Moth bean is a small-seeded, protein-rich, and abiotic stress-resilient legume grown in arid and semi-arid areas of South Asia. Cultivation of this underutilized legume can reduce the dependency on commercialized Vigna species for food and nutrient security in underdeveloped countries. However, low yield remains one of the major limitations in the wider adoption of the crop among farmers in South Asian countries. To address this challenge, the present study employs genome-wide association studies to dissect the genetic basis of seed weight, a very important trait directly related to seed size and yield. The study used a diverse panel of 327 genotypes, which were phenotyped for 100-seed weight trait across three environments. By employing four multi-locus GWAS methods and 8518 SNP markers, we identified 17 significant SNPs across the genome associated with seed weight. The important seed size/seed development-associated candidate genes anchoring these SNPs were S-protein-like protein, purple acid phosphatase, kinetochore protein spc25 isoform X2 and CBL-interacting protein kinase 8-like protein. Four trait-associated SNPs/genomic regions identified in this study exhibited significant effects on the 100-seed weight trait. Genes associated with two of these SNPs (SNP2374: “g20155.t2” encoding purple acid phosphatase, and SNP5696: “g29506.t1” encoding kinetochore protein spc25 isoform X2) showed prominent upregulation in flower and early developing seed tissues/pod development stages suggesting their role in regulating seed size in moth bean. Trait-based markers developed from these candidate genes could potentially accelerate the marker-assisted breeding program to enhance seed weight and overall productivity of moth bean.

AbstractAs a fast-growing legume species, moth bean (Vigna aconitifolia)has a unique habit of sustaining in conditions of higher temperatures and drought. This grain legume is also valued for it seeds which have one of the highest contents of proteins amongst all grain legumes. This plant can be a rich source of genomic resources, which can be applied to improve abiotic stress response in allied grain legumes and also help understand the biological processes governing their overall development. Here we generate ade novogenome assembly ofVigna aconitifoliausing PacBio High-Fidelity reads and Hi-C sequencing data, with a total size of 409 Mb and contig N50 of more than 30Mb. We also annotated the genome for repeat sequences, found that the moth bean genome comprises of about 54% of repetitive sequences, and predicted 36950 protein-coding genes. Using the available RNA-Seq data for moth bean, we have developed a differential expression profile for various tissues of moth bean using the whole genome as a reference and identified simple sequence repeats that could be developed into viable molecular markers. This nascent study will provide insight into the identification of agronomically important genes and accelerate the genetic improvement of moth bean as well as other legume crops.

Background Moth bean ( Vigna aconitifolia ) is an underutilized, protein-rich legume that is grown in arid and semi-arid areas of south Asia and is highly resistant to abiotic stresses such as heat and drought. Despite its economic importance, the crop remains unexplored at the genomic level for genetic diversity and trait mapping studies. To date, there is no report of SNP marker discovery and association mapping of any trait in this crop. Therefore, this study aimed to dissect the genetic diversity, population structure and marker-trait association for the flowering trait in a diversity panel of 428 moth bean accessions using genotyping by sequencing (GBS) approach. Results A total of 9078 high-quality single nucleotide polymorphisms (SNPs) were discovered by genotyping of 428 moth bean accessions. Model-based structure analysis and PCA grouped the moth bean accessions into two subpopulations. Cluster analysis revealed accessions belonging to the Northwestern region of India had higher variability than accessions from the other regions suggesting that this region represents its center of diversity. AMOVA revealed more variations within individuals (74%) and among the individuals (24%) than among the populations (2%). Marker-trait association analysis using seven multi-locus models including mrMLM, FASTmrEMMA FASTmrEMMA, ISIS EM-BLASSO, MLMM, BLINK and FarmCPU revealed 29 potential genomic regions for the trait days to 50% flowering, which were consistently detected in three or more models. Analysis of the allelic effect of the major genomic regions explaining phenotypic variance of more than 10% and those detected in at least 2 environments showed 4 genomic regions with significant phenotypic effect on this trait. Further, we also analyzed genetic relationships among the Vigna species using SNP markers. The genomic localization of moth bean SNPs on genomes of closely related Vigna species demonstrated that maximum numbers of SNPs were getting localized on Vigna mungo. This suggested that the moth bean is most closely related to V. mungo. Conclusion Our study shows that the north-western regions of India represent the center of diversity of the moth bean. Further, the study revealed flowering-related genomic regions/candidate genes which can be potentially exploited in breeding programs to develop early-maturity moth bean varieties.

Mung bean [Vigna radiata (L.) Wilczek] is one of the upsurging, highly economical, nutritive Asiatic leguminous crops. The crop is getting higher attention in terms of the consumption and production worldwide being an important source of amino acids, proteins, dietary fibre and unsaturated fatty acids. It possesses folate and iron in significant amount along with several phytochemicals. The short life cycle and nitrogen-fixing ability make it more suitable for sowing along with other crops. In spite of several advantages, it has got less attention in terms of development of morphophysiological and molecularly diverse varieties. Mung bean has a small genome, and fortunately it has been sequenced; therefore, it may be utilized as an exemplary plant to understand other legumes. Development of wild mung bean pool from diverse origins and environmental conditions would help to conserve the genetic wealth of the crop. Higher yields, shorter maturity period, higher harvest index, photoperiod insensitivity, resistance to major insect pests/diseases, compact canopy and synchronous maturity are some of the important objectives for crop improvement in mung bean. This chapter reviews the morphophysiological and molecular diversity of mung bean and also gives an insight about mutagenesis, plant protection and abiotic stresses associated with the crop.

As a fast-growing legume species, moth bean (Vigna aconitifolia) has a unique habit of sustaining in conditions of higher temperatures and drought. This grain legume is also valued for it seeds which have one of the highest contents of proteins amongst all grain legumes. This plant can be a rich source of genomic resources, which can be applied to improve abiotic stress response in allied grain legumes and also help understand the biological processes governing their overall development. Here we generate a de novo genome assembly of Vigna aconitifolia using PacBio High-Fidelity reads and Hi-C sequencing data, with a total size of 409 Mb and contig N50 of more than 30Mb. We also annotated the genome for repeat sequences, found that the moth bean genome comprises of about 54% of repetitive sequences, and predicted 36950 protein-coding genes. Using the available RNA-Seq data for moth bean, we have developed a differential expression profile for various tissues of moth bean using the whole genome as a reference and identified simple sequence repeats that could be developed into viable molecular markers. This nascent study will provide insight into the identification of agronomically important genes and accelerate the genetic improvement of moth bean as well as other legume crops.

Much has been learned about how plants acclimate to stressful environments, but the molecular basis of stress adaptation and the potential involvement of epigenetic regulation remain poorly understood. Here, we examined if salt stress induces mutagenesis in suspension cultured plant cells and if DNA methylation affects the mutagenesis using whole genome resequencing analysis. We generated suspension cell cultures from two Arabidopsis DNA methylation-deficient mutants and wild-type plants, and subjected the cultured cells to stepwise increases in salt stress intensity over 40 culture cycles. We show that ddc (drm1 drm2 cmt3) mutant cells can adapt to grow in 175 mM NaCl-containing growth medium and exhibit higher adaptability compared to wild type Col-0 and nrpe1 cells, which can adapt to grow in only 125 mM NaCl-containing growth medium. Salt treated nrpe1 and ddc cells but not wild type cells accumulate more mutations compared with their respective untreated cells. There is no enrichment of stress responsive genes in the list of mutated genes in salt treated cells compared to the list of mutated genes in untreated cells. Our results suggest that DNA methylation prevents the induction of mutagenesis by salt stress in plant cells during stress adaptation.

Tree species are characterized by their perennial growth habit, woody morphology, long juvenile period phase, mostly outcrossing behaviour, highly heterozygosity genetic makeup, and relatively high genetic diversity. The economically important trees have been an integral part of the human life system due to their provision of timber, fruit, fodder, and medicinal and/or health benefits. Despite its widespread application in agriculture, industrial and medicinal values, the molecular aspects of key economic traits of many tree species remain largely unexplored. Over the past two decades, research on forest tree genomics has generally lagged behind that of other agronomic crops. Genomic research on trees is motivated by the need to support genetic improvement programmes mostly for food trees and timber, and develop diagnostic tools to assist in recommendation for optimum conservation, restoration and management of natural populations. Research on long-lived woody perennials is extending our molecular knowledge and understanding of complex life histories and adaptations to the environment, enriching a field that has traditionally drawn its biological inference from a few short-lived herbaceous species. These concerns have fostered research aimed at deciphering the genomic basis of complex traits that are related to the adaptive value of trees. This review summarizes the highlights of tree genomics and offers some priorities for accelerating progress in the next decade.

Transferability of SSR markers from related species/genera is a rapid and cost-effective method to enhance genomic database of genetically neglected crops. Monotypic genus Tecomella undulata, a pharmacologically important endangered timber tree, found in hyper arid regions is one such genetic resource limited species, wherein neither SSR identification nor cross transferability studies have been initiated. Transferability of 69 cross-genera SSR primers selected from other members of family bignoniaceae (Incarvillea sinensis, I. mairei, Jacaranda copaia, Tabebuia aurea and Arrabidaea chica) showed 40.58% (28 primers) transferability amplifying 1–10 amplicons ranging in the size from 80to 600 bp in 24 accessions of T. undulata. Per cent marker transferability varied from 66.67% (A. chica) to 38.89% (J. copaia) among the genera tested while no transferable markers could be identified from I. sinensis. Transferability of simple di-/tri-nucleotide repeat (34.2–37.5%) and complex nucleotide sequence (60.0%) based SSR motifs were higher as compared to penta-/hexa-nucleotide based repeat motifs. Within the 28 transferable markers, 26 (92.86%) were polymorphic while 2 (7.14%) were monomorphic. Average number of alleles per primer was 5.39 while average polymorphic alleles per locus were 5.11. The PIC values of SSR markers ranged from 0.23 to 0.85 with an average of 0.59. Efficiency of the identified cross species SSR markers was tested for diversity analysis using a set of 24 trees (8 each of yellow, orange and red flower colour morphotypes). The 24 samples clustered into six groups with similarity coefficient ranging from 0.29 to 0.67, while six accessions formed distinct out groups. Distribution of accessions in the SSR dendrogram showed no correlation with flower colour. More diversity (99%) was observed within populations compared to that existing between populations (1%). The present study can enrich the genomic background of T. undulata by identifying suitable polymorphic markers from confamiliar species that can be applied for genetic diversity studies, mapping of QTLs and cultivar identification as well.

The agriculture sector is facing major challenges of food safety, production and risk of diseases under the changing climatic conditions. Nanomaterial has high proportion of the atoms, different surface compositions, density sites and relativities with respect to adsorption and redox reactions. These advantages of the nanomaterial can be exploited for its application in agriculture. Nanotechnology has the potential to transform the food industry by changing the way food is produced, processed, packaged, transported and consumed. The up-coming innovations in the agricultural field that are due to nanotechnology are reviewed. For example, the prospective of smart sensors for combating crop pathogens, disease forecasting, nano-catalysts for enhancing the effectiveness of herbicides and pesticides, nanotubes for removing water-borne pathogens, encapsulation of pesticides, nanofertilizers, etc., are discussed. In agriculture, synthetic agrochemicals need to be replaced by biopolymer materials in order to reduce the deleterious effects of resistance in plant pathogens, harm to non-target organisms and deterioration of soil health. Nevertheless, the toxicity level of the nanoparticles should be defined properly along with the risk assessment and its adverse effect on human health. The development of regulation, legislation, databases and alarm systems is required in order to exploit the benefits of this budding technology.

Substantial genetic diversity exists in the natural populations of desert teak which needs to be conserved in-situ as well as ex-situ to ensure sustainable utilization and survival of this endangered tree.

A simple method has been developed for clonal propagation of mature trees of Tecomella undulata (Sm.) Seem, a medicinally important deciduous timber tree of hot arid regions, via multiple shoot proliferation from axillary buds after examining the role of season influences and physico–chemical conditions on micropropagation. Spring season (March–April) was the best period for contamination free establishment of explants and maximum sprouting of healthy axillary buds. Shoots proliferated directly from the explant nodes cultured on Murashige and Skoog’s medium containing cytokinins, BAP supporting better growth compared to kinetin during shoot induction as well as multiplication phase. Cytokinin concentration influenced the bud induction frequency and optimal response of 2.6 buds per explant was achieved in 86.66% explants on media supplemented with 10 µM BAP. Stunted shoot buds with excessive callus were observed when cytokinin concentration was increased beyond optimal levels. Ascorbic acid (50 mg/l), arginine and citric acid (25 mg/l each) were added to proliferation and multiplication media for reducing callus proliferation and better shoot growth. Among the media (B5, MS, NN, WPM and SH) tested, SH was best for shoot multiplication. Shoot cultures were multiplied by regular subculture of axillary shoots on SH medium containing 5.0 µM each of BAP and kinetin. Shoots produced roots when cultured on ½× SH medium + 10 μM IBA. Regenerated plantlets were successfully transferred to field after hardening and acclimatization. Genetic homogeneity of tissue culture raised plants was confirmed by generation of monomorphic DNA fragments with Start codon targeted and intersimple sequence repeat (ISSR) markers.

Genetic variation and relationships among 37 cultivars of Ziziphus mauritiana (Lamk.) native of India were analyzed using start codon targeted (SCoT), inter-simple sequence repeats (ISSR), and ribosomal DNA (rDNA) markers. High level of polymorphism among SCoT (61.6%) and ISSR (61%) primers with higher PIC values ranging from 63.1 to 90.4% of SCoT and 47.3 to 88.8% of ISSR primers was recorded. SCoT and ISSR dendrograms revealed similarity coefficients ranging from 0.80 to 0.92 and 0.79 to 0.96, respectively, and clearly delineated all the cultivars of Z. mauritiana into well-supported distinct clusters. Greater Gst signifies higher amount of differentiation observed over multiple loci among seven Z. mauritiana populations. On the other hand, higher gene flow demonstrating a very high migration rate between Z. mauritiana populations indicated higher rates of transfer of alleles or genes from one population to another. The genetic diversity of population 1 (Rajasthan) was the richest among all the seven populations. The largest genetic distance was measured between Maharashtra and West Bengal and the least between Rajasthan and Punjab cultivars. Most of the genetic diversity exists within population rather than among populations. Substantial variation in the ITS-1 region signifies its phylogenetic utility specifically in assessing genetic diversity in Z. mauritiana. The clustering patterns using three molecular marker systems vis-à-vis place of origin exhibited no consistency in grouping of Z. mauritiana cultivars as cultivars from the same place of origin were genetically cataloged into different SCoT, ISSR, and ITS phylogram clusters indicating wide genetic diversity and distribution across agro-climatic zones validating the robustness of marker systems tested.

Tecomella undulata (Sm.) Seem commonly called Rohida or Desert teak (family bignoniaceae) is an important agroforestry tree having an important pharmacological and therapeutic uses. Its distribution is restricted to hot arid regions of India and Pakistan having < 150 to 500 mm annual rainfall. Genetic diversity status of this important endangered timber tree species designated state flower of Rajasthan remains unrevealed. Genetic diversity of 21 populations (108 accessions) encompassing yellow, red and orange coloured flower bearing morphotypes collected from all 12 districts of western Rajasthan, India, has been examined using start codon targeted (SCoT) polymorphism for the first time. Fingerprinting with 22 SCoT primers (out of 36 screened) generated 294 amplicons of 100 to 3000 bp size, of which 212 (71.6%) were polymorphic. Amplicon number varied from 4 (SCoT-9) to 24 (SCoT-15) with an average of 13.4 amplicons per primer. Average polymorphism information content (PIC), Nei's diversity index (H) and Shannon index (I) were 0.54, 0.22 and 0.36, respectively. Dendrogram generated using unweighted pair-group method with arithmetic mean (UPGMA) delineated the 108 accessions into 5 clusters while 2 accessions out grouped. Principal coordinate analysis (PCoA) also revealed similar clustering. High level of genetic differentiation among accessions/populations was attributed to cross pollination and continuous evolution under harsh agro-climatic conditions.

Discovery of plant growth regulators have materialized Haberlandt's concept of totipotency coined more than a century ago. A number of tissue culture based biotechniques are now possible due to the ability of growth regulators to influence morphogenesis. Physiological functions of most of the classical PGRs have been studied for decades, however, discovery of chemicals that interfere with synthesis, transport and action of endogenous growth regulators have further improved our knowledge regarding the role of these plant growth regulators in plant's growth and development. This review summarizes the role of such interfering and inhibiting compounds in in vitro growth and development of plants.

Introduction and selection of fast-growing exotic tree and shrub species into the arid regions of Indian subcontinent is imperative to ensure a sustained livelihood under harsh agro-climatic conditions in the region. Large scale mortality of perennials, mechanized agriculture, industrialization and population explosion, increased demand of fuel and fodder, and cutting of trees without adequate reforestation has also fueled the concern for saving such fragile ecosystems from degradation. Prosopis, a multipurpose, leguminous, nitrogen fixing genus encompassing approximately 45 species of trees and shrubs remains one of the most widely accepted genera in the arid regions as many of the species of the genus are highly adapted for survival in arid, semi-arid and usar lands. However, there is an urgent need to modify and improve the undesirable features like thorniness, bushy architecture, slow growth rate and high alkaloid content in leaves of important Prosopis spp. by developing tailored genotypes suitable for plantation and rapid growth in these dry regions. Limited progress has been made for improvement of the genus through conventional breeding programs due to lack of identified superior parental lines, lack of knowledge about extent of hybridization possible between species, genetic linkage maps and QTL linkage maps. Conventional propagation methods i.e., through seeds and rooting of cuttings are in place, but have limitations for development of genetically uniform planting material on a larger scale. Therefore, application of modern tools of biotechnology need to be standardized for harnessing maximum benefits from this plant. Improvement of this genus through genetic transformation requires an efficient regeneration system, which is yet to be perfected for large scale production of planting material. Genetic diversity studies, taxonomic delineation of species and subspecies and also the breeding programs can be more robustly addressed using molecular markers. An attempt has been made to review the need and the scope of genetic improvement of this important genus using modern tools of biotechnology. Key words: Fabaceae, Prosopis, micropropagation, molecular markers, tree improvement

Tecomella undulata (Sm.) Seem (family Bignoniaceae) is an economically and pharmaceutically important timber tree of arid regions of India. Overexploitation of natural stands coupled with minimal conservation and reforestation efforts has led to its incorporation in list of endangered species. This monotypic genus can be propagated only through seeds as nomethods are available for its vegetative propagation. Therefore, protocol for multiplication of T. undulata via direct regeneration using nodal segments from mature trees has been standardized. Authentication of genetic homogeneity of these in vitro-raised plants is necessary for commercial-scale application of the developed micropropagation protocol. PCR-based molecular markers which have emerged as simple, fast, reliable, and labor-effective tools for testing the genetic homogeneity of in vitro-raised plants were used in the present study. Arbitrary (random amplified polymorphic DNA, RAPD), semi-arbitrary (inter-simple sequence repeat, ISSR; start codon targeted (SCoT) polymorphism), and sequence-based (simple sequence repeat, SSR) markers were used. DNA samples of shoots maintained in vitro for 2 years collected after every 4 subculture cycles (of 3 weeks each) and field-transferred plantlets were compared with the mother tree DNA using 131 primers (25 each of RAPD, ISSR, SCoT and 56 SSR). Scorable unambiguous and reproducible DNA fragments were produced by 77 (21 RAPD, 20 ISSR, 22 SCoT and 14 SSR) primers. A total of 71, 93, 94, and 42 distinct and scorable DNA fragments were produced by RAPD, ISSR, SCoT, and SSR primers respectively with an average of 3.38, 4.65, 4.27, and 3.0 DNA fragments per primer. The true-to-type nature of the in vitro-raised plants of T. undulata undergoing up to 32 subculture passages over a period of approximately 2 years was authenticated by monomorphic DNA fragments amplified with all primer combinations. Therefore, the developed micropropagation protocol can be safely used on a commercial scale for multiplying T. undulata plants.

A diverse array of growth regulators interact at the cellular level to produce physiological and morphological effects on plant growth, morphology and yield. The five conventional growth regulators viz. auxins, cytokinins, gibberellins, abscisic acid and ethylene are being used in plant cell, tissue and organ cultures for decades, while many of them, like non-purine cytokinins, polyamines, jasmonates, brassinosteroids, oligosaccharides, sterols, phosphoinositosides, salicylic acid and systemins, have recently been discovered and tested for their effects in vitro. However, many have not yet been examined for their effects on in vitro growth and development of plants. In this review, we attempted to summarize the progress that has been made over the past two decades towards understanding the role of non conventional PGRs in plant growth and development.