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

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Not AvailableGrain legumes are a key food source for ensuring global food security and sustaining agriculture. However, grain legume production is challenged by growing disease incidence due to global climate change. Ascochyta blight (AB) is a major disease, causing substantial yield losses in grain legumes worldwide. Harnessing the untapped reserve of global grain legume germplasm, landraces, and crop wild relatives (CWRs) could help minimize yield losses caused by AB infection in grain legumes. Several genetic determinants controlling AB resistance in various grain legumes have been identified following classical genetic and conventional breeding approaches. However, the advent of molecular markers, biparental quantitative trait loci (QTL) mapping, genome-wide association studies, genomic resources developed from various genome sequence assemblies, and whole-genome resequencing of global germplasm has revealed AB-resistant gene(s)/QTL/genomic regions/haplotypes on various linkage groups. These genomics resources allow plant breeders to embrace genomics-assisted selection for developing/transferring AB-resistant genomic regions to elite cultivars with great precision. Likewise, advances in functional genomics, especially transcriptomics and proteomics, have assisted in discovering possible candidate gene(s) and proteins and the underlying molecular mechanisms of AB resistance in various grain legumes. We discuss how emerging cutting-edge next-generation breeding tools, such as rapid generation advancement, field-based high-throughput phenotyping tools, genomic selection, and CRISPR/Cas9, could be used for fast-tracking AB-resistant grain legumes to meet the increasing demand for grain legume-based protein diets and thus ensuring global food security.Not Availabl

Breeding approaches and genomics technologies to increase crop yield under low-temperature stress

Alarmingly rising temperature extremities present a substantial impediment to the projected target of 70% more food production by 2050. Low-temperature (LT) stress severely constrains crop production worldwide, thereby demanding an urgent yet sustainable solution. Considerable research progress has been achieved on this front. Here, we review the crucial cellular and metabolic alterations in plants that follow LT stress along with the signal transduction and the regulatory network describing the plant cold tolerance. The significance of plant genetic resources to expand the genetic base of breeding programmes with regard to cold tolerance is highlighted. Also, the genetic architecture of cold tolerance trait as elucidated by conventional QTL mapping and genome-wide association mapping is described. Further, global expression profiling techniques including RNA-Seq along with diverse omics platforms are briefly discussed to better understand the underlying mechanism and prioritize the candidate gene (s) for downstream applications. These latest additions to breeders’ toolbox hold immense potential to support plant breeding schemes that seek development of LT-tolerant cultivars. High-yielding cultivars endowed with greater cold tolerance are urgently required to sustain the crop yield under conditions severely challenged by low-temperature

Genomics enabled breeding approaches for improving cadmium stress tolerance in plants

Heavy metal (HM) toxicity is a considerable challenge that the current agricultural production systems and human population face worldwide. Among the HMs with pronounced toxic effects, cadmium (Cd) potentially contaminates a range of vital agricultural resources including soil and water together with severely impacting crop performance. Besides, gradual accumulation of Cd in food chain poses a global threat to food safety and environmental sustainability. Plants are equipped with meticulously orchestrated physiological and molecular mechanisms to respond and acclimatize to Cd-challenged scenarios. However, limited understanding about the HM toxicity mechanism involving metal uptake/transport, associated candidate gene (s) or QTLs and signaling crosstalk has greatly constrained breeding capacities to improve plants for HM tolerance. In the context, quantifying genetic variation for Cd tolerance accompanied by appropriate breeding schemes allowing the most efficient utilization of the estimated variation should be essentially undertaken. Concurrently, efforts are needed to facilitate fast-track introgression of genomic segments harboring candidate gene(s)/QTL for Cd tolerance to high yielding yet Cd-susceptible backgrounds. Advances in plant molecular biology have introduced refined techniques and methods to pinpoint genetic factors describing plant Cd tolerance. Ancillary to conventional breeding and marker assisted selection methods are modern transgenic technologies that offer attractive means to precisely interrogate the relevant molecular networks and manipulate the key Cd-related genes in plants

Salinity stress response and ‘omics’ approaches for improving salinity stress tolerance in major grain legumes

Grain legume crops are important to global food security being an affordable source of dietary protein and essential mineral nutrients to human population, especially in the developing countries. The global productivity of grain legume crops is severely challenged by the salinity stress particularly in the face of changing climates coupled with injudicious use of irrigation water and improper agricultural land management. Plants adapt to sustain under salinity-challenged conditions through evoking complex molecular mechanisms. Elucidating the underlying complex mechanisms remains pivotal to our knowledge about plant salinity response. Improving salinity tolerance of plants demand enriching cultivated gene pool of grain legume crops through capitalizing on ‘adaptive traits’ that contribute to salinity stress tolerance. Here, we review the current progress in understanding the genetic makeup of salinity tolerance and highlight the role of germplasm resources and omics advances in improving salt tolerance of grain legumes. In parallel, scope of next generation phenotyping platforms that efficiently bridge the phenotyping–genotyping gap and latest research advances including epigenetics is also discussed in context to salt stress tolerance. Breeding salt-tolerant cultivars of grain legumes will require an integrated “omics-assisted” approach enabling accelerated improvement of salt-tolerance traits in crop breeding programs

Enriching nutrient density in staple crops using modern “-Omics” Tools

A sizeable proportion of the global population faces nutritional disorders. Notably, the poorest regions in the developing world share considerably large segment of malnourished people. Given the rising prevalence of nutritional disorders, sustainable solutions urgently need to be in place in order to tackle the menace of hidden hunger. An array of improvement strategies is suggested to meet the growing challenge. These strategies involve dietary diversification, food supplementation/fortification, and biofortification using nutritional breeding approaches, genetic engineering, and agronomic interventions. The mounting concerns about environmental safety and poor economic status of the target population further put a limit on the large-scale use of micronutrient-rich fertilizers. Hence, crop biofortification via conventional and molecular breeding stands to be the most economic, readily accessible, and globally accepted strategy. For some obvious reasons, staple crops that serve the daily dietary needs of the maximum population in the developing world are targeted for nutritional enhancement. As a prerequisite, survey of the germplasm pools is needed to quantify the exploitable genetic variation that exists in the crop gene pool. Further, modern omics approaches like genomics, proteomics, metabolomics, and ionomics will definitely advance our knowledge about the genetic makeup, molecular networks, and physiological alternations involved in the process of mineral accumulation and subsequent partitioning of minerals to edible plant parts. Similarly, engineering metabolic pathways through genetic modification holds great relevance for expediting the development of nutrient-dense food crops. We expect that the “omics” assisted nutritional breeding, as the most potential biofortification strategy, will be greatly helpful in achieving the nutritional security of over two billion nutrient-deficient people worldwide

Integrated “omics” approaches to sustain global productivity of major grain legumes under heat stress

Grain legumes serve as key sources of dietary protein to the global human population. Consequence of high-temperature (HT) stress is increasingly evident as drastically lost production of different crops including grain legumes worldwide, thus putting the global food security under great threat. In a changing climate scenario, cool season-adapted grain legumes frequently encounter heat stress (HS) during their reproductive phase, thus witnessing serious yield losses. To combat the emerging challenges of HT stress, an integrated approach demanding collaborative efforts from various disciplines of plant science should be in place. This review summarizes major impacts of HT stress on grain legume, and captures the relevance of crop genetic resources to HS tolerance in these crops. Measurement of physiological traits assumes key place in view of ever-increasing precision of next-generation phenotyping assays. We also discuss the significance of genetic inheritance and QTL discovery and evolving “omics” science for developing HS tolerance grain legume crops

Advances in “omics” approaches to tackle drought stress in grain legumes

Grain legumes being affordable sources of proteins, vitamins and essential micronutrients are key to human nutrition worldwide. However, frequent drought episodes present serious threat to grain legume production worldwide. Advances in legume omics in concert with evolving phenotyping and breeding techniques hold great promise to improve drought response of these crops. These resources could underpin prebreeding efforts to expedite discovery and deployment of novel drought tolerance traits into elite backgrounds. Fast-track transfer of traits that confer drought tolerance using marker technologies has been demonstrated in grain legumes like chickpea. However, complex genetic architecture of drought tolerance demands embracing more efficient tools like genomic selection (GS) for accelerated trait improvement. Recent studies on GS for addressing complex traits like drought tolerance have yielded encouraging results in these crops. Recently, speed breeding (SB) protocols have also been optimized for the improvement of long-day/day-neutral grain legumes. Efficacy of SB protocols with regard to complex traits awaits further evidences though. There remains immense scope for integrating SB with GS and gene editing to deliver drought-tolerant cultivars

Heat stress in crop plants: Its nature, impacts and integrated breeding strategies to improve heat tolerance

Increasing severity of high temperature worldwide presents an alarming threat to the humankind. As evident by massive yield losses in various food crops, the escalating adverse impacts of heat stress (HS) are putting the global food as well as nutritional security at great risk. Intrinsically, plants respond to high temperature stress by triggering a cascade of events and adapt by switching on numerous stress-responsive genes. However, the complex and poorly understood mechanism of heat tolerance (HT), limited access to the precise phenotyping techniques, and above all, the substantial G × E effects offer major bottlenecks to the progress of breeding for improving HT. Therefore, focus should be given to assess the crop diversity, and targeting the adaptive/morpho-physiological traits while making selections. Equally important is the rapid and precise introgression of the HT-related gene(s)/QTLs to the heat-susceptible cultivars to recover the genotypes with enhanced HT. Therefore, the progressive tailoring of the heat-tolerant genotypes demands a rational integration of molecular breeding, functional genomics and transgenic technologies reinforced with the next-generation phenomics facilities

Analysis of an intraspecific RIL population uncovers genomic segments harbouring multiple QTL for seed relevant traits in lentil (Lens culinaris L.)

Improving seed related traits remains key objective in lentil breeding. In recent years, genomic resources have shown great promise to accelerate crop improvement. However, limited genomic resources in lentil greatly restrict the use of genomics assisted breeding. The present investigation aims to build an intraspecific genetic linkage map and identify the QTL associated with important seed relevant traits using 94 recombinant inbreds (WA 8649090 × Precoz). A total of 288 polymorphic DNA markers including simple sequence repeat (SSR), inter simple sequence repeat (ISSR) and random amplified polymorphic DNA (RAPD) were assayed on mapping population. The resultant genetic linkage map comprised 220 loci spanning 604.2 cM of the lentil genome, with average inter-marker distance of 2.74 cM. QTL mapping in this RIL population uncovered a total of 18 QTL encompassing nine major and nine minor QTL. All major QTL were detected for seed related traits viz., seed diameter (SD), seed thickness (ST), seed weight (SW) and seed plumpness (SP) across two locations. A considerable proportion of the phenotypic variation (PV) was accounted to these QTL. For instance, one major QTL on LG5 controlling SW (QTL 15) explained 50% PV in one location, while the same QTL accounted for 34.18% PV in other location. Importantly, the genomic region containing multiple QTL for different seed traits was mapped to a 17-cM region on LG5. The genomic region harbouring QTL for multiple traits opens up exciting opportunities for genomics assisted improvement of lentil