Transcriptome analysis to identify putative floral-specific genes and flowering regulatory-related genes of sweet potato

First systematic review of the last 30 years of research on sweetpotato: elucidating the frontiers and hotspots

Sweetpotato is an economically important crop, and it has various advantages over other crops in addressing global food security and climate change. Although substantial articles have been published on the research of various aspects of sweetpotato biology, there are no specific reports to systematically crystallize the research achievements. The current review takes the lead in conducting a keyword-centric spatiotemporal dimensional bibliometric analysis of articles on sweetpotato research using CiteSpace software to comprehensively clarify the development status, research hotspot, and development trend in the past 30 years (1993-2022). Quantitative analysis was carried out on the publishing countries, institutions, disciplines, and scholars to understand the basic status of sweetpotato research; then, visual analysis was conducted on high-frequency keywords, burst keywords, and keyword clustering; the evolution of major research hotspots and the development trend in different periods were summarized. Finally, the three main development stages-preliminary stage (1993-2005), rapid stage (2006-2013), and diversified mature stage (2014-2022)-were reviewed and analyzed in detail. Particularly, the development needs of sweetpotato production in improving breeding efficiency, enhancing stress tolerance, coordinating high yield with high quality and high resistance, and promoting demand were discussed, which will help to comprehensively understand the development dynamics of sweetpotato research from different aspects of biological exploration.

CRISPR/Cas9: an advanced platform for root and tuber crops improvement

Root and tuber crops (RTCs), which include cassava, potato, sweet potato, and yams, principally function as staple crops for a considerable fraction of the world population, in addition to their diverse applications in nutrition, industry, and bioenergy sectors. Even then, RTCs are an underutilized group considering their potential as industrial raw material. Complexities in conventional RTC improvement programs curb the extensive exploitation of the potentials of this group of crop species for food, energy production, value addition, and sustainable development. Now, with the advent of whole-genome sequencing, sufficient sequence data are available for cassava, sweet potato, and potato. These genomic resources provide enormous scope for the improvement of tuber crops, to make them better suited for agronomic and industrial applications. There has been remarkable progress in RTC improvement through the deployment of new strategies like gene editing over the last decade. This review brings out the major areas where CRISPR/Cas technology has improved tuber crops. Strategies for genetic transformation of RTCs with CRISPR/Cas9 constructs and regeneration of edited lines and the bottlenecks encountered in their establishment are also discussed. Certain attributes of tuber crops requiring focus in future research along with putative editing targets are also indicated. Altogether, this review provides a comprehensive account of developments achieved, future lines of research, bottlenecks, and major experimental concerns regarding the establishment of CRISPR/Cas9-based gene editing in RTCs.

Transcriptomic analysis reveals mechanisms for the different drought tolerance of sweet potatoes

Drought is a common environmental stress with great negative impacts on plant growth, development and geographical distribution as well as agriculture and food production. Sweet potato is characterized by starchy, fresh and pigmented tuber, and is regarded as the seventh most important food crop. However, there has been no comprehensive study of the drought tolerance mechanism of different sweet potato cultivars to date. Here, we studied the mechanism for drought response of seven sweet potato drought-tolerant cultivars using the drought coefficients, physiological indicators and transcriptome sequencing. The seven sweet potato cultivars were classified into four groups of drought tolerance performance. A large number of new genes and transcripts were identified, with an average of about 8000 new genes per sample. Alternative splicing events in sweet potato, which were dominated by first exon and last exon alternative splicing, were not conserved among different cultivars and not significantly affected by drought stress. Furthermore, different drought-tolerance mechanisms were revealed through differentially expressed gene analysis and functional annotation. Two drought-sensitive cultivars, Shangshu-9 and Xushu-22, mainly resisted drought stress by up-regulating plant signal transduction. The other drought-sensitive cultivar Jishu-26 responded to drought stress by down-regulating isoquinoline alkaloid biosynthesis and nitrogen/carbohydrate metabolism. In addition, the drought-tolerant cultivar Chaoshu-1 and drought-preferred cultivar Z15-1 only shared 9% of differentially expressed genes, as well as many opposite metabolic pathways in response to drought. They mainly regulated flavonoid and carbohydrate biosynthesis/metabolism in response to drought, while Z15-1 increased photosynthesis and carbon fixation capacity. The other drought-tolerant cultivar Xushu-18 responded to drought stress by regulating the isoquinoline alkaloid biosynthesis and nitrogen/carbohydrate metabolism. The extremely drought-tolerant cultivar Xuzi-8 was almost unaffected by drought stress and responded to drought environment only by regulating the cell wall. These findings provide important information for the selection of sweet potatoes for specific purposes.

Transcriptome analysis reveals the effects of grafting on sweetpotato scions during the full blooming stages

BACKGROUND

Sweetpotato (Ipomoea batatas) is a hexaploid plant and generally most genotypes do not flower at all in sub-tropics. Heterografting was carried out between sweetpotato cultivar 'Xushu 18' and Japanese morning glory (Ipomoea nil). With sweetpotato as 'scion' and I. nil as 'rootstock', sweetpotato was induced flowering in the autumn. However, little is known about the molecular mechanisms underlying sweetpotato responses to grafting, especially during the full blooming stages.

OBJECTIVES

To investigate the poorly understood molecular responses underlying the grafting-induced phenotypic processes in sweetpotato at full anthesis.

METHODS

In this study, to explore the transcriptome diversity and complexity of sweetpotato, PacBio Iso-Seq and Illumina RNA-seq analysis were combined to obtain full-length transcripts and to profile the changes in gene expression of five tissues: scion flowers (SF), scion leaves (SL), scion stems (SS), own-rooted leaves (OL) and own-rooted stems (OS).

RESULTS

A total of 138,151 transcripts were generated with an average length of 2255 bp, and more than 72% (100,396) of the transcripts were full-length. During full blooming, to examine the difference in gene expression of sweetpotato under grafting and natural growth conditions, 7905, 7795 and 15,707 differentially expressed genes were detected in pairwise comparisons of OS versus SS, OL versus SL and SL versus SF, respectively. Moreover, differential transcription of genes associated with anthocyanin biosynthesis, light pathway and photosynthesis, ethylene signal transduction pathway was observed in scion responses to grafting.

CONCLUSION

Our study is useful in understanding the molecular basis of grafting-induced flowering in grafted sweetpotatoes, and will lay a foundation for further research on sweetpotato breeding in the future.

Comparative Analysis of CDPK Family in Maize, Arabidopsis, Rice, and Sorghum Revealed Potential Targets for Drought Tolerance Improvement

Calcium dependent protein kinases (CDPKs) play significant role in regulation of plant growth and development in response to various stresses including drought. A set of 32 CDPK genes identified in maize were further used for searching of orthologs in the model plant Arabidopsis (72) and major food crops such as rice (78) and sorghum (91). We comprehensively studied the phylogenetic relationship, annotations, gene duplications, gene structure, divergence time, 3-D protein structures and tissue-specific drought induced expression of CDPK genes in all four species. Variation in intron frequency in the studied species was one of the reasons for the functional diversity of CDPK genes to various stress responses. Protein kinase and protein kinase C phosphorylation site domains were the most conserved motifs identified in all species. Four groups were identified from the sequence-based phylogenetic analysis, in which maize CDPKs were clustered in group III. Expression data showed that the CDPK genes were highly expressed in leaf of maize, rice, and sorghum whereas in Arabidopsis the maximum expression was observed in root. The expression assay showed 5, 6, 11, and 9 were the commonly and differentially expressed drought-related orthologous genes in maize, Arabidopsis, rice, and sorghum, respectively. 3-D protein structure were predicted for the nine genes (Arabidopsis: 2, maize: 2, rice: 3, and sorghum: 2) showing differential expression in at least three species. The predicted 3-D structures were further evaluated and validated by Ramachandran plot, ANOLEA, ProSA, and Verify-3D. The superimposed 3-D structure of drought-related orthologous proteins retained similar folding pattern owing to their conserved nature. Functional annotation revealed the involvement of CDPK genes in various pathways such as osmotic homeostasis, cell protection, and root growth. The interactions of CDPK genes in various pathways play crucial role in imparting drought tolerance through different ABA and MAPK signaling cascades. These selected candidate genes could be targeted in development of drought tolerant genotypes in maize, rice, and sorghum through appropriate breeding approaches. Our comparative experiments of CDPK genes could also be extended in the drought stress breeding programmes of the related species.

Isolation and Abiotic Stress Resistance Analyses of a Catalase Gene from Ipomoea batatas (L.) Lam

As an indicator of the antioxidant capability of plants, catalase can detoxify reactive oxygen species (ROS) generated by environmental stresses. Sweet potato is one of the top six most important crops in the world. However, its catalases remain largely unknown. In this study, a catalase encoding gene, IbCAT2 (accession number: KY615708), was identified and cloned from sweet potato cv. Xushu 18. It contained a 1479 nucleotides' open reading frame (ORF). S-R-L, Q-K-L, and a putative calmodulin binding domain were located at the C-terminus of IbCAT2, which suggests that IbCAT2 could be a peroxisomal catalase. Next-generation sequencing (NGS) based quantitative analyses showed that IbCAT2 was mainly expressed in young leaves and expanding tuberous roots under normal conditions. When exposed to 10% PEG6000 or 200 mmol/L NaCl solutions, IbCAT2 was upregulated rapidly in the first 11 days and then downregulated, although different tissues showed different degree of change. Overexpression of IbCAT2 conferred salt and drought tolerance in Escherichia coli and Saccharomyces cerevisiae. The positive response of IbCAT2 to abiotic stresses suggested that IbCAT2 might play an important role in stress responses.

Challenges to genome sequence dissection in sweetpotato

The development of next generation sequencing (NGS) technologies has enabled the determination of whole genome sequences in many non-model plant species. However, genome sequencing in sweetpotato (Ipomoea batatas (L.) Lam) is still difficult because of the hexaploid genome structure. Previous studies suggested that a diploid wild relative, I. trifida (H.B.K.) Don., is the most possible ancestor of sweetpotato. Therefore, the genetic and genomic features of I. trifida have been studied as a potential reference for sweetpotato. Meanwhile, several research groups have begun the challenging task of directly sequencing the sweetpotato genome. In this manuscript, we review the recent results and activities of large-scale genome and transcriptome analysis related to genome sequence dissection in sweetpotato under the sections as follows: I. trifida genome and transcript sequencing, genome sequences of I. nil (Japanese morning glory), transcript sequences in sweetpotato, chloroplast sequences, transposable elements and transfer DNA. The recent international activities of de novo whole genome sequencing in sweetpotato are also described. The large-scale publically available genome and transcript sequence resources and the international genome sequencing streams are expected to promote the genome sequence dissection in sweetpotato.

Improvement for agronomically important traits by gene engineering in sweetpotato

Sweetpotato is the seventh most important food crop in the world. It is mainly used for human food, animal feed, and for manufacturing starch and alcohol. This crop, a highly heterozygous, generally self-incompatible, outcrossing polyploidy, poses numerous challenges for the conventional breeding. Its productivity and quality are often limited by abiotic and biotic stresses. Gene engineering has been shown to have the great potential for improving the resistance to these stresses as well as the nutritional quality of sweetpotato. To date, an Agrobacterium tumefaciens-mediated transformation system has been developed for a wide range of sweetpotato genotypes. Several genes associated with salinity and drought tolerance, diseases and pests resistance, and starch, carotenoids and anthocyanins biosynthesis have been isolated and characterized from sweetpotato. Gene engineering has been used to improve abiotic and biotic stresses resistance and quality of this crop. This review summarizes major research advances made so far in improving agronomically important traits by gene engineering in sweetpotato and suggests future prospects for research in this field.

A genome-wide BAC-end sequence survey provides first insights into sweetpotato (Ipomoea batatas (L.) Lam.) genome composition

Background

Sweetpotato, Ipomoea batatas (L.) Lam., is an important food crop widely grown in the world. However, little is known about the genome of this species because it is a highly heterozygous hexaploid. Gaining a more in-depth knowledge of sweetpotato genome is therefore necessary and imperative. In this study, the first bacterial artificial chromosome (BAC) library of sweetpotato was constructed. Clones from the BAC library were end-sequenced and analyzed to provide genome-wide information about this species.

Results

The BAC library contained 240,384 clones with an average insert size of 101 kb and had a 7.93–10.82 × coverage of the genome, and the probability of isolating any single-copy DNA sequence from the library was more than 99%. Both ends of 8310 BAC clones randomly selected from the library were sequenced to generate 11,542 high-quality BAC-end sequences (BESs), with an accumulative length of 7,595,261 bp and an average length of 658 bp. Analysis of the BESs revealed that 12.17% of the sweetpotato genome were known repetitive DNA, including 7.37% long terminal repeat (LTR) retrotransposons, 1.15% Non-LTR retrotransposons and 1.42% Class II DNA transposons etc., 18.31% of the genome were identified as sweetpotato-unique repetitive DNA and 10.00% of the genome were predicted to be coding regions. In total, 3,846 simple sequences repeats (SSRs) were identified, with a density of one SSR per 1.93 kb, from which 288 SSRs primers were designed and tested for length polymorphism using 20 sweetpotato accessions, 173 (60.07%) of them produced polymorphic bands. Sweetpotato BESs had significant hits to the genome sequences of I. trifida and more matches to the whole-genome sequences of Solanum lycopersicum than those of Vitis vinifera, Theobroma cacao and Arabidopsis thaliana.

Conclusions

The first BAC library for sweetpotato has been successfully constructed. The high quality BESs provide first insights into sweetpotato genome composition, and have significant hits to the genome sequences of I. trifida and more matches to the whole-genome sequences of Solanum lycopersicum. These resources as a robust platform will be used in high-resolution mapping, gene cloning, assembly of genome sequences, comparative genomics and evolution for sweetpotato.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3302-1) contains supplementary material, which is available to authorized users.

De novo transcriptome analysis in radish (Raphanus sativus L.) and identification of critical genes involved in bolting and flowering

Background

The appropriate timing of bolting and flowering is pivotal for reproductive success in Brassicaceae crops including radish (Raphanus sativus L.). Although several flowering regulatory pathways had been described in some plant species, no study on genetic networks of bolting and flowering regulation was performed in radish. In this study, to generate dataset of radish unigene sequences for large-scale gene discovery and functional pathway identification, a cDNA library from mixed radish leaves at different developmental stages was subjected to high-throughput RNA sequencing (RNA-seq).

Results

A total of 54.64 million clean reads and 111,167 contigs representing 53,642 unigenes were obtained from the radish leaf transcriptome. Among these, 50,385 unigenes were successfully annotated by BLAST searching against the public protein databases. Functional classification and annotation indicated that 42,903 and 15,382 unique sequences were assigned to 55 GO terms and 25 COG categories, respectively. KEGG pathway analysis revealed that 25,973 unigenes were classified into 128 functional pathways, among which 24 candidate genes related to plant circadian rhythm were identified. Moreover, 142 potential bolting and flowering-related genes involved in various flowering pathways were identified. In addition, seven critical bolting and flowering-related genes were isolated and profiled by T-A cloning and RT-qPCR analysis. Finally, a schematic network model of bolting and flowering regulation and pathways was put forward in radish.

Conclusions

This study is the first report on systematic identification of bolting and flowering-related genes based on transcriptome sequencing and assembly in radish. These results could provide a foundation for further investigating bolting and flowering regulatory networks in radish, and facilitate dissecting molecular genetic mechanisms underlying bolting and flowering in Brassicaceae vegetable crops.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2633-2) contains supplementary material, which is available to authorized users.

Transcriptomic Analysis Identifies Differentially Expressed Genes (DEGs) Associated with Bolting and Flowering in Radish (Raphanus sativus L.)

The transition of vegetative growth to bolting and flowering is an important process in the life cycle of plants, which is determined by numerous genes forming an intricate network of bolting and flowering. However, no comprehensive identification and profiling of bolting and flowering-related genes have been carried out in radish. In this study, RNA-Seq technology was applied to analyze the differential gene expressions during the transition from vegetative stage to reproductive stage in radish. A total of 5922 differentially expressed genes (DEGs) including 779 up-regulated and 5143 down-regulated genes were isolated. Functional enrichment analysis suggested that some DEGs were involved in hormone signaling pathways and the transcriptional regulation of bolting and flowering. KEGG-based analysis identified 37 DEGs being involved in phytohormone signaling pathways. Moreover, 95 DEGs related to bolting and flowering were identified and integrated into various flowering pathways. Several critical genes including FT, CO, SOC1, FLC, and LFY were characterized and profiled by RT-qPCR analysis. Correlation analysis indicated that 24 miRNA-DEG pairs were involved in radish bolting and flowering. Finally, a miRNA-DEG-based schematic model of bolting and flowering regulatory network was proposed in radish. These outcomes provided significant insights into genetic control of radish bolting and flowering, and would facilitate unraveling molecular regulatory mechanism underlying bolting and flowering in root vegetable crops.

RNA-seq Analysis of Overexpressing Ovine AANAT Gene of Melatonin Biosynthesis in Switchgrass

Melatonin serves important functions in the promotion of growth and anti-stress regulation by efficient radical scavenging and regulation of antioxidant enzyme activity in various plants. To investigate its regulatory roles and metabolism pathways, the transcriptomic profile of overexpressing the ovine arylalkylamine N-acetyltransferase (oAANAT) gene, encoding the penultimate enzyme in melatonin biosynthesis, was compared with empty vector control using RNA-seq in switchgrass, a model plant of cellulosic ethanol conversion. The 85.22 million high quality reads that were assembled into 135,684 unigenes were generated by Illumina sequencing for transgenic oAANAT switchgrass with an average sequence length of 716 bp. A total of 946 differentially expression genes in transgenic line comparing to control switchgrass, including 737 up-regulated and 209 down-regulated genes, were mainly enriched with two main functional patterns of melatonin identifying by gene ontology analysis: the growth regulator and stress tolerance. Furthermore, KEGG maps indicated that the biosynthetic pathways of secondary metabolite (phenylpropanoids, flavonoids, steroids, stilbenoid, diarylheptanoid, and gingerol) and signaling pathways (MAPK signaling pathway, estrogen signaling pathway) were involved in melatonin metabolism. This study substantially expands the transcriptome information for switchgrass and provides valuable clues for identifying candidate genes involved in melatonin biosynthesis and elucidating the mechanism of melatonin metabolism.

Development and Identification of SSR Markers Associated with Starch Properties and β-Carotene Content in the Storage Root of Sweet Potato (Ipomoea batatas L.)

Sweet potato (Ipomoea batatas L.) is a nutritious food crop and, based on the high starch content of its storage root, a potential bioethanol feedstock. Enhancing the nutritional value and starch quantity of storage roots are important goals of sweet potato breeding programs aimed at developing improved varieties for direct consumption, processing, and industrial uses. However, developing improved lines of sweet potato is challenging due to the genetic complexity of this plant and the lack of genome information. Short sequence repeat (SSR) markers are powerful molecular tools for tracking important loci in crops and for molecular-based breeding strategies; however, few SSR markers and marker-trait associations have hitherto been identified in sweet potato. In this study, we identified 1824 SSRs by using a de novo assembly of publicly available ESTs and mRNAs in sweet potato, and designed 1476 primer pairs based on SSR-containing sequences. We mapped 214 pairs of primers in a natural population comprised of 239 germplasms, and identified 1278 alleles with an average of 5.972 alleles per locus and a major allele frequency of 0.7702. Population structure analysis revealed two subpopulations in this panel of germplasms, and phenotypic characterization demonstrated that this panel is suitable for association mapping of starch-related traits. We identified 32, 16, and 17 SSR markers associated with starch content, β-carotene content, and starch composition in the storage root, respectively, using association analysis and further evaluation of a subset of sweet potato genotypes with various characteristics. The SSR markers identified here can be used to select varieties with desired traits and to investigate the genetic mechanism underlying starch and carotenoid formation in the starchy roots of sweet potato.

De Novo Transcriptome Sequencing of the Orange-Fleshed Sweet Potato and Analysis of Differentially Expressed Genes Related to Carotenoid Biosynthesis

Sweet potato, Ipomoea batatas (L.) Lam., is an important food crop worldwide. The orange-fleshed sweet potato is considered to be an important source of beta-carotene. In this study, the transcriptome profiles of an orange-fleshed sweet potato cultivar “Weiduoli” and its mutant “HVB-3” with high carotenoid content were determined by using the high-throughput sequencing technology. A total of 13,767,387 and 9,837,090 high-quality reads were produced from Weiduoli and HVB-3, respectively. These reads were de novo assembled into 58,277 transcripts and 35,909 unigenes with an average length of 596 bp and 533 bp, respectively. In all, 874 differentially expressed genes (DEGs) were obtained between Weiduoli and HVB-3, 401 of which were upregulated and 473 were downregulated in HVB-3 compared to Weiduoli. Of the 697 DEGs annotated, 316 DEGs had GO terms and 62 DEGs were mapped onto 50 pathways. The 22 DEGs and 31 transcription factors involved in carotenoid biosynthesis were identified between Weiduoli and HVB-3. In addition, 1,725 SSR markers were detected. This study provides the genomic resources for discovering the genes involved in carotenoid biosynthesis of sweet potato and other plants.

Exploring the polyadenylated RNA virome of sweet potato through high-throughput sequencing

BACKGROUND

Viral diseases are the second most significant biotic stress for sweet potato, with yield losses reaching 20% to 40%. Over 30 viruses have been reported to infect sweet potato around the world, and 11 of these have been detected in China. Most of these viruses were detected by traditional detection approaches that show disadvantages in detection throughput. Next-generation sequencing technology provides a novel, high sensitive method for virus detection and diagnosis.

METHODOLOGY/PRINCIPAL FINDINGS

We report the polyadenylated RNA virome of three sweet potato cultivars using a high throughput RNA sequencing approach. Transcripts of 15 different viruses were detected, 11 of which were detected in cultivar Xushu18, whilst 11 and 4 viruses were detected in Guangshu 87 and Jingshu 6, respectively. Four were detected in sweet potato for the first time, and 4 were found for the first time in China. The most prevalent virus was SPFMV, which constituted 88% of the total viral sequence reads. Virus transcripts with extremely low expression levels were also detected, such as transcripts of SPLCV, CMV and CymMV. Digital gene expression (DGE) and reverse transcription polymerase chain reaction (RT-PCR) analyses showed that the highest viral transcript expression levels were found in fibrous and tuberous roots, which suggest that these tissues should be optimum samples for virus detection.

CONCLUSIONS/SIGNIFICANCE

A total of 15 viruses were presumed to present in three sweet potato cultivars growing in China. This is the first insight into the sweet potato polyadenylated RNA virome. These results can serve as a basis for further work to investigate whether some of the 'new' viruses infecting sweet potato are pathogenic.

Scanning of transposable elements and analyzing expression of transposase genes of sweet potato [Ipomoea batatas]

BACKGROUND

Transposable elements (TEs) are the most abundant genomic components in eukaryotes and affect the genome by their replications and movements to generate genetic plasticity. Sweet potato performs asexual reproduction generally and the TEs may be an important genetic factor for genome reorganization. Complete identification of TEs is essential for the study of genome evolution. However, the TEs of sweet potato are still poorly understood because of its complex hexaploid genome and difficulty in genome sequencing. The recent availability of the sweet potato transcriptome databases provides an opportunity for discovering and characterizing the expressed TEs.

METHODOLOGY/PRINCIPAL FINDINGS

We first established the integrated-transcriptome database by de novo assembling four published sweet potato transcriptome databases from three cultivars in China. Using sequence-similarity search and analysis, a total of 1,405 TEs including 883 retrotransposons and 522 DNA transposons were predicted and categorized. Depending on mapping sets of RNA-Seq raw short reads to the predicted TEs, we compared the quantities, classifications and expression activities of TEs inter- and intra-cultivars. Moreover, the differential expressions of TEs in seven tissues of Xushu 18 cultivar were analyzed by using Illumina digital gene expression (DGE) tag profiling. It was found that 417 TEs were expressed in one or more tissues and 107 in all seven tissues. Furthermore, the copy number of 11 transposase genes was determined to be 1-3 copies in the genome of sweet potato by Real-time PCR-based absolute quantification.

CONCLUSIONS/SIGNIFICANCE

Our result provides a new method for TE searching on species with transcriptome sequences while lacking genome information. The searching, identification and expression analysis of TEs will provide useful TE information in sweet potato, which are valuable for the further studies of TE-mediated gene mutation and optimization in asexual reproduction. It contributes to elucidating the roles of TEs in genome evolution.