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Desert ecosystems have limited resources and harsh climatic conditions and cannot support cropping in most farming models. Recently, microbial applications have emerged as promising strategies to enhance plant survival and adaptation in such extreme environments. However, the beneficial microbes and our understanding of their functional roles and adaptation mechanisms in desert ecosystems remain underexplored. This study reports the isolation and characterization of the Pseudomonas sp. R4-79 strain from the arid environment of Wadi Rum, Jordan, associated with the desert plant Ifloga spicata . The genome of Pseudomonas sp. R4-79, sequenced at 275 × PacBio coverage, consists of a 6.18 Mbp chromosome encoding 5,445 proteins, including gene clusters for siderophores, phenazines, hydrogen cyanide, and phytohormones, as well as secretion systems (T2SS, T4SS, T6SS, and TAT). Genomic and phenotypic analyses revealed that Pseudomonas sp. R4-79 belongs to the genus P. granadensis and exhibits plant growth-promoting attributes and substantial biocontrol potential. Pseudomonas sp. R4-79 effectively suppressed key phytopathogens, including the necrotrophic fungus Botrytis cinerea in vitro , as well as Pseudomonas syringae pv. tomato DC3000 and root-knot nematodes ( Meloidogyne incognita ) in vivo in Arabidopsis and tomato . This work suggests that P. granadensis R4-79 could represent an effective biocontrol agent to improve crop yield in sustainable agriculture.

Global climate change increasingly challenges agriculture with flooding and salinity. Among strategies to enhance crop resilience to these stresses, we tested several endophytic bacterial strains from mangroves, which are permanently exposed to flooding and high salinity. We show several strains that can enhance flooding and salinity tolerance in Arabidopsis and rice plants. Two strains and their combination massively enhanced the growth and yield of Oryza sativa cv. Nipponbare under both soil and hydroponic growth conditions with and without salt treatment. The bacteria-induced transcriptome changes in O. sativa roots, particularly related to ABA-signaling and lignin and suberin deposition in root tissues, explain the altered responses of colonized rice plants to hypoxic and saline stress conditions. Importantly, bacterially colonized rice plants exhibited enhanced yield and improved grain quality. These results show that microbes can be a powerful tool for enhancing the yield and resilience of rice to hypoxic and saline stress conditions.

The scarcity of freshwater resources resulting in a significant yield loss presents a pressing challenge in agriculture. To address this issue, utilizing abundantly available saline water could offer a smart solution. In this study, we demonstrate that the genome sequence rhizosphere bacterium Tritonibacter mobilis AK171, a halophilic marine bacterium recognized for its ability to thrive in saline and waterlogged environments, isolated from mangroves, has the remarkable ability to enable plant growth using saline irrigation. AK171 is characterized as rod-shaped cells, displays agile movement in free-living conditions, and adopts a rosette arrangement in static media. Moreover, The qualitative evaluation of PGP traits showed that AK171 could produce siderophores and IAA but could not solubilize phosphate nor produce hydrolytic enzymes it exhibits a remarkable tolerance to high temperatures and salinity. In this study, we conducted a comprehensive genome sequence analysis of T. mobilis AK171 to unravel the genetic mechanisms underlying its plant growth-promoting abilities in such challenging conditions. Our analysis revealed diverse genes and pathways involved in the bacterium’s adaptation to salinity and waterlogging stress. Notably, T. mobilis AK171 exhibited a high level of tolerance to salinity and waterlogging through the activation of stress-responsive genes and the production of specific enzymes and metabolites. Additionally, we identified genes associated with biofilm formation, indicating its potential role in establishing symbiotic relationships with host plants. Furthermore, our analysis unveiled the presence of genes responsible for synthesizing antimicrobial compounds, including tropodithietic acid (TDA), which can effectively control phytopathogens. This genomic insight into T. mobilis AK171 provides valuable information for understanding the molecular basis of plant-microbial interactions in saline and waterlogged environments. It offers potential applications for sustainable agriculture in challenging conditions.

Activity of root apical meristem (RAM) at the root apex is critical for stress-mediated modulation of root-architecture. Chickpea, like other legumes, possesses a basic open root meristem. Deep sequencing was used to perform microRNA expression profiling in root apex of chickpea ( Cicer arietinum L.) in order to investigate post-transcriptional regulation of gene expression in this tissue in response to salinity and water deficit. Five small RNA libraries prepared from chickpea root apices at different stages of stress treatments were sequenced to obtain 284 unique miRNA sequences including 60 novel miRNAs belonging to total 255 families. Two hundred and fiftynine miRNAs were differentially expressed in stress. Six hundred and nine mRNA targets involved in diverse cellular processes were predicted for 244 miRNAs. Stress-responsive expression patterns of selected miRNAs, inverse expression patterns of their target genes and the target-cleavage sites were validated. Three candidate miRNA-target gene relationships were validated in transient expression system in chickpea. The miRNA expression profiling under salinity and water deficiency in a legume root apex and the reported function of their target genes suggested important roles of miRNA-mediated post-transcriptional regulation of gene expression involved in re-patterning of root hair cells, lateral root formation and high-affinity K + -uptake under these stresses.

Key messageLaser microdissection applied on the developing rice endosperm revealed tissue- and stage-specific regulators modulating programmed cell death and desiccation tolerance mechanisms in the central starchy endosperm following starch metabolism.Rice (Oryza sativa L.) filial seed tissues are heterozygous in its function, which accumulate distinct storage compounds spatially in starchy endosperm and aleurone. In this study, we identified the 18 tissue- and stage-specific gene co-regulons in the developing endosperm by isolating four fine tissues dorsal aleurone layer (AL), central starchy endosperm (CSE), dorsal starchy endosperm (DSE), and lateral starchy endosperm (LSE) at two developmental stages (7 days after flowering, DAF and 12DAF) using laser microdissection (LM) coupled with gene expression analysis of a 44 K microarray. The derived co-expression regulatory networks depict that distinct set of starch biosynthesis genes expressed preferentially at first in CSE at 7 DAF and extend its spatial expression to LSE and DSE by 12 DAF. Interestingly, along with the peak of starch metabolism we noticed accumulation of transcripts related to phospholipid and glycolipid metabolism in CSE during 12 DAF. The spatial distribution of starch accumulation in distinct zones of starchy endosperm contains specific transcriptional factors and hormonal-regulated genes. Genes related to programmed cell death (PCD) were specifically expressed in CSE at 12DAF, when starch accumulation was already completed in that tissue. The aleurone layer present in the outermost endosperm accumulates transcripts of lipid, tricarboxylic acid metabolism, several transporters, while starch metabolism and PCD is not pronounced. These regulatory cascades are likely to play a critical role in determining the positional fate of cells and offer novel insights into the molecular physiological mechanisms of endosperm development from early to middle storage phase.

Chickpea ( Cicer arietinum L.) is an important pulse legume crop. We previously reported a draft genome assembly of the desi chickpea cultivar ICC 4958. Here we report an advanced version of the ICC 4958 genome assembly (version 2.0) generated using additional sequence data and an improved genetic map. This resulted in 2.7-fold increase in the length of the pseudomolecules and substantial reduction of sequence gaps. The genome assembly covered more than 94% of the estimated gene space and predicted the presence of 30,257 protein-coding genes including 2230 and 133 genes encoding potential transcription factors (TF) and resistance gene homologs, respectively. Gene expression analysis identified several TF and chickpea-specific genes with tissue-specific expression and displayed functional diversification of the paralogous genes. Pairwise comparison of pseudomolecules in the desi (ICC 4958) and the earlier reported kabuli (CDC Frontier) chickpea assemblies showed an extensive local collinearity with incongruity in the placement of large sequence blocks along the linkage groups, apparently due to use of different genetic maps. Single nucleotide polymorphism (SNP)-based mining of intra-specific polymorphism identified more than four thousand SNPs differentiating a desi group and a kabuli group of chickpea genotypes.

Summary Resistant starch (RS) is the portion of starch that escapes gastrointestinal digestion and acts as a substrate for fermentation of probiotic bacteria in the gut. Aside from enhancing gut health, RS contributes to a lower glycemic index. A genome‐wide association study coupled with targeted gene association studies was conducted utilizing a diverse panel of 281 resequenced Indica rice lines comprising of ~2.2 million single nucleotide polymorphisms. Low‐to‐intermediate RS phenotypic variations were identified in the rice diversity panel, resulting in novel associations of RS to several genes associated with amylopectin biosynthesis and degradation. Selected rice lines encoding superior alleles of SSIIa with medium RS and inferior alleles with low RS groups were subjected to detailed transcriptomic, metabolomic, non‐starch dietary fibre (DF), starch structural and textural attributes. The gene regulatory networks highlighted the importance of a protein phosphatase alongside multiple genes of starch metabolism. Metabolomics analyses resulted in the identification of several metabolite hubs (carboxylic acid, sugars and polyamines) in the medium RS group. Among DF, mannose and galactose from the water‐insoluble fraction were found to be highly associated with low and medium RS lines, respectively. Starch structural analyses revealed that a moderate increase in RS is also linked to an elevation of amylose 1 and amylose 2 fractions. Although rice lines with medium RS content negatively affected textural and viscosity properties in comparison to low RS, the textural property of medium RS lines was in the same acceptable range as IR64, a rice mega variety popular in Asia.

Background Pseudomonas argentinensis SA190 is a desert-adapted, plant-associated bacterium with demonstrated potential to enhance plant growth under abiotic stress. In this study, we conducted a comprehensive genomic and functional characterization of SA190 to uncover the molecular mechanisms underlying its biofilm formation, root colonization, and plant growth-promoting traits. Results The SA190 genome consists of a single circular chromosome (5.07 Mb, 64% GC) encoding 4561 predicted ORFs. Functional annotation revealed genes related to phosphate solubilization ( pqq operon), antifungal activity, and stress mitigation, including ACC deaminase. AntiSMASH analysis identified eight biosynthetic gene clusters linked to secondary metabolite production, including siderophores, terpenes, and β-lactones. Metabolic profiling demonstrated selective utilization of root exudate-associated sugars, consistent with rhizosphere adaptation. By a Tn5 transposon mutagenesis approach, we identified key regulators required for biofilm formation. Biofilm mutants deficient in wspC , rpoE , and fliD were differentially compromised in plant colonization and plant growth promotion under ambient and/or drought conditions. Conclusion Our study suggests that SA190 is a metabolically streamlined yet ecologically versatile PGPB and provides functional insights into its potential application as a bioinoculant for sustainable agriculture in arid environments.

Summary To address the future food security in Asia, we need to improve the genetic gain of grain yield while ensuring the consumer acceptance. This study aimed to identify novel genes influencing the number of upper secondary rachis branches (USRB) to elevate superior grains without compromising grain quality by studying the genetic variance of 310 diverse O. sativa var. indica panel using single‐ and multi‐locus genome‐wide association studies (GWAS), gene set analyses and gene regulatory network analysis. GWAS of USRB identified 230 significant (q‐value < 0.05) SNPs from chromosomes 1 and 2. GWAS targets narrowed down using gene set analyses identified large effect association on an important locus LOC_Os02g50790/LOC_Os02g50799 encoding a nuclear‐pore anchor protein (OsTPR). The superior haplotype derived from non‐synonymous SNPs identified in OsTPR was specifically associated with increase in USRB with superior grains being low chalk. Through haplotype mining, we further demonstrated the synergy of offering added yield advantage due to superior allele of OsTPR in elite materials with low glycaemic index (GI) property. We further validated the importance of OsTPR using recombinant inbred lines (RILs) population by introgressing a superior allele of OsTPR into elite materials resulted in raise in productivity in high amylose background. This confirmed a critical role for OsTPR in influencing yield while maintaining grain and nutritional quality.

Rice lines with slower starch digestibility provide opportunities in mitigating the global rise in type II diabetes and related non-communicable diseases. However, screening for low glycemic index (GI) in rice breeding programs is not possible due to time and cost constraints. This study evaluated the feasibility of using in vitro cooked grain amylolysis, starch mobilization patterns during seed germination, and variation in starch structure and composition in the mature seed to differentiate patterns of starch digestibility. Mobilization patterns of total starch, resistant starch, amylose and amylopectin chains, and free sugars during seed germination revealed that the process is analogous to digestion in the human gastrointestinal tract. The combination of these biochemical markers can be used as an alternative measure to predict GI. Additionally, transcriptome analysis of stored mRNA transcripts in high and low GI lines detected differences in starch metabolism and confirmed the importance of seed storage pathways in influencing digestibility. Pathway analyses supported by metabolomics data revealed that resistant starch, cell wall non-starch polysaccharides and flavonoids potentially contribute to slower digestibility. These new insights can guide precision breeding programs to produce low GI rice with acceptable cooking quality to help mitigate the burden of diet-associated lifestyle diseases.