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【Objective】Magnesium transporters（MGTs）are vital for magnesium transportation, thus analyzing the basic information, the physiological and chemical characteristics of the MeMGT gene family in cassava serves as a foundational step for understanding the functions of these genes.【Method】In this study, we identified and named 13 putative MeMGTs genes in cassava（Manihot esculenta Crantz）based on the cassava genome database through homologous sequence alignments, designated as MeMGT2; 1-MeMGT10; 2. We conducted chromosomal localization, conserved motif analysis, and phylogenetic analysis of the MeMGT family genes. Additionally, we predicted the biochemical properties, structure, and function of the corresponding proteins. 【Result】Chromosomal analysis revealed that the 13 MeMGTs genes were distributed across 8 chromosomes, each containing 4 to 13 exons. Tissue-specific expression patterns indicated differential expressions of MeMGTs genes across various developmental stages. MeMGT4; 2 was mainly expressed in cassava fibrous root and storage root, which might potentially play a role in storage root development, and MeMGT7 was mainly expressed in cassava leave, vein and stem with function possibly involved in long-distance Mg2+ transport. Cis-acting element analysis revealed the presence of numerous photoresponsive and hormone-responsive elements in the promoter regions of MeMGTs genes, suggesting regulation by multiple factors. Phylogenetic analysis of the MGT gene family categorized these genes into five distinct clusters between cassava and selected model species. Protein sequence analysis identified MeMGTs member proteins as hydrophilic proteins with two conserved transmembrane domains and a Gly-Met-Asn (GMN) tripeptide motif, devoid of signal peptides. Phosphorylation analysis indicated the presence of phosphorylation sites, including serine, threonine, and tyrosine sites, which may contribute to the functionality of MeMGTs member proteins.【Conclusion】MeMGTs genes are regulated by various elements including light, hormone, drought and cold responses, might play a crucial role in the growth, development and adversity stress of cassava. [ABSTRACT FROM AUTHOR]

Tea or tea shrub is a plant of the Camellia sinensis species, the leaves of which, previously prepared in a special way, are the traditional raw material for the production of tea products. Varietal gene identification of tea allows us to increase the level of assessment of the authenticity of tea raw materials and tea products. It is predominantly based on DNA technologies for the detection and interpretation of SNP markers (Single Nucleotide Polymorphism), represented by a wide arsenal of both expensive high-tech methods and publicly available laboratory approaches. Species gene identification of the raw material composition of tea-based soft drinks is an equally important area of research due to the risk of falsification of this type of product. The purpose of this study was to find methodological approaches to the varietal gene identification of tea raw materials and to the species gene identification of the raw material composition of tea-based soft drinks. As a result of a bioinformatics study to identify polymorphic restriction sites in the nucleotide sequences of Camellia sinensis genome loci, diagnostically significant restriction enzymes were selected that were capable of detecting SNPs and identifying tea genotypes using the analyzed markers. At the same time, 16 loci had potential for practical application, of which 11 belonged to the group of the most informative SNP markers. A post-analytical assessment of tea varieties was carried out with them regarding their genotypic affiliation and identifiability as part of solving the first task of the study. To achieve the second task, a molecular genetic approach to the species identification of the raw composition of soft drinks based on green tea was tested. The study included the analysis of experimental drinks (with natural flavoring “Lemon” and synthetic flavoring “Peach 716”), as well as commercial concentrates “TIAKVA” (based on extracts from the coarse stems of green or black tea). The methods used in the work were PCR (Polymerase Chain Reaction), RFLP (Restriction Fragment Length Polymorphism) and direct sequencing of the amplified chloroplast DNA locus. The combination of two methods (PCR and sequencing) showed its effectiveness in establishing the belonging of the analyzed nucleic acid samples to the Camellia sinensis species, the raw material base of the studied drinks and concentrates. However, to unlock the authentication potential of PCR with primers #1 and #2 combined with RFLP analysis, it will be necessary to select diagnostically significant restriction enzymes suitable for generating species-specific combinations of PCR-RFLP profiles of marker sequence.

In order to elucidate the basic properties of Vigna radiata 7S (Vr7S) globulin genes and their expression patterns during seed growth and development, the physicochemical properties, structural characteristics, protein tertiary structures, phylogenetic relationship and expression profiles of 10 Vr7S globulin genes were studied using bioinformatics and reverse transcription-polymerase chain reaction (RT-PCR). The results showed that the proteins encoded by the Vr7S globulin genes consisted of 246 to 594 amino acid residues, with isoelectric point (pI) ranging from 5.02 to 6.40, and molecular mass ranging from 27.82 to 70.02 kDa. All Vr7S globulin genes contained 3–7 exons, 2–6 introns, and 5–8 conserved motifs. Vr7S B1 had one conserved cupin domain, while the other nine genes contained two cupin domains. Vr7S globulin had four types of tertiary structures including α-helix and β-chain. In the conserved cupin domain, 67 conserved amino acid residues were shared by mung bean and other species, and mung bean 7S globulin genes had the closest homology adzuki bean 7S globulin genes followed by those of French bean, pigeon pea and soybean. The RNA sequencing (RNA-Seq) and RT-PCR expression profiles of mung bean seeds at different development stages showed that the expression level of the Vr7S globulin genes increased with the maturity of mung bean seeds, which was consistent with the expression pattern of 7S globulin genes in other legume species. These results indicated that the Vr7S globulin genes played a positive role in regulating the generation of mung bean seed storage protein. This study may lay a foundation for further analyzing the biological function of the Vr7S globulin genes in the seed development of mung bean.

Abstract Background The auxin/indole-3-acetic acid (Aux/IAA) gene family is a crucial element of the auxin signaling pathway, significantly influencing plant growth and development. Hence, we conducted a comprehensive investigation of Aux/IAAs gene family using the Sp75 and Monoe-Viroflay genomes in spinach. Results A total of 24 definitive Aux/IAA genes were identified, exhibiting diverse attributes in terms of amino acid length, molecular weight, and isoelectric points. This diversity underscores potential specific roles within the family, such as growth regulation and stress response. Structural analysis revealed significant variations in gene length and molecular weight. These variations indicate distinct roles within the Aux/IAA gene family. Chromosomal distribution analysis exhibited a dispersed pattern, with chromosomes 4 and 1 hosting the highest and lowest numbers of Aux/IAA genes, respectively. Phylogenetic analysis grouped the identified genes into distinct clades, revealing potential evolutionary relationships. Notably, the phylogenetic tree highlighted specific gene clusters suggesting shared genetic ancestry and potential functional synergies within spinach. Expression analysis under NAA treatment unveiled gene-specific and time-dependent responses, with certain genes exhibiting distinct temporal expression patterns. Specifically, SpoIAA5 displayed a substantial increase at 2 h post-NAA treatment, while SpoIAA7 and SpoIAA9 demonstrated continuous rises, peaking at the 4-hour time point. Conclusions These observations indicate a complex interplay of gene-specific and temporal regulation in response to auxin. Moreover, the comparison with other plant species emphasized both shared characteristics and unique features in Aux/IAA gene numbers, providing insights into the evolutionary dynamics of this gene family. This comprehensive characterization of Aux/IAA genes in spinach not only establishes the foundation for understanding their specific functions in spinach development but also provides a valuable resource for experimental validation and further exploration of their roles in the intricate network of auxin signaling pathways.

Laccase (LAC), a copper-containing polyphenol oxidase, is an important pathogenic factor of pathogenic fungi, and has been identified as an important virulence factor in numerous pathogenic fungi. LAC is encoded by a gene family and belongs to the class of multicopper oxidases. The study aimed to identify the LAC genes in Athelia bombacina (Link) Pers, and their interactions with the host. The expression levels of the LAC genes were quantified using RT-qPCR. The LAC activity, level of malondialdehyde (MDA) and activities of protective enzymes in 'Huangguan' pears during the interaction were measured. The AbLac4 gene deletion mutant strain was constructed. Six LAC genes were identified in A. bombacina, distributed across three chromosomes. Interspecies collinearity analysis suggested that LAC genes could serve as crucial pathogenic factors in A. bombacina. The LAC gene family can be classified into three distinct subgroups. Among the subgroups, variations were observed in their characteristic sequences and conserved motifs. However, the LAC genes within the same subgroup exhibited a high degree of conservation. The genes showed diverse expression profiles, with their promoters harboring multiple stress-responsive elements. Signal peptide prediction showed that all LAC proteins, with the exception of the AbLac3 protein, possessed signal peptides, indicating that they are secretory proteins. The subcellular localization analysis showed that all LAC proteins may be localized extracellularly. RT-qPCR revealed differential expression patterns among LAC genes; specifically, AbLac1 and AbLac4 exhibited distinct expression dynamics during the infection process. The LAC activity first increased and then decreased, with the highest increase rate occurring in the early stage of culture. The MDA content and catalase (CAT) activity at the inoculated site were found to be significantly higher than the uninoculated control. In addition, the deletion of AbLac4 gene reduced the growth rate and pathogenic ability of A. bombacina. This investigation found that AbLac1 and AbLac4 may play pivotal roles in mediating host interactions, and the fruit may combat pathogen infection through increasing the activities of CAT, phenylalanine ammonia lyase and peroxidase. This study provides valuable new insights into the pathogenic mechanisms of A. bombacina, significantly contributing to the field. [ABSTRACT FROM AUTHOR]

Copyright of Acta Edulis Fungi is the property of Acta Edulis Fungi and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

The Sahiwal breed of dairy cattle holds significant importance in Pakistan, mostly attributed to its ability to withstand high temperatures, resilience to diseases, and satisfactory performance when fed low-quality roughages. Domestication and breeding of mammals have exerted a consistent selection pressure on a wide range of characteristics in many domesticated species, resulting in discernible genetic modifications at the individual genome level. The study aimed to discover and analyze potential indicators of recent selection in Sahiwal cattle, specifically identifying the genes and quantitative trait loci associated with these selection indicators. The study utilized a sample size of 98 Sahiwal bulls. The genotyping of all animals was conducted using the BovineHD140k BeadChip. After undergoing quality control measures, 87 samples as well as 74,070 SNPs located throughout 29 autosomes were selected as well as included in the study. The selection signatures were examined using the iHS and the Tajima D approach. The result reveals the current positive selections on BTA 1, 2, 6, 11, 12, 15, 17, 21, and 27 with the iHS test, while for the Tajima D test, the current positive selections were detected on BTA 1, 2, 3, 4, 5, 6, 7, 9, 10, 14, 18, 20, 23, and 24. A total of 47 genes were detected within selection regions associated with vital economic traits. The QTL enrichment analysis has shown eight substantial QTLs in BTA19 and BTA20 linked with milk, production, as well as reproduction traits. Therefore, understanding the selection signatures and candidate genes that influence important economic traits can provide foundational knowledge that can be used effectively to gain insight into the underlying mechanisms controlling these traits in Sahiwal cattle. [ABSTRACT FROM AUTHOR]

Copyright of Revista Chapingo Serie Horticultura is the property of Universidad Autonoma Chapingo and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Shipin Kexue/ Food Science is the property of Food Science Editorial Department and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Background: The auxin/indole-3-acetic acid (Aux/IAA) gene family is a crucial element of the auxin signaling pathway, significantly influencing plant growth and development. Hence, we conducted a comprehensive investigation of Aux/IAAs gene family using the Sp75 and Monoe-Viroflay genomes in spinach. Results: A total of 24 definitive Aux/IAA genes were identified, exhibiting diverse attributes in terms of amino acid length, molecular weight, and isoelectric points. This diversity underscores potential specific roles within the family, such as growth regulation and stress response. Structural analysis revealed significant variations in gene length and molecular weight. These variations indicate distinct roles within the Aux/IAA gene family. Chromosomal distribution analysis exhibited a dispersed pattern, with chromosomes 4 and 1 hosting the highest and lowest numbers of Aux/IAA genes, respectively. Phylogenetic analysis grouped the identified genes into distinct clades, revealing potential evolutionary relationships. Notably, the phylogenetic tree highlighted specific gene clusters suggesting shared genetic ancestry and potential functional synergies within spinach. Expression analysis under NAA treatment unveiled gene-specific and time-dependent responses, with certain genes exhibiting distinct temporal expression patterns. Specifically, SpoIAA5 displayed a substantial increase at 2 h post-NAA treatment, while SpoIAA7 and SpoIAA9 demonstrated continuous rises, peaking at the 4-hour time point. Conclusions: These observations indicate a complex interplay of gene-specific and temporal regulation in response to auxin. Moreover, the comparison with other plant species emphasized both shared characteristics and unique features in Aux/IAA gene numbers, providing insights into the evolutionary dynamics of this gene family. This comprehensive characterization of Aux/IAA genes in spinach not only establishes the foundation for understanding their specific functions in spinach development but also provides a valuable resource for experimental validation and further exploration of their roles in the intricate network of auxin signaling pathways. [ABSTRACT FROM AUTHOR]

PREMISE: Robust standards to evaluate quality and completeness are lacking in eukaryotic structural genome annotation, as genome annotation software is developed using model organisms and typically lacks benchmarking to comprehensively evaluate the quality and accuracy of the final predictions. The annotation of plant genomes is particularly challenging due to their large sizes, abundant transposable elements, and variable ploidies. This study investigates the impact of genome quality, complexity, sequence read input, and method on protein-coding gene predictions. METHODS: The impact of repeat masking, long-read and short-read inputs, and de novo and genome-guided protein evidence was examined in the context of the popular BRAKER and MAKER workflows for five plant genomes. The annotations were benchmarked for structural traits and sequence similarity. RESULTS: Benchmarks that reflect gene structures, reciprocal similarity search alignments, and mono-exonic/multi-exonic gene counts provide a more complete view of annotation accuracy. Transcripts derived from RNA-read alignments alone are not sufficient for genome annotation. Gene prediction workflows that combine evidence-based and ab initio approaches are recommended, and a combination of short and long reads can improve genome annotation. Adding protein evidence from de novo assemblies, genome-guided transcriptome assemblies, or full-length proteins from OrthoDB generates more putative false positives as implemented in the current workflows. Post-processing with functional and structural filters is highly recommended. DISCUSSION: While the annotation of non-model plant genomes remains complex, this study provides recommendations for inputs and methodological approaches. We discuss a set of best practices to generate an optimal plant genome annotation and present a more robust set of metrics to evaluate the resulting predictions.

Simple Summary: The tea geometrid (Ectropis obliqua (Prout)) is a major defoliator of tea plants and seriously affects the tea quality and yield in China. The females release three Type-II sex pheromone components for mate communication, but knowledge about the biosynthesis of these compounds is still limited. In this study, we screened for the candidate genes in the sex pheromone biosynthetic pathway with a combination of comparative RNAseq, phylogenetic relationship, and tissue expression pattern analyses. A total of seven tentative biosynthetic enzymes were identified, including two ELOs (ELO3 and ELO5), two FARs (FAR2 and FAR9), one DEC (CYP4G173), one LIP (LIP1), and one epoxidase (CYP340BD1). Overall, our results provide a foundation for further functional elucidation of the vital genes involved in E. obliqua sex pheromone biosynthesis. Ectropis obliqua, a notorious tea pest, produces a Type-II sex pheromone blend for mate communication. This blend contains (Z,Z,Z)-3,6,9-octadecatriene, (Z,Z)-3,9-cis-6,7-epoxy-octadecadiene, and (Z,Z)-3,9-cis-6,7-epoxy-nonadecadiene. To elucidate the genes related to the biosynthesis of these sex pheromone components, transcriptome sequencing of the female E. obliqua pheromone gland and the abdomen without pheromone gland was performed. Comparative RNAseq analyses identified 52 putative genes, including 7 fatty acyl-CoA elongases (ELOs), 9 fatty acyl-CoA reductases (FARs), 1 decarbonylase (DEC), 3 lipophorins (LIPs), and 32 cytochrome P450 enzymes (CYPs). Tissue expression profiles revealed that two ELOs (ELO3 and ELO5), two FARs (FAR2 and FAR9), one DEC (CYP4G173), and one LIP (LIP1) displayed either abdomen-centric or -specific expression, suggesting potential roles in sex pheromone biosynthesis within the oenocytes of E. obliqua. Furthermore, the tissue expression patterns, combined with phylogenetic analysis, showed that CYP340BD1, which was expressed specifically and predominantly only in the pheromone gland, was clustered with the previously reported epoxidases, highlighting its potential role in the epoxidation of the unsaturated polytriene sex pheromone components. Collectively, our research provides valuable insights into the genes linked to sex pheromone biosynthesis. [ABSTRACT FROM AUTHOR]

OVATE family proteins (OFPs) are a kind of plant-specific transcription factor, which play important roles in the growth and development of plants. Here, we performed a genome-wide investigation of the OFP gene family members in the wild diploid strawberry (Fragaria vesca, 2n = 14), and analyzed their physical and chemical properties, gene structure, phylogeny, expression patterns, and the subcellular localizations of these genes. Fourteen OFP genes from F.vesca were identified. Collinearity analysis showed ten pairs of collinearity between F. vesca and Arabidopsis. Phylogenetic analysis divided FvOFP genes into five different clades. The expression patterns of the FvOFP genes assayed in different tissues of F. vesca by Reverse Transcription Quantitative Polymerase Chain Reaction (RT-qPCR) showed that FvOFP1, FvOFP11, FvOFP12, and FvOFP14 were highly expressed in achene and their expression was further verified in the fruits at different developmental stages. Additionally, the subcellular localizations of FvOFP1, FvOFP11, FvOFP12, and FvOFP14 were preliminarily analyzed in tobacco leaves. The results showed clear fluorescent signals in the nucleus. Our results provided a comprehensive understanding of the potential function of FvOFP genes in strawberries. [ABSTRACT FROM AUTHOR]

Data heterogeneity, particularly noted in fields such as genetics, has been identified as a key feature of big data, posing significant challenges to innovation in knowledge and information. This paper focuses on characterizing and understanding the so-called ''curse of heterogeneity'' in gene identification for low infant birth weight from a statistical learning perspective. Owing to the computational and analytical advantages of expectile regression in handling heterogeneity, this paper proposes a flexible, regularized, partially linear additive expectile regression model for high-dimensional heterogeneous data. Unlike most existing works that assume Gaussian or sub-Gaussian error distributions, we adopt a more realistic, less stringent assumption that the errors have only finite moments. Additionally, we derive a two-step algorithm to address the reduced optimization problem and demonstrate that our method, with a probability approaching one, achieves optimal estimation accuracy. Furthermore, we demonstrate that the proposed algorithm converges at least linearly, ensuring the practical applicability of our method. Monte Carlo simulations reveal that our method's resulting estimator performs well in terms of estimation accuracy, model selection, and heterogeneity identification. Empirical analysis in gene trait expression further underscores the potential for guiding public health interventions.

Background: TRIM proteins, recognized as a class of E3 ubiquitin ligases, are increasingly acknowledged for their antipathogen immune functions in mammals and fish. In the Chinese soft-shelled turtle (Pelodiscus sinensis), a secondary aquatic reptile that occupies a unique evolutionary position, the TRIM gene has rarely been reported. Methods and results: In the present study, 48 PsTRIM proteins were identified from the genome of Pelodiscus sinensis via Hidden Markov Model (HMM) searches and Signal Transduction ATPases with Numerous Domains (SMART) analysis. These PsTRIMs were found across 43 distinct scaffolds, and phylogenetic analyses classified them into three principal clades. The PsTRIMs feature a conserved assembly of either RING-B-box-coiled-coil (RBCC) or B-box-coiled-coil (BBC) domains at the N-terminus, in addition to eight unique domains at the C-terminus, including the B30.2 domain, 19 of which were identified. Expression profiling revealed ubiquitous expression of the 48 PsTRIMs across various P. sinensis tissues. Notably, seven PsTRIMs exhibited significant differential expression in liver transcriptomes following infection with Aeromonas hydrophila. Weighted gene coexpression network analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis implicated PsTRIM14 and PsTRIM28 as key players in host defense against bacterial invasion. Real-time quantitative PCR results indicated that PsTRIM1, PsTRIM2, PsTRIM14, and PsTRIM28 experienced marked upregulation in P. sinensis livers at 12 h post-infection with A. hydrophila. Conclusions: Our study is the first to comprehensively identify and analyze the functions of TRIM genes in P. sinensis, unveiling their considerable diversity and potential roles in modulating immune responses. [ABSTRACT FROM AUTHOR]

Background: Light is essential for kiwifruit development, in which photoresponse factors contributes greatly to the quality formation. 'Light sensitive hypocotyls, also known as light-dependent short hypocotyls' (LSH) gene family can participate in fruit development as photoresponse factor. However, the key LSH gene that determine kiwifruit development remains unclear. This study aim to screen and identify the key gene AaLSH9 in A. arguta. Materials and methods: Genome-wide identification of the LSH gene family was used to analyse LSH genes in kiwifruit. Homologous cloning was used to confirm the sequence of candidate LSH genes. qRT-PCR and cluster analysis of expression pattern were used to screen the key AaLSH9 gene. Subcellular localization of AaLSH9 in tobacco leaves and overexpression of AaLSH9 in Arabidopsis thaliana hy5 mutant plants were used to define the acting place in cell and identify molecular function, respectively. Results: We identified 15 LSH genes, which were divided into two sub-families namely A and B. Domain analysis of A and B showed that they contained different domain organizations, which possibly played key roles in the evolution process. Three LSH genes, AaLSH2, AaLSH9, and AaLSH11, were successfully isolated from Actinidia arguta. The expression pattern and cluster analysis of these three AaLSH genes suggested AaLSH9 might be a key photoresponse gene participating in fruit development in A. arguta. Subcellular localization showed AaLSH9 protein was located in the nucleus. The overexpression of AaLSH9 gene in Arabidopsis thaliana hy5 mutant plants partially complemented the long hypocotyls of hy5 mutant, implying AaLSH9 played a key role as photoresponse factor in cells. In addition, the seed coat color of A. thaliana over-expressing AaLSH9 became lighter than the wide type A.thaliana. Finally, AaCOP1 was confirmed as photoresponse factor to participate in developmental process by stable transgenic A. thaliana. Conclusions: AaLSH9 can be involved in kiwifruit (A. arguta) development as key photoresponse factor. Our results not only identified the photoresponse factors AaLSH9 and AaCOP1 but also provided insights into their key role in fruit quality improvement in the process of light response. [ABSTRACT FROM AUTHOR]

Proteins containing the homologous E6-AP carboxyl-terminal (HECT) domain are a class of E3 ubiquitin ligases involved in the ubiquitin–proteasome pathway, which plays an irreplaceable role in plant growth, development, and stress resistance. However, a phylogenetic analysis and expression profile of the HECT gene (PtrHECT) in the model plant Populus trichocarpa (Torr. & Gray) have not been reported. In this study, we identified 13 PtrHECT genes using genome-wide analysis, and then these were divided into four groups. The protein interaction networks showed that the PtrHECT protein may interact with PTR6 and participate in ABA signal regulation. Abiotic stress is the main environmental factor limiting plant growth and development. The qRT-PCR results showed that PtrHECT1, 4, 7, 8, and 9 were significantly up-regulated in leaves at each time point under drought stress, and most PtrHECT genes responded to both drought and high salt stress, consistent with their promoter sequence analysis, revealing the presence of an important number of phytohormone-responsive and stress-related cis-regulatory elements. This study provides useful information for further analysis of the functions of the HECT gene family in P. trichocarpa. [ABSTRACT FROM AUTHOR]

Salinity greatly affects the production of soybeans in arid and semi-arid lands around the world. The responses of soybeans to salt stress at germination, emergence, and other seedling stages have been evaluated in multitudes of studies over the past decades. Considerable salt-tolerant accessions have been identified. The association between salt tolerance responses during early and later growth stages may not be as significant as expected. Genetic analysis has confirmed that salt tolerance is distinctly tied to specific soybean developmental stages. Our understanding of salt tolerance mechanisms in soybeans is increasing due to the identification of key salt tolerance genes. In this review, we focus on the methods of soybean salt tolerance screening, progress in forward genetics, potential mechanisms involved in salt tolerance, and the importance of translating laboratory findings into field experiments via marker-assisted pyramiding or genetic engineering approaches, and ultimately developing salt-tolerant soybean varieties that produce high and stable yields. Progress has been made in the past decades, and new technologies will help mine novel salt tolerance genes and translate the mechanism of salt tolerance into new varieties via effective routes. [ABSTRACT FROM AUTHOR]

The current study focuses on identifying the candidate genes of a grain yield QTL from a double haploid population, Westonia × Kauz. The QTL region spans 20 Mbp on the IWGSC whole-genome sequence flank with 90K SNP markers. The IWGSC gene annotation revealed 16 high-confidence genes and 41 low-confidence genes. Bioinformatic approaches, including functional gene annotation, ontology investigation, pathway exploration, and gene network study using publicly available gene expression data, enabled the short-listing of four genes for further confirmation. Complete sequencing of those four genes demonstrated that only two genes are polymorphic between the parental cultivars, which are the ferredoxin-like protein gene and the tetratricopeptide-repeat (TPR) protein gene. The two genes were selected for downstream investigation. Two SNP variations were observed in the exon for both genes, with one SNP resulting in changes in amino acid sequence. qPCR-based gene expression showed that both genes were highly expressed in the high-yielding double haploid lines along with the parental cultivar Westonia. In contrast, their expression was significantly lower in the low-yielding lines in the other parent. It can be concluded that these two genes are the contributing genes to the grain yield QTL. [ABSTRACT FROM AUTHOR]

Plant trehalose has been regarded to play a key role in various biological processes during the growth and development stages. Trehalose-6-phosphate synthase (TPS) and trehalose-6-phosphate phosphatase (TPP) are two important enzymes for the synthesis of plant trehalose. Up till now, the TPS and TPP gene families have been identified and characterized in numerous higher plant species, but are rarely recorded in peanuts (Arachis hypogaea). In this study, a comprehensive search was performed to identify all putative TPS and TPP proteins in the peanut genome using Arabidopsis TPS and TPP proteins as queries. We then analyzed the characteristics of TPS and TPP members, including physic-chemical parameters, subcellular localization, phylogeny relationships, gene duplication, and expression patterns by various computational tools. As a result, a total of 17 ArahyTPS and 15 ArahyTPP genes were identified and annotated in the peanut genome, which was expanded by segmental duplication events. Our Neighbor-Joining based phylogenetic tree indicated that the ArahyTPS and ArahyTPP proteins could be categorized into three and two major branches. Gene structures and protein features analysis exhibited that the ArahyTPS and ArahyTPP proteins shared high structural and functional similarities. Based on previous RNA-Seq datasets, a majority of the ArahyTPS and ArahyTPP genes were found to specifically express in at least one major organ/tissue during the growth and development. This work will not only lead to a solid foundation on reveal the potential roles of ArahyTPS and ArahyTPP gene families in peanuts but also provide evidence to related trehalose research in other higher plant species. [ABSTRACT FROM AUTHOR]

The ZRT/IRT-like proteins (ZIPs) play critical roles in the absorption, transport, and intracellular balance of metal ions essential for various physiological processes in plants. However, little is known about the pan-genomic characteristics and properties of ZIP genes in cucumber (Cucumis sativus L.). In this study, we identified 10 CsZIP genes from the pan-genome of 13 C. sativus accessions. Among them, only CsZIP10 showed no variation in protein sequence length. We analyzed the gene structure, conserved domains, promoter cis-elements, and phylogenetic relationships of these 10 CsZIP genes derived from "9930". Based on phylogenetic analysis, the CsZIP genes were classified into three branches. Amino acid sequence comparison revealed the presence of conserved histidine residues in the ZIP proteins. Analysis of promoter cis-elements showed that most promoters contained elements responsive to plant hormones. Expression profiling in different tissues showed that most CsZIP genes were expressed at relatively low levels in C. sativus leaves, stems, and tendrils, and CsZIP7 and CsZIP10 were specifically expressed in roots, indicating their potential involvement in the absorption and transport of metal ions. Transcriptomic data indicated that these 10 ZIP genes displayed responses to both downy mildew and powdery mildew, and CsZIP1 was significantly downregulated after both salt and heat treatments. In conclusion, this study deepens our understanding of the ZIP gene family and enhances our knowledge of the biological functions of CsZIP genes in C. sativus. [ABSTRACT FROM AUTHOR]

Rice is a valuable crop used for food throughout the world. To develop modern, productive and disease resistant rice varieties, it is necessary to accelerate the breeding process using molecular biology methods. The purpose of the current study was to identify alleles of six blast resistance genes (Pi-1, Pi-2, Pi-33, Pi-40, Pi-ta and Pi-b) in the selected rice samples using MAS (marker-associated selection method). The objects of the study were 446 breeding rice samples sent to the laboratory of cell breeding for analysis by breeders from the laboratory for rice breeding and seed production of the FSBSI «ARC «Donskoy». Identification of genes in them was carried out differentially and was determined by the pedigree of the samples. In order to determine the alleles of the blast resistance genes Pi-1, Pi-2 and Pi-33, all 446 samples were studied, for the Pi-40 gene there were studied 20 samples, for the Pi-ta gene there were studied 316 samples. For DNA extraction, there was used a Russian-made kit ‘DNA-Extran-3’. PCR was performed using specific primers of the target genes. Identification of reaction products was performed on agarosegels after photographing in ultraviolet light. As a result of the study, there were identified the rice samples which carried from 1 to 5 blast resistance genes in various combinations. There have been identified 14 samples that possess a set of 5 resistance genes, such as 2723, 2724, 2727, 2728, 2729, 2730, 2733, 2735, 2736, 5007, 5671, 5673, 5450/2 and 2450/2. The information obtained from the results of the study could then be used by breeders to use valuable genotypes as donors in crosses, as well as to select promising breeding material resistant to blast disease.

【Objective】Capsicum chinense is one of the main cultivated species of pepper, which generally has a strong fruit aroma formed by branched chain esters. AAT (alcohol acyl-CoA transferase) catalyzes the last step in the synthesis of branched chain esters and has an important impact on its content. Identification of the AAT gene family in C. chinense and analysis on its expression patterns will provide references for its functional studies.【Method】Bioinformatics and real-time quantitative PCR analysis were applied to identify the AAT gene family of C. chinense and analyze its expression patterns.【Result】Ten members of the AAT gene family were identified and named CcAAT1-CcAAT10 according to their distribution order on six chromosomes. Physicochemical properties prediction revealed that the length of amino acid sequence encoded by AAT gene family range from 256 to 683 aa, with their molecular mass ranging from 29 to 77 kDa, and isoelectric point ranging from 5.34 to 8.79. Average hydrophobic coefficients of them were all negative values. Their instability indexes ranged 23.76 to 51.02. Protein structure prediction showed that their secondary structure was dominated by α-helices and irregular convolutions, and the tertiary structure varied widely. Subcellular localization prediction revealed that all CcAAT were located in the cytoplasm and 16 cis-regulatory elements were found on their gene promoter. Spatiotemporal expression analysis showed that CcAAT5 and CcAAT6 had no detectable expression, CcAAT8 was specifically expressed in flowers and fruits, CcAAT1, CcAAT3 and CcAAT7 were highly expressed in leaves, and CcAAT4 was highly expressed in roots.【Conclusion】It clarified the expression pattern of the AAT gene family in C. chinense and it was hypothesized that CcAAT8 might be a key gene affecting the content of branched chain esters.

【Objective】Sesuvium portulacastrum, a typical coastal and mangrove associate plant, is capable of retaining sand and protecting banks. It can grow normally in seawater and has a strong salt tolerance. Na+/H+ exchange (NHX) plays a key role in salt tolerance and plant growth with development. In order to understand the role of NHX in salt tolerance of S. portulacastrum, the NHX genes were identified and analyzed.【Method】In this study, the S. portulacastrum NHX genes were identified by using informatic method through its full length transcriptome data. Their physicochemical properties, conserved motifs and evolutionary relationships were analyzed, and the expression patterns of NHX genes under s alt stress were studied by quantative real-time PCR (qRT-PCR).【Result】The results showed that 12 SpNHX genes were identified from S. portulacastrum and named as SpNHX1 to SpNHX12. The number of amino acids ranged from 276 to 554, with the molecular weight ranged from 31.22 to 61.21 kD, isoelectric point from 5.55 to 8.64, and instability ind ex from 32.14 to 50.54. All the proteins were hydrophobic. Phylogenetic analysis showed that SpNHX proteins can be divided into two subgroups. Similar conserved motifs composition was found in each subgroup. Multiple sequence alignment results showed that all SpNHX proteins had Na+/H+ exchange conserved domains. RNA-seq data and qRT-PCR results showed that SpNHX genes were induced to different degrees under salt stress, and SpNHX1, SpNHX9, SpNHX10, SpNHX11 and SpNHX12 were significantly up-regulated under salt stress.【Conclusion】This study clarified the expression patterns of NHXs in S. portulacastrum under high salt stress, indicating that SpNHX1, SpNHX9, SpNHX10, SpNHX11 and SpNHX12 may be involved in the response of S. portulacastrum to salt stress, which provided a theoretical basis for further research on the role of NHX in the process of salt tolerance of S. portulacastrum.

Laccase (LAC), a copper-containing polyphenol oxidase, is an important pathogenic factor of pathogenic fungi, and has been identified as an important virulence factor in numerous pathogenic fungi. LAC is encoded by a gene family and belongs to the class of multicopper oxidases. The study aimed to identify the LAC genes in Athelia bombacina (Link) Pers, and their interactions with the host. The expression levels of the LAC genes were quantified using RT-qPCR. The LAC activity, level of malondialdehyde (MDA) and activities of protective enzymes in ‘Huangguan’ pears during the interaction were measured. The AbLac4 gene deletion mutant strain was constructed. Six LAC genes were identified in A. bombacina, distributed across three chromosomes. Interspecies collinearity analysis suggested that LAC genes could serve as crucial pathogenic factors in A. bombacina. The LAC gene family can be classified into three distinct subgroups. Among the subgroups, variations were observed in their characteristic sequences and conserved motifs. However, the LAC genes within the same subgroup exhibited a high degree of conservation. The genes showed diverse expression profiles, with their promoters harboring multiple stress-responsive elements. Signal peptide prediction showed that all LAC proteins, with the exception of the AbLac3 protein, possessed signal peptides, indicating that they are secretory proteins. The subcellular localization analysis showed that all LAC proteins may be localized extracellularly. RT-qPCR revealed differential expression patterns among LAC genes; specifically, AbLac1 and AbLac4 exhibited distinct expression dynamics during the infection process. The LAC activity first increased and then decreased, with the highest increase rate occurring in the early stage of culture. The MDA content and catalase (CAT) activity at the inoculated site were found to be significantly higher than the uninoculated control. In addition, the deletion of AbLac4 gene reduced the growth rate and pathogenic ability of A. bombacina. This investigation found that AbLac1 and AbLac4 may play pivotal roles in mediating host interactions, and the fruit may combat pathogen infection through increasing the activities of CAT, phenylalanine ammonia lyase and peroxidase. This study provides valuable new insights into the pathogenic mechanisms of A. bombacina, significantly contributing to the field.

SPL transcription factors are widely involved in plant growth and development, stress response and so on. At present, there is no study on the STM (SPL with transmembrane motif) transcription factor in Dendrobium officinale. In order to explore the role of STM in the growth, development and stress response of D. officinale, four STM transcription factors were identified at the whole genome of D. officinale, and bioinformatics analysis of DoSTM gene family members were carried out. The expression of DoSTM in different tissue parts and different stress treatments were studied by reverse transcription PCR. The results were as follows: (1)DoSTM1-4 were hydrophilic proteins with SBP conserved domains and some hormone response sites. (2)Four DoSTM were expressed in root, stem and leaf, and the relative expression of DoSTM2 was the lowest in leaf; there was no significant differences in the relative expression level of DoSTM1/3/4. (3)The relative expression level of DoSTM1-4 changed significantly under low temperature, high temperature and drought stress, and the expression of DoSTM1/3/4 decreased most significantly. Therefore, it is speculated that DoSTM is related to hormone response, temperature change response and drought resistance in plants. These conclusions provide the reference for the further research on STM transcription factor of D. officinale.

In order to explore the relationship between dehydrin (DHN) and core browning in late-harvested Yali pears, this study identified and characterized the PbDHN3 gene based on bioinformatics methods, and analyzed the expression pattern of this gene during the core browning process under rapid cooling and slow cooling conditions. The results showed that the open reading frame (ORF) of PbDHN3 was 564 bp in length, encoding 187 amino acids, and having a conserved domain of dehydrin superfamily comprising two Y segments, one S segment and three K segments (Y2SK3). Bioinformatics analysis showed that PbDHN3 was a hydrophilic stable protein with a molecular mass of 19.77 kDa and an isoelectric point of 7.98. The secondary structure consists of α-helix, irregular coil, extended chain and β-turn. PbDHN3 was located in the nucleus and contained no signal peptide or transmembrane structure. It was a non-secretory protein. The results of homology analysis showed that PbDHN3 was more than 89.74% similar to the DHN of five other plants such as apples. Phylogenetic analysis showed that PbDHN3 had the closest relationship with the DHN of Pyrus ussuriensis × Pyrus communis. The results of promoter analysis showed that PbDHN3 contained basic promoter elements and other cis-acting elements, which were consistent with the predicted results of the upland cotton GhDHN1 and the wheat TaDHN2 promoter regions, and all of them included hormone response elements and light response elements. The results of real-time fluorescence polymerase chain reaction (PCR) analysis showed that the expression of the DHN3 gene was significantly up-regulated during the core browning process of Yali pears under rapid cooling conditions, which was closely related to the browning of the core. This study provides a theoretical basis for further exploring the function of the PbDHN3 gene and clarifying the mechanism of core browning of Yali pears.

Betalains provide Chenopodium quinoa bright color, and the key enzyme genes for betalain biosynthesis include CYP76AD, DODA, and GTs. In this study, 59 CqCYP76AD, CqDODA and CqGTs genes in quinoa were identified and characterized by gene structural characteristics, phylogenetic relationships and gene expression patterns. The CqCYP76AD genes were divided into ɑ, β and γ types, CqDODA into ɑ and β types, and CqGTs into CqcDOPA5GT, CqB5GT and CqB6GT types according to phylogenetic relationships. The analysis of co-linearity identified eight pairs of duplicated genes which were subjected to purifying selection during evolution. CqCYP76AD and CqDODA, as well as CqcDOPA5GT and CqB5GT may have been evolutionarily linked in genetic inheritance, based on gene location and gene structure study. The tissue expression specificity of CqCYP76AD, CqDODA, and CqGTs genes in response to seed germination and cold stress was studied by RNA-Seq data. The genes CqCYP76AD, CqDODA, and CqGTs were involved in betalain biosynthesis and cold stress. CqCYP76AD, CqDODA, CqcDOPA5GT and CqB5GT gene sequences were consistent in the eight quinoa samples and showed significant variations in expression. In contrast, the inconsistency between changes in gene expression and betalain accumulation indicates that other factors may influence betalain biosynthesis in quinoa. This study offers the theoretical basis for the roles of the CqCYP76AD, CqDODA, and CqGTs genes in betalain biosynthesis and cold stress in quinoa, as well as a guide for the full utilization of betalains in quinoa plants.

【Objective】 Capsicum chinense is one of the main cultivated species of pepper, which generally has a strong fruit aroma formed by branched chain esters. AAT (alcohol acyl-CoA transferase) catalyzes the last step in the synthesis of branched chain esters and has an important impact on its content. Identification of the AAT gene family in C. chinense and analysis on its expression patterns will provide references for its functional studies.【Method】Bioinformatics and real-time quantitative PCR analysis were applied to identify the AAT gene family of C. chinense and analyze its expression patterns.【Result】Ten members of the AAT gene family were identified and named CcAAT1-CcAAT10 according to their distribution order on six chromosomes. Physicochemical properties prediction revealed that the length of amino acid sequence encoded by AAT gene family range from 256 to 683 aa, with their molecular mass ranging from 29 to 77 kDa, and isoelectric point ranging from 5.34 to 8.79. Average hydrophobic coefficients of them were all negative values. Their instability indexes ranged 23.76 to 51.02. Protein structure prediction showed that their secondary structure was dominated by α-helices and irregular convolutions, and the tertiary structure varied widely. Subcellular localization prediction revealed that all CcAAT were located in the cytoplasm and 16 cis-regulatory elements were found on their gene promoter. Spatiotemporal expression analysis showed that CcAAT5 and CcAAT6 had no detectable expression, CcAAT8 was specifically expressed in flowers and fruits, CcAAT1, CcAAT3 and CcAAT7 were highly expressed in leaves, and CcAAT4 was highly expressed in roots.【Conclusion】It clarified the expression pattern of the AAT gene family in C. chinense and it was hypothesized that CcAAT8 might be a key gene affecting the content of branched chain esters. [ABSTRACT FROM AUTHOR]

【Objective】Sesuvium portulacastrum, a typical coastal and mangrove associate plant, is capable of retaining sand and protecting banks. It can grow normally in seawater and has a strong salt tolerance. Na+ /H+ exchange (NHX) plays a key role in salt tolerance and plant growth with development. In order to understand the role of NHX in salt tolerance of S. portulacastrum, the NHX genes were identified and analyzed. 【Method】In this study, the S. portulacastrum NHX genes were identified by using informatic method through its full length transcriptome data. Their physicochemical properties, conserved motifs and evolutionary relationships were analyzed, and the expression patterns of NHX genes under s alt stress were studied by quantative real-time PCR (qRT-PCR).【Result】The results showed that 12 SpNHX genes were identified from S. portulacastrum and named as SpNHX1 to SpNHX12. The number of amino acids ranged from 276 to 554, with the molecular weight ranged from 31.22 to 61.21 kD, isoelectric point from 5.55 to 8.64, and instability ind ex from 32.14 to 50.54. All the proteins were hydrophobic. Phylogenetic analysis showed that SpNHX proteins can be divided into two subgroups. Similar conserved motifs composition was found in each subgroup. Multiple sequence alignment results showed that all SpNHX proteins had Na+ /H+ exchange conserved domains. RNA-seq data and qRT-PCR results showed that SpNHX genes were induced to different degrees under salt stress, and SpNHX1, SpNHX9, SpNHX10, SpNHX11 and SpNHX12 were significantly up-regulated under salt stress. 【Conclusion】This study clarified the expression patterns of NHXs in S. portulacastrum under high salt stress, indicating that SpNHX1, SpNHX9, SpNHX10, SpNHX11 and SpNHX12 may be involved in the response of S. portulacastrum to salt stress, which provided a theoretical basis for further research on the role of NHX in the process of salt tolerance of S. portulacastrum. [ABSTRACT FROM AUTHOR]

Micronutrient deficiencies, particularly of iron (Fe) and zinc (Zn), in the diet contribute to health issues and hidden hunger. Enhancing the Fe and Zn content in globally staple food crops like rice is necessary to address food malnutrition. A Genome-Wide Association Study (GWAS) was conducted using 85 diverse rice accessions from the Democratic Republic of Congo (DRC) to identify genomic regions associated with grain Fe and Zn content. The Fe content ranged from 0.95 to 8.68 mg/100 g on a dry weight basis (dwb) while Zn content ranged from 0.87 to 3.8 mg/100 g (dwb). Using MLM and FarmCPU models, we found 10 significant SNPs out of which one SNP on chromosome 11 was associated with the variation in Fe content and one SNP on chromosome 4 was associated with the Zn content, and both were commonly detected by the two models. Candidate genes belonging to transcription regulator activities, including the bZIP family genes and MYB family genes, as well as transporter activities involved in Fe and Zn homeostasis were identified in the vicinity of the SNP markers and selected. The identified SNP markers hold promise for marker-assisted selection in rice breeding programs aimed at enhancing Fe and Zn content in rice. This study provides valuable insights into the genetic factors controlling Fe and Zn uptake and their transport and accumulation in rice, offering opportunities for developing biofortified rice varieties to combat malnutrition among rice consumers. [ABSTRACT FROM AUTHOR]

Objective To construct and identify Nrf2 knockout mouse model. Methods A pair of male and female heterozygous (Nrf2-/+) mice were introduced to breed F1 mice. Male and female Nrf2-/+ mice from F1 generation were bred to obtain F2 generation mice. DNA was extracted from the tail tissue of mice at 5 days of age and their genotype was determined by PCR and agarose gel electrophoresis. NRF2 protein was extracted and coding gene was knocked out from the lung tissues of mice. The expression of NRF2 protein was detected by Western blot, and the identification results were confirmed laterally. Results Homozygous (Nrf2-/-) mice continued to mate and obtain homozygous mice. Three genotypes were identified when F1 was mated with F2 generation heterozygous mice: wild type (Nrf2+/+), heterozygous (Nrf2+/-) and homozygous (Nrf2-/-). The genotypes of offspring mice were successfully identified by PCR. NRF2 protein expression in lung tissue of Nrf2 knockout mice was significantly lower than that of wild-type mice (P＜0.05). Conclusions The mouse model with Nrf2 knockout is successfully bred in this study, which provides a new experimental tool for further exploring the role and mechanism of NRF2.

Ectropis obliqua, a notorious tea pest, produces a Type-II sex pheromone blend for mate communication. This blend contains (Z,Z,Z)-3,6,9-octadecatriene, (Z,Z)-3,9-cis-6,7-epoxy-octadecadiene, and (Z,Z)-3,9-cis-6,7-epoxy-nonadecadiene. To elucidate the genes related to the biosynthesis of these sex pheromone components, transcriptome sequencing of the female E. obliqua pheromone gland and the abdomen without pheromone gland was performed. Comparative RNAseq analyses identified 52 putative genes, including 7 fatty acyl-CoA elongases (ELOs), 9 fatty acyl-CoA reductases (FARs), 1 decarbonylase (DEC), 3 lipophorins (LIPs), and 32 cytochrome P450 enzymes (CYPs). Tissue expression profiles revealed that two ELOs (ELO3 and ELO5), two FARs (FAR2 and FAR9), one DEC (CYP4G173), and one LIP (LIP1) displayed either abdomen-centric or -specific expression, suggesting potential roles in sex pheromone biosynthesis within the oenocytes of E. obliqua. Furthermore, the tissue expression patterns, combined with phylogenetic analysis, showed that CYP340BD1, which was expressed specifically and predominantly only in the pheromone gland, was clustered with the previously reported epoxidases, highlighting its potential role in the epoxidation of the unsaturated polytriene sex pheromone components. Collectively, our research provides valuable insights into the genes linked to sex pheromone biosynthesis.

OVATE family proteins (OFPs) are a kind of plant-specific transcription factor, which play important roles in the growth and development of plants. Here, we performed a genome-wide investigation of the OFP gene family members in the wild diploid strawberry (Fragaria vesca, 2n = 14), and analyzed their physical and chemical properties, gene structure, phylogeny, expression patterns, and the subcellular localizations of these genes. Fourteen OFP genes from F.vesca were identified. Collinearity analysis showed ten pairs of collinearity between F. vesca and Arabidopsis. Phylogenetic analysis divided FvOFP genes into five different clades. The expression patterns of the FvOFP genes assayed in different tissues of F. vesca by Reverse Transcription Quantitative Polymerase Chain Reaction (RT-qPCR) showed that FvOFP1, FvOFP11, FvOFP12, and FvOFP14 were highly expressed in achene and their expression was further verified in the fruits at different developmental stages. Additionally, the subcellular localizations of FvOFP1, FvOFP11, FvOFP12, and FvOFP14 were preliminarily analyzed in tobacco leaves. The results showed clear fluorescent signals in the nucleus. Our results provided a comprehensive understanding of the potential function of FvOFP genes in strawberries.

• This is a report on Class III peroxidase genes (POD) in the moss Dicranum scoparium. • We identified 22 genes encoding PODs and cloned two for verification. • The physicochemical properties of these proteins were analysed in silico. • Specific genes were differentially upregulated by a variety of abiotic stresses. • Results indicated that PODs are important in the abiotic stress tolerance of the moss. Class III peroxidases (POD: EC 1.11.1.7) are classical secretory plant peroxidases belonging to a large multigene family with diverse functions. Members of the POD family have been well-studied and characterized in many plants, including three species of bryophytes, but not from the moss Dicranum scoparium Hedw. Ecologically, D. scoparium is a very important species, which has a widespread distribution throughout the Holarctic. Here we present the first comprehensive report on the POD gene family in D. scoparium, identifying 22 genes encoding PODs (DsPODs), two of which were cloned for verification. All genes were deposited to GenBank under the third-party annotation (Accession numbers TPA: BK061169 – BK061190). Here, we present an in silico study of the physicochemical properties of these proteins. Analyses of conserved domains and subcellular localization suggested that DsPODs have classical peroxidase domain structure; they are secretory proteins and most of them are extracellular. Eight DsPODs highly homologous to Class III peroxidases from the mosses Pohlia nutans and Physcomitrium patens were further microcharacterized. All eight DsPODs possess a haem ligand and active sites necessary for enzymatic activity; they also contained sites for posttranslational modifications. Prediction of secondary structure indicated that these proteins mainly consist of α-helices and random coils. Experiments involving the reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) showed that DsPOD1, DsPOD2, DsPOD6 , and DsPOD8 are differentially upregulated in response to stress. The stresses applied here included CdCl 2 , paraquat, unfavorable temperatures, and a hydration-desiccation-rehydration cycle. Our results indicate that Class III PODs contribute to the abiotic stress tolerance of D. scoparium , and specific DsPOD genes may play diverse roles in the response of the moss to stress. [ABSTRACT FROM AUTHOR]

Sesquiterpenes are characteristic components and important quality criterions for agarwood. Although sesquiterpenes are well-known to be biosynthesized by sesquiter- pene synthases (TPSs), to date, only a few TPS genes involved in agarwood formation have been reported. Here, two new TPS genes, namely, TPS9 and TPS12, were iso- lated from Aquilaria sinensis (Lour.) Gilg, and their functions were examined in Es- cherichia coli BL21(DE3), with farnesyl pyrophosphate (FPP) and geranyl pyrophos- phate (GPP) as the substrate of the corresponding enzyme activities. They were both identified as a multiproduct enzymes. After incubation with FPP, TPS9 liberated β- farnesene and cis-sesquisabinene hydrate as main products, with cedrol and another unidentified sesquiterpene as minor products. TPS12 catalyzes the formation of β- farnesene, nerolidol, -eudesmol, and hinesol. After incubation with GPP, TPS9 gen- erated citronellol and geraniol as main products, with seven minor products. TPS12 converted GPP into four monoterpenes, with citral as the main product, and three minor products. Both TPS9 and TPS12 showed much higher expression in the two major tissues emitting floral volatiles: flowers and agarwood. Further, RT-PCR anal- ysis showed TPS9 and TPS12 are typical genes mainly expressed during later stages of stress response, which is better known than that of chromone derivatives. This study will advance our understanding of agarwood formation and provide a solid theoreti- cal foundation for clarifying its mechanism in A. sinensis. [ABSTRACT FROM AUTHOR]

Background: Drought stress is a major constraint for rice production worldwide. Reproductive stage drought stress (RSDS) leads to heavy yield losses in rice. The prospecting of new donor cultivars for identification and introgression of QTLs of major effect (Quantitative trait locus) for drought tolerance is crucial for the development of drought-resilient rice varieties. Methods and results: Our study aimed to map QTLs associated with yield and its related traits under RSDS conditions. A saturated linkage map was constructed using 3417 GBS (Genotyping by sequencing) derived SNP (Single nucleotide polymorphism) markers spanning 1924.136 cM map length with an average marker density of 0.56 cM, in the F3 mapping population raised via cross made between the traditional ahu rice cultivar, Koniahu (drought tolerant) and a high-yielding variety, Disang (drought susceptible). Using the Inclusive composite interval mapping approach, 35 genomic regions governing yield and related traits were identified in pooled data from 198 F3 and F4 segregating lines evaluated for two consecutive seasons under both RSDS and irrigated control conditions. Of the 35 QTLs, 23 QTLs were identified under RSDS with LOD (Logarithm of odds) values ranging between 2.50 and 7.83 and PVE (phenotypic variance explained) values of 2.95–12.42%. Two major QTLs were found to be linked to plant height (qPH1.29) and number of filled grains per panicle (qNOG5.12) under RSDS. Five putative QTLs for grain yield namely, qGY2.00, qGY5.05, qGY6.16, qGY9.19, and qGY10.20 were identified within drought conditions. Fourteen QTL regions having ≤ 10 Mb QTL interval size were further analysed for candidate gene identification and a total of 4146 genes were detected out of these 2263 (54.63%) genes were annotated to at least one gene ontology (GO) term. Conclusion: Several QTLs associated with grain yield and yield components and putative candidate genes were identified. The putative QTLs and candidate genes identified could be employed to augment drought resilience in rice after further validation through MAS strategies. [ABSTRACT FROM AUTHOR]

Soluble N-ethylmaleimide-sensitive factor attachment protein receptors (R-SNAREs) mainly promoted the assembly of the SNARE complex to drive the final membrane fusion step of membrane transport. Previous research on R-SNAREs has mainly focused on development and growth and has rarely been involved in abiotic stress, especially in cotton. Here, we performed a comprehensive analysis of R-SNARE genes in upland cotton. In total, 51 Gh-R-SNARE genes across six phylogenetic groups were unevenly distributed on 21 chromosomes. Cis elements related to plant growth and response to abiotic stress responses were found in the promoter region of Gh-R-SNAREs. Nine Gh-R-SNARE genes were obviously upregulated under drought stress conditions by RNA-seq and qRT-PCR analysis. Among them, GhVAMP72l might be the key candidate gene contributing to drought stress tolerance in cotton by virus-induced gene silencing (VIGS) assay. These results provide valuable insights for the functional analysis of cotton RSNAREs in response to drought stress and highlight potential beneficial genes for genetic improvement and breeding in cotton. [ABSTRACT FROM AUTHOR]

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SPL transcription factors are widely involved in plant growth and development, stress response and so on. At present, there is no study on the STM(SPL with transmembrane motif)transcription factor in Dendrobium officinale. In order to explore the role of STM in the growth, development and stress response of D. officinale, four STM transcription factors were identified at the whole genome of D. officinale, and bioinformatics analysis of DoSTM gene family members were carried out. The expression of DoSTM in different tissue parts and different stress treatments were studied by reverse transcription PCR. The results were as follows:(1)DoSTM1-4 were hydrophilic proteins with SBP conserved domains and some hormone response sites.(2)Four DoSTM were expressed in root, stem and leaf, and the relative expression of DoSTM2 was the lowest in leaf; there was no significant differences in the relative expression level of DoSTM1/3/4.(3)The relative expression level of DoSTM1-4 changed significantly under low temperature, high temperature and drought stress, and the expression of DoSTM1/3/4 decreased most significantly. Therefore, it is speculated that DoSTM is related to hormone response, temperature change response and drought resistance in plants. These conclusions provide the reference for the further research on STM transcription factor of D. officinale. [ABSTRACT FROM AUTHOR]

Lipid droplet-associated proteins (LDAPs) play essential roles in tissue growth and development and in drought stress responses in plants. Cotton is an important fiber and cash crop; however, the LDAP family has not been characterized in cotton. In this study, a total of 14, six, seven, and seven genes were confirmed as LDAP family members in Gossypium hirsutum, Gossypium raimondii, Gossypium arboreum, and Gossypium stocksii, respectively. Additionally, expansion in the LDAP family occurred with the formation of Gossypium, which is mirrored in the number of LDAPs found in five Malvaceae species (Gossypioides kirkii, Bombax ceiba, Durio zibethinus, Theobroma cacao, and Corchorus capsularis), Arabidopsis thaliana, and Carica papaya. The phylogenetic tree showed that the LDAP genes in cotton can be divided into three groups (I, II, and III). The analysis of gene structure and conserved domains showed that LDAPs derived from group I (LDAP1/2/3) are highly conserved during evolution, while members from groups II and III had large variations in both domains and gene structures. The gene expression pattern analysis of LDAP genes showed that they are expressed not only in the reproductive organs (ovule) but also in vegetative organs (root, stem, and leaves). The expression level of two genes in group III, GhLDAP6_At/Dt, were significantly higher in fiber development than in other tissues, indicating that it may be an important regulator of cotton fiber development. In group III, GhLDAP2_At/Dt, especially GhLDAP2_Dt was strongly induced by various abiotic stresses. Decreasing the expression of GhLDAP2_Dt in cotton via virus-induced gene silencing increased the drought sensitivity, and the over-expression of GhLDAP2_Dt led to increased tolerance to mannitol-simulated osmotic stress at the germination stage. Thus, we conclude that GhLDAP2_Dt plays a positive role in drought tolerance. [ABSTRACT FROM AUTHOR]

Abstract Background Selecting and prioritizing candidate disease genes is necessary before conducting laboratory studies as identifying disease genes from a large number of candidate genes using laboratory methods, is a very costly and time-consuming task. There are many machine learning-based gene prioritization methods. These methods differ in various aspects including the feature vectors of genes, the used datasets with different structures, and the learning model. Creating a suitable feature vector for genes and an appropriate learning model on a variety of data with different and non-Euclidean structures, including graphs, as well as the lack of negative data are very important challenges of these methods. The use of graph neural networks has recently emerged in machine learning and other related fields, and they have demonstrated superior performance for a broad range of problems. Methods In this study, a new semi-supervised learning method based on graph convolutional networks is presented using the novel constructing feature vector for each gene. In the proposed method, first, we construct three feature vectors for each gene using terms from the Gene Ontology (GO) database. Then, we train a graph convolution network on these vectors using protein–protein interaction (PPI) network data to identify disease candidate genes. Our model discovers hidden layer representations encoding in both local graph structure as well as features of nodes. This method is characterized by the simultaneous consideration of topological information of the biological network (e.g., PPI) and other sources of evidence. Finally, a validation has been done to demonstrate the efficiency of our method. Results Several experiments are performed on 16 diseases to evaluate the proposed method's performance. The experiments demonstrate that our proposed method achieves the best results, in terms of precision, the area under the ROC curve (AUCs), and F1-score values, when compared with eight state-of-the-art network and machine learning-based disease gene prioritization methods. Conclusion This study shows that the proposed semi-supervised learning method appropriately classifies and ranks candidate disease genes using a graph convolutional network and an innovative method to create three feature vectors for genes based on the molecular function, cellular component, and biological process terms from GO data.

Cellulose synthase (CESA) is a key enzyme in the synthesis of cellulose, which plays an important role in cell wall construction and plant growth and development. In this study, seven CesA genes of P. massoniana were identified by searching the transcriptome data. Bioinformatics analysis showed that the putative CESA proteins were composed of 984–1101 amino acids, each containing the typical motifs of CESA proteins. Phylogenetic analysis showed that Transcript4609, Tran-script2643 and Transcript1263 were clustered into three groups with proteins related to regulating secondary wall synthesis, while Transcript691, Transcript1283, Transcript418 and Transcript556 were categorized into three clades with those associated with the formation of the primary cell walls. RT-qPCR analysis showed that the CesA genes were differentially expressed in different tissues, and most of the genes were induced by different abiotic stress and hormones. Transcript4609, Tran-script2643 and Transcript1263 were mainly expressed in the xylem and could respond to drought and salt stress induced by ABA, MeJA, ETH and SA hormones, indicating that these three CesA genes may play an important role in the response to abiotic stress in P. massoniana. This study revealed the possible biochemical and physiological functions of the CesA gene in P. massoniana, which can provide a basis for further exploration of the function of the CesA gene in cell wall formation and the response to external stress. [ABSTRACT FROM AUTHOR]

Particle Swarm Optimization (PSO) has a limitation of early convergence and needs to be improved to find the global optima. The main objective here is to improve its exploration capability without deteriorating the exploitation capability. For this purpose, a modified version of PSO, namely Elitist Random Swapped Particle Swarm Optimization (ERSPSO), has been proposed. The elitist (fittest) particles in the swarm guide the other particles to improve their position. To enhance exploration in the search process a swapping of the randomly selected parts of the elitist particle positions (candidate solution) has been made. Consequently, a perturbation is applied to further improve the exploration. The proposed ERSPSO has been applied to the full benchmark set of 25 functions (CEC 2005) as well as complex real life problems like 'Gene selection by sample classification'. The new variant ERSPSO has been validated by the statistical metrics, convergence plot, sensitivity analysis using convergence behaviour, p-values using Wilcoxon rank sum test and Friedman rank test. For sample classification in Gene selection, VkNN (a new variant of kNN) is proposed which performs better than kNN in classification accuracy. The combined ERSPSO-VkNN is tested in 6 microarray datasets including 4 diseases. In most of the datasets (5 datasets out of 6) ERSPSO-VkNN performs better than the state-of-the-art methods. In different datasets, the percentage of classification accuracy of ERSPSO-VkNN varies between 89.29 and 100%. Finally, a biological verification is performed to show that many of the selected genes are biologically significant according to the reporting in current literature. [ABSTRACT FROM AUTHOR]

The cytokinin two‐component signal transduction system (TCS) is involved in many biological processes, including hormone signal transduction and plant growth regulation. Although cytokinin TCS has been well characterized in Arabidopsis thaliana, its role in tomato remains elusive.In this study, we characterized the diversity and function of response regulator (RR) genes, a critical component of TCS, in tomato. In total, we identified 31 RR genes in the tomato genome. These SlRR genes were classified into three subgroups (type‐A, type‐B and type‐C).Various stress‐responsive cis‐elements were present in the tomato RR gene promoters. Their expression responses under pesticide treatment were evaluated by transcriptome analysis. Their expression under heat, cold, ABA, salinity and NaHCO3 treatments was further investigated by qRT‐PCR and complemented with the available transcription data under these treatments. Specifically, SlRR13 expression was significantly upregulated under salinity, drought, cold and pesticide stress and was downregulated under ABA treatment. SlRR23 expression was induced under salt treatment, while the transcription level of SlRR1 was increased under cold and decreased under salt stress.We also found that GATA transcription factors played a significant role in the regulation of SlRR genes. Based on our results, tomato SlRR genes are involved in responses to abiotic stress in tomato and could be implemented in molecular breeding approaches to increase resistance of tomato to environmental stresses. [ABSTRACT FROM AUTHOR]

Objective To construct and identify Nrf2 knockout mouse model. Methods A pair of male and female heterozygous(Nrf2-/+) mice were introduced to breed F1 mice. Male and female Nrf2-/+ mice from F1 generation were bred to obtain F2 generation mice. DNA was extracted from the tail tissue of mice at 5 days of age and their genotype was determined by PCR and agarose gel electrophoresis. NRF2 protein was extracted and coding gene was knocked out from the lung tissues of mice. The expression of NRF2 protein was detected by Western blot, and the identification results were confirmed laterally. Results Homozygous(Nrf2-/-) mice continued to mate and obtain homozygous mice. Three genotypes were identified when F1 was mated with F2 generation heterozygous mice: wild type(Nrf2+/+), heterozygous(Nrf2+/-) and homozygous(Nrf2-/-). The genotypes of offspring mice were successfully identified by PCR. NRF2 protein expression in lung tissue of Nrf2 knockout mice was significantly lower than that of wild-type mice（P＜0.05）. Conclusions The mouse model with Nrf2 knockout is successfully bred in this study, which provides a new experimental tool for further exploring the role and mechanism of NRF2. [ABSTRACT FROM AUTHOR]

The coronavirus disease 2019 (COVID-19), as a severe respiratory disease, affects many parts of the body, and approximately 20–85% of patients exhibit functional impairment of the senses of smell and taste, some of whom even experience the permanent loss of these senses. These symptoms are not life-threatening but severely affect patients' quality of life and increase the risk of depression and anxiety. The pathological mechanisms of these symptoms have not been fully identified. In the current study, we aimed to identify the important biomarkers at the expression level associated with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection-mediated loss of taste or olfactory ability, and we have suggested the potential pathogenetic mechanisms of COVID-19 complications. We designed a machine-learning-based approach to analyze the transcriptome of 577 COVID-19 patient samples, including 84 COVID-19 samples with a decreased ability to taste or smell and 493 COVID-19 samples without impairment. Each sample was represented by 58,929 gene expression levels. The features were analyzed and sorted by three feature selection methods (least absolute shrinkage and selection operator, light gradient boosting machine, and Monte Carlo feature selection). The optimal feature sets were obtained through incremental feature selection using two classification algorithms: decision tree (DT) and random forest (RF). The top genes identified by these multiple methods (H3-5, NUDT5, and AOC1) are involved in olfactory and gustatory impairments. Meanwhile, a high-performance RF classifier was developed in this study, and three sets of quantitative rules that describe the impairment of olfactory and gustatory functions were obtained based on the optimal DT classifiers. In summary, this study provides a new computation analysis and suggests the latent biomarkers (genes and rules) for predicting olfactory and gustatory impairment caused by COVID-19 complications. [ABSTRACT FROM AUTHOR]

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