A sweetpotato gene index established by de novo assembly of pyrosequencing and Sanger sequences and mining for gene-based microsatellite markers

Schafleitner, Roland; Tincopa, Luz; Palomino, Omar; Rossel, Genoveva; Robles, Ronald; Alagon, Rocio; Rivera, Carlos; Quispe, Cynthia; Rojas, Luís; Pacheco, Jaime A; Solis, Julio; Cerna, Diogenes; Kim, Ji Young; Hou, Jack P.; Simon, Reinhard

doi:10.1186/1471-2164-11-604

Cited by 80 publications

(83 citation statements)

References 23 publications

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“…When annotated to nr database, many contigs could not be matched the known non-redundant protein, especially in the stems (52.24%). Compared with previous transcriptome study on Ipomoea batatas (Schafleitner et al, 2010;Wang et al, 2010;Tao et al, 2012, Xie et al, 2012Ma et al, 2016), more transcripts in hexaploid I. trifida had significant BLASTX hits to the nr database than these in cultivar 'Xushu18' (40.42%) (Tao et al, 2012) and less than variety 'Georgia Jet' (72.48%) (Firon et al, 2013), and it also less than diploid I. trifida (76.68%) (Cao et al, 2016). This may be because of the characters with hexaploid genome and wild.…”

Section: Discussionmentioning

confidence: 91%

Comparative transcriptome to reveal the drought tolerance mechanism in hexaploid <i>Ipomoea trifida</i>

Ma¹,

Lin²,

Feng³

et al. 2017

mpb

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Hexaploid Ipomoea trifida (I. trifida), a wild relative of sweetpotato [Ipomoea batatas (L.) Lam.], has plentiful superior genes and a variety of anti-adversity characteristics genetically, and used as a distant hybridization materials in sweetpotato breeding. However, insufficient transcriptomic and genomic resources of hexaploid I. trifida are available for understanding the molecular mechanism underlying drought tolerance. In this study, we are the first to report a reference transcriptome using leaf, stem and root tissues under drought-stressed condition from hexaploid I. trifida, which is helpful to generate a large number of transcripts associated with drought tolerance for gene discovery. In this study, a total of 191,231, 226,262, and 171,841 contigs with a mean length of 1,100, 1,038 and 1,106 bp were obtained from the three tissues, respectively. In our assembled sequences, 62.38%, 50.08% and 47.76% of all contigs in the three tissues could be annotated to the nr database. Based on the Gene ontology (GO) analysis, 39,193, 49,997 and 34,887 contigs in leaves, roots and stems could assign with GO terms, and totaled 69 contigs up-regulated expression. In the annotated genes, we identified six transcription factors and two genes involved in drought-stress responses. Furthermore, the gene expression profiles of 15 putative genes associated with drought tolerance were analyzed to verify the reliability of the transcriptome using quantitative real-time PCR (qRT-PCR). These results provide a foundation for understanding the molecular mechanisms underlying drought stress of hexaploid I. trifida, and promoting its further utilization in sweetpotato breeding.

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Section: Discussionmentioning

confidence: 91%

Comparative transcriptome to reveal the drought tolerance mechanism in hexaploid <i>Ipomoea trifida</i>

Ma¹,

Lin²,

Feng³

et al. 2017

mpb

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“…The sequences of 405 published expressed sequence tags (EST) SSR primers (Buteler et al 1999;Hu et al 2004;Schafleitner et al 2010;Wang et al 2011) were obtained for this study. The primers were redesigned by addition of the M13 tail universal primer sequence (TGTAAAACGACGGCCAGT) to the 5 0 end of the forward primer sequence and then synthesized by Eurofins Genomics (Huntsville, Alabama).…”

Section: Plant Materialsmentioning

confidence: 99%

“…Nextgeneration sequencing will also contribute to simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) marker discovery for use in marker assisted selection (MAS) and genomic selection for developing SPW resistant cultivars. With the low number of sweetpotato SSR markers published to date compared to other major crops (Buteler et al 1999;Hu et al 2004;Schafleitner et al 2010;Wang et al 2011), and no SNPs at all, genomic improvement of SPW resistance is still in its infancy.…”

Section: Introductionmentioning

confidence: 99%

“…In this study, we used logistic regression to associate published SSR markers (Buteler et al 1999;Hu et al 2004;Schafleitner et al 2010;Wang et al 2011) to SPW resistance in the 'New Kawogo' x 'Beauregard' bi-parental population, which is segregating for SPW resistance and other agronomic traits. This is the first time that co-dominantly inherited SSR markers have been used to identify SPW resistance loci in sweetpotato.…”

Section: Introductionmentioning

confidence: 99%

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Identification of simple sequence repeat markers for sweetpotato weevil resistance

et al. 2017

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The development of sweetpotato [Ipomoea batatas (L.) Lam] germplasm with resistance to sweetpotato weevil (SPW) requires an understanding of the biochemical and genetic mechanisms of resistance to optimize crop resistance. The African sweetpotato landrace, 'New Kawogo', was reported to be moderately resistant to two species of SPW, Cylas puncticollis and Cylas brunneus. Resistance has been associated with the presence of hydroxycinnamic acids esters (HCAs), but the underlying genetic basis remains unknown. To determine the genetic basis of this resistance, a bi-parental sweetpotato population from a cross between the moderately resistant, whitefleshed 'New Kawogo' and the highly susceptible, orange-fleshed North American variety 'Beauregard' was evaluated for SPW resistance and genotyped with simple sequence repeat (SSR) markers to identify weevil resistance loci. SPW resistance was measured on the basis of field storage root SPW damage severity and total HCA ester concentrations. Moderate broad sense heritability (H 2 = 0.49) was observed for weevil resistance in the population. Mean genotype SPW severity scores ranged from 1.0 to 9.0 and 25 progeny exhibited transgressive segregation for SPW resistance. Mean genotype total HCA ester concentrations were significantly different (P \ 0.0001). A weak but significant correlation (r = 0.103, P = 0.015) was observed between total HCA ester concentration and SPW severity. A total of five and seven SSR markers were associated with field SPW severity and total HCA ester concentration, respectively. Markers IBS11, IbE5 and IbJ544b showed significant association with both field and HCA-based resistance,

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“…The genomic resources of this crop are much more deficient than those of other important crop species. Due to the development and usage of next-generation sequencing technology, several sweet potato transcriptomes have been released (Schafleitner et al, 2010;Wang et al, 2010;Tao et al, 2012;Xie et al, 2012;Tao et al, 2013). Although the complete genome sequence has not yet been published, it is encouraging that scientists have been attempting to construct a genetic map for sweet potato and have recently released the de novo whole-genome sequencing results of the diploid ancestor (Hirakawa et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

Cloning and characterization of a serine/threonine protein phosphatase2A-encoding gene IbPP2A1 from Ipomoea batatas (L.) Lam.

Xu¹,

Yong²,

Shao³

et al. 2017

Turk J Biol

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Sweet potato is one of the most important food crops with strong environmental adaptability. Protein phosphatase 2A (PP2A) is a major intracellular protein phosphatase that plays crucial roles in hormone signal transduction and abiotic stress response. Characterization of PP2A can elucidate the mechanisms of stress resistance in this crop. In this study, a total of 15 PP2A transcripts, including nine regulatory subunit-encoding sequences and six catalytic subunit-encoding sequences, were identified from sweet potato and found to be expressed at varying levels. Only one contained a complete open reading frame and encoded a B regulatory subunit (termed IbPP2A1). Ten polymorphic sites were distributed in the coding region of this gene, but most did not result in amino acid change. RNA sequencing-based digital gene expression profiling showed that this PP2A gene was primarily expressed in fibrous roots and developing tuberous roots under natural conditions. After drought, salinity, and alkaline stress treatment, the expression of IbPP2A1 was obviously upregulated in stems and tuberous roots at 2 days, whereas the expression of IbPP2A1 in leaves was only upregulated by drought stress at 2 days. However, heterogeneous expression of IbPP2A1 did not enhance abiotic stress tolerance in recombinant Saccharomyces cerevisiae. The results described here indicate that IbPP2A1 is an abiotic stress-responsive gene, but it could not work alone in vitro. This study provides a preliminary but global insight into PP2A proteins in sweet potato for further investigations on improving stress tolerance in this crop.

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A sweetpotato gene index established by de novo assembly of pyrosequencing and Sanger sequences and mining for gene-based microsatellite markers

Cited by 80 publications

References 23 publications

Comparative transcriptome to reveal the drought tolerance mechanism in hexaploid <i>Ipomoea trifida</i>

Comparative transcriptome to reveal the drought tolerance mechanism in hexaploid <i>Ipomoea trifida</i>

Identification of simple sequence repeat markers for sweetpotato weevil resistance

Cloning and characterization of a serine/threonine protein phosphatase2A-encoding gene IbPP2A1 from Ipomoea batatas (L.) Lam.

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