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.

Comparative physiological and transcriptome analysis between potassium-deficiency tolerant and sensitive sweetpotato genotypes in response to potassium-deficiency stress

BACKGROUND

Sweetpotato is a typical ''potassium (K+) favoring'' food crop, which root differentiation process needs a large supply of potassium fertilizer and determine the final root yield. To further understand the regulatory network of the response to low potassium stress, here we analyze physiological and biochemical characteristics, and investigated root transcriptional changes in two sweetpotato genotypes, namely, - K tolerant "Xu32" and - K susceptible"NZ1".

RESULT

We found Xu32 had the higher capability of K+ absorption than NZ1 with better growth performance, higher net photosynthetic rate and higher chlorophyll contents under low potassium stress, and identified 889 differentially expressed genes (DEGs) in Xu32, 634 DEGs in NZ1, 256 common DEGs in both Xu32 and NZ1. The Gene Ontology (GO) term in molecular function enrichment analysis revealed that the DEGs under low K+ stress are predominately involved in catalytic activity, binding, transporter activity and antioxidant activity. Moreover, the more numbers of identified DEGs in Xu32 than that in NZ1 responded to K+-deficiency belong to the process of photosynthesis, carbohydrate metabolism, ion transport, hormone signaling, stress-related and antioxidant system may result in different ability to K+-deficiency tolerance. The unique genes in Xu32 may make a great contribution to enhance low K+ tolerance, and provide useful information for the molecular regulation mechanism of K+-deficiency tolerance in sweetpotato.

CONCLUSIONS

The common and distinct expression pattern between the two sweetpotato genotypes illuminate a complex mechanism response to low potassium exist in sweetpotato. The study provides some candidate genes, which can be used in sweetpotato breeding program for improving low potassium stress tolerance.

Review: Defense responses in sweetpotato (Ipomoea batatas L.) against biotic stress

Sweetpotato (Ipomoea batatas L.) is regarded as amongst the world's most important crops for food, vegetable, forage, and raw material for starch and alcohol production. Since pest attack and disease infection are the main limiting aspects frequently causing the yield loss and quality degradation of sweetpotato, it is a great demand to develop the effective defense strategies for maintaining productivity. In the past decade, many studies have focused on dynamic analysis at the physiological, biochemical, and molecular responses of sweetpotatoes to environmental challenges. This review offers an overview of the defense mechanisms against biotic stresses in sweetpotato observed so far, particularly insect herbivory and pathogen infections. The defenses of sweetpotato include the regulation of the toxic and anti-digestive proteins, plant-derived compounds, physical barrier formation, and sugar distribution. Ipomoelin and sporamin have been extensively researched for the defense against herbivore wounding. Herbivory-induced plant volatiles, chlorogenic acid, and latex phytochemicals play important roles in defenses for insect herbivory. Induction of IbSWEET10 reduces sugar content to mediate F. oxysporum resistance. Therefore, these researches provide the genetic strategies for improving resistance bioengineering and breeding of sweetpotato crops and future prospects for research in this field.

Using machine learning for image-based analysis of sweetpotato root sensory attributes

The sweetpotato breeding process involves assessing different phenotypic traits, such as the sensory attributes, to decide which varieties to progress to the next stage during the breeding cycle. Sensory attributes like appearance, taste, colour and mealiness are important for consumer acceptability and adoption of new varieties. Therefore, measuring these sensory attributes is critical to inform the selection of varieties during breeding. Current methods using a trained human panel enable screening of different sweetpotato sensory attributes. Despite this, such methods are costly and time-consuming, leading to low throughput, which remains the biggest challenge for breeders. In this paper, we describe an approach to apply machine learning techniques with image-based analysis to predict flesh-colour and mealiness sweetpotato sensory attributes. The developed models can be used as high-throughput methods to augment existing approaches for the evaluation of flesh-colour and mealiness for different sweetpotato varieties. The work involved capturing images of boiled sweetpotato cross-sections using the DigiEye imaging system, data pre-processing for background elimination and feature extraction to develop machine learning models to predict the flesh-colour and mealiness sensory attributes of different sweetpotato varieties. For flesh-colour the trained Linear Regression and Random Forest Regression models attained R 2 values of 0.92 and 0.87, respectively, against the ground truth values given by a human sensory panel. In contrast, the Random Forest Regressor and Gradient Boosting model attained R 2 values of 0.85 and 0.80, respectively, for the prediction of mealiness. The performance of the models matched the desirable R 2 threshold of 0.80 for acceptable comparability to the human sensory panel showing that this approach can be used for the prediction of these attributes with high accuracy. The machine learning models were deployed and tested by the sweetpotato breeding team at the International Potato Center in Uganda. This solution can automate and increase throughput for analysing flesh-colour and mealiness sweetpotato sensory attributes. Using machine learning tools for analysis can inform and quicken the selection of promising varieties that can be progressed for participatory evaluation during breeding cycles and potentially lead to increased chances of adoption of the varieties by consumers.

Heterotic gains, transgressive segregation and fitness cost of sweetpotato weevil resistance expression in a partial diallel cross of sweetpotato

Heterosis-exploiting breeding schemes are currently under consideration as a means of accelerating genetic gains in sweetpotato (Ipomoea batatas) breeding. This study was aimed at establishing heterotic gains, fitness costs and transgressive segregation associated with sweetpotato weevil (SPW) resistance in a partial diallel cross of sweetpotato. A total of 1896 clones were tested at two sites, for two seasons each in Uganda. Data on weevil severity (WED), weevil incidence (WI), storage root yield (SRY) and dry matter content (DM) were obtained. Best linear unbiased predictors (BLUPs) for each clone across environments were used to estimate heterotic gains and for regression analyses to establish relationships between key traits. In general, low mid-parent heterotic gains were detected with the highest favorable levels recorded for SRY (14.7%) and WED (- 7.9%). About 25% of the crosses exhibited desirable and significant mid-parent heterosis for weevil resistance. Over 16% of the clones displayed superior transgressive segregation, with the highest percentages recorded for SRY (21%) and WED (18%). A yield penalty of 10% was observed to be associated with SPW resistance whereas no decline in DM was detected in relation to the same. Chances of improving sweetpotato through exploiting heterosis in controlled crosses using parents of mostly similar background are somewhat minimal, as revealed by the low heterotic gains. The yield penalty detected due to SPW resistance suggests that a trade-off may be necessary between maximizing yields and developing weevil-resistant cultivars if the current needs for this crop are to be met in weevil-prone areas.

Early root phenotyping in sweetpotato (Ipomoea batatas L.) uncovers insights into root system architecture variability

Background

We developed a novel, non-destructive, expandable, ebb and flow soilless phenotyping system to deliver a capable way to study early root system architectural traits in stem-derived adventitious roots of sweetpotato (Ipomoea batatas L.). The platform was designed to accommodate up to 12 stems in a relatively small area for root screening. This platform was designed with inexpensive materials and equipped with an automatic watering system.

Methods

To test this platform, we designed a screening experiment for root traits using two contrasting sweetpotato genotypes, 'Covington' and 'NC10-275'. We monitored and imaged root growth, architecture, and branching patterns every five days up to 20 days.

Results

We observed significant differences in both architectural and morphological root traits for both genotypes tested. After 10 days, root length, surface root area, and root volume were higher in 'NC10-275' compared to 'Covington'. However, average root diameter and root branching density were higher in 'Covington'.

Conclusion

These results validated the effective and efficient use of this novel root phenotyping platforming for screening root traits in early stem-derived adventitious roots. This platform allowed for monitoring and 2D imaging of root growth over time with minimal disturbance and no destructive root sampling. This platform can be easily tailored for abiotic stress experiments, and permit root growth mapping and temporal and dynamic root measurements of primary and secondary adventitious roots. This phenotyping platform can be a suitable tool for examining root system architecture and traits of clonally propagated material for a large set of replicates in a relatively small space.

Genome-wide identification and expression analysis of the polygalacturonase gene family in sweetpotato

BACKGROUND

Polygalacturonase (PG), a crucial enzyme involved in pectin degradation, is associated with various plants' developmental and physiological processes such as seed germination, fruit ripening, fruit softening and plant organ abscission. However, the members of PG gene family in sweetpotato (Ipomoea batatas) have not been extensively identified.

RESULTS

In this study, there were 103 PG genes identified in sweetpotato genome, which were phylogenetically clustered into divergent six clades. The gene structure characteristics of each clade were basically conserved. Subsequently, we renamed these PGs according to their locations of the chromosomes. The investigation of collinearity between the PGs in sweetpotato and other four species, contained Arabidopsis thaliana, Solanum lycopersicum, Malus domestica and Ziziphus jujuba, revealed important clues about the potential evolution of the PG family in sweetpotato. Gene duplication analysis showed that IbPGs with collinearity relationships were all derived from segmental duplications, and these genes were under purifying selection. In addition, each promoter region of IbPG proteins contained cis-acting elements related to plant growth and development processes, environmental stress responses and hormone responses. Furthermore, the 103 IbPGs were differentially expressed in various tissues (leaf, stem, proximal end, distal end, root body, root stalk, initiative storage root and fibrous root) and under different abiotic stresses (salt, drought, cold, SA, MeJa and ABA treatment). IbPG038 and IbPG039 were down-regulated with salt, SA and MeJa treatment. According to the further investigation, we found that IbPG006, IbPG034 and IbPG099 had different patterns under the drought and salt stress in fibrous root of sweetpotato, which provided insights into functional differences among these genes.

CONCLUSION

A total of 103 IbPGs were identified and classified into six clades from sweetpotato genome. The results of RNA-Seq and qRT-PCR suggested that IbPG006, IbPG034 and IbPG099 might play a significant role in tissue specificity as well as drought and salt stress responses, which showed valuable information for further functional characterization and application of the IbPGs.

Genome-wide comparative analysis of the valine glutamine motif containing genes in four Ipomoea species

BACKGROUND

Genes with valine glutamine (VQ) motifs play an essential role in plant growth, development, and resistance to biotic and abiotic stresses. However, little information on the VQ genes in sweetpotato and other Ipomoea species is available.

RESULTS

This study identified 55, 58, 50 and 47 VQ genes from sweetpotato (I. batatas), I.triflida, I. triloba and I. nil, respectively. The phylogenetic analysis revealed that the VQ genes formed eight clades (I-VII), and the members in the same group exhibited similar exon-intron structure and conserved motifs distribution. The distribution of the VQ genes among the chromosomes of Ipomoea species was disproportional, with no VQ genes mapped on a few of each species' chromosomes. Duplication analysis suggested that segmental duplication significantly contributes to their expansion in sweetpotato, I.trifida, and I.triloba, while the segmental and tandem duplication contributions were comparable in I.nil. Cis-regulatory elements involved in stress responses, such as W-box, TGACG-motif, CGTCA-motif, ABRE, ARE, MBS, TCA-elements, LTR, and WUN-motif, were detected in the promoter regions of the VQ genes. A total of 30 orthologous groups were detected by syntenic analysis of the VQ genes. Based on the analysis of RNA-seq datasets, it was found that the VQ genes are expressed distinctly among different tissues and hormone or stress treatments. A total of 40 sweetpotato differentially expressed genes (DEGs) refer to biotic (sweetpotato stem nematodes and Ceratocystis fimbriata pathogen infection) or abiotic (cold, salt and drought) stress treatments were detected. Moreover, IbVQ8, IbVQ25 and IbVQ44 responded to the five stress treatments and were selected for quantitative reverse-transcription polymerase chain reaction (qRT-PCR) analysis, and the results were consistent with the transcriptome analysis.

CONCLUSIONS

Our study may provide new insights into the evolution of VQ genes in the four Ipomoea genomes and contribute to the future molecular breeding of sweetpotatoes.

Improving the quality of barren rocky soil by culturing sweetpotato, with special reference to plant-microbes-soil interactions

Biological process is an effective strategy to improve soil quality in agroecosystems. Sweetpotato has long been cultivated in barren rocky soil (BRS) to improve soil fertility and obtain considerably high yield. However, how sweetpotato cultivation affects soil quality is still unclear. We cultured sweetpotato in virgin BRS, and investigated its transcriptome, rhizospheric microbial community and soil properties. A high sweetpotato yield (22.69 t.ha^-1) was obtained through upregulating the expression of genes associated with stress resistance, nitrogen/phosphorus/potassium (N/P/K) uptake, and root exudates transport. Meanwhile, the rhizospheric microbial diversity in BRS increased, and the rhizospheric microbial community structure became more similar to that of fertile soil, which might benefit from the increased root exudates. Notably, the relative abundances of N-fixing and P/K-solubilizing microbes increased, and the copy number of nifH increased 6.67 times. Moreover, the activities of acid, neutral, and alkaline phosphatases increased strongly from 0.63, 0.02, and 1.15-1.58, 0.31, and 2.11 mg phenol·g^-1·d^-1, respectively, and total carbon, dissolved organic carbon, available N/P content also increased, while bulk density and pH of BRS decreased, indicating the enhanced soil fertility. Our study found sweetpotato cultivation improved BRS quality through shaping microbial communities, which has important guiding significance for sustainable agriculture.

RETRACTED: Genome-wide analysis of the B-box gene family in the sweetpotato wild ancestor Ipomoea trifida and determination of the function of IbBBX28 in the regulation of flowering time of Arabidopsis

This article has been retracted: please see Elsevier Policy on Article Withdrawal (https://www.elsevier.com/about/our-business/policies/article-withdrawal). This article has been retracted at the request of of the Editors-in-Chief. A large part of the article is highly similar to the paper previously published by Wenqian Hou, Lei Ren, Yang Zhang, Haoyun Sun, Tianye Shi, Yulan Gu, Aimin Wang, Daifu Ma, Zongyun Li and Lei Zhang in Scientia Horticulturae 288 (2021) 110374 https://doi.org/10.1016/j.scienta.2021.110374. In particular, a large part of the two articles shows a study on the same gene family in the same plant, with similar methodological approaches, resulting in a series of highly similar figures. One of the conditions of submission of a paper for publication is that authors declare explicitly that their work is original and has not appeared in a publication elsewhere. Re-use of any data should be appropriately cited. As such this article represents a severe abuse of the scientific publishing system. The scientific community takes a very strong view on this matter and apologies are offered to readers of the journal that this was not detected during the submission process.

Comparative transcriptome profiling of sweetpotato storage roots during curing-mediated wound healing

Sweetpotato (Ipomoea batatas L. Lam) is an economically important crop that is cultivated for its storage roots. Storage roots provide a source of valuable nutrients, processed foods, animal feeds, and pigments. Sweetpotato storage roots spoil during post-harvest handling because of wounding, which makes them more susceptible to disease-causing microorganisms. Curing to promote wound healing is a common method to control microbial spoilage during post-harvest storage. However, molecular mechanisms underlying the process of curing in sweetpotato storage roots are unknown. To better understand the biology behind curing, the transcriptome of the sweetpotato cultivar, Pungwonmi, was studied using RNA-seq. Storage roots of sweetpotato were treated at 33 °C (Curing) and 13 °C (Control) for 3 days. RNA-seq data identified 78,781 unigenes and 3,366 differentially expressed genes by over log2 fold change (FC) > 2 and <-2. During curing, DEGs encoded genes related to drought/salt stress responses, phyto-hormones (e.g., auxin, ethylene and jasmonic acid), and proteolysis, were up-regulated, whereas those related to redox state, phyto-hormones (e.g., salicylic acid and brassinosteroids), and lignin and flavonoid biosynthesis were down-regulated. Additionally, among the candidate genes, DEGs encoded genes related to proteolysis and pathogen defense, such as protease inhibitors and lipid transfer proteins, were highly up-regulated during curing and storage. This study provides a valuable resource to further understand the molecular basis of curing-mediated wound healing in sweetpotato storage roots. Moreover, genes revealed in this work could present targets for the development of sweetpotato varieties with improved post-harvest storage characteristics.

Genome-wide survey and expression analysis of GRAS transcription factor family in sweetpotato provides insights into their potential roles in stress response

BACKGROUND

The plant-specific GRAS transcription factors play pivotal roles in various adverse environmental conditions. Numerous GRAS genes have been explored and characterized in different plants, however, comprehensive survey on GRASs in sweetpotato is lagging.

RESULTS

In this study, 72 putative sweetpotato IbGRAS genes with uneven distribution were isolated on 15 chromosomes and classified into 12 subfamilies supported by gene structures and motif compositions. Moreover, both tandem duplication and segmental duplication events played critical roles in the expansion of sweetpotato GRAS genes, and the collinearity between IbGRAS genes and the related orthologs from nine other plants further depicted evolutionary insights into GRAS gene family. RNA-seq analysis under salt stress and qRT-PCR detection of 12 selected IbGRAS genes demonstrated their significant and varying inductions under multiple abiotic stresses (salt, drought, heat and cold) and hormone treatments (ABA, ACC and JA). Consistently, the promoter regions of IbGRAS genes harbored a series of stress- and hormone-associated cis-acting elements. Among them, IbGRAS71, the potential candidate for breeding tolerant plants, was characterized as having transactivation activity in yeasts, while IbGRAS-2/-4/-9 did not. Moreover, a complex interaction relationship between IbGRASs was observed through the interaction network analysis and yeast two-hybrid assays.

CONCLUSIONS

Our results laid a foundation for further functional identifications of IbGRAS genes, and multiple members may serve as potential regulators for molecular breeding of tolerant sweetpotato.

Exploration of molecular mechanism of intraspecific cross-incompatibility in sweetpotato by transcriptome and metabolome analysis

Cross-incompatibility, frequently happening in intraspecific varieties, has seriously restricted sweetpotato breeding. However, the mechanism of sweetpotato intraspecific cross-incompatibility (ICI) remains largely unexplored, especially for molecular mechanism. Treatment by inducible reagent developed by our lab provides a method to generate material for mechanism study, which could promote incompatible pollen germination and tube growth in the ICI group. Based on the differential phenotypes between treated and untreated samples, transcriptome and metabolome were employed to explore the molecular mechanism of sweetpotato ICI in this study, taking varieties 'Guangshu 146' and 'Shangshu 19', a typical incompatible combination, as materials. The results from transcriptome analysis showed oxidation-reduction, cell wall metabolism, plant-pathogen interaction, and plant hormone signal transduction were the essential pathways for sweetpotato ICI regulation. The differentially expressed genes (DEGs) enriched in these pathways were the important candidate genes to response ICI. Metabolome analysis showed that multiple differential metabolites (DMs) involved oxidation-reduction were identified. The most significant DM identified in comparison between compatible and incompatible samples was vitexin-2-O-glucoside, a flavonoid metabolite. Corresponding to it, cytochrome P450s were the most DEGs identified in oxidation-reduction, which were implicated in flavonoid biosynthesis. It further suggested oxidation-reduction play an important role in sweetpotato ICI regulation. To validate function of oxidation-reduction, reactive oxygen species (ROS) was detected in compatible and incompatible samples. The green fluorescence was observed in incompatible but not in compatible samples. It indicated ROS regulated by oxidation-reduction is important pathway to response sweetpotato ICI. The results in this study would provide valuable insights into molecular mechanisms for sweetpotato ICI.

Identification and function analysis of bHLH genes in response to cold stress in sweetpotato

Basic/helix-loop-helix (bHLH) transcription factors are involved in various metabolic and physiological processes in plants. Sweetpotato (Ipomoea batatas (L.) Lam.) is an important crop in China but is highly susceptible to cold stress. However, little information on the bHLH gene family is available, and the function of this family in response to cold stress has not been revealed in sweetpotato. Here, 110 IbbHLHs were identified and classified into 17 categories based on phylogenetic relationships, conserved motifs and gene structure analyses. Except for 5 IbbHLHs, 90 IbbHLHs were putative E-box-binding proteins including 70 IbbHLHs belonging to G-box, whereas 15 IbbHLHs were putative non-E box-binding proteins based on DNA-binding analysis. In total, 37 pairs of segmental duplicated genes and 5 pairs of tandem duplication genes were identified within the IbbHLH gene family. The transcript level of 20 IbbHLHs was regulated by cold stress based on RNA-seq data, and 8 genes were selected for further quantitative real-time PCR (qRT-PCR) analysis. IbHLH8 and IbHLH92 are involved in network interaction with several genes related to abiotic and biotic stresses under cold treatment. IbbHLH79, an ICE1-like gene, was isolated and overexpressed in sweetpotato. The IbbHLH79 protein can activate the CBF (C-repeat Binding Factor) pathway, and IbbHLH79-overexpressing transgenic plants display enhanced cold tolerance. Taken together, these results provide valuable information on the IbbHLH gene family; in addition, several IbbHLHs may regulate cold stress, and the results suggest IbbHLH79 will be useful for molecular breeding of enhanced cold tolerance in sweetpotato.

The sweetpotato GIGANTEA gene promoter is co-regulated by phytohormones and abiotic stresses in Arabidopsis thaliana

GIGANTEA (GI) is known to play significant roles in various molecular pathways. Nevertheless, the underlying mechanism of the transcriptional regulation of GI remains obscure in sweetpotato. In the present study, a 1518-bp promoter sequence was obtained from the Ipomoea batatas GIGANTEA (IbGI) gene, and several potential cis-elements responsive to light, phytohormones and abiotic stresses were identified by in silico analysis. In order to functionally validate the IbGI promoter, the 5' deletion analysis of the promoter was performed by cloning the full-length promoter (D0) and its four deletion fragments, D1 (1235 bp), D2 (896 bp), D3 (549 bp) and D4 (286 bp), upstream of the β-glucuronidase (GUS) reporter gene. Then, these were stably transformed in Arabidopsis plants. All transgenic seedlings exhibited stable GUS activity in the condition of control, but with decreased activity in the condition of most treatments. Interestingly, merely D1 seedlings that contained an abscisic acid responsive cis-element (ABRE-element) had an extremely powerful GUS activity under the treatment of ABA, which implies that fragment spanning nucleotides of -1235 to -896 bp might be a crucial component for the responses of ABA. Eight different types of potential transcriptional regulators of IbGI were isolated by Y1H, including TGA2.2, SPLT1 and GADPH, suggesting the complex interaction mode of protein-DNA on the IbGI promoter. Taken together, these present results help to better understand the transcriptional regulation mechanism of the IbGI gene, and provides an insight into the IbGI promoter, which can be considered as an alternation for breeding transgenic plants.

The sweetpotato β-amylase gene IbBAM1.1 enhances drought and salt stress resistance by regulating ROS homeostasis and osmotic balance

Abiotic stressors, such as drought and high salinity, seriously affect plant growth, productivity, and quality. Maintaining reactive oxygen species (ROS) homeostasis and osmotic balance plays a crucial role in abiotic stress tolerance. β-amylase (BAM) hydrolyzes α-1,4-glycosidic bonds by releasing maltose from starch in the regulation of soluble sugars. However, the function and mechanism of BAMs related to abiotic stress resistance remain unclear in sweetpotato (Ipomoea batatas (L.) Lam.). In this study, we isolated a novel β-amylase gene IbBAM1.1, which was strongly induced by PEG6000, NaCl, and maltose treatments in sweetpotato variety Yanshu25. Overexpression of IbBAM1.1 conferred enhanced tolerance to the drought and high salinity stressors in Arabidopsis thaliana. The activity of β-amylase and the degradation of starch were promoted under drought or salt stress. Accordingly, the contents of osmoprotectants, including maltose and proline were significantly higher in the transgenic lines than those in wild type (WT) plants. Less ROS, such as H₂O₂ and O₂^-, accumulated in the overexpressing lines than in WT plants. Superoxide dismutase activity was strongly enhanced and the level of malondialdehyde was lower under the drought or salt treatment in transgenic plants. Taken together, these results demonstrate that IbBAM1.1 acted as a positive regulator, at least in part, by regulating the level of osmoprotectants to balance the osmotic pressure and activate the scavenging system to maintain ROS homeostasis in the plants.

Overexpression of IbLfp in sweetpotato enhances the low-temperature storage ability of tuberous roots

Sweetpotato (Ipomoea batatas [L.] Lam) is a prospective food crop that ensures food and nutrition security under the dynamic changes in global climate. Peroxidase (POD) is a multifunctional enzyme involved in diverse plant physiological processes, including stress tolerance and cell wall lignification. Although various POD genes were cloned and functionally characterized in sweetpotato, the role of POD in lignification and low-temperature storage ability of sweetpotato tuberous roots is yet to be investigated. In this study, we isolated the cold-induced lignin forming peroxidase (IbLfp) gene of sweetpotato, and analyzed its physiological functions. IbLfp showed more predominant expression in fibrous roots than in other tissues. Moreover, IbLfp expression was up-regulated in leaves and roots under cold stress, and was altered by other abiotic stresses. Tuberous roots of transgenic sweetpotato lines overexpressing IbLfp (LP lines) showed improved tolerance to low temperature, with lower malondialdehyde and hydrogen peroxide contents than non-transgenic sweetpotato plants under cold stress. The enhanced cold tolerance of LP lines could be attributed to the increased basal activity of POD, which is involved in reactive oxygen species (ROS) scavenging. Moreover, greater accumulation of lignin could also contribute to the enhanced cold tolerance of LP lines, as lignin acts as a protective barrier against invading pathogens, which is a secondary symptom of chilling injury in sweetpotato. Overall, the results of this study enhance our understanding of the function of POD in low-temperature storage of sweetpotato tuberous roots.

Overexpression of 4-hydroxyphenylpyruvate dioxygenase (IbHPPD) increases abiotic stress tolerance in transgenic sweetpotato plants

Tocopherols are lipid-soluble compounds regarded as vitamin E compounds and they function as antioxidants in scavenging lipid peroxyl radicals and quenching reactive oxygen species (ROS). In our previous studies, we isolated five tocopherol biosynthesis genes from sweetpotato (Ipomoea batatas [L.] Lam) plants including 4-hydroxyphenylpyruvate dioxygenase (IbHPPD). HPPD is the first regulatory enzyme in vitamin E biosynthesis and serves to catalyze in the first steps α-tocopherol and plastoquinone biosynthesis by converting 4-hydroxyphenylpyruvate (HPP) to homogentisic acid (HGA). In this study, we generated transgenic sweetpotato plants overexpressing IbHPPD under the control of cauliflower mosaic virus (CaMV) 35S promoter (referred to as HP plants) via Agrobacterium-mediated transformation to understand the function of IbHPPD in sweetpotato. Three transgenic lines (HP3, HP14 and HP15) with high transcript levels of IbHPPD were selected for further characterization. Compared with non-transgenic (NT) plants, HP plants exhibited enhanced tolerance to multiple environmental stresses, including salt, drought, and oxidative stresses. In addition, HP plants showed increased tolerance to the herbicide sulcotrione, which is involved in the inhibition of the HPPD. Interestingly, after stress treatments, HP plants also showed higher abscisic acid (ABA) contents than NT plants. Under dehydrated condition, HP plants displayed an elevated α-tocopherol content to 19-27% in leaves compared with NT plants. These results indicate that increased abiotic stress tolerance in HP plants is related to inducing enhancement of α-tocopherol and ABA contents.

Tuberous roots of transgenic sweetpotato overexpressing IbCAD1 have enhanced low-temperature storage phenotypes

Lignin is associated with cell wall rigidity, water and solute transport, and resistance to diverse stresses in plants. Lignin consists of polymerized monolignols (p-coumaryl, coniferyl, and sinapyl alcohols), which are synthesized by cinnamyl alcohol dehydrogenase (CAD) in the phenylpropanoid pathway. We previously investigated cold-induced IbCAD1 expression by transcriptome profiling of cold-stored tuberous roots of sweetpotato (Ipomoea batatas [L.] Lam). In this study, we confirmed that IbCAD1 expression levels depended on the sweetpotato root type and were strongly induced by several abiotic stresses. We generated transgenic sweetpotato plants overexpressing IbCAD1 (TC plants) to investigate CAD1 physiological functions in sweetpotato. TC plants displayed lower root weights and lower ratios of tuberous roots to pencil roots than non-transgenic (NT) plants. The lignin contents in tuberous roots of NT and TC plants differed slightly, but these differences were not significant. By contrast, monolignol levels and syringyl (S)/guaiacyl (G) ratios were higher in TC plants than NT plants, primarily owing to syringyl unit accumulation. Tuberous roots of TC plants displayed enhanced low-temperature (4 °C) storage with lower malondialdehyde and H₂O₂ contents than NT plants. We propose that high monolignol levels in TC tuberous roots served as substrates for increased peroxidase activity, thereby enhancing antioxidation capacity against cold stress-induced reactive oxygen species. Increased monolignol contents and/or increased S/G ratios might contribute to pathogen-induced stress tolerance as a secondary chilling-damage response in sweetpotato. These results provide novel information about CAD1 function in cold stress tolerance and root formation mechanisms in sweetpotato.

Characterization of Nucleotide Binding -Site-Encoding Genes in Sweetpotato, Ipomoea batatas(L.) Lam., and Their Response to Biotic and Abiotic Stresses

Sweetpotato, Ipomoea batatas (L.) Lam., is an important and widely grown crop, yet its production is affected severely by biotic and abiotic stresses. The nucleotide binding site (NBS)-encoding genes have been shown to improve stress tolerance in several plant species. However, the characterization of NBS-encoding genes in sweetpotato is not well-documented to date. In this study, a comprehensive analysis of NBS-encoding genes has been conducted on this species by using bioinformatics and molecular biology methods. A total of 315 NBS-encoding genes were identified, and 260 of them contained all essential conserved domains while 55 genes were truncated. Based on domain architectures, the 260 NBS-encoding genes were grouped into 6 distinct categories. Phylogenetic analysis grouped these genes into 3 classes: TIR, CC (I), and CC (II). Chromosome location analysis revealed that the distribution of NBS-encoding genes in chromosomes was uneven, with a number ranging from 1 to 34. Multiple stress-related regulatory elements were detected in the promoters, and the NBS-encoding genes' expression profiles under biotic and abiotic stresses were obtained. According to the bioinformatics analysis, 9 genes were selected for RT-qPCR analysis. The results revealed that IbNBS75, IbNBS219, and IbNBS256 respond to stem nematode infection; Ib-NBS240, IbNBS90, and IbNBS80 respond to cold stress, while IbNBS208, IbNBS71, and IbNBS159 respond to 30% PEG treatment. We hope these results will provide new insights into the evolution of NBS-encoding genes in the sweetpotato genome and contribute to the molecular breeding of sweetpotato in the future.

Effects of exogenous phytohormones on chlorogenic acid accumulation and pathway-associated gene expressions in sweetpotato stem tips

Sweetpotato (Ipomoea batatas [L.] Lam.) stem tips, which contain high concentrations of chlorogenic acid (CGA), are useful as a physiologically functional food to protect against some serious diseases. According to previous studies, exogenous application of phytohormones may be an effective agrotechnical measure to control CGA biosynthesis through the transcriptional regulation of pathway gene expressions. To understand the mechanism of CGA biosynthesis in sweetpotato, we investigated the effects of exogenous phytohormones on CGA metabolism in stem tips of sweetpotato. A significantly elevated CGA content was observed in salicylic acid (SA)-treated sweetpotato stem tips at 72 h, as well as in those subjected to abscisic acid (ABA) or gibberellic acid (GA) treatments. Dynamic expression change of seven enzyme genes involved in sweetpotato CGA biosynthesis were analyzed to determine correlations between transcript levels and CGA accumulation. As revealed by the differential expression of these genes under distinct phytohormone treatments, the regulation of specific pathway genes is a critical determinant of the accumulation of CGA in sweetpotato stem tips. We also found that several hormone-responsive sites, such as those for ABA, GA, SA, and jasmonic acid (JA), were present in the promoter regions of sweetpotato CGA biosynthestic pathway genes. Collectively, phytohormones can regulate the transcription of CGA synthesis-related genes and ultimately affect CGA accumulation in sweetpotato stem tips, whereas the regulatory differences are mirrored by cis-acting elements in the corresponding pathway gene promoters.

Analysis of β-amylase gene (Amyβ) variation reveals allele association with low enzyme activity and increased firmness in cooked sweetpotato (Ipomoea batatas) from East Africa

β-amylase is a thermostable enzyme that hydrolyses starch during cooking of sweetpotato (Ipomoea batatas) storage roots, thereby influencing eating quality. Its activity is known to vary amongst genotypes but the genetic diversity of the beta-amylase gene (Amyβ) is not well studied. Amyβ has a highly conserved region between exon V and VI, forming part of the enzyme's active site. To determine the gene diversity, a 2.3 kb fragment, including the conserved region of the Amyβ gene was sequenced from 25 sweetpotato genotypes. The effect of sequence variation on gene expression, enzyme activity, and firmness in cooked roots was determined. Six genotypes carrying several SNPs within exon V, linked with an AT or ATGATA insertion in intron V were unique and clustered together. The genotypes also shared an A336E substitution in the amino acid sequence, eight residues upstream of a substrate-binding Thr344. The genotypes carrying this allele exhibited low gene expression and low enzyme activity. Enzyme activity was negatively correlated with firmness (R = -0.42) in cooked roots. This is the first report of such an allele, associated with low enzyme activity. These results suggest that genetic variation within the AmyB locus can be utilized to develop markers for firmness in sweetpotato breeding.

Comparative analysis of chloroplast genomes of cultivars and wild species of sweetpotato (Ipomoea batatas [L.] Lam)

Background

Sweetpotato (Ipomoea batatas [L.] Lam.) is an important food crop. However, the genetic information of the nuclear genome of this species is difficult to determine accurately because of its large genome and complex genetic background. This drawback has limited studies on the origin, evolution, genetic diversity and other relevant studies on sweetpotato.

Results

The chloroplast genomes of 107 sweetpotato cultivars were sequenced, assembled and annotated. The resulting chloroplast genomes were comparatively analysed with the published chloroplast genomes of wild species of sweetpotato. High similarity and certain specificity were found among the chloroplast genomes of Ipomoea spp. Phylogenetic analysis could clearly distinguish wild species from cultivars. Ipomoea trifida and Ipomoea tabascana showed the closest relationship with the cultivars, and different haplotypes of ycf1 could be used to distinguish the cultivars from their wild relatives. The genetic structure was analyzed using variations in the chloroplast genome. Compared with traditional nuclear markers, the chloroplast markers designed based on the InDels on the chloroplast genome showed significant advantages.

Conclusions

Comparative analysis of chloroplast genomes of 107 cultivars and several wild species of sweetpotato was performed to help analyze the evolution, genetic structure and the development of chloroplast DNA markers of sweetpotato.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07544-y.

A novel sweetpotato RING-H2 type E3 ubiquitin ligase gene IbATL38 enhances salt tolerance in transgenic Arabidopsis

Arabidopsis Toxicos en Levadura (ATL) proteins compose a subfamily of E3 ubiquitin ligases and play major roles in regulating plant growth, cold, drought, oxidative stresses response and pathogen defense in plants. However, the role in enhancing salt tolerance has not been reported to date. Here, we cloned a novel RING-H2 type E3 ubiquitin ligase gene, named IbATL38, from sweetpotato cultivar Lushu 3. This gene was highly expressed in the leaves of sweetpotato and strongly induced by NaCl and abscisic acid (ABA). This IbATL38 was localized to nucleus and plasm membrane and possessed E3 ubiquitin ligase activity. Overexpression of IbATL38 in Arabidopsis significantly enhanced salt tolerance, along with inducible expression of a series of stress-responsive genes and prominently decrease of H₂O₂ content. These results suggest that IbATL38 as a novel E3 ubiquitin ligase may play an important role in salt stress response.

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. β-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 β-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.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07436-1.

First Report of Root-Knot Nematode Meloidogyne enterolobii Infecting Sweetpotato in the State of Rio Grande do Norte, Brazil

The sweetpotato (Ipomoea batatas L., Convolvulaceae family) originated in Latin America and is currently cultivated worldwide. The storage roots, rich in calories, have made this crop one of the main caloric sources for low-income populations, especially in developing countries. Brazil annually produces about 805,000 tons, with the Northeast region responsible for 34% of this production (Albuquerque et al. 2020). In October 2019, sweetpotato plants cv. Campina, from a field in the region of Touros, state of Rio Grande do Norte (RN), Brazil (5°12'31"S 35°34'42"W), presented deformed storage roots, with galls, typical of root-knot nematodes. The roots were sent to the Nematology Laboratory (LabNema) where 14,032 eggs and 3,312 second-stage juveniles (J2s) of Meloidogyne sp., in 10 g of roots, were recovered. The species of adults was identified through morphological, biochemical, and phylogenetic analysis. The perineal region of females (n = 10) presented an oval shape, with a high and semi-trapezoidal dorsal arch and streak-free perivulval region. The labial region of males (n=10) presented high and rounded head cap, labial region slightly set off from the body, without annulations. The morphological characters were compatible with the original description of Meloidogyne enterolobii (Yang and Eisenback 1983). The phenotype of esterase isoenzymes showed two major bands (VS1-S1) also characteristic of M. enterolobii (Esbenshade and Triantaphyllou 1985). Sequences of 18S rDNA (~1200bp) of individual females (Holterman et al. 2006) obtained from sweetpotatoes before (SPme1 and 2) and after inoculation (SPme3 and 6), and from guava, used as M. enterolobii species control, were submitted to Bayesian analysis. The sequences presented genetic diversity among them resulting from seven SNPs (Single Nucleotide Polymorphism) and 99.4 to 99.9% identity with M. enterolobii sequences deposited in the NCBI GenBank (accession numbers MW209034-MW209039). The pathogenicity test was carried out under greenhouse conditions, in which 3,000 eggs and J2s from the original population isolated of M. enterolobii were inoculated in sweetpotato seedlings cv. Campina (n = 6). After three months, the roots presented galls and deformations typical of root-knot nematodes, while non-inoculated plants did not present any symptoms. An average of 15,900 eggs and J2s of M. enterolobii (RF = 5.3) were recovered from the roots, proving that sweetpotatoes were a host of this species. Meloidogyne enterolobii is known to cause great damage to sweetpotato (Ye et al. 2020). In Brazil, Meloidogyne nematode had been reported once, isolated from a sweetpotato field in the Ceara state and the species suggested by the authors according to esterase electrophoresis was M. enterolobii. Nonetheless, the authors did not present taxonomic, isoenzyme phenotypes and molecular species identification integratively, nor included pathogenicity tests (Silva et al. 2016). Therefore, it is the first time that M. enterolobii, with reliable identification by different methods, including sequencing, was detected in commercial sweetpotato fields in the RN state and in Brazil. The local farmers reported that this nematode deforms the storage roots which make them useless for commercialization, resulting in minimal losses of 50% of production in the infested areas. Furthermore, as sweetpotatoes are vegetatively propagated, the spread of this nematode through planting material is favored. Considering the importance of this crop in Brazil, this report is essential for control measures of this pathogen to be taken in order to avoid its spread to other regions.

Identification of Shaker K+ channel family members in sweetpotato and functional exploration of IbAKT1

The Shaker K⁺ channel family plays a vital role in potassium absorption and stress resistance in plants. However little information on the genes family is available about sweetpotato. In the present study, eleven sweetpotato Shaker K⁺ channel genes were identified and classified into five groups based on phylogenetic relationships, conserved motifs, and gene structure analyses. Based on synteny analysis, four duplicated gene pairs were identified, derived from both ancient and recent duplication, whereas only one resulted from tandem duplication events. Different expression pattern of Shaker K⁺ channel genes in roots of Xu32 and NZ1 resulted in different K⁺ deficiency tolerances, suggesting there is different mechanism of K⁺ uptake in sweetpotato cultivars with different K⁺-tolerance levels. Quantitative real-time PCR analysis revealed that the shaker K⁺ channel genes responded to drought and high salt stresses. Higher K⁺ influx under normal condition and lower K⁺ efflux under K⁺ deficiency stress were observed in IbAKT1 overexpressing transgenic roots than in adventitious roots, which indicated that IbAKT1 may play an important role in the regulation of K⁺ deficiency tolerance in sweetpotato. This is the first genome-wide analysis of Shaker K⁺ channel genes and the first functional analysis of IbAKT1 in sweetpotato. Our results provide valuable information on the gene structure, evolution, expression and functions of the Shaker K⁺ channel gene family in sweetpotato.

Mechanisms of low cadmium accumulation in storage root of sweetpotato (Ipomoea batatas L.)

Sweetpotato (Ipomoea batatas L.) possess great application prospects due to their low cadmium (Cd) concentration within their storage roots despite growth on Cd-polluted fields. The mechanisms of low Cd accumulation in storage root is not entirely clear. We found that the blocking effect of Cd uptake in the root absorption system and the characteristics of Cd distribution in storage root play a decisive role in the regulation of low Cd accumulation in storage root. Cd absorbed from the rhizosphere mainly accumulated in feeder roots in Cd dose-dependent accumulation analyses. Meanwhile, we found that Cd absorbed by the peels of storage root was mainly transported from peels to shoots, rather than directly into the fleshed storage root. Further analysis indicated that Cd uptake, transport, and distribution in sweetpotato hinges on whether Cd enters the plant plasma membrane by either the symplast or apoplast pathway. The Cd concentration in feeder root decreased after respiratory inhibitors CCCP and DNP treatment and increased after the culture temperature was raised from 28 ℃ to 35 ℃. Non-invasive microelectrode Cd flux measurements further revealed that Cd uptake in feeder root was affected greatly by the Cd concentration of the solution and was markedly reduced by respiratory inhibitor CCCP. Relative to the elongation zone and mature zone, the meristematic zone was the main site of Cd uptake in the root absorption system. This study suggests that inhibition of Cd uptake by the root absorption system and the characteristics of Cd distribution in storage root are the main reasons for low cadmium accumulation in storage root.

Transcriptomic and targeted metabolomic analysis identifies genes and metabolites involved in anthocyanin accumulation in tuberous roots of sweetpotato (Ipomoea batatas L.)

Purple-fleshed sweetpotato (PFSP) accumulates high amounts of anthocyanins that are beneficial to human health. Although biosynthesis of such secondary metabolites has been well studied in aboveground organs of many plants, the mechanisms underlying anthocyanin accumulation in underground tuberous roots of sweetpotato are less understood. To identify genes and metabolites involved in anthocyanin accumulation in sweetpotato, we performed comparative transcriptomic and metabolomic analysis of (PFSP) and white-fleshed sweetpotato (WFSP). Anthocyanin-targeted metabolome analysis revealed that delphinidin, petunidin, and rosinidin were the key metabolites conferring purple pigmentation in PFSP as they were highly enriched in PFSP but absent in WFSP. Transcriptomic analysis identified 358 genes that were potentially implicated in multiple pathways for the biosynthesis of anthocyanins. Although most of the genes were previously known for their roles in anthocyanin biosynthesis, we identified 26 differentially expressed genes that are involved in Aux/IAA-ARF signaling. Gene-metabolite correlation analysis also revealed novel genes that are potentially involved in the anthocyanin accumulation in sweetpotato. Taken together, this study provides insights into the genes and metabolites underlying anthocyanin enrichment in underground tuberous roots of sweetpotato.

Changes in cell wall components and polysaccharide-degrading enzymes in relation to differences in texture during sweetpotato storage root growth

Sweetpotato has special texture characteristics, which directly affect the eating quality and post-production processing quality of sweetpotato. To investigate the texture change mechanism of sweetpotato during the growth process, this study selected two varieties with significant differences in texture from 35 varieties. The storage roots were sampled at 50, 80, 110, and 140 days after planting. Measure the texture parameters, the cell wall composition content, cell wall-related enzyme activities and the expression of expansin genes of sweetpotato storage roots. The results show that the hardness, adhesiveness and chewiness parameters of 'Yushu No 10' were significantly lower than those of 'Mianfen No 1', they have significantly different texture properties. In terms of cell wall composition, the soluble pectin content of 'Yushu No 10' was more than twice that of 'Mianfen No 1', whereas the insoluble pectin content was lower than that of 'Mianfen No 1', with the cellulose content of 'Yushu No 10' being significantly higher than that of 'Mianfen No 1'. In terms of cell wall-related enzymes, 'Yushu No 10' hardness gumminess and chewiness had a significant correlation with hemicellulose activity, and 'Mianfen No 1' had insignificant correlation with four cell wall-related enzymes. Expansin genes were also expressed differently during the various stages of root tubers expansin. The expressions of IbEXP1, IbEXP2 and IbEXPL1 were significantly correlated with the changes in cell wall component content, and were related to the qualitative structure changes. The research conclusion shows that the texture changes during the growth of sweetpotato are related to cell wall composition, cell wall-related enzyme activity changes, and the expression of expansin genes. This study provides theoretical guidance for in-depth study of texture changes of sweetpotato, post-harvest processing and utilization and quality improvement of storage roots.

Selection of flooding stress tolerant sweetpotato cultivars based on biochemical and phenotypic characterization

Sweetpotato [Ipomoea batatas (L.) Lam] serves as a sustainable food source and ensures nutrition security in the face of climate change. Recently, farmers have developed increased interest in replacing rice with sweetpotato in paddy fields for higher income. However, sweetpotato is more susceptible to flooding stress than other abiotic stresses including drought and salinity. Here, we selected flooding tolerant sweetpotato cultivars based on biochemical characterization. Young seedlings of 33 sweetpotato cultivars were subjected to flooding stress for 20 days, and Yeonjami (YJM) was identified as the most flooding tolerant sweetpotato cultivar. Plant growth and biochemical characteristics of YJM were compared with those of Jeonmi (JM), a flooding sensitive sweetpotato cultivar. Under flooding stress, YJM showed higher content of chlorophyll and lower inhibition of plant height and fibrous root length than JM. Biochemical characterization revealed that although malondialdehyde and hydrogen peroxide contents were increased in fibrous roots of both cultivars, the amount of increase was 4-fold lower in YJM than in JM. Additionally, leaves of YJM showed higher ascorbate peroxidase activity than those of JM under flooding stress. Our results suggest that high membrane stability and antioxidant capacity are important flooding tolerance factors in sweetpotato. Furthermore, several flooding tolerance-related genes involved in starch and sucrose metabolism, fermentation, and cell wall loosening showed earlier induction and higher transcript levels in YJM leaves and fibrous roots than in JM tissues under flooding stress. Thus, phenotypic and biochemical characterization suggests that YJM could be used as a flooding tolerant sweetpotato cultivar.

Proteomic and metabolic profile analysis of low-temperature storage responses in Ipomoea batata Lam. tuberous roots

BACKGROUND

Sweetpotato (Ipomoea batatas L.) is one of the seven major food crops grown worldwide. Cold stress often can cause protein expression pattern and substance contents variations for tuberous roots of sweetpotato during low-temperature storage. Recently, we developed proteometabolic profiles of the fresh sweetpotatoes (cv. Xinxiang) in an attempt to discern the cold stress-responsive mechanism of tuberous root crops during post-harvest storage.

RESULTS

For roots stored under 4 °C condition, the CI index, REC and MDA content in roots were significantly higher than them at control temperature (13 °C). The activities of SOD, CAT, APX, O₂^.- producing rate, proline and especially soluble sugar contents were also significantly increased. Most of the differentially expressed proteins (DEPs) were implicated in pathways related to metabolic pathway, especially phenylpropanoids and followed by starch and sucrose metabolism. L-ascorbate peroxidase 3 and catalase were down-regulated during low temperature storage. α-amylase, sucrose synthase and fructokinase were significantly up-regulated in starch and sucrose metabolism, while β-glucosidase, glucose-1-phosphate adenylyl-transferase and starch synthase were opposite. Furthermore, metabolome profiling revealed that glucosinolate biosynthesis, tropane, piperidine and pyridine alkaloid biosynthesis as well as protein digestion and absorption played a leading role in metabolic pathways of roots. Leucine, tryptophan, tyrosine, isoleucine and valine were all significantly up-regulated in glucosinolate biosynthesis.

CONCLUSIONS

Our proteomic and metabolic profile analysis of sweetpotatoes stored at low temperature reveal that the antioxidant enzymes activities, proline and especially soluble sugar content were significantly increased. Most of the DEPs were implicated in phenylpropanoids and followed by starch and sucrose metabolism. The discrepancy between proteomic (L-ascorbate peroxidase 3 and catalase) and biochemical (CAT/APX activity) data may be explained by higher H₂O₂ levels and increased ascorbate redox states, which enhanced the CAT/APX activity indirectly. Glucosinolate biosynthesis played a leading role in metabolic pathways. Leucine, tryptophan, tyrosine, isoleucine and valine were all significantly up-regulated in glucosinolate biosynthesis.

Optimization of reference genes for qRT-PCR analysis of microRNA expression under abiotic stress conditions in sweetpotato

Sweetpotato (Ipomoea batatas. L) is an important food crop, harvested for its nutrient-rich tuberous roots. Drought and salt stresses are two major factors limiting the sweetpotato production. Since microRNAs (miRNAs) are well known to play crucial roles in regulation of plant stress responses, quantitative profiling of miRNA expression under stress conditions will facilitate identification and genetic manipulation of novel miRNAs to improve stress tolerance. Real-time quantitative reverse transcription PCR (qRT-PCR) is a commonly used tool for this purpose, but not without challenges. Although stem-loop and poly(A)-tail modified qRT-PCR methods were developed for characterizing miRNA expression, accurate profiling of miRNAs is still difficult in many plant species because of a lack of reliable reference genes for normalizing miRNA transcripts. To identify reference genes that are suitable for normalizing miRNA expression in sweetpotato, the expression stability of eight candidate miRNAs and two commonly used reference genes were tested in 96 samples involving four tissues and two cultivars under drought and salt stress treatments. Data analysis using the geNorm, NormFinder and Bestkeeper algorithms demonstrated that miRn60, miR482, and their combination were reliable references. We further validated the reference genes by expression analysis of the well-characterized miR319 and miR156 that regulate drought and salt stress responses, respectively. The reference genes identified in this study will facilitate future miRNA analysis under abiotic stress conditions in sweetpotato.

Continuous Storage Root Formation and Bulking in Sweetpotato

This study investigated the phenotypic variation of continuous storage root formation and bulking (CSRFAB) growth patterns underlying the development of sweetpotato genotypes for identification of potential varieties adapted to piecemeal harvesting for small scale farmers. The research was conducted between September 2016 and August 2017 in Uganda. Genotypes from two distinct sweetpotato genepool populations (Population Uganda A and Population Uganda B) comprising 130 genotypes, previously separated using 31 simple sequence repeat (SSR) markers were used. Measurements (4 harvest times with 4 plants each) were repeated on genotypes in a randomized complete block design with 2 replications in 2 locations for 2 seasons. We developed a scoring scale of 1 to 9 and used it to compare growth changes between consecutive harvests. Data analysis was done using residual or restricted maximum likelihood (REML). Data showed a non-linear growth pattern within and between locations, seasons, and genotypes for most traits. Some genotypes displayed early initiation and increase of bulking, while others showed late initiation. Broad sense heritability of CSRFAB was low due to large GxE interactions but higher in other traits  probably due to high genetic influence and the effectiveness of the methodology. A high level of reproducibility (89%) was observed comparing 2016B and 2017A seasons (A and B are first and second season, respectively) at the National Crops Resources Research Institute (NaCRRI), Namulonge, Uganda. Choosing CSRFAB genotypes can more than double the sweetpotato production (average maximum yield of 13.1 t/ha for discontinuous storage root formation and bulking (DSRFAB) versus 28.6 t/ha for CSRFAB, demonstrating the importance of this underresearched component of storage root yield.

Induced biosynthesis of chlorogenic acid in sweetpotato leaves confers the resistance against sweetpotato weevil attack

Sweetpotato weevil is among the most harmful pests in some major sweetpotato growing areas with warm climates. To enable the future establishment of safe weevil-resistance strategies, anti-weevil metabolites from sweetpotato should be investigated. In the present study, we pretreated sweetpotato leaves with exogenous chlorogenic acid and then exposed them to sweetpotato weevils to evaluate this compound's anti-insect activity. We found that chlorogenic acid applied to sweetpotato conferred significant resistance against sweetpotato-weevil feeding. We also observed enhanced levels of chlorogenic acid in response to weevil attack in sweetpotato leaves. To clarify how sweetpotato weevils regulate the generation of chlorogenic acid, we examined key elements of plant-herbivore interaction: continuous wounding and phytohormones participating in chlorogenic acid formation. According to our results, sweetpotato weevil-derived continuous wounding induces increases in phytohormones, including jasmonic acid, salicylic acid, and abscisic acid. These phytohormones can upregulate expression levels of genes involved in chlorogenic acid formation, such as IbPAL, IbC4H and IbHQT, thereby leading to enhanced chlorogenic acid generation. This information should contribute to understanding of the occurrence and formation of natural anti-weevil metabolites in sweetpotato in response to insect attack and provides critical targets for the future breeding of anti-weevil sweetpotato cultivars.

Identification of QTL for resistance to root rot in sweetpotato (Ipomoea batatas (L.) Lam) with SSR linkage maps

BACKGROUND

Sweetpotato root rot is a devastating disease caused by Fusarium solani that seriously endangers the yield of sweetpotato in China. Although there is currently no effective method to control the disease, breeding of resistant varieties is the most effective and economic option. Moreover, quantitative trait locus (QTL) associated with resistance to root rot have not yet been reported, and the biological mechanisms of resistance remain unclear in sweetpotato. Thus, increasing our knowledge about the mechanism of disease resistance and identifying resistance loci will assist in the development of disease resistance breeding.

RESULTS

In this study, we constructed genetic linkage maps of sweetpotato using a mapping population consisting of 300 individuals derived from a cross between Jizishu 1 and Longshu 9 by simple sequence repeat (SSR) markers, and mapped seven QTLs for resistance to root rot. In total, 484 and 573 polymorphic SSR markers were grouped into 90 linkage groups for Jizishu 1 and Longshu 9, respectively. The total map distance for Jizishu 1 was 3974.24 cM, with an average marker distance of 8.23 cM. The total map distance for Longshu 9 was 5163.35 cM, with an average marker distance of 9.01 cM. Five QTLs (qRRM_1, qRRM_2, qRRM_3, qRRM_4, and qRRM_5) were located in five linkage groups of Jizishu 1 map explaining 52.6-57.0% of the variation. Two QTLs (qRRF_1 and qRRF_2) were mapped on two linkage groups of Longshu 9 explaining 57.6 and 53.6% of the variation, respectively. Furthermore, 71.4% of the QTLs positively affected the variation. Three of the seven QTLs, qRRM_3, qRRF_1, and qRRF_2, were colocalized with markers IES43-5mt, IES68-6 fs**, and IES108-1 fs, respectively.

CONCLUSIONS

To our knowledge, this is the first report on the construction of a genetic linkage map for purple sweetpotato (Jizishu 1) and the identification of QTLs associated with resistance to root rot in sweetpotato using SSR markers. These QTLs will have practical significance for the fine mapping of root rot resistance genes and play an important role in sweetpotato marker-assisted breeding.

A novel sucrose transporter gene IbSUT4 involves in plant growth and response to abiotic stress through the ABF-dependent ABA signaling pathway in Sweetpotato

BACKGROUND

To maintain sweetpotato (Ipomoea batatas (L.) Lam) growth and yield, sucrose must be transported from the leaves to the roots. Sucrose transporters or carriers (SUTs or SUCs) transport sucrose and are involved in plant growth and response to abiotic stress. However, the mechanisms of SUTs in sweetpotato abiotic stress resistance remains to be determined.

RESULTS

In the present study, we cloned a novel IbSUT4 gene; the protein encoded by this gene is localized in the tonoplast and plasma membrane. The plant growth was promoted in the IbSUT4 transgenic Arabidopsis thaliana lines, with increased expression of AtFT, a regulator of flowering time in plants. Over-expression of IbSUT4 in Arabidopsis thaliana resulted in higher sucrose content in the roots and lower sucrose content in the leaves, as compared to the wild-type (WT) plants, leading to improved stress tolerance during seedling growth. Moreover, we systematically analyzed the mechanisms of IbSUT4 in response to abiotic stress. The results suggest that the ABRE-motif was localized in the IbSUT4 promoter region, and the expression of the ABA signaling pathway genes (i.e., ABF2, ABF4, SnRK2.2, SnRK2.3, and PYL8/RCAR3) were induced, and the expression of ABI1 was inhibited.

CONCLUSIONS

Our dates provide evidence that IbSUT4 is not only involved in plant growth but also is an important positive regulator in plant stress tolerance through the ABF-dependent ABA signaling pathway.

Continuous Storage Root Formation and Bulking in Sweetpotato

This study investigated the phenotypic variation of continuous storage root formation and bulking (CSRFAB) growth patterns underlying the development of sweetpotato genotypes for identification of potential varieties adapted to piecemeal harvesting for small scale farmers. The research was conducted between September 2016 and August 2017 in Uganda. Genotypes from two distinct sweetpotato genepool populations (Population Uganda A and Population Uganda B) comprising 130 genotypes, previously separated using 31 simple sequence repeat (SSR) markers were used. Measurements (4 harvest times with 4 plants each) were repeated on genotypes in a randomized complete block design with 2 replications in 2 locations for 2 seasons. We developed a scoring scale of 1 to 9 and used it to compare growth changes between consecutive harvests. Data analysis was done using residual or restricted maximum likelihood (REML) in GenStat 18th Edition. There were strong linear and quadratic trends over time (P<0.001) indicating a non-linear growth pattern within and between locations, seasons, and genotypes for most traits. Some genotypes displayed early initiation and a determinate linear increase of bulking, while others showed late initiation following a quadratic growth pattern. Broad sense heritability of CSRFAB would be low due to large GxE interactions, however, it was relatively high (50.5%) compared to other yield related traits indicating high genetic influence and accuracy of the developed method to quantify yield overtime. A high level of reproducibility (89%) was observed comparing 2016B and 2017A seasons (A and B are first and second season, respectively) at the National Crops Resources Research Institute (NaCRRI), Namulonge, Uganda. Choosing CSRFAB genotypes can more than double the sweetpotato production (average maximum yield of 13.1 t/ha for discontinuous storage root formation and bulking (DSRFAB) versus 28.6 t/ha for CSRFAB demonstrating the importance of this underresearched component of storage root yield.

Genome-wide association study identified candidate genes controlling continuous storage root formation and bulking in hexaploid sweetpotato

BACKGROUND

Continuous storage root formation and bulking (CSRFAB) in sweetpotato is an important trait from agronomic and biological perspectives. Information about the molecular mechanisms underlying CSRFAB traits is lacking.

RESULTS

Here, as a first step toward understanding the genetic basis of CSRFAB in sweetpotato, we performed a genome-wide association study (GWAS) using phenotypic data from four distinct developmental stages and 33,068 single nucleotide polymorphism (SNP) and insertion-deletion (indel) markers. Based on Bonferroni threshold (p-value < 5 × 10- 7), we identified 34 unique SNPs that were significantly associated with the complex trait of CSRFAB at 150 days after planting (DAP) and seven unique SNPs associated with discontinuous storage root formation and bulking (DCSRFAB) at 90 DAP. Importantly, most of the loci associated with these identified SNPs were located within genomic regions (using Ipomoea trifida reference genome) previously reported for quantitative trait loci (QTL) controlling similar traits. Based on these trait-associated SNPs, 12 and seven candidate genes were respectively annotated for CSRFAB and DCSRFAB traits. Congruent with the contrasting and inverse relationship between discontinuous and continuous storage root formation and bulking, a DCSRFAB-associated candidate gene regulates redox signaling, involved in auxin-mediated lateral root formation, while CSRFAB is enriched for genes controlling growth and senescence.

CONCLUSION

Candidate genes identified in this study have potential roles in cell wall remodeling, plant growth, senescence, stress, root development and redox signaling. These findings provide valuable insights into understanding the functional networks to develop strategies for sweetpotato yield improvement. The markers as well as candidate genes identified in this pioneering research for CSRFAB provide important genomic resources for sweetpotato and other root crops.

IbINH positively regulates drought stress tolerance in sweetpotato

Invertase inhibitor (INH) post-translationally regulates the activity of invertase, which hydrolyzes sucrose into glucose and fructose, and plays essential roles in plant growth and development. However, little is known about the role of INH in growth and responses to environmental challenges in sweetpotato. Here, we identified and characterized an INH-like gene (IbINH) from sweetpotato. IbINH belongs to the pectin methylesterase inhibitor super family. IbINH transcript was the most abundant in storage roots. IbINH mRNA levels were significantly up-regulated in response to drought, abscisic acid (ABA), salicyclic acid (SA) and jasmonic acid (JA) treatments. Overexpressing IbINH in sweetpotato (SI plants) led to the decrease of plant growth and the increase of drought tolerance, while down-regulation of IbINH (RI plants) by RNAi technology resulted in vigorous growth and drought sensitivity. Furthermore, sucrose was increased and hexoses was decreased in SI plants, but the opposite results were observed in RI plants. Moreover, higher levels of sugars were accumulated in SI plants in comparison to non-transgenic plants (NT plants) and RI plants during water deficit. In addition, ABA biosynthesis-involved and abiotic stress response-involved genes were prominently up-regulated in SI plants under drought stress. Taken together, these results indicate that IbINH mediates plant growth and drought stress tolerance in sweetpotato via induction of source-sink strength and ABA-regulated pathway.

Genome-wide genetic diversity detection and population structure analysis in sweetpotato (Ipomoea batatas) using RAD-seq

Sweetpotato (Ipomoea batatas L.) is one of the most important food and grain-forage crops globally. It has been planted in >100 countries. Due to the complexity of the sweetpotato genome, its research is far behind other major food crops. At present, limited information about the sweetpotato genome is available. Thus, it is central to find an efficient approach for the investigation of sweetpotato genome. In this study, RAD-seq (Restriction site-associated DNA sequencing) was used to evaluate sweetpotato genetic structure diversity and to develop relevant SSR markers. The study yielded >128 Gb reliable sequence data from 81 sweetpotato accessions. By analyzing polymorphic tags from each accession, a total of 55,622 restriction-site associated DNA sequencing tags (RAD-seq) were found, containing 907,010 SNP. Genetic analysis divided 81 accessions into five major clusters based on their SNP genotype, which matches the results of genetic analysis and the genetic family tree. In addition, 18,320 SSRs loci were detected and 9336 SSR primer pairs were developed. Eighty-three primer pairs were amplified in different sweetpotato genotypes, 76 of which successfully amplified polymorphism bands. These results provide significant information about sweetpotato genome, which can be used to identify novel gene and to further develop the gene chip. And more significant, clustering results based on the SNP genotype provide an essential reference for breeders to match parent plants in breeding program. Additionally, SSR markers developed in this study will supply a wealth of markers for marker-assisted selection in sweetpotato breeding.

Transgenic sweetpotato plants overexpressing tocopherol cyclase display enhanced α-tocopherol content and abiotic stress tolerance

Oxidative stress caused by reactive oxygen species (ROS) under various environmental stresses significantly reduces plant productivity. Tocopherols (collectively known as vitamin E) are a group of lipophilic antioxidants that protect cellular components against oxidative stress. Previously, we isolated five tocopherol biosynthesis genes from sweetpotato (Ipomoea batatas [L.] Lam) plants, including tocopherol cyclase (IbTC). In this study, we generated transgenic sweetpotato plants overexpressing IbTC under the control of cauliflower mosaic virus (CaMV) 35S promoter (referred to as TC plants) via Agrobacterium-mediated transformation to understand the function of IbTC in sweetpotato. Three transgenic lines (TC2, TC9, and TC11) with high transcript levels of IbTC were selected for further characterization. High performance liquid chromatography (HPLC) analysis revealed that α-tocopherol was the most predominant form of tocopherol in sweetpotato tissues. The content of α-tocopherol was 1.6-3.3-fold higher in TC leaves than in non-transgenic (NT) leaves. No significant difference was observed in the tocopherol content of storage roots between TC and NT plants. Additionally, compared with NT plants, TC plants showed enhanced tolerance to multiple environmental stresses, including salt, drought, and oxidative stresses, and showed consistently higher levels of photosystem II activity and chlorophyll content, indicating abiotic stress tolerance. These results suggest IbTC as a strong candidate gene for the development of sweetpotato cultivars with increased α-tocopherol levels and enhanced abiotic stress tolerance.

A single amino acid change at position 96 (Arg to His) of the sweetpotato Orange protein leads to carotenoid overaccumulation

IbOr-R96H resulted in carotenoid overaccumulation and enhanced abiotic stress tolerance in transgenic sweetpotato calli. The Orange (Or) protein is involved in the regulation of carotenoid accumulation and tolerance to various environmental stresses. Sweetpotato IbOr, with strong holdase chaperone activity, protects a key enzyme, phytoene synthase (PSY), in the carotenoid biosynthetic pathway and stabilizes a photosynthetic component, oxygen-evolving enhancer protein 2-1 (PsbP), under heat and oxidative stresses in plants. Previous studies of various plant species demonstrated that a single-nucleotide polymorphism (SNP) from Arg to His in Or protein promote a high level of carotenoid accumulation. Here, we showed that the substitution of a single amino acid at position 96 (Arg to His) of wild-type IbOr (referred to as IbOr-R96H) dramatically increases carotenoid accumulation. Sweetpotato calli overexpressing IbOr-WT or IbOr-Ins exhibited 1.8- or 4.3-fold higher carotenoid contents than those of the white-fleshed sweetpotato Yulmi (Ym) calli, and IbOr-R96H overexpression substantially increased carotenoid accumulation by up to 23-fold in sweetpotato calli. In particular, IbOr-R96H transgenic calli contained 88.4-fold higher levels of β-carotene than those in Ym calli. Expression levels of carotenogenesis-related genes were significantly increased in IbOr-R96H transgenic calli. Interestingly, transgenic calli overexpressing IbOr-R96H showed increased tolerance to salt and heat stresses, with similar levels of malondialdehyde to those in calli expressing IbOr-WT or IbOr-Ins. These results suggested that IbOr-R96H is a useful target for the generation of efficient industrial plants, including sweetpotato, to cope with growing food demand and climate change by enabling sustainable agriculture on marginal lands.

NHX1 and eIF4A1-stacked transgenic sweetpotato shows enhanced tolerance to drought stress

Co-expression of Na⁺/H⁺ antiporter NHX1 and DEAD-box RNA helicase eIF4A1 from Arabidopsis positively regulates drought stress tolerance by improving ROS scavenging capacity and maintaining membrane integrity in sweetpotato. Plants evolve multiple strategies for stress adaptation in nature. To improve sweetpotato resistance to drought stress, transgenic sweetpotato plants overexpressing the Arabidopsis Na⁺/H⁺ antiporter, NHX1, and the translation initiation factor elF4A1 were characterized for phenotypic traits and physiological performance. Without drought treatment, the NHX1-elF4A1 stacked lines (NE lines) showed normal, vigorous growth comparable to the WT plants. The NE plants showed dense green foliage with delayed leaf senescence and developed more roots than WT plants under drought treatment for 18 days. Compared to WT plants, higher level of reactive oxygen scavenging capacity was detected in NE lines as indicated by reduced H₂O₂ accumulation as well as increased superoxide dismutase activity and proline content. The relative ion leakage and malondialdehyde content were reduced in NE plants, indicating improved maintenance of intact membranes system. Both NE plants and NHX1-overexpressing plants (N lines) showed larger aerial parts and well-developed root system compared to WT plants under the drought stress conditions, likely due to the improved antioxidant capacity. The NE plants showed better ROS scavenging than N-line plants. All N- and NE-line plants produced normal storage roots with similar yields as WT in the field under normal growth conditions. These results demonstrated the potential to enhance sweetpotato productivity through stacking genes that are involved in ion compartmentalization and translation initiation.

A novel sweetpotato bZIP transcription factor gene, IbbZIP1, is involved in salt and drought tolerance in transgenic Arabidopsis

The overexpression of IbbZIP1 leads to a significant upregulation of abiotic-related genes, suggesting that IbbZIP1 gene confers salt and drought tolerance in transgenic Arabidopsis. Basic region/leucine zipper motif (bZIP) transcription factors regulate flower development, seed maturation, pathogen defense, and stress signaling in plants. Here, we cloned a novel bZIP transcription factor gene, named IbbZIP1, from sweetpotato [Ipomoea batatas (L.) Lam.] line HVB-3. The full length of IbbZIP1 exhibited transactivation activity in yeast. The expression of IbbZIP1 in sweetpotato was strongly induced by NaCl, PEG6000, and abscisic acid (ABA). Its overexpression in Arabidopsis significantly enhanced salt and drought tolerance. Under salt and drought stresses, the transgenic Arabidopsis plants showed significant upregulation of the genes involved in ABA and proline biosynthesis and reactive oxygen species scavenging system, significant increase of ABA and proline contents and superoxide dismutase activity and significant decrease of H₂O₂ content. These results demonstrate that the IbbZIP1 gene confers salt and drought tolerance in transgenic Arabidopsis. This study provides a novel bZIP gene for improving the tolerance of sweetpotato and other plants to abiotic stresses.

Phenotyping viral infection in sweetpotato using a high-throughput chlorophyll fluorescence and thermal imaging platform

BACKGROUND

Virus diseases caused by co-infection with Sweet potato feathery mottle virus (SPFMV) and Sweetpotato chlorotic stunt virus (SPCSV) are a severe problem in the production of sweetpotato (Ipomoea batatas L.). Traditional molecular virus detection methods include nucleic acid-based and serological tests. In this study, we aimed to validate the use of a non-destructive imaging-based plant phenotype platform to study plant-virus synergism in sweetpotato by comparing four virus treatments with two healthy controls.

RESULTS

By monitoring physiological and morphological effects of viral infection in sweetpotato over 29 days, we quantified photosynthetic performance from chlorophyll fluorescence (ChlF) imaging and leaf thermography from thermal infrared (TIR) imaging among sweetpotatoes. Moreover, the differences among different treatments observed from ChlF and TIR imaging were related to virus accumulation and distribution in sweetpotato. These findings were further validated at the molecular level by related gene expression in both photosynthesis and carbon fixation pathways.

CONCLUSION

Our study validated for the first time the use of ChlF- and TIR-based imaging systems to distinguish the severity of virus diseases related to SPFMV and SPCSV in sweetpotato. In addition, we demonstrated that the operating efficiency of PSII and photochemical quenching were the most sensitive parameters for the quantification of virus effects compared with maximum quantum efficiency, non-photochemical quenching, and leaf temperature.

Continuous Storage Root Formation and Bulking in Sweetpotato

This study investigated the phenotypic variation of continuous storage root formation and bulking (CSRFAB) growth patterns underlying the development of sweetpotato genotypes for identification of potential varieties adapted to piecemeal harvesting for small scale farmers. The research was conducted between September 2016 and August 2017 in Uganda. Genotypes from two distinct sweetpotato genepool populations (Population Uganda A and Population Uganda B) comprising 130 genotypes, previously separated using 31 simple sequence repeat (SSR) markers were used. Measurements (4 harvest times with 4 plants each) were repeated on genotypes in a randomized complete block design with 2 replications in 2 locations for 2 seasons. We developed a scoring scale of 1 to 9 and used it to compare growth changes between consecutive harvests. Data analysis was done using residual or restricted maximum likelihood (REML) in GenStat 18th Edition. There were strong linear and quadratic trends over time (P<0.001) indicating a non-linear growth pattern within and between locations, seasons, and genotypes for most traits. Some genotypes displayed early initiation and a determinate linear increase of bulking, while others showed late initiation following a quadratic growth pattern. Broad sense heritability of CSRFAB would be low due to large GxE interactions, however, it was relatively high (50.5%) compared to other yield related traits indicating high genetic influence and accuracy of the developed method to quantify yield overtime. A high level of reproducibility (89%) was observed comparing 2017A and 2017B seasons (A and B are first and second season, respectively) at the National Crops Resources Research Institute (NaCRRI), Namulonge, Uganda. Choosing CSRFAB genotypes can more than double the sweetpotato production (average maximum yield of 13.1 t/ha for discontinuous storage root formation and bulking (DSRFAB) versus 28.6 t/ha for CSRFAB demonstrating the importance of this underresearched component of storage root yield.

Transcriptomic changes in sweetpotato peroxidases in response to infection with the root-knot nematode Meloidogyne incognita

A previous transcriptomic analysis of the roots of susceptible and resistant cultivars of sweetpotato (Ipomoea batatas) identified genes that were likely to contribute to protection against infection with the root-knot nematode Meloidogyne incognita. The current study examined the roles of peroxidase genes in sweetpotato defense responses during root-knot nematode infection, using the susceptible (cv. Yulmi) and resistant (cv. Juhwangmi) cultivars. Differentially expressed genes were assigned to gene ontology categories to predict their functional roles and associated biological processes. Comparison with Arabidopsis peroxidases identified a group of genes orthologous to Arabidopsis PEROXIDASE 52 (AtPrx52). An analysis of sweetpotato peroxidase genes determined their roles in protecting plants against root-knot nematode infection and enabled identification of important peroxidases. The interactions involved in sweetpotato resistance to nematode infection are discussed.

Uncovering anthocyanin biosynthesis related microRNAs and their target genes by small RNA and degradome sequencing in tuberous roots of sweetpotato

BACKGROUND

Compared with white-fleshed sweetpotato (WFSP), purple-fleshed sweetpotato (PFSP) is a desirable resource for functional food development because of the abundant anthocyanin accumulation in its tuberous roots. Some studies have shown that the expression regulation mediated by miRNA plays an important role in anthocyanin biosynthesis in plants. However, few miRNAs and their corresponding functions related to anthocyanin biosynthesis in tuberous roots of sweetpotato have been known.

RESULTS

In this study, small RNA (sRNA) and degradome libraries from the tuberous roots of WFSP (Xushu-18) and PFSP (Xuzishu-3) were constructed, respectively. Totally, 191 known and 33 novel miRNAs were identified by sRNA sequencing, and 180 target genes cleaved by 115 known ib-miRNAs and 5 novel ib-miRNAs were identified by degradome sequencing. Of these, 121 miRNAs were differently expressed between Xushu-18 and Xuzishu-3. Integrated analysis of sRNA, degradome sequencing, GO, KEGG and qRT-PCR revealed that 26 differentially expressed miRNAs and 36 corresponding targets were potentially involved in the anthocyanin biosynthesis. Of which, an inverse correlation between the expression of ib-miR156 and its target ibSPL in WFSP and PFSP was revealed by both qRT-PCR and sRNA sequencing. Subsequently, ib-miR156 was over-expressed in Arabidopsis. Interestingly, the ib-miR156 over-expressing plants showed suppressed abundance of SPL and a purplish phenotype. Concomitantly, upregulated expression of four anthocyanin pathway genes was detected in transgenic Arabidopsis plants. Finally, a putative ib-miRNA-target model involved in anthocyanin biosynthesis in sweetpotato was proposed.

CONCLUSIONS

The results represented a comprehensive expression profiling of miRNAs related to anthocyanin accumulation in sweetpotato and provided important clues for understanding the regulatory network of anthocyanin biosynthesis mediated by miRNA in tuberous crops.