The AVRDC - The World Vegetable Center mungbean (Vigna radiata) core and mini core collections

Deciphering PDH1's role in mung bean domestication: a genomic perspective on pod dehiscence

Mung bean (Vigna radiata) stands as a crucial legume crop in Asia, contributing to food security. However, our understanding of the underlying genetic foundation governing domesticated agronomic traits, especially those linked to pod architecture, remains largely unexplored. In this study, we delved into the genomic divergence between wild and domesticated mung bean varieties, leveraging germplasm obtained from diverse sources. Our findings unveiled pronounced variation in promoter regions (35%) between the two mung bean subpopulations, suggesting substantial changes in gene expression patterns during domestication. Leveraging transcriptome analysis using distinct reproductive stage pods and subpopulations, we identified candidate genes responsible for pod and seed architecture development, along with Genome-Wide Association Studies (GWAS) and Quantitative Trait Locus (QTL) analysis. Notably, our research conclusively confirmed PDH1 as a parallel domesticated gene governing pod dehiscence in legumes. This study imparts valuable insights into the genetic underpinnings of domesticated agronomic traits in mung bean, and simultaneously highlighting the parallel domestication of pivotal traits within the realm of legume crops.

Genetic diversity and candidate genes for transient waterlogging tolerance in mungbean at the germination and seedling stages

Mungbean [Vigna radiata var. radiata (L.) Wilczek] production in Asia is detrimentally affected by transient soil waterlogging caused by unseasonal and increasingly frequent extreme precipitation events. While mungbean exhibits sensitivity to waterlogging, there has been insufficient exploration of germplasm for waterlogging tolerance, as well as limited investigation into the genetic basis for tolerance to identify valuable loci. This research investigated the diversity of transient waterlogging tolerance in a mini-core germplasm collection of mungbean and identified candidate genes for adaptive traits of interest using genome-wide association studies (GWAS) at two critical stages of growth: germination and seedling stage (i.e., once the first trifoliate leaf had fully-expanded). In a temperature-controlled glasshouse, 292 genotypes were screened for tolerance after (i) 4 days of waterlogging followed by 7 days of recovery at the germination stage and (ii) 8 days of waterlogging followed by 7 days of recovery at the seedling stage. Tolerance was measured against drained controls. GWAS was conducted using 3,522 high-quality DArTseq-derived SNPs, revealing five significant associations with five phenotypic traits indicating improved tolerance. Waterlogging tolerance was positively correlated with the formation of adventitious roots and higher dry masses. FGGY carbohydrate kinase domain-containing protein was identified as a candidate gene for adventitious rooting and mRNA-uncharacterized LOC111241851, Caffeoyl-CoA O-methyltransferase At4g26220 and MORC family CW-type zinc finger protein 3 and zinc finger protein 2B genes for shoot, root, and total dry matter production. Moderate to high broad-sense heritability was exhibited for all phenotypic traits, including seed emergence (81%), adventitious rooting (56%), shoot dry mass (81%), root dry mass (79%) and SPAD chlorophyll content (70%). The heritability estimates, marker-trait associations, and identification of sources of waterlogging tolerant germplasm from this study demonstrate high potential for marker-assisted selection of tolerance traits to accelerate breeding of climate-resilient mungbean varieties.

Genome-wide association studies for phenological and agronomic traits in mungbean (Vigna radiata L. Wilczek)

Mungbean (Vigna radiata L. Wilczek) is one of the important warm-season food legumes, contributing substantially to nutritional security and environmental sustainability. The genetic complexity of yield-associated agronomic traits in mungbean is not well understood. To dissect the genetic basis of phenological and agronomic traits, we evaluated 153 diverse mungbean genotypes for two phenological (days to heading and days to maturity) and eight agronomic traits (leaf nitrogen status using SPAD, plant height, number of primary branches, pod length, number of pods per plant, seeds per pod, 100-seed weight, and yield per plant) under two environmental conditions. A wide array of phenotypic variability was apparent among the studied genotypes for all the studied traits. The broad sense of heritability of traits ranged from 0.31 to 0.95 and 0.21 to 0.94 at the Delhi and Ludhiana locations, respectively. A total of 55,634 genome-wide single nucleotide polymorphisms (SNPs) were obtained by the genotyping-by-sequencing method, of which 15,926 SNPs were retained for genome-wide association studies (GWAS). GWAS with Bayesian information and linkage-disequilibrium iteratively nested keyway (BLINK) model identified 50 SNPs significantly associated with phenological and agronomic traits. In total, 12 SNPs were found to be significantly associated with phenological traits across environments, explaining 7%-18.5% of phenotypic variability, and 38 SNPs were significantly associated with agronomic traits, explaining 4.7%-27.6% of the phenotypic variability. The maximum number of SNPs (15) were located on chromosome 1, followed by seven SNPs each on chromosomes 2 and 8. The BLAST search identified 19 putative candidate genes that were involved in light signaling, nitrogen responses, phosphorus (P) transport and remobilization, photosynthesis, respiration, metabolic pathways, and regulating growth and development. Digital expression analysis of 19 genes revealed significantly higher expression of 12 genes, viz. VRADI01G08170, VRADI11G09170, VRADI02G00450, VRADI01G00700, VRADI07G14240, VRADI03G06030, VRADI02G14230, VRADI08G01540, VRADI09G02590, VRADI08G00110, VRADI02G14240, and VRADI02G00430 in the roots, cotyledons, seeds, leaves, shoot apical meristems, and flowers. The identified SNPs and putative candidate genes provide valuable genetic information for fostering genomic studies and marker-assisted breeding programs that improve yield and agronomic traits in mungbean.

Demographic history and distinct selection signatures of two domestication genes in mungbean

Domestication is the long and complex process underlying the evolution of crops, in which artificial directional selection transformed wild progenitors into the desired form, affecting genomic variation and leaving traces of selection at targeted loci. However, whether genes controlling important domestication traits follow the same evolutionary pattern expected under the standard selective sweep model remains unclear. With whole-genome resequencing of mungbean (Vigna radiata), we investigated this issue by resolving its global demographic history and targeted dissection of the molecular footprints of genes underlying 2 key traits representing different stages of domestication. Mungbean originated in Asia, and the Southeast Asian wild population migrated to Australia about 50 thousand generations ago. Later in Asia, the cultivated form diverged from the wild progenitor. We identified the gene associated with the pod shattering resistance trait, VrMYB26a, with lower expression across cultivars and reduced polymorphism in the promoter region, reflecting a hard selective sweep. On the other hand, the stem determinacy trait was associated with VrDet1. We found that 2 ancient haplotypes of this gene have lower gene expression and exhibited intermediate frequencies in cultivars, consistent with selection favoring independent haplotypes in a soft selective sweep. In mungbean, contrasting signatures of selection were identified from the detailed dissection of 2 important domestication traits. The results suggest complex genetic architecture underlying the seemingly simple process of directional artificial selection and highlight the limitations of genome-scan methods relying on hard selective sweeps.

Genome-wise association study identified genomic regions associated with drought tolerance in mungbean (Vigna radiata (L.) R. Wilczek)

A total of 282 mungbean accessions were resequenced to identify genome-wide variants and construct a highly precise variant map, and drought tolerance-related loci and superior alleles were identified by GWAS. Mungbean (Vigna radiata (L.) R. Wilczek) is an important food legume crop that is highly adapted to drought environments, but severe drought significantly curtails mungbean production. Here, we resequenced 282 mungbean accessions to identify genome-wide variants and constructed a highly precise map of mungbean variants. A genome-wide association study was performed to identify genomic regions for 14 drought tolerance-related traits in plants grown under stress and well-watered conditions over three years. One hundred forty-six SNPs associated with drought tolerance were detected, and 26 candidate loci associated with more than two traits were subsequently selected. Two hundred fifteen candidate genes were identified at these loci, including eleven transcription factor genes, seven protein kinase genes and other protein coding genes that may respond to drought stress. Furthermore, we identified superior alleles that were associated with drought tolerance and positively selected during the breeding process. These results provide valuable genomic resources for molecular breeding and will accelerate future efforts aimed at mungbean improvement.

Mining legume germplasm for genetic gains: An Indian perspective

Legumes play a significant role in food and nutritional security and contribute to environmental sustainability. Although legumes are highly beneficial crops, it has not yet been possible to enhance their yield and production to a satisfactory level. Amid a rising population and low yield levels, per capita average legume consumption in India has fallen by 71% over the last 50 years, and this has led to protein-related malnutrition in a large segment of the Indian population, especially women and children. Several factors have hindered attempts to achieve yield enhancement in grain legumes, including biotic and abiotic pressures, a lack of good ideotypes, less amenability to mechanization, poorer responsiveness to fertilizer input, and a poor genetic base. Therefore, there is a need to mine the approximately 0.4 million ex situ collections of legumes that are being conserved in gene banks globally for identification of ideal donors for various traits. The Indian National Gene Bank conserves over 63,000 accessions of legumes belonging to 61 species. Recent initiatives have been undertaken in consortia mode with the aim of unlocking the genetic potential of ex situ collections and conducting large-scale germplasm characterization and evaluation analyses. We assume that large-scale phenotyping integrated with omics-based science will aid the identification of target traits and their use to enhance genetic gains. Additionally, in cases where the genetic base of major legumes is narrow, wild relatives have been evaluated, and these are being exploited through pre-breeding. Thus far, >200 accessions of various legumes have been registered as unique donors for various traits of interest.

Nutritional, functional, and bioactive properties of african underutilized legumes

Globally, legumes are vital constituents of diet and perform critical roles in maintaining well-being owing to the dense nutritional contents and functional properties of their seeds. While much emphasis has been placed on the major grain legumes over the years, the neglected and underutilized legumes (NULs) are gaining significant recognition as probable crops to alleviate malnutrition and give a boost to food security in Africa. Consumption of these underutilized legumes has been associated with several health-promoting benefits and can be utilized as functional foods due to their rich dietary fibers, vitamins, polyunsaturated fatty acids (PUFAs), proteins/essential amino acids, micro-nutrients, and bioactive compounds. Despite the plethora of nutritional benefits, the underutilized legumes have not received much research attention compared to common mainstream grain legumes, thus hindering their adoption and utilization. Consequently, research efforts geared toward improvement, utilization, and incorporation into mainstream agriculture in Africa are more convincing than ever. This work reviews some selected NULs of Africa (Adzuki beans (Vigna angularis), African yam bean (Sphenostylis stenocarpa), Bambara groundnut (Vigna subterranea), Jack bean (Canavalia ensiformis), Kidney bean (Phaseolus vulgaris), Lima bean (Phaseolus lunatus), Marama bean (Tylosema esculentum), Mung bean, (Vigna radiata), Rice bean (Vigna Umbellata), and Winged bean (Psophocarpus tetragonolobus)), and their nutritional, and functional properties. Furthermore, we highlight the prospects and current challenges associated with the utilization of the NULs and discusses the strategies to facilitate their exploitation as not only sources of vital nutrients, but also their integration for the development of cheap and accessible functional foods.

Modeling of Flowering Time in Vigna radiata with Artificial Image Objects, Convolutional Neural Network and Random Forest

Flowering time is an important target for breeders in developing new varieties adapted to changing conditions. In this work, a new approach is proposed in which the SNP markers influencing time to flowering in mung bean are selected as important features in a random forest model. The genotypic and weather data are encoded in artificial image objects, and a model for flowering time prediction is constructed as a convolutional neural network. The model uses weather data for only a limited time period of 5 days before and 20 days after planting and is capable of predicting the time to flowering with high accuracy. The most important factors for model solution were identified using saliency maps and a Score-CAM method. Our approach can help breeding programs harness genotypic and phenotypic diversity to more effectively produce varieties with a desired flowering time.

High-quality genome assembly and pan-genome studies facilitate genetic discovery in mung bean and its improvement

Mung bean is an economically important legume crop species that is used as a food, consumed as a vegetable, and used as an ingredient and even as a medicine. To explore the genomic diversity of mung bean, we assembled a high-quality reference genome (Vrad_JL7) that was ∼479.35 Mb in size, with a contig N50 length of 10.34 Mb. A total of 40,125 protein-coding genes were annotated, representing ∼96.9% of the genetic region. We also sequenced 217 accessions, mainly landraces and cultivars from China, and identified 2,229,343 high-quality single-nucleotide polymorphisms (SNPs). Population structure revealed that the Chinese accessions diverged into two groups and were distinct from non-Chinese lines. Genetic diversity analysis based on genomic data from 750 accessions in 23 countries supported the hypothesis that mung bean was first domesticated in south Asia and introduced to east Asia probably through the Silk Road. We constructed the first pan-genome of mung bean germplasm and assembled 287.73 Mb of non-reference sequences. Among the genes, 83.1% were core genes and 16.9% were variable. Presence/absence variation (PAV) events of nine genes involved in the regulation of the photoperiodic flowering pathway were identified as being under selection during the adaptation process to promote early flowering in the spring. Genome-wide association studies (GWASs) revealed 2,912 SNPs and 259 gene PAV events associated with 33 agronomic traits, including a SNP in the coding region of the SWEET10 homolog (jg24043) involved in crude starch content and a PAV event in a large fragment containing 11 genes for color-related traits. This high-quality reference genome and pan-genome will provide insights into mung bean breeding.

Resequencing of 558 Chinese mungbean landraces identifies genetic loci associated with key agronomic traits

Mungbean is a warm-season annual food legume and plays important role in supplying food and nutritional security in many tropical countries. However, the genetic basis of its agronomic traits remains poorly understood. Therefore, we resequenced 558 Chinese mungbean landraces and produced a comprehensive map of mungbean genomic variation. We phenotyped all landraces in six different environments. Genome-wide association studies (GWAS) produced 110 signals significantly associated with nine agronomic traits, for which several candidate genes were identified. Overall, this study provides new insight into the genetic architecture of mungbean agronomic traits. Moreover, the genome-wide variations identified here should be valuable resources for future breeding studies of this important food legume.

A multiple phenotype imputation method for genetic diversity and core collection in Taiwanese vegetable soybean

Establishment of vegetable soybean (edamame) [Glycine max (L.) Merr.] germplasms has been highly valued in Asia and the United States owing to the increasing market demand for edamame. The idea of core collection (CC) is to shorten the breeding program so as to improve the availability of germplasm resources. However, multidimensional phenotypes typically are highly correlated and have different levels of missing rate, often failing to capture the underlying pattern of germplasms and select CC precisely. These are commonly observed on correlated samples. To overcome such scenario, we introduced the "multiple imputation" (MI) method to iteratively impute missing phenotypes for 46 morphological traits and jointly analyzed high-dimensional imputed missing phenotypes (EC impu ) to explore population structure and relatedness among 200 Taiwanese vegetable soybean accessions. An advanced maximization strategy with a heuristic algorithm and PowerCore was used to evaluate the morphological diversity among the EC impu . In total, 36 accessions (denoted as CC impu ) were efficiently selected representing high diversity and the entire coverage of the EC impu . Only 4 (8.7%) traits showed slightly significant differences between the CC impu and EC impu . Compared to the EC impu , 96% traits retained all characteristics or had a slight diversity loss in the CC impu . The CC impu exhibited a small percentage of significant mean difference (4.51%), and large coincidence rate (98.1%), variable rate (138.76%), and coverage (close to 100%), indicating the representativeness of the EC impu . We noted that the CC impu outperformed the CC raw in evaluation properties, suggesting that the multiple phenotype imputation method has the potential to deal with missing phenotypes in correlated samples efficiently and reliably without re-phenotyping accessions. Our results illustrated a significant role of imputed missing phenotypes in support of the MI-based framework for plant-breeding programs.

Thirty Years of Mungbean Genome Research: Where Do We Stand and What Have We Learned?

Mungbean is a socioeconomically important legume crop in Asia that is currently in high demand by consumers and industries both as dried beans and in plant-based protein foods. Marker-assisted and genomics-assisted breeding are promising approaches to efficiently and rapidly develop new cultivars with improved yield, quality, and resistance to biotic and abiotic stresses. Although mungbean was at the forefront of research at the dawn of the plant genomics era 30 years ago, the crop is a "slow runner" in genome research due to limited genomic resources, especially DNA markers. Significant progress in mungbean genome research was achieved only within the last 10 years, notably after the release of the VC1973A draft reference genome constructed using next-generation sequencing technology, which enabled fast and efficient DNA marker development, gene mapping, and identification of candidate genes for complex traits. Resistance to biotic stresses has dominated mungbean genome research to date; however, research is on the rise. In this study, we provide an overview of the past progress and current status of mungbean genomics research. We also discuss and evaluate some research results to provide a better understanding of mungbean genomics.

CRISPR/Cas9 is a powerful tool for precise genome editing of legume crops: a review

Legumes are an imperative source of food and proteins across the globe. They also improve soil fertility through symbiotic nitrogen fixation (SNF). Genome editing (GE) is now a novel way of developing desirable traits in legume crops. Genome editing tools like clustered regularly interspaced short palindromic repeats (CRISPR) system permits a defined genome alteration to improve crop performance. This genome editing tool is reliable, cost-effective, and versatile, and it has to deepen in terms of use compared to other tools. Recently, many novel variations have drawn the attention of plant geneticists, and efforts are being made to develop trans-gene-free cultivars for ensuring biosafety measures. This review critically elaborates on the recent development in genome editing of major legumes crops. We hope this updated review will provide essential informations for the researchers working on legumes genome editing. In general, the CRISPR/Cas9 novel GE technique can be integrated with other techniques like omics approaches and next-generation tools to broaden the range of gene editing and develop any desired legumes traits. Regulatory ethics of CRISPR/Cas9 are also discussed.

Population Genetics and Development of a Core Collection from Elite Germplasms of Xanthoceras sorbifolium Based on Genome-Wide SNPs

Xanthoceras sorbifolium is one of the most important species of woody oil. In this study, whole genome re-sequencing of 119 X. sorbifolium germplasms was conducted and, after filtering, 105,685,557 high-quality SNPs were identified, which were used to perform population genetics and core collection development analyses. The results from the phylogenetic, population structure, and principal component analyses showed a high level of agreement, with 119 germplasms being classified into three main groups. The germplasms were not completely classified based on their geographical origins and flower colors; furthermore, the genetic backgrounds of these germplasms were complex and diverse. The average polymorphsim information content (PIC) values for the three inferred groups clustered by structure analysis and the six classified color groups were 0.2445 and 0.2628, respectively, indicating a low to medium informative degree of genetic diversity. Moreover, a core collection containing 29.4% (35) out of the 119 X. sorbifolium germplasms was established. Our results revealed the genetic diversity and structure of X. sorbifolium germplasms, and the development of a core collection will be useful for the efficient improvement of breeding programs and genome-wide association studies.

Dissecting the Root Phenotypic and Genotypic Variability of the Iowa Mung Bean Diversity Panel

Mung bean [Vigna radiata (L.) Wilczek] is a drought-tolerant, short-duration crop, and a rich source of protein and other valuable minerals, vitamins, and antioxidants. The main objectives of this research were (1) to study the root traits related with the phenotypic and genetic diversity of 375 mung bean genotypes of the Iowa (IA) diversity panel and (2) to conduct genome-wide association studies of root-related traits using the Automated Root Image Analysis (ARIA) software. We collected over 9,000 digital images at three-time points (days 12, 15, and 18 after germination). A broad sense heritability for days 15 (0.22-0.73) and 18 (0.23-0.87) was higher than that for day 12 (0.24-0.51). We also reported root ideotype classification, i.e., PI425425 (India), PI425045 (Philippines), PI425551 (Korea), PI264686 (Philippines), and PI425085 (Sri Lanka) that emerged as the top five in the topsoil foraging category, while PI425594 (unknown origin), PI425599 (Thailand), PI425610 (Afghanistan), PI425485 (India), and AVMU0201 (Taiwan) were top five in the drought-tolerant and nutrient uptake "steep, cheap, and deep" ideotype. We identified promising genotypes that can help diversify the gene pool of mung bean breeding stocks and will be useful for further field testing. Using association studies, we identified markers showing significant associations with the lateral root angle (LRA) on chromosomes 2, 6, 7, and 11, length distribution (LED) on chromosome 8, and total root length-growth rate (TRL_GR), volume (VOL), and total dry weight (TDW) on chromosomes 3 and 5. We discussed genes that are potential candidates from these regions. We reported beta-galactosidase 3 associated with the LRA, which has previously been implicated in the adventitious root development via transcriptomic studies in mung bean. Results from this work on the phenotypic characterization, root-based ideotype categories, and significant molecular markers associated with important traits will be useful for the marker-assisted selection and mung bean improvement through breeding.

Zinc Oxide Nanoparticles Interplay With Physiological and Biochemical Attributes in Terminal Heat Stress Alleviation in Mungbean (Vigna radiata L.)

Gradually rising atmospheric temperature is the vital component of the environment, which is anticipated as the riskiest abiotic stress for crop growth. Nanotechnology revolutionizing the agricultural sectors, notably, zinc oxide nanoparticles (nano-ZnO) has captured intensive research interests due to their distinctive properties and numerous applications against abiotic stresses. Mungbean (Vigna radiata L.), being a summer crop, is grown all over the world at an optimum temperature of 28-30°C. A rise in temperature above this range, particularly during the flowering stage, can jeopardize the potential performance of the plant. Hence, an outdoor study was performed to evaluate the effect of multiple suspensions of nano-ZnO (0, 15, 30, 45, and 60 mg l^-1) on physicochemical attributes and yield of mungbean crop under heat stress. Heat stress was induced by fine-tuning of sowing time as: S1 is the optimal sowing time having day/night temperatures <40/25°C and S2 and S3 are late sown that were above >40/25°C during the flowering stage. In vitro studies on Zn release from nano-ZnO by inductively coupled plasma mass spectroscopy (ICPMS) disclosed that the Zn release and particles uptake from nano-ZnO were concentration-dependent. Exogenous foliar application of nano-ZnO significantly upstreamed the production of antioxidants and osmolytes to attenuate the shocks of heat stress in S2 and S3. Likewise, nano-ZnO substantially rebated the production of reactive oxygen species in both S2 and S3 that was associated with curtailment in lipid peroxidation. Adding to that, foliar-applied nano-ZnO inflates not only the chlorophyll contents and gas exchange attributes, but also the seeds per pod (SPP) and pods per plant (PPP), which results in the better grain yield under heat stress. Thus, among all the sowing dates, S1 statistically performed better than S2 and S3, although foliar exposure of nano-ZnO boosted up mungbean performance under both the no heat and heat-induced environments. Hence, foliar application of nano-ZnO can be suggested as an efficient way to protect the crop from heat stress-mediated damages with the most negligible chances of nanoparticles delivery to environmental compartments that could be possible in case of soil application.

Core Collections: Is There Any Value for Cotton Breeding?

Global plant breeding activities are reliant on the available genetic variation held in extant varieties and germplasm collections. Throughout the mid- to late 1900s, germplasm collecting efforts were prioritized for breeding programs to archive precious material before it disappeared and led to the development of the numerous large germplasm resources now available in different countries. In recent decades, however, the maintenance and particularly the expansion of these germplasm resources have come under threat, and there has been a significant decline in investment in further collecting expeditions, an increase in global biosecurity restrictions, and restrictions placed on the open exchange of some commercial germplasm between breeders. The large size of most genebank collections, as well as constraints surrounding the availability and reliability of accurate germplasm passport data and physical or genetic characterization of the accessions in collections, limits germplasm utilization by plant breeders. To overcome these constraints, core collections, defined as a representative subset of the total germplasm collection, have gained popularity. Core collections aim to increase germplasm utilization by containing highly characterized germplasm that attempts to capture the majority of the variation in a whole collection. With the recent availability of many new genetic tools, the potential to unlock the value of these resources can now be realized. The Commonwealth Scientific and Industrial Research Organisation (CSIRO) cotton breeding program supplies 100% of the cotton cultivars grown in Australia. The program is reliant on the use of plant genetic resources for the development of improved cotton varieties to address emerging challenges in pest and disease resistance as well as the global changes occurring in the climate. Currently, the CSIRO germplasm collection is actively maintained but underutilized by plant breeders. This review presents an overview of the Australian cotton germplasm resources and discusses the appropriateness of a core collection for cotton breeding programs.

A review on metabolites and pharmaceutical potential of food legume crop mung bean (Vigna radiata L. Wilczek)

Mung bean or moong or green gram, an important grain legume, is cultivated mainly in Asian countries and other parts of the world as a food crop. It is a highly nutritious grain legume with a high content of easily digestible proteins (20-32%), carbohydrates (53.3-67.1%), lipids (0.71-1.85%), vitamins, minerals, and fiber. It also contains some antinutrients such as tannins, phytic acid, hemagglutinin, polyphenols, and trypsin inhibitors in low concentrations. The sprouting of seeds leads to dynamic changes in metabolites with a decrease in antinutrient content and an increase in the nutritional value. In addition to these nutrients and antinutrients, the plant also contains various other phytochemicals such as alkaloids, flavonoids, saponins, phenols, glycosides, and bioactive peptides, which exhibit an array of pharmaceutically important properties such as anti-inflammatory, antinociceptive, antimicrobial, antioxidant, antidiabetic, lipid metabolism regulation, antihypertensive, antiallergic, and antitumor. Being rich in nutritional value and other phytochemical components, the plant can be explored further for its pharmaceutical properties and used as an efficient food additive in the preparation of different types of dietary supplements or food-derived drugs.

A Critical Review of the Current Global Ex Situ Conservation System for Plant Agrobiodiversity. II. Strengths and Weaknesses of the Current System and Recommendations for Its Improvement

In this paper, we review gene bank operations that have an influence on the global conservation system, with the intention to identify critical aspects that should be improved for optimum performance. We describe the role of active and base collections and the importance of linking germplasm conservation and use, also in view of new developments in genomics and phenomics that facilitate more effective and efficient conservation and use of plant agrobiodiversity. Strengths, limitations, and opportunities of the existing global ex situ conservation system are discussed, and measures are proposed to achieve a rational, more effective, and efficient global system for germplasm conservation and sustainable use. The proposed measures include filling genetic and geographic gaps in current ex situ collections; determining unique accessions at the global level for long-term conservation in virtual base collections; intensifying existing international collaborations among gene banks and forging collaborations with the botanic gardens community; increasing investment in conservation research and user-oriented supportive research; improved accession-level description of the genetic diversity of crop collections; improvements of the legal and policy framework; and oversight of the proposed network of global base collections.

A Novel Disease of Mung Bean, Phytophthora Stem Rot Caused by a New Forma Specialis of Phytophthora vignae

An emerging soilborne disease resembling Phytophthora stem rot was observed on mung bean plants grown in Anhui, China. To identify the causal agent, diseased plants and soil samples from 13 fields were collected to isolate the pathogen. Twenty-two Phytophthora isolates were recovered from the samples and detailed identification was conducted. Based on morphological and molecular characterizations, all of the isolates were consistently identified as P. vignae. Phylogenetic analysis using eight nuclear loci sequences of the internal transcribed spacer region, rRNA gene large subunit, a partial sequence of the β-tubulin gene, translation elongation factor 1α, 60S ribosomal protein L10, the enolase gene, heat shock protein 90, and triose phosphate isomerase/glyceraldehyde-3-phosphate dehydrogenase and a mitochondrial locus cytochrome c oxidase subunit I revealed that the mung bean isolates grouped in the same clade as P. vignae and its two formae speciales, P. vignae f. sp. adzukicola and P. vignae f. sp. vignae. A host specificity test showed that the mung bean isolates of P. vignae were pathogenic toward mung bean with a much stronger virulence and toward adzuki bean with a relatively weak virulence, but they were nonpathogenic to the other tested legume crops, including soybean, cowpea, pea, common bean, faba bean, and chickpea. The host range of mung bean isolates significantly differs from those of P. vignae f. sp. adzukicola and P. vignae f. sp. vignae based on our results and on previous studies. Thus, the pathogen causing Phytophthora stem rot of mung bean is proposed as a new forma specialis of P. vignae, designated as P. vignae f. sp. mungcola.

Field-Relevant New Sources of Resistance to Anthracnose Caused by Colletotrichum truncatum in a Mungbean Mini-Core Collection

Anthracnose is a prevalent disease of mungbean in Asian countries and Sub-Saharan Africa. It is caused by multiple Colletotrichum species. The high levels of anthracnose resistance in mungbean have not been studied in depth in India, but genetic resistance is desired. In this study, we identified the causal agent of mungbean anthracnose in two regions of India as Colletotrichum truncatum through morphological and molecular methods. A set of 296 mungbean mini-core accessions developed by WorldVeg was screened under a natural disease pressure from July to September (kharif season) in 2016, 2017, and 2018 in Hyderabad (a hot spot for anthracnose) to identify anthracnose resistance. Based on disease severity scores, 22 accessions were consistently anthracnose resistant under the categories of immune, highly resistant, and resistant with scores ranging from ≥1.0 to ≤3.0 during the period of study. Furthermore, based on the agronomic performance, anthracnose resistance in Hyderabad, and other desirable traits, a subset of 74 mungbean accessions was selected from 296 mini-core accessions. These accessions were evaluated under natural disease pressure from July to September in 2018 and 2019 in Palampur (another hot spot for anthracnose) to determine the variation in anthracnose resistance. Out of the 74 accessions, two accessions were resistant in 2018; in 2019, one was immune, nine were highly resistant, and 15 were resistant. Combined analysis of variance of 65 accessions common in Hyderabad and Palampur revealed highly significant effects of environment, genotype (accessions), and genotype × environment interaction on the disease severity. The combined GGE biplot analysis of data across years and locations confirmed that the seven accessions MC-24, MC-51, MC-75, MC-127, MC-207, MC-208, and MC-292 were resistant during 2016 to 2018 in Hyderabad, and only in 2019 in Palampur, and the same accessions were moderately resistant in 2018 in Palampur. The seven resistant accessions identified from both test locations could be used as potential donors in the anthracnose resistance breeding program.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Assessment of root phenotypes in mungbean mini-core collection (MMC) from the World Vegetable Center (AVRDC) Taiwan

Mungbean (Vigna radiata L.) is an important food grain legume, but its production capacity is threatened by global warming, which can intensify plant stress and limit future production. Identifying new variation of key root traits in mungbean will provide the basis for breeding lines with effective root characteristics for improved water uptake to mitigate heat and drought stress. The AVRDC mungbean mini core collection consisting of 296 genotypes was screened under modified semi-hydroponic screening conditions to determine the variation for fourteen root-related traits. The AVRDC mungbean mini core collection displayed wide variations for the primary root length, total surface area, and total root length, and based on agglomerative hierarchical clustering eight homogeneous groups displaying different root traits could be identified. Germplasm with potentially favorable root traits has been identified for further studies to identify the donor genotypes for breeding cultivars with enhanced adaptation to water-deficit stress and other stress conditions.

Transcriptome Analysis of Resistance to Fusarium Wilt in Mung Bean (Vigna radiata L.)

Fusarium wilt is a destructive soil-borne disease that threatens the production of mung bean. Mung bean lines Zheng8-4 and Zheng8-20 show high resistance and high susceptibility to Fusarium wilt, respectively. Transcriptome analysis was carried out to identify candidate genes involved in Fusarium wilt resistance using Zheng8-4 and Zheng8-20 at 0, 0.5, 1, 2, and 4 days post inoculation (dpi). Differential expression analysis showed that 3,254 genes responded to pathogen infection and were differentially expressed in the resistant and susceptible lines. Weighted gene co-expression network analysis (WGCNA) was also performed to identify five modules highly correlated with Fusarium wilt resistance, in which 453 differentially expressed genes (DEGs) were considered likely to be involved in Fusarium wilt resistance. Among these DEGs, we found 24 genes encoding resistance (R) proteins, 22 encoding protein kinases, 20 belonging to transcription factor families, 34 encoding proteins with oxidoreductase activity, 17 involved in stimulation/stress responses, and 54 annotated to pathogen resistance-related pathways. Finally, 27 annotated genes were further selected as candidate genes of Fusarium wilt resistance in mung bean. This study identifies novel potential resistance-related genes against Fusarium wilt and provides a theoretical basis for further investigation of Fusarium wilt resistance in mung bean breeding.

Plant Biodiversity and Genetic Resources Matter!

Plant biodiversity is the foundation of our present-day food supply (including functional food and medicine) and offers humankind multiple other benefits in terms of ecosystem functions and resilience to climate change, as well as other perturbations. This Special Issue on 'Plant Biodiversity and Genetic Resources' comprises 32 papers covering a wide array of aspects from the definition and identification of hotspots of wild and domesticated plant biodiversity to the specifics of conservation of genetic resources of crop genepools, including breeding and research materials, landraces and crop wild relatives which collectively are the pillars of modern plant breeding, as well as of localized breeding efforts by farmers and farming communities. The integration of genomics and phenomics into germplasm and genebank management enhances the value of crop germplasm conserved ex situ, and is likely to increase its utilization in plant breeding, but presents major challenges for data management and the sharing of this information with potential users. Furthermore, also a better integration of in situ and ex situ conservation efforts will contribute to a more effective conservation and certainly to a more sustainable and efficient utilization. Other aspects such as policy, access and benefit-sharing that directly impact the use of plant biodiversity and genetic resources, as well as balanced nutrition and enhanced resilience of production systems that depend on their increased use, are also being treated. The editorial concludes with six key messages on plant biodiversity, genetic erosion, genetic resources and plant breeding, agricultural diversification, conservation of agrobiodiversity, and the evolving role and importance of genebanks.

Transcriptome analysis provides molecular evidences for growth and adaptation of plant roots in cadimium-contaminated environments

Cadmium (Cd) is a detrimental element that can be toxic to plants. The physiological and biochemical responses of plants to Cd stress have been extensively studied, but the molecular mechanisms remain unclear. The present study showed that Cd severely inhibited the growth of roots and shoots and reduced plant biomass of mung bean seedlings. To further investigate the gene profiles and molecular processes in response Cd stress, transcriptome analyses of mung bean roots exposed to 100 μM Cd for 1, 5, and 9 days were performed. Cd treatment significantly decreased global gene expression levels at 5 and 9 d compared with the control. A total of 6737, 10279, and 9672 differentially expressed genes (DEGs) were identified in the 1-, 5-, and 9-day Cd-treated root tissues compared with the controls, respectively. Based on the analysis of DEG function annotation and enrichment, a pattern of mung bean roots response to Cd stress was proposed. The processes detoxification and antioxidative defense were involved in the early response of mung bean roots to Cd. Cd stress downregulated the expressions of a series of genes involved in cell wall biosynthesis, cell division, DNA replication and repair, and photosynthesis, while genes involved in signal transduction and regulation, transporters, secondary metabolisms, defense systems, and mitochondrial processes were upregulated in response to Cd, which might be contributed to the improvement of plant tolerance. Our results provide some novel insights into the molecular processes for growth and adaption of mung bean roots in response to Cd and many candidate genes for further biotechnological manipulations to improve plant tolerance to heavy metals.

Genome-wide association study in accessions of the mini-core collection of mungbean (Vigna radiata) from the World Vegetable Gene Bank (Taiwan)

BACKGROUND

Mungbean (Vigna radiata (L.) R. Wilczek, or green gram) is important tropical and sub-tropical legume and a rich source of dietary protein and micronutrients. In this study we employ GWAS to examine the genetic basis of variation in several important traits in mungbean, using the mini-core collection established by the World Vegetable Center, which includes 296 accessions that represent the major market classes. This collection has been grown in a common field plot in southern European part of Russia in 2018.

RESULTS

We used 5041 SNPs in 293 accessions that passed strict filtering for genetic diversity, linkage disequilibrium, population structure and GWAS analysis. Polymorphisms were distributed among all chromosomes, but with variable density. Linkage disequilibrium decayed in approximately 105 kb. Four distinct subgroups were identified within 293 accessions with 70% of accessions attributed to one of the four populations. By performing GWAS on the mini-core collection we have found several loci significantly associated with two important agronomical traits. Four SNPs associated with possibility of maturation in Kuban territory of Southern Russia in 2018 were identified within a region of strong linkage which contains genes encoding zinc finger A20 and an AN1 domain stress-associated protein.

CONCLUSIONS

The core collection of mungbean established by the World Vegetable Center is a valuable resource for mungbean breeding. The collection has been grown in southern European part of Russia in 2018 under incidental stresses caused by abnormally hot weather and different photoperiod. We have found several loci significantly associated with color of hypocotyl and possibility of maturation under these stressful conditions. SNPs associated with possibility of maturation localize to a region on chromosome 2 with strong linkage, in which genes encoding zinc finger A20 and AN1 domain stress associated protein (SAP) are located. Phenotyping of WorldVeg collection for maturation traits in temperate climatic locations is important as phenology remains a critical breeding target for mungbean. As demand rises for mungbean, production in temperate regions with shorter growing seasons becomes crucial to keep up with needs. Uncovering SNPs for phenology traits will speed breeding efforts.

Dynamical climatic model for time to flowering in Vigna radiata

BACKGROUND

Phenology data collected recently for about 300 accessions of Vigna radiata (mungbean) is an invaluable resource for investigation of impacts of climatic factors on plant development.

RESULTS

We developed a new mathematical model that describes the dynamic control of time to flowering by daily values of maximal and minimal temperature, precipitation, day length and solar radiation. We obtained model parameters by adaptation to the available experimental data. The models were validated by cross-validation and used to demonstrate that the phenology of adaptive traits, like flowering time, is strongly predicted not only by local environmental factors but also by plant geographic origin and genotype.

CONCLUSIONS

Of local environmental factors maximal temperature appeared to be the most critical factor determining how faithfully the model describes the data. The models were applied to forecast time to flowering of accessions grown in Taiwan in future years 2020-2030.

A SNP-Based Genome-Wide Association Study to Mine Genetic Loci Associated to Salinity Tolerance in Mungbean (Vigna radiata L.)

Mungbean (Vigna radiata (L.) R. Wilzeck var. radiata) is a protein-rich short-duration legume that fits well as a rotation crop into major cereal production systems of East and South-East Asia. Salinity stress in arid areas affects mungbean, being more of a glycophyte than cereals. A significant portion of the global arable land is either salt or sodium affected. Thus, studies to understand and improve salt-stress tolerance are imminent. Here, we conducted a genome-wide association study (GWAS) to mine genomic loci underlying salt-stress tolerance during seed germination of mungbean. The World Vegetable Center (WorldVeg) mungbean minicore collection representing the diversity of mungbean germplasm was utilized as the study panel and variation for salt stress tolerance was found in this germplasm collection. The germplasm panel was classed into two agro-climatic groups and showed significant differences in their germination abilities under salt stress. A total of 5288 SNP markers obtained through genotyping-by-sequencing (GBS) were used to mine alleles associated with salt stress tolerance. Associated SNPs were identified on chromosomes 7 and 9. The associated region at chromosome 7 (position 2,696,072 to 2,809,200 bp) contains the gene Vradi07g01630, which was annotated as the ammonium transport protein (AMT). The associated region in chromosome 9 (position 19,390,227 bp to 20,321,817 bp) contained the genes Vradi09g09510 and Vradi09g09600, annotated as OsGrx_S16-glutaredoxin subgroup II and dnaJ domain proteins respectively. These proteins were reported to have functions related to salt-stress tolerance.

Genetic variation for root architectural traits in response to phosphorus deficiency in mungbean at the seedling stage

Roots enable the plant to survive in the natural environment by providing anchorage and acquisition of water and nutrients. In this study, root architectural traits of 153 mungbean genotypes were compared under optimum and low phosphorus (P) conditions. Significant variations and medium to high heritability were observed for the root traits. Total root length was positively and significantly correlated with total root surface area, total root volume, total root tips and root forks under both optimum P (r = 0.95, r = 0.85, r = 0.68 and r = 0.82 respectively) and low P (r = 0.95, r = 0.82, r = 0.71 and r = 0.81 respectively). The magnitudes of the coefficient of variations were relatively higher for root forks, total root tips and total root volume. Total root length, total root surface area and total root volume were major contributors of variation and can be utilized for screening of P efficiency at the seedling stage. Released Indian mungbean varieties were found to be superior for root traits than other genotypic groups. Based on comprehensive P efficiency measurement, IPM-288, TM 96–25, TM 96–2, M 1477, PUSA 1342 were found to be the best highly efficient genotypes, whereas M 1131, PS-16, Pusa Vishal, M 831, IC 325828 were highly inefficient. Highly efficient genotypes identified would be valuable genetic resources for P efficiency for utilizing in the mungbean breeding programme.

Green gram and black gram: prospects of cultivation and breeding in Russian Federation

Diversifcation of crop production in the Russian Federation could be partly achieved by the introduction and production of minor and underutilized crops. Green gram or mung bean (Vigna radiata(L.) R. Wilczek) and black gram or urd (V. mungo(L.) Hepper) are grain legume crops cultivated in limited areas in the Russian Federation. Meanwhile, green gram occupies about 8.5 % of the world production area under pulses (without soybean). It is cultivated mainly in countries of Southeast Asia, but production is expanding to the entire subtropical belt of the globe. In our country these crops can be successfully grown on irrigation in a number of regions in the southern area of the European part and the Russian Far East, where the temperatures during their vegetation are about 28–30 °C and always above 15 °C. The purpose of this paper is to summarize the world’s experience in breeding improvement of mung bean and urd as crops with promise for cultivation in certain soil and climatic zones of the Russian Federation. The world production, use of these high-protein crops, history and peculiarities of breeding, including in the USSR, are covered. To expand the production of both crops in the Russian Federation, their popularization and development of breeding are required. Basic requirements for modern varieties include resistance to biotic and abiotic stressors which can be introgressed from wild relatives. The great importance of both crops in the Asian countries led to the rapid development of molecular researches there. The genome of black gram has been fully sequenced, the genome of green gram has been partly sequenced. Some genes and QTL of adaptability traits have been marked and mapped in a number of wild species of the genusVigna. The role of wild relatives in the breeding of crops concerned is discussed. In the world genebanks, signifcant genetic resources of mung bean and urd have been accumulated. All this creates prerequisites for the development of marker-assistant and genomic breeding.

Biotic and Abiotic Constraints in Mungbean Production-Progress in Genetic Improvement

Mungbean [Vigna radiata (L.) R. Wilczek var. radiata] is an important food and cash legume crop in Asia. Development of short duration varieties has paved the way for the expansion of mungbean into other regions such as Sub-Saharan Africa and South America. Mungbean productivity is constrained by biotic and abiotic factors. Bruchids, whitefly, thrips, stem fly, aphids, and pod borers are the major insect-pests. The major diseases of mungbean are yellow mosaic, anthracnose, powdery mildew, Cercospora leaf spot, halo blight, bacterial leaf spot, and tan spot. Key abiotic stresses affecting mungbean production are drought, waterlogging, salinity, and heat stress. Mungbean breeding has been critical in developing varieties with resistance to biotic and abiotic factors, but there are many constraints still to address that include the precise and accurate identification of resistance source(s) for some of the traits and the traits conferred by multi genes. Latest technologies in phenotyping, genomics, proteomics, and metabolomics could be of great help to understand insect/pathogen-plant, plant-environment interactions and the key components responsible for resistance to biotic and abiotic stresses. This review discusses current biotic and abiotic constraints in mungbean production and the challenges in genetic improvement.

In silico genome-wide identification and characterization of the glutathione S-transferase gene family in Vigna radiata

Plant glutathione S-transferases (GSTs) are integral to normal plant metabolism and biotic and abiotic stress tolerance. The GST gene family has been characterized in diverse plant species using molecular biology and bioinformatics approaches. In the current study, in silico analysis identified 44 GSTs in Vigna radiata. Of the total 44 GSTs identified, chromosomal locations of 31 GSTs were confirmed. The pI value of GST proteins ranged from 5.10 to 9.40. The predicted molecular weights ranged from 13.12 to 50 kDa. Subcellular localization analysis revealed that all GSTs were predominantly localized in the cytoplasm. The active site amino acids were confirmed to be serine in tau, phi, theta, zeta, and TCHQD; cysteine in lambda, DHAR, and omega; and tyrosine in EF1G. The gene architecture conformed to the two-exon/one-intron and three-exon/two-intron organization in the case of tau and phi classes, respectively. MEME analysis identified 10 significantly conserved motifs with the width of 8-50 amino acids. The motifs identified were either specific to a specific GST class or were shared by multiple GST classes. The results of the current study will be of potential importance in the characterization of the GST gene family in V. radiata, an economically important leguminous crop.

Genetic Characterization of Chinese fir from Six Provinces in Southern China and Construction of a Core Collection

Large ex situ germplasm collections of plants generally contain significant diversity. A set of 700 well-conserved Chinese fir (Cunninghamia lanceolata (Lamb.) Hook) clones from six provinces in southern China in the ex situ gene bank of Longshan State Forest, was analyzed using 21 simple sequence repeat markers, with the aim of assessing the genetic diversity of these germplasm resources. Genetic analysis revealed extensive genetic variation among the accessions, with an average of 8.31 alleles per locus and a mean Shannon index of 1.331. Excluding loci with null alleles, we obtained a low level of genetic differentiation among provinces, consistent with the interpopulation genetic variation (1%). Three clusters were identified by STRUCTURE, which did not match the individuals’ geographical provenances. Ten traits related to growth and wood properties were quantified in these individuals, and there was substantial variation in all traits across individuals, these provide a potential source of variation for genetic improvement of the Chinese fir. Screening large collections for multiple-trait selective breeding programs is laborious and expensive; a core collection of 300 accessions, representative of the germplasm, was established, based on genotypic and phenotypic data. The identified small, but diverse, collections will be useful for further genome-wide association studies.

Salinity and High Temperature Tolerance in Mungbean [Vigna radiata (L.) Wilczek] from a Physiological Perspective

Biotic and abiotic constraints seriously affect the productivity of agriculture worldwide. The broadly recognized benefits of legumes in cropping systems-biological nitrogen fixation, improving soil fertility and broadening cereal-based agro-ecologies, are desirable now more than ever. Legume production is affected by hostile environments, especially soil salinity and high temperatures (HTs). Among legumes, mungbean has acceptable intrinsic tolerance mechanisms, but many agro-physiological characteristics of the Vigna species remain to be explored. Mungbean has a distinct advantage of being short-duration and can grow in wide range of soils and environments (as mono or relay legume). This review focuses on salinity and HT stresses on mungbean grown as a fallow crop (mungbean-rice-wheat to replace fallow-rice-wheat) and/or a relay crop in cereal cropping systems. Salinity tolerance comprises multifaceted responses at the molecular, physiological and plant canopy levels. In HTs, adaptation of physiological and biochemical processes gradually may lead to improvement of heat tolerance in plants. At the field level, managing or manipulating cultural practices can mitigate adverse effects of salinity and HT. Greater understanding of physiological and biochemical mechanisms regulating these two stresses will contribute to an evolving profile of the genes, proteins, and metabolites responsible for mungbean survival. We focus on abiotic stresses in legumes in general and mungbean in particular, and highlight gaps that need to be bridged through future mungbean research. Recent findings largely from physiological and biochemical fronts are examined, along with a few agronomic and farm-based management strategies to mitigate stress under field conditions.

Genome-wide resequencing of KRICE_CORE reveals their potential for future breeding, as well as functional and evolutionary studies in the post-genomic era

Background

Rice germplasm collections continue to grow in number and size around the world. Since maintaining and screening such massive resources remains challenging, it is important to establish practical methods to manage them. A core collection, by definition, refers to a subset of the entire population that preserves the majority of genetic diversity, enhancing the efficiency of germplasm utilization.

Results

Here, we report whole-genome resequencing of the 137 rice mini core collection or Korean rice core set (KRICE_CORE) that represents 25,604 rice germplasms deposited in the Korean genebank of the Rural Development Administration (RDA). We implemented the Illumina HiSeq 2000 and 2500 platform to produce short reads and then assembled those with 9.8 depths using Nipponbare as a reference. Comparisons of the sequences with the reference genome yielded more than 15 million (M) single nucleotide polymorphisms (SNPs) and 1.3 M INDELs. Phylogenetic and population analyses using 2,046,529 high-quality SNPs successfully assigned rice accessions to the relevant rice subgroups, suggesting that these SNPs capture evolutionary signatures that have accumulated in rice subpopulations. Furthermore, genome-wide association studies (GWAS) for four exemplary agronomic traits in the KRIC_CORE manifest the utility of KRICE_CORE; that is, identifying previously defined genes or novel genetic factors that potentially regulate important phenotypes.

Conclusion

This study provides strong evidence that the size of KRICE_CORE is small but contains high genetic and functional diversity across the genome. Thus, our resequencing results will be useful for future breeding, as well as functional and evolutionary studies, in the post-genomic era.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2734-y) contains supplementary material, which is available to authorized users.

Transcriptomic analysis reveals the gene expression profile that specifically responds to IBA during adventitious rooting in mung bean seedlings

BACKGROUND

Auxin plays a critical role in inducing adventitious rooting in many plants. Indole-3-butyric acid (IBA) is the most widely employed auxin for adventitious rooting. However, the molecular mechanisms by which auxin regulate the process of adventitious rooting are less well known.

RESULTS

The RNA-Seq data analysis indicated that IBA treatment greatly increased the amount of clean reads and the amount of expressed unigenes by 24.29 % and 27.42 % and by 4.3 % and 5.04 % at two time points, respectively, and significantly increased the numbers of unigenes numbered with RPKM = 10-100 and RPKM = 500-1000 by 13.04 % and 3.12 % and by 24.66 % and 108.2 % at two time points, respectively. Gene Ontology (GO) enrichment analysis indicated that the enrichment of down-regulated GOs was 2.87-fold higher than that of up-regulated GOs at stage 1, suggesting that IBA significantly down-regulated gene expression at 6 h. The GO functional category indicated that IBA significantly up- or down-regulated processes associated with auxin signaling, ribosome assembly and protein synthesis, photosynthesis, oxidoreductase activity and extracellular region, secondary cell wall biogenesis, and the cell wall during the development process. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment indicated that ribosome biogenesis, plant hormone signal transduction, pentose and glucuronate interconversions, photosynthesis, phenylpropanoid biosynthesis, sesquiterpenoid and triterpenoid biosynthesis, ribosome, cutin, flavonoid biosynthesis, and phenylalanine metabolism were the pathways most highly regulated by IBA. A total of 6369 differentially expressed (2-fold change > 2) unigenes (DEGs) with 3693 (58 %) that were up-regulated and 2676 (42 %) down-regulated, 5433 unigenes with 2208 (40.6 %) that were up-regulated and 3225 (59.4 %) down-regulated, and 7664 unigenes with 3187 (41.6 %) that were up-regulated and 4477 (58.4 %) down-regulated were detected at stage 1, stage 2, and between stage 1 and stage 2, respectively, suggesting that IBA treatment increased the number of DEGs. A total of 143 DEGs specifically involved in plant hormone signaling and 345 transcription factor (TF) genes were also regulated by IBA. qRT-PCR validation of the 36 genes with known functions indicated a strong correlation with the RNA-Seq data.

CONCLUSIONS

The changes in GO functional categories, KEGG pathways, and global DEG profiling during adventitious rooting induced by IBA were analyzed. These results provide valuable information about the molecular traits of IBA regulation of adventitious rooting.

De Novo Characterization of the Mung Bean Transcriptome and Transcriptomic Analysis of Adventitious Rooting in Seedlings Using RNA-Seq

Adventitious rooting is the most important mechanism underlying vegetative propagation and an important strategy for plant propagation under environmental stress. The present study was conducted to obtain transcriptomic data and examine gene expression using RNA-Seq and bioinformatics analysis, thereby providing a foundation for understanding the molecular mechanisms controlling adventitious rooting. Three cDNA libraries constructed from mRNA samples from mung bean hypocotyls during adventitious rooting were sequenced. These three samples generated a total of 73 million, 60 million, and 59 million 100-bp reads, respectively. These reads were assembled into 78,697 unigenes with an average length of 832 bp, totaling 65 Mb. The unigenes were aligned against six public protein databases, and 29,029 unigenes (36.77%) were annotated using BLASTx. Among them, 28,225 (35.75%) and 28,119 (35.62%) unigenes had homologs in the TrEMBL and NCBI non-redundant (Nr) databases, respectively. Of these unigenes, 21,140 were assigned to gene ontology classes, and a total of 11,990 unigenes were classified into 25 KOG functional categories. A total of 7,357 unigenes were annotated to 4,524 KOs, and 4,651 unigenes were mapped onto 342 KEGG pathways using BLAST comparison against the KEGG database. A total of 11,717 unigenes were differentially expressed (fold change>2) during the root induction stage, with 8,772 unigenes down-regulated and 2,945 unigenes up-regulated. A total of 12,737 unigenes were differentially expressed during the root initiation stage, with 9,303 unigenes down-regulated and 3,434 unigenes up-regulated. A total of 5,334 unigenes were differentially expressed between the root induction and initiation stage, with 2,167 unigenes down-regulated and 3,167 unigenes up-regulated. qRT-PCR validation of the 39 genes with known functions indicated a strong correlation (92.3%) with the RNA-Seq data. The GO enrichment, pathway mapping, and gene expression profiles reveal molecular traits for root induction and initiation. This study provides a platform for functional genomic research with this species.

Genomic resources in mungbean for future breeding programs

Among the legume family, mungbean (Vigna radiata) has become one of the important crops in Asia, showing a steady increase in global production. It provides a good source of protein and contains most notably folate and iron. Beyond the nutritional value of mungbean, certain features make it a well-suited model organism among legume plants because of its small genome size, short life-cycle, self-pollinating, and close genetic relationship to other legumes. In the past, there have been several efforts to develop molecular markers and linkage maps associated with agronomic traits for the genetic improvement of mungbean and, ultimately, breeding for cultivar development to increase the average yields of mungbean. The recent release of a reference genome of the cultivated mungbean (V. radiata var. radiata VC1973A) and an additional de novo sequencing of a wild relative mungbean (V. radiata var. sublobata) has provided a framework for mungbean genetic and genome research, that can further be used for genome-wide association and functional studies to identify genes related to specific agronomic traits. Moreover, the diverse gene pool of wild mungbean comprises valuable genetic resources of beneficial genes that may be helpful in widening the genetic diversity of cultivated mungbean. This review paper covers the research progress on molecular and genomics approaches and the current status of breeding programs that have developed to move toward the ultimate goal of mungbean improvement.