Temporal patterns of gene expression associated with tuberous root formation and development in sweetpotato (Ipomoea batatas)

Identification of cotton PIP5K genes and role of GhPIP5K9a in primary root development

Phosphatidylinositol 4 phosphate 5-kinase (PIP5K) is crucial for the phosphatidylinositol (PI) signaling pathway. It plays a significant role in plant growth and development, as well as stress response. However, its effects on cotton are unknown. This study identified PIP5K genes from four cotton species and conducted bioinformatic analyses, with a particular emphasis on the functions of GhPIP5K9a in primary roots. The results showed that cotton PIP5Ks were classified into four subgroups. Analysis of gene structure and motif composition showed obvious conservation within each subgroup. Synteny analysis suggested that the PIP5K gene family experienced significant expansion due to both whole-genome duplication (WGD) and segmental duplication. Transcriptomic data analysis revealed that the majority of GhPIP5K genes had the either low or undetectable levels of expression. Moreover, GhPIP5K9a is highly expressed in the root and was located in plasmalemma. Suppression of GhPIP5K9a transcripts resulted in longer primary roots, longer primary root cells and increased auxin polar transport-related genes expression, and decreased abscisic acid (ABA) content, indicating that GhPIP5K9a negatively regulates cotton primary root growth. This study lays the foundation for further exploration of the role of the PIP5K genes in cotton.

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.

Transcriptome profiling reveals the genes involved in tuberous root expansion in Pueraria (Pueraria montana var. thomsonii)

BACKGROUND

Pueraria is a dry root commonly used in Traditional Chinese Medicine or as food and fodder, and tuberous root expansion is an important agronomic characteristic that influences its yield. However, no specific genes regulating tuberous root expansion in Pueraria have been identified. Therefore, we aimed to explore the expansion mechanism of Pueraria at six developmental stages (P1-P6), by profiling the tuberous roots of an annual local variety "Gange No.1" harvested at 105, 135, 165, 195, 225, and 255 days after transplanting.

RESULTS

Observations of the tuberous root phenotype and cell microstructural morphology revealed that the P3 stage was a critical boundary point in the expansion process, which was preceded by a thickening diameter and yield gain rapidly of the tuberous roots, and followed by longitudinal elongation at both ends. A total of 17,441 differentially expressed genes (DEGs) were identified by comparing the P1 stage (unexpanded) against the P2-P6 stages (expanded) using transcriptome sequencing; 386 differential genes were shared across the six developmental stages. KEGG pathway enrichment analysis showed that the DEGs shared by P1 and P2-P6 stages were mainly involved in pathways related to the "cell wall and cell cycle", "plant hormone signal transduction", "sucrose and starch metabolism", and "transcription factor (TF)". The finding is consistent with the physiological data collected on changes in sugar, starch, and hormone contents. In addition, TFs including bHLHs, AP2s, ERFs, MYBs, WRKYs, and bZIPs were involved in cell differentiation, division, and expansion, which may relate to tuberous root expansion. The combination of KEGG and trend analyses revealed six essential candidate genes involved in tuberous root expansion; of them, CDC48, ARF, and EXP genes were significantly upregulated during tuberous root expansion while INV, EXT, and XTH genes were significantly downregulated.

CONCLUSION

Our findings provide new insights into the complex mechanisms of tuberous root expansion in Pueraria and candidate target genes, which can aid in increasing Pueraria yield.

Deciphering the hormone regulatory mechanisms of storage root initiation in sweet potato: challenges and future prospects

Sweet potato (Ipomoea batatas) is an economically important food crop that is grown primarily for its edible storage roots. Several researchers have consequently been conducting studies to increase sweet potato yield, and an important aspect of this research involves understanding how storage root initiation occurs. Although significant progress has been made, several challenges associated with studying this crop have resulted in lagging progress compared to other crops and thus sweet potato storage root initiation is not clearly understood. This article highlights the most important aspects of the hormone signalling processes during storage root initiation that needs to be investigated further and suggests candidate genes that should be prioritized for further study, based on their importance in storage organ formation in other crops. Lastly, ways of overcoming the challenges associated with studying this crop are suggested.

Sweet potato ADP-glucose pyrophosphorylase small subunit affects vegetative growth, starch content and storage root yield

The development of storage roots is a key factor determining the yields of crop plants, including sweet potato. Here, using combined bioinformatic and genomic approaches, we identified a sweet potato yield-related gene, ADP-glucose pyrophosphorylase (AGP) small subunit (IbAPS). We found that IbAPS positively affects AGP activity, transitory starch biosynthesis, leaf development, chlorophyll metabolism, and photosynthesis, ultimately affecting the source strength. IbAPS overexpression in sweet potato led to increased vegetative biomass and storage root yield. RNAi of IbAPS resulted in reduced vegetative biomass, accompanied with a slender stature and stunted root development. In addition to the effects on root starch metabolism, we found that IbAPS affects other storage root development-associated events, including lignification, cell expansion, transcriptional regulation, and production of the storage protein sporamins. A combinatorial analysis based on transcriptomes, as well as morphological and physiological data, revealed that IbAPS affects several pathways that determine development of vegetative tissues and storage roots. Our work establishes an important role of IbAPS in concurrent control of carbohydrate metabolism, plant growth, and storage root yield. We showed that upregulation of IbAPS results in superior sweet potato with increased green biomass, starch content, and storage root yield. The findings expand our understanding of the functions of AGP enzymes and advances our ability to increase the yield of sweet potato and, perhaps, other crop plants.

Integrated metabolic and transcriptional analysis reveals the role of carotenoid cleavage dioxygenase 4 (IbCCD4) in carotenoid accumulation in sweetpotato tuberous roots

BACKGROUND

Plant carotenoids are essential for human health, having wide uses in dietary supplements, food colorants, animal feed additives, and cosmetics. With the increasing demand for natural carotenoids, plant carotenoids have gained great interest in both academic and industry research worldwide. Orange-fleshed sweetpotato (Ipomoea batatas) enriched with carotenoids is an ideal feedstock for producing natural carotenoids. However, limited information is available regarding the molecular mechanism responsible for carotenoid metabolism in sweetpotato tuberous roots.

RESULTS

In this study, metabolic profiling of carotenoids and gene expression analysis were conducted at six tuberous root developmental stages of three sweetpotato varieties with different flesh colors. The correlations between the expression of carotenoid metabolic genes and carotenoid levels suggested that the carotenoid cleavage dioxygenase 4 (IbCCD4) and 9-cis-epoxycarotenoid cleavage dioxygenases 3 (IbNCED3) play important roles in the regulation of carotenoid contents in sweetpotato. Transgenic experiments confirmed that the total carotenoid content decreased in the tuberous roots of IbCCD4-overexpressing sweetpotato. In addition, IbCCD4 may be regulated by two stress-related transcription factors, IbWRKY20 and IbCBF2, implying that the carotenoid accumulation in sweeetpotato is possibly fine-tuned in responses to stress signals.

CONCLUSIONS

A set of key genes were revealed to be responsible for carotenoid accumulation in sweetpotato, with IbCCD4 acts as a crucial player. Our findings provided new insights into carotenoid metabolism in sweetpotato tuberous roots and insinuated IbCCD4 to be a target gene in the development of new sweetpotato varieties with high carotenoid production.

Transcriptomic analysis of tuberous root in two sweet potato varieties reveals the important genes and regulatory pathways in tuberous root development

Background

Tuberous root formation and development is a complex process in sweet potato, which is regulated by multiple genes and environmental factors. However, the regulatory mechanism of tuberous root development is unclear.

Results

In this study, the transcriptome of fibrous roots (R0) and tuberous roots in three developmental stages (Rl, R2, R3) were analyzed in two sweet potato varieties, GJS-8 and XGH. A total of 22,914 and 24,446 differentially expressed genes (DEGs) were identified in GJS-8 and XGH respectively, 15,920 differential genes were shared by GJS-8 and XGH. KEGG pathway enrichment analysis showed that the DEGs shared by GJS-8 and XGH were mainly involved in “plant hormone signal transduction” “starch and sucrose metabolism” and “MAPK signal transduction”. Trihelix transcription factor (Tai6.25300) was found to be closely related to tuberous root enlargement by the comprehensive analysis of these DEGs and weighted gene co-expression network analysis (WGCNA).

Conclusion

A hypothetical model of genetic regulatory network for tuberous root development of sweet potato is proposed, which emphasizes that some specific signal transduction pathways like “plant hormone signal transduction” “Ca²⁺signal” “MAPK signal transduction” and metabolic processes including “starch and sucrose metabolism” and “cell cycle and cell wall metabolism” are related to tuberous root development in sweet potato. These results provide new insights into the molecular mechanism of tuberous root development in sweet potato.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08670-x.

Dynamic network biomarker analysis discovers IbNAC083 in the initiation and regulation of sweet potato root tuberization

The initiation and development of storage roots (SRs) are intricately regulated by a transcriptional regulatory network. One key challenge is to accurately pinpoint the tipping point during the transition from pre-swelling to SRs and to identify the core regulators governing such a critical transition. To solve this problem, we performed a dynamic network biomarker (DNB) analysis of transcriptomic dynamics during root development in Ipomoea batatas (sweet potato). First, our analysis identified stage-specific expression patterns for a significant proportion (>9%) of the sweet potato genes and unraveled the chronology of events that happen at the early and later stages of root development. Then, the results showed that different root developmental stages can be depicted by co-expressed modules of sweet potato genes. Moreover, we identified the key components and transcriptional regulatory network that determine root development. Furthermore, through DNB analysis an early stage, with a root diameter of 3.5 mm, was identified as the critical period of SR swelling initiation, which is consistent with morphological and metabolic changes. In particular, we identified a NAM/ATAF/CUC (NAC) domain transcription factor, IbNAC083, as a core regulator of this initiation in the DNB-associated network. Further analyses and experiments showed that IbNAC083, along with its associated differentially expressed genes, induced dysfunction of metabolism processes, including the biosynthesis of lignin, flavonol and starch, thus leading to the transition to swelling roots.

Tuber and Tuberous Root Development

Root and tuber crops have been an important part of human nutrition since the early days of humanity, providing us with essential carbohydrates, proteins, and vitamins. Today, they are especially important in tropical and subtropical regions of the world, where they help to feed an ever-growing population. Early induction and storage organ size are important agricultural traits, as they determine yield over time. During potato tuberization, environmental and metabolic status are sensed, ensuring proper timing of tuberization mediated by phloem-mobile signals. Coordinated cellular restructuring and expansion growth, as well as controlled storage metabolism in the tuber, are executed. This review summarizes our current understanding of potato tuber development and highlights similarities and differences to important tuberous root crop species like sweetpotato and cassava. Finally, we point out knowledge gaps that need to be filled before a complete picture of storage organ development can emerge.

Gene Regulatory Network Guided Investigations and Engineering of Storage Root Development in Root Crops

The plasticity of plant development relies on its ability to balance growth and stress resistance. To do this, plants have established highly coordinated gene regulatory networks (GRNs) of the transcription factors and signaling components involved in developmental processes and stress responses. In root crops, yields of storage roots are mainly determined by secondary growth driven by the vascular cambium. In relation to this, a dynamic yet intricate GRN should operate in the vascular cambium, in coordination with environmental changes. Despite the significance of root crops as food sources, GRNs wired to mediate secondary growth in the storage root have just begun to emerge, specifically with the study of the radish. Gene expression data available with regard to other important root crops are not detailed enough for us directly to infer underlying molecular mechanisms. Thus, in this review, we provide a general overview of the regulatory programs governing the development and functions of the vascular cambium in model systems, and the role of the vascular cambium on the growth and yield potential of the storage roots in root crops. We then undertake a reanalysis of recent gene expression data generated for major root crops and discuss common GRNs involved in the vascular cambium-driven secondary growth in storage roots using the wealth of information available in Arabidopsis. Finally, we propose future engineering schemes for improving root crop yields by modifying potential key nodes in GRNs.

Involvement of nitrogen in storage root growth and related gene expression in sweet potato (Ipomoea batatas)

Nitrogen (N) could affect storage root growth and development of sweet potato. To manage external N concentration fluctuations, plants have developed a wide range of strategies, such as growth changes and gene expression. Five sweet potato cultivars were used to analyse the functions of N in regulating storage root growth. Growth responses and physiological indicators were measured to determine the physiological changes regulated by different N concentrations. Expression profiles of related genes were analysed via microarray hybridization data and qRT-PCR analysis to reveal the molecular mechanisms of storage root growth regulated by different N concentrations. The growth responses and physiological indicators of the five cultivars were changed by N concentration. The root fresh weight of two of the sweet potato cultivars, SS19 and GS87, was higher under low N concentrations compared with the other cultivars. SS19 and GS87 were found to be having greater tolerance to low N concentration. The expression of N metabolism and storage root growth related genes was regulated by N concentration in sweet potato. These results reveal that N significantly regulated storage root growth. SS19 and GS87 were more tolerant to low N concentration and produced greater storage root yield (at 30 days). Furthermore, several N response genes were involved in both N metabolism and storage root growth.

Mobile RNAs and proteins: Prospects in storage organ development of tuber and root crops

Storage tuber and root crops make up a significant portion of the world's subsistence food supply. Because of their importance in food security, yield enhancement has become a priority. A major focus has been to understand the biology of belowground storage organ development. Considerable insights have been gained studying tuber development in potato. We now know that two mobile signals, a full-length mRNA, StBEL5, and a protein, StSP6A, play pivotal roles in regulating tuber development. Under favorable conditions, these signals move from leaves to a belowground modified stem (stolon) and regulate genes that activate tuberization. Overexpression of StBEL5 or StSP6A increases tuber yield even under non-inductive conditions. The mRNAs of two close homologs of StBEL5, StBEL11 and StBEL29, are also known to be mobile but act as repressors of tuberization. Polypyrimidine tract-binding proteins (PTBs) are RNA-binding proteins that facilitate the movement of these mRNAs. Considering their role in tuberization, it is possible that these mobile signals play a major role in storage root development as well. In this review, we explore the presence of these signals and their relevance in the development and yield potential of several important storage root crops.

RNA-Seq and iTRAQ reveal multiple pathways involved in storage root formation and development in sweet potato (Ipomoea batatas L.)

BACKGROUND

Sweet potato (Ipomoea batatas L.) is the sixth most important food crop in the world. The formation and development of storage roots in sweet potato is a highly complicated and genetically programmed process. However, the underlying mechanisms of storage root development have not yet been elucidated.

RESULTS

To better understand the molecular mechanisms involved in storage root development, a combined analysis of the transcriptome and proteome of sweet potato fibrous roots (F) and storage roots at four different stages (D1, D3, D5 and D10) was performed in the present study. A total of 26,273 differentially expressed genes were identified in a comparison between the fibrous root library and four storage root libraries, while 2558 proteins showed a 1.0-fold or greater expression difference as indicated by isobaric tags for relative and absolute quantitation (iTRAQ) analysis. The combination of the transcriptome and proteome analyses and morphological and physiological data revealed several critical pathways involved in storage root formation and development. First, genes/proteins involved in the development of meristems/cambia and starch biosynthesis were all significantly upregulated in storage roots compared with fibrous roots. Second, multiple phytohormones and the genes related to their biosynthesis showed differential expression between fibrous roots and storage roots. Third, a large number of transcription factors were differentially expressed during storage root initiation and development, which suggests the importance of transcription factor regulation in the development of storage roots. Fourth, inconsistent gene expression was found between the transcriptome and proteome data, which indicated posttranscriptional regulatory activity during the development of storage roots.

CONCLUSION

Overall, these results reveal multiple events associated with storage root development and provide new insights into the molecular mechanisms underlying the regulatory networks involved in storage root development.

The wild sweetpotato (Ipomoea trifida) genome provides insights into storage root development

BACKGROUND

Sweetpotato (Ipomoea batatas (L.) Lam.) is the seventh most important crop in the world and is mainly cultivated for its underground storage root (SR). The genetic studies of this species have been hindered by a lack of high-quality reference sequence due to its complex genome structure. Diploid Ipomoea trifida is the closest relative and putative progenitor of sweetpotato, which is considered a model species for sweetpotato, including genetic, cytological, and physiological analyses.

RESULTS

Here, we generated the chromosome-scale genome sequence of SR-forming diploid I. trifida var. Y22 with high heterozygosity (2.20%). Although the chromosome-based synteny analysis revealed that the I. trifida shared conserved karyotype with Ipomoea nil after the separation, I. trifida had a much smaller genome than I. nil due to more efficient eliminations of LTR-retrotransposons and lack of species-specific amplification bursts of LTR-RTs. A comparison with four non-SR-forming species showed that the evolution of the beta-amylase gene family may be related to SR formation. We further investigated the relationship of the key gene BMY11 (with identity 47.12% to beta-amylase 1) with this important agronomic trait by both gene expression profiling and quantitative trait locus (QTL) mapping. And combining SR morphology and structure, gene expression profiling and qPCR results, we deduced that the products of the activity of BMY11 in splitting starch granules and be recycled to synthesize larger granules, contributing to starch accumulation and SR swelling. Moreover, we found the expression pattern of BMY11, sporamin proteins and the key genes involved in carbohydrate metabolism and stele lignification were similar to that of sweetpotato during the SR development.

CONCLUSIONS

We constructed the high-quality genome reference of the highly heterozygous I. trifida through a combined approach and this genome enables a better resolution of the genomics feature and genome evolutions of this species. Sweetpotato SR development genes can be identified in I. trifida and these genes perform similar functions and patterns, showed that the diploid I. trifida var. Y22 with typical SR could be considered an ideal model for the studies of sweetpotato SR development.

Partial Replacement of Maltodextrin by Sweet Potato Flour (Ipomoea Batatas L. Lamarck) in the Development of a Shake Beverage

Sweet potato flour contains low-glycemic complex carbohydrates and, when it is ingested, prevents insulin spikes and prolongs the feeling of satiety. The aim of this study was to elaborate and to verify the acceptability of the shake with the total or partial substitution of maltodextrin for sweet potato flour. To elaborate the shake beverage, we used a 22 factorial design, with three central points, thus generating seven formulations. For the taste, color, texture, appearance, acceptance and attitude of purchase properties, sensory tests were conducted using a nine-point hedonic scale and panelists (n = 50). The highest acceptability formulations, formulations 3 (10% sweet potato flour; 25% maltodextrin) and 7 (0% sweet potato flour; 25% maltodextrin), were submitted to pH, moisture, ash, protein, lipid, crude fiber and total carbohydrate analyses. The statistical difference between the formulations from the T test (p < 0.05) was verified for the moisture, ash and lipid parameters. Formulation 3 presented higher values of moisture (93.26 ± 0.57) and lipids (1.91 ± 0.01), and formulation 7 had higher values of ash (0.39 ± 0.01). The results of the sensorial and physicochemical analyses of the shake indicate that sweet potato flour shows potential for the elaboration of this drink.

Conservation of polypyrimidine tract binding proteins and their putative target RNAs in several storage root crops

Background

Polypyrimidine-tract binding proteins (PTBs) are ubiquitous RNA-binding proteins in plants and animals that play diverse role in RNA metabolic processes. PTB proteins bind to target RNAs through motifs rich in cytosine/uracil residues to fine-tune transcript metabolism. Among tuber and root crops, potato has been widely studied to understand the mobile signals that activate tuber development. Potato PTBs, designated as StPTB1 and StPTB6, function in a long-distance transport system by binding to specific mRNAs (StBEL5 and POTH1) to stabilize them and facilitate their movement from leaf to stolon, the site of tuber induction, where they activate tuber and root growth. Storage tubers and root crops are important sustenance food crops grown throughout the world. Despite the availability of genome sequence for sweet potato, cassava, carrot and sugar beet, the molecular mechanism of root-derived storage organ development remains completely unexplored. Considering the pivotal role of PTBs and their target RNAs in potato storage organ development, we propose that a similar mechanism may be prevalent in storage root crops as well.

Results

Through a bioinformatics survey utilizing available genome databases, we identify the orthologues of potato PTB proteins and two phloem-mobile RNAs, StBEL5 and POTH1, in five storage root crops - sweet potato, cassava, carrot, radish and sugar beet. Like potato, PTB1/6 type proteins from these storage root crops contain four conserved RNA Recognition Motifs (characteristic of RNA-binding PTBs) in their protein sequences. Further, 3´ UTR (untranslated region) analysis of BEL5 and POTH1 orthologues revealed the presence of several cytosine/uracil motifs, similar to those present in potato StBEL5 and POTH1 RNAs. Using RT-qPCR assays, we verified the presence of these related transcripts in leaf and root tissues of these five storage root crops. Similar to potato, BEL5-, PTB1/6- and POTH1-like orthologue RNAs from the aforementioned storage root crops exhibited differential accumulation patterns in leaf and storage root tissues.

Conclusions

Our results suggest that the PTB1/6-like orthologues and their putative targets, BEL5- and POTH1-like mRNAs, from storage root crops could interact physically, similar to that in potato, and potentially, could function as key molecular signals controlling storage organ development in root crops.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4502-7) contains supplementary material, which is available to authorized users.

Transcriptome profiling and digital gene expression analysis of sweet potato for the identification of putative genes involved in the defense response against Fusarium oxysporum f. sp. batatas

Sweet potato production is constrained by Fusarium wilt, which is caused by Fusarium oxysporum f. sp. batatas (Fob). The identification of genes related to disease resistance and the underlying mechanisms will contribute to improving disease resistance via sweet potato breeding programs. In the present study, we performed de novo transcriptome assembly and digital gene expression (DGE) profiling of sweet potato challenged with Fob using Illumina HiSeq technology. In total, 89,944,188 clean reads were generated from 12 samples and assembled into 101,988 unigenes with an average length of 666 bp; of these unigenes, 62,605 (61.38%) were functionally annotated in the NCBI non-redundant protein database by BLASTX with a cutoff E-value of 10-5. Clusters of Orthologous Groups (COG), Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations were examined to explore the unigenes' functions. We constructed four DGE libraries for the sweet potato cultivars JinShan57 (JS57, highly resistant) and XinZhongHua (XZH, highly susceptible), which were challenged with pathogenic Fob. Genes that were differentially expressed in the four libraries were identified by comparing the transcriptomes. Various genes that were differentially expressed during defense, including chitin elicitor receptor kinase 1 (CERK), mitogen-activated protein kinase (MAPK), WRKY, NAC, MYB, and ethylene-responsive transcription factor (ERF), as well as resistance genes, pathogenesis-related genes, and genes involved in salicylic acid (SA) and jasmonic acid (JA) signaling pathways, were identified. These data represent a sequence resource for genetic and genomic studies of sweet potato that will enhance the understanding of the mechanism of disease resistance.

Transcriptomic profiling of taproot growth and sucrose accumulation in sugar beet (Beta vulgaris L.) at different developmental stages

In sugar beet (Beta vulgaris L.), taproot weight and sucrose content are the important determinants of yield and quality. However, high yield and low sucrose content are two tightly bound agronomic traits. The advances in next-generation sequencing technology and the publication of sugar beet genome have provided a method for the study of molecular mechanism underlying the regulation of these two agronomic traits. In this work, we performed comparative transcriptomic analyses in the high taproot yield cultivar SD13829 and the high sucrose content cultivar BS02 at five developmental stages. More than 50,000,000 pair-end clean reads for each library were generated. When taproot turned into the rapid growth stage at the growth stage of 82 days after emergence (DAE), eighteen enriched gene ontology (GO) terms, including cell wall, cytoskeleton, and enzyme linked receptor protein signaling pathway, occurred in both cultivars. Differentially expressed genes (DEGs) of paired comparison in both cultivars were enriched in the cell wall GO term. For pathway enrichment analyses of DEGs that were respectively generated at 82 DAE compared to 59 DAE (the earlier developmental stage before taproot turning into the rapid growth stage), plant hormone signal transduction pathway was enriched. At 82 DAE, the rapid enlarging stage of taproot, several transcription factor family members were up-regulated in both cultivars. An antagonistic expression of brassinosteroid- and auxin-related genes was also detected. In SD13829, the growth strategy was relatively focused on cell enlargement promoted by brassinosteroid signaling, whereas in BS02, it was relatively focused on secondarily cambial cell division regulated by cytokinin, auxin and brassinosteroid signaling. Taken together, our data demonstrate that the weight and sucrose content of taproot rely on its growth strategy, which is controlled by brassinosteroid, auxin, cytokinin, and gibberellin.

Comparative analysis of the root transcriptomes of cultivated sweetpotato (Ipomoea batatas [L.] Lam) and its wild ancestor (Ipomoea trifida [Kunth] G. Don)

BACKGROUND

The complex process of formation of storage roots (SRs) from adventitious roots affects sweetpotato yield. Identifying the genes that are uniquely expressed in the SR forming cultivated species, Ipomoea batatas (Ib), and its immediate ancestral species, Ipomoea trifida (It), which does not form SRs, may provide insights into the molecular mechanisms underlying SR formation in sweetpotato.

RESULTS

Illumina paired-end sequencing generated ~208 and ~200 million reads for Ib and It, respectively. Trinity assembly of the reads resulted in 98,317 transcripts for Ib and 275,044 for It, after post-assembly removal of trans-chimeras. From these sequences, we identified 4,865 orthologous genes in both Ib and It, 60 paralogous genes in Ib and 2,286 paralogous genes in It. Among paralogous gene sets, transcripts encoding the transcription factor RKD, which may have a role in nitrogen regulation and starch formation, and rhamnogalacturonate lyase (RGL) family proteins, which produce the precursors of cell wall polysaccharides, were found only in Ib. In addition, transcripts encoding a K⁺ efflux antiporter (KEA5) and the ERECTA protein kinase, which function in phytohormonal regulation and root proliferation, respectively, were also found only in Ib. qRT-PCR indicated that starch and sucrose metabolism genes, such as those encoding ADP-glucose pyrophosphorylase and beta-amylase, showed lower expression in It than Ib, whereas lignin genes such as caffeoyl-CoA O-methyltransferase (CoMT) and cinnamyl alcohol dehydrogenase (CAD) showed higher expression in It than Ib. A total of 7,067 and 9,650 unique microsatellite markers, 1,037,396 and 495,931 single nucleotide polymorphisms (SNPs) and 103,439 and 69,194 InDels in Ib and It, respectively, were also identified from this study.

CONCLUSION

The detection of genes involved in the biosynthesis of RGL family proteins, the transcription factor RKD, and genes encoding a K⁺ efflux antiporter (KEA5) and the ERECTA protein kinase only in I. batatas indicate that these genes may have important functions in SR formation in sweetpotato. Potential molecular markers (SNPs, simple sequence repeats and InDels) and sequences identified in this study may represent a valuable resource for sweetpotato gene annotation and may serve as important tools for improving SR formation in sweetpotato through breeding.

Transcriptome-wide mining suggests conglomerate of genes associated with tuberous root growth and development in Aconitum heterophyllum Wall

Tuberous roots of Aconitum heterophyllum constitute storage organ for secondary metabolites, however, molecular components contributing to their formation are not known. The transcriptomes of A. heterophyllum were analyzed to identify possible genes associated with tuberous root development by taking clues from genes implicated in other plant species. Out of 18 genes, eight genes encoding GDP-mannose pyrophosphorylase (GMPase), SHAGGY, Expansin, RING-box protein 1 (RBX1), SRF receptor kinase (SRF), β-amylase, ADP-glucose pyrophosphorylase (AGPase) and Auxin responsive factor 2 (ARF2) showed higher transcript abundance in roots (13-171 folds) compared to shoots. Comparative expression analysis of those genes between tuberous root developmental stages showed 11-97 folds increase in transcripts in fully developed roots compared to young rootlets, thereby implying their association in biosynthesis, accumulation and storage of primary metabolites towards root biomass. Cluster analysis revealed a positive correlation with the gene expression data for different stages of tuberous root formation in A. heterophyllum. The outcome of this study can be useful in genetic improvement of A. heterophyllum for root biomass yield.

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.