GsSRK, a G-type lectin S-receptor-like serine/threonine protein kinase, is a positive regulator of plant tolerance to salt stress

High-Resolution Mass Spectrometry Approach for Proteomic and Metabolomic Analyses of High-Protein Soybean Seeds

Soybeans are a valuable source of vegetable protein and edible oil. Fast neutron (FN) radiation was employed to produce large chromosomal deletions in soybean Glycine max (L.) Merrill. We conducted proteomic and metabolomic profiling of a high-protein soybean mutant (G15FN-12) developed through FN mutagenesis to identify the metabolic pathways that underlie the elevated protein content. A deletion of 137 genes located on chromosome-12 had occurred in G15FN-12. Tandem tag-based protein profiling of the mutant and wild type identified 6098 proteins, of which 175 showed increased abundance and 239 showed decreased abundance in the mutant seeds. Using liquid chromatography-mass spectrometry (LC-MS)-based metabolomic profiling, we identified 610 metabolites, of which 294 metabolites showed increased and 157 showed reduced content in mutant seeds as compared to wild type. Proteomic and metabolomic profiling revealed a decrease in ubiquitin-proteasome-associated proteins and an increase in heat shock proteins in the mutant seed. We hypothesize that decreased protein degradation, together with enhanced refolding of misfolded protein by molecular chaperones, contributes to elevated protein content in the mutant seed. The development of value-added seed traits such as increased protein using advanced metabolic engineering techniques can be achieved by further exploring the metabolic pathways identified in this investigation.

Functional and transcriptomic characterization of the receptor-like protein kinase gene GmHSL1b involved in salt stress tolerance in soybean roots

The survival and adaptation of plants to adverse environmental conditions is crucial and is facilitated by receptor-like kinases, which act as cell surface receptors for a variety of signals. In this study, we identified a gene, GmHSL1b, encoding a receptor-like protein kinase that is responsive to abscisic acid (ABA) hormonal signals and is involved in the plant's response to drought and salt stresses. Subcellular localization assays have demonstrated that the GmHSL1b protein is located in the plasma membrane. Overexpression of the GmHSL1b gene in soybean enhanced root growth and development, as well as the plant's tolerance to salt stress, while the gmhsl1b mutant revealed increased sensitivity to salt stress. Comparative transcriptome analysis showed that some genes associated with various biological processes, such as mitogen-activated protein kinase (MAPK) cascade signaling, plant hormone signaling, cell wall remodeling, calcium signaling, and defense response mechanisms are differentially expressed in GmHSL1b overexpressing roots. Our research indicated that GmHSL1b can regulate the expression level of the candidate aquaporin GmPIP2-1, thereby affecting cell water content and the accumulation of reactive oxygen species (ROS) under salt stress. These findings indicate that the GmHSL1b participates in regulating root development and enhancing the tolerance to salt stress, thus offering insights for boosting crop adaptability to environmental stresses.

Multi-omics analysis of hexaploid triticale that show molecular responses to salt stress during seed germination

The development of a salt-tolerant hexaploid triticale cultivar offers an economical and efficient solution for utilizing marginal land. Understanding how hexaploid triticales respond to salt stress is essential if this goal is to be achieved. A genome-wide association study (GWAS), along with transcriptome and proteome analyses, were used in the present study to determine the molecular responses to salt stress in hexaploid triticale. In total, 81 marker-trait associations for 10 salt-tolerance traits were identified in 153 hexaploid triticale accessions, explaining 0.71% to 56.98% of the phenotypic variation, and 54 GWAS-associated genes were uncovered. A total of 67, 88, and 688 differential expression genes were co-expressed at both the transcriptomic and proteomic levels after 4, 12, and 18 h of salt stress, respectively. Among these differentially expressed genes, six appeared in the coincident expression trends for both the transcriptomic and proteomic levels at the seed germination stage. A total of nine common KEGG pathways were enriched at both the transcriptomic and proteomic levels at 4, 12, and 18 h. After integrating GWAS-target genes with transcriptomics and proteomics approaches that the candidate gene late embryogenesis abundant protein 14 (LEA14) was up-regulated at the transcriptomic and proteomic levels. LEA14 contained important stress-responsive cis-acting regulatory elements that could be dynamically regulated by the binding of transcription factors (TFs). This suggested that LEA14 was a key gene associated with salt tolerance in hexaploid triticale and could respond quickly to salt stress. This study improved understanding about the potential molecular mechanisms associated with hexaploid triticale salt tolerance and contributed to the breeding of salt-tolerant germplasms and the utilization of saline soils.

Identification and Characterization of the LecRLKs Gene Family in Maize, and Its Role Under Biotic and Abiotic Stress

Plant lectin receptor-like kinases (LecRLKs) are plant membrane protein receptor kinases. Lectin-like receptor kinases play a crucial role in regulating plant growth, development, and responses to environmental stimuli. It can rapidly respond to both biotic and abiotic stresses while mediating mechanisms of plant immune responses. This study represents the first identification of the LecRLK family genes in maize. It analyzes the gene structure, chromosomal locations, phylogenetic classification, promoter homoeotropic elements, and expression patterns under both biotic and abiotic stresses. The results indicate that these genes possess kinase and transmembrane domains, along with specific L-type or G-type extracellular domains. Most ZmLecRLK gene promoters contain cis-acting elements that are responsive to known hormones and stressors. Furthermore, these genes have been identified as being sensitive to both biotic and abiotic stresses. This discovery establishes a significant theoretical foundation for the selection of corn varieties in adverse environments. Additionally, it provides a basis for further in-depth exploration of the molecular regulatory mechanisms of LecRLK family genes.

Quantitative N-glycoproteomics characterization of differential N-glycosylation in Sorghum bicolor under salinity stress

Salt stress is one of the significant environmental stresses that severely affect plant growth and development. Here, we report quantitative N-glycoproteomics characterization of differential N-glycosylation in Sorghum bicolor under low, median and high salinity stress. 21,621 intact N-glycopeptides coming from the combination of 127 N-glycan structures on 6574 N-glycosites from 5321 proteins were identified; differential N-glycosylation was observed for 682 N-glycoproteins which are mainly involved in the pathways of biosynthesis of secondary metabolites, biosynthesis of amino acids and several metabolic pathways. 41 N-glycan structures modifying on 338 N-glycopeptides from 122 glycoproteins were co-quantified and deregulated under at least one salt stress, including enzymes of energy production and carbohydrate metabolisms, cell wall organization related proteins, glycosyltransferases and so on. Intriguingly, with increasing salt concentration, there was an increase in the percentage of complex N-glycans on the altered N-glycopeptides. Furthermore, the observation of glycoproteins with distinct salt sensitivity is noteworthy, particularly the upregulated hyposensitive glycoproteins that predominantly undergo complex N-glycan modification. This is the first N-glycoproteome description of salt stress response at the intact N-glycopeptide level in sorghum and a further validation of data reported here would likely provide deeper insights into the stress physiology of this important crop plant.

Restriction site-associated DNA sequencing (RAD-seq) of tea plant (Camellia sinensis) in Sichuan province, China, provides insights into free amino acid and polyphenol contents of tea

Worldwide, tea is a popular beverage; within the realm of Chinese tea, Sichuan tea holds particular significance for its role in the origin and composition of Chinese tea cultivars. Sichuan tea is noted for its rich content of free amino acids (FAAs) and tea polyphenols (TPs), which has made it an important subject for studying genetic diversity and the genes regulating these compounds. In this study, 139 varieties of tea were collected from areas in Sichuan Province, China, with similar geographical and climatic conditions. The FAA content was approximately 3% and the TP content was approximately 17%. Using RAD sequencing, 5,656,224 variant loci were identified, primarily comprising SNPs (94.17%) and indels (5.83%). Evolutionary analysis revealed that genetic divergence was not closely linked to the collection location. Population structure analysis confirmed a division into two main populations having a similar composition to the phylogenetic clusters. Screening for FAA-related SNPs identified significant loci associated with 33 genes that potentially regulate FAA content. Similarly, TP-related analysis pinpointed 8 SNPs significantly linked to 20 candidate genes. Notably, genetic associations hinted at the genes involved in the stress response and the accumulation of phenolic compounds, enhancing the understanding of determinants of tea quality. This research underscores the potential for molecular breeding based on genetic insights, suggesting pathways to improve the FAA and TP contents in tea. These findings not only provide a solid foundation for exploring gene-chemical interactions but also offer practical strategies for improving the nutritional and sensory attributes of tea cultivars through informed breeding practices.

In silico analysis of L- and G-type lectin receptor kinases in tomato: evolution, diversity, and abiotic responses

Solanum lycopersicum (family: Solanaceae) is a crucial crop and model organism for many phenotypic traits, and its sequenced genome provides valuable insights into plant biology and crop improvement. This study investigated lectin receptor-like kinases (LecRLKs) in tomato, focusing on L-type and G-type families. Mining the tomato genome (ITAG2.4) revealed 161 putative lectin genes across seven families, with GNA-related genes being the most abundant. Gene duplication analysis indicated that tandem and segmental duplications were the primary mechanisms driving LecRLK gene family expansion, particularly for G-type LecRLKs. These duplicated genes showed evidence of both purifying and negative selection, suggesting functional conservation and sub-functionalization. L-type and G-type LecRLKs exhibited diverse domain rearrangement architectures and subcellular localizations, with G-type LecRLKs showing greater expansion and architectural diversity. Differential expression analysis during abiotic stress (drought, heat, and cold stress) revealed key responsive genes. During drought stress, 63.2% of L-type and 18.5% of G-type LecRLK genes were expressed, with L-type Solyc09g005000.1 and G-type Solyc03g078360.1 genes showing significant 2-fold upregulation. Heat stress (42 °C) induced the upregulation of L-type Solyc04g071000.1 and G-type Solyc03g078360.1 and Solyc04g008400.1, particularly after 12-24 h of exposure. Promoter analysis revealed numerous stress-related cis-elements. Transcription factor predictions and miRNA targeting sites suggest complex regulatory mechanisms. This comprehensive in silico characterization of tomato LecRLKs, including their expansion patterns and evolutionary pressures, provides insights into their potential roles in abiotic stress responses and lays the groundwork for enhancing crop resilience through targeted breeding or genetic engineering approaches.

Genome-Wide Identification of the Lectin Receptor-like Kinase Gene Family in Avena sativa and Its Role in Salt Stress Tolerance

Lectin receptor-like kinases (LecRLKs) are membrane-bound receptor genes found in many plant species. They are involved in perceiving stresses and responding to the environment. Oat (Avena sativa; 2n = 6x = 42) are an important food and forage crop with potential in drought, saline, or alkaline soils. Here, we present a comprehensive genome-wide analysis of the LecRLK gene family in A. sativa and the crop's wild relatives A. insularis (4x) and A. longiglumis (2x), unveiling a rich diversity with a total of 390 LecRLK genes identified, comprising 219 G-types, 168 L-types, and 3 C-types in oats. Genes were unevenly distributed across the oat chromosomes. GFP constructs show that family members were predominantly located in the plasma membrane. Expression under salt stress demonstrated functional redundancy and differential expression of LecRLK gene family members in oats: 173 members of this family were involved in the response to salt stress, and the expression levels of three C-type genes in the root and leaf were significantly increased under salt stress. The results show the diversity, evolutionary dynamics, and functional implications of the LecRLK gene family in A. sativa, setting a foundation for defining its roles in plant development and stress resilience, and suggesting its potential agricultural application for crop improvement.

Transcriptome profiling of two rice varieties reveals their molecular responses under high night-time temperature

High night-time temperatures (HNT) pose a threat to the sustainability of crop production, including rice. HNT can affect crop productivity and quality by influencing plant physiology, morphology, and phenology. The ethylene perception inhibitor, 1-methylcyclopropene (1-MCP), can minimize HNT-induced damage to plant membranes, thereby preventing decrease in rice yield. In this study, we employed a transcriptome approach to investigate the effects of HNT, 1-MCP, and their interaction on two Texas rice varieties, Antonio and Colorado. The plants were exposed to temperatures of 25°C (ambient night-time temperature, ANT) and 30°C (HNT) using an infrared heating system from the booting stage until harvest, while 1-MCP was applied at the booting stage of rice development. Several physiological and agronomical traits were evaluated under each condition to assess plant responses. Leaf tissues were collected from the plants grown in the ANT and HNT conditions after the heat stress and 1-MCP treatments. Based on agronomic performance, Colorado was less negatively affected than Antonio under HNT, showing a slight reduction in spikelet fertility and leaf photosynthetic rate but no significant reduction in yield. The application of 1-MCP significantly mitigated the adverse effects of HNT in Antonio. However, no significant differences were observed in yield and leaf photosynthetic rate in Colorado. Furthermore, transcriptomic data revealed distinct responsive mechanisms in Antonio and Colorado in response to both HNT and 1-MCP. Several ethylene and senescence-related transcription factors (TFs) were identified only in Antonio, suggesting that 1-MCP affected the ethylene signaling pathway in Antonio but not in Colorado. These findings contribute to our understanding of the physiological differences between varieties exhibiting susceptible and tolerant responses to high night-time temperatures, as well as their response to 1-MCP and ethylene regulation under 1-MCP.

Natural variations of maize ZmLecRK1 determine its interaction with ZmBAK1 and resistance patterns to multiple pathogens

Maize (Zea mays) is one of the most important crops in the world, but its yield and quality are seriously affected by diverse diseases. Identifying broad-spectrum resistance genes is crucial for developing effective strategies to control the disease in maize. In a genome-wide study in maize, we identified a G-type lectin receptor kinase ZmLecRK1, as a new resistance protein against Pythium aphanidermatum, one of the causal pathogens of stalk rot in maize. Genetic analysis showed that the specific ZmLecRK1 allele can confer resistance to multiple pathogens in maize. The cell death and disease resistance phenotype mediated by the resistant variant of ZmLecRK1 requires the co-receptor ZmBAK1. A naturally occurring A404S variant in the extracellular domain of ZmLecRK1 determines the ZmLecRK1-ZmBAK1 interaction and the formation of ZmLecRK1-related protein complexes. Interestingly, the ZmLecRK1 susceptible variant was found to possess the amino acid S404 that is present in the ancestral variants of ZmLecRK1 and conserved among the majority of grass species, while the resistance variant of ZmLecRK1 with A404 is only present in a few maize inbred lines. Substitution of S by A at position 404 in ZmLecRK1-like proteins of sorghum and rice greatly enhances their ability to induce cell death. Further transcriptomic analysis reveals that ZmLecRK1 likely regulates gene expression related to the pathways in cell wall organization or biogenesis in response to pathogen infection. Taken together, these results suggest that the ZmLecRK1 resistance variant enhances its binding affinity to the co-receptor ZmBAK1, thereby enhancing the formation of active complexes for defense in maize. Our work highlights the biotechnological potential for generating disease-resistant crops by precisely modulating the activity of ZmLecRK1 and its homologs through targeted base editing.

Vitis rotundifolia Genes Introgressed with RUN1 and RPV1: Poor Recombination and Impact on V. vinifera Berry Transcriptome

Thanks to several Vitis vinifera backcrosses with an initial V. vinifera L. × V. rotundifolia (previously Muscadinia rotundifolia) interspecific cross, the MrRUN1/MrRPV1 locus (resistance to downy and powdery mildews) was introgressed in genotypes phenotypically close to V. vinifera varieties. To check the consequences of introgressing parts of the V. rotundifolia genome on gene expression during fruit development, we conducted a comparative RNA-seq study on single berries from different V. vinifera cultivars and V. vinifera × V. rotundifolia hybrids, including 'G5' and two derivative microvine lines, 'MV102' (resistant) and 'MV32' (susceptible) segregating for the MrRUN1/RPV1 locus. RNA-Seq profiles were analyzed on a comprehensive set of single berries from the end of the herbaceous plateau to the ripe stage. Pair-end reads were aligned both on V. vinifera PN40024.V4 reference genome, V. rotundifolia cv 'Trayshed' and cv 'Carlos', and to the few resistance genes from the original V. rotundifolia cv '52' parent available at NCBI. Weighted Gene Co-expression Network Analysis (WGCNA) led to classifying the differentially expressed genes into 15 modules either preferentially correlated with resistance or berry phenology and composition. Resistance positively correlated transcripts predominantly mapped on the 4-5 Mb distal region of V. rotundifolia chromosome 12 beginning with the MrRUN1/MrRPV1 locus, while the negatively correlated ones mapped on the orthologous V. vinifera region, showing this large extremity of LG12 remained recalcitrant to internal recombination during the successive backcrosses. Some constitutively expressed V. rotundifolia genes were also observed at lower densities outside this region. Genes overexpressed in developing berries from resistant accessions, either introgressed from V. rotundifolia or triggered by these in the vinifera genome, spanned various functional groups, encompassing calcium signal transduction, hormone signaling, transcription factors, plant-pathogen-associated interactions, disease resistance proteins, ROS and phenylpropanoid biosynthesis. This transcriptomic insight provides a foundation for understanding the disease resistance inherent in these hybrid cultivars and suggests a constitutive expression of NIR NBS LRR triggering calcium signaling. Moreover, these results illustrate the magnitude of transcriptomic changes caused by the introgressed V. rotundifolia background in backcrossed hybrids, on a large number of functions largely exceeding the ones constitutively expressed in single resistant gene transformants.

Advances in CircRNAs in the Past Decade: Review of CircRNAs Biogenesis, Regulatory Mechanisms, and Functions in Plants

Circular RNA (circRNA) is a type of non-coding RNA with multiple biological functions. Whole circRNA genomes in plants have been identified, and circRNAs have been demonstrated to be widely present and highly expressed in various plant tissues and organs. CircRNAs are highly stable and conserved in plants, and exhibit tissue specificity and developmental stage specificity. CircRNAs often interact with other biomolecules, such as miRNAs and proteins, thereby regulating gene expression, interfering with gene function, and affecting plant growth and development or response to environmental stress. CircRNAs are less studied in plants than in animals, and their regulatory mechanisms of biogenesis and molecular functions are not fully understood. A variety of circRNAs in plants are involved in regulating growth and development and responding to environmental stress. This review focuses on the biogenesis and regulatory mechanisms of circRNAs, as well as their biological functions during growth, development, and stress responses in plants, including a discussion of plant circRNA research prospects. Understanding the generation and regulatory mechanisms of circRNAs is a challenging but important topic in the field of circRNAs in plants, as it can provide insights into plant life activities and their response mechanisms to biotic or abiotic stresses as well as new strategies for plant molecular breeding and pest control.

Multiple transcription factors involved in the response of Chinese cabbage against Plasmodiophora brassicae

Clubroot disease, which is caused by the obligate biotrophic protist Plasmodiophora brassicae, leads to the formation of galls, commonly known as pathogen-induced tumors, on the roots of infected plants. The identification of crucial regulators of host tumor formation is essential to unravel the mechanisms underlying the proliferation and differentiation of P. brassicae within plant cells. To gain insight into this process, transcriptomic analysis was conducted to identify key genes associated with both primary and secondary infection of P. brassicae in Chinese cabbage. Our results demonstrate that the k-means clustering of subclass 1, which exhibited specific trends, was closely linked to the infection process of P. brassicae. Of the 1610 differentially expressed genes (DEGs) annotated in subclass 1, 782 were identified as transcription factors belonging to 49 transcription factor families, including bHLH, B3, NAC, MYB_related, WRKY, bZIP, C2H2, and ERF. In the primary infection, several genes, including the predicted Brassica rapa probable pectate lyase, RPM1-interacting protein 4-like, L-type lectin-domain-containing receptor kinase, G-type lectin S-receptor-like serine, B. rapa photosystem II 22 kDa protein, and MLP-like protein, showed significant upregulation. In the secondary infection stage, 45 of 50 overlapping DEGs were upregulated. These upregulated DEGs included the predicted B. rapa endoglucanase, long-chain acyl-CoA synthetase, WRKY transcription factor, NAC domain-containing protein, cell division control protein, auxin-induced protein, and protein variation in compound-triggered root growth response-like and xyloglucan glycosyltransferases. In both the primary and secondary infection stages, the DEGs were predicted to be Brassica rapa putative disease resistance proteins, L-type lectin domain-containing receptor kinases, ferredoxin-NADP reductases, 1-aminocyclopropane-1-carboxylate synthases, histone deacetylases, UDP-glycosyltransferases, putative glycerol-3-phosphate transporters, and chlorophyll a-binding proteins, which are closely associated with plant defense responses, biosynthetic processes, carbohydrate transport, and photosynthesis. This study revealed the pivotal role of transcription factors in the initiation of infection and establishment of intracellular parasitic relationships during the primary infection stage, as well as the proliferation and differentiation of the pathogen within the host cell during the secondary infection stage.

LORE receptor homomerization is required for 3-hydroxydecanoic acid-induced immune signaling and determines the natural variation of immunosensitivity within the Arabidopsis genus

The S-domain-type receptor-like kinase (SD-RLK) LIPOOLIGOSACCHARIDE-SPECIFIC REDUCED ELICITATION (LORE) from Arabidopsis thaliana is a pattern recognition receptor that senses medium-chain 3-hydroxy fatty acids, such as 3-hydroxydecanoic acid (3-OH-C10:0), to activate pattern-triggered immunity. Here, we show that LORE homomerization is required to activate 3-OH-C10:0-induced immune signaling. Fluorescence lifetime imaging in Nicotiana benthamiana demonstrates that AtLORE homomerizes via the extracellular and transmembrane domains. Co-expression of AtLORE truncations lacking the intracellular domain exerts a dominant negative effect on AtLORE signaling in both N. benthamiana and A. thaliana, highlighting that homomerization is essential for signaling. Screening for 3-OH-C10:0-induced reactive oxygen species production revealed natural variation within the Arabidopsis genus. Arabidopsis lyrata and Arabidopsis halleri do not respond to 3-OH-C10:0, although both possess a putative LORE ortholog. Both LORE orthologs have defective extracellular domains that bind 3-OH-C10:0 to a similar level as AtLORE, but lack the ability to homomerize. Thus, ligand binding is independent of LORE homomerization. Analysis of AtLORE and AlyrLORE chimera suggests that the loss of AlyrLORE homomerization is caused by several amino acid polymorphisms across the extracellular domain. Our findings shed light on the activation mechanism of LORE and the loss of 3-OH-C10:0 perception within the Arabidopsis genus.

Deciphering miRNA-lncRNA-mRNA interaction through experimental validation of miRNAs, lncRNAs, and miRNA targets on mRNAs in Cajanus cajan

Pigeon pea (Cajanus cajan) is widely cultivated for its nutritional and medicinal value yet remains an orphan crop as productivity has not been improved because of a lack of genome and non-coding genome information. Non-coding RNAs, like miRNAs and long non-coding RNAs (lncRNAs), are involved in regulation of growth, metabolism, development, and stress response, and have a critical role in post-transcriptional gene regulation (PTGR). We attempted to elucidate the roles of miRNAs and lncRNAs in pigeon pea through experimental validation of computationally predicted miRNAs and lncRNAs and targets of miRNAs on mRNAs. We experimentally validated 20 miRNAs and 11 lncRNAs. We predicted cleavage sites of three miRNA targets: serine/threonine-protein kinase, polygalacturonase, beta-galactosidase. We identified 469 targets of 265 miRNAs and their functional annotations using computational methods. We built a miRNA-mRNA-lncRNA network model, with the miRNAs targeting both mRNAs and lncRNAs, to obtain information on the interplay of these three molecules. A confirmed interaction through experimental validation was established between miRNA, namely cca-miR1535a targeting the mRNA for beta-galactosidase, as well as the lncRNA cca-lnc-020033. Our findings increase knowledge of the non-coding genome of pigeon pea and their roles in PTGR and in improving agronomic traits of this pulse crop.

Overexpression of a plasmalemma Na+/H+ antiporter from the halophyte Nitraria sibirica enhances the salt tolerance of transgenic poplar

The plasmalemma Na+/H+ antiporter Salt Overly Sensitive 1 (SOS1) is responsible for the efflux of Na+ from the cytoplasm, an important determinant of salt resistance in plants. In this study, an ortholog of SOS1, referred to as NsSOS1, was cloned from Nitraria sibirica, a typical halophyte that grows in deserts and saline-alkaline land, and its expression and function in regulating the salt tolerance of forest trees were evaluated. The expression level of NsSOS1 was higher in leaves than in roots and stems of N. sibirica, and its expression was upregulated under salt stress. Histochemical staining showed that β-glucuronidase (GUS) driven by the NsSOS1 promoter was strongly induced by abiotic stresses and phytohormones including salt, drought, low temperature, gibberellin, and methyl jasmonate, suggesting that NsSOS1 is involved in the regulation of multiple signaling pathways. Transgenic 84 K poplar (Populus alba × P. glandulosa) overexpressing NsSOS1 showed improvements in survival rate, root biomass, plant height, relative water levels, chlorophyll and proline levels, and antioxidant enzyme activities versus non-transgenic poplar (NT) under salt stress. Transgenic poplars accumulated less Na+ and more K+ in roots, stems, and leaves, which had a lower Na+/K+ ratio compared to NT under salt stress. These results indicate that NsSOS1-mediated Na+ efflux confers salt tolerance to transgenic poplars, which show more efficient photosynthesis, better scavenging of reactive oxygen species, and improved osmotic adjustment under salt stress. Transcriptome analysis of transgenic poplars confirmed that NsSOS1 not only mediates Na+ efflux but is also involved in the regulation of multiple metabolic pathways. The results provide insight into the regulatory mechanisms of NsSOS1 and suggest that it could be used to improve the salt tolerance of forest trees.

Weighted gene co-expression network analysis reveals hub genes regulating response to salt stress in peanut

Peanut (Arachis hypogaea L.) is an important oilseed crop worldwide. However, soil salinization becomes one of the main limiting factors of peanut production. Therefore, developing salt-tolerant varieties and understanding the molecular mechanisms of salt tolerance is important to protect peanut yield in saline areas. In this study, we selected four peanut varieties with contrasting response to salt challenges with T1 and T2 being tolerance and S1 and S2 being susceptible. High-throughput RNA sequencing resulted in more than 314.63 Gb of clean data from 48 samples. We identified 12,057 new genes, 7,971of which have functional annotations. KEGG pathway enrichment analysis of uniquely expressed genes in salt-tolerant peanut revealed that upregulated genes in the root are involved in the MAPK signaling pathway, fatty acid degradation, glycolysis/gluconeogenesis, and upregulated genes in the shoot were involved in plant hormone signal transduction and the MAPK signaling pathway. Na+ content, K+ content, K+/ Na+, and dry mass were measured in root and shoot tissues, and two gene co-expression networks were constructed based on weighted gene co-expression network analysis (WGCNA) in root and shoot. In this study, four key modules that are highly related to peanut salt tolerance in root and shoot were identified, plant hormone signal transduction, phenylpropanoid biosynthesis, starch and sucrose metabolism, flavonoid biosynthesis, carbon metabolism were identified as the key biological processes and metabolic pathways for improving peanut salt tolerance. The hub genes include genes encoding ion transport (such as HAK8, CNGCs, NHX, NCL1) protein, aquaporin protein, CIPK11 (CBL-interacting serine/threonine-protein kinase 11), LEA5 (late embryogenesis abundant protein), POD3 (peroxidase 3), transcription factor, and MAPKKK3. There were some new salt-tolerant genes identified in peanut, including cytochrome P450, vinorine synthase, sugar transport protein 13, NPF 4.5, IAA14, zinc finger CCCH domain-containing protein 62, beta-amylase, fatty acyl-CoA reductase 3, MLO-like protein 6, G-type lectin S-receptor-like serine/threonine-protein kinase, and kinesin-like protein KIN-7B. The identification of key modules, biological pathways, and hub genes in this study enhances our understanding of the molecular mechanisms underlying salt tolerance in peanuts. This knowledge lays a theoretical foundation for improving and innovating salt-tolerant peanut germplasm.

Comparative analysis of infected cassava root transcriptomics reveals candidate genes for root rot disease resistance

Cassava root-rot incited by soil-borne pathogens is one of the major diseases that reduces root yield. Although the use of resistant cultivars is the most effective method of management, the genetic basis for root-rot resistance remains poorly understood. Therefore, our work analyzed the transcriptome of two contrasting genotypes (BRS Kiriris/resistant and BGM-1345/susceptible) using RNA-Seq to understand the molecular response and identify candidate genes for resistance. Cassava seedlings (resistant and susceptible to root-rot) were both planted in infested and sterilized soil and samples from Initial-time and Final-time periods, pooled. Two controls were used: (i) seedlings collected before planting in infested soil (absolute control) and, (ii) plants grown in sterilized soil (mock treatments). For the differentially expressed genes (DEGs) analysis 23.912 were expressed in the resistant genotype, where 10.307 were differentially expressed in the control treatment, 15 DEGs in the Initial Time-period and 366 DEGs in the Final Time-period. Eighteen candidate genes from the resistant genotype were related to plant defense, such as the MLP-like protein 31 and the peroxidase A2-like gene. This is the first model of resistance at the transcriptional level proposed for the cassava × root-rot pathosystem. Gene validation will contribute to screening for resistance of germplasm, segregating populations and/or use in gene editing in the pursuit to develop most promising cassava clones with resistance to root-rot.

Haplotype-resolved T2T reference genomes for wild and domesticated accessions shed new insights into the domestication of jujube

Chinese jujube (Ziziphus jujuba Mill.) is one of the most important deciduous tree fruits in China, with substantial economic and nutritional value. Jujube was domesticated from its wild progenitor, wild jujube (Z. jujuba var. spinosa), and both have high medicinal value. Here we report the 767.81- and 759.24-Mb haplotype-resolved assemblies of a dry-eating 'Junzao' jujube (JZ) and a wild jujube accession (SZ), using a combination of multiple sequencing strategies. Each assembly yielded two complete haplotype-resolved genomes at the telomere-to-telomere (T2T) level, and ~81.60 and 69.07 Mb of structural variations were found between the two haplotypes within JZ and SZ, respectively. Comparative genomic analysis revealed a large inversion on each of chromosomes 3 and 4 between JZ and SZ, and numerous genes were affected by structural variations, some of which were associated with starch and sucrose metabolism. A large-scale population analysis of 672 accessions revealed that wild jujube originated from the lower reaches of the Yellow River and was initially domesticated at local sites. It spread widely and was then independently domesticated at the Shanxi-Shaanxi Gorge of the middle Yellow River. In addition, we identified some new selection signals regions on genomes, which are involved in the tissue development, pollination, and other aspects of jujube tree morphology and fertilization domestication. In conclusion, our study provides high-quality reference genomes of jujube and wild jujube and new insights into the domestication history of jujube.

Overexpression of the WRKY transcription factor gene NtWRKY65 enhances salt tolerance in tobacco (Nicotiana tabacum)

BACKGROUND

Salt stress severely inhibits plant growth, and the WRKY family transcription factors play important roles in salt stress resistance. In this study, we aimed to characterize the role of tobacco (Nicotiana tabacum) NtWRKY65 transcription factor gene in salinity tolerance.

RESULTS

This study characterized the role of tobacco (Nicotiana tabacum) NtWRKY65 transcription factor gene in salinity tolerance using four NtWRKY65 overexpression lines. NtWRKY65 is localized to the nucleus, has transactivation activity, and is upregulated by NaCl treatment. Salinity treatment resulted in the overexpressing transgenic tobacco lines generating significantly longer roots, with larger leaf area, higher fresh weight, and greater chlorophyll content than those of wild type (WT) plants. Moreover, the overexpressing lines showed elevated antioxidant enzyme activity, reduced malondialdehyde content, and leaf electrolyte leakage. In addition, the Na+ content significantly decreased, and the K+/Na+ ratio was increased in the NtWRKY65 overexpression lines compared to those in the WT. These results suggest that NtWRKY65 overexpression enhances salinity tolerance in transgenic plants. RNA-Seq analysis of the NtWRKY65 overexpressing and WT plants revealed that NtWRKY65 might regulate the expression of genes involved in the salt stress response, including cell wall component metabolism, osmotic stress response, cellular oxidant detoxification, protein phosphorylation, and the auxin signaling pathway. These results were consistent with the morphological and physiological data. These findings indicate that NtWRKY65 overexpression confers enhanced salinity tolerance.

CONCLUSIONS

Our results indicated that NtWRKY65 is a critical regulator of salinity tolerance in tobacco plants.

Screening candidate genes for fruit size based on QTL-seq in Chinese jujube

Introduction

Fruit size is an important economic trait affecting jujube fruit quality, which has always been the focus of marker-assisted breeding of jujube traits. However, despite a large number of studies have been carried out, the mechanism and key genes regulating jujube fruit size are mostly unknown.

Methods

In this study, we used a new analysis method Quantitative Trait Loci sequencing (QTL-seq) (bulked segregant analysis) to screen the parents 'Yuhong' and 'Jiaocheng 5' with significant phenotypic differences and mixed offspring group with extreme traits of large fruit and small fruit, respectively, and, then, DNA mixed pool sequencing was carried out to further shortening the QTL candidate interval for fruit size trait and excavated candidate genes for controlling fruit size.

Results

The candidate intervals related to jujube fruit size were mainly located on chromosomes 1, 5, and 10, and the frequency of chromosome 1 was the highest. Based on the QTL-seq results, the annotation results of ANNOVAR were extracted from 424 SNPs (single-nucleotide polymorphisms) and 164 InDels (insertion-deletion), from which 40 candidate genes were selected, and 37 annotated candidate genes were found in the jujube genome. Four genes (LOC107428904, LOC107415626, LOC125420708, and LOC107418290) that are associated with fruit size growth and development were identified by functional annotation of the genes in NCBI (National Center for Biotechnology Information). The genes can provide a basis for further exploration and identification on genes regulating jujube fruit size.

Discussion

In summary, the data obtained in this study revealed that QTL intervals and candidate genes for fruit size at the genomic level provide valuable resources for future functional studies and jujube breeding.

Chromosome-level genome of Ambrosia trifida provides insights into adaptation and the evolution of pollen allergens

Ambrosia trifida (giant ragweed) is an invasive plant that can cause serious damage to natural ecosystems and severe respiratory allergies. However, the genomic basis of invasive adaptation and pollen allergens in Ambrosia species remain largely unknown. Here, we present a 1.66 Gb chromosome-scale reference genome for giant ragweed and identified multiple types of genome duplications, which are responsible for its rapid environmental adaptation and pollen development. The largest copies number and species-specific expansions of resistance-related gene families compared to Heliantheae alliance might contribute to resist stresses, pathogens and rapid adaptation. To extend the knowledge of evolutionary process of allergic pollen proteins, we predicted 26 and 168 potential pollen allergen candidates for giant ragweed and other Asteraceae plant species by combining machine learning and identity screening. Interestingly, we observed a specific tandemly repeated array for potential allergenic pectate lyases among Ambrosia species. Rapid evolutionary rates on putative pectate lyase allergens may imply a crucial role of nonsynonymous mutations on amino acid residues for plant biological function and allergenicity. Altogether, this study provides insight into the molecular ecological adaptation and putative pollen allergens prediction that will be helpful in promoting invasion genomic research and evolution of putative pollen allergy in giant ragweed.

Genome-wide identification of PYL/PYR-PP2C (A)-SnRK2 genes in Eutrema and their co-expression analysis in response to ABA and abiotic stresses

ABA signaling core components PYR/PYL, group A PP2C and SnRK2 play important roles in various environmental stress responses of plants. This study identified 14 PYR/PYL, 9 PP2C (A), and 10 SnRK2 genes from halophytic Eutrema. Phylogenetic analysis showed 4 EsPYR/PYL, 4 EsPP2C (A) and 3 EsSnRK2 subfamilies characterized, which was supported by their gene structures and protein motifs. Large-scale segmental duplication event was demonstrated to be a major contributor to expansion of the EsPYL-PP2C (A)-SnRK2 gene families. Synteny relationship analysis revealed more orthologous PYL-PP2C (A)-SnRK2 gene pairs located in collinear blocks between Eutrema and Brassica than that between Eutrema and Arabidopsis. RNA-seq and qRT-PCR revealed EsABI1, EsABI2 and EsHAL2 showed a significantly up-regulated expression in leaves and roots in response to ABA, NaCl or cold stress. Three markedly co-expression modules of ABA/R-brown, NaCl/L-lightsteelblue1 and Cold/R-lightgreen were uncovered to contain EsPYL-PP2C (A)-SnRK2 genes by WGCNA analysis. GO and KEGG analysis indicated that the genes of ABA/R-brown module containing EsHAB1, EsHAI2 and EsSnRK2.6 were enriched in proteasome pathway. Further, EsHAI2-OE transgenic Arabidopsis lines showed significantly enhanced seeds germination and seedlings growth. This work provides a new insight for elucidating potential molecular functions of PYL-PP2C (A)-SnRK2 responding to ABA and abiotic stresses.

Comparative analysis of the carrot miRNAome in response to salt stress

Soil salinity adversely affects the yield and quality of crops, including carrot. During salt stress, plant growth and development are impaired by restricted water uptake and ion cytotoxicity, leading to nutrient imbalance and oxidative burst. However, the molecular mechanisms of the carrot plant response to salt stress remain unclear. The occurrence and expression of miRNAs that are potentially involved in the regulation of carrot tolerance to salinity stress were investigated. The results of small RNA sequencing revealed that salt-sensitive (DH1) and salt-tolerant (DLBA) carrot varieties had different miRNA expression profiles. A total of 95 miRNAs were identified, including 71 novel miRNAs, of which 30 and 23 were unique to DH1 and DLBA, respectively. The comparison of NGS and qPCR results allowed identification of two conserved and five novel miRNA involved in carrot response to salt stress, and which differentiated the salt-tolerant and salt-sensitive varieties. Degradome analysis supported by in silico-based predictions and followed by expression analysis of exemplary target genes pointed at genes related to proline, glutathione, and glutamate metabolism pathways as potential miRNA targets involved in salt tolerance, and indicated that the regulation of osmoprotection and antioxidant protection, earlier identified as being more efficient in the tolerant variety, may be controlled by miRNAs. Furthermore, potential miRNA target genes involved in chloroplast protection, signal transduction and the synthesis and modification of cell wall components were indicated in plants growing in saline soil.

PWL1, a G-type lectin receptor-like kinase, positively regulates leaf senescence and heat tolerance but negatively regulates resistance to Xanthomonas oryzae in rice

Plant leaf senescence, caused by multiple internal and environmental factors, has an important impact on agricultural production. The lectin receptor-like kinase (LecRLK) family members participate in plant development and responses to biotic and abiotic stresses, but their roles in regulating leaf senescence remain elusive. Here, we identify and characterize a rice premature withered leaf 1 (pwl1) mutant, which exhibits premature leaf senescence throughout the plant life cycle. The pwl1 mutant displayed withered and whitish leaf tips, decreased chlorophyll content, and accelerated chloroplast degradation. Map-based cloning revealed an amino acid substitution (Gly412Arg) in LOC_Os03g62180 (PWL1) was responsible for the phenotypes of pwl1. The expression of PWL1 was detected in all tissues, but predominantly in tillering and mature leaves. PWL1 encodes a G-type LecRLK with active kinase and autophosphorylation activities. PWL1 is localized to the plasma membrane and can self-associate, mainly mediated by the plasminogen-apple-nematode (PAN) domain. Substitution of the PAN domain significantly diminished the self-interaction of PWL1. Moreover, the pwl1 mutant showed enhanced reactive oxygen species (ROS) accumulation, cell death, and severe DNA fragmentation. RNA sequencing analysis revealed that PWL1 was involved in the regulation of multiple biological processes, like carbon metabolism, ribosome, and peroxisome pathways. Meanwhile, interfering of biological processes induced by the PWL1 mutation also enhanced heat sensitivity and resistance to bacterial blight and bacterial leaf streak with excessive accumulation of ROS and impaired chloroplast development in rice. Natural variation analysis indicated more variations in indica varieties, and the vast majority of japonica varieties harbour the PWL1Hap1 allele. Together, our results suggest that PWL1, a member of LecRLKs, exerts multiple roles in regulating plant growth and development, heat-tolerance, and resistance to bacterial pathogens.

PaLectinL7 enhances salt tolerance of sweet cherry by regulating lignin deposition in connection with PaCAD1

Lectin receptor-like kinases (LecRLKs), a large family of plant receptor-like kinases, play an important role in plant response to abiotic stresses. However, little information is available about the roles of LecRLKs in the salt stress response of sweet cherry (Prunus avium). Here, an L-type LecRLK gene (PaLectinL7) was characterized from sweet cherry. Subcellular localization analysis revealed that PaLectinL7 is a plasma membrane protein. The expression of PaLectinL7 was up-regulated by salt, drought and exogenously gibberellin treatments. Overexpression of PaLectinL7 in the roots of Gisela 6 enhanced its tolerance to salt stress. Additionally, transcriptome analysis showed that lignin metabolic-related genes were regulated by PaLectinL7 overexpression. Meanwhile, the lignin contents and associated enzymes (CAD and COMT) rose concurrently with PaLectinL7 overexpression under salt stress. We also found that PaCAD1, a key enzyme involved in lignin metabolism, interacted with PaLectinL7 and could be phosphorylated by PaLectinL7 in vitro, suggesting that PaLectinL7 may regulate the enzyme activity of PaCAD1. Therefore, these results indicated that PaLectinL7, as a membrane-bound regulator, promoted lignin deposition by regulating the activities of enzymes related to lignin metabolism, thus enhancing salt tolerance.

Emerging Roles of Receptor-like Protein Kinases in Plant Response to Abiotic Stresses

The productivity of plants is hindered by unfavorable conditions. To perceive stress signals and to transduce these signals to intracellular responses, plants rely on membrane-bound receptor-like kinases (RLKs). These play a pivotal role in signaling events governing growth, reproduction, hormone perception, and defense responses against biotic stresses; however, their involvement in abiotic stress responses is poorly documented. Plant RLKs harbor an N-terminal extracellular domain, a transmembrane domain, and a C-terminal intracellular kinase domain. The ectodomains of these RLKs are quite diverse, aiding their responses to various stimuli. We summarize here the sub-classes of RLKs based on their domain structure and discuss the available information on their specific role in abiotic stress adaptation. Furthermore, the current state of knowledge on RLKs and their significance in abiotic stress responses is highlighted in this review, shedding light on their role in influencing plant-environment interactions and opening up possibilities for novel approaches to engineer stress-tolerant crop varieties.

Plant lectins: Classical molecules with emerging roles in stress tolerance

Biotic and abiotic stresses impose adverse effects on plant's development, growth, and production. For the past many years, researchers are trying to understand the stress induced responses in plants and decipher strategies to produce stress tolerant crops. It has been demonstrated that molecular networks encompassing an array of genes and functional proteins play a key role in generating responses to combat different stresses. Newly, there has been a resurgence of interest to explore the role of lectins in modulating various biological responses in plants. Lectins are naturally occurring proteins that form reversible linkages with their respective glycoconjugates. To date, several plant lectins have been recognized and functionally characterized. However, their involvement in stress tolerance is yet to be comprehensively analyzed in greater detail. The availability of biological resources, modern experimental tools, and assay systems has provided a fresh impetus for plant lectin research. Against this backdrop, the present review provides background information on plant lectins and recent knowledge on their crosstalks with other regulatory mechanisms, which play a remarkable role in plant stress amelioration. It also highlights their versatile role and suggests that adding more information to this under-explored area will usher in a new era of crop improvement.

Twenty years of mining salt tolerance genes in soybean

Current combined challenges of rising food demand, climate change and farmland degradation exert enormous pressure on agricultural production. Worldwide soil salinization, in particular, necessitates the development of salt-tolerant crops. Soybean, being a globally important produce, has its genetic resources increasingly examined to facilitate crop improvement based on functional genomics. In response to the multifaceted physiological challenge that salt stress imposes, soybean has evolved an array of defences against salinity. These include maintaining cell homeostasis by ion transportation, osmoregulation, and restoring oxidative balance. Other adaptations include cell wall alterations, transcriptomic reprogramming, and efficient signal transduction for detecting and responding to salt stress. Here, we reviewed functionally verified genes that underly different salt tolerance mechanisms employed by soybean in the past two decades, and discussed the strategy in selecting salt tolerance genes for crop improvement. Future studies could adopt an integrated multi-omic approach in characterizing soybean salt tolerance adaptations and put our existing knowledge into practice via omic-assisted breeding and gene editing. This review serves as a guide and inspiration for crop developers in enhancing soybean tolerance against abiotic stresses, thereby fulfilling the role of science in solving real-life problems.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01383-3.

Comparative transcriptome profiling of near isogenic lines PBW343 and FLW29 to unravel defense related genes and pathways contributing to stripe rust resistance in wheat

Stripe rust (Sr), caused by Puccinia striiformis f. sp. tritici (Pst), is the most devastating disease that poses serious threat to the wheat-growing nations across the globe. Developing resistant cultivars is the most challenging aspect in wheat breeding. The function of resistance genes (R genes) and the mechanisms by which they influence plant-host interactions are poorly understood. In the present investigation, comparative transcriptome analysis was carried out by involving two near-isogenic lines (NILs) PBW343 and FLW29. The seedlings of both the genotypes were inoculated with Pst pathotype 46S119. In total, 1106 differentially expressed genes (DEGs) were identified at early stage of infection (12 hpi), whereas expressions of 877 and 1737 DEGs were observed at later stages (48 and 72 hpi) in FLW29. The identified DEGs were comprised of defense-related genes including putative R genes, 7 WRKY transcriptional factors, calcium, and hormonal signaling associated genes. Moreover, pathways involved in signaling of receptor kinases, G protein, and light showed higher expression in resistant cultivar and were common across different time points. Quantitative real-time PCR was used to further confirm the transcriptional expression of eight critical genes involved in plant defense mechanism against stripe rust. The information about genes are likely to improve our knowledge of the genetic mechanism that controls the stripe rust resistance in wheat, and data on resistance response-linked genes and pathways will be a significant resource for future research.

Genetic architecture of leaf morphology revealed by integrated trait module in Catalpa bungei

Leaves are crucial for maintaining plant growth and development via photosynthesis, and their function is simultaneously regulated by a suite of phenotypic traits. Although much is known about the genetic architecture of individual leaf traits, unraveling the genetic basis of complex leaf morphology remains a challenge. Based on the functional correlation and coordination of multi-traits, we divided 15 leaf morphological traits into three modules, comprising size (area, length, width, and perimeter), shape (leaf lobes, aspect ratio, circularity, rectangularity, and the relevant ratios), and color (red, green, and blue) for an ornamental tree species, Catalpa bungei. A total of 189 significant single-nucleotide polymorphisms were identified in the leaves of C. bungei: 35, 82, and 76 in the size, shape, and color modules, respectively. Four quantitative trait loci were common between the size and shape modules, which were closely related according to phenotype correlation, genetic mapping, and mRNA analysis. The color module was independent of them. Synergistic changes in the aspect ratio, leaf lobe, and circularity suggest that these traits could be the core indicators of the leaf shape module. The LAS and SRK genes, associated with leaf lobe and circularity, were found to function in plant defense mechanisms and the growth of leaves. The associations between the SRK and CRK2 genes and the leaf lobe and circularity traits were further verified by RT-qPCR. Our findings demonstrate the importance of integrating multi-trait modules to characterize leaf morphology and facilitate a holistic understanding of the genetic architecture of intraspecific leaf morphology diversity.

Bactericidal and plant defense elicitation activities of Eucalyptus oil decrease the severity of infections by Xylella fastidiosa on almond plants

The activity of Eucalyptus essential oil against eleven strains pertaining to six species of plant pathogenic bacteria was studied using growth inhibition and contact assays. All strains were susceptible to the formulation EGL2, and Xylella fastidiosa subspecies and Xanthomonas fragariae were the most sensitive. The bactericidal effect was strong causing 4.5 to 6.0 log reductions in survival in 30 min at concentrations in the range of 0.75 to 15.0 μl/ml depending on the bacteria tested. Transmission electron microscopy of the formulation EGL2 against the three X. fastidiosa subspecies studied allowed the observation of a strong lytic effect on bacterial cells. In addition, the preventive spray application of EGL2 to potted pear plants subsequently inoculated with Erwinia amylovora significantly decreased the severity of infections. Almond plants treated by endotherapy or soil drenching, and then inoculated with X. fastidiosa showed a significant decrease in disease severity as well as in the levels of the pathogen, depending on the strategy used (endotherapy/soil drenching, preventive/curative). The treatment by endotherapy in almond plants induced the expression of several genes involved in plant defense. It was concluded that the reduction of infections by the Eucalyptus oil treatments was due to the combination of its bactericidal and plant defense induction activities.

Genetic Analyses of Seed Longevity in Capsicum annuum L. in Cold Storage Conditions

Seed longevity is the most important trait in the genebank management system. No seed can remain infinitely viable. There are 1241 accessions of Capsicum annuum L. available at the German Federal ex situ genebank at IPK Gatersleben. C. annuum (Capsicum) is the most economically important species of the genus Capsicum. So far, there is no report that has addressed the genetic basis of seed longevity in Capsicum. Here, we convened a total of 1152 Capsicum accessions that were deposited in Gatersleben over forty years (from 1976 to 2017) and assessed their longevity by analyzing the standard germination percentage after 5-40 years of storage at -15/-18 °C. These data were used to determine the genetic causes of seed longevity, along with 23,462 single nucleotide polymorphism (SNP) markers covering all of the 12 Capsicum chromosomes. Using the association-mapping approach, we identified a total of 224 marker trait associations (MTAs) (34, 25, 31, 35, 39, 7, 21 and 32 MTAs after 5-, 10-, 15-, 20-, 25-, 30-, 35- and 40-year storage intervals) on all the Capsicum chromosomes. Several candidate genes were identified using the blast analysis of SNPs, and these candidate genes are discussed.

Can cereal-legume intercrop systems contribute to household nutrition in semi-arid environments: A systematic review and meta-analysis

Introduction

Intercropping cereals with legumes can intensify rainfed cereal monocropping for improved household food and nutritional security. However, there is scant literature confirming the associated nutritional benefits.

Methodology

A systematic review and meta-analysis of nutritional water productivity (NWP) and nutrient contribution (NC) of selected cereal-legume intercrop systems was conducted through literature searches in Scopus, Web of Science and ScienceDirect databases. After the assessment, only nine articles written in English that were field experiments comprising grain cereal and legume intercrop systems were retained. Using the R statistical software (version 3.6.0), paired t-tests were used to determine if differences existed between the intercrop system and the corresponding cereal monocrop for yield (Y), water productivity (WP), NC, and NWP.

Results

The intercropped cereal or legume yield was 10 to 35% lower than that for the corresponding monocrop system. In most instances, intercropping cereals with legumes improved NY, NWP, and NC due to their added nutrients. Substantial improvements were observed for calcium (Ca), where NY, NWP, and NC improved by 658, 82, and 256%, respectively.

Discussion

Results showed that cereal-legume intercrop systems could improve nutrient yield in water-limited environments. Promoting cereal- legume intercrops that feature nutrient-dense legume component crops could contribute toward addressing the SDGs of Zero Hunger (SDG 3), Good Health and Well-3 (SDG 2) and Responsible consumption and production (SDG 12).

Proteomics approach to investigating osmotic stress effects on pistachio

Osmotic stress can occur due to some stresses such as salinity and drought, threatening plant survival. To investigate the mechanism governing the pistachio response to this stress, the biochemical alterations and protein profile of PEG-treated plants was monitored. Also, we selected two differentially abundant proteins to validate via Real-Time PCR. Biochemical results displayed that in treated plants, proline and phenolic content was elevated, photosynthetic pigments except carotenoid decreased and MDA concentration were not altered. Our findings identified a number of proteins using 2DE-MS, involved in mitigating osmotic stress in pistachio. A total of 180 protein spots were identified, of which 25 spots were altered in response to osmotic stress. Four spots that had photosynthetic activities were down-regulated, and the remaining spots were up-regulated. The biological functional analysis of protein spots exhibited that most of them are associated with the photosynthesis and metabolism (36%) followed by stress response (24%). Results of Real-Time PCR indicated that two of the representative genes illustrated a positive correlation among transcript level and protein expression and had a similar trend in regulation of gene and protein. Osmotic stress set changes in the proteins associated with photosynthesis and stress tolerance, proteins associated with the cell wall, changes in the expression of proteins involved in DNA and RNA processing occur. Findings of this research will introduce possible proteins and pathways that contribute to osmotic stress and can be considered for improving osmotic tolerance in pistachio.

Integrated GWAS and transcriptomic analysis reveal the candidate salt-responding genes regulating Na+/K+ balance in barley (Hordeum vulgare L.)

Salt stress is one of the main abiotic stresses affecting crop yield and quality. Barley has strong salt tolerance, however, the underlying genetic basis is not fully clear, especially in the seedling stage. This study examined the ionic changes in barley core germplasms under the control and salt conditions. Genome-wide association study (GWAS) analysis revealed 54 significant SNPs from a pool of 25,342 SNPs distributed in 7 chromosomes (Chr) of the Illumina Barley 50K SNP array. These SNPs are associated with ion homeostasis traits, sodium (Na⁺) and potassium (K⁺) content, and Na⁺/K⁺ ratio representing five genomic regions on Chr 2, 4, 5, 6, and 7 in the leaves of worldwide barley accessions. And there are 3 SNP peaks located on the Chr 4, 6, and 7, which could be the "hot spots" regions for mining and identifying candidate genes for salt tolerance. Furthermore, 616 unique candidate genes were screened surrounding the significant SNPs, which are associated with transport proteins, protein kinases, binding proteins, and other proteins of unknown function. Meanwhile, transcriptomic analysis (RNA-Seq) was carried out to compare the salt-tolerant (CM72) and salt-sensitive (Gairdner) genotypes subjected to salt stress. And there was a greater accumulation of differentially expressed genes(DEGs) in Gairdner compared to CM72, mainly enriched in metabolic pathway, biosynthesis of secondary metabolites, photosynthesis, signal transduction,emphasizing the different transcriptional response in both genotypes following salt exposure. Combined GWAS and RNA-Seq analysis revealed 5 promising salt-responding genes (PGK2, BASS3, SINAT2, AQP, and SYT3) from the hot spot regions, which were verified between the salt-tolerant and salt-sensitive varieties by qRT-PCR. In all, these results provide candidate SNPs and genes responsible for salinity responding in barley, and a new idea for studying such genetic basis in similar crops.

Hrip1 enhances tomato resistance to yellow leaf curl virus by manipulating the phenylpropanoid biosynthesis and plant hormone pathway

Tomato yellow leaf curl virus (TYLCV) causes tremendous losses of tomato worldwide. An elicitor Hrip1, which produced by Alternaria tenuissima, can serve as a pathogen-associated molecular patterns (PAMPs) to trigger the immune defense response in Nicotiana benthamiana. Here, we show that Hrip1 can be targeted to the extracellular space and significantly delayed the development of symptoms caused by TYLCV in tomato. In basis of RNA-seq profiling, we find that 1621 differential expression genes (DEGs) with the opposite expression patterns are enriched in plant response to biotic stress between Hrip1 treatment and TYLCV infection of tomato. Thirty-two known differential expression miRNAs with the opposite expression patterns are identified by small RNA sequencing and the target genes of these miRNAs are significantly enriched in phenylpropanoid biosynthesis, plant hormone signal transduction and peroxisome. Based on the Pearson correlation analysis, 13 negative and 21 positive correlations are observed between differential expression miRNAs and DEGs. These miRNAs, which act as a key mediator of tomato resistance to TYLCV induced by Hrip1, regulate the expression of phenylpropanoid biosynthesis and plant hormone signal transduction-related genes. Taken together, our results provide an insight into tomato resistance to TYLCV induced by PAMP at transcriptional and posttranscriptional levels.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-022-03426-6.

Molecular plasticity to soil water deficit differs between sessile oak (Quercus Petraea (Matt.) Liebl.) high- and low-water use efficiency genotypes

Water use efficiency (WUE) is an important adaptive trait for soil water deficit. The molecular and physiological bases of WUE regulation in crops have been studied in detail in the context of plant breeding. Knowledge for most forest tree species lags behind, despite the need to identify populations or genotypes able to cope with the longer, more intense drought periods likely to result from climate warming. We aimed to bridge this gap in knowledge for sessile oak (Quercus petraea (Matt.) Liebl.), one of the most ecologically and economically important tree species in Europe, using a factorial design including trees with contrasted phenotypic values (low and high WUE) and two watering regimes (control and drought). By monitoring the ecophysiological response, we first qualified genotypes for their WUE (by using instantaneous and long-term measures). We then performed RNA-seq to quantify gene expression for the three most extreme genotypes exposed to the two watering regimes. By analyzing the interaction term, we were able to capture the molecular strategy of each group of plants for coping with drought. We identified putative candidate genes potentially involved in the regulation of transpiration rate in high-WUE phenotypes. Regardless of water availability, trees from the high-WUE phenotypic class overexpressed genes associated with drought responses, and in the control of stomatal density and distribution, and displayed a downregulation of genes associated with early stomatal closure and high transpiration rate. Fine physiological screening of sessile oaks with contrasting WUE, and their molecular characterization (i) highlighted subtle differences in transcription between low- and high-WUE genotypes, identifying key molecular players in the genetic control of this trait and (ii) revealed the genes underlying the molecular strategy that evolved in each group to potentially cope with water deficit, providing new insight into the within-species diversity in drought adaptation strategies.

Insights into the regulation of wild soybean tolerance to salt-alkaline stress

Soybean is an important grain and oil crop. In China, there is a great contradiction between soybean supply and demand. China has around 100 million ha of salt-alkaline soil, and at least 10 million could be potentially developed for cultivated land. Therefore, it is an effective way to improve soybean production by breeding salt-alkaline-tolerant soybean cultivars. Compared with wild soybean, cultivated soybean has lost a large number of important genes related to environmental adaptation during the long-term domestication and improvement process. Therefore, it is greatly important to identify the salt-alkaline tolerant genes in wild soybean, and investigate the molecular basis of wild soybean tolerance to salt-alkaline stress. In this review, we summarized the current research regarding the salt-alkaline stress response in wild soybean. The genes involved in the ion balance and ROS scavenging in wild soybean were summarized. Meanwhile, we also introduce key protein kinases and transcription factors that were reported to mediate the salt-alkaline stress response in wild soybean. The findings summarized here will facilitate the molecular breeding of salt-alkaline tolerant soybean cultivars.

Coastal Wild Grapevine Accession (Vitis vinifera L. ssp. sylvestris) Shows Distinct Late and Early Transcriptome Changes under Salt Stress in Comparison to Commercial Rootstock Richter 110

Increase in soil salinity, driven by climate change, is a widespread constrain for viticulture across several regions, including the Mediterranean basin. The implementation of salt-tolerant varieties is sought after to reduce the negative impact of salinity in grape production. An accession of wild grapevine (Vitis vinifera L. ssp. sylvestris), named AS1B, found on the coastline of Asturias (Spain), could be of interest toward the achievement of salt-tolerant varieties, as it demonstrated the ability to survive and grow under high levels of salinity. In the present study, AS1B is compared against widely cultivated commercial rootstock Richter 110, regarding their survival capabilities, and transcriptomic profiles analysis allowed us to identify the genes by employing RNA-seq and gene ontology analyses under increasing salinity and validate (via RT-qPCR) seven salinity-stress-induced genes. The results suggest contrasting transcriptomic responses between AS1B and Richter 110. AS1B is more responsive to a milder increase in salinity and builds up specific mechanisms of tolerance over a sustained salt stress, while Richter 110 maintains a constitutive expression until high and prolonged saline inputs, when it mainly shows responses to osmotic stress. The genetic basis of AS1B's strategy to confront salinity could be valuable in cultivar breeding programs, to expand the current range of salt-tolerant rootstocks, aiming to improve the adaptation of viticulture against climate change.

Transcriptome and Metabolome Analyses Revealed the Response Mechanism of Sugar Beet to Salt Stress of Different Durations

Salinity is one of the most serious threats to agriculture worldwide. Sugar beet is an important sugar-yielding crop and has a certain tolerance to salt; however, the genome-wide dynamic response to salt stress remains largely unknown in sugar beet. In the present study, physiological and transcriptome analyses of sugar beet leaves and roots were compared under salt stress at five time points. The results showed that different salt stresses influenced phenotypic characteristics, leaf relative water content and root activity in sugar beet. The contents of chlorophyll, malondialdehyde (MDA), the activities of peroxidase (POD), superoxide dismutase (SOD), and catalase (CAT) were also affected by different salt stresses. Compared with control plants, there were 7391 and 8729 differentially expressed genes (DEGs) in leaves and roots under salt stress, respectively. A total of 41 hub genes related to salt stress were identified by weighted gene co-expression network analysis (WGCNA) from DEGs, and a transcriptional regulatory network based on these genes was constructed. The expression pattern of hub genes under salt stress was confirmed by qRT-PCR. In addition, the metabolite of sugar beet was compared under salt stress for 24 h. A total of 157 and 157 differentially accumulated metabolites (DAMs) were identified in leaves and roots, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis further indicated that DEGs and DAMs act on the starch and sucrose metabolism, alpha-linolenic acid metabolism, phenylpropanoid biosynthesis and plant hormone signal transduction pathway. In this study, RNA-seq, WGCNA analysis and untargeted metabolomics were combined to investigate the transcriptional and metabolic changes of sugar beet during salt stress. The results provided new insights into the molecular mechanism of sugar beet response to salt stress, and also provided candidate genes for sugar beet improvement.

Genome-Wide Association Studies of Maize Seedling Root Traits under Different Nitrogen Levels

Nitrogen (N) is one of the important factors affecting maize root morphological construction and growth development. An association panel of 124 maize inbred lines was evaluated for root and shoot growth at seedling stage under normal N (CK) and low N (LN) treatments, using the paper culture method. Twenty traits were measured, including three shoot traits and seventeen root traits, a genome-wide association study (GWAS) was performed using the Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK) methods. The results showed that LN condition promoted the growth of the maize roots, and normal N promoted the growth of the shoots. A total of 185 significant SNPs were identified, including 27 SNPs for shoot traits and 158 SNPs for root traits. Four important candidate genes were identified. Under LN conditions, the candidate gene Zm00001d004123 was significantly correlated with the number of crown roots, Zm00001d025554 was correlated with plant height. Under CK conditions, the candidate gene Zm00001d051083 was correlated with the length and area of seminal roots, Zm00001d050798 was correlated with the total root length. The four candidate genes all responded to the LN treatment. The research results provide genetic resources for the genetic improvement of maize root traits.

Combined GWAS and Transcriptome Analyses Provide New Insights Into the Response Mechanisms of Sunflower Against Drought Stress

Sunflower is one of the most important oil crops in the world, and drought stress can severely limit its production and quality. To understand the underlying mechanism of drought tolerance, and identify candidate genes for drought tolerance breeding, we conducted a combined genome-wide association studies (GWAS) and RNA-seq analysis. A total of 226 sunflower inbred lines were collected from different regions of China and other countries. Eight phenotypic traits were evaluated under control and drought stress conditions. Genotyping was performed using a Specific-Locus Amplified Fragment Sequencing (SLAF-seq) approach. A total of 934.08 M paired-end reads were generated, with an average Q30 of 91.97%. Based on the 243,291 polymorphic SLAF tags, a total of 94,162 high-quality SNPs were identified. Subsequent analysis of linkage disequilibrium (LD) and population structure in the 226 accessions was carried out based on the 94,162 high-quality SNPs. The average LD decay across the genome was 20 kb. Admixture analysis indicated that the entire population most likely originated from 11 ancestors. GWAS was performed using three methods (MLM, FarmCPU, and BLINK) simultaneously. A total of 80 SNPs showed significant associations with the 8 traits (p < 1.062 × 10-6). Next, a total of 118 candidate genes were found. To obtain more reliable candidate genes, RNA-seq analysis was subsequently performed. An inbred line with the highest drought tolerance was selected according to phenotypic traits. RNA was extracted from leaves at 0, 7, and 14 days of drought treatment. A total of 18,922 differentially expressed genes were obtained. Gene ontology and Kyoto Encyclopedia of Genes and Genomes analysis showed up-regulated genes were mainly enriched in the branched-chain amino acid catabolic process, while the down-regulated genes were mainly enriched in the photosynthesis-related process. Six DEGs were randomly selected from all DEGs for validation; these genes showed similar patterns in RNA-seq and RT-qPCR analysis, with a correlation coefficient of 0.8167. Through the integration of the genome-wide association study and the RNA-sequencing, 14 candidate genes were identified. Four of them (LOC110885273, LOC110872899, LOC110891369, LOC110920644) were abscisic acid related protein kinases and transcription factors. These genes may play an important role in sunflower drought response and will be used for further study. Our findings provide new insights into the response mechanisms of sunflowers against drought stress and contribute to further genetic breeding.

SNP markers identification by genome wide association study for chemical quality traits of coffee (Coffea spp.) Germplasm

BACKGROUND

Coffee quality is an important selection criterion for coffee breeding. Metabolite profiling and Genome-Wide Association Studies (GWAS) effectively dissect the genetic background of complex traits such as metabolites content (caffeine, trigonelline, and 5-caffeoylquinic acid (5-CQA)) in coffee that affect quality. Therefore, it is important to determine the metabolic profiles of Coffea spp. genotypes. This study aimed to identify Single Nucleotide Polymorphisms (SNPs) within Coffea spp. genotypes through GWAS and associate these significant SNPs to the metabolic profiles of the different genotypes.

METHODS AND RESULTS

A total of 1,739 SNP markers were obtained from 80 genotypes using the DArTseq™ method. Caffeine, trigonelline, and 5-CQA content were determined in coffee leaves using Ultra-Performance Liquid Chromatography/tandem mass spectrometry (UPLC-MS/MS) analyses. The GWAS was carried out using the Genome Association and Prediction Integrated Tool (GAPIT) software and a compressed mixed linear model. Finally, a total of three significant SNP markers out of ten were identified. One SNP, located in the coffee chromosome (Chr) 8, was significantly associated with caffeine. The two remaining SNPs, located in Chr 4 and 5, were significantly associated with trigonelline and six SNPs markers were associated with 5-CQA in Chr 1, 5 and 10, but these six markers were not significant.

CONCLUSIONS

These significant SNP sequences were associated with protein ubiquitination, assimilation, and wall receptor kinases. Therefore, these SNPs might be useful hits in subsequent quality coffee breeding programs.

Integrated analysis of the lncRNA/circRNA-miRNA-mRNA expression profiles reveals novel insights into potential mechanisms in response to root-knot nematodes in peanut

Background

Peanut is the most essential oil and food crop globally due to its high oil and protein content. Root-knot nematode infects peanut roots, causing poor development and severely limiting peanut yields worldwide. The discovery of peanut genome identified a considerable number of genetic loci controlling the peanut root-knot nematode; however, the molecular mechanism of root-knot nematode remains unknown.

Results

The heterogeneous response to root-knot nematode stress in peanut roots was identified using whole-transcriptome RNA-seq. A total of 430 mRNAs, 111 miRNAs, 4453 lncRNAs, and 123 circRNAs were found to have differential expression between infected and non-infected peanuts. The expression profiles of the lncRNA/circRNA-miRNA-mRNA network were developed to understand the potential pathways that lead to root-knot nematodes in peanut roots. During root-knot nematodes stress, a total of 10 lncRNAs, 4 circRNAs, 5 miRNAs, and 13 mRNAs can create competing endogenous RNA and participate in the oxidation–reduction process as well as other biological metabolism processes in peanuts. The findings will highlight the role of peanut ceRNAs in response to root-knot nematodes.

Conclusion

The GO classification and KEGG pathway enrichment study of core regulatory networks revealed that ceRNAs are involved in oxidation–reduction, peroxidase activity, lignin synthesis in the xylem, and flavonoid synthesis. Overall, these findings may help researchers better understand the role of non-coding RNAs in response to root-knot nematodes.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08470-3.

Strategies of tolerance reflected in two North American maple genomes

The first chromosome‐scale assemblies for North American members of the Acer genus, sugar maple (Acer saccharum) and boxelder (Acer negundo), as well as transcriptomic evaluation of the abiotic stress response in A. saccharum are reported. This integrated study describes in‐depth aspects contributing to each species' approach to tolerance and applies current knowledge in many areas of plant genome biology with Acer physiology to help convey the genomic complexities underlying tolerance in broadleaf tree species.

GmLecRlk, a Lectin Receptor-like Protein Kinase, Contributes to Salt Stress Tolerance by Regulating Salt-Responsive Genes in Soybean

Soybean [Glycine max (L.) Merr.] is an important oil crop that provides valuable resources for human consumption, animal feed, and biofuel. Through the transcriptome analysis in our previous study, GmLecRlk (Glyma.07G005700) was identified as a salt-responsive candidate gene in soybean. In this study, qRT-PCR analysis showed that the GmLecRlk gene expression level was significantly induced by salt stress and highly expressed in soybean roots. The pCAMBIA3300-GmLecRlk construct was generated and introduced into the soybean genome by Agrobacterium rhizogenes. Compared with the wild type (WT), GmLecRlk overexpressing (GmLecRlk-ox) soybean lines had significantly enhanced fresh weight, proline (Pro) content, and catalase (CAT) activity, and reduced malondialdehyde (MDA) and H2O2 content under salt stress. These results show that GmLecRlk gene enhanced ROS scavenging ability in response to salt stress in soybean. Meanwhile, we demonstrated that GmLecRlk gene also conferred soybean salt tolerance when it was overexpressed alone in soybean hairy root. Furthermore, the combination of RNA-seq and qRT-PCR analysis was used to determine that GmLecRlk improves the salt tolerance of soybean by upregulating GmERF3, GmbHLH30, and GmDREB2 and downregulating GmGH3.6, GmPUB8, and GmLAMP1. Our research reveals a new mechanism of salt resistance in soybean, which exposes a novel avenue for the cultivation of salt-resistant varieties.

Distinct GmASMTs are involved in regulating transcription factors and signalling cross-talk across embryo development, biotic, and abiotic stress in soybean

N-Acetylserotonin O-methyltransferase (ASMT) is the final enzyme involved in melatonin biosynthesis. Identifying the expression of ASMT will reveal the regulatory role in the development and stress conditions in soybean. To identify and characterize ASMT in soybean (GmASMT), we employed genome-wide analysis, gene structure, cis-acting elements, gene expression, co-expression network analysis, and enzyme assay. We found seven pairs of segmental and tandem duplication pairs among the 44 identified GmASMTs by genome-wide analysis. Notably, co-expression network analysis reported that distinct GmASMTs are involved in various stress response. For example, GmASMT3, GmASMT44, GmASMT17, and GmASMT7 are involved in embryo development, heat, drought, aphid, and soybean cyst nematode infections, respectively. These distinct networks of GmASMTs were associated with transcription factors (NAC, MYB, WRKY, and ERF), stress signalling, isoflavone and secondary metabolites, calcium, and calmodulin proteins involved in stress regulation. Further, GmASMTs demonstrated auxin-like activities by regulating the genes involved in auxin transporter (WAT1 and NRT1/PTR) and auxin-responsive protein during developmental and biotic stress. The current study identified the key regulatory role of GmASMTs during development and stress. Hence GmASMT could be the primary target in genetic engineering for crop improvement under changing environmental conditions.

Modelling of gene loss propensity in the pangenomes of three Brassica species suggests different mechanisms between polyploids and diploids

Plant genomes demonstrate significant presence/absence variation (PAV) within a species; however, the factors that lead to this variation have not been studied systematically in Brassica across diploids and polyploids. Here, we developed pangenomes of polyploid Brassica napus and its two diploid progenitor genomes B. rapa and B. oleracea to infer how PAV may differ between diploids and polyploids. Modelling of gene loss suggests that loss propensity is primarily associated with transposable elements in the diploids while in B. napus, gene loss propensity is associated with homoeologous recombination. We use these results to gain insights into the different causes of gene loss, both in diploids and following polyploidization, and pave the way for the application of machine learning methods to understanding the underlying biological and physical causes of gene presence/absence.