Genome-Wide Identification, Evolution, and Expression of GDSL-Type Esterase/Lipase Gene Family in Soybean

Genome-wide identification of the GDSL-type esterase/lipase protein (GELP) gene family in Ricinus communis and its transcriptional regulation during germination and seedling establishment under different abiotic stresses

GDSL-type esterase/lipase protein (GELP) genes are crucial in the specialized lipid metabolism, in the responses to abiotic stresses, and in the regulation of plant homeostasis. R. communis is an important oilseed crop species that can sustain growth and productivity when exposed to harsh environmental conditions. Herein, we raised the question of whether the GELP gene family could be involved in the acquisition of R. communis tolerance to abiotic stresses during seed germination and seedling establishment. Thus, we used bioinformatics and transcriptomics to characterize the R. communis GELP gene family. R. communis genome possesses 96 GELP genes that were characterized by extensive bioinformatics, including phylogenetic analysis, subcellular localization, exon-intron distribution, the analysis of regulatory cis-elements, tandem duplication, and physicochemical properties. Transcriptomics indicated that numerous RcGELP genes are readily responsive to high-temperature and salt stresses and might be potential candidates for genome editing techniques to develop abiotic stress-tolerant crops.

Genetic insights into superior grain number traits: a QTL analysis of wheat-Agropyron cristatum derivative pubing3228

BACKGROUND

Agropyron cristatum (L.) is a valuable genetic resource for expanding the genetic diversity of common wheat. Pubing3228, a novel wheat-A. cristatum hybrid germplasm, exhibits several desirable agricultural traits, including high grain number per spike (GNS). Understanding the genetic architecture of GNS in Pubing3228 is crucial for enhancing wheat yield. This study aims to analyze the specific genetic regions and alleles associated with high GNS in Pubing3228.

METHODS

The study employed a recombination inbred line (RIL) population derived from a cross between Pubing3228 and Jing4839 to investigate the genetic regions and alleles linked to high GNS. Quantitative Trait Loci (QTL) analysis and candidate gene investigation were utilized to explore these traits.

RESULTS

A total of 40 QTLs associated with GNS were identified across 16 chromosomes, accounting for 4.25-17.17% of the total phenotypic variation. Five QTLs (QGns.wa-1D, QGns.wa-5 A, QGns.wa-7Da.1, QGns.wa-7Da.2 and QGns.wa-7Da.3) accounter for over 10% of the phenotypic variation in at least two environments. Furthermore, 94.67% of the GNS QTL with positive effects originated from Pubing3228. Candidate gene analysis of stable QTLs identified 11 candidate genes for GNS, including a senescence-associated protein gene (TraesCS7D01G148000) linked to the most significant SNP (AX-108,748,734) on chromosome 7D, potentially involved in reallocating nutrients from senescing tissues to developing seeds.

CONCLUSION

This study provides new insights into the genetic mechanisms underlying high GNS in Pubing3228, offering valuable resources for marker-assisted selection in wheat breeding to enhance yield.

Genome-wide identification and expression analysis of TIFY genes under MeJA, cold and PEG-induced drought stress treatment in Dendrobium huoshanense

The TIFY family consists of plant-specific genes that regulates multiple plant functions, including developmental and defense responses. Here, we performed a comprehensive genomic analysis of TIFY genes in Dendrobium huoshanense. Our analysis encompassed their phylogenetic relationships, gene structures, chromosomal distributions, promoter regions, and patterns of collinearity. A total of 16 DhTIFY genes were identified, and classified into distinct clusters named JAZ, PPD, ZIM, and TIFY based on their phylogenetic relationship. These DhTIFYs exhibited an uneven distribution across 7 chromosomes. The expansion of the DhTIFY gene family appears to have been significantly influenced by whole-genome and segmental duplication events. The ratio of non-synonymous to synonymous substitutions (Ka/Ks) implies that the purifying selection has been predominant, maintaining a constrained functional diversification after duplication events. Gene structure analysis indicated that DhTIFYs exhibited significant structural variation, particularly in terms of gene organization and intron numbers. Moreover, numerous cis-acting elements related to hormone signaling, developmental processes, and stress responses were identified within the promoter regions. Subsequently, qRT-PCR experiments demonstrated that the expression of DhTIFYs is modulated in response to MeJA (Methyl jasmonate), cold, and drought treatment. Collectively, these results enhance our understanding of the functional dynamics of TIFY genes in D. huoshanense and may pinpoint potential candidates for detailed examination of the biological roles of TIFY genes.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-024-01442-9.

Proteome profiling of vascular sap regarding Eucalyptus grandis, Eucalyptus urophylla, and Eucalyptus camaldulensis

The plant vascular system is a key element for long-distance communication. Understanding its composition may provide valuable information on how plants grow and develop themselves. In this study, a quantitative proteome dataset of the vascular sap proteome of three commercially important Eucalyptus species was shown. Protein extraction was carried out using a pressure bomb, whereas only in silico predicted extracellular proteins were considered as part of the sap proteome. A total of 132 different proteins were identified in all three Eucalyptus species and the most abundant proteome subset within all three species was comprised of proteins involved in the carbohydrate metabolic process, proteolysis, components of membrane, and defense response. The sap proteome of the species E. grandis and E. urophylla revealed the highest similarities. Functional classification indicated that the sap proteome of E. grandis and E. urophylla are mostly comprised of proteins involved in defense response and proteolysis; whereas no prominent functional class was observed for the E. camaldulensis species. Quantitative comparison highlighted characteristic sap proteins in each of the Eucalyptus species. The results that could be found in this study can be used as a reference for the proteome sap analysis of Eucalyptus plants grown under different conditions.

Comparative transcriptome analysis of two contrasting genotypes provides new insights into the drought response mechanism in pigeon pea (Cajanus cajan L. Millsp.)

BACKGROUND

Despite plant's ability to adapt and withstand challenging environments, drought poses a severe threat to their growth and development. Although pigeon pea is already quite resistant to drought, the prolonged dehydration induced by the aberrant climate poses a serious threat to their survival and productivity.

OBJECTIVE

Comparative physiological and transcriptome analyses of drought-tolerant (CO5) and drought-sensitive (CO1) pigeon pea genotypes subjected to drought stress were carried out in order to understand the molecular basis of drought tolerance in pigeon pea.

METHODS

The transcriptomic analysis allowed us to examine how drought affects the gene expression of C. cajan. Using bioinformatics tools, the unigenes were de novo assembled, annotated, and functionally evaluated. Additionally, a homology-based sequence search against the droughtDB database was performed to identify the orthologs of the DEGs.

RESULTS

1102 potential drought-responsive genes were found to be differentially expressed genes (DEGs) between drought-tolerant and drought-sensitive genotypes. These included Abscisic acid insensitive 5 (ABI5), Nuclear transcription factor Y subunit A-7 (NF-YA7), WD40 repeat-containing protein 55 (WDR55), Anthocyanidin reductase (ANR) and Zinc-finger homeodomain protein 6 (ZF-HD6) and were highly expressed in the tolerant genotype. Further, GO analysis revealed that the most enriched classes belonged to biosynthetic and metabolic processes in the biological process category, binding and catalytic activity in the molecular function category and nucleus and protein-containing complex in the cellular component category. Results of KEGG pathway analysis revealed that the DEGs were significantly abundant in signalling pathways such as plant hormone signal transduction and MAPK signalling pathways. Consequently, in our investigation, we have identified and validated by qPCR a group of genes involved in signal reception and propagation, stress-specific TFs, and basal regulatory genes associated with drought response.

CONCLUSION

In conclusion, our comprehensive transcriptome dataset enabled the discovery of candidate genes connected to pathways involved in pigeon pea drought response. Our research uncovered a number of unidentified genes and transcription factors that could be used to understand and improve susceptibility to drought.

Identification, evolution, and expression of GDSL-type Esterase/Lipase (GELP) gene family in three cotton species: a bioinformatic analysis

BACKGROUND

GDSL esterase/lipases (GELPs) play important roles in plant growth, development, and response to biotic and abiotic stresses. Presently, an extensive and in-depth analysis of GELP family genes in cotton is still not clear enough, which greatly limits the further understanding of cotton GELP function and regulatory mechanism.

RESULTS

A total of 389 GELP family genes were identified in three cotton species of Gossypium hirsutum (193), G. arboreum (97), and G. raimondii (99). These GELPs could be classified into three groups and eight subgroups, with the GELPs in same group to have similar gene structures and conserved motifs. Evolutionary event analysis showed that the GELP family genes tend to be diversified at the spatial dimension and certain conservative at the time dimension, with a trend of potential continuous expansion in the future. The orthologous or paralogous GELPs among different genomes/subgenomes indicated the inheritance from genome-wide duplication during polyploidization, and the paralogous GELPs were derived from chromosomal segment duplication or tandem replication. GELP genes in the A/D subgenome underwent at least three large-scale replication events in the evolutionary process during the period of 0.6-3.2 MYA, with two large-scale evolutionary events between 0.6-1.8 MYA that were associated with tetraploidization, and the large-scale duplication between 2.6-9.1 MYA that occurred during diploidization. The cotton GELPs indicated diverse expression patterns in tissue development, ovule and fiber growth, and in response to biotic and abiotic stresses, combining the existing cis-elements in the promoter regions, suggesting the GELPs involvements of functions to be diversification and of the mechanisms to be a hormone-mediated manner.

CONCLUSIONS

Our results provide a systematic and comprehensive understanding the function and regulatory mechanism of cotton GELP family, and offer an effective reference for in-depth genetic improvement utilization of cotton GELPs.

Isolation and Characterization of Extracellular Vesicles from Arabidopsis thaliana Cell Culture and Investigation of the Specificities of Their Biogenesis

Over recent years, extracellular vesicles (EVs), commonly termed exosomes, have gained prominence for their potential as natural nanocarriers. It has now been recognized that plants also secrete EVs. Despite this discovery, knowledge about EV biogenesis in plant cell cultures remains limited. In our study, we have isolated and meticulously characterized EVs from the callus culture of the model plant, Arabidopsis thaliana. Our findings indicate that the abundance of EVs in calli was less than that in the plant's apoplastic fluid. This difference was associated with the transcriptional downregulation of the endosomal sorting complex required for transport (ESCRT) genes in the calli cells. While salicylic acid increased the expression of ESCRT components, it did not enhance EV production. Notably, EVs from calli contained proteins essential for cell wall biogenesis and defense mechanisms, as well as microRNAs consistent with those found in intact plants. This suggests that plant cell cultures could serve as a feasible source of EVs that reflect the characteristics of the parent plant species. However, further research is essential to determine the optimal conditions for efficient EV production in these cultured cells.

Dissecting the genetic basis of drought responses in common bean using natural variation

The common bean (Phaseolus vulgaris L) is the most important legume for human consumption, contributing 30% of the total daily protein intake in developing countries. A major limitation for its cultivation is drought, which causes more than 60% of the annual losses. Among physiological adaptations to drought, delaying senescence and extending the photosynthetic capacity can improve crop productivity. This strategy is known as functional "stay-green" (SG) and has been discussed as a goal in plant breeding to alleviate the loss of yield under water scarcity conditions. The genetic components behind SG traits have been explored specially in cereals, but they are to date poorly studied in the common bean. For this, we screened 71 common bean cultivars belonging to the three most important gene-pools, Mesoamerica, Andes and Europe, selected to cover the natural variation of the species. Phenotyping experiments under terminal drought during long-days in greenhouse conditions, identified six photoperiod insensitive cultivars of European origin with a clear SG phenotype. Using SNP data produced from whole genome re-sequencing data, we obtained 10 variants significantly associated to the SG phenotype on chromosomes 1, 3, 7, 8, 9 and 10 that are in close proximity to gene models with functional annotations related to hormone signaling and anti-oxidant production. Calculating pairwise FST between subgroups of cultivars divided according to their drought response (susceptibility, escape, recovery or SG), we identified up to 29 genomic windows accounting for 1,45Mb that differentiate SG cultivars; these signals were especially strong on chromosomes 1, 5 and 10. Within these windows, we found genes directly involved in photosynthetic processes and trehalose synthesis. Altogether, these signals represent good targets for further characterization and highlight the multigenic nature of the SG response in legumes.

Towards carotenoid biofortification in wheat: identification of XAT-7A1, a multicopy tandem gene responsible for carotenoid esterification in durum wheat

Yellow pigment content, mainly due to the accumulation of carotenoids, is a quality trait in durum wheat grain as it confers the bright yellow color to pasta preferred by consumers. Also, carotenoids are essential nutrients exerting important biological functions in human health. Consequently, biofortification strategies have been developed in many crops to increase carotenoid content. In this context, carotenoid esterification is emerging as a new breeding target for wheat biofortification, as carotenoid esters have been found to promote both carotenoid accumulation and stability. Until recently, no carotenoid esters have been identified in significant proportions in durum wheat grains, and interspecific breeding programs have been started to transfer esterification ability from common wheat and Hordeum chilense.In this work, XAT-7A1 is identified as the gene responsible for carotenoid esterification in durum wheat. Sequencing, copy number variation and mapping results show that XAT-7A1 is organized as tandem or proximal GDSL esterase/lipase copies in chromosome 7A. Three XAT-7A1 haplotypes are described: Type 1 copies, associated with high levels of carotenoid esters (diesters and monoesters) production and high expression in grain development; Type 2 copies, present in landraces with low levels of carotenoid esters (monoesters) or no esters; and Type 3 copies, without the signal peptide, resulting in zero-ester phenotypes.The identification of XAT-7A1 is a necessary step to make the carotenoid esterification ability available for durum and bread wheat breeding, which should be focused on the Type 1 XAT-7A1 haplotype, which may be assessed as a single gene since XAT-7A1 copies are inherited together.

Metallochaperone protein OsHIPP17 regulates the absorption and translocation of cadmium in rice (Oryza sativa L.)

Heavy metal-associated isoprenylated plant proteins (HIPPs) play vital roles in regulating heavy metal responding activities in plants. Yet only a handful of studies have characterized the functions of HIPPs. In this study, a novel HIPP member OsHIPP17 was functionally characterized, which was involved in the tolerance of yeast and plants to cadmium (Cd). The Cd accumulation in yeast cells was increased due to the overexpression of OsHIPP17. Nevertheless, the overexpression of OsHIPP17 in Arabidopsis thaliana resulted in compromised growth under Cd stress. Meanwhile, the mutation of OsHIPP17 resulted in 38.9-40.9 % increase of Cd concentration in rice roots as well as 14.3-20.0 % decrease of Cd translocation factor. Further investigation of the genes responsible for Cd absorption and transporter indicated that the expression levels of these genes were also perturbed. In addition, two OsHIPP17-interacting proteins, OsHIPP24 and OsLOL3 were identified in a yeast two hybrid assay. Further analysis of their functions revealed that OsHIPP24 or OsLOL3 may be involved in the regulation of Cd tolerance by OsHIPP17 in rice. All above results implied that OsHIPP17 may affect Cd resistance by regulating the absorption and translocation of Cd in rice.

GDSL Esterase/Lipase GELP1 Involved in the Defense of Apple Leaves against Colletotrichum gloeosporioides Infection

GDSL esterases/lipases are a subclass of lipolytic enzymes that play critical roles in plant growth and development, stress response, and pathogen defense. However, the GDSL esterase/lipase genes involved in the pathogen response of apple remain to be identified and characterized. Thus, in this study, we aimed to analyze the phenotypic difference between the resistant variety, Fuji, and susceptible variety, Gala, during infection with C. gloeosporioides, screen for anti-disease-associated proteins in Fuji leaves, and elucidate the underlying mechanisms. The results showed that GDSL esterase/lipase protein GELP1 contributed to C. gloeosporioides infection defense in apple. During C. gloeosporioides infection, GELP1 expression was significantly upregulated in Fuji. Fuji leaves exhibited a highly resistant phenotype compared with Gala leaves. The formation of infection hyphae of C. gloeosporioides was inhibited in Fuji. Moreover, recombinant His:GELP1 protein suppressed hyphal formation during infection in vitro. Transient expression in Nicotiana benthamiana showed that GELP1-eGFP localized to the endoplasmic reticulum and chloroplasts. GELP1 overexpression in GL-3 plants increased resistance to C. gloeosporioides. MdWRKY15 expression was upregulated in the transgenic lines. Notably, GELP1 transcript levels were elevated in GL-3 after salicylic acid treatment. These results suggest that GELP1 increases apple resistance to C. gloeosporioides by indirectly regulating salicylic acid biosynthesis.

Relationships between some transcription factors and concordantly expressed drought stress-related genes in bread wheat

The challenge of climate change makes it mandatory to improve tolerance to drought stress in bread wheat (Triticum aestivum) via biotechnological approaches. Drought stress experiment was conducted followed by RNA-Seq analysis for leaves of two wheat cultivars namely Giza 168 and Gemmiza 10 with contrasting genotypes. Expression patterns of the regulated stress-related genes and concordantly expressed TFs were detected, then, validated via qPCR for two loss-of-function mutants in Arabidopsis background harboring mutated genes analogue to those in wheat. Drought-stress related genes were searched for concordantly expressed TFs and a total of eight TFs were shown to coexpress with 14 stress-related genes. Among these genes, one TF belongs to the zinc finger protein CONSTANS family and proved via qPCR to drive expression of a gene encoding a speculative TF namely zinc transporter 3-like and two other stress related genes encoding tryptophan synthase alpha chain and asparagine synthetase. Known functions of the two TFs under drought stress complement those of the two concordantly expressed stress-related genes, thus, it is likely that they are related. This study highlights the possibility to utilize metabolic engineering approaches to decipher and incorporate existing regulatory frameworks under drought stress in future breeding programs of bread wheat.

Genome-wide identification and functional analysis of ICE genes reveal that Gossypium thurberi "GthICE2" is responsible for cold and drought stress tolerance

Cold stress has been found to have a negative impact on cotton growth and annual production. To address this issue, the utilization of cold-tolerant gene resources from wild species of Gossypium is crucial for genetic improvements in cultivated cotton. ICE (inducer of CBF expression) are the key regulators of cold tolerance in plants, however, there is relatively little information on ICE genes in cotton. Herein, we performed comprehensive bioinformatics analyses of the ICE gene family in eight cotton species. Phylogenetic analysis showed that 52 ICE genes were clustered into four subgroups. Cis-regulatory elements analysis suggests that the expression of ICE genes might be regulated by light, plant hormones, and various environment stresses. Higher expression of GthICE2 was observed in leaves as compared to roots and stems, in response to cold, drought, and exogenous hormone ABA. Furthermore, overexpression of GthICE2 in A. thaliana led to higher germination and survival rates, longer root length, lower ion leakage, and induction under cold and drought stress. Histochemical staining showed that oxidative damage in transgenic lines was much lower compared to wild-type plants. Lower MDA contents and higher SOD and POD activities were observed in overexpressed plants. Y1H and LUC assays revealed that GthICE2 might activate the expression of GthCBF4, a cold-responsive gene, by connecting with the MYC cis-element present in the promoter of GthCBF4. GthICE2 confers cold and drought stress tolerance in cotton. Our findings add significantly to the existing knowledge regarding cold stress tolerance and helps to elucidate cold response mechanisms in cotton.

Multi-locus genome-wide association study of chickpea reference set identifies genetic determinants of Pratylenchus thornei resistance

Pratylenchus thornei is an economically important species of root-lesion nematode adversely affecting chickpea (Cicer arietinum) yields globally. Integration of resistant crops in farming systems is recognised as the most effective and sustainable management strategy for plant-parasitic nematodes. However, breeding for P. thornei resistance in chickpea is limited by the lack of genetic diversity. We deployed a genome-wide association approach to identify genomic regions and candidate genes associated with P. thornei resistance in 285 genetically diverse chickpea accessions. Chickpea accessions were phenotyped for P. thornei resistance in replicated glasshouse experiments performed for two years (2018 and 2020). Whole genome sequencing data comprising 492,849 SNPs were used to implement six multi-locus GWAS models. Fourteen chickpea genotypes were found to be resistant to P. thornei. Of the six multi-locus GWAS methods deployed, FASTmrMLM was found to be the best performing model. In all, 24 significant quantitative trait nucleotides (QTNs) were identified, of which 13 QTNs were associated with lower nematode population density and 11 QTNs with higher nematode population density. These QTNs were distributed across all of the chickpea chromosomes, except chromosome 8. We identified, receptor-linked kinases (RLKs) on chromosomes 1, 4 and 6, GDSL-like Lipase/Acylhydrolase on chromosome 3, Aspartic proteinase-like and Thaumatin-like protein on chromosome 4, AT-hook DNA-binding and HSPRO2 on chromosome 6 as candidate genes for P. thornei resistance in the chickpea reference set. New sources of P. thornei resistant genotypes were identified that can be harnessed into breeding programs and putative candidate P. thornei resistant genes were identified that can be explored further to develop molecular markers and accelerate the incorporation of improved P. thornei resistance into elite chickpea cultivars.

Genome-wide exploration of the GDSL-type esterase/lipase gene family in rapeseed reveals several BnGELP proteins active during early seedling development

The Gly-Asp-Ser-Leu (GDSL)-type esterase/lipase proteins (GELP) are one of the most important families of lipolytic enzymes and play prominent roles in seed germination and early seedling establishment through mobilizing the lipids stored in seeds. However, there are no comprehensive studies systematically investigating the GELP gene family in Brassica napus (BnGELP), and their biological significance to these physiological processes are far from understood. In the present study, a total of 240 BnGELP genes were identified in B. napus cultivar "Zhongshuang 11" (ZS11), which is nearly 2.3-fold more GELP genes than in Arabidopsis thaliana. The BnGELP genes clustered into 5 clades based on phylogenetic analysis. Ten BnGELPs were identified through zymogram analysis of esterase activity followed by mass spectrometry, among which five clustered into the clade 5. Gene and protein architecture, gene expression, and cis-element analyses of BnGELP genes in clade 5 suggested that they may play different roles in different tissues and in response to different abiotic stresses. BnGELP99 and BnGELP159 were slightly induced by cold, which may be attributed to two low-temperature responsive cis-acting regulatory elements present in their promoters. An increased activity of esterase isozymes by cold was also observed, which may reflect other cold inducible esterases/lipases in addition to the ten identified BnGELPs. This study provides a systemic view of the BnGELP gene family and offers a strategy for researchers to identify candidate esterase/lipase genes responsible for lipid mobilization during seed germination and early seedling establishment.

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.

Bioengineering of Soybean Oil and Its Impact on Agronomic Traits

Soybean is a major oil crop and is also a dominant source of nutritional protein. The 20% seed oil content (SOC) of soybean is much lower than that in most oil crops and the fatty acid composition of its native oil cannot meet the specifications for some applications in the food and industrial sectors. Considerable effort has been expended on soybean bioengineering to tailor fatty acid profiles and improve SOC. Although significant advancements have been made, such as the creation of high-oleic acid soybean oil and high-SOC soybean, those genetic modifications have some negative impacts on soybean production, for instance, impaired germination or low protein content. In this review, we focus on recent advances in the bioengineering of soybean oil and its effects on agronomic traits.

The binding pocket properties were fundamental to functional diversification of the GDSL-type esterases/lipases gene family in cotton

Cotton is one of the most important crops in the world. GDSL-type esterases/lipases (GELPs) are widely present in all kingdoms and play an essential role in regulating plant growth, development, and responses to abiotic and biotic stresses. However, the molecular mechanisms underlying this functional diversity remain unclear. Here, based on the identification of the GELP gene family, we applied genetic evolution and molecular simulation techniques to explore molecular mechanisms in cotton species. A total of 1502 GELP genes were identified in 10 cotton species. Segmental duplication and differences in evolutionary rates are the leading causes of the increase in the number and diversity of GELP genes during evolution for ecological adaptation. Structural analysis revealed that the GELP family has high structural diversity. Moreover, molecular simulation studies have demonstrated significant differences in the properties of the binding pockets among cotton GELPs. In the process of adapting to the environment, GELPs not only have segmental duplication but also have different evolutionary rates, resulting in gene diversity. This diversity leads to significant differences in the 3D structure and binding pocket properties and, finally, to functional diversity. These findings provide a reference for further functional analyses of plant GELPs.

Genome wide identification of GDSL gene family explores a novel GhirGDSL26 gene enhancing drought stress tolerance in cotton

BACKGROUND

Current climate change scenarios are posing greater threats to the growth and development of plants. Thus, significant efforts are required that can mitigate the negative effects of drought on the cotton plant. GDSL esterase/lipases can offer an imperative role in plant development and stress tolerance. However, thesystematic and functional roles of the GDSL gene family, particularly in cotton under water deficit conditions have not yet been explored.

RESULTS

In this study, 103, 103, 99, 198, 203, 239, 249, and 215 GDSL proteins were identified in eight cotton genomes i.e., Gossypium herbaceum (A1), Gossypium arboretum (A2), Gossypium raimondii (D5), Gossypium hirsutum (AD1), Gossypium barbadense (AD2), Gossypium tomentosum (AD3), Gossypium mustelinum (AD4), Gossypium darwinii (AD5), respectively. A total of 198 GDSL genes of Gossypium hirsutum were divided into eleven clades using phylogenetic analysis, and the number of GhirGDSL varied among different clades. The cis-elements analysis showed that GhirGDSL gene expression was mainly related to light, plant hormones, and variable tense environments. Combining the results of transcriptome and RT-qPCR, GhirGDSL26 (Gh_A01G1774), a highly up-regulated gene, was selected for further elucidating its tole in drought stress tolerance via estimating physiological and biochemical parameters. Heterologous expression of the GhirGDSL26 gene in Arabidopsis thaliana resulted in a higher germination and survival rates, longer root lengths, lower ion leakage and induced stress-responsive genes expression under drought stress. This further highlighted that overexpressed plants had a better drought tolerance as compared to the wildtype plants. Moreover, 3, 3'-diaminobenzidine (DAB) and Trypan staining results indicated reduced oxidative damage, less cell membrane damage, and lower ion leakage in overexpressed plants as compared to wild type. Silencing of GhirGDSL26 in cotton via VIGS resulting in a susceptible phenotype, higher MDA and H₂O₂ contents, lower SOD activity, and proline content.

CONCLUSION

Our results demonstrated that GhirGDSL26 plays a critical role in cotton drought stress tolerance. Current findings enrich our knowledge of GDSL genes in cotton and provide theoretical guidance and excellent gene resources for improving drought tolerance in cotton.

Genome-wide identification, characterization, evolution, and expression pattern analyses of the typical thioredoxin gene family in wheat (Triticum aestivum L.)

Typical thioredoxin (TRX) plays an important role in maintaining redox balance in plants. However, the typical TRX genes in wheat still need to be comprehensively and deeply studied. In this research, a total of 48 typical TaTRX genes belonging to eight subtypes were identified via a genome-wide search in wheat, and the gene structures, protein conserved motifs, and protein 3D structures of the same subtype were very similar. Evolutionary analysis showed that there are two pairs of tandem duplication genes and 14 clusters of segmental duplication genes in typical TaTRX family members; TaTRX15, TaTRX36, and TaTRX42 had positive selection compared with the orthologs of their ancestral species; rice and maize have 11 and 13 orthologous typical TRXs with wheat, respectively. Gene Ontology (GO) analysis indicated that typical TaTRXs were involved in maintaining redox homeostasis in wheat cells. Estimation of ROS content, determination of antioxidant enzyme activity, and gene expression analysis in a line overexpressing one typical TaTRX confirmed that TRX plays an important role in maintaining redox balance in wheat. A predictive analysis of cis-acting elements in the promoter region showed that typical TaTRXs were extensively involved in various hormone metabolism and response processes to stress. The results predicted using public databases or verified using RT-qPCR show that typical TaTRXs were able to respond to biotic and abiotic stresses, and their expression in wheat was spatiotemporal. A total of 16 wheat proteins belonging to four different families interacting with typical TaTRXs were predicted. The above comprehensive analysis of typical TaTRX genes can enrich our understanding of this gene family in wheat and provide valuable insights for further gene function research.

Phosphoprotein Profile of Rice (Oryza sativa L.) Seedlings under Osmotic Stress after Pretreatment with Chitosan

This study aims to identify novel chitosan (CTS)-responsive phosphoproteins in Leung Pratew 123 (LPT123) and Khao Dawk Mali 105 (KDML105) as drought-sensitive rice cultivars and differences in the CTS response. Rice seeds were soaked in CTS solution before germination, and 2- and 4-week-old rice seedlings sprayed with CTS before osmotic stress comprised the following four groups: (1) seedlings treated with distilled water; (2) seedlings treated with CTS; (3) seedlings pretreated with distilled water and subjected to osmotic stress; and (4) seedlings pretreated with CTS and subjected to osmotic stress. Phosphoproteins of leaf tissues were enriched using immobilized metal affinity chromatography (IMAC) before tryptic digestion and analysis via LC-MS. Phosphoprotein profiling analyses led to the identification of 4721 phosphoproteins representing 1052 and 1040 unique phosphoproteins in the LPT123 and KDML105 seedlings, respectively. In response to CTS pretreatment before osmotic stress, 22 differently expressed proteins were discovered, of which 10 and 12 were identified in the LPT123 and KDML105, respectively. These proteins are typically involved in signaling, transport, protein folding, protein degradation, and metabolism. This study provides fruitful data to understand the signal transduction mechanisms of rice seedlings pretreated with CTS before exposure to osmotic stress.

Genome-Wide Classification and Phylogenetic Analyses of the GDSL-Type Esterase/Lipase (GELP) Family in Flowering Plants

GDSL-type esterase/lipase (GELP) enzymes have key functions in plants, such as developmental processes, anther and pollen development, and responses to biotic and abiotic stresses. Genes that encode GELP belong to a complex and large gene family, ranging from tens to more than hundreds of members per plant species. To facilitate functional transfer between them, we conducted a genome-wide classification of GELP in 46 plant species. First, we applied an iterative phylogenetic method using a selected set of representative angiosperm genomes (three monocots and five dicots) and identified 10 main clusters, subdivided into 44 orthogroups (OGs). An expert curation for gene structures, orthogroup composition, and functional annotation was made based on a literature review. Then, using the HMM profiles as seeds, we expanded the classification to 46 plant species. Our results revealed the variable evolutionary dynamics between OGs in which some expanded, mostly through tandem duplications, while others were maintained as single copies. Among these, dicot-specific clusters and specific amplifications in monocots and wheat were characterized. This approach, by combining manual curation and automatic identification, was effective in characterizing a large gene family, allowing the establishment of a classification framework for gene function transfer and a better understanding of the evolutionary history of GELP.

Identification of Two GDSL-Type Esterase/Lipase Genes Related to Tissue-Specific Lipolysis in Dendrobium catenatum by Multi-Omics Analysis

Dendrobium catenatum is an important herb and widely cultivated in China. GDSL-Type Esterase/Lipase proteins (GELPs) are widely distributed in plants and play crucial roles in stress responses, plant growth, and development. However, no identification or functional analysis of GELPs was reported in D. catenatum. This study identifies 52 GELPs in D. catenatum genome, which is classified into four groups by phylogenetic analysis. Four conservative blocks (Ser-Gly-Asn-His) are found in most GELP domains. Transcriptome analysis reveals the expression profiles of GELPs in different organs and flowering phases. Co-expression analysis of the transcriptome and lipidome identifies a GELP gene, Dca016600, that positively correlates with 23 lipids. The purified Dca016600 protein shows the optimum pH is active from 8.0 to 8.5, and the optimum temperature is active from 30 °C to 40 °C. The kinetic study provides V_max (233.43 μmol·min^-1·mg^-1) and K_m (1.49 mM) for substrate p-nitrophenyl palmitate (p-NPP). Integrated analysis of the transcriptome and proteome identifies a GELP gene, Dca005399, which is specially induced by freezing. Interestingly, Dca005399 shows high expression in symbiotic germination seeds and sepals. This study provides new insights into the function of D. catenatum GELPs in plant development and stress tolerance.

Mutation in BrGGL7 gene encoding a GDSL esterase / lipase causes male sterility in Chinese cabbage (Brassica rapa L. ssp. pekinensis)

MutMap and KASP analyses revealed that the BrGGL7 gene is responsible for the male-sterile trait of ftms1 in Chinese cabbage, with functional verification in Arabidopsis. The application of a male-sterile line is an ideal approach of hybrid seed production in Chinese cabbage. In this study, we obtained a male-sterile mutant (ftms1) from the double haploid line 'FT' using ethyl methane sulfonate (EMS) mutagenesis. The mutant was completely sterile due to abnormal enlargement and vacuolization of the tapetum cells. A single recessive nuclear gene was found to control male sterility in the mutant, while MutMap and KASP analyses identified BraA05g022470.3C (BrGGL7), which encodes a GDSL esterase / lipase, as the candidate mutant gene. A single nucleotide substitution from C to T occurred within the domain of BrGGL7 in ftms1, resulting in premature translation termination in the fourth exon. Meanwhile, qRT-PCR analysis indicated that BrGGL7 was prominently expressed in the anthers, and expression was greater in the wild-type 'FT' than ftms1. Genetic complementation of the orthologous Arabidopsis ggl7 mutant further confirmed the role of BrGGL7 in pollen development. These findings suggest that BrGGL7 plays a fundamental role in pollen formation, providing important insight into the molecular mechanisms underlying male sterility in Chinese cabbage.

Genome-Wide Analysis of the GDSL Genes in Pecan (Carya illinoensis K. Koch): Phylogeny, Structure, Promoter Cis-Elements, Co-Expression Networks, and Response to Salt Stresses

The Gly-Asp-Ser-Leu (GDSL)-lipase family is a large subfamily of lipolytic enzymes that plays an important role in plant growth and defense against environmental stress. However, little is known about their function in pecans (Carya illinoensis K. Koch). In this study, 87 CilGDSLs were identified and divided into 2 groups and 12 subgroups using phylogenetic analysis; members of the same sub-branch had conserved gene structure and motif composition. The majority of the genes had four introns and were composed of an α-helix and a β-strand. Subcellular localization analysis revealed that these genes were localized in the extracellular matrix, chloroplasts, cytoplasm, nucleus, vacuole, and endoplasmic reticulum, and were validated by transient expression in tobacco mesophyll cells. Furthermore, the analysis of the promoter cis-elements for the CilGDSLs revealed the presence of plant anaerobic induction regulatory, abscisic acid response, light response elements, jasmonic acid (JA) response elements, etc. The qRT-PCR analysis results in “Pawnee” with salt treatment showed that the CilGDSL42.93 (leaf) and CilGDSL39.88 (root) were highly expressed in different tissues. After salt stress treatment, isobaric tags for relative and absolute quantitation (iTRAQ) analysis revealed the presence of a total of ten GDSL proteins. Moreover, the weighted gene co-expression network analysis (WGCNA) showed that one set of co-expressed genes (module), primarily CilGDSL41.11, CilGDSL39.49, CilGDSL34.85, and CilGDSL41.01, was significantly associated with salt stress in leaf. In short, some of them were shown to be involved in plant defense against salt stress in this study.

Genome-wide analysis of the VQ motif-containing gene family and expression profiles during phytohormones and abiotic stresses in wheat (Triticum aestivum L.)

BACKGROUND

VQ motif-containing (VQ) proteins are cofactors of transcriptional regulation that are widely involved in plant growth and development and respond to various stresses. The VQ gene family has been identified and characterized for many plants, but there is little research on VQ gene family proteins in wheat (Triticum aestivum L.).

RESULTS

In this study, 113 TaVQ genes (40 homoeologous groups) were identified in the wheat genome. TaVQ proteins all contain the conserved motif FxxhVQxhTG, and most of the TaVQ genes do not contain introns. Phylogenetic analysis demonstrated that TaVQ proteins can be divided into 8 subgroups (I-VIII). The chromosomal location mapping analysis indicated that TaVQ genes are disproportionally distributed on 21 wheat chromosomes. Gene duplication analysis revealed that segmental duplication significantly contributes to the expansion of the TaVQ gene family. Gene expression analysis demonstrated that the expression pattern of TaVQ genes varies in different tissues. The results of quantitative real-time PCR (qRT-PCR) found that TaVQ genes displayed different expression levels under different phytohormones and abiotic stresses. The cis-elements analysis of the promoter region demonstrated that stress responses, hormone responses, growth and development, and WRKY binding elements are all widely distributed. Additionally, a potential regulatory network between TaVQ proteins and WRKY transcription factors was visualized.

CONCLUSION

This study systematically analyzed the wheat TaVQ gene family, providing a reference for further functional characterization of TaVQ genes in wheat.

Genome-Wide Analysis of the Soybean TIFY Family and Identification of GmTIFY10e and GmTIFY10g Response to Salt Stress

TIFY proteins play crucial roles in plant abiotic and biotic stress responses. Our transcriptome data revealed several TIFY family genes with significantly upregulated expression under drought, salt, and ABA treatments. However, the functions of the GmTIFY family genes are still unknown in abiotic stresses. We identified 38 GmTIFY genes and found that TIFY10 homologous genes have the most duplication events, higher selection pressure, and more obvious response to abiotic stresses compared with other homologous genes. Expression pattern analysis showed that GmTIFY10e and GmTIFY10g genes were significantly induced by salt stress. Under salt stress, GmTIFY10e and GmTIFY10g transgenic Arabidopsis plants showed higher root lengths and fresh weights and had significantly better growth than the wild type (WT). In addition, overexpression of GmTIFY10e and GmTIFY10g genes in soybean improved salt tolerance by increasing the PRO, POD, and CAT contents and decreasing the MDA content; on the contrary, RNA interference plants showed sensitivity to salt stress. Overexpression of GmTIFY10e and GmTIFY10g in Arabidopsis and soybean could improve the salt tolerance of plants, while the RNAi of GmTIFY10e and GmTIFY10g significantly increased sensitivity to salt stress in soybean. Further analysis demonstrated that GmTIFY10e and GmTIFY10g genes changed the expression levels of genes related to the ABA signal pathway, including GmSnRK2, GmPP2C, GmMYC2, GmCAT1, and GmPOD. This study provides a basis for comprehensive analysis of the role of soybean TIFY genes in stress response in the future.

Plant GDSL Esterases/Lipases: Evolutionary, Physiological and Molecular Functions in Plant Development

GDSL esterases/lipases (GELPs), present throughout all living organisms, have been a very attractive research subject in plant science due mainly to constantly emerging properties and functions in plant growth and development under both normal and stressful conditions. This review summarizes the advances in research on plant GELPs in several model plants and crops, including Arabidopsis, rice, maize and tomato, while focusing on the roles of GELPs in regulating plant development and plant-environment interactions. In addition, the possible regulatory network and mechanisms of GELPs have been discussed.

Predication of the Effector Proteins Secreted by Fusarium sacchari Using Genomic Analysis and Heterogenous Expression

One of the causative agents of pokkah boeng disease (PBD), which affects sugarcane crops globally, is the fungus Fusarium sacchari. These fungal infections reduce sugar quality and yield, resulting in severe economic losses. Effector proteins play important roles in the interactions between pathogenic fungi and plants. Here, we used bioinformatic prediction approaches to identify 316 candidate secreted effector proteins (CSEPs) in the complete genome of F. sacchari. In total, 95 CSEPs contained known conserved structures, representing 40 superfamilies and 18 domains, while an additional 91 CSEPs contained seven known motifs. Of the 130 CSEPs containing no known domains or motifs, 14 contained one of four novel motifs. A heterogeneous expression system in Nicotiana benthamiana was used to investigate the functions of 163 CSEPs. Seven CSEPs suppressed BAX-triggered programmed cell death in N. benthamiana, while four caused cell death in N. benthamiana. The expression profiles of these eleven CSEPs during F. sacchari infection suggested that they may be involved in sugarcane-F. sacchari interaction. Our results establish a basis for further studies of the role of effector molecules in pathogen–sugarcane interactions, and provide a framework for future predictions of pathogen effector molecules.

Expression, characterization, and immobilization of a novel SGNH esterase Est882 and its potential for pyrethroid degradation

The widely-used pyrethroid pesticides have attracted public attention because of their potentials to cause environmental pollution and toxic effects on non-target organisms. Esterase is a kind of hydrolytic enzyme that can catalyze the cleavage or formation of ester bonds. it plays a pivotal role in the decomposition of pyrethroids and esters containing industrial pollutants through the hydrolysis of ester bonds. Here, a new esterase gene est882 was successfully screened, which encodes Est882, a SGNH family esterase composed of 294 amino acids. It was heterogeneously expressed, identified and immobilized. Multiple sequence alignment showed that Est882 had a typical GDS(X) conserved motif and a catalytic triad composed of Ser79, Asp269 and His275. Phylogenetic analysis showed that Est882 shall belong to a new esterase family. Biochemical characterization demonstrated that the optimum condition was 40°C and pH 9.0. Est882 immobilization was studied with mesoporous silica SBA-15 as the carrier and found to significantly improve the tolerance and stability of Est882. Its optimum pH increased to 10.0 and stabilized within pH 8.0-11.0. Free Est882 can effectively degrade various pyrethroids within 30 min, with a degradation rate above 80%. The immobilized Est882 yet degraded more than 70% of pyrethroids within 30 min. The present study indicated that Est882 has outstanding potential in bioremediation of a pyrethroid-polluted environment. These characteristics endow Est882 with potential values in various industrial applications and hydrolysis of pyrethroid residues.

R2R3-MYBs in Durum Wheat: Genome-Wide Identification, Poaceae-Specific Clusters, Expression, and Regulatory Dynamics Under Abiotic Stresses

MYB transcription factors (TFs) represent one of the biggest TF families in plants, being involved in various specific plant processes, such as responses to biotic and abiotic stresses. The implication of MYB TFs in the tolerance mechanisms to abiotic stress is particularly interesting for crop breeding, since environmental conditions can negatively affect growth and productivity. Wheat is a worldwide-cultivated cereal, and is a major source of plant-based proteins in human food. In particular, durum wheat plays an important role in global food security improvement, since its adaptation to hot and dry conditions constitutes the base for the success of wheat breeding programs in future. In the present study, a genome-wide identification of R2R3-MYB TFs in durum wheat was performed. MYB profile search and phylogenetic analyses based on homology with Arabidopsis and rice MYB TFs led to the identification of 233 R2R3-TdMYB (Triticum durum MYB). Three Poaceae-specific MYB clusters were detected, one of which had never been described before. The expression of eight selected genes under different abiotic stress conditions, revealed that most of them responded especially to salt and drought stress. Finally, gene regulatory network analyses led to the identification of 41 gene targets for three TdR2R3-MYBs that represent novel candidates for functional analyses. This study provides a detailed description of durum wheat R2R3-MYB genes and contributes to a deeper understanding of the molecular response of durum wheat to unfavorable climate conditions.

Genome-Wide Analysis of DEAD-box RNA Helicase Family in Wheat (Triticum aestivum) and Functional Identification of TaDEAD-box57 in Abiotic Stress Responses

DEAD-box RNA helicases constitute the largest subfamily of RNA helicase superfamily 2 (SF2), and play crucial roles in plant growth, development, and abiotic stress responses. Wheat is one of the most important cereal crops in worldwide, and abiotic stresses greatly restrict its production. So far, the DEAD-box RNA helicase family has yet to be characterized in wheat. Here, we performed a comprehensive genome-wide analysis of the DEAD-box RNA helicase family in wheat, including phylogenetic relationships, chromosomal distribution, duplication events, and protein motifs. A total of 141 TaDEAD-box genes were identified and found to be unevenly distributed across all 21 chromosomes. Whole genome/segmental duplication was identified as the likely main driving factor for expansion of the TaDEAD-box family. Expression patterns of the 141 TaDEAD-box genes were compared across different tissues and under abiotic stresses to identify genes to be important in growth or stress responses. TaDEAD-box57-3B was significantly up-regulated under multiple abiotic stresses, and was therefore selected for further analysis. TaDEAD-box57-3B was localized to the cytoplasm and plasma membrane. Ectopic expression of TaDEAD-box57-3B in Arabidopsis improved tolerance to drought and salt stress as measured by germination rates, root lengths, fresh weights, and survival rates. Transgenic lines also showed higher levels of proline and chlorophyll and lower levels of malonaldehyde (MDA) than WT plants in response to drought or salt stress. In response to cold stress, the transgenic lines showed significantly better growth and higher survival rates than WT plants. These results indicate that TaDEAD-box57-3B may increase tolerance to drought, salt, and cold stress in transgenic plants through regulating the degree of membrane lipid peroxidation. This study provides new insights for understanding evolution and function in the TaDEAD-box gene family.

QTL dissection and mining of candidate genes for Ascochyta fabae and Orobanche crenata resistance in faba bean (Vicia faba L.)

BACKGROUND

Ascochyta blight caused by Ascochyta fabae Speg. and broomrape (Orobanche crenata) are among the economically most significant pathogens of faba bean. Several QTLs conferring resistance against the two pathogens have been identified and validated in different genetic backgrounds. The aim of this study was to saturate the most stable QTLs for ascochyta and broomrape resistance in two Recombinant Inbred Line (RIL) populations, 29H x Vf136 and Vf6 x Vf136, to identify candidate genes conferring resistance against these two pathogens.

RESULTS

We exploited the synteny between faba bean and the model species Medicago truncatula by selecting a set of 219 genes encoding putative WRKY transcription factors and defense related proteins falling within the target QTL intervals, for genotyping and marker saturation in the two RIL populations. Seventy and 50 of the candidate genes could be mapped in 29H x Vf136 and Vf6 x Vf136, respectively. Besides the strong reduction of the QTL intervals, the mapping process allowed replacing previous dominant and pedigree-specific RAPD flanking markers with robust and transferrable SNP markers, revealing promising candidates for resistance against the two pathogens.

CONCLUSIONS

Although further efforts in association mapping and expression studies will be required to corroborate the candidate genes for resistance, the fine-mapping approach proposed here increases the genetic resolution of relevant QTL regions and paves the way for an efficient deployment of useful alleles for faba bean ascochyta and broomrape resistance through marker-assisted breeding.

Genome-Wide Identification and Characterization of Soybean GmLOR Gene Family and Expression Analysis in Response to Abiotic Stresses

The LOR (LURP-one related) family genes encode proteins containing a conserved LOR domain. Several members of the LOR family genes are required for defense against Hyaloperonospora parasitica (Hpa) in Arabidopsis. However, there are few reports of LOR genes in response to abiotic stresses in plants. In this study, a genome-wide survey and expression levels in response to abiotic stresses of 36 LOR genes from Glycine max were conducted. The results indicated that the GmLOR gene family was divided into eight subgroups, distributed on 14 chromosomes. A majority of members contained three extremely conservative motifs. There were four pairs of tandem duplicated GmLORs and nineteen pairs of segmental duplicated genes identified, which led to the expansion of the number of GmLOR genes. The expansion patterns of the GmLOR family were mainly segmental duplication. A heatmap of soybean LOR family genes showed that 36 GmLOR genes exhibited various expression patterns in different tissues. The cis-acting elements in promoter regions of GmLORs include abiotic stress-responsive elements, such as dehydration-responsive elements and drought-inducible elements. Real-time quantitative PCR was used to detect the expression level of GmLOR genes, and most of them were expressed in the leaf or root except that GmLOR6 was induced by osmotic and salt stresses. Moreover, GmLOR4/10/14/19 were significantly upregulated after PEG and salt treatments, indicating important roles in the improvement of plant tolerance to abiotic stress. Overall, our study provides a foundation for future investigations of GmLOR gene functions in soybean.

Genome-Wide Identification of GDSL-Type Esterase/Lipase Gene Family in Dasypyrum villosum L. Reveals That DvGELP53 Is Related to BSMV Infection

GDSL-type esterase/lipase proteins (GELPs) characterized by a conserved GDSL motif at their N-terminus belong to the lipid hydrolysis enzyme superfamily. In plants, GELPs play an important role in plant growth, development and stress response. The studies of the identification and characterization of the GELP gene family in Triticeae have not been reported. In this study, 193 DvGELPs were identified in Dasypyrum villosum and classified into 11 groups (clade A–K) by means of phylogenetic analysis. Most DvGELPs contain only one GDSL domain, only four DvGELPs contain other domains besides the GDSL domain. Gene structure analysis indicated 35.2% DvGELP genes have four introns and five exons. In the promoter regions of the identified DvGELPs, we detected 4502 putative cis-elements, which were associated with plant hormones, plant growth, environmental stress and light responsiveness. Expression profiling revealed 36, 44 and 17 DvGELPs were highly expressed in the spike, the root and the grain, respectively. Further investigation of a root-specific expressing GELP, DvGELP53, indicated it was induced by a variety of biotic and abiotic stresses. The knockdown of DvGELP53 inhibited long-distance movement of BSMV in the tissue of D. villosum. This research provides a genome-wide glimpse of the D. villosum GELP genes and hints at the participation of DvGELP53 in the interaction between virus and plants.

Expression Pattern and Functional Analyses of Arabidopsis Guard Cell-Enriched GDSL Lipases

There are more than 100 GDSL lipases in Arabidopsis, but only a few members have been functionally investigated. Moreover, no reports have ever given a comprehensive analysis of GDSLs in stomatal biology. Here, we systematically investigated the expression patterns of 19 putative Guard-cell-enriched GDSL Lipases (GGLs) at various developmental stages and in response to hormone and abiotic stress treatments. Gene expression analyses showed that these GGLs had diverse expression patterns. Fifteen GGLs were highly expressed in guard cells, with seven preferentially in guard cells. Most GGLs were localized in endoplasmic reticulum, and some were also localized in lipid droplets and nucleus. Some closely homologous GGLs exhibited similar expression patterns at various tissues and in response to hormone and abiotic stresses, or similar subcellular localization, suggesting the correlation of expression pattern and biological function, and the functional redundancy of GGLs in plant development and environmental adaptations. Further phenotypic identification of ggl mutants revealed that GGL7, GGL14, GGL22, and GGL26 played unique and redundant roles in stomatal dynamics, stomatal density and morphology, and plant water relation. The present study provides unique resources for functional insights into these GGLs to control stomatal dynamics and development, plant growth, and adaptation to the environment.

Albedo- and Flavedo-Specific Transcriptome Profiling Related to Penicillium digitatum Infection in Citrus Fruit

Penicillium digitatum is the main postharvest pathogen of citrus fruit. Although the inner fruit peel part (albedo) is less resistant than the outer part (flavedo) to P. digitatum, the global mechanisms involved in their different susceptibility remain unknown. Here, we examine transcriptome differences between both tissues at fruit harvest and in their early responses to infection. At harvest, not only was secondary metabolism, involving phenylpropanoids, waxes, and terpenoids, generally induced in flavedo vs. albedo, but also energy metabolism, transcription factors (TFs), and biotic stress-related hormones and proteins too. Flavedo-specific induced responses to infection might be regulated in part by ERF1 TF, and are related to structural plant cell wall reinforcement. Other induced responses may be related to H₂O₂, the synthesis of phenylpropanoids, and the stress-related proteins required to maintain basal defense responses against virulent pathogens, whereas P. digitatum represses some hydrolase-encoding genes that play different functions and auxin-responsive genes in this peel tissue. In infected albedo, the repression of transport and signal transduction prevail, as does the induction of not only the processes related to the synthesis of flavonoids, indole glucosinolates, cutin, and oxylipins, but also the specific genes that elicit plant immunity against pathogens.

High-Throughput Sequencing-Based Identification of miRNAs and Their Target mRNAs in Wheat Variety Qing Mai 6 Under Salt Stress Condition

Soil salinization is one of the major abiotic stresses that adversely affect the yield and quality of crops such as wheat, a leading cereal crop worldwide. Excavating the salt-tolerant genes and exploring the salt tolerance mechanism can help breeding salt-tolerant wheat varieties. Thus, it is essential to identify salt-tolerant wheat germplasm resources. In this study, we carried out a salt stress experiment using Qing Mai 6 (QM6), a salt-tolerant wheat variety, and sequenced the miRNAs and mRNAs. The differentially expressed miRNAs and mRNAs in salt stress conditions were compared with the control. As results, a total of eight salt-tolerance-related miRNAs and their corresponding 11 target mRNAs were identified. Further analysis revealed that QM6 enhances salt tolerance through increasing the expression level of genes related to stress resistance, antioxidation, nutrient absorption, and lipid metabolism balance, and the expression of these genes was regulated by the identified miRNAs. The resulting data provides a theoretical basis for future research studies on miRNAs and novel genes related to salt tolerance in wheat in order to develop genetically improved salt-tolerant wheat varieties.

Genome-Wide Analysis of the DUF4228 Family in Soybean and Functional Identification of GmDUF4228 -70 in Response to Drought and Salt Stresses

Domain of unknown function 4228 (DUF4228) proteins are a class of proteins widely found in plants, playing an important role in response to abiotic stresses. However, studies on the DUF4228 family in soybean (Glycine max L.) are sparse. In this study, we identified a total of 81 DUF4228 genes in soybean genome, named systematically based on their chromosome distributions. Results showed that these genes were unevenly distributed on the 20 chromosomes of soybean. The predicted soybean DUF4228 proteins were identified in three groups (Groups I-III) based on a maximum likelihood phylogenetic tree. Genetic structure analysis showed that most of the GmDUF4228 genes contained no introns. Expression profiling showed that GmDUF4228 genes were widely expressed in different organs and tissues in soybean. RNA-seq data were used to characterize the expression profiles of GmDUF4228 genes under the treatments of drought and salt stresses, with nine genes showing significant up-regulation under both drought and salt stress further functionally verified by promoter (cis-acting elements) analysis and quantitative real-time PCR (qRT-PCR). Due to its upregulation under drought and salt stresses based on both RNA-seq and qRT-PCR analyses, GmDUF4228-70 was selected for further functional analysis in transgenic plants. Under drought stress, the degree of leaf curling and wilting of the GmDUF4228-70-overexpressing (GmDUF4228-70-OE) line was lower than that of the empty vector (EV) line. GmDUF4228-70-OE lines also showed increased proline content, relative water content (RWC), and chlorophyll content, and decreased contents of malondialdehyde (MDA), H2O2, and O2-. Under salt stress, the changes in phenotypic and physiological indicators of transgenic plants were the same as those under drought stress. In addition, overexpression of the GmDUF4228-70 gene promoted the expression of marker genes under both drought and salt stresses. Taken together, the results indicated that GmDUF4228 genes play important roles in response to abiotic stresses in soybean.

The Role of Chloroplast Membrane Lipid Metabolism in Plant Environmental Responses

Plants are nonmotile life forms that are constantly exposed to changing environmental conditions during the course of their life cycle. Fluctuations in environmental conditions can be drastic during both day–night and seasonal cycles, as well as in the long term as the climate changes. Plants are naturally adapted to face these environmental challenges, and it has become increasingly apparent that membranes and their lipid composition are an important component of this adaptive response. Plants can remodel their membranes to change the abundance of different lipid classes, and they can release fatty acids that give rise to signaling compounds in response to environmental cues. Chloroplasts harbor the photosynthetic apparatus of plants embedded into one of the most extensive membrane systems found in nature. In part one of this review, we focus on changes in chloroplast membrane lipid class composition in response to environmental changes, and in part two, we will detail chloroplast lipid-derived signals.

Genomic-Wide Analysis of the PLC Family and Detection of GmPI-PLC7 Responses to Drought and Salt Stresses in Soybean

Phospholipase C (PLC) performs significant functions in a variety of biological processes, including plant growth and development. The PLC family of enzymes principally catalyze the hydrolysis of phospholipids in organisms. This exhaustive exploration of soybean GmPLC members using genome databases resulted in the identification of 15 phosphatidylinositol-specific PLC (GmPI-PLC) and 9 phosphatidylcholine-hydrolyzing PLC (GmNPC) genes. Chromosomal location analysis indicated that GmPLC genes mapped to 10 of the 20 soybean chromosomes. Phylogenetic relationship analysis revealed that GmPLC genes distributed into two groups in soybean, the PI-PLC and NPC groups. The expression patterns and tissue expression analysis showed that GmPLCs were differentially expressed in response to abiotic stresses. GmPI-PLC7 was selected to further explore the role of PLC in soybean response to drought and salt stresses by a series of experiments. Compared with the transgenic empty vector (EV) control lines, over-expression of GmPI-PLC7 (OE) conferred higher drought and salt tolerance in soybean, while the GmPI-PLC7-RNAi (RNAi) lines exhibited the opposite phenotypes. Plant tissue staining and physiological parameters observed from drought- and salt-stressed plants showed that stress increased the contents of chlorophyll, oxygen free radical (O2 -), hydrogen peroxide (H2O2) and NADH oxidase (NOX) to amounts higher than those observed in non-stressed plants. This study provides new insights in the functional analysis of GmPLC genes in response to abiotic stresses.