QTL Mapping of Genome Regions Controlling Manganese Uptake in Lentil Seed

Integrated breeding approaches to enhance the nutritional quality of food legumes

Global food security, both in terms of quantity and quality remains as a challenge with the increasing population. In parallel, micronutrient deficiency in the human diet leads to malnutrition and several health-related problems collectively known as "hidden hunger" more prominent in developing countries around the globe. Biofortification is a potential tool to fortify grain legumes with micronutrients to mitigate the food and nutritional security of the ever-increasing population. Anti-nutritional factors like phytates, raffinose (RFO's), oxalates, tannin, etc. have adverse effects on human health upon consumption. Reduction of the anti-nutritional factors or preventing their accumulation offers opportunity for enhancing the intake of legumes in diet besides increasing the bioavailability of micronutrients. Integrated breeding methods are routinely being used to exploit the available genetic variability for micronutrients through modern "omic" technologies such as genomics, transcriptomics, ionomics, and metabolomics for developing biofortified grain legumes. Molecular mechanism of Fe/Zn uptake, phytate, and raffinose family oligosaccharides (RFOs) biosynthesis pathways have been elucidated. Transgenic, microRNAs and genome editing tools hold great promise for designing nutrient-dense and anti-nutrient-free grain legumes. In this review, we present the recent efforts toward manipulation of genes/QTLs regulating biofortification and Anti-nutrient accumulation in legumes using genetics-, genomics-, microRNA-, and genome editing-based approaches. We also discuss the success stories in legumes enrichment and recent advances in development of low Anti-nutrient lines. We hope that these emerging tools and techniques will expedite the efforts to develop micronutrient dense legume crop varieties devoid of Anti-nutritional factors that will serve to address the challenges like malnutrition and hidden hunger.

Estimating genetic variability among diverse lentil collections through novel multivariate techniques

Lentil is an important food legume throughout the world and Pakistan stands at 18^th position with 8,610 tons production from 17,457 hectares. It is rich in protein, carbohydrates, fat, fiber, and minerals that can potentially meet food security and malnutrition issues, particularly in South Asia. Two hundred and twenty lentil genotypes representing Pakistan (178), Syria (14), and the USA (22) including 6 from unknown origins were studied for yield, yield contributing traits, and cooking time (CT). Genotype 6122 (Pakistan) performed the best during both years with seed yield per plant (SY) 68±1.7 g, biological yield per plant (BY) 264±2.8 g, pod size (PS) 0.61±0.01 cm, number of seeds per pod (NSP) 2, cooking time (CT) 11 minutes, with no hard seed (HS). The genotypes 6122 (Pakistan) and 6042 (Syria) produced the highest BY, hence these have the potential to be an efficient source of fodder, particularly during extreme winter months. The genotypes 5698 (Pakistan) and 6015 (USA) were late in maturity during 2018–19 while 24783 and 5561 matured early in 2019. A minimum CT of 10 minutes was taken by the genotypes 6074 and 5745 of Pakistani origin. The lowest CT saves energy, time, and resources, keeps flavor, texture, and improves protein digestibility, hence the genotypes with minimum CT are recommended for developing better lentil cultivars. Pearson correlation matrix revealed significant association among several traits, especially SY with BY, PS, and NSP which suggests their use for the future crop improvement program. The PCA revealed a considerable reduction in components for the selection of suitable genotypes with desired traits that could be utilized for future lentil breeding. Structural Equational Model (SEM) for SY based on covariance studies indicated the perfect relationship among variables. Further, hierarchical cluster analysis establishes four clusters for 2017–18, whereas seven clusters for 2018–19. Cluster 4 of 2017–18 and cluster 5 of 2018–19 exhibited the genotypes with the best performance for most of the traits (SY, BY, PS, NSP, CT, and HS). Based on heritability; HSW, SY, BY, NSP were highly heritable, hence these traits are expected for selecting genotypes with genes of interest and for future lentil cultivars. In conclusion, 10 genotypes (5664, 5687, 6084, 6062, 6122, 6058, 6087, 5689, 6042 and 6074) have been suggested to evaluate under multi-location environments for selection of the best one/s or could be utilized in hybridization in future lentil breeding programs.

Omics Path to Increasing Productivity in Less-Studied Crops Under Changing Climate-Lentil a Case Study

Conventional breeding techniques for crop improvement have reached their full potential, and hence, alternative routes are required to ensure a sustained genetic gain in lentils. Although high-throughput omics technologies have been effectively employed in major crops, less-studied crops such as lentils have primarily relied on conventional breeding. Application of genomics and transcriptomics in lentils has resulted in linkage maps and identification of QTLs and candidate genes related to agronomically relevant traits and biotic and abiotic stress tolerance. Next-generation sequencing (NGS) complemented with high-throughput phenotyping (HTP) technologies is shown to provide new opportunities to identify genomic regions and marker-trait associations to increase lentil breeding efficiency. Recent introduction of image-based phenotyping has facilitated to discern lentil responses undergoing biotic and abiotic stresses. In lentil, proteomics has been performed using conventional methods such as 2-D gel electrophoresis, leading to the identification of seed-specific proteome. Metabolomic studies have led to identifying key metabolites that help differentiate genotypic responses to drought and salinity stresses. Independent analysis of differentially expressed genes from publicly available transcriptomic studies in lentils identified 329 common transcripts between heat and biotic stresses. Similarly, 19 metabolites were common across legumes, while 31 were common in genotypes exposed to drought and salinity stress. These common but differentially expressed genes/proteins/metabolites provide the starting point for developing high-yielding multi-stress-tolerant lentils. Finally, the review summarizes the current findings from omic studies in lentils and provides directions for integrating these findings into a systems approach to increase lentil productivity and enhance resilience to biotic and abiotic stresses under changing climate.

Intelligent Characterization of Lentil Genetic Resources: Evolutionary History, Genetic Diversity of Germplasm, and the Need for Well-Represented Collections

The genetic and phenotypic characterization of crops allows us to elucidate their evolutionary and domestication history, the genetic basis of important traits, and the use of variation present in landraces and wild relatives to enhance resilience. In this context, we aim to provide an overview of the main genetic resources developed for lentil and their main outcomes, and to suggest protocols for continued work on this important crop. Lens culinaris is the third-most-important cool-season grain and its use is increasing as a quick-cooking, nutritious, plant-based source of protein. L. culinaris was domesticated in the Fertile Crescent, and six additional wild taxa (L. orientalis, L. tomentosus, L. odemensis, L. lamottei, L. ervoides, and L. nigricans) are recognized. Numerous genetic diversity studies have shown that wild relatives present high levels of genetic variation and provide a reservoir of alleles that can be used for breeding programs. Furthermore, the integration of genetics/genomics and breeding techniques has resulted in identification of quantitative trait loci and genes related to attributes of interest. Genetic maps, massive genotyping, marker-assisted selection, and genomic selection are some of the genetic resources generated and applied in lentil. In addition, despite its size (∼4 Gbp) and complexity, the L. culinaris genome has been assembled, allowing a deeper understanding of its architecture. Still, major knowledge gaps exist in lentil, and a deeper understanding and characterization of germplasm resources, including wild relatives, is critical to lentil breeding and improvement. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Recording of lentil seed descriptors Basic Protocol 2: Lentil seed imaging Basic Protocol 3: Lentil seed increase Basic Protocol 4: Recording of primary lentil seed INCREASE descriptors.

Enhancing the Nutritional Quality of Major Food Crops Through Conventional and Genomics-Assisted Breeding

Nutritional stress is making over two billion world population malnourished. Either our commercially cultivated varieties of cereals, pulses, and oilseed crops are deficient in essential nutrients or the soils in which these crops grow are becoming devoid of minerals. Unfortunately, our major food crops are poor sources of micronutrients required for normal human growth. To overcome the problem of nutritional deficiency, greater emphasis should be laid on the identification of genes/quantitative trait loci (QTLs) pertaining to essential nutrients and their successful deployment in elite breeding lines through marker-assisted breeding. The manuscript deals with information on identified QTLs for protein content, vitamins, macronutrients, micro-nutrients, minerals, oil content, and essential amino acids in major food crops. These QTLs can be utilized in the development of nutrient-rich crop varieties. Genome editing technologies that can rapidly modify genomes in a precise way and will directly enrich the nutritional status of elite varieties could hold a bright future to address the challenge of malnutrition.

Manganese in the Diet: Bioaccessibility, Adequate Intake, and Neurotoxicological Effects

Manganese (Mn) is an essential element that participates in several biological processes. Mn serves as a cofactor for several enzymes, such as glutamine synthetase and oxidoreductases, that have an important role in the defense of the organisms against oxidative stress. The diet is the main source of Mn intake for humans, and adequate daily intake levels for this metal change with age. Moreover, in higher amounts, Mn may be toxic, mainly to the brain. Here, we provide an overview of Mn occurrence in food, addressing its bioaccessibility and discussing the dietary standard and recommended intake of Mn consumption. In addition, we review some mechanisms underlying Mn-induced neurotoxicity.

Genome-Wide SNP Identification and Association Mapping for Seed Mineral Concentration in Mung Bean (Vigna radiata L.)

Mung bean (Vigna radiata L.) quality is dependent on seed chemical composition, which in turn determines the benefits of its consumption for human health and nutrition. While mung bean is rich in a range of nutritional components, such as protein, carbohydrates and vitamins, it remains less well studied than other legume crops in terms of micronutrients. In addition, mung bean genomics and genetic resources are relatively sparse. The objectives of this research were three-fold, namely: to develop a genome-wide marker system for mung bean based on genotyping by sequencing (GBS), to evaluate diversity of mung beans available to breeders in the United States and finally, to perform a genome-wide association study (GWAS) for nutrient concentrations based on a seven mineral analysis using inductively coupled plasma (ICP) spectroscopy. All parts of our research were performed with 95 cultivated mung bean genotypes chosen from the USDA core collection representing accessions from 13 countries. Overall, we identified a total of 6,486 high quality single nucleotide polymorphisms (SNPs) from the GBS dataset and found 43 marker × trait associations (MTAs) with calcium, iron, potassium, manganese, phosphorous, sulfur or zinc concentrations in mung bean grain produced in either of two consecutive years' field experiments. The MTAs were scattered across 35 genomic regions explaining on average 22% of the variation for each seed nutrient in each year. Most of the gene regions provided valuable candidate loci to use in future breeding of new varieties of mung bean and further the understanding of genetic control of nutritional properties in the crop. Other SNPs identified in this study will serve as important resources to enable marker-assisted selection (MAS) for nutritional improvement in mung bean and to analyze cultivars of mung bean.

Legume biofortification is an underexploited strategy for combatting hidden hunger

Legumes are the world's primary source of dietary protein and are particularly important for those in developing economies. However, the biofortification potential of legumes remains underexploited. Legumes offer a diversity of micronutrients and amino acids, exceeding or complementing the profiles of cereals. As such, the enhancement of legume nutritional composition presents an appealing target for addressing the "hidden hunger" of global micronutrient malnutrition. Affecting ~2 billion people, micronutrient malnutrition causes severe health effects ranging from stunted growth to reduced lifespan. An increased availability of micronutrient-enriched legumes, particularly to those in socio-economically deprived areas, would serve the dual functions of ameliorating hidden hunger and increasing the positive health effects associated with legumes. Here, we give an updated overview of breeding approaches for the nutritional improvement of legumes, and crucially, we highlight the importance of considering nutritional improvement in a wider ecological context. Specifically, we review the potential of the legume microbiome for agronomic trait improvement and highlight the need for increased genetic, biochemical, and environmental data resources. Finally, we state that such resources should be complemented by an international and multidisciplinary initiative that will drive crop improvement and, most importantly, ensure that research outcomes benefit those who need them most.