ACRE, a class of AP2/ERF transcription factors, activates the expression of sweet potato ß-amylase and sporamin genes through the sugar-responsible element CMSRE-1.

Sugars, synthesized by photosynthesis in source organs, are loaded and utilized as an energy source and carbon skeleton in sink organs, and also known to be important signal molecules regulating gene expression in higher plants. The expression of genes coding for sporamin and ß-amylase, the two most abundant proteins in storage roots of sweet potato, is coordinately induced by sugars. We previously reported on the identification of the carbohydrate metabolic signal-responsible element-1 (CMSRE-1) essential for the sugar-responsible expression of two genes. However, transcription factors that bind to this sequence have not been identified. In this study, we performed yeast one-hybrid screening using the sugar-responsible minimal promoter region of the ß-amylase gene as bait and a library composed only transcription factor cDNAs of Arabidopsis. Two clones, named Activator protein binding to CMSRE-1 (ACRE), encoding AP2/ERF transcription factors were isolated. ACRE showed transactivation activity of the sugar-responsible minimal promoter in a CMSRE-1-dependent manner in Arabidopsis protoplasts. Electric mobility shift assay (EMSA) using recombinant proteins and transient co-expression assay in Arabidopsis protoplasts revealed that ACRE could actually act to the CMSRE-1. Among the DEHYDRATION -RESPONSIVE ELEMENT BINDING FACTOR (DREB) subfamily, almost all homologs including ACRE, could act on the DRE, while only three ACREs could act to the CMSRE-1. Moreover, ACRE-homologs of Japanese morning glory also have the same property of DNA-binding preference and transactivation activity through the CMSRE-1. These findings suggested that ACRE plays an important role in the mechanism regulating the sugar-responsible gene expression through the CMSRE-1 conserved across plant species.

Saccharopolyspora ipomoeae sp. nov., an Actinomycete Isolated from Sweet Potato Field Soils.

During the course of the isolation of actinobacteria from sweet potato field soils collected from Phra Nakhon Si Ayutthaya province of Thailand, strain TS4A08T was isolated and subjected to a polyphasic taxonomic approach. The 16S rRNA gene sequence analysis of strain TS4A08T revealed that it is closely related to the type strains of Saccharopolyspora aridisoli, and Saccharopolyspora endophytica with 98.7%, and 98.6% similarity, respectively. However, phylogenetic analyses using 16S rRNA gene and genome sequences indicated that strain TS4A08T clustered with Saccharopolyspora flava AS4.1520T (98.2% similarity), well-supported by bootstrap values, and formed distinct line from the two closest strains. The average nucleotide identity (ANI) values and digital DNA-DNA hybridization (dDDH) values between the genome sequences of strain TS4A08T and the closest type strains of S. aridisoli, S. endophytica, and S. flava, were 86.1-93.2% and 33.1-49.6%, respectively, which were less than the threshold for the species delineation. The genome size and the DNA G + C content of strain TS4A08T were 6.6 Mbp and 70.5%, respectively. The strain grew well at 25-37 °C, pH range of 7-9, and NaCl concentration of 0-5% (w/v). Whole-cell hydrolysates contained meso-diaminopimelic acid. The major fatty acids were iso-C16:0, anteiso-C17:0, and iso-C15:0. Strain TS4A08T exhibited phosphatidylcholine in its polar lipid profile, with MK-9(H4) being the predominant isoprenologue. The strain exhibits typical chemotaxonomic properties of the genus Saccharopolyspora, including arabinose, galactose, and ribose as whole-cell sugars. Strain TS4A08T represents a novel species within the genus Saccharopolyspora, for which the name Saccharopolyspora ipomoeae sp. nov. is proposed. The type strain is TS4A08T (= TBRC 17271T = NBRC 115967T).

Genome-Wide Identification and Expression Analysis of the Starch Synthase Gene Family in Sweet Potato and Two of Its Closely Related Species.

The starch synthase (SS) plays important roles in regulating plant growth and development and responding to adversity stresses. Although the SS family has been studied in many crops, it has not been fully identified in sweet potato and its two related species. In the present study, eight SSs were identified from Ipomoea batatas (I. batata), Ipomoea trifida (I. trifida), and Ipomoea trlioba (I. trlioba), respectively. According to the phylogenetic relationships, they were divided into five subgroups. The protein properties, chromosomal location, phylogenetic relationships, gene structure, cis-elements in the promoter, and interaction network of these proteins were also analyzed; stress expression patterns were systematically analyzed; and real-time polymerase chain reaction (qRT-PCR) analysis was performed. Ipomoea batatas starch synthase (IbSSs) were highly expressed in tuber roots, especially Ipomoea batatas starch synthase 1 (IbSS1) and Ipomoea batatas starch synthase 6 (IbSS6), which may play an important role in root development and starch biosynthesis. At the same time, the SS genes respond to potassium deficiency, hormones, cold, heat, salt, and drought stress. This study offers fresh perspectives for enhancing knowledge about the roles of SSs and potential genes to enhance productivity, starch levels, and resistance to environmental stresses in sweet potatoes.

Genome-Wide Identification and Expression Analysis of the DMP and MTL Genes in Sweetpotato (Ipomoea batatas L.).

Sweetpotato (Ipomoea batatas L.) is a strategic crop with both economic and energy value. However, improving sweetpotato varieties through traditional breeding approaches can be a time-consuming and labor-intensive process due to the complex genetic nature of sweetpotato as a hexaploid species (2n = 6x = 90). Double haploid (DH) breeding, based on in vivo haploid induction, provides a new approach for rapid breeding of crops. The success of haploid induction can be achieved by manipulating specific genes. Two of the most critical genes, DMP (DUF679 membrane proteins) and MTL (MATRILINEAL), have been shown to induce haploid production in several species. Here, we identified and characterized DMP and MTL genes in sweetpotato using gene family analysis. In this study, we identified 5 IbDMPs and 25 IbpPLAs. IbDMP5 and IbPLAIIs (IbPLAIIκ, IbPLAIIλ, and IbPLAIIµ) were identified as potential haploid induction (HI) genes in sweetpotato. These results provide valuable information for the identification and potential function of HI genes in sweetpotato and provide ideas for the breeding of DH lines.

Salicylic acid and jasmonic acid biosynthetic pathways are simultaneously activated in transgenic Arabidopsis expressing the rolB/C gene from Ipomoea batatas.

The Agrobacterium rhizogenes root oncogenic locus (rol) genes interfere with hormone balance by altering their synthesis and/or recognition, giving rise to varied impacts on the physiological characteristics of plants and cell cultures. The homolog of the rolB and rolC genes from Ipomoea batatas, named Ib-rolB/C, similarly induces morphological and physiological alterations in transgenic Arabidopsis thaliana; however, its role in plant hormonal homeostasis has not been previously defined. In this study, we found that external application of salicylic acid (SA) and methyl jasmonate (MeJA) significantly upregulated Ib-rolB/C in detached I. batatas leaves. Furthermore, heterologous expression of Ib-rolB/C in A. thaliana markedly enhanced the accumulation of SA and MeJA, and to a lesser extent, elevated abscisic acid (ABA) levels, through the modulation of genes specific to hormone biosynthesis. Even though the RolB/RolC homolog protein has a notable structural resemblance to the RolB protein from A. rhizogenes, it exhibits a distinct localization pattern, predominantly residing in the cytoplasm and certain discrete subcellular structures, instead of the nucleus. Consequently, the functions of RolB/RolC in both naturally and artificially transgenic plants are linked to changes in the hormonal state of the cells, though the underlying signaling pathways remain to be elucidated.

Genome-Wide Identification and Expression Analysis of the DA1 Gene Family in Sweet Potato and Its Two Diploid Relatives.

The DA1-like gene family plays a crucial role in regulating seed and organ size in plants. The DA1 gene family has been identified in several species but has not yet been reported in sweet potatoes. In this study, nine, eleven, and seven DA1s were identified in cultivated sweet potato (Ipomoea batatas, 2n = 6x = 90) and its two diploid wild relatives, I. trifida (2n = 2x = 30) and I. triloba (2n = 2x = 30), respectively. The DA1 genes were classified into three subgroups based on their phylogenetic relationships with Arabidopsis thaliana and Oryza sativa (rice). Their protein physiological properties, chromosomal localization, phylogenetic relationships, gene structure, promoter cis-elements, and expression patterns were systematically analyzed. The qRT-PCR results showed that the expression levels of four genes, IbDA1-1, IbDA1-3, IbDA1-6, and IbDA1-7, were higher in the sweet potato leaves than in the roots, fiber roots, and stems. In our study, we provide a comprehensive comparison and further the knowledge of DA1-like genes in sweet potatoes, and provide a theoretical basis for functional studies.

Biosynthesis of Scopoletin in Sweet Potato Confers Resistance against Fusarium oxysporum.

Fusarium wilt is a severe fungal disease caused by Fusarium oxysporum in sweet potato. We conducted transcriptome analysis to explore the resistance mechanism of sweet potato against F. oxysporum. Our findings highlighted the role of scopoletin, a hydroxycoumarin, in enhancing resistance. In vitro experiments confirmed that scopoletin and umbelliferone had inhibitory effects on the F. oxysporum growth. We identified hydroxycoumarin synthase genes IbF6'H2 and IbCOSY that are responsible for scopoletin production in sweet potatoes. The co-overexpression of IbF6'H2 and IbCOSY in tobacco plants produced the highest scopoletin levels and disease resistance. This study provides insights into the molecular basis of sweet potato defense against Fusarium wilt and identifies valuable genes for breeding wilt-resistant cultivars.

Integrated transcriptomic and CGAs analysis revealed IbGLK1 is a key transcription factor for chlorogenic acid accumulation in sweetpotato (Ipomoea batatas [L.] Lam.) blades.

Sweetpotato blades are rich in the functional secondary metabolite chlorogenic acid (CGA), which deepen potential for effective utilization of the blade in industry. In this study, we evaluated the type and content of CGA in the blades of 16 sweetpotato genotypes and analyzed the correlation between CGA content and antioxidant capacity. Then we isolated and characterized IbGLK1, a GARP-type transcription factor, by comparative transcriptome analysis. A subcellular localization assay indicated that IbGLK1 is located in the nucleus. Overexpression and silencing of IbGLK1 in sweetpotato blade resulted in a 0.90-fold increase and 1.84-fold decrease, respectively, in CGA content compared to the control. Yeast one-hybrid and dual-luciferase assays showed that IbGLK1 binds and activates the promoters of IbHCT, IbHQT, IbC4H, and IbUGCT, resulting in the promotion of CGA biosynthesis. In conclusion, our study provides insights into a high-quality gene for the regulation of CGA metabolism and germplasm resources for breeding sweetpotato.

Comparative analysis of chloroplast and mitochondrial genomes of sweet potato provides evidence of gene transfer.

The increasing number of plant mitochondrial DNA genomes (mtDNA) sequenced reveals the extent of transfer from both chloroplast DNA genomes (cpDNA) and nuclear DNA genomes (nDNA). This study created a library and assembled the chloroplast and mitochondrial genomes of the leafy sweet potato better to understand the extent of mitochondrial and chloroplast gene transfer. The full-length chloroplast genome of the leafy sweet potato (OM808940) is 161,387 bp, with 132 genes annotated, including 87 protein-coding genes, 8 rRNA genes, and 37 tRNA genes. The mitochondrial genome (OM808941) was 269,578 bp in length and contained 69 functional genes, including 39 protein-coding genes, 6 rRNA genes, and 24 tRNA genes. 68 SSR loci were found in the leafy sweet potato organelle genome, including 54 in the chloroplast genome and 14 in the mitochondria genome. In the sweet potato mitochondrial genome, most genes have RNA editing sites, and the conversion ratio from hydrophilic amino acids to hydrophobic amino acids is the highest, reaching 47.12%. Horizontal transfer occurs in the sweet potato organelle genome and nuclear genome. 40 mitochondrial genome segments share high homology with 14 chloroplast genome segments, 33 of which may be derived from chloroplast genome horizontal transfer. 171 mitochondrial genome sequences come from the horizontal transfer of nuclear genome. The phylogenetic analysis of organelle genes revealed that the leafy sweet potato was closely related to the tetraploid wild species Ipomoea tabascana and the wild diploid species Ipomoea trifida.

Genome-Wide Analysis of the Lateral Organ Boundaries Domain (LBD) Gene Family in Sweet Potato (Ipomoea batatas).

The LBD family is a plant-specific transcription factor family that plays an important role in a variety of biological processes. However, the function of IbLBD genes in sweet potato remains unclear. In this study, we identified a total of 53 IbLBD genes in sweet potato. Genetic structure showed that most of the IbLBD genes contained only two exons. Following the phylogenetic investigation, the IbLBD gene family was separated into Class I (45 members) and Class II (8) members. Both classes of proteins contained relatively conservative Motif1 and Motif2 domains. The chromosomal locations, gene duplications, promoters, PPI network, and GO annotation of the sweet potato LBD genes were also investigated. Furthermore, gene expression profiling and real-time quantitative PCR analysis showed that the expression of 12 IbLBD genes altered in six separate tissues and under various abiotic stresses. The IbLBD genes belonging to Class I were mostly expressed in the primary root, the pencil root, and the leaves of sweet potatoes, while the genes belonging to Class II were primarily expressed in the various sweet potato roots. The IbLBD genes belonging to Class I were mostly expressed in the primary root, the pencil root, and the leaves of sweet potatoes, while the genes belonging to Class II were primarily expressed in the fibrous root, pencil root, and tuber root.

IbMYC2 Contributes to Salt and Drought Stress Tolerance via Modulating Anthocyanin Accumulation and ROS-Scavenging System in Sweet Potato.

Basic helix-loop-helix (bHLH) transcription factors extensively affect various physiological processes in plant metabolism, growth, and abiotic stress. However, the regulation mechanism of bHLH transcription factors in balancing anthocyanin biosynthesis and abiotic stress in sweet potato (Ipomoea batata (L.) Lam.) remains unclear. Previously, transcriptome analysis revealed the genes that were differentially expressed among the purple-fleshed sweet potato cultivar 'Jingshu 6' and its anthocyanin-rich mutant 'JS6-5'. Here, we selected one of these potential genes, IbMYC2, which belongs to the bHLH transcription factor family, for subsequent analyses. The expression of IbMYC2 in the JS6-5 storage roots is almost four-fold higher than Jingshu 6 and significantly induced by hydrogen peroxide (H2O2), methyl jasmonate (MeJA), NaCl, and polyethylene glycol (PEG)6000. Overexpression of IbMYC2 significantly enhances anthocyanin production and exhibits a certain antioxidant capacity, thereby improving salt and drought tolerance. In contrast, reducing IbMYC2 expression increases its susceptibility. Our data showed that IbMYC2 could elevate the expression of anthocyanin synthesis pathway genes by binding to IbCHI and IbDFR promoters. Additionally, overexpressing IbMYC2 activates genes encoding reactive oxygen species (ROS)-scavenging and proline synthesis enzymes under salt and drought conditions. Taken together, these results demonstrate that the IbMYC2 gene exercises a significant impact on crop quality and stress resistance.

A simple and efficient in planta transformation method based on the active regeneration capacity of plants.

Plant genetic transformation strategies serve as essential tools for the genetic engineering and advanced molecular breeding of plants. However, the complicated operational protocols and low efficiency of current transformation strategies restrict the genetic modification of most plant species. This paper describes the development of the regenerative activity-dependent in planta injection delivery (RAPID) method based on the active regeneration capacity of plants. In this method, Agrobacterium tumefaciens is delivered to plant meristems via injection to induce transfected nascent tissues. Stable transgenic plants can be obtained by subsequent vegetative propagation of the positive nascent tissues. The method was successfully used for transformation of plants with strong regeneration capacity, including different genotypes of sweet potato (Ipomoea batatas), potato (Solanum tuberosum), and bayhops (Ipomoea pes-caprae). Compared with traditional transformation methods, RAPID has a much higher transformation efficiency and shorter duration, and it does not require tissue culture procedures. The RAPID method therefore overcomes the limitations of traditional methods to enable rapid in planta transformation and can be potentially applied to a wide range of plant species that are capable of active regeneration.

Genome-wide identification and expression analyses of CYP450 genes in sweet potato (Ipomoea batatas L.).

BACKGROUND: Cytochrome P450 monooxygenases (CYP450s) play a crucial role in various biochemical reactions involved in the synthesis of antioxidants, pigments, structural polymers, and defense-related compounds in plants. As sweet potato (Ipomoea batatas L.) holds significant economic importance, a comprehensive analysis of CYP450 genes in this plant species can offer valuable insights into the evolutionary relationships and functional characteristics of these genes. RESULTS: In this study, we successfully identified and categorized 95 CYP450 genes from the sweet potato genome into 5 families and 31 subfamilies. The predicted subcellular localization results indicate that CYP450s are distributed in the cell membrane system. The promoter region of the IbCYP450 genes contains various cis-acting elements related to plant hormones and stress responses. In addition, ten conserved motifs (Motif1-Motif10) have been identified in the IbCYP450 family proteins, with 5 genes lacking introns and only one exon. We observed extensive duplication events within the CYP450 gene family, which may account for its expansion. The gene duplication analysis results showed the presence of 15 pairs of genes with tandem repeats. Interaction network analysis reveals that IbCYP450 families can interact with multiple target genes and there are protein-protein interactions within the family. Transcription factor interaction analysis suggests that IbCYP450 families interact with multiple transcription factors. Furthermore, gene expression analysis revealed tissue-specific expression patterns of CYP450 genes in sweet potatoes, as well as their response to abiotic stress and plant hormones. Notably, quantitative real-time polymerase chain reaction (qRT‒PCR) analysis indicated the involvement of CYP450 genes in the defense response against nonbiological stresses in sweet potatoes. CONCLUSIONS: These findings provide a foundation for further investigations aiming to elucidate the biological functions of CYP450 genes in sweet potatoes.

IbNIEL-mediated degradation of IbNAC087 regulates jasmonic acid-dependent salt and drought tolerance in sweet potato.

Sweet potato (Ipomoea batatas [L.] Lam.) is a crucial staple and bioenergy crop. Its abiotic stress tolerance holds significant importance in fully utilizing marginal lands. Transcriptional processes regulate abiotic stress responses, yet the molecular regulatory mechanisms in sweet potato remain unclear. In this study, a NAC (NAM, ATAF1/2, and CUC2) transcription factor, IbNAC087, was identified, which is commonly upregulated in salt- and drought-tolerant germplasms. Overexpression of IbNAC087 increased salt and drought tolerance by increasing jasmonic acid (JA) accumulation and activating reactive oxygen species (ROS) scavenging, whereas silencing this gene resulted in opposite phenotypes. JA-rich IbNAC087-OE (overexpression) plants exhibited more stomatal closure than wild-type (WT) and IbNAC087-Ri plants under NaCl, polyethylene glycol, and methyl jasmonate treatments. IbNAC087 functions as a nuclear transcriptional activator and directly activates the expression of the key JA biosynthesis-related genes lipoxygenase (IbLOX) and allene oxide synthase (IbAOS). Moreover, IbNAC087 physically interacted with a RING-type E3 ubiquitin ligase NAC087-INTERACTING E3 LIGASE (IbNIEL), negatively regulating salt and drought tolerance in sweet potato. IbNIEL ubiquitinated IbNAC087 to promote 26S proteasome degradation, which weakened its activation on IbLOX and IbAOS. The findings provide insights into the mechanism underlying the IbNIEL-IbNAC087 module regulation of JA-dependent salt and drought response in sweet potato and provide candidate genes for improving abiotic stress tolerance in crops.

Purple Sweet Potato Polysaccharide Exerting an Anti-inflammatory Effect via a TLR-Mediated Pathway by Regulating Polarization and Inhibiting the Inflammasome Activation.

Purple sweet potato polysaccharide (PSPP-1) is a novel glucan; this study aimed to examine the anti-inflammatory effect of PSPP-1 and elucidate its potential mechanisms. Lipopolysaccharide (LPS)-induced RAW264.7 was used as the model of inflammation, cell viability, and levels of nitric oxide (NO), reactive oxygen species (ROS), and calcium ion (Ca2+) were analyzed. ELISA and qPCR were used to assess the productions and mRNA expression of cytokines, and Western blotting was used to assess protein expressions in the TLR-mediated pathway, macrophage polarization, and inflammasome activation. The results demonstrated PSPP-1 inhibited cell proliferation and markedly decreased NO, ROS, and Ca2+ levels. Moreover, PSPP-1 suppressed the secretions and mRNA expressions of pro-inflammatory cytokines and increased those of anti-inflammatory cytokines. Furthermore, PSPP-1 could exert anti-inflammatory effects through different pathways mediated by both TLR2 and TLR4, which modulated the expressions of essential proteins in the myeloid differentiation factor 88 (MyD88)-dependent and toll/IL-1 receptor domain-containing adaptor-inducing interferon-ß (TRIF)-dependent signaling pathways. PSPP-1 even regulated the polarization of M1/M2 macrophages and inhibited the nucleotide oligomerization domain-like receptor protein 3 (NLRP3) inflammasome activation. These findings indicate that PSPP-1 can suppress LPS-induced inflammation via multiple pathways and may be a potential agent for therapeutic inflammation-related pathophysiological processes and disorders.

IbMYB73 targets abscisic acid-responsive IbGER5 to regulate root growth and stress tolerance in sweet potato.

Root development influences plant responses to environmental conditions, and well-developed rooting enhances plant survival under abiotic stress. However, the molecular and genetic mechanisms underlying root development and abiotic stress tolerance in plants remain unclear. In this study, we identified the MYB transcription factor-encoding gene IbMYB73 by cDNA-amplified fragment length polymorphism and RNA-seq analyses. IbMYB73 expression was greatly suppressed under abiotic stress in the roots of the salt-tolerant sweet potato (Ipomoea batatas) line ND98, and its promoter activity in roots was significantly reduced by abscisic acid (ABA), NaCl, and mannitol treatments. Overexpression of IbMYB73 significantly inhibited adventitious root growth and abiotic stress tolerance, whereas IbMYB73-RNAi plants displayed the opposite pattern. IbMYB73 influenced the transcription of genes involved in the ABA pathway. Furthermore, IbMYB73 formed homodimers and activated the transcription of ABA-responsive protein IbGER5 by binding to an MYB binding sites I motif in its promoter. IbGER5 overexpression significantly inhibited adventitious root growth and abiotic stress tolerance concomitantly with a reduction in ABA content, while IbGER5-RNAi plants showed the opposite effect. Collectively, our results demonstrated that the IbMYB73-IbGER5 module regulates ABA-dependent adventitious root growth and abiotic stress tolerance in sweet potato, which provides candidate genes for the development of elite crop varieties with well-developed root-mediated abiotic stress tolerance.

High-throughput characterization and phenotyping of resistance and tolerance to virus infection in sweetpotato.

Breeders have made important efforts to develop genotypes able to resist virus attacks in sweetpotato, a major crop providing food security and poverty alleviation to smallholder farmers in many regions of Sub-Saharan Africa, Asia and Latin America. However, a lack of accurate objective quantitative methods for this selection target in sweetpotato prevents a consistent and extensive assessment of large breeding populations. In this study, an approach to characterize and classify resistance in sweetpotato was established by assessing total yield loss and virus load after the infection of the three most common viruses (SPFMV, SPCSV, SPLCV). Twelve sweetpotato genotypes with contrasting reactions to virus infection were grown in the field under three different treatments: pre-infected by the three viruses, un-infected and protected from re-infection, and un-infected but exposed to natural infection. Virus loads were assessed using ELISA, (RT-)qPCR, and loop-mediated isothermal amplification (LAMP) methods, and also through multispectral reflectance and canopy temperature collected using an unmanned aerial vehicle. Total yield reduction compared to control and the arithmetic sum of (RT-)qPCR relative expression ratios were used to classify genotypes into four categories: resistant, tolerant, susceptible, and sensitives. Using 14 remote sensing predictors, machine learning algorithms were trained to classify all plots under the said categories. The study found that remotely sensed predictors were effective in discriminating the different virus response categories. The results suggest that using machine learning and remotely sensed data, further complemented by fast and sensitive LAMP assays to confirm results of predicted classifications could be used as a high throughput approach to support virus resistance phenotyping in sweetpotato breeding.

Genome-wide identification, characterization, and expression analysis of the sweet potato (Ipomoea batatas [L.] Lam.) ARF, Aux/IAA, GH3, and SAUR gene families.

BACKGROUND: Auxins are known to have roles in the tuberization process in sweet potato (Ipomoea batatas [L.] Lam.) and these effects are mediated by various auxin signalling gene families. In this study, an analysis of the sweet potato genome was performed to identify the ARF, Aux/IAA, GH3, and SAUR auxin signalling gene family members in this crop. RESULTS: A total of 29 ARF, 39 Aux/IAA, 13 GH3, and 200 SAUR sequences were obtained, and their biochemical properties and gene expression profiles were analysed. The sequences were relatively conserved based on exon-intron structure, motif analysis, and phylogenetic tree construction. In silico expression analyses of the genes in fibrous and storage roots indicated that many sequences were not differentially expressed in tuberizing and non-tuberizing roots. However, some ARF, Aux/IAA, and SAUR genes were up-regulated in tuberizing storage roots compared to non-tuberizing fibrous roots while many GH3 genes were down-regulated. Additionally, these genes were expressed in a variety of plant parts, with some genes being highly expressed in shoots, leaves, and stems while others had higher expression in the roots. Some of these genes are up-regulated during the plant's response to various hormone treatments and abiotic stresses. Quantitative RT-PCR confirmation of gene expression was also conducted, and the results were concordant with the in silico analyses. A protein-protein interaction network was predicted for the differentially expressed genes, suggesting that these genes likely form part of a complex regulatory network that controls tuberization. These results confirm those of existing studies that show that auxin signalling genes have numerous roles in sweet potato growth and development. CONCLUSION: This study provides useful information on the auxin signalling gene families in Ipomoea batatas and suggests putative candidates for further studies on the role of auxin signalling in tuberization and plant development.

RNA-Sequencing Analysis Revealed Genes Associated with Sweet Potato (Ipomoea batatas (L.) Lam.) Responses to Stem Rot during Different Infection Stages.

The sweet potato, which is an important tuber crop in China, is susceptible to a variety of pathogens and insect pests during cultivation and production. Stem rot is a common sweet potato disease that seriously affects tuber yield and quality. Unfortunately, there have been relatively few studies on the mechanism mediating the stem rot resistance of sweet potatoes. In this study, a transcriptome sequencing analysis was completed using Xushu 48 samples at different stages (T1, T2, and T3) of the stem rot infection. The T1 vs. T2, T1 vs. T3, and T2 vs. T3 comparisons detected 44,839, 81,436, and 61,932 differentially expressed genes (DEGs), respectively. The DEGs encoded proteins primarily involved in alanine, aspartate, and glutamate metabolism (ko00250), carbon fixation in photosynthetic organisms (ko00710), and amino sugar and nucleotide sugar metabolism (ko00520). Furthermore, some candidate genes induced by phytopathogen infections were identified, including gene-encoding receptor-like protein kinases (RLK5 and RLK7), an LRR receptor-like serine/threonine protein kinase (SERK1), and transcription factors (bHLH137, ERF9, MYB73, and NAC053). The results of this study provide genetic insights that are relevant to future explorations of sweet potato stem rot resistance, while also providing the theoretical basis for breeding sweet potato varieties that are resistant to stem rot and other diseases.

Transcriptome-Based Comparative Expression Profiling of Sweet Potato during a Compatible Response with Root-Knot Nematode Meloidogyne incognita Infection.

M. incognita, a root-knot nematode (RKN), infects the roots of several important food crops, including sweet potato (Ipomoea batatas Lam.), and severely reduces yields. However, the molecular mechanisms underlying infection remain unclear. Previously, we investigated differential responses to RKN invasion in susceptible and resistant sweet potato cultivars through RNA-seq-based transcriptome analysis. In this study, gene expression similarities and differences were examined in RKN-susceptible sweet potato cultivars during the compatible response to RKN infection. Three susceptible cultivars investigated in previous research were used: Dahomi (DHM), Shinhwangmi (SHM), and Yulmi (YM). Of the three cultivars, YM had the highest number of genes with altered expression in response to infection. YM was also the cultivar with the highest susceptibility to RKN. Comparisons among cultivars identified genes that were regulated in more than one cultivar upon infection. Pairwise comparisons revealed that YM and DHM shared the most regulated genes, whereas YM and SHM shared the lowest number of regulated genes. Five genes were up-regulated, and two were down-regulated, in all three cultivars. Among these, four genes were highly up-regulated in all cultivars: germin-like protein, anthranilate synthase α subunit, isocitrate lyase, and uncharacterized protein. Genes were also identified that were uniquely regulated in each cultivar in response to infection, suggesting that susceptible cultivars respond to infection through shared and cultivar-specific pathways. Our findings expand the understanding of the compatible response to RKN invasion in sweet potato roots and provide useful information for further research on RKN defense mechanisms.