Genome-wide systematic survey and analysis of the RNA helicase gene family and their response to abiotic stress in sweetpotato.

Sweetpotato (Ipomoea batatas (L.) Lam.) holds a crucial position as one of the staple foods globally, however, its yields are frequently impacted by environmental stresses. In the realm of plant evolution and the response to abiotic stress, the RNA helicase family assumes a significant role. Despite this importance, a comprehensive understanding of the RNA helicase gene family in sweetpotato has been lacking. Therefore, we conducted a comprehensive genome-wide analysis of the sweetpotato RNA helicase family, encompassing aspects such as chromosome distribution, promoter elements, and motif compositions. This study aims to shed light on the intricate mechanisms underlying the stress responses and evolutionary adaptations in sweetpotato, thereby facilitating the development of strategies for enhancing its resilience and productivity. 300 RNA helicase genes were identified in sweetpotato and categorized into three subfamilies, namely IbDEAD, IbDEAH and IbDExDH. The collinearity relationship between the sweetpotato RNA helicase gene and 8 related homologous genes from other species was explored, providing a reliable foundation for further study of the sweetpotato RNA helicase gene family's evolution. Furthermore, through RNA-Seq analysis and qRT-PCR verification, it was observed that the expression of eight RNA helicase genes exhibited significant responsiveness to four abiotic stresses (cold, drought, heat, and salt) across various tissues of ten different sweetpotato varieties. Sweetpotato transgenic lines overexpressing the RNA helicase gene IbDExDH96 were generated using A.rhizogenes-mediated technology. This approach allowed for the preliminary investigation of the role of sweetpotato RNA helicase genes in the response to cold stress. Notably, the promoters of RNA helicase genes contained numerous cis-acting elements associated with temperature, hormone, and light response, highlighting their crucial role in sweetpotato abiotic stress response.

Systematic identification and expression analysis of bHLH gene family reveal their relevance to abiotic stress response and anthocyanin biosynthesis in sweetpotato.

BACKGROUND: bHLH transcription factors play significant roles in regulating plant growth and development, stress response, and anthocyanin biosynthesis. Sweetpotato is a pivotal food and industry crop, but little information is available on sweetpotato bHLH genes. RESULTS: Herein, 227 putative IbbHLH genes were defined on sweetpotato chromosomes, and fragment duplications were identified as the dominant driving force for IbbHLH expansion. These IbbHLHs were divided into 26 subfamilies through phylogenetic analysis, as supported by further analysis of exon-intron structure and conserved motif composition. The syntenic analysis between IbbHLHs and their orthologs from other plants depicted evolutionary relationships of IbbHLHs. Based on the transcriptome data under salt stress, the expression of 12 IbbHLHs was screened for validation by qRT-PCR, and differential and significant transcriptions under abiotic stress were detected. Moreover, IbbHLH123 and IbbHLH215, which were remarkably upregulated by stress treatments, had obvious transactivation activity in yeasts. Protein interaction detections and yeast two-hybrid assays suggested an intricate interaction correlation between IbbHLHs. Besides, transcriptome screening revealed that multiple IbbHLHs may be closely related to anthocyanin biosynthesis based on the phenotype (purple vs. white tissues), which was confirmed by subsequent qRT-PCR analysis. CONCLUSIONS: These results shed light on the promising functions of sweetpotato IbbHLHs in abiotic stress response and anthocyanin biosynthesis.

The unique sweet potato NAC transcription factor IbNAC3 modulates combined salt and drought stresses.

Plants often simultaneously experience combined stresses rather than a single stress, causing more serious damage, but the underlying mechanisms remain unknown. Here, we identified the stress-induced IbNAC3 from sweet potato (Ipomoea batatas) as a nucleus-localized transcription activator. IbNAC3 contains a unique activation domain whose MKD sequence confers transactivation activities to multiple other TFs and is essential for the activated expression of downstream target genes. Ectopic expression of IbNAC3 conferred tolerance to single and combined salt and drought stresses in Arabidopsis (Arabidopsis thaliana), and a group of NAM, ATAF1/2, and CUC2 (NAC) TFs, including ANAC011, ANAC072, ANAC083, ANAC100, and NAP, interacted with IbNAC3, and the specific domains responsible for each interaction varied. Intriguingly, IbNAC3 repressed the interaction among the five NACs, and knockout or mutation of ANAC011 and ANAC072 dramatically impaired combined stress tolerance. IbNAC3-ANAC072 and IbNAC3-NAP modules synergistically activated the MICROTUBULE-RELATED E3 LIGASE57 (MREL57) gene. Consistently, mutation of MREL57 and overexpression of WAVE-DAM-PENED2-LIKE7, encoding a target protein of MREL57, both remarkably impaired combined stress tolerance. Moreover, transgenic plants displayed abscisic acid (ABA) hyposensitivity by directly promoting the transcription of ENHANCED RESPONSE TO ABA 1, a key negative regulator of ABA signaling. The data unravel the unique IbNAC3 TF functions as a pivotal component in combined stress tolerance by integrating multiple regulatory events and ubiquitin pathways, which is essential for developing high-tolerant plants in natural environments.

Role of Soil and Foliar-Applied Carbon Dots in Plant Iron Biofortification and Cadmium Mitigation by Triggering Opposite Iron Signaling in Roots.

In China, iron (Fe) availability is low in most soils but cadmium (Cd) generally exceeds regulatory soil pollution limits. Thus, biofortification of Fe along with mitigation of Cd in edible plant parts is important for human nutrition and health. Carbon dots (CDs) are considered as potential nanomaterials for agricultural applications. Here, Salvia miltiorrhiza-derived CDs are an efficient modulator of Fe, manganese (Mn), zinc (Zn), and Cd accumulation in plants. CDs irrigation (1 mg mL-1 , performed every week starting at the jointing stage for 12 weeks) increased Fe content by 18% but mitigated Cd accumulation by 20% in wheat grains. This finding was associated with the Fe3+ -mobilizing properties of CDs from the soil and root cell wall, as well as endocytosis-dependent internalization in roots. The resulting excess Fe signaling mitigated Cd uptake via inhibiting TaNRAMP5 expression. Foliar spraying of CDs enhanced Fe (44%), Mn (30%), and Zn (19%) content with an unchanged Cd accumulation in wheat grains. This result is attributed to CDs-enhanced light signaling, which triggered shoot-to-root Fe deficiency response. This study not only reveals the molecular mechanism underlying CDs modulation of Fe signaling in plants but also provides useful strategies for concurrent Fe biofortification and Cd mitigation in plant-based foods.

Long-Term Soil Drought Limits Starch Accumulation by Altering Sucrose Transport and Starch Synthesis in Sweet Potato Tuberous Root.

In this study, the influences of long-term soil drought with three levels [soil-relative water content (SRWC) (75 ± 5)%, as the control; SRWC (55 ± 5)%, mild drought; SRWC (45 ± 5)%, severe drought] were investigated on sucrose-starch metabolism in sweet potato tuberous roots (TRs) by pot experiment. Compared to the control, drought stress increased soluble sugar and sucrose content by 4-60% and 9-75%, respectively, but reduced starch accumulation by 30-66% through decreasing the starch accumulate rate in TRs. In the drought-treated TRs, the inhibition of sucrose decomposition was attributed to the reduced activities of acid invertase (AI) and alkaline invertase (AKI) and the IbA-INV3 expression, rather than sucrose synthase (SuSy), consequently leading to the increased sucrose content in TRs. In addition, starch synthesis was inhibited mainly by reducing ADP-glucose pyrophosphorylase (AGPase), granular starch synthase (GBSS) and starch branching enzyme (SBE) activities in TRs under drought stress, and AGPase was the rate-limiting enzyme. Furthermore, soil drought remarkably up-regulated the IbSWEET11, IbSWEET605, and IbSUT4 expressions in Jishu 26 TRs, while it down-regulated or had no significant differences in Xushu 32 and Ningzishu 1 TRs. These results suggested that the sucrose-loading capability in Jishu 26 TRs were stronger than that in Xushu 32 and Ningzishu 1 TRs. Moreover, IbA-INV3, IbAGPS1, IbAGPS2, IbGBSSI and IbSBEII play important roles in different drought-tolerant cultivars under drought stress.

IbINV Positively Regulates Resistance to Black Rot Disease Caused by Ceratocystis fimbriata in Sweet Potato.

Black rot disease, caused by Ceratocystis fimbriata Ellis & Halsted, severely affects both plant growth and post-harvest storage of sweet potatoes. Invertase (INV) enzymes play essential roles in hydrolyzing sucrose into glucose and fructose and participate in the regulation of plant defense responses. However, little is known about the functions of INV in the growth and responses to black rot disease in sweet potato. In this study, we identified and characterized an INV-like gene, named IbINV, from sweet potato. IbINV contained a pectin methylesterase-conserved domain. IbINV transcripts were most abundant in the stem and were significantly induced in response to C. fimbriata, salicylic acid, and jasmonic acid treatments. Overexpressing IbINV in sweet potato (OEV plants) led to vigorous growth and high resistance to black rot disease, while the down-regulation of IbINV by RNA interference (RiV plants) resulted in reduced plant growth and high sensitivity to black rot disease. Furthermore, OEV plants contained a decreased sucrose content and increased hexoses content, which might be responsible for the increased INV activities; not surprisingly, RiV plants showed the opposite effects. Taken together, these results indicate that IbINV positively regulates plant growth and black rot disease resistance in sweet potato, mainly by modulating sugar metabolism.

A systematical genome-wide analysis and screening of WRKY transcription factor family engaged in abiotic stress response in sweetpotato.

BACKGROUND: WRKY transcription factors play pivotal roles in regulating plant multiple abiotic stress tolerance, however, a genome-wide systematical analysis of WRKY genes in sweetpotato is still missing. RESULTS: Herein, 84 putative IbWRKYs with WRKY element sequence variants were identified in sweetpotato reference genomes. Fragment duplications, rather than tandem duplications, were shown to play prominent roles in IbWRKY gene expansion. The collinearity analysis between IbWRKYs and the related orthologs from other plants further depicted evolutionary insights into IbWRKYs. Phylogenetic relationships displayed that IbWRKYs were divided into three main groups (I, II and III), with the support of the characteristics of exon-intron structures and conserved protein motifs. The IbWRKY genes, mainly from the group Ib, displayed remarkable and diverse expression profiles under multiple abiotic stress (NaCl, PEG6000, cold and heat) and hormone (ABA, ACC, JA and SA) treatments, which were determined by RNA-seq and qRT-PCR assays, suggesting their potential roles in mediating particular stress responses. Moreover, IbWRKY58L could interact with IbWRKY82 as revealed by yeast two-hybrid based on the protein interaction network screening. And abiotic stress-remarkably induced IbWRKY21L and IbWRKY51 were shown to be localized in the nucleus and had no transactivation activities. CONCLUSION: These results provide valuable insights into sweetpotato IbWRKYs and will lay a foundation for further exploring functions and possible regulatory mechanisms of IbWRKYs in abiotic stress tolerance.

Chromosome painting reveals the genomic structure of three polyploid species of Ipomoea.

Cultivated sweetpotato [Ipomoea batatas (L.) Lam.] from the family Convolvulaceae is a hexaploid species with 2n = 6x = 90 and has been controversial regarding its nature as an autopolyploid arising within a species or an allopolyploid forming between species. Here, we developed oligonucleotide-based painting probes for two chromosomes of I. nil, a model diploid Ipomoea species. Using these probes, we revealed the pairing behavior of homoeologous chromosomes in I. batatas and its two possible polyploid ancestral species, tetraploid I. tabascana (2n = 4x = 60) and hexaploid I. trifida (2n = 6x = 90). Chromosome painting analysis revealed a high percentage of quadrivalent formation in zygotene-pachytene cells of I. tabascana, which supported that I. tabascana was an autotetraploid likely derived by doubling of structurally similar and homologous genomes rather than a hybrid between I. batatas and I. trifida (2x). A high frequency of hexavalent/bivalent and tetravalent pairing was observed in I. trifida (6x) and I. batatas. However, the percentage of hexavalent pairing in I. trifida (6x) was far higher than that in I. batatas. Thus, the present results tend to support that I. trifida (6x) is an autohexaploid, while I. batatas is more likely to be a segmental allohexaploid.

Karyotypic stability of Fragaria (strawberry) species revealed by cross-species chromosome painting.

Chromosome karyotyping analysis is particularly useful in determining species relationships and the origin of polyploid species. Identification of individual chromosomes is the foundation for karyotype development. For Fragaria (strawberry) species, definitive identification of the individual chromosomes is extremely difficult because of their small size and similar shape. Here, we identified all chromosomes for 11 representative Fragaria species with different ploidy using a set of oligonucleotide-based probes developed in Fragaria vesca. Comprehensive molecular cytogenetic karyotypes were established based on the individually identified chromosomes. In addition, we used oligo probes to assign the 5S and 45S rDNA loci to specific chromosomes in 16 Fragaria species. We found that these Fragaria species maintained a remarkably conserved karyotype. No inter-chromosomal structural rearrangements at the cytological level were observed in any of the chromosomes among these species. Despite karyotypic stability and similarity, variations in the signal intensity of oligo probes were observed among the homologous chromosomes in several polyploid species. Moreover, most Fragaria species also showed differences in the distribution patterns of 45S and 5S rDNA. These data provide new insights into the origins of several polyploid Fragaria species.

A bacterial F-box effector suppresses SAR immunity through mediating the proteasomal degradation of OsTrxh2 in rice.

Plant bacterial pathogens usually cause diseases by secreting and translocating numerous virulence effectors into host cells and suppressing various host immunity pathways. It has been demonstrated that the extensive ubiquitin systems of host cells are frequently interfered with or hijacked by numerous pathogenic bacteria, through various strategies. Some type-III secretion system (T3SS) effectors of plant pathogens have been demonstrated to impersonate the F-box protein (FBP) component of the SKP1/CUL1/F-box (SCF) E3 ubiquitin system for their own benefit. Although numerous putative eukaryotic-like F-box effectors have been screened for different bacterial pathogens by bioinformatics analyses, the targets of most F-box effectors in host immune systems remain unknown. Here, we show that XopI, a putative F-box effector of African Xoo (Xanthomonas oryzae pv. oryzae) strain BAI3, strongly inhibits the host's OsNPR1-dependent resistance to Xoo. The xopI knockout mutant displays lower virulence in Oryza sativa (rice) than BAI3. Mechanistically, we identify a thioredoxin protein, OsTrxh2, as an XopI-interacting protein in rice. Although OsTrxh2 positively regulates rice immunity by catalyzing the dissociation of OsNPR1 into monomers in rice, the XopI effector serves as an F-box adapter to form an OSK1-XopI-OsTrxh2 interaction complex, and further disrupts OsNPR1-mediated resistance through proteasomal degradation of OsTrxh2. Our results indicate that XopI targets OsTrxh2 and further represses OsNPR1-dependent signaling, thereby subverting systemic acquired resistance (SAR) immunity in rice.

Genome-wide in silico identification and expression analysis of beta-galactosidase family members in sweetpotato [Ipomoea batatas (L.) Lam].

BACKGROUND: Sweetpotato (Ipomoea batatas (L.) Lam.) serves as an important food source for human beings. ß-galactosidase (bgal) is a glycosyl hydrolase involved in cell wall modification, which plays essential roles in plant development and environmental stress adaptation. However, the function of bgal genes in sweetpotato remains unclear. RESULTS: In this study, 17 ß-galactosidase genes (Ibbgal) were identified in sweetpotato, which were classified into seven subfamilies using interspecific phylogenetic and comparative analysis. The promoter regions of Ibbgals harbored several stress, hormone and light responsive cis-acting elements. Quantitative real-time PCR results displayed that Ibbgal genes had the distinct expression patterns across different tissues and varieties. Moreover, the expression profiles under various hormonal treatments, abiotic and biotic stresses were highly divergent in leaves and root. CONCLUSIONS: Taken together, these findings suggested that Ibbgals might play an important role in plant development and stress responses, which provided evidences for further study of bgal function and sweetpotato breeding.

Antifungal effect of volatile organic compounds produced by Pseudomonas chlororaphis subsp. aureofaciens SPS-41 on oxidative stress and mitochondrial dysfunction of Ceratocystis fimbriata.

Ceratocystis fimbriata is the pathogen of black rot disease, which widely exists in sweet potato producing areas all over the world. The antifungal activity of volatile organic compounds (VOCs) released by Pseudomonas chlororaphis subsp. aureofaciens SPS-41 against C. fimbriata was reported in our previous study. In this study, we attempted to reveal the underlying antifungal mechanism of SPS-41 volatiles. Our results showed that the VOCs released by SPS-41 caused the morphological change of hyphae, destroyed the integrity of cell membrane, reduced the content of ergosterol, and induced massive accumulation of reactive oxygen species in C. fimbriata cells. Furthermore, SPS-41 fumigation decreased the mitochondrial membrane potential, acetyl-CoA and pyruvate content of C. fimbriata cells, as well as the mitochondrial dehydrogenases activity. In addition, the VOCs generated by SPS-41 reduced the intracellular ATP content and increased the extracellular ATP content of C. fimbriata. In summary, SPS-41 fumigation exerted its antifungal activity by inducing oxidative stress and mitochondrial dysfunction in C. fimbriata.

Potassium Fertilization Stimulates Sucrose-to-Starch Conversion and Root Formation in Sweet Potato (Ipomoea batatas (L.) Lam.).

A field experiment was established to study sweet potato growth, starch dynamic accumulation, key enzymes and gene transcription in the sucrose-to-starch conversion and their relationships under six K2O rates using Ningzishu 1 (sensitive to low-K) and Xushu 32 (tolerant to low-K). The results indicated that K application significantly improved the biomass accumulation of plant and storage root, although treatments at high levels of K, i.e., 300-375 kg K2O ha-1, significantly decreased plant biomass and storage root yield. Compared with the no-K treatment, K application enhanced the biomass accumulation of plant and storage root by 3-47% and 13-45%, respectively, through promoting the biomass accumulation rate. Additionally, K application also enhanced the photosynthetic capacity of sweet potato. In this study, low stomatal conductance and net photosynthetic rate (Pn) accompanied with decreased intercellular CO2 concentration were observed in the no-K treatment at 35 DAT, indicating that Pn was reduced mainly due to stomatal limitation; at 55 DAT, reduced Pn in the no-K treatment was caused by non-stomatal factors. Compared with the no-K treatment, the content of sucrose, amylose and amylopectin decreased by 9-34%, 9-23% and 6-19%, respectively, but starch accumulation increased by 11-21% under K supply. The activities of sucrose synthetase (SuSy), adenosine-diphosphate-glucose pyrophosphorylase (AGPase), starch synthase (SSS) and the transcription of Susy, AGP, SSS34 and SSS67 were enhanced by K application and had positive relationships with starch accumulation. Therefore, K application promoted starch accumulation and storage root yield through regulating the activities and genes transcription of SuSy, AGPase and SSS in the sucrose-to-starch conversion.

Research progress of plant cytogenetics in Jiangsu province.

Cytogenetics was established based on the "Chromosome theory of inheritance", proposed by Boveri and Sutton and evidenced by Morgan's lab in early stage of the 20 th centrary. With rapid development of related research areas, especially molecular genetics, cytogenetics developed from traditional into a new era, molecular cytogenetics in late 1960s. Featured by an established technique named DNA in situ hybridization (ISH), molecular cytogenetics has been applied in various research areas. ISH provids vivid and straightforward figures showing the virtual presence of DNA, RNA or proteins. In combination with genomics and cell biology tools, ISH and derived techniques have been widely used in studies of the origin, evolution, domestication of human, animal and plant, as well as wide hybridization and chromosome engineering. The physical location and order of DNA sequences revealed by ISH enables the detection of chromosomal re-arrangments among related species and gaps of assembled genome sequences. In addition, ISH using RNA or protein probes can reveal the location and quantification of transcripted RNA or translated protein. Since the 1970s, scientists from universities or institutes belonging to the Jiangsu Society of Genetics have initiated cytogenetics researches using various plant species. In recent years, research platforms for molecular cytogenetics have also been well established in Nanjing Agricultural University, Yangzhou University, Nanjing Forestry University, Jiangsu Xuhuai Academy of Agricultural Sciences, and Jiangsu Normal University. The application of molecular cytogenetics in plant evolution, wide hybridization, chromosome engineering, chromosome biology, genomics has been successful. Significant progresses have been achieved, both in basic and applied researches. In this paper, we will review main research progresses of plant cytogenetics in Jiangsu province, and discuss the potential development of this research area.

[Application of QAMS for quality evaluation and control of Chinese patent medicines:taking Bufonis Venenum-contained preparations as examples].

As a new strategy capable of uncovering the characteristics of traditional Chinese medicines, the quantitative analysis of multi-components by single-marker(QAMS) has been widely employed for the quality evaluation of Chinese medicinal materials, slices, and extracts. However, its application in the assessment of Chinese patent medicines is yet to be explored. By referring to the determination of three bufogenins in Bufonis Venenum by QAMS described in Chinese Pharmacopoeia(2020 Edition), this paper selected seven representative preparations containing Bufonis Venenum and explored whether the relative correction factors(RCFs) of cinobufagin(CB) to bufalin(BF) and resibufogenin(RB) could be directly used for the quality control of Bufonis Venenum-contained preparations. Based on the qualitative analyses under the same chromatographic conditions as used for toad venom, combing specificity test, five preparations such as Yatong Yili Pills, Houzheng Pills, Xiongdan Jiuxin Pills, Liushen Pills and Niuhuang Xiaoyan Pills, were expected to use validated RCFs for the direct determination of three components. Taking Houzheng Pills as an example, the methodological validation of bufalin, cinobufagin and resibufogenin was carried out, and the recoveries of bufalin, cinobufagin and resibufogenin were 90.64%-106.1%. The obvious difference was not observed between the contents of bufalin and resibufogenin in 24 batches of preparation samples by QAMS and external reference method. In the tested samples, the content of bufalin, cinobufagin and resibufogenin were 1.27-2.61, 2.44-5.66 and 0.988-3.16 mg·g~(-1) in 10 batches of Liushen Pills samples. The contents of bufalin, cinobufagin and resibufogenin were 0.760-1.32, 1.35-2.39 and 0.600-1.55 mg·g~(-1) in 10 batches of Houzheng Pills samples from three manufacturers. The obtained data contribute to improving the quality standard of Bufonis Venenum-contained preparations, and they also provide some ideas for the application of QAMS in the quality evaluation and control of Chinese patent medicines.

High-throughput deep sequencing reveals the important role that microRNAs play in the salt response in sweet potato (Ipomoea batatas L.).

BACKGROUND: MicroRNAs (miRNAs), a class of small regulatory RNAs, have been proven to play important roles in plant growth, development and stress responses. Sweet potato (Ipomoea batatas L.) is an important food and industrial crop that ranks seventh in staple food production. However, the regulatory mechanism of miRNA-mediated abiotic stress response in sweet potato remains unclear. RESULTS: In this study, we employed deep sequencing to identify both conserved and novel miRNAs from salinity-exposed sweet potato cultivars and its untreated control. Twelve small non-coding RNA libraries from NaCl-free (CK) and NaCl-treated (Na150) sweet potato leaves and roots were constructed for salt-responsive miRNA identification in sweet potatoes. A total of 475 known miRNAs (belonging to 66 miRNA families) and 175 novel miRNAs were identified. Among them, 51 (22 known miRNAs and 29 novel miRNAs) were significantly up-regulated and 76 (61 known miRNAs and 15 novel miRNAs) were significantly down-regulated by salinity stress in sweet potato leaves; 13 (12 known miRNAs and 1 novel miRNAs) were significantly up-regulated and 9 (7 known miRNAs and 2 novel miRNAs) were significantly down-regulated in sweet potato roots. Furthermore, 636 target genes of 314 miRNAs were validated by degradome sequencing. Deep sequencing results confirmed by qRT-PCR experiments indicated that the expression of most miRNAs exhibit a negative correlation with the expression of their targets under salt stress. CONCLUSIONS: This study provides insights into the regulatory mechanism of miRNA-mediated salt response and molecular breeding of sweet potatoes though miRNA manipulation.

Selection of stable reference genes for gene expression analysis in sweet potato (Ipomoea batatas L.).

Gene expression analysis is one of the most common and important studies in biology and biomedicine. No matter for traditional blotting analysis or currently commonly used PCR strategy, all need a stable reference gene for normalizing the gene expression. To screen and select housekeeping genes as the most stable reference genes, quantitative real-time PCR (qRT-PCR) was employed to analyze the expression of sixteen commonly used reference genes (IbelF, Ibα-tubulin, IbHIS, IbCOX, IbGAPDH, IbH2B1, IbARF, IbCYC, Ibß-tubulin, IbACT, IbEFl-a, IbG14, IbPLD, IbRPL2, IbUBQ, IbUBI) in five different tissues under two different temperature stresses in sweet potato. Data analysis by the Delta CT, geNorm, NormFinder, and BestKeeper programs revealed that IbelF is the most stable gene and IbUBI is the least stable gene as reference. Our study also shows that combination of two or more genes as reference is a better choice, rendering more substantiated expression data for comparison. This study provides evidence for selecting reference genes in sweet potato gene expression analysis.

High throughput sequencing identifies chilling responsive genes in sweetpotato (Ipomoea batatas Lam.) during storage.

Sweetpotato (Ipomoea batatas L.) is a globally important economic food crop. It belongs to Convolvulaceae family and origins in the tropics; however, sweetpotato is sensitive to cold stress during storage. In this study, we performed transcriptome sequencing to investigate the sweetpotato response to chilling stress during storage. A total of 110,110 unigenes were generated via high-throughput sequencing. Differentially expressed genes (DEGs) analysis showed that 18,681 genes were up-regulated and 21,983 genes were down-regulated in low temperature condition. Many DEGs were related to the cell membrane system, antioxidant enzymes, carbohydrate metabolism, and hormone metabolism, which are potentially associated with sweetpotato resistance to low temperature. The existence of DEGs suggests a molecular basis for the biochemical and physiological consequences of sweetpotato in low temperature storage conditions. Our analysis will provide a new target for enhancement of sweetpotato cold stress tolerance in postharvest storage through genetic manipulation.

The Interaction Network and Signaling Specificity of Two-Component System in Arabidopsis.

Two-component systems (TCS) in plants have evolved into a more complicated multi-step phosphorelay (MSP) pathway, which employs histidine kinases (HKs), histidine-containing phosphotransfer proteins (HPts), and response regulators (RRs) to regulate various aspects of plant growth and development. How plants perceive the external signals, then integrate and transduce the secondary signals specifically to the desired destination, is a fundamental characteristic of the MSP signaling network. The TCS elements involved in the MSP pathway and molecular mechanisms of signal transduction have been best understood in the model plant Arabidopsis thaliana. In this review, we focus on updated knowledge on TCS signal transduction in Arabidopsis. We first present a brief description of the TCS elements; then, the protein-protein interaction network is established. Finally, we discuss the possible molecular mechanisms involved in the specificity of the MSP signaling at the mRNA and protein levels.

SlSTE1 promotes abscisic acid-dependent salt stress-responsive pathways via improving ion homeostasis and reactive oxygen species scavenging in tomato.

High salinity is one of the major limiting factors that reduces crop productivity and quality. Herein, we report that small SALT TOLERANCE ENHANCER1 (STE1) protein without any known conserved domains is required for tomato salt tolerance. Overexpression (OE) of SlSTE1 enhanced the tolerance to multiple chloride salts (NaCl, KCl, and LiCl) and oxidative stress, along with elevated antioxidant enzyme activities, increased abscisic acid (ABA) and chlorophyll contents, and reduced malondialdehyde (MDA) and reactive oxygen species (ROS) accumulations compared to that of wild-type (WT) plants. Moreover, decreased K+ efflux and increased H+ efflux were detected in the OE plants, which induced a higher K+ /Na+ ratio. In contrast, SlSTE1-RNAi plants displayed decreased tolerance to salt stress. RNA-seq data revealed 1 330 differentially expressed genes in the OE plants versus WT plants under salt stress, and the transcription of numerous and diverse genes encoding transcription factors, stress-related proteins, secondary metabolisms, kinases, and hormone synthesis/signaling-related proteins (notably ABA and 1-aminocyclopropane-1-carboxylate) was greatly elevated. Furthermore, SlSTE1-OE plants showed increased sensitivity to ABA, and the results suggest that SlSTE1 promotes ABA-dependent salt stress-responsive pathways by interacting with SlPYLs and SlSnRK2s. Collectively, our findings reveal that the small SlSTE1 protein confers salt tolerance via ABA signaling and ROS scavenging and improves ion homeostasis in tomato.