plant growth through genetic or agronomic practices. Traditional plant breeding techniques and genetic engineering approaches are key to crop biofortification. Here, we summarize recent advances in genomics that have contributed towards the progress of crop biofortification. Rapidly evolving technologies like high-density genotyping assays have accelerated harnessing gains associated with natural variation of mineral contents available in crop wild relatives and landraces. The genetic nature of the mineral composition is being resolved, thus furthering the understanding of trait architecture. Conventional QTL mapping techniques have made significant contribution towards this end. New molecular breeding techniques like genome-wide association study (GWAS) and genomic selection (GS) are opening new avenues for capturing the maximum variation for elemental content, majorly explained by small-effect QTL. The potential of GS in this respect is enhanced several fold with the increasing availability of rapid generation advancement systems and high-throughput elemental profiling platforms. Evidences from latest research involving cutting-edge omics techniques including metabolomics help better elucidate nutrient metabolism in plants. Increasing the efficiency of biofortification breeding could enhance the rate of delivery of nutritionally rich cultivars of food crops, which will be easily accessible to a larger segment of nutrient-deficient people in the most cost-efficient way.

Chickpea is a well-recognized global grain legume that plays an important role for providing plant-based protein security to global human population. Given the rising uncertainties in global climate coupled with growing occurrence of various pests and diseases and a range of abiotic stresses, global chickpea production is seriously challenged. Therefore, conventional breeding approaches are not adequate to meet the rising demand for chickpea. Evolving genomic technologies have yielded considerable success in accelerating molecular breeding program in various crops. To this end, unprecedented advances in genome sequencing technologies facilitated largely by next-generation sequencing (NGS) technologies have allowed decoding of whole genome sequences of both cultivated and wild species of chickpea. These developments have opened up great opportunity to improve the efficiency of chickpea breeding programs through deployment of large-scale genomic tools. Efforts are underway to re-sequence multiple genomes for identifying new haplotypes of traits of breeding importance in the crop from wider germplasm resources such as the core collection and reference sets. Taken together, these massive genomic resources including the high-density genotyping assays have allowed chickpea breeders to embrace modern breeding techniques like genomic selection (GS) for enhancing genetic gain. This chapter focuses on the genomics-assisted improvement of chickpea, with an emphasis on the traits that impart resilience to changing climate. In addition to genomics, we highlight progress and possibilities of transgenic research for improving tolerance against biotic and abiotic stress resistance in chickpea. Moreover, the introduction of novel breeding schemes such as “speed breeding”, CRISPR/Cas9-based genome editing holds great promise for accelerating the genetic gains projected to meet the ever-increasing demand for plant-based proteins.

Pigeonpea owing to its ability to sustain harsh environment and limited input/water requirement remains an excellent remunerative crop in the face of increasing climatic adversities. With nearly 70% share in global pigeonpea production, India is the leading pigeonpea producing country. Since the mid-1900s, constant research efforts directed to improve yield and resistance levels of pigeonpea have resulted in the development and deployment of several commercially accepted cultivars in India, accommodating into diverse agro-climatic zones. However, the crop productivity needs incremental improvements in order to meet the growing nutritional demands, especially in developing countries like India where pigeonpea forms a dominant part of vegetarian diet. Empowering crop improvement strategies with genomic tool kit is imperative to attain the project gains in crop yield. In the context, adoption of next-generation sequencing (NGS) technology has helped establish a wide range of genomic resources to support pigeonpea breeding, and the existing molecular tool kit includes genome-wide genetic markers, transcriptome/genome assemblies, and candidate genes/QTLs for target traits. Similarly, availability of whole mitochondrial genome sequence and derived DNA markers is immensely relevant in order to furthering the understanding of cytoplasmic male sterility (CMS) system and hybrid breeding. This chapter covers the progress of developing modern genomic resources in pigeonpea and highlights their vital role in designing future crop breeding schemes.