Genome-Wide Analysis and Expression Profiling of Rice Hybrid Proline-Rich Proteins in Response to Biotic and Abiotic Stresses, and Hormone Treatment

Ubiquitin Ligase Gene OsPUB57 Negatively Regulates Rice Blast Resistance

The ubiquitination and degradation of proteins are widely involved in plant biotic and abiotic stress responses. E3 ubiquitin ligases play an important role in the ubiquitination of specific proteins. In this study, we identified the function of a U-box E3 ubiquitin ligase gene OsPUB57 in rice. Expression analyses revealed that OsPUB57 was mainly expressed in the aboveground part of rice. Drought, salt, cold, JA (jasmonic acid), PAMPs (pathogen-associated molecular patterns) or Magnaportheoryzae treatment could significantly suppress the expression of OsPUB57 in rice. Compared with wild-type plants, OsPUB57-overexpressing plants showed a decrease in resistance to M. oryzae, while the mutant plants exhibited an enhancement of M. oryzae resistance. The expression level detection indicated that OsPUB57 negatively regulates rice blast resistance, probably by down-regulating the expression of the defense-related genes OsPR1a and OsAOS2. This study provides a candidate gene for the genetic improvement of rice blast resistance.

CRISPR/Cas9-based genome editing and functional analysis of SlHyPRP1 and SlDEA1 genes of Solanum lycopersicum L. in imparting genetic tolerance to multiple stress factors

CRISPR/Cas is a breakthrough genome editing system because of its precision, target specificity, and efficiency. As a speed breeding system, it is more robust than the conventional breeding and biotechnological approaches for qualitative and quantitative trait improvement. Tomato (Solanum lycopersicum L.) is an economically important crop, but its yield and productivity have been severely impacted due to different abiotic and biotic stresses. The recently identified SlHyPRP1 and SlDEA1 are two potential negative regulatory genes in response to different abiotic (drought and salinity) and biotic stress (bacterial leaf spot and bacterial wilt) conditions in S. lycopersicum L. The present study aimed to evaluate the drought, salinity, bacterial leaf spot, and bacterial wilt tolerance response in S. lycopersicum L. crop through CRISPR/Cas9 genome editing of SlHyPRP1 and SlDEA1 and their functional analysis. The transient single- and dual-gene SlHyPRP1 and SlDEA1 CRISPR-edited plants were phenotypically better responsive to multiple stress factors taken under the study. The CRISPR-edited SlHyPRP1 and SlDEA1 plants showed a higher level of chlorophyll and proline content compared to wild-type (WT) plants under abiotic stress conditions. Reactive oxygen species accumulation and the cell death count per total area of leaves and roots under biotic stress were less in CRISPR-edited SlHyPRP1 and SlDEA1 plants compared to WT plants. The study reveals that the combined loss-of-function of SlHyPRP1 along with SlDEA1 is essential for imparting significant multi-stress tolerance (drought, salinity, bacterial leaf spot, and bacterial wilt) in S. lycopersicum L. The main feature of the study is the detailed genetic characterization of SlDEA1, a poorly studied 8CM family gene in multi-stress tolerance, through the CRISPR/Cas9 gene editing system. The study revealed the key negative regulatory role of SlDEA1 that function together as an anchor gene with SlHyPRP1 in imparting multi-stress tolerance in S. lycopersicum L. It was interesting that the present study also showed that transient CRISPR/Cas9 editing events of SlHyPRP1 and SlDEA1 genes were successfully replicated in stably generated parent-genome-edited line (GEd0) and genome-edited first-generation lines (GEd1) of S. lycopersicum L. With these upshots, the study's key findings demonstrate outstanding value in developing sustainable multi-stress tolerance in S. lycopersicum L. and other crops to cope with climate change.

An Integration of Linkage Mapping and GWAS Reveals the Key Genes for Ear Shank Length in Maize

Ear shank length (ESL) has significant effects on grain yield and kernel dehydration rate in maize. Herein, linkage mapping and genome-wide association study were combined to reveal the genetic architecture of maize ESL. Sixteen quantitative trait loci (QTL) were identified in the segregation population, among which five were repeatedly detected across multiple environments. Meanwhile, 23 single nucleotide polymorphisms were associated with the ESL in the association panel, of which four were located in the QTL identified by linkage mapping and were designated as the population-common loci. A total of 42 genes residing in the linkage disequilibrium regions of these common variants and 12 of them were responsive to ear shank elongation. Of the 12 genes, five encode leucine-rich repeat receptor-like protein kinases, proline-rich proteins, and cyclin11, respectively, which were previously shown to regulate cell division, expansion, and elongation. Gene-based association analyses revealed that the variant located in Cyclin11 promoter affected the ESL among different lines. Cyclin11 showed the highest expression in the ear shank 15 days after silking among diverse tissues of maize, suggesting its role in modulating ESL. Our study contributes to the understanding of the genetic mechanism underlying maize ESL and genetic modification of maize dehydration rate and kernel yield.

Silveira S, Brommonschenkel SH, Fontes EPB. RLPredictiOme, a Machine Learning-Derived Method for High-Throughput Prediction of Plant Receptor-like Proteins, Reveals Novel Classes of Transmembrane Receptors

Cell surface receptors play essential roles in perceiving and processing external and internal signals at the cell surface of plants and animals. The receptor-like protein kinases (RLK) and receptor-like proteins (RLPs), two major classes of proteins with membrane receptor configuration, play a crucial role in plant development and disease defense. Although RLPs and RLKs share a similar single-pass transmembrane configuration, RLPs harbor short divergent C-terminal regions instead of the conserved kinase domain of RLKs. This RLP receptor structural design precludes sequence comparison algorithms from being used for high-throughput predictions of the RLP family in plant genomes, as has been extensively performed for RLK superfamily predictions. Here, we developed the RLPredictiOme, implemented with machine learning models in combination with Bayesian inference, capable of predicting RLP subfamilies in plant genomes. The ML models were simultaneously trained using six types of features, along with three stages to distinguish RLPs from non-RLPs (NRLPs), RLPs from RLKs, and classify new subfamilies of RLPs in plants. The ML models achieved high accuracy, precision, sensitivity, and specificity for predicting RLPs with relatively high probability ranging from 0.79 to 0.99. The prediction of the method was assessed with three datasets, two of which contained leucine-rich repeats (LRR)-RLPs from Arabidopsis and rice, and the last one consisted of the complete set of previously described Arabidopsis RLPs. In these validation tests, more than 90% of known RLPs were correctly predicted via RLPredictiOme. In addition to predicting previously characterized RLPs, RLPredictiOme uncovered new RLP subfamilies in the Arabidopsis genome. These include probable lipid transfer (PLT)-RLP, plastocyanin-like-RLP, ring finger-RLP, glycosyl-hydrolase-RLP, and glycerophosphoryldiester phosphodiesterase (GDPD, GDPDL)-RLP subfamilies, yet to be characterized. Compared to the only Arabidopsis GDPDL-RLK, molecular evolution studies confirmed that the ectodomain of GDPDL-RLPs might have undergone a purifying selection with a predominance of synonymous substitutions. Expression analyses revealed that predicted GDPGL-RLPs display a basal expression level and respond to developmental and biotic signals. The results of these biological assays indicate that these subfamily members have maintained functional domains during evolution and may play relevant roles in development and plant defense. Therefore, RLPredictiOme provides a framework for genome-wide surveys of the RLP superfamily as a foundation to rationalize functional studies of surface receptors and their relationships with different biological processes.

Identification and analysis of proline-rich proteins and hybrid proline-rich proteins super family genes from Sorghum bicolor and their expression patterns to abiotic stress and zinc stimuli

Systematic genome-wide analysis of Sorghum bicolor revealed the identification of a total of 48 homologous genes comprising 21 proline-rich proteins (PRPs) and 27 hybrid proline-rich proteins (HyPRPs). Comprehensive scrutiny of these gene homologs was conducted for gene structure, phylogenetic investigations, chromosome mapping, and subcellular localization of proteins. Promoter analysis uncovered the regions rich with phosphorous- (BIHD), ammonium-, sulfur-responsive (SURE), and iron starvation-responsive (IRO2) along with biotic, abiotic, and development-specific cis-elements. Further, PRPs exhibit more methylation and acetylation sites in comparison with HyPRPs. miRNAs have been predicted which might play a role in cleavage and translation inhibition. Several of the SbPRP genes were stimulated in a tissue-specific manner under drought, salt, heat, and cold stresses. Additionally, exposure of plants to abscisic acid (ABA) and zinc (Zn) also triggered PRP genes in a tissue-dependent way. Among them, SbPRP17 has been found upregulated markedly in all tissues irrespective of the stress imposed. The expressions of SbHyPRPs, especially SbHyPRP2, SbHyPRP6, and SbHyPRP17 were activated under all stresses in all three tissues. On the other hand, SbHyPRP8 (root only) and SbHyPRP12 (all three tissues) were highly responsive to cold stress and ABA while SbHyPRP26 was induced by drought and Zn in the stem. Taken together, this study indicates the critical roles that SbPRPs and SbHyPRPs play during diverse abiotic stress conditions and notably the plausible roles that these genes play upon exposure to zinc, the crucial micronutrient in plants.

Transcriptome analysis of tea (Camellia sinensis) leaves in response to ammonium starvation and recovery

The tea plant is a kind of ammonium-preferring crop, but the mechanism whereby ammonium (NH₄ ⁺) regulate its growth is not well understood. The current study focused on the effects of NH₄ ⁺ on tea plants. Transcriptomic analysis was performed to investigate the early- and late-stage NH₄ ⁺ deprivation and resupply in tea plants shoots. Through short- and long-term NH₄ ⁺ deficiency, the dynamic response to NH₄ ⁺ stress was investigated. The most significant effects of NH₄ ⁺ deficiency were found to be on photosynthesis and gene ontology (GO) enrichment varied with the length of NH₄ ⁺ deprivation. Enriched KEGG pathways were also different when NH₄ ⁺ was resupplied at different concentrations which may indicate reasons for tolerance of high NH₄ ⁺ concentration. Using weighted gene co-expression network analysis (WGCNA), modules related to significant tea components, tea polyphenols and free amino acids, were identified. Hence, NH₄ ⁺ could be regarded as a signaling molecule with the response of catechins shown to be higher than that of amino acids. The current work represents a comprehensive transcriptomic analysis of plant responses to NH₄ ⁺ and reveals many potential genes regulated by NH₄ ⁺ in tea plants. Such findings may lead to improvements in nitrogen efficiency of tea plants.

Characterization of evolutionarily distinct rice BAHD-Acyltransferases provides insight into their plausible role in rice susceptibility to Rhizoctonia solani

Plants produce diverse secondary metabolites in response to different environmental cues including pathogens. The modification of secondary metabolites, including acylation, modulates their biological activity, stability, transport, and localization. A plant-specific BAHD-acyltransferase (BAHD-AT) gene family members catalyze the acylation of secondary metabolites. Here we characterized the rice (Oryza sativa L.) BAHD-ATs at the genome-wide level and endeavor to define their plausible role in the tolerance against Rhizoctonia solani AG1-IA. We identified a total of 85 rice OsBAHD-AT genes and classified them into five canonical clades based on their phylogenetic relationship with characterized BAHD-ATs from other plant species. The time-course RNA sequencing (RNA-seq) analysis of OsBAHD-AT genes and qualitative real-time polymerase chain reaction (qRT-PCR) validation showed higher expression in sheath blight susceptible rice genotype. Furthermore, the DNA methylation analysis revealed higher hypomethylation of OsBAHD-AT genes that corresponds to their higher expression in susceptible rice genotype, indicating epigenetic regulation of OsBAHD-AT genes in response to R. solani AG1-IA inoculation. The results shown here indicate that BAHD-ATs may have a negative role in rice tolerance against R. solani AG1-IA possibly mediated through the brassinosteroid (BR) signaling pathway. Altogether, the present analysis suggests the putative functions of several OsBAHD-AT genes, which will provide a blueprint for their functional characterization and to understand the rice-R. solani AG1-IA interaction.

Genome-Wide Association Study Dissects Resistance Loci against Bacterial Blight in a Diverse Rice Panel from the 3000 Rice Genomes Project

BACKGROUND

Bacterial blight (BB), caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of the most devastating bacterial diseases of rice in temperate and tropical regions. Breeding and deployment of resistant cultivars carrying major resistance (R) genes has been the most effective approach for BB management. However, because of specific interaction of each R gene with the product of the corresponding pathogen avirulence or effector gene, new pathogen strains that can overcome the deployed resistance often emerge rapidly. To deal with ever-evolving Xoo, it is necessary to identify novel R genes and resistance quantitative trait loci (QTL).

RESULTS

BB resistance of a diverse panel of 340 accessions from the 3000 Rice Genomes Project (3 K RGP) was evaluated by artificial inoculation with four representative Xoo strains, namely Z173 (C4), GD1358 (C5), V from China and PXO339 (P9a) from Philippines. Using the 3 K RG 4.8mio filtered SNP Dataset, a total of 11 QTL associated with BB resistance on chromosomes 4, 5, 11 and 12 were identified through a genome-wide association study (GWAS). Among them, eight resistance loci, which were narrowed down to relatively small genomic intervals, coincided with previously reported QTL or R genes, e.g. xa5, xa25, xa44(t). The other three QTL were putative novel loci associated with BB resistance. Linear regression analysis showed a dependence of BB lesion length on the number of favorable alleles, suggesting that pyramiding QTL using marker-assisted selection would be an effective approach for improving resistance. In addition, the Hap2 allele of LOC_Os11g46250 underlying qC5-11.1 was validated as positively regulating resistance against strain C5.

CONCLUSIONS

Our findings provide valuable information for the genetic improvement of BB resistance and application of germplasm resources in rice breeding programs.

SlHyPRP1 and DEA1, the multiple stress responsive eight-cysteine motif family genes of tomato (Solanum lycopersicum L.) are expressed tissue specifically, localize and interact at cytoplasm and plasma membrane in vivo

Owing to rapid global climate change, the occurrence of multiple abiotic stresses is known to influence the outburst of biotic stress factors which affects crop productivity. Therefore, it is essential to understand the molecular and cell biology of key genes associated with multiple stress responses in crop plants. SlHyPRP1 and DEA1, the members of eight-cysteine motif (8CM) family genes have been recently identified as putative regulators of multiple stress responses in tomato (Solanum lycopersicum L.). In order to gain deeper insight into cell and molecular biology of SlHyPRP1 and DEA1, we performed their expression analysis in three tomato cultivars and in vivo cell biological analysis. The semi-quantitative PCR and qRT-PCR results showed the higher expression of SlHyPRP1 and DEA1 in leaf, stem, flower and root tissues as compared to fruit and seed tissues in all three cultivars. The expression levels of SlHyPRP1 and DEA1 were found to be relatively higher in a wilt susceptible tomato cultivar (Arka Vikas) than a multiple disease resistant cultivar (Arka Abhed). In vivo cell biological analysis through Gateway cloning and Bi-FC assay revealed the predominant sub-cellular localization and strong protein-protein interaction of SlHyPRP1 and DEA1 at the cytoplasm and plasma membrane. Moreover, SlHyPRP1 showed in vivo interaction with stress responsive proteins WRKY3 and MST1. Our findings suggest that SlHyPRP1 with DEA1 are co-expressed with tissue specificity and might function together by association with WRKY3 and MST1 in plasma membrane for regulating multiple stress responses in the tomato plant.

Multivariate Analysis of Amino Acids and Health Beneficial Properties of Cantaloupe Varieties Grown in Six Locations in the United States

Cantaloupe is a good dietary source of amino acids, including γ-aminobutyric acid (GABA), glutamine, and citrulline. However, the levels of these amino acids vary among different cantaloupe varieties grown in different locations. Understanding the variation in amino acid contents provides fundamentally important information for quality control and improving melon varieties. To examine this variation, we measured the amino acid contents in cantaloupes grown in six locations in the United States (Texas, Georgia, North Carolina, California, Indiana, and Arizona). Principal component analyses were applied to analyze the effect of growing location on the amino acid profiles in different varieties. The GABA content ranged from 1006.14 ± 64.77 to 3187.12 ± 64.96 µg/g and citrulline ranged from 92.65 ± 9.52 to 464.75 ± 34.97 µg/g depending on the variety and location. Total phenolic contents, α-amylase inhibition, and antioxidant activities were also measured. Tuscan type Da Vinci had significantly higher phenolic contents in Arizona (381.99 ± 16.21 µg/g) but had the lowest level when grown in California (224.56 ± 14.62 µg/g). Our analyses showed significant differences in amino acid levels, phenolics contents, and antioxidant activity in the cantaloupe varieties based on the growing location. These findings underline the importance of considering growing location in the selection and improvement of cantaloupe varieties.