Metabolomics-Driven Mining of Metabolite Resources: Applications and Prospects for Improving Vegetable Crops.

Vegetable crops possess a prominent nutri-metabolite pool that not only contributes to the crop performance in the fields, but also offers nutritional security for humans. In the pursuit of identifying, quantifying and functionally characterizing the cellular metabolome pool, biomolecule separation technologies, data acquisition platforms, chemical libraries, bioinformatics tools, databases and visualization techniques have come to play significant role. High-throughput metabolomics unravels structurally diverse nutrition-rich metabolites and their entangled interactions in vegetable plants. It has helped to link identified phytometabolites with unique phenotypic traits, nutri-functional characters, defense mechanisms and crop productivity. In this study, we explore mining diverse metabolites, localizing cellular metabolic pathways, classifying functional biomolecules and establishing linkages between metabolic fluxes and genomic regulations, using comprehensive metabolomics deciphers of the plant's performance in the environment. We discuss exemplary reports covering the implications of metabolomics, addressing metabolic changes in vegetable plants during crop domestication, stage-dependent growth, fruit development, nutri-metabolic capabilities, climatic impacts, plant-microbe-pest interactions and anthropogenic activities. Efforts leading to identify biomarker metabolites, candidate proteins and the genes responsible for plant health, defense mechanisms and nutri-rich crop produce are documented. With the insights on metabolite-QTL (mQTL) driven genetic architecture, molecular breeding in vegetable crops can be revolutionized for developing better nutritional capabilities, improved tolerance against diseases/pests and enhanced climate resilience in plants.

Inter-Genera Colonization of Ocimum tenuiflorum Endophytes in Tomato and Their Complementary Effects on Na+/K+ Balance, Oxidative Stress Regulation, and Root Architecture Under Elevated Soil Salinity.

Endophytic bacilli of ethano-botanical plant Ocimum tenuiflorum were screened for salt stress-alleviating traits in tomato. Four promising O. tenuiflorum endophytes (Bacillus safensis BTL5, Bacillus haynesii GTR8, Bacillus paralicheniformis GTR11, and Bacillus altitudinis GTS16) were used in this study. Confocal scanning laser microscopic studies revealed the inter-genera colonization of O. tenuiflorum endophytes in tomato plants, giving insights for widening the applicability of potential endophytes to other crops. Furthermore, in a pot trial under 150 mM NaCl concentration, the inoculated endophytes contributed in reducing salt toxicity and improving recovery from salt-induced oxidative stress by different mechanisms. Reduction in reactive oxygen species (ROS) (sub-cellular H2O2 and superoxide) accumulation was observed besides lowering programmed cell death and increasing chlorophyll content. Endophyte inoculation supplemented the plant antioxidant enzyme system via the modulation of enzymatic antioxidants, viz., peroxidase, ascorbate peroxidase, superoxide dismutase, and catalase, apart from increasing proline and total phenolics. Antioxidants like proline have dual roles of antioxidants and osmoregulation, which might also have contributed to improved water relation under elevated salinity. Root architecture, viz., root length, projection area, surface area, average diameter, tips, forks, crossings, and the number of links, was improved upon inoculation, indicating healthy root growth and enhanced nutrient flow and water homeostasis. Regulation of Na+/K+ balance and water homeostasis in the plants were also evident from the modulation in the expression of abiotic stress-responsive genes, viz., LKT1, NHX1, SOS1, LePIP2, SlERF16, and SlWRKY39. Shoot tissues staining with light-excitable Na+ indicator Sodium GreenTM Tetra (tetramethylammonium) salt showed low sodium transport and accumulation in endophyte-inoculated plants. All four endophytes exhibited different mechanisms for stress alleviation and indicated complementary effects on plant growth. Furthermore, this could be harnessed in the form of a consortium for salt stress alleviation. The present study established inter-genera colonization of O. tenuiflorum endophytes in tomato and revealed its potential in maintaining Na+/K+ balance, reducing ROS, and improving root architecture under elevated salinity.

Stage-dependent concomitant microbial fortification improves soil nutrient status, plant growth, antioxidative defense system and gene expression in rice.

Stage-dependent concomitant fortification of rice (Oryza sativa L.) varieties PB1612 and CO51 with microbial inoculants Trichoderma asperellum and Pseudomonas fluorescens as seed coating, seedling root inoculation and soil application enhanced growth, activated antioxidant enzymes and modulated defence-related genes in plants. Microbial inoculants improved shoot height, tiller numbers, fresh weight and dry biomass. Co-inoculation was more impactful in enhancing plant growth and development as compared to single inoculation. Single and co-inoculation improved organic carbon (OC) and N, P and K content in the soil substantially. Mean values between control and co-inoculation varied significantly for OC in PB1612 (p0.001) and CO51 (p0.019) and phosphorus content in PB1612 (p0.044) and CO51 (p0.021). Microbial inoculation enhanced soil nutrients and increased their bioavailability for the plants. Total polyphenolics, flavonoids and protein content increased in the leaves following microbial inoculation. Enhanced non-enzymatic antioxidant parameters (ABTS, DPPH, Fe-ion reducing power and Fe-ion chelation) was found in microbe inoculated rice reflecting high free radical scavenging activity in polyphenolics-rich leaf extracts. Increased enzyme activity of superoxide dismutase (SOD), glutathione reductase (GR), phenylalanine ammonia-lyase (PAL), peroxidase (PO), glutathione peroxidase (GPX), ascorbate peroxidase (APX) and catalase (CAT) showed improved ROS scavenging in rice plants having co-inoculation. Over-expression of PAL, cCuZn-SOD and CAT genes in microbial inoculated rice plants was recorded. The study concludes that plant stage-wise concomitant fortification by microbial inoculants could play multi-pronged manifestations at physiological, biochemical and molecular level in rice to positively influence growth, development and defense attributes in plants.

Sphingobacterium sp. BHU-AV3 Induces Salt Tolerance in Tomato by Enhancing Antioxidant Activities and Energy Metabolism.

Salt tolerant bacteria can be helpful in improving a plant's tolerance to salinity. Although plant-bacteria interactions in response to salt stress have been characterized, the precise molecular mechanisms by which bacterial inoculation alleviates salt stress in plants are still poorly explored. In the present study, we aimed to determine the role of a salt-tolerant plant growth-promoting rhizobacteria (PGPR) Sphingobacterium BHU-AV3 for improving salt tolerance in tomato through investigating the physiological responses of tomato roots and leaves under salinity stress. Tomato plants inoculated with BHU-AV3 and challenged with 200 mM NaCl exhibited less senescence, positively correlated with the maintenance of ion balance, lowered reactive oxygen species (ROS), and increased proline content compared to the non-inoculated plants. BHU-AV3-inoculated plant leaves were less affected by oxidative stress, as evident from a reduction in superoxide contents, cell death, and lipid peroxidation. The reduction in ROS level was associated with the increased antioxidant enzyme activities along with multiple-isoform expression [peroxidase (POD), polyphenol oxidase (PPO), and superoxide dismutase (SOD)] in plant roots. Additionally, BHU-AV3 inoculation induced the expression of proteins involved in (i) energy production [ATP synthase], (ii) carbohydrate metabolism (enolase), (iii) thiamine biosynthesis protein, (iv) translation protein (elongation factor 1 alpha), and the antioxidant defense system (catalase) in tomato roots. These findings have provided insight into the molecular mechanisms of bacteria-mediated alleviation of salt stress in plants. From the study, we can conclude that BHU-AV3 inoculation effectively induces antioxidant systems and energy metabolism in tomato roots, which leads to whole plant protection during salt stress through induced systemic tolerance.

Microbial inoculation in rice regulates antioxidative reactions and defense related genes to mitigate drought stress.

Microbial inoculation in drought challenged rice triggered multipronged steps at enzymatic, non-enzymatic and gene expression level. These multifarious modulations in plants were related to stress tolerance mechanisms. Drought suppressed growth of rice plants but inoculation with Trichoderma, Pseudomonas and their combination minimized the impact of watering regime. Induced PAL gene expression and enzyme activity due to microbial inoculation led to increased accumulation of polyphenolics in plants. Enhanced antioxidant concentration of polyphenolics from microbe inoculated and drought challenged plants showed substantially high values of DPPH, ABTS, Fe-ion reducing power and Fe-ion chelation activity, which established the role of polyphenolic extract as free radical scavengers. Activation of superoxide dismutase that catalyzes superoxide (O2-) and leads to the accumulation of H2O2 was linked with the hypersensitive cell death response in leaves. Microbial inoculation in plants enhanced activity of peroxidase, ascorbate peroxidase, glutathione peroxidase and glutathione reductase enzymes. This has further contributed in reducing ROS burden in plants. Genes of key metabolic pathways including phenylpropanoid (PAL), superoxide dismutation (SODs), H2O2 peroxidation (APX, PO) and oxidative defense response (CAT) were over-expressed due to microbial inoculation. Enhanced expression of OSPiP linked to less-water permeability, drought-adaptation gene DHN and dehydration related stress inducible DREB gene in rice inoculated with microbial inoculants after drought challenge was also reported. The impact of Pseudomonas on gene expression was consistently remained the most prominent. These findings suggested that microbial inoculation directly caused over-expression of genes linked with defense processes in plants challenged with drought stress. Enhanced enzymatic and non-enzymatic antioxidant reactions that helped in minimizing antioxidative load, were the repercussions of enhanced gene expression in microbe inoculated plants. These mechanisms contributed strongly towards stress mitigation. The study demonstrated that microbial inoculants were successful in improving intrinsic biochemical and molecular capabilities of rice plants under stress. Results encouraged us to advocate that the practice of growing plants with microbial inoculants may find strategic place in raising crops under abiotic stressed environments.

Identification, characterization and expression profiles of Fusarium udum stress-responsive WRKY transcription factors in Cajanus cajan under the influence of NaCl stress and Pseudomonas fluorescens OKC.

The WRKY gene family has never been identified in pigeonpea (Cajanus cajan). Therefore, objective of the present study was to identify the WRKY gene family in pigeonpea and characterize the Fusarium udum stress-responsive WRKY genes under normal, NaCl-stressed and Pseudomonas fluorescens OKC (a plant growth-promoting bacterial strain) treated conditions. The aim was to characterize the Fusarium udum stress-responsive WRKY genes under some commonly occurring field conditions. We identified 97 genes in the WRKY family of pigeonpea, using computational prediction method. The gene family was then classified into three groups through phylogenetic analysis of the homologous genes from the representative plant species. Among the 97 identified WRKY genes 35 were further classified as pathogen stress responsive genes. Functional validation of the 35 WRKY genes was done through generating transcriptional profiles of the genes from root tissues of pigeonpea plants under the influence of P. fluorescens OKC after 24 h of stress application (biotic: Fusarium udum, abiotic: NaCl). The entire experiment was conducted in two pigeonpea cultivars Asha (resistant to F. udum) and Bahar (susceptible to F. udum) and the results were concluded on the basis of transcriptional regulation of the WRKY genes in both the pigeonpea cultivars. The results revealed that among the 35 tentatively identified biotic stress responsive CcWRKY genes, 26 were highly F. udum responsive, 17 were better NaCl responsive compared to F. udum and 11 were dual responsive to both F. udum and NaCl. Application of OKC was able to enhance transcript accumulation of the individual CcWRKY genes to both the stresses when applied individually but not in combined challenge of the two stresses. The results thus indicated that CcWRKY genes play a vital role in the defense signaling against F. udum and some of the F. udum responsive CcWRKYs (at least 11 in pigeonpea) are also responsive to abiotic stresses such as NaCl. Further, plant beneficial microbes such as P. fluorescens OKC also help pegionpea to defend itself against the two stresses (F. udum and NaCl) through enhanced expression of the stress responsive CcWRKY genes when the stresses are applied individually.

Trichoderma mediate early and enhanced lignifications in chickpea during Fusarium oxysporum f. sp. ciceris infection.

Lignifications in secondary cell walls play a significant role in defense mechanisms of plants against the invading pathogens. In the present study, we investigated Trichoderma strain specific lignifications in chickpea plants pre-treated with 10 potential Trichoderma strains and subsequently challenged with the wilt pathogen Fusarium oxysporum f. sp. ciceris (Foc). Trichoderma-induced lignifications in chickpea were observed through histochemical staining and expression of some genes of the lignin biosynthetic pathway. Lignifications were observed in transverse sections of shoots near the soil line through histochemical staining and expression pattern of the target genes was observed in root tissues through semi quantitative RT-PCR at different time intervals after inoculation of F. oxysporum f. sp. ciceris. Lignin deposition and expression pattern of the target genes were variable in each treatment. Lignifications were enhanced in all 10 Trichoderma strain treated and F. oxysporum f. sp. ciceris challenged chickpea plants. However, four Trichoderma strains viz., T-42, MV-41, DFL, and RO, triggered significantly high lignifications compared to the other six strains. Time course studies showed that effective Trichoderma isolates induced lignifications very early compared to the other strains and the process of lignifications nearly completes within 6 days of pathogen challenge. Thus, from the results it can be concluded that effective Trichoderma strains trigger lignifications very early in chickpea under Foc challenge and provide better protection to chickpea plants.

Trichoderma asperellum T42 Reprograms Tobacco for Enhanced Nitrogen Utilization Efficiency and Plant Growth When Fed with N Nutrients.

Trichoderma spp., are saprophytic fungi that can improve plant growth through increased nutrient acquisition and change in the root architecture. In the present study, we demonstrate that Trichoderma asperellum T42 mediate enhancement in host biomass, total nitrogen content, nitric oxide (NO) production and cytosolic Ca2+ accumulation in tobacco. T42 inoculation enhanced lateral root, root hair length, root hair density and root/shoot dry mass in tobacco under deprived nutrients condition. Interestingly, these growth attributes were further elevated in presence of T42 and supplementation of NO3- and NH4+ nutrients to tobacco at 40 and 70 days, particularly in NO3- supplementation, whereas no significant increment was observed in nia30 mutant. In addition, NO production was more in tobacco roots in T42 inoculated plants fed with NO3- nutrient confirming NO generation was dependent on NR pathway. NO3- dependent NO production contributed to increase in lateral root initiation, Ca2+ accumulation and activities of nitrate transporters (NRTs) in tobacco. Higher activities of several NRT genes in response to T42 and N nutrients and suppression of ammonium transporter (AMT1) suggested that induction of high affinity NRTs help NO3- acquisition through roots of tobacco. Among the NRTs NRT2.1 and NRT2.2 were more up-regulated compared to the other NRTs. Addition of sodium nitroprusside (SNP), relative to those supplied with NO3-/NH4+ nutrition and T42 treated plants singly, and with application of NO inhibitor, cPTIO, confirmed the altered NO fluorescence intensity in tobacco roots. Our findings suggest that T42 promoted plant growth significantly ant N content in the tobacco plants grown under N nutrients, notably higher in NO3-, providing insight of the strategy for not only tobacco but probably for other crops as well to adapt to fluctuating nitrate availability in soil.

Compatible Rhizosphere-Competent Microbial Consortium Adds Value to the Nutritional Quality in Edible Parts of Chickpea.

Chickpea is used as a high-energy and protein source in diets of humans and livestock. Moreover, chickpea straw can be used as alternative of forage in ruminant diets. The present study evaluates the effect of beneficial microbial inoculation on enhancing the nutritional values in edible parts of chickpea. Two rhizosphere-competent compatible microbes (Pseudomonas fluorescens OKC and Trichoderma asperellum T42) were selected and applied to seeds either individually or in consortium before sowing. Chickpea seeds treated with the microbes showed enhanced plant growth [88.93% shoot length at 60 days after sowing (DAS)] and biomass accumulation (21.37% at 120 DAS). Notably, the uptake of mineral nutrients, viz., N (90.27, 91.45, and 142.64%), P (14.13, 58.73, and 56.84%), K (20.5, 9.23, and 35.98%), Na (91.98, 101.66, and 36.46%), Ca (16.61, 29.46, and 16%), and organic carbon (28.54, 17.09, and 18.54%), was found in the seed, foliage, and pericarp of the chickpea plants, respectively. Additionally, nutritional quality, viz., total phenolic (59.7, 2.8, and 17.25%), protein (9.78, 18.53, and 7.68%), carbohydrate content (26.22, 30.21, and 26.63%), total flavonoid content (3.11, 9.15, and 7.81%), and reducing power (112.98, 75.42, and 111.75%), was also found in the seed, foliage, and pericarp of the chickpea plants. Most importantly, the microbial-consortium-treated plants showed the maximum increase of nutrient accumulation and enhancement in nutritional quality in all edible parts of chickpea. Nutritional partitioning in different edible parts of chickpea was also evident in the microbial treatments compared to their uninoculated ones. The results thus clearly demonstrated microbe-mediated enhancement in the dietary value of the edible parts of chickpea because seeds are consumed by humans, whereas pericarp and foliage (straw) are used as an alternative of forage and roughage in ruminant diets.

Trichoderma asperellum (T42) and Pseudomonas fluorescens (OKC)-Enhances Resistance of Pea against Erysiphe pisi through Enhanced ROS Generation and Lignifications.

Plant signaling mechanisms are not completely understood in plant-fungal biotrophic pathogen interactions. Further how such interactions are influenced by compatible rhizosphere microbes are also not well-studied. Therefore, we explored the pea-Erysiphe pisi (obligate biotroph) system to understand the interaction and applied compatible rhizospheric bio-agents Trichoderma asperellum (T42) and Pseudomonas fluorescens (OKC) singly or in combination to assess their influence on the host while under the pathogen challenge. Transcript accumulation pattern of some vital genes in the lignin biosynthetic pathway in pea under E. pisi challenge indicated enhanced activation of the pathway. Interestingly, transcript accumulations were even higher in the bio-agent treated plants compared to untreated plants after pathogen inoculation particularly in co-inoculated treatments. Further, down regulation of the lignifications-associated ABC transporter gene in the pathogen challenged plants possibly is an indication of passive diffusion of monolignols across the membrane from symplast. Additionally, up regulation of NADPH oxidase gene revealed ROS generation in the challenged plants which was confirmed through spectrophotometric estimation of H2O2. Up regulation of laccase and peroxidase along with higher H2O2 generation points out their involvement in lignifications which was further confirmed through cross section analysis of pea stems that showed increased lignifications in pathogen challenged plants co-inoculated with the bioagents. Interestingly, pathogen responsive MAPK homologs MAPK3/MAPK6 and the enzyme serine threonine kinase that activates MAPKs were down regulated and the results possibly indicate non-participation of the MAPK cascade in this interaction. Therefore, it can be concluded that the microbial treatments enhanced pea resistance to E. pisi by generation of ROS and lignifications.

Multiple post-domestication origins of kabuli chickpea through allelic variation in a diversification-associated transcription factor.

Chickpea (Cicer arietinum) is among the founder crops domesticated in the Fertile Crescent. One of two major forms of chickpea, the so-called kabuli type, has white flowers and light-colored seed coats, properties not known to exist in the wild progenitor. The origin of the kabuli form has been enigmatic. We genotyped a collection of wild and cultivated chickpea genotypes with 538 single nucleotide polymorphisms (SNPs) and examined patterns of molecular diversity relative to geographical sources and market types. In addition, we examined sequence and expression variation in candidate anthocyanin biosynthetic pathway genes. A reduction in genetic diversity and extensive genetic admixture distinguish cultivated chickpea from its wild progenitor species. Among germplasm, the kabuli form is polyphyletic. We identified a basic helix-loop-helix (bHLH) transcription factor at chickpea's B locus that conditions flower and seed colors, orthologous to Mendel's A gene of garden pea, whose loss of function is associated invariantly with the kabuli type of chickpea. From the polyphyletic distribution of the kabuli form in germplasm, an absence of nested variation within the bHLH gene and invariant association of loss of function of bHLH among the kabuli type, we conclude that the kabuli form arose multiple times during the phase of phenotypic diversification after initial domestication of cultivated chickpea.

Plant genotype, microbial recruitment and nutritional security.

Agricultural food products with high nutritional value should always be preferred over food products with low nutritional value. Efforts are being made to increase nutritional value of food by incorporating dietary supplements to the food products. The same is more desirous if the nutritional value of food is increased under natural environmental conditions especially in agricultural farms. Fragmented researches have demonstrated possibilities in achieving the same. The rhizosphere is vital in this regard for not only health and nutritional status of plants but also for the microorganisms colonizing the rhizosphere. Remarkably robust composition of plant microbiome with respect to other soil environments clearly suggests the role of a plant host in discriminating its colonizers (Zancarini et al., 2012). A large number of biotic and abiotic factors are believed to manipulate the microbial communities in the rhizosphere. However, plant genotype has proven to be the key in giving the final shape of the rhizosphere microbiome (Berendsen et al., 2012; Marques et al., 2014).

Pseudomonas fluorescens and Trichoderma asperellum Enhance Expression of Gα Subunits of the Pea Heterotrimeric G-protein during Erysiphe pisi Infection.

We investigated the transcript accumulation patterns of all three subunits of heterotrimeric G-proteins (Gα1 and 2, Gß, and Gγ) in pea under stimulation of two soil-inhabiting rhizosphere microbes Pseudomonas fluorescens OKC and Trichoderma asperellum T42. The microbes were either applied individually or co-inoculated and the transcript accumulation patterns were also investigated after challenging the same plants with a fungal biotrophic pathogen Erysiphe pisi. We observed that mostly the transcripts of Gα 1 and 2 subunits were accumulated when the plants were treated with the microbes (OKC and T42) either individually or co-inoculated. However, transcript accumulations of Gα subunits were highest in the T42 treatment particularly under the challenge of the biotroph. Transcript accumulations of the other two subunits Gß and Gγ were either basal or even lower than the basal level. There was an indication for involvement of JA-mediated pathway in the same situations as activation of LOX1 and COI1 were relatively enhanced in the microbe co-inoculated treatments. Non-increment of SA content as well as transcripts of SA-dependent PR1 suggested non-activation of the SA-mediated signal transduction in the interaction of pea with E. pisi under the stimuli of OKC and T42. Gα1 and 2 transcript accumulations were further correlated with peroxidases activities, H2O2 generation and accumulation in ABA in pea leaves under OKC and T42 stimulations and all these activities were positively correlated with stomata closure at early stage of the biotroph challenge. The microbe-induced physiological responses in pea leaves finally led to reduced E. pisi development particularly in OKC and T42 co-inoculated plants. We conclude that OKC and T42 pretreatment stimulate transcript accumulations of the Gα1 and Gα2 subunits of the heterotrimeric G protein, peroxidases activities and phenol accumulation in pea during infection by E. pisi. The signal transduction was possibly mediated through JA in pea under the stimulus of the microbes and the cumulative effect of the co-inoculated microbes had a suppressive effect on E. pisi conidial development on pea leaves.

Solid waste management of temple floral offerings by vermicomposting using Eisenia fetida.

Recycling of temple waste (TW) mainly comprising of floral offerings was done through vermitechnology using Eisenia fetida and its impact on seed germination and plant growth parameters was studied by comparing with kitchen waste (KW) and farmyard waste (FYW) vermicompost (VC). The worm biomass was found to be maximum in TW VC compared to KW and FYW VCs at both 40 and 120days old VCs. Physico-chemical analysis of worm-worked substrates showed better results in TW VC especially in terms of electrical conductivity, C/N, C/P and TK. 10% TW VC-water extract (VCE) showed stimulatory effect on germination percentage of chickpea seeds while KW and FYW VCE proved effective at higher concentration. Variation in growth parameters was also observed with change in the VC-soil ratio and TW VC showed enhanced shoot length, root length, number of secondary roots and total biomass at 12.5% VC compared to KW and FYW VC.

Large-scale development of cost-effective single-nucleotide polymorphism marker assays for genetic mapping in pigeonpea and comparative mapping in legumes.

Single-nucleotide polymorphisms (SNPs, >2000) were discovered by using RNA-seq and allele-specific sequencing approaches in pigeonpea (Cajanus cajan). For making the SNP genotyping cost-effective, successful competitive allele-specific polymerase chain reaction (KASPar) assays were developed for 1616 SNPs and referred to as PKAMs (pigeonpea KASPar assay markers). Screening of PKAMs on 24 genotypes [23 from cultivated species and 1 wild species (Cajanus scarabaeoides)] defined a set of 1154 polymorphic markers (77.4%) with a polymorphism information content (PIC) value from 0.04 to 0.38. One thousand and ninety-four PKAMs showed polymorphisms between parental lines of the reference mapping population (C. cajan ICP 28 × C. scarabaeoides ICPW 94). By using high-quality marker genotyping data on 167 F(2) lines from the population, a comprehensive genetic map comprising 875 PKAMs with an average inter-marker distance of 1.11 cM was developed. Previously mapped 35 simple sequence repeat markers were integrated into the PKAM map and an integrated genetic map of 996.21 cM was constructed. Mapped PKAMs showed a higher degree of synteny with the genome of Glycine max followed by Medicago truncatula and Lotus japonicus and least with Vigna unguiculata. These PKAMs will be useful for genetics research and breeding applications in pigeonpea and for utilizing genome information from other legume species.

Genetic patterns of domestication in pigeonpea (Cajanus cajan (L.) Millsp.) and wild Cajanus relatives.

Pigeonpea (Cajanus cajan) is an annual or short-lived perennial food legume of acute regional importance, providing significant protein to the human diet in less developed regions of Asia and Africa. Due to its narrow genetic base, pigeonpea improvement is increasingly reliant on introgression of valuable traits from wild forms, a practice that would benefit from knowledge of its domestication history and relationships to wild species. Here we use 752 single nucleotide polymorphisms (SNPs) derived from 670 low copy orthologous genes to clarify the evolutionary history of pigeonpea (79 accessions) and its wild relatives (31 accessions). We identified three well-supported lineages that are geographically clustered and congruent with previous nuclear and plastid sequence-based phylogenies. Among all species analyzed Cajanus cajanifolius is the most probable progenitor of cultivated pigeonpea. Multiple lines of evidence suggest recent gene flow between cultivated and non-cultivated forms, as well as historical gene flow between diverged but sympatric species. Evidence supports that primary domestication occurred in India, with a second and more recent nested population bottleneck focused in tropical regions that is the likely consequence of pigeonpea breeding. We find abundant allelic variation and genetic diversity among the wild relatives, with the exception of wild species from Australia for which we report a third bottleneck unrelated to domestication within India. Domesticated C. cajan possess 75% less allelic diversity than the progenitor clade of wild Indian species, indicating a severe "domestication bottleneck" during pigeonpea domestication.

Effect of plant growth-promoting Rhizobacteria and culture filtrate of Sclerotium rolfsii on phenolic and salicylic acid contents in chickpea (Cicer arietinum).

Two plant growth-promoting rhizobacteria (PGPR), viz., Pseudomonas fluorescens strain Pf4 and P. aeruginosa strain Pag, protected chickpea ( Cicer arietinum) plants from Sclerotium rolfsii infection when applied singly or in combination as seed treatment. Pag gave the best protection to the seedlings, applied either singly (mortality 16%) or in combination with Pf4 (mortality 17%) compared with 44% and 24% mortality in control and Pf4 treatment, respectively. The two PGPR strains induced the synthesis of specific phenolic acids, salicylic acid (SA), as well as total phenolics at different growth stages of chickpea seedlings with varied amount. The maximum amount of total phenolics was recorded in all the aerial parts of 4-week-old plants. Gallic, ferulic, chlorogenic, and cinnamic acids were the major phenolic acids detected in high-performance liquid chromatography (HPLC) analysis. Induction of such phenolic acids in the seedlings was observed up to 6 weeks in comparison with control. Salicylic acid (SA) was induced frequently during the first 3 weeks of growth only. Between the two strains, Pag was more effective in inducing phenolic acid synthesis applied either singly or in combination with strain Pf4 during the entire 6 weeks of growth of chickpea. In the presence of a culture filtrate of S. rolfsii, the two Pseudomonas strains induced more phenolic acids in treated than in non-treated and control plants. The occurrence of salicylic acid was frequent in the first 24 h, but infrequent at 48 and 96 h. Foliar spray of Pseudomonas strains also enhanced the phenolic acid content as well as total phenolics within 24 h of application. Gallic, chlorogenic, and cinnamic acids were consistently discerned in the treated leaves, whereas SA was absent even up to 96 h of application. Resistance in chickpea plants by Pseudomonas strains through induction of phenolic compounds as well as induced systemic resistance via SA-dependent pathway was evident.