A Novel Insight into Functional Divergence of the MST Gene Family in Rice Based on Comprehensive Expression Patterns

Genome-wide identification and investigation of monosaccharide transporter gene family based on their evolution and expression analysis under abiotic stress and hormone treatments in maize (Zea mays L.)

BACKGROUND

Monosaccharide transporter (MST) family, as a carrier for monosaccharide transport, plays an important role in carbon partitioning and widely involves in plant growth and development, stress response, and signaling transduction. However, little information on the MST family genes is reported in maize (Zea mays), especially in response to abiotic stresses. In this study, the genome-wide identification of MST family genes was performed in maize.

RESULT

A total of sixty-six putative members of MST gene family were identified and divided into seven subfamilies (including SPT, PMT, VGT, INT, pGlcT, TMT, and ERD) using bioinformatics approaches, and gene information, phylogenetic tree, chromosomal location, gene structure, motif composition, and cis-acting elements were investigated. Eight tandem and twelve segmental duplication events were identified, which played an important role in the expansion of the ZmMST family. Synteny analysis revealed the evolutionary features of MST genes in three gramineous crop species. The expression analysis indicated that most of the PMT, VGT, and ERD subfamilies members responded to osmotic and cadmium stresses, and some of them were regulated by ABA signaling, while only a few members of other subfamilies responded to stresses. In addition, only five genes were induced by NaCl stress in MST family.

CONCLUSION

These results serve to understand the evolutionary relationships of the ZmMST family genes and supply some insight into the processes of monosaccharide transport and carbon partitioning on the balance between plant growth and development and stress response in maize.

Meta-analysis of identified genomic regions and candidate genes underlying salinity tolerance in rice (Oryza sativa L.)

Rice output has grown globally, yet abiotic factors are still a key cause for worry. Salinity stress seems to have the more impact on crop production out of all abiotic stresses. Currently one of the most significant challenges in paddy breeding for salinity tolerance with the help of QTLs, is to determine the QTLs having the best chance of improving salinity tolerance with the least amount of background noise from the tolerant parent. Minimizing the size of the QTL confidence interval (CI) is essential in order to primarily include the genes responsible for salinity stress tolerance. By considering that, a genome-wide meta-QTL analysis on 768 QTLs from 35 rice populations published from 2001 to 2022 was conducted to identify consensus regions and the candidate genes underlying those regions responsible for the salinity tolerance, as it reduces the confidence interval (CI) to many folds from the initial QTL studies. In the present investigation, a total of 65 MQTLs were extracted with an average CI reduced from 17.35 to 1.66 cM including the smallest of 0.01 cM. Identification of the MQTLs for individual traits and then classifying the target traits into correlated morphological, physiological and biochemical aspects, resulted in more efficient interpretation of the salinity tolerance, identifying the candidate genes and to understand the salinity tolerance mechanism as a whole. The results of this study have a huge potential to improve the rice genotypes for salinity tolerance with the help of MAS and MABC.

Knockout of the sugar transporter OsSTP15 enhances grain yield by improving tiller number due to increased sugar content in the shoot base of rice (Oryza sativa L.)

Sugar transporter proteins (STPs) play critical roles in regulating plant stress tolerance, growth, and development. However, the role of STPs in regulating crop yield is poorly understood. This study elucidates the mechanism by which knockout of the sugar transporter OsSTP15 enhances grain yield via increasing the tiller number in rice. We found that OsSTP15 is specifically expressed in the shoot base and vascular bundle sheath of seedlings and encodes a plasma membrane-localized high-affinity glucose efflux transporter. OsSTP15 knockout enhanced sucrose and trehalose-6-phosphate (Tre6P) synthesis in leaves and improved sucrose transport to the shoot base by inducing the expression of sucrose transporters. Higher glucose, sucrose, and Tre6P contents were observed at the shoot base of stp15 plants. Transcriptome and metabolome analyses of the shoot base demonstrated that OsSTP15 knockout upregulated the expression of cytokinin (CK) synthesis- and signaling pathway-related genes and increased CK levels. These findings suggest that OsSTP15 knockout represses glucose export from the cytoplasm and simultaneously enhances sugar transport from source leaves to the shoot base by promoting the synthesis of sucrose and Tre6P in leaves. Subsequent accumulation of glucose, sucrose, and Tre6P in the shoot base promotes tillering by stimulating the CK signaling pathway.

Genome-wide analysis of sugar transporter genes in maize (Zea mays L.): identification, characterization and their expression profiles during kernel development

Sugar transporters (STs) play a crucial role in the development of maize kernels. However, very limited information about STs in maize is known. In this study, sixty-eight ZmST genes were identified from the maize genome and classified into eight major groups based on phylogenetic relationship. Gene structure analysis revealed that members within the same group shared similar exon numbers. Synteny analysis indicated that ZmSTs underwent 15 segmental duplication events under purifying selection. Three-dimensional structure of ZmSTs demonstrated the formation of a compact helix bundle composed of 8-13 trans-membrane domains. Various development-related cis-acting elements, enriched in promoter regions, were correlated with the transcriptional response of ZmSTs during kernel development. Transcriptional expression profiles exhibited expression diversity of various ZmST genes in roots, stems, leaves, tassels, cobs, embryos, endosperms and seeds tissues. During kernel development, the expression of 24 ZmST genes was significantly upregulated in the early stage of grain filling. This upregulation coincided with the sharply increased grain-filling rate observed in the early stage. Overall, our findings shed light on the characteristics of ZmST genes in maize and provide a foundation for further functional studies.

Genome-wide identification and expression profiling analysis of DIR gene family in Setaria italica

Dirigent (DIR) proteins play essential roles in regulating plant growth and development, as well as enhancing resistance to abiotic and biotic stresses. However, the whole-genome identification and expression profiling analysis of DIR gene family in millet (Setaria italica (Si)) have not been systematically understood. In this study, we conducted genome-wide identification and expression analysis of the S. italica DIR gene family, including gene structures, conserved domains, evolutionary relationship, chromosomal locations, cis-elements, duplication events, gene collinearity and expression patterns. A total of 38 SiDIR members distributed on nine chromosomes were screened and identified. SiDIR family members in the same group showed higher sequence similarity. The phylogenetic tree divided the SiDIR proteins into six subfamilies: DIR-a, DIR-b/d, DIR-c, DIR-e, DIR-f, and DIR-g. According to the tertiary structure prediction, DIR proteins (like SiDIR7/8/9) themselves may form a trimer to exert function. The result of the syntenic analysis showed that tandem duplication may play the major driving force during the evolution of SiDIRs. RNA-seq data displayed higher expression of 16 SiDIR genes in root tissues, and this implied their potential functions during root development. The results of quantitative real-time PCR (RT-qPCR) assays revealed that SiDIR genes could respond to the stress of CaCl2, CdCl, NaCl, and PEG6000. This research shed light on the functions of SiDIRs in responding to abiotic stress and demonstrated their modulational potential during root development. In addition, the membrane localization of SiDIR7/19/22 was confirmed to be consistent with the forecast. The results above will provide a foundation for further and deeper investigation of DIRs.

Starving the enemy: how plant and microbe compete for sugar on the border

As the primary energy source for a plant host and microbe to sustain life, sugar is generally exported by Sugars Will Eventually be Exported Transporters (SWEETs) to the host extracellular spaces or the apoplast. There, the host and microbes compete for hexose, sucrose, and other important nutrients. The host and microbial monosaccharide transporters (MSTs) and sucrose transporters (SUTs) play a key role in the "evolutionary arms race". The result of this competition hinges on the proportion of sugar distribution between the host and microbes. In some plants (such as Arabidopsis, corn, and rice) and their interacting pathogens, the key transporters responsible for sugar competition have been identified. However, the regulatory mechanisms of sugar transporters, especially in the microbes require further investigation. Here, the key transporters that are responsible for the sugar competition in the host and pathogen have been identified and the regulatory mechanisms of the sugar transport have been briefly analyzed. These data are of great significance to the increase of the sugar distribution in plants for improvement in the yield.

GhSTP18, a member of sugar transport proteins family, negatively regulates salt stress in cotton

The sugar transporter protein (STP) family has been shown to play important roles in plant growth, development, and stress response. However, it has not been studied in cotton compared to other major crops. In this study, we identified 90 STP genes from four cotton species, performed bioinformatic analysis, and focused on the role of GhSTP18 in salt stress. According to our results, cotton STP proteins were divided into four subgroups according to the phylogenetic tree. A synteny analysis suggested that whole-genome duplication (WGD) and segmental duplication were key drivers in the expansion of the STP gene family. The transcriptomic data analysis showed that 29 GhSTP genes exhibited sink-specific expression. Quantitative real time-polymerase chain reaction (qRT-PCR) analyses revealed that expression of GhSTP18 was induced by salt treatment, heat treatment, cold treatment, and drought treatment, and continuously increased during a salt stress time course. Notably, GhSTP18 encodes a plasma membrane-localized galactose transporter. Suppression of GhSTP18 transcription by a virus-induced gene silencing (VIGS) assay reduced sensitivity to salt stress in cotton, indicating that GhSTP18 negatively regulates plant salt tolerance. These results provide an important reference and resource for further studying and deploying STP genes for cotton improvement.

Genome-Wide Identification and an Evolution Analysis of Tonoplast Monosaccharide Transporter (TMT) Genes in Seven Gramineae Crops and Their Expression Profiling in Rice

The tonoplast monosaccharide transporter (TMT) family plays essential roles in sugar transport and plant growth. However, there is limited knowledge about the evolutionary dynamics of this important gene family in important Gramineae crops and putative function of rice TMT genes under external stresses. Here, the gene structural characteristics, chromosomal location, evolutionary relationship, and expression patterns of TMT genes were analyzed at a genome-wide scale. We identified six, three, six, six, four, six, and four TMT genes, respectively, in Brachypodium distachyon (Bd), Hordeum vulgare (Hv), Oryza rufipogon (Or), Oryza sativa ssp. japonica (Os), Sorghum bicolor (Sb), Setaria italica (Si), and Zea mays (Zm). All TMT proteins were divided into three clades based on the phylogenetic tree, gene structures, and protein motifs. The transcriptome data and qRT-PCR experiments suggested that each clade members had different expression patterns in various tissues and multiple reproductive tissues. In addition, the microarray datasets of rice indicated that different rice subspecies responded differently to the same intensity of salt or heat stress. The Fst value results indicated that the TMT gene family in rice was under different selection pressures in the process of rice subspecies differentiation and later selection breeding. Our findings pave the way for further insights into the evolutionary patterns of the TMT gene family in the important Gramineae crops and provide important references for characterizing the functions of rice TMT genes.

Molecular insights into the responses of barley to yellow mosaic disease through transcriptome analysis

BACKGROUND

Barley (Hordeum vulgare L.) represents the fourth most essential cereal crop in the world, vulnerable to barley yellow mosaic virus (BaYMV) and/or barley mild mosaic virus (BaMMV), leading to the significant yield reduction. To gain a better understanding of the mechanisms regarding barley crop tolerance to virus infection, we employed a transcriptome sequencing approach and investigated global gene expression among three barley varieties under both infected and control conditions.

RESULTS

High-throughput sequencing outputs revealed massive genetic responses, reflected by the barley transcriptome after BaYMV and/or BaMMV infection. Significant enrichments in peptidase complex and protein processing in endoplasmic reticulum were clustered through Gene ontology and KEGG analysis. Many genes were identified as transcription factors, antioxidants, disease resistance genes and plant hormones and differentially expressed between infected and uninfected barley varieties. Importantly, general response genes, variety-specific and infection-specific genes were also discovered. Our results provide useful information for future barley breeding to resist BaYMV and BaMMV.

CONCLUSIONS

Our study elucidates transcriptomic adaptations in barley response to BaYMV/BaMMV infection through high-throughput sequencing technique. The analysis outcome from GO and KEGG pathways suggests that BaYMV disease induced regulations in multiple molecular-biology processes and signalling pathways. Moreover, critical DEGs involved in defence and stress tolerance mechanisms were displayed. Further functional investigations focusing on these DEGs contributes to understanding the molecular mechanisms of plant response to BaYMV disease infection, thereby offering precious genetic resources for breeding barley varieties resistant to BaYMV disease.

Genome-Wide Identification and Expression Pattern Analysis of Dirigent Members in the Genus Oryza

Dirigent (DIR) members have been shown to play essential roles in plant growth, development and adaptation to environmental changes. However, to date, there has been no systematic analysis of the DIR members in the genus Oryza. Here, 420 genes were identified from nine rice species to have the conserved DIR domain. Importantly, the cultivated rice species Oryza sativa has more DIR family members than the wild rice species. DIR proteins in rice could be classified into six subfamilies based on phylogeny analysis. Gene duplication event analysis suggests that whole genome/segmental duplication and tandem duplication are the primary drivers for DIR genes' evolution in Oryza, while tandem duplication is the main mechanism of gene family expansion in the DIR-b/d and DIR-c subfamilies. Analysis of the RNA sequencing data indicates that OsjDIR genes respond to a wide range of environmental factors, and most OsjDIR genes have a high expression level in roots. Qualitative reverse transcription PCR assays confirmed the responsiveness of OsjDIR genes to the undersupply of mineral elements, the excess of heavy metals and the infection of Rhizoctonia solani. Furthermore, there exist extensive interactions between DIR family members. Taken together, our results shed light on and provide a research foundation for the further exploration of DIR genes in rice.

Overexpression of LjPLT3 Enhances Salt Tolerance in Lotus japonicus

Intracellular polyols are used as osmoprotectants by many plants under environmental stress. However, few studies have shown the role of polyol transporters in the tolerance of plants to abiotic stresses. Here, we describe the expression characteristics and potential functions of Lotus japonicus polyol transporter LjPLT3 under salt stress. Using LjPLT3 promoter-reporter gene plants showed that LjPLT3 was expressed in the vascular tissue of L. japonicus leaf, stem, root, and nodule. The expression was also induced by NaCl treatment. Overexpression of LjPLT3 in L. japonicus modified the growth rate and saline tolerance of the transgenic plants. The OELjPLT3 seedlings displayed reduced plant height under both nitrogen-sufficient and symbiotic nitrogen fixation conditions when 4 weeks old. The nodule number of OELjPLT3 plants was reduced by 6.7–27.4% when 4 weeks old. After exposure to a NaCl treatment in Petri dishes for 10 days, OELjPLT3 seedlings had a higher chlorophyll concentration, fresh weight, and survival rate than those in the wild type. For symbiotic nitrogen fixation conditions, the decrease in nitrogenase activity of OELjPLT3 plants was slower than that of the wild type after salt treatment. Compared to the wild type, both the accumulation of small organic molecules and the activity of antioxidant enzymes were higher under salt stress. Considering the concentration of lower reactive oxygen species (ROS) in transgenic lines, we speculate that overexpression of LjPLT3 in L. japonicus might improve the ROS scavenging system to alleviate the oxidative damage caused by salt stress, thereby increasing plant salinity tolerance. Our results will direct the breeding of forage legumes in saline land and also provide an opportunity for the improvement of poor and saline soils.

Transcriptional landscape of Brachypodium distachyon roots during interaction with Bacillus velezensis strain B26

Plant growth promoting rhizobacteria (PGPR) communicate with plants through roots. The molecular mechanism by which plants and PGPR respond to each other is not very well known. In the current study, we did RNA sequence analysis of Brachypodium distachyon Bd21-3 roots inoculated with PGPR, Bacillus velezensis strain B26. From our list of differentially expressed genes, we concentrated on transcripts that have a high possibility of participating in plant-PGPR interaction. Transcripts associated to the hormone signalling pathway were differentially expressed. We identified the upregulation of various transcripts linked to ion transporters. Reduction in expression of defense signalling genes indicated that B26 suppresses the plant defense mechanisms to begin successful interaction with roots. Transcripts associated with lignin branch of the phenylpropanoid pathway were upregulated as well, leading to more accumulation of lignin in the cell wall which enhances mechanical strength of plants. Overall, this study is an excellent resource for investigating associations between plant-PGPR interactions.

Genome-wide characterization of the inositol transporters gene family in Populus and functional characterization of PtINT1b in response to salt stress

Inositol transporters (INTs) can mediate the transmembrane transport of inositol, and play crucial roles in plant growth, development and stress resistance. However, the INT gene family in Populus has not been reported. Herein, nine INT genes were identified in the Populus trichocarpa genome and divided into three clades. Tandem duplication and whole-genome duplication events could induce the expansion of PtINT gene family. It was worth noting that PtINT1c* and 1d* formed by twice tandem gene duplication events of PtINT1b, but both had undergone partial structural loss during evolution. PtINT2_p1* and PtINT2_p2* might be originated from one INT2 gene by stop codon- and start codon-gain variants. Different members of PtINTs were localized to the plasma membrane or vacuolar membrane. PtINTs had diversified tissue expression profiles, and many members were significantly induced or suppressed after salt and drought treatments. PtINT1b was induced by drought and salinity stresses, and encoded a vacuolar inositol transporter. Overexpression of PtINT1b rendered the transgenic Arabidopsis plants more resistant to salt stress. In conclusion, this study provides valuable clues for future research on the function of PtINTs, and PtINT1b was identified as a candidate gene for genetic engineering to enhance salinity tolerance in plants.

The functional analysis of sugar transporter proteins in sugar accumulation and pollen tube growth in pummelo (Citrus grandis)

Sugar transporter proteins (STPs) play vital roles in sugar transport and allocation of carbon sources in plants. However, the evolutionary dynamics of this important gene family and their functions are still largely unknown in citrus, which is the largest fruit crop in the world. In this study, fourteen non-redundant CgSTP family members were identified in pummelo (Citrus grandis). A comprehensive analysis based on the biochemical characteristics, the chromosomal location, the exon-intron structures and the evolutionary relationships demonstrated the conservation and the divergence of CgSTPs. Moreover, CgSTP4, 11, 13, 14 were proofed to be localized in plasma membrane and have glucose transport activity in yeast. The hexose content were significantly increased with the transient overexpression of CgSTP11 and CgSTP14. In addition, antisense repression of CgSTP4 induced the shorter pollen tube length in vitro, implying the potential role of CgSTP4 in pummelo pollen tube growth. Taken together, this work explored a framework for understanding the physiological role of CgSTPs and laid a foundation for future functional studies of these members in citrus species.

Exploration of Sugar and Starch Metabolic Pathway Crucial for Pollen Fertility in Rice

Starch is the primary storage carbohydrate in mature pollen grains in many crop plants, including rice. Impaired starch accumulation causes male sterility because of the shortage of energy and building blocks for pollen germination and pollen tube growth. Thus, starch-defective pollen is applicable for inducing male sterility and hybrid rice production. Despite the importance of pollen starch, the details of the starch biosynthesis and breakdown pathway in pollen are still largely unknown. As pollen is isolated from the maternal tissue, photoassimilate transported from leaves must pass through the apoplastic space from the anther to the filial pollen, where it is stored as starch. Several sugar transporters and enzymes are involved in this process, but many are still unknown. Thus, the current review provides possible scenarios for sucrose transport and metabolic pathways that lead to starch biosynthesis and breakdown in rice pollen.

Sugar transporter TaSTP3 activation by TaWRKY19/61/82 enhances stripe rust susceptibility in wheat

Sugar efflux from host plants is essential for pathogen survival and proliferation. Sugar transporter-mediated redistribution of host sugar contributes to the outcomes of plant-pathogen interactions. However, few studies have focused on how sugar translocation is strategically manipulated during host colonization. To elucidate this question, the wheat sugar transport protein (STP) TaSTP3 responding to Puccinia striiformis f. sp. tritici (Pst) infection was characterized for sugar transport properties in Saccharomyces cerevisiae and its potential role during Pst infection by RNA interference and overexpression in wheat. In addition, the transcription factors regulating TaSTP3 expression were further determined. The results showed that TaSTP3 is localized to the plasma membrane and functions as a sugar transporter of hexose and sucrose. TaSTP3 confers enhanced wheat susceptibility to Pst, and overexpression of TaSTP3 resulted in increased sucrose accumulation and transcriptional suppression of defense-related genes. Furthermore, TaWRKY19, TaWRKY61 and TaWRKY82 were identified as positive transcriptional regulators of TaSTP3 expression. Our findings reveal that the Pst-induced sugar transporter TaSTP3 is transcriptionally activated by TaWRKY19/61/82 and facilitates wheat susceptibility to stripe rust possibly through elevated sucrose concentration, and suggest TaSTP3 as a strong target for engineering wheat resistance to stripe rust.

Genome-wide identification and expression profiling of sugar transporter genes in tobacco

Sugars are both nutrients and important signal molecules in higher plants. Sugar transporters (STs) are involved in sugar loading and unloading and facilitate sugar transport across membranes. Tobacco (Nicotiana tabacum) is a model plant and one of the most significant plants economically. In our research, 92 N. tabacum ST (NtST) genes were identified and classified into eight distinct subfamilies in the tobacco genome based on phylogenetic analysis. Exon-intron analysis revealed that each subfamily manifested closely associated gene architectural features based on a comparable number or length of exons. Tandem repetition and purifying selection were the main factors of NtST gene evolution. A search for cis-regulatory elements in the promoter sequences of the NtST gene families suggested that they are probably regulated by light, plant hormones, and abiotic stress factors. We performed a comprehensive expression study in different tissues, viarious abiotic and phytohormone stresses. The results revealed different expression patterns and the functional diversification of NtST genes. The resulting data showed that NtSFP1 was highly expressed all measured five tobacco tissues, and also regulated by the MeJA, and temperature stress. In addition, the virus-induced NibenSFP1 silencing in tobacco and detected dramatically enhanced glucose content, indicating the NtSFP1 might regulate the glucose content and involved in MeJA signaling way to response the temperature stress. In general, our findings provide useful information on understanding the roles of STs in phytohormone signaling way and abiotic stresses in N. tabacum.

Source-To-Sink Transport of Sugar and Its Role in Male Reproductive Development

Sucrose is produced in leaf mesophyll cells via photosynthesis and exported to non-photosynthetic sink tissues through the phloem. The molecular basis of source-to-sink long-distance transport in cereal crop plants is of importance due to its direct influence on grain yield-pollen grains, essential for male fertility, are filled with sugary starch, and rely on long-distance sugar transport from source leaves. Here, we overview sugar partitioning via phloem transport in rice, especially where relevant for male reproductive development. Phloem loading and unloading in source leaves and sink tissues uses a combination of the symplastic, apoplastic, and/or polymer trapping pathways. The symplastic and polymer trapping pathways are passive processes, correlated with source activity and sugar gradients. In contrast, apoplastic phloem loading/unloading involves active processes and several proteins, including SUcrose Transporters (SUTs), Sugars Will Eventually be Exported Transporters (SWEETs), Invertases (INVs), and MonoSaccharide Transporters (MSTs). Numerous transcription factors combine to create a complex network, such as DNA binding with One Finger 11 (DOF11), Carbon Starved Anther (CSA), and CSA2, which regulates sugar metabolism in normal male reproductive development and in response to changes in environmental signals, such as photoperiod.

The regulatory role of CARBON STARVED ANTHER-mediated photoperiod-dependent male fertility in rice

Environmental signals, especially daylength, play important roles in determining fertility in photoperiod-sensitive genic male sterile (PGMS) lines that are critical to sustain production of high-yielding hybrid rice (Oryza sativa) varieties. However, the mechanisms by which PGMS lines perceive changes in photoperiod and transmit those signals to elicit downstream effects are not well understood. In this study, we compared the transcriptomes from the leaves and anthers of carbon starved anther (csa), a PGMS line, to wild-type (WT) tissues under different photoperiods. Components of circadian clock in the leaves, including Circadian Clock-Associated 1 and Pseudo-Response Regulator (PRR95), played vital roles in sensing the photoperiod signals. Photoperiod signals were weakly transduced to anthers, where gene expression was mainly controlled by the CSA allele. CSA played a critical role in regulating sugar metabolism and cell wall synthesis in anthers under short-day conditions, and transcription of key genes inducing csa-directed sterility was upregulated under long-day (LD) conditions though not to WT levels, revealing a mechanism to explain the partial restoration of fertility in rice under LD conditions. Eight direct targets of CSA regulation were identified, all of which were genes involved in sugar metabolism and transport (cell wall invertases, SWEETs, and monosaccharide transporters) expressed only in reproductive tissues. Several hub genes coordinating the effects of CSA regulation were identified as critical elements determining WT male fertility and further analysis of these and related genes will reveal insights into how CSA coordinates sugar metabolism, cell wall biosynthesis, and photoperiod sensing in rice anther development.

Genome-wide identification of sugar transporter gene family in Brassicaceae crops and an expression analysis in the radish

BACKGROUND

Sugar not only is an important biomacromolecule that plays important roles in plant growth, development, and biotic and abiotic stress tolerance but also provides a skeleton for other macromolecules, such as proteins and nucleic acids. Sugar transporter proteins (STPs) play essential roles in plant sugar transport and ultimately affect the abovementioned life processes. However, the evolutionary dynamics of this important gene family in Brassicaceae crops are still largely unknown, and the functional differentiation of radish STP genes remains unclear.

RESULTS

In the present study, a comparative genomic study of STP genes in five representative Brassicaceae crops was conducted, and a total of 25, 25, 28, 36 and 49 STP genes were individually identified in Raphanus sativus (Rs), Brassica oleracea (Bo), B. rapa (Br), B. napus (Bn) and B. juncea (Bj), which were divided into four clades by phylogenetic analysis. The number of STP genes was no direct correlation with genome size and the total number of coding genes in Brassicaceae crops, and their physical and chemical properties showed no significant difference. Expression analysis showed that radish STP genes play vital roles not only in flower and seedpod development but also under heavy metal (cadmium, chromium and lead), NaCl and PEG-6000 stresses, Agrobacterium tumefaciens infection, and exogenous sugar treatment. RsSTP13.2 was significantly upregulated in the resistant radish cultivar by A. tumefaciens infection and induced by heavy metal, NaCl and PEG-6000 stress, indicating that it is involved in resistance to both biotic and abiotic stress in radish.

CONCLUSIONS

The present study provides insights into the evolutionary patterns of the STP gene family in Brassicaceae genomes and provides a theoretical basis for future functional analysis of STP genes in Brassicaceae crops.

Genome-wide exploration of sugar transporter (sweet) family proteins in Fabaceae for Sustainable protein and carbon source

Sugar transporter proteins (STPs) are membrane proteins required for sugar transport throughout cellular membranes. They plays an imperative role in sugar transmission across the plant and determinants of crop yield. However, the analysis of these important STPs Sugars Will Eventually be Exported Transporters (SWEET) family in legumes is still not well-documented and remains unclear. Therefore, the in-silico analysis of STPs has been performed to unravel their cellular, molecular, and structural composition in legume species. This study conducted a systematic search for STPs in Cajanus cajan using the Blastp algorithm to understand its molecular basis. Here, we performed a comprehensive analysis of 155 identified SWEET proteins across 12 legumes species, namely (Cajanus cajan, Glycine max, Vigna radiate, Vigna angularis, Medicago truncatula, Lupinus angustifolius, Glycine soja, Spatholobus suberectus, Cicer arietinum, Arachis ipaensis, Arachis hypogaea, Arachis duranensis). The amino acid composition and motif analysis revealed that SWEET proteins are rich in essential amino acids such as leucine, valine, isoleucine, phenylalanine, and serine while less profuse in glutamine, tryptophan, cysteine, and histidine. A total of four main conserved motifs of SWEET proteins are also highly abundant in these amino acids. The present study deciphered the details on primary physicochemical properties, secondary, tertiary structure, and phylogenetic analysis of SWEETs protein. Majorities of SWEET proteins (72.26%) are in stable form with an average instability index of 36.5%, and it comprises a higher fraction of positively charged amino acid Arg + Lys residues. Secondary structure analysis shown that these proteins are richer in alpha-helix (40%) than extended strand (30%) and random coil (25%), respectively. Furthermore, to infer their mechanism at a structural and functional level which play an essential roles in growth, development, and stress responses. This study will be useful to examine photosynthetic productivity, embryo sugar content, seed quality, and yield enhancement in Fabaceae for a sustainable source of essential amino acids and carbon source.

Global Survey, Expressions and Association Analysis of CBLL Genes in Peanut

Cystathionine γ-synthase (CGS), methionine γ-lyase (MGL), cystathionine β-lyase (CBL) and cystathionine γ-lyase (CGL) share the Cys_Met_Meta_PP domain and play important roles in plant stress response and development. In this study, we defined the genes containing the Cys_Met_Meta_PP domain (PF01053.20) as CBL-like genes (CBLL). Twenty-nine CBLL genes were identified in the peanut genome, including 12 from cultivated peanut and 17 from wild species. These genes were distributed unevenly at the ends of different chromosomes. Evolution, gene structure, and motif analysis revealed that CBLL proteins were composed of five different evolutionary branches. Chromosome distribution pattern and synteny analysis strongly indicated that whole-genome duplication (allopolyploidization) contributed to the expansion of CBLL genes. Comparative genomics analysis showed that there were three common collinear CBLL gene pairs among peanut, Arabidopsis, grape, and soybean, but no collinear CBLL gene pairs between peanut and rice. The prediction results of cis-acting elements showed that AhCBLLs, AdCBLLs, and AiCBLLs contained different proportions of plant growth, abiotic stress, plant hormones, and light response elements. Spatial expression profiles revealed that almost all AhCBLLs had significantly higher expression in pods and seeds. All AhCBLLs could respond to heat stress, and some of them could be rapidly induced by cold, salt, submergence, heat and drought stress. Furthermore, one polymorphic site in AiCBLL7 was identified by association analysis which was closely associated with pod length (PL), pod width (PW), hundred pod weight (HPW) and hundred seed weight (HSW). The results of this study provide a foundation for further research on the function of the CBLL gene family in peanut.

Tonoplast inositol transporters: Roles in plant abiotic stress response and crosstalk with other signals

Inositol transporters (INT) are thought to be the pivotal transporters for vital metabolites, in particular lipids, minerals, and sugars. These transporters play an important role in transitional metabolism and various signaling pathways in plants through regulating the transduction of messages from hormones, neurotransmitters, and immunologic and growth factors. Extensive studies have been conducted on animal INT, with promising outcomes. However, only few recent studies have highlighted the importance and complexity of INT genes in the regulation of plant physiology stages, including growth and tolerance to stress conditions. The present review summarizes the most recent findings concerning the role of INT or inositol genes in plant metabolism and the response mechanisms triggered by external stressors. Moreover, we highlight the emerging role of vacuoles and vacuolar INT in plant molecular transition and their related roles in plant growth and development. INTs are the essential mediators of inositol uptake and its intracellular broadcasting for various metabolic pathways where they play crucial roles. Additionally, we report evidence on Na⁺/inositol transporters, which until now have only been characterized in animals, as well as H⁺/inositol symporters and their kinetic functions and physiological role and suggest their roles and operating mode in plants. A more comprehensive understanding of the INT functioning system, in particular the coordinated movement of inositol and the relation between inositol generation and other important plant signaling pathways, would greatly advance the study of plant stress adaptation.

Genome-Wide Identification and Expression Profiles of 13 Key Structural Gene Families Involved in the Biosynthesis of Rice Flavonoid Scaffolds

Flavonoids are a class of key polyphenolic secondary metabolites with broad functions in plants, including stress defense, growth, development and reproduction. Oryza sativa L. (rice) is a well-known model plant for monocots, with a wide range of flavonoids, but the key flavonoid biosynthesis-related genes and their molecular features in rice have not been comprehensively and systematically characterized. Here, we identified 85 key structural gene candidates associated with flavonoid biosynthesis in the rice genome. They belong to 13 families potentially encoding chalcone synthase (CHS), chalcone isomerase (CHI), flavanone 3-hydroxylase (F3H), flavonol synthase (FLS), leucoanthocyanidin dioxygenase (LDOX), anthocyanidin synthase (ANS), flavone synthase II (FNSII), flavanone 2-hydroxylase (F2H), flavonoid 3′-hydroxylase (F3′H), flavonoid 3′,5′-hydroxylase (F3′5′H), dihydroflavonol 4-reductase (DFR), anthocyanidin reductase (ANR) and leucoanthocyanidin reductase (LAR). Through structural features, motif analyses and phylogenetic relationships, these gene families were further grouped into five distinct lineages and were examined for conservation and divergence. Subsequently, 22 duplication events were identified out of a total of 85 genes, among which seven pairs were derived from segmental duplication events and 15 pairs were from tandem duplications, demonstrating that segmental and tandem duplication events play important roles in the expansion of key flavonoid biosynthesis-related genes in rice. Furthermore, these 85 genes showed spatial and temporal regulation in a tissue-specific manner and differentially responded to abiotic stress (including six hormones and cold and salt treatments). RNA-Seq, microarray analysis and qRT-PCR indicated that these genes might be involved in abiotic stress response, plant growth and development. Our results provide a valuable basis for further functional analysis of the genes involved in the flavonoid biosynthesis pathway in rice.

Genome-Wide Identification and Analysis of the Metallothionein Genes in Oryza Genus

Metallothionein (MT) proteins are low molecular mass, cysteine-rich, and metal-binding proteins that play an important role in maintaining metal homeostasis and stress response. However, the evolutionary relationships and functional differentiation of MT in the Oryza genus remain unclear. Here we identified 53 MT genes from six Oryza genera, including O. sativa ssp. japonica, O. rufipogon, O. sativa ssp. indica, O. nivara, O. glumaepatula, and O. barthii. The MT genes were clustered into four groups based on phylogenetic analysis. MT genes are unevenly distributed on chromosomes; almost half of the MT genes were clustered on chromosome 12, which may result from a fragment duplication containing the MT genes on chromosome 12. Five pairs of segmental duplication events and ten pairs of tandem duplication events were found in the rice MT family. The Ka/Ks values of the fifteen duplicated MT genes indicated that the duplicated MT genes were under a strong negative selection during evolution. Next, combining the promoter activity assay with gene expression analysis revealed different expression patterns of MT genes. In addition, the expression of OsMT genes was induced under different stresses, including NaCl, CdCl₂, ABA, and MeJ treatments. Additionally, we found that OsMT genes were mainly located in chloroplasts. These results imply that OsMT genes play different roles in response to these stresses. All results provide important insights into the evolution of the MT gene family in the Oryza genus, and will be helpful to further study the function of MT genes.

Genome-Wide Identification, Expansion Mechanism and Expression Profiling Analysis of GLABROUS1 Enhancer-Binding Protein (GeBP) Gene Family in Gramineae Crops

The GLABROUS1 enhancer-binding protein (GeBP) gene family encodes a typical transcription factor containing a noncanonical Leucine (Leu-)-zipper motif that plays an essential role in regulating plant growth and development, as well as responding to various stresses. However, limited information on the GeBP gene family is available in the case of the Gramineae crops. Here, 125 GeBP genes from nine Gramineae crops species were phylogenetically classified into four clades using bioinformatics analysis. Evolutionary analyses showed that whole genome duplication (WGD) and segmental duplication play important roles in the expansion of the GeBP gene family. The various gene structures and protein motifs revealed that the GeBP genes play diverse functions in plants. In addition, the expression profile analysis of the GeBP genes showed that 13 genes expressed in all tested organs and stages of development in rice, with especially high levels of expression in the leaf, palea, and lemma. Furthermore, the hormone- and metal-induced expression patterns showed that the expression levels of most genes were affected by various biotic stresses, implying that the GeBP genes had an important function in response to various biotic stresses. Furthermore, we confirmed that OsGeBP11 and OsGeBP12 were localized to the nucleus through transient expression in the rice protoplast, indicating that GeBPs function as transcription factors to regulate the expression of downstream genes. This study provides a comprehensive understanding of the origin and evolutionary history of the GeBP genes family in Gramineae, and will be helpful in a further functional characterization of the GeBP genes.

A synthetic cytokinin influences the accumulation of leaf soluble sugars and sugar transporters, and enhances the drought adaptability in rice

Oryza sativa cv. PTT1 (Pathumthani1) was treated with phenyl-urea-based synthetic cytokinin under drought stress. Soluble sugar contents were examined in rice flag leaves at tillering and grain-filling stages. The same leaf samples were used to analyze the differential abundance intensities of proteins related to metabolism and transport of soluble sugars, and the process of senescence. The results showed drought-induced accumulation of hexose sugars (glucose and fructose) in rice flag leaves, which could be corroborated with enhanced accumulation of MST8 under drought stress. On the other hand, cytokinin-treated plants maintained the normal contents of hexose sugar in their flag leaves under drought stress, alike well-watered plants. In the case of sucrose, cytokinin treatment reduced its accumulation at tillering stage, but the results were reversed at the grain-filling stage, where the cytokinin-treated plants maintained significantly higher contents of sucrose under drought stress. Growth stage dependent variations in sucrose contents corroborated with the accumulation of SPS (SPS1, SPS2, and SPS5) proteins, implicated in sucrose biosynthesis. In our study, among the proteins involved in sucrose transport, SUT1 transporter was induced by drought stress at both the growth stages, whereas SUT2 transporter accumulated equally in all the treatments. However, cytokinin treatment reversed the effect of drought on the accumulation of SUT1. Similarly, SWEET5, and SWEET13 proteins, which were induced by drought stress treatment, were inhibited by cytokinin treatment. However, the accumulation SWEET6, SWEET7, and SWEET15 was not influenced by the treatment of cytokinin in the flag leaves of rice. In addition, cytokinin treatment reduced the leaf wilting, enhanced the fresh weight and grain yield, and curtailed the accumulation of proteins involved in drought-induced senescence. In conclusion, the cytokinin treatment had a positive agro-economic impact on the rice plants and provided better drought adaptability.

Differential regulation of drought stress by biological membrane transporters and channels

Stress arising due to abiotic factors affects the plant's growth and productivity. Among several existing abiotic stressors like cold, drought, heat, salinity, heavy metal, etc., drought condition tends to affect the plant's growth by inducing two-point effect, i.e., it disturbs the water balance as well as induces toxicity by disturbing the ion homeostasis, thus hindering the growth and productivity of plants, and to survive under this condition, plants have evolved several transportation systems that are involved in regulating the drought stress. The role of membrane transporters has gained interest since genetic engineering came into existence, and they were found to be the important modulators for tolerance, avoidance, ion movements, stomatal movements, etc. Here in this comprehensive review, we have discussed the role of transporters (ABA, protein, carbohydrates, etc.) and channels that aids in withstanding the drought stress as well as the regulatory role of transporters involved in osmotic adjustments arising due to drought stress. This review also provides a gist of hydraulic conductivity by roots that are involved in regulating the drought stress.

Plant sugars: Homeostasis and transport under abiotic stress in plants

The sessile nature of plants' life is endowed with a highly evolved defense system to adapt and survive under environmental extremes. To combat such stresses, plants have developed complex and well-coordinated molecular and metabolic networks encompassing genes, metabolites, and acclimation responses. These modulate growth, photosynthesis, osmotic maintenance, and carbohydrate homeostasis. Under a given stress condition, sugars act as key players in stress perception, signaling, and are a regulatory hub for stress-mediated gene expression ensuring responses of osmotic adjustment, scavenging of reactive oxygen species, and maintaining the cellular energy status through carbon partitioning. Several sugar transporters are known to regulate carbohydrate partitioning and key signal transduction steps involved in the perception of biotic and abiotic stresses. Sugar transporters such as SUGARS WILL EVENTUALLY BE EXPORTED TRANSPORTER (SWEETs), SUCROSE TRANSPORTERS (SUTs), and MONOSACCHARIDE TRANSPORTERS (MSTs) are involved in sugar loading and unloading as well as long-distance transport (source to sink) besides orchestrating oxidative and osmotic stress tolerance. It is thus necessary to understand the structure-function relationship of these sugar transporters to fine-tune the abiotic stress-modulated responses. Advances in genomics have unraveled many sugars signaling components playing a key role in cross-talk in abiotic stress pathways. An integrated omics approach may aid in the identification and characterization of sugar transporters that could become targets for developing stress tolerance plants to mitigate climate change effects and improve crop yield. In this review, we have presented an up-to-date analysis of the sugar homeostasis under abiotic stresses as well as describe the structure and functions of sugar transporters under abiotic stresses.

Comprehensive Analysis of Evolutionary Characterization and Expression for Monosaccharide Transporter Family Genes in Nelumbo nucifera

Sugar transporters, an important class of transporters for sugar function, regulate many processes associated with growth, maturation, and senescence processes in plants. In this study, a total of 35 NuMSTs were identified in the Nelumbo nucifera genome and grouped by conserved domains and phylogenetic analysis. Additionally, we identified 316 MST genes in 10 other representative plants and performed a comparative analysis with Nelumbo nucifera genes, including evolutionary trajectory, gene duplication, and expression pattern. A large number of analyses across plants and algae indicated that the MST family could have originated from STP and Glct, expanding to form STP and SFP by dispersed duplication. Finally, a quantitative real-time polymerase chain reaction and cis-element analysis showed that some of them may be regulated by plant hormones (e.g., abscisic acid), biotic stress factors, and abiotic factors (e.g., drought, excessive cold, and light). We found that under the four abiotic stress conditions, only NuSTP5 expression was upregulated, generating a stress response, and ARBE and LTR were present in NuSTP5. In summary, our findings are significant for understanding and exploring the molecular evolution and mechanisms of NuMSTs in plants.

OsClo5 functions as a transcriptional co-repressor by interacting with OsDi19-5 to negatively affect salt stress tolerance in rice seedlings

Caleosins constitute a small protein family with one calcium-binding EF-hand motif. They are involved in the regulation of development and response to abiotic stress in plants. Nevertheless, how they impact salt stress tolerance in rice is largely unknown. Thereby, biochemical and molecular genetic experiments were carried out, and the results revealed that OsClo5 was able to bind calcium and phospholipids in vitro and localized in the nucleus and endoplasmic reticulum in rice protoplasts. At the germination and early seedlings stages, overexpression transgenic lines and T-DNA mutant lines exhibited reduced and increased tolerance to salt stress, respectively, compared with the wild-type. Yeast two-hybrid, bimolecular fluorescence complementation and in vitro pull-down assays demonstrated that the EF-hand motif of OsClo5 was essential for the interactions with itself and OsDi19-5. Yeast one-hybrid, electrophoretic migration shift and dual-luciferase reporter assays identified OsDi19-5 as a transcriptional repressor via the TACART cis-element in the promoters of two salt stress-related target genes, OsUSP and OsMST. In addition, OsClo5 enhanced the inhibitory effect of OsDi19-5 in the tobacco transient system, which was confirmed by qRT-PCR analysis in rice seedlings under salt stress. The collective results deepen the understanding of the molecular mechanism underlying the roles of caleosin in the salt stress response. These findings will also inform efforts to improve salt tolerance of rice.

Interpopulation differences of retroduplication variations (RDVs) in rice retrogenes and their phenotypic correlations

Retroduplication variation (RDV), a type of retrocopy polymorphism, is considered to have essential biological significance, but its effect on gene function and species phenotype is still poorly understood. To this end, we analyzed the retrocopies and RDVs in 3,010 rice genomes. We calculated the RDV frequencies in the genome of each rice population; detected the mutated, ancestral and expressed retrogenes in rice genomes; and analyzed their RDV influence on rice phenotypic traits. Collectively, 73 RDVs were identified, and 14 RDVs in ancestral retrogenes can significantly affect rice phenotypes. Our research reveals that RDV plays an important role in rice migration, domestication and evolution. We think that RDV is a good molecular breeding marker candidate. To our knowledge, this is the first study on the relationship between retrogene function, expression, RDV and species phenotype.

Early Response to Dehydration Six-Like Transporter Family: Early Origin in Streptophytes and Evolution in Land Plants

Carbon management by plants involves the activity of many sugar transporters, which play roles in sugar subcellular partitioning and reallocation at the whole organism scale. Among these transporters, the early response to dehydration six-like (ESL) monosaccharide transporters (MSTs) are still poorly characterized although they represent one of the largest sugar transporter subfamilies. In this study, we used an evolutionary genomic approach to infer the evolutionary history of this multigenic family. No ESL could be identified in the genomes of rhodophytes, chlorophytes, and the brown algae Ectocarpus siliculosus, whereas one ESL was identified in the genome of Klebsormidium nitens providing evidence for the early emergence of these transporters in Streptophytes. A phylogenetic analysis using the 519 putative ESL proteins identified in the genomes of 47 Embryophyta species and being representative of the plant kingdom has revealed that ESL protein sequences can be divided into three major groups. The first and second groups originated in the common ancestor of all spermaphytes [ζ: 340 million years ago (MYA)] and of angiosperms (ε: 170-235 MYA), respectively, and the third group originated before the divergence of rosids and asterids (γ/1R: 117 MYA). In some eudicots (Vitales, Malpighiales, Myrtales, Sapindales, Brassicales, Malvales, and Solanales), the ESL family presents remarkable expansions of gene copies associated with tandem duplications. The analysis of non-synonymous and synonymous substitutions for the dN/dS ratio of the ESL copies of the genus Arabidopsis has revealed that ESL genes are evolved under a purifying selection even though the progressive increase of dN/dS ratios in the three groups suggests subdiversification phenomena. To further explore the possible acquisition of novel functions by ESL MSTs, we identified the gene structure and promoter cis-acting elements for Arabidopsis thaliana ESL genes. The expression profiling of Arabidopsis ESL unraveled some gene copies that are almost constitutively expressed, whereas other gene copies display organ-preferential expression patterns. This study provides an evolving framework to better understand the roles of ESL transporters in plant development and response to environmental constraints.

Micro-Evolution Analysis Reveals Diverged Patterns of Polyol Transporters in Seven Gramineae Crops

Polyol transporters (PLTs), also called polyol/monosaccharide transporters, is of significance in determining plant development and sugar transportation. However, the diverged evolutionary patterns of the PLT gene family in Gramineae crops are still unclear. Here a micro-evolution analysis was performed among the seven Gramineae representative crops using whole-genome sequences, i.e., Brachypodium distachyon (Bd), Hordeum vulgare (Hv), Oryza rufipogon (Or), Oryza sativa (Os), Sorghum bicolor (Sb), Setaria italica (Si), and Zea mays (Zm), leading to the identification of 12, 11, 12, 15, 20, 24, and 20 PLT genes, respectively. In this study, all PLT genes were divided into nine orthogroups (OGs). However, the number of PLT genes and the distribution of PLT OGs were not the same in these seven Gramineae species, and different OGs were also subject to different purification selection pressures. These results indicated that the PLT OGs of the PLT gene family have been expanded or lost unevenly in all tested species. Then, our results of gene duplication events confirmed that gene duplication events promoted the expansion of the PLT gene family in some Gramineous plants, namely, Bd, Or, Os, Si, Sb, and Zm, but the degree of gene family expansion, the type of PLT gene duplication, and the differentiation time of duplicate gene pairs varied greatly among these species. In addition, the sequence alignment and the internal repeat analysis of all PLTs protein sequences implied that the PLT protein sequences may originate from an internal repeat duplication of an ancestral six transmembrane helical units. Besides that, the protein motifs result highlighted that the PLT protein sequences were highly conserved, whereas the functional differentiation of the PLT genes was characterized by different gene structures, upstream elements, as well as co-expression analysis. The gene expression analysis of rice and maize showed that the PLT genes have a wide range of expression patterns, suggesting diverse biological functions. Taken together, our finding provided a perspective on the evolution differences and the functional characterizations of PLT genes in Gramineae representative crops.

Genome-Wide Identification and Expression Profiling of Monosaccharide Transporter Genes Associated with High Harvest Index Values in Rapeseed (Brassica napus L.)

Sugars are important throughout a plant’s lifecycle. Monosaccharide transporters (MST) are essential sugar transporters that have been identified in many plants, but little is known about the evolution or functions of MST genes in rapeseed (Brassica napus). In this study, we identified 175 MST genes in B. napus, 87 in Brassica oleracea, and 83 in Brassica rapa. These genes were separated into the sugar transport protein (STP), polyol transporter (PLT), vacuolar glucose transporter (VGT), tonoplast monosaccharide transporter (TMT), inositol transporter (INT), plastidic glucose transporter (pGlcT), and ERD6-like subfamilies, respectively. Phylogenetic and syntenic analysis indicated that gene redundancy and gene elimination have commonly occurred in Brassica species during polyploidization. Changes in exon-intron structures during evolution likely resulted in the differences in coding regions, expression patterns, and functions seen among BnMST genes. In total, 31 differentially expressed genes (DEGs) were identified through RNA-seq among materials with high and low harvest index (HI) values, which were divided into two categories based on the qRT-PCR results, expressed more highly in source or sink organs. We finally identified four genes, including BnSTP5, BnSTP13, BnPLT5, and BnERD6-like14, which might be involved in monosaccharide uptake or unloading and further affect the HI of rapeseed. These findings provide fundamental information about MST genes in Brassica and reveal the importance of BnMST genes to high HI in B. napus.

Genome-wide identification, expression, and association analysis of the monosaccharide transporter (MST) gene family in peanut (Arachis hypogaea L.)

In this study, we reported the genome-wide analysis of the whole sugar transporter gene family of a legume species, peanut (Arachis hypogaea L.), including the chromosome locations, gene structures, phylogeny, expression patterns, as well as comparative genomic analysis with Arabidopsis, rice, grape, and soybean. A total of 76 AhMST genes (AhMST1-76) were identified from the peanut genome and located unevenly in 20 chromosomes. Phylogeny analysis indicated that the AhMSTs can be divided into eight groups including two undefined peanut-specific groups. Transcriptional profiles revealed that many AhMST genes showed tissue-specific expression, the majority of the AhMST genes mainly expressed in sink organs and floral organ of peanut. Chromosome distribution pattern and synteny analysis strongly indicated that genome-wide segmental and tandem duplication contributed to the expansion of peanut MST genes. Four common orthologs (AhMST9, AhMST13, AhMST40, and AhMST43) between peanut and the other four species were identified by comparative genomic analysis, which might play important roles in maintaining the growth and development of plant. Furthermore, four polymorphic sites in AhMST11, AhMST13, and AhMST60 were significantly correlated with hundred pod weight (HPW) and hundred seed weight (HSW) by association analysis. In a word, these results will provide new insights for understanding the functions of AhMST family members to sugar transporting and the potential for yield improvement in peanut.

TaSTP13 contributes to wheat susceptibility to stripe rust possibly by increasing cytoplasmic hexose concentration

BACKGROUND

Biotrophic fungi make intimate contact with host cells to access nutrients. Sugar is considered as the main carbon sources absorbed from host cells by pathogens. Partition, exchanges and competition for sugar at plant-pathogen interfaces are controlled by sugar transporters. Previous studies have indicated that the leaf rust resistance (Lr) gene Lr67, a natural mutation of TaSTP13 encoding a wheat sugar transport protein, confers partial resistance to all three wheat rust species and powdery mildew possibly due to weakened sugar transport activity of TaSTP13 by heterodimerization. However, one major problem that remains unresolved concerns whether TaSTP13 participates in wheat susceptibility to rust and mildew.

RESULTS

In this study, expression of TaSTP13 was highly induced in wheat leaves challenged by Puccinia striiformis f. sp. tritici (Pst) and certain abiotic treatments. TaSTP13 was localized in the plasma membrane and functioned as homooligomers. In addition, a functional domain for its transport activity was identified in yeast. Suppression of TaSTP13 reduced wheat susceptibility to Pst by barley stripe mosaic virus-induced gene silencing (VIGS). While overexpression of TaSTP13 promoted Arabidopsis susceptibility to powdery mildew and led to increased glucose accumulation in the leaves.

CONCLUSIONS

These results indicate that TaSTP13 is transcriptionally induced and contributes to wheat susceptibility to stripe rust, possibly by promoting cytoplasmic hexose accumulation for fungal sugar acquisition in wheat-Pst interactions.

TaSTP13 contributes to wheat susceptibility to stripe rust possibly by increasing cytoplasmic hexose concentration

BACKGROUND

Biotrophic fungi make intimate contact with host cells to access nutrients. Sugar is considered as the main carbon sources absorbed from host cells by pathogens. Partition, exchanges and competition for sugar at plant-pathogen interfaces are controlled by sugar transporters. Previous studies have indicated that the leaf rust resistance (Lr) gene Lr67, a natural mutation of TaSTP13 encoding a wheat sugar transport protein, confers partial resistance to all three wheat rust species and powdery mildew possibly due to weakened sugar transport activity of TaSTP13 by heterodimerization. However, one major problem that remains unresolved concerns whether TaSTP13 participates in wheat susceptibility to rust and mildew.

RESULTS

In this study, expression of TaSTP13 was highly induced in wheat leaves challenged by Puccinia striiformis f. sp. tritici (Pst) and certain abiotic treatments. TaSTP13 was localized in the plasma membrane and functioned as homooligomers. In addition, a functional domain for its transport activity was identified in yeast. Suppression of TaSTP13 reduced wheat susceptibility to Pst by barley stripe mosaic virus-induced gene silencing (VIGS). While overexpression of TaSTP13 promoted Arabidopsis susceptibility to powdery mildew and led to increased glucose accumulation in the leaves.

CONCLUSIONS

These results indicate that TaSTP13 is transcriptionally induced and contributes to wheat susceptibility to stripe rust, possibly by promoting cytoplasmic hexose accumulation for fungal sugar acquisition in wheat-Pst interactions.

Characterization and Functional Divergence of a Novel DUF668 Gene Family in Rice Based on Comprehensive Expression Patterns

The domain of unknown function (DUF) superfamily encodes proteins of unknown functions in plants. Among them, DUF668 family members in plants possess a 29 amino-acid conserved domain, and this family has not been described previously. Here, we report this plant-specific novel DUF668 gene family containing 12 OsDUF668 genes in rice (Oryza sativa) and 91 DUF668s for the other seven plant species. In our study, DUF668 genes were present in both dicot and monocot plants, indicating that DUF668 is a conserved gene family that originated by predating the dicot–monocot divergence. Based on the gene structure and motif composition, the DUF668 family consists of two distinct clades, I and II in the phylogenetic tree. Remarkably, OsDUF668 genes clustered on the chromosomes merely show close phylogenetic relationships, suggesting that gene duplications or collinearity seldom happened. Cis-elements prediction display that over 80% of DUF668s contain phytohormone and light responsiveness factors. Further comprehensive experimental analyses of the OsDUF668 family are implemented in 22 different tissues, five hormone treatments, seven environmental factor stresses, and two pathogen-defense related stresses. The OsDUF668 genes express ubiquitously in analyzed rice tissues, and seven genes show tissue-specific high expression profiles. All OsDUF668s respond to drought, and some of Avr9/Cf-9 rapidly elicited genes resist to salt, wound, and rice blast with rapidly altered expression patterns. These findings imply that OsDUF668 is essential for drought-enduring and plant defense. Together, our results bring the important role of the DUF668 gene family in rice development and fitness to the fore.

Sugar Transporter Proteins (STPs) in Gramineae Crops: Comparative Analysis, Phylogeny, Evolution, and Expression Profiling

Sugar transporter proteins (STPs), such as H⁺/sugar symporters, play essential roles in plants’ sugar transport, growth, and development, and possess an important potential to enhance plants’ performance of multiple agronomic traits, especially crop yield and stress tolerance. However, the evolutionary dynamics of this important gene family in Gramineae crops are still not well-documented and functional differentiation of rice STP genes remain unclear. To address this gap, we conducted a comparative genomic study of STP genes in seven representative Gramineae crops, which are Brachypodium distachyon (Bd), Hordeum vulgare (Hv), Setaria italica (Si), Sorghum bicolor (Sb), Zea mays (Zm), Oryza rufipogon (Or), and Oryza sativa ssp. japonica (Os). In this case, a total of 177 STP genes were identified and grouped into four clades. Of four clades, the Clade I, Clade III, and Clade IV showed an observable number expansion compared to Clade II. Our results of identified duplication events and divergence time of duplicate gene pairs indicated that tandem, Whole genome duplication (WGD)/segmental duplication events play crucial roles in the STP gene family expansion of some Gramineae crops (expect for Hv) during a long-term evolutionary process. However, expansion mechanisms of the STP gene family among the tested species were different. Further selective force studies revealed that the STP gene family in Gramineae crops was under purifying selective forces and different clades and orthologous groups with different selective forces. Furthermore, expression analysis showed that rice STP genes play important roles not only in flower organs development but also under various abiotic stresses (cold, high-temperature, and submergence stresses), blast infection, and wounding. The current study highlighted the expansion and evolutionary patterns of the STP gene family in Gramineae genomes and provided some important messages for the future functional analysis of Gramineae crop STP genes.

Expansion and Evolutionary Patterns of Glycosyltransferase Family 8 in Gramineae Crop Genomes and Their Expression under Salt and Cold Stresses in Oryza sativa ssp. japonica

Plant cell walls play a fundamental role in several ways, providing structural support for cells, resistance against pathogens and facilitating the communication between cells. The glycosyltransferase family 8 (GT8) is involved in the formation of the plant cell wall. However, the evolutionary relationship and the functional differentiation of this important gene family remain obscure in Gramineae crop genomes. In the present investigation, we identified 269 GT8 genes in the seven Gramineae representative crop genomes, namely, 33 in Hordeum vulgare, 37 in Brachypodium distachyon, 40 in Oryza sativa ssp. japonica, 41 in Oryza rufipogon, 36 in Setaria italica, 37 in Sorghum bicolor, and 45 in Zea mays. Phylogenetic analysis suggested that all identified GT8 proteins belonged to seven subfamilies: galacturonosyltransferase (GAUT), galacturonosyltransferase-like (GATL), GATL-related (GATR), galactinol synthase (GolS), and plant glycogenin-like starch initiation proteins A (PGSIP-A), PGSIP-B, and PGSIP-C. We estimated that the GAUT subfamily might be further divided into four subgroups (I–IV) due to differentiation of gene structures and expression patterns. Our orthogroup analysis identified 22 orthogroups with different sizes. Of these orthogroups, several orthogroups were lost in some species, such as S. italica and Z. mays. Moreover, lots of duplicate pairs and collinear pairs were discovered among these species. These results indicated that multiple duplication modes led to the expansion of this important gene family and unequal loss of orthogroups and subfamilies might have happened during the evolutionary process. RNA-seq, microarray analysis, and qRT-PCR analyses indicated that GT8 genes are critical for plant growth and development, and for stresses responses. We found that OsGolS1 was significantly up-regulated under salt stress, while OsGAUT21, OsGATL2, and OsGATL5 had remarkable up-regulation under cold stress. The current study highlighted the expansion and evolutionary patterns of the GT8 gene family in these seven Gramineae crop genomes and provided potential candidate genes for future salt- and cold- resistant molecular breeding studies in O. sativa.

Comparative Genomic and Transcriptomic Analysis Suggests the Evolutionary Dynamic of GH3 Genes in Gramineae Crops

Glycoside hydrolase 3 (GH3) gene family belongs to auxin-responsive gene families and is tightly linked with hormone homeostasis and signaling pathways. However, our knowledge about the evolutionary dynamic of GH3 genes in Gramineae crops is limited. In this study, a comparative genomic and transcriptomic analysis was conducted to study evolutionary patterns and the driving selective forces of GH3 gene family in six representative Gramineae crops, namely, Setaria italica (Si), Zea mays (Zm), Sorghum bicolor (Sb), Hordeum vulgare (Hv), Brachypodium distachyon (Bd), and Oryza sativa ssp. japonica (Os). A total of 17, 13, 11, 9, 8, and 11 GH3 proteins (GH3s) were identified in Si, Zm, Sb, Hv, Bd, and Os, respectively. Phylogenetic, conserved motif, and gene structural analyses could divide all GH3s into two groups (I and II), and all GH3s consisted of seven orthogroups (Ors) on the basis of Or identification result. We further found that genes in the same Or showed similar sequence and structural features, whereas genes in the same groups exhibited intrinsic differences in exon numbers and intron lengths. These results revealed GH3 genes in the same groups have been differentiated. Obvious differences in total numbers of GH3 genes, Ors, and duplication events among these six tested Gramineae crops reflected lineage-specific expansions and homologous gene loss/gain of GH3 gene family during the evolutionary process. In addition, selective force and expression analyses indicated that all GH3 genes were constrained by strong purifying selection, and GH3 genes in conserved Ors showed higher expression levels than that in unconserved Ors. The current study highlighted different evolutionary patterns of GH3 genes in Gramineae crops resulted from different evolutionary rates and duplication events and provided a vital insight into the functional divergence of GH3 genes.