Genome-Wide Association Study (GWAS) for Identifying SNPs and Genes Related to Phosphate-Induced Phenotypic Traits in Tomato (Solanum lycopersicum L.).

Phosphate (P) is a crucial macronutrient for normal plant growth and development. The P availability in soils is a limitation factor, and understanding genetic factors playing roles in plant adaptation for improving P uptake is of great biological importance. Genome-wide association studies (GWAS) have become indispensable tools in unraveling the genetic basis of complex traits in various plant species. In this study, a comprehensive GWAS was conducted on diverse tomato (Solanum lycopersicum L.) accessions grown under normal and low P conditions for two weeks. Plant traits such as shoot height, primary root length, plant biomass, shoot inorganic content (SiP), and root inorganic content (RiP) were measured. Among several models of GWAS tested, the Bayesian-information and linkage disequilibrium iteratively nested keyway (BLINK) models were used for the identification of single nucleotide polymorphisms (SNPs). Among all the traits analyzed, significantly associated SNPs were recorded for PB, i.e., 1 SNP (SSL4.0CH10_49261145) under control P, SiP, i.e., 1 SNP (SSL4.0CH08_58433186) under control P and 1 SNP (SSL4.0CH08_51271168) under low P and RiP i.e., 2 SNPs (SSL4.0CH04_37267952 and SSL4.0CH09_4609062) under control P and 1 SNP (SSL4.0CH09_3930922) under low P condition. The identified SNPs served as genetic markers pinpointing regions of the tomato genome linked to P-responsive traits. The novel candidate genes associated with the identified SNPs were further analyzed for their protein-protein interactions using STRING. The study provided novel candidate genes, viz. Solyc10g050370 for PB under control, Solyc08g062490, and Solyc08g062500 for SiP and Solyc09g010450, Solyc09g010460, Solyc09g010690, and Solyc09g010710 for RiP under low P condition. These findings offer a glimpse into the genetic diversity of tomato accessions' responses to P uptake, highlighting the potential for tailored breeding programs to develop P-efficient tomato varieties that could adapt to varying soil conditions, making them crucial for sustainable agriculture and addressing global challenges, such as soil depletion and food security.

Combinatorial impacts of elevated CO2 and temperature affect growth, development, and fruit yield in Capsicum chinense Jacq.

Hot chilli ('Bhut Jolokia') (Capsicum chinense Jacq.) is the hottest chilli widely grown in the North-Eastern region of India for its high pungency. However, little information is available on its physiology, growth and developmental parameters including yield. Therefore, the present research was undertaken to study the physiological responses of Bhut Jolokia under elevated CO2 (eCO2) and temperature. Two germplasms from two different agro-climatic zones (Assam and Manipur) within the North-East region of India were collected based on the pungency. The present study explored the interactive effect of eCO2 [at 380, 550, 750 ppm (parts per million)] and temperature (at ambient, > 2 °C above ambient, and > 4 °C above ambient) on various physiological processes, and expression of some photosynthesis and capsaicin related genes in both the germplasms. Results revealed an increase (> 1-2 fold) in the net photosynthetic rate (Pn), carbohydrate content, and C: N ratio in 'Bhut Jolokia' under eCO2 and elevated temperature regimes compared to ambient conditions within the germplasms. Gene expression studies revealed an up-regulation of photosynthesis-related genes such as Cs RuBPC2 (Ribulose biphosphate carboxylase 2) and Cs SPS (Sucrose phosphate synthase) which, explained the higher Pn under eCO2 and temperature conditions. Both the germplasm showed better performance under CTGT-II (Carbon dioxide Temperature Gradient Tunnel having 550 ppm CO2 and temperature of 2 °C above ambient) in terms of various physiological parameters and up-regulation of key photosynthesis-related genes. An up-regulation of the Cs  capsaicin synthase gene was also evident in the study, which could be due to the metabolite readjustment in 'Bhut Jolokia'. In addition, the cultivar from Manipur (cv. 1) had less fruit drop compared to the cultivar from Assam (cv. 2) in CTGT II. The data indicated that 550 ppm of eCO2 and temperature elevation of > 2 °C above the ambient with CTGT-II favored the growth and development of 'Bhut Jolokia'. Thus, results suggest that Bhut Jolokia grown under the elevation of CO2 up to 550 ppm and temperature above 2 °C than ambient may support the growth, development, and yield. Supplementary Information: The online version contains supplementary material available at 10.1007/s12298-023-01294-9.

Recent trends in root phenomics of plant systems with available methods- discrepancies and consonances.

The phenotyping of plant roots is a challenging task and poses a major lacuna in plant root research. Roots rhizospheric zone is affected by several environmental cues among which salinity, drought, heavy metal and soil pH are key players. Among biological factors, fungal, nematode and bacterial interactions with roots are vital for improving nutrient uptake efficiency in plants. The subterranean nature of a plant root and the limited number of approaches for root phenotyping offers a great challenge to the plant breeders to select a desirable root trait under different stress conditions. Identification of key root traits can provide a basic understanding for generating crop plants with enhanced ability to withstand various biotic or abiotic stresses. For instance, crops with improved soil exploration potential, phosphate uptake efficiency, water use efficiency and others. Laboratory methods such as hydroponics, rhizotron, rhizoslide and luminescence observatory for roots do not provide precise and desired root quantification attributes. Though 3D imaging by X-ray computed tomography (X-ray-CT) and magnetic resonance imaging techniques are complex, however, it provides the most applicable and practically relevant data for quantifying root system architecture traits. This review outlines the current developments in root studies including recent approaches viz. X-ray-CT, MRI, thermal infrared imaging and minirhizotron. Although root phenotyping is a laborious procedure, it offers multiple advantages by removing discrepancies and providing the actual practical significance of plant roots for breeding programs.

Paclobutrazol improves surface water use efficiency by regulating allometric trait behavior in maize.

Paclobutrazol (PBZ) role in drought management of maize is least understood. In maize, root traits are linked with surface water management. Over three years, early and terminal deficit irrigation (EDI and TDI) with or without PBZ were imposed on DKC-9144 and PG-2475 maize varieties. Several allometric parameters viz. stem height, stem diameter, leaf area and root traits along with physiological processes were measured. Implication of these parameters in the management of soil surface irrigation in terms of water use efficiency (WUE) was demonstrated in maize. Increased number of lateral roots and root number density in DKC-9144 provided more surface area for water absorption for better management of EDI. Root growth rates showed a similar pattern with root length, root surface areas, and root numbers in EDI. Elevated expressions of ZmRTCL, ZmRTCS and ZmARF34 in EDI and EDI plus PBZ were associated with seminal roots and root laterals initiation. Under TDI alone or in combination with PBZ, root lengths (BRL, CRL, SRL) and root surface areas varied in DKC-9144 and PG-2475 over control. Furthermore, correlation analysis showed that decrease in WUE under TDI was significantly associated with a reduction in stem thickness and leaf surface area. For WUE_N in TDI and PBZ plus TDI, structural equation modelling proposed, brace root surface area (BRSA_N) as a positive contributor, while a negative contributor was seminal root surface area (SRSA_N). Present study explained the importance of specific root traits and their association with other allometric parameters for improving WUE in DKC-9144 variety of maize and the crop in general.

Green synthesis of zinc oxide nanoparticles using Eucalyptus lanceolata leaf litter: characterization, antimicrobial and agricultural efficacy in maize.

In the present study, green synthesis of zinc oxide nanoparticles (ZnO NP) using Eucalyptus lanceolatus (leaf litter) extract was explored after characterization with UV spectrophotometery, Fourier Transform Infrared analysis, X-ray diffraction and TEM studies. ZnO NPs stability was ensured with - 32.1 mV zeta potential, while TEM showed ZnO NP as hexagonal structure (100 nm). In vitro antimicrobial activity showed potential of ZnO NP against pathogens causing diseases in maize plants. Both in vitro and in vivo studies of ZnO NP and ZnSO4 (200 ppm and 400 ppm) over a two year period (2019, 2020) were conducted on Zea mays L. var. PG2458. ZnO NP seed priming improved seed vigor index, germination percentage, shoot and root length and fresh biomass. Foliar application improved stem diameter and leaf surface area. Physiological status was relatively better, while reproductive attributes got altered to guide resource allocation for better cob growth and biomass with ZnO NP. Leaf, cob, grain and total Zn was maximum for 200 ppm ZnO NP. Translocation of Zn from leaf to cob and cob to grain was faster for ZnO NP compared to ZnSO4. Higher concentration (400 ppm) of ZnO NPs and ZnSO4 proved phytotoxic for plant growth attributes. Supplementary Information: The online version contains supplementary material available at 10.1007/s12298-022-01136-0.

Plants Metabolome Study: Emerging Tools and Techniques.

Metabolomics is now considered a wide-ranging, sensitive and practical approach to acquire useful information on the composition of a metabolite pool present in any organism, including plants. Investigating metabolomic regulation in plants is essential to understand their adaptation, acclimation and defense responses to environmental stresses through the production of numerous metabolites. Moreover, metabolomics can be easily applied for the phenotyping of plants; and thus, it has great potential to be used in genome editing programs to develop superior next-generation crops. This review describes the recent analytical tools and techniques available to study plants metabolome, along with their significance of sample preparation using targeted and non-targeted methods. Advanced analytical tools, like gas chromatography-mass spectrometry (GC-MS), liquid chromatography mass-spectroscopy (LC-MS), capillary electrophoresis-mass spectrometry (CE-MS), fourier transform ion cyclotron resonance-mass spectrometry (FTICR-MS) matrix-assisted laser desorption/ionization (MALDI), ion mobility spectrometry (IMS) and nuclear magnetic resonance (NMR) have speed up precise metabolic profiling in plants. Further, we provide a complete overview of bioinformatics tools and plant metabolome database that can be utilized to advance our knowledge to plant biology.

Nickel excess affects phenology and reproductive attributes of Asterella wallichiana and Plagiochasma appendiculatum growing in natural habitats.

Bryophytes are potent metal absorbers, thriving well on heavy metal (HM)-polluted soils. Mechanisms controlling uptake, compartmentalization and impacts of HMs on bryophytes life cycle are largely unknown. The current study is an effort to decipher mechanisms of nickel (Ni) excess-induced effects on the phenological events of two bryophytes, Asterella wallichiana and Plagiochasma apendiculatum growing in natural habitats. Observations revealed Ni-excess induced negative impacts on abundance, frequency of occurrence of reproductive organs, population viability and morphological traits, spore viability and physiological attributes of both the liverworts. Results led us conclude that P. appendiculatum survived better with the lowest impact on its life cycle events than A. wallichiana under Ni excess in natural habitats. Our findings collectively provide insights into the previously unknown mechanisms of Ni-induced responses in liverworts with respect to phenological attributes, as well as demonstrate the potential of P. appendiculatum to survive better in Ni excess habitats.

TransDetect Identifies a New Regulatory Module Controlling Phosphate Accumulation.

Identifying transcription factor (TFs) cooperation controlling target gene expression is still an arduous challenge. The accuracy of current methods at genome scale significantly drops with the increase in number of genes, which limits their applicability to more complex genomes, like animals and plants. Here, we developed an algorithm, TransDetect, able to predict TF combinations controlling the expression level of a given gene. TransDetect was used to identify novel TF modules regulating the expression of Arabidopsis (Arabidopsis thaliana) phosphate transporter PHO1;H3 comprising MYB15, MYB84, bHLH35, and ICE1. These TFs were confirmed to interact between themselves and with the PHO1;H3 promoter. Phenotypic and genetic analyses of TF mutants enable the organization of these four TFs and PHO1;H3 in a new gene regulatory network controlling phosphate accumulation in zinc-dependent manner. This demonstrates the potential of TransDetect to extract directionality in nondynamic transcriptomes and to provide a blueprint to identify gene regulatory network involved in a given biological process.

Paclobutrazol induces tolerance in tomato to deficit irrigation through diversified effects on plant morphology, physiology and metabolism.

Dwindling water resources combined with meeting the demands for food security require maximizing water use efficiency (WUE) both in rainfed and irrigated agriculture. In this regard, deficit irrigation (DI), defined as the administration of water below full crop-water requirements (evapotranspiration), is a valuable practice to contain irrigation water use. In this study, the mechanism of paclobutrazol (Pbz)-mediated improvement in tolerance to water deficit in tomato was thoroughly investigated. Tomato plants were subjected to normal irrigated and deficit irrigated conditions plus Pbz application (0.8 and 1.6 ppm). A comprehensive morpho-physiological, metabolomics and molecular analysis was undertaken. Findings revealed that Pbz application reduced plant height, improved stem diameter and leaf number, altered root architecture, enhanced photosynthetic rates and WUE of tomato plants under deficit irrigation. Pbz differentially induced expression of genes and accumulation of metabolites of the tricarboxylic acid (TCA) cycle, γ-aminobutyric acid (GABA-shunt pathway), glutathione ascorbate (GSH-ASC)-cycle, cell wall and sugar metabolism, abscisic acid (ABA), spermidine (Spd) content and expression of an aquaporin (AP) protein under deficit irrigation. Our results suggest that Pbz application could significantly improve tolerance in tomato plants under limited water availability through selective changes in morpho-physiology and induction of stress-related molecular processes.

Involvement of Asada-Halliwell Pathway During Phytoremediation of Chromium (VI) in Brassica juncea L. Plants.

Brassica juncea (Indian mustard) L. plants were exposed to different concentrations (0.0, 0.1, 0.3 and 0.5 mM) of Chromium (Cr) and harvested after 30 and 60 days of sowing for the analysis of growth parameters, metal uptake and oxidative stress markers. Significant accumulation of Cr (VI) by B. juncea L. plants resulted in the reduced growth and modulations in the pool of various biochemical stress markers. The toxic effects of Cr (VI) on growth and other stress markers (protein content, lipid peroxidation and antioxidative enzymes viz.SOD, CAT, POD, APOX, GR, DHAR and MDHAR) in B. juncea L. were observed to be concentration and time dependent. Effect of Cr (VI) on biochemical parameters was differential and their maximum activities of SOD, POD, APX, GR, DHAR and lipid peroxidation were recorded at 0.5 mM concentration in 30 days old plants. Whereas, trend in the activities of most of the stress markers was reversed in 60 days old plants. The results obtained from the study suggested that Cr (VI) stress inhibited growth of B. juncea L. plants is directly interrelated with its accumulation and resulted in the modulation in activities of various stress markers.