BackgroundThe tuberous root of sweetpotato is an important agricultural and biological organ. There are not sufficient transcriptomic and genomic data in public databases for understanding of the molecular mechanism underlying the tuberous root formation and development. Thus, high throughput transcriptome sequencing is needed to generate enormous transcript sequences from sweetpotato root for gene discovery and molecular marker development.ResultsIn this study, more than 59 million sequencing reads were generated using Illumina paired-end sequencing technology. De novo assembly yielded 56,516 unigenes with an average length of 581 bp. Based on sequence similarity search with known proteins, a total of 35,051 (62.02%) genes were identified. Out of these annotated unigenes, 5,046 and 11,983 unigenes were assigned to gene ontology and clusters of orthologous group, respectively. Searching against the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG) indicated that 17,598 (31.14%) unigenes were mapped to 124 KEGG pathways, and 11,056 were assigned to metabolic pathways, which were well represented by carbohydrate metabolism and biosynthesis of secondary metabolite. In addition, 4,114 cDNA SSRs (cSSRs) were identified as potential molecular markers in our unigenes. One hundred pairs of PCR primers were designed and used for validation of the amplification and assessment of the polymorphism in genomic DNA pools. The result revealed that 92 primer pairs were successfully amplified in initial screening tests.ConclusionThis study generated a substantial fraction of sweetpotato transcript sequences, which can be used to discover novel genes associated with tuberous root formation and development and will also make it possible to construct high density microarrays for further characterization of gene expression profiles during these processes. Thousands of cSSR markers identified in the present study can enrich molecular markers and will facilitate marker-assisted selection in sweetpotato breeding. Overall, these sequences and markers will provide valuable resources for the sweetpotato community. Additionally, these results also suggested that transcriptome analysis based on Illumina paired-end sequencing is a powerful tool for gene discovery and molecular marker development for non-model species, especially those with large and complex genome.

BackgroundCurrently there exists a limited availability of genetic marker resources in sweetpotato (Ipomoea batatas), which is hindering genetic research in this species. It is necessary to develop more molecular markers for potential use in sweetpotato genetic research. With the newly developed next generation sequencing technology, large amount of transcribed sequences of sweetpotato have been generated and are available for identifying SSR markers by data mining.ResultsIn this study, we investigated 181,615 ESTs for the identification and development of SSR markers. In total, 8,294 SSRs were identified from 7,163 SSR-containing unique ESTs. On an average, one SSR was found per 7.1 kb of EST sequence with tri-nucleotide motifs (42.9%) being the most abundant followed by di- (41.2%), tetra- (9.2%), penta- (3.7%) and hexa-nucleotide (3.1%) repeat types. The top five motifs included AG/CT (26.9%), AAG/CTT (13.5%), AT/TA (10.6%), CCG/CGG (5.8%) and AAT/ATT (4.5%). After removing possible duplicate of published EST-SSRs of sweetpotato, a total of non-repeat 7,958 SSR motifs were identified. Based on these SSR-containing sequences, 1,060 pairs of high-quality SSR primers were designed and used for validation of the amplification and assessment of the polymorphism between two parents of one mapping population (E Shu 3 Hao and Guang 2k-30) and eight accessions of cultivated sweetpotatoes. The results showed that 816 primer pairs could yield reproducible and strong amplification products, of which 195 (23.9%) and 342 (41.9%) primer pairs exhibited polymorphism between E Shu 3 Hao and Guang 2k-30 and among the 8 cultivated sweetpotatoes, respectively.ConclusionThis study gives an insight into the frequency, type and distribution of sweetpotato EST-SSRs and demonstrates successful development of EST-SSR markers in cultivated sweetpotato. These EST-SSR markers could enrich the current resource of molecular markers for the sweetpotato community and would be useful for qualitative and quantitative trait mapping, marker-assisted selection, evolution and genetic diversity studies in cultivated sweetpotato and related Ipomoea species.

BackgroundThe tuberous root of sweetpotato is undisputedly an important organ from agronomic and biological perspectives. Little is known regarding the regulatory networks programming tuberous root formation and development.ResultsHere, as a first step toward understanding these networks, we analyzed and characterized the genome-wide transcriptional profiling and dynamics of sweetpotato root in seven distinct developmental stages using a customized microarray containing 39,724 genes. Analysis of these genes identified temporal programs of gene expression, including hundreds of transcription factor (TF) genes. We found that most genes active in roots were shared across all developmental stages, although significant quantitative changes in gene abundance were observed for 5,368 (including 435 TFs) genes. Clustering analysis of these differentially expressed genes pointed out six distinct expression patterns during root development. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that genes involved in different processes were enriched at specific stages of root development. In contrast with the large number of shared expressed genes in root development, each stage or period of root development has only a small number of specific genes. In total, 712 (including 27 TFs) and 1,840 (including 115 TFs) genes were identified as root-stage and root-period specific, respectively at the level of microarray. Several of the specific TF genes are known regulators of root development, including DA1-related protein, SHORT-ROOT and BEL1-like. The remaining TFs with unknown roles would also play critical regulatory roles during sweetpotato tuberous root formation and development.ConclusionsThe results generated in this study provided spatiotemporal patterns of root gene expression in support of future efforts for understanding the underlying molecular mechanism that control sweetpotato yield and quality.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0567-5) contains supplementary material, which is available to authorized users.

Purple-fleshed sweetpotatoes (PFSPs) are considered to be a healthy food and there are many methods to process in family. This study aimed to investigate the effects of various domestic cooking on the anthocyanin variation and antioxidant activity of a newly bred purple-fleshed cultivar Guangzishu 9 (GZ9) with anthocyanin content up to 1,500 mg/100g dry weight. As a result, total 15 individual anthocyanins were separated and identified by using UPLC-QTOF-MS. Top three anthocyanins were cyanidin 3-dicaffeoyl sophoroside-5-glucoside, cyanidin 3-caffeoyl- p-coumaryl sophoroside-5-glucoside and peonidin 3-caffeoyl-p-hydroxybenzoyl sophoroside-5-glucoside, which accounting for 57.27% of the total anthocyanin content. Acylated anthocyanins were the major constituents in GZ9, and the type of anthocyanins was dominated by cyanidin. Boiling, steaming and mircrowaving had no significant effect on the total anthocyanin content. But baking, frying, air-frying and stir-frying reduced 11–45% of total anthocyanin content. Through ABTS + radical scavenging capacity and reducing power, antioxidant variations were also observed during different family cooking, and the variation had a strong correlation with total anthocyanin content.

Since 2006, stem and root rot of sweetpotato has been observed in fields at a number of sweetpotato-production areas in Huidong, Haifeng, Puning, and Zhanjiang counties and Guangzhou City in Guangdong Province of China. Initially, the leaves turn yellow, and a black, water-soaked rot occurs on the bottom of the stems that gradually extends to the top of the stems. Finally, the entire plant collapses and dies. Bacteria were consistently isolated from stems of diseased seedlings by streaking on nutrient agar. Twelve representative isolates were chosen for further characterization. All strains grew at 37°C, were gram negative, facultatively anaerobic, and rod shaped with peritrichous flagella. The strains were negative for oxidase and positive for catalase and tryptophanase (indole production) They fermented glucose, reduced nitrates to nitrites, degraded pectate, produced phosphatase and lecithinase, and utilized citrate, tartrate, malonate, glucose, sucrose, fructose, and maltose, but not trehalose and lactose. These characteristics were similar to those of Erwinia chrysanthemi (Pectobacterium chrysanthemi) (1). PCR was performed on the 16S rDNA gene from isolate H12 (1,503 bp; GenBank Accession No. GU252371) with primers 27f (5′-GAGAGTTTGATCCTGGCTCAG-3′) and reverse primer (5′-GGCTACCTTGTTACGACTTC-3′). Subsequently, PCR products were sequenced. Results of sequence analysis showed the sequence of isolated strain H12 was 99% identical to that of E. chrysanthemi, 99% identical to that of type strain CFBP 1269T of Dickeya dadantii (Accession No. AF520707), and 98% identical to that of type strain CFBP 1200T of D. dianthicola (Accession No. AF520708). Recently, E. chrysanthemi was transferred to Dickeya gen. nov., but it was difficult to identify the species within the genus Dickeya. Seedlings (20 to 30 cm) were planted in 10-cm-diameter plastic pots containing sterilized field soil at room temperature. Four days later, five stem tops of sweetpotato were injected with a bacteria suspension (108 CFU/ml) of approximately 100 μl to fulfill Koch's postulates. Five control plants were inoculated with sterile distilled water. The experiment was conducted three times. All plants were incubated in a chamber at 30°C with high humidity. One to two days after inoculation, symptoms were observed in all inoculated plants and appeared to be identical to those observed in the field. No symptoms were noted on the control plants. The bacterium was reisolated from symptomatic stems of sweetpotato plants. This pathogen was previously reported on sweetpotato in the United States in 1974 (2). To our knowledge, this is the first report of a Dickeya sp. (E. chrysanthemi) causing bacterial stem and root rot of sweetpotato in China. References: (1) D. J. Brenner et al. Page 670 in: Bergey's Manual of Systematic Bacteriology. 2nd ed. Springer, New York, 2005. (2) N. W. Schaad et al. Phytopathology 67:302, 1977.

Summary Four inoculation methods were investigated for assessing the clonal variation of eucalypts in susceptibility to bacterial wilt (Ralstonia solanacearum). The results showed that these inoculation methods obviously differed in the disease infection process, clonal variation and clonal mean repeatability in susceptibility of stock materials inoculated. For each inoculation method, the clonal effect was consistently significant over the assessment period. Root-collar suspension injection method (RSI) yielded the highest relative clonal variation (0.67±0.086) and clonal mean repeatability (0.92±0.038) in both disease infected incidence and severity at the end of assessment, attributable to the enhanced genetic variation or low environment effect. For a given inoculation method, an early assessment time might exist for maximizing relative clonal variation or repeatability. It is desirable in breeding to adopt an inoculation method and/or efficient assessment time with high clonal variance component, which would in turn improve the efficiency of clonal screening.

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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 GS87were 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.