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Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae).

Blanca J, Cañizares J, Roig C, Ziarsolo P, Nuez F, Picó B - BMC Genomics (2011)

Bottom Line: We present the first broad survey of gene sequences and allelic variation in C. pepo, where limited prior genomic information existed.The transcriptome provides an invaluable new tool for biological research.The developed molecular markers are the basis for future genetic linkage and quantitative trait loci analysis, and will be essential to speed up the process of breeding new and better adapted squash varieties.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute for the Conservation and Breeding of Agricultural Biodiversity, Universidad Politécnica de Valencia (COMAV-UPV), Camino de Vera s/n, 46022 Valencia, Spain.

ABSTRACT

Background: Cucurbita pepo belongs to the Cucurbitaceae family. The "Zucchini" types rank among the highest-valued vegetables worldwide, and other C. pepo and related Cucurbita spp., are food staples and rich sources of fat and vitamins. A broad range of genomic tools are today available for other cucurbits that have become models for the study of different metabolic processes. However, these tools are still lacking in the Cucurbita genus, thus limiting gene discovery and the process of breeding.

Results: We report the generation of a total of 512,751 C. pepo EST sequences, using 454 GS FLX Titanium technology. ESTs were obtained from normalized cDNA libraries (root, leaves, and flower tissue) prepared using two varieties with contrasting phenotypes for plant, flowering and fruit traits, representing the two C. pepo subspecies: subsp. pepo cv. Zucchini and subsp. ovifera cv Scallop. De novo assembling was performed to generate a collection of 49,610 Cucurbita unigenes (average length of 626 bp) that represent the first transcriptome of the species. Over 60% of the unigenes were functionally annotated and assigned to one or more Gene Ontology terms. The distributions of Cucurbita unigenes followed similar tendencies than that reported for Arabidopsis or melon, suggesting that the dataset may represent the whole Cucurbita transcriptome. About 34% unigenes were detected to have known orthologs of Arabidopsis or melon, including genes potentially involved in disease resistance, flowering and fruit quality. Furthermore, a set of 1,882 unigenes with SSR motifs and 9,043 high confidence SNPs between Zucchini and Scallop were identified, of which 3,538 SNPs met criteria for use with high throughput genotyping platforms, and 144 could be detected as CAPS. A set of markers were validated, being 80% of them polymorphic in a set of variable C. pepo and C. moschata accessions.

Conclusion: We present the first broad survey of gene sequences and allelic variation in C. pepo, where limited prior genomic information existed. The transcriptome provides an invaluable new tool for biological research. The developed molecular markers are the basis for future genetic linkage and quantitative trait loci analysis, and will be essential to speed up the process of breeding new and better adapted squash varieties.

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Related in: MedlinePlus

Length distribution of the Cucurbita ESTs. Data obtained after sequencing, with a half run of 454 GS FLX Titanium each one of the two Cucurbita cDNA libraries (Zucchini, Mu-16; Scallop, UPV-196), and processing the 454 raw reads, are presented.
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Figure 1: Length distribution of the Cucurbita ESTs. Data obtained after sequencing, with a half run of 454 GS FLX Titanium each one of the two Cucurbita cDNA libraries (Zucchini, Mu-16; Scallop, UPV-196), and processing the 454 raw reads, are presented.

Mentions: We performed a half 454 GS FLX Titanium run on each of the two libraries constructed from leaves, flowers and roots from two C. pepo cultivars with contrasting plant, flower and fruit phenotypes, MU16 (C. pepo subsp. pepo cv Zucchini) and UPV196 (C. pepo subsp. pepo cv Scallop). A total of 407,723 and 392,370 raw sequence reads were obtained from each library (Table 1). Raw reads were processed using the Ngs_backbone software [53] to eliminate adapter sequences, low quality chromatograms and sequences of less than 100 base pairs (bp). This analysis gave rise to 261,962 and 250,789 processed sequences, comprising 164.6 Mbp of sequence, with an average length of 318.7 and 323.4 bp, respectively. The length distribution of these expressed sequence tags (ESTs) is shown in Figure 1. More than 85% ESTs fell between 200 and 500 bp in length.


Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae).

Blanca J, Cañizares J, Roig C, Ziarsolo P, Nuez F, Picó B - BMC Genomics (2011)

Length distribution of the Cucurbita ESTs. Data obtained after sequencing, with a half run of 454 GS FLX Titanium each one of the two Cucurbita cDNA libraries (Zucchini, Mu-16; Scallop, UPV-196), and processing the 454 raw reads, are presented.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3049757&req=5

Figure 1: Length distribution of the Cucurbita ESTs. Data obtained after sequencing, with a half run of 454 GS FLX Titanium each one of the two Cucurbita cDNA libraries (Zucchini, Mu-16; Scallop, UPV-196), and processing the 454 raw reads, are presented.
Mentions: We performed a half 454 GS FLX Titanium run on each of the two libraries constructed from leaves, flowers and roots from two C. pepo cultivars with contrasting plant, flower and fruit phenotypes, MU16 (C. pepo subsp. pepo cv Zucchini) and UPV196 (C. pepo subsp. pepo cv Scallop). A total of 407,723 and 392,370 raw sequence reads were obtained from each library (Table 1). Raw reads were processed using the Ngs_backbone software [53] to eliminate adapter sequences, low quality chromatograms and sequences of less than 100 base pairs (bp). This analysis gave rise to 261,962 and 250,789 processed sequences, comprising 164.6 Mbp of sequence, with an average length of 318.7 and 323.4 bp, respectively. The length distribution of these expressed sequence tags (ESTs) is shown in Figure 1. More than 85% ESTs fell between 200 and 500 bp in length.

Bottom Line: We present the first broad survey of gene sequences and allelic variation in C. pepo, where limited prior genomic information existed.The transcriptome provides an invaluable new tool for biological research.The developed molecular markers are the basis for future genetic linkage and quantitative trait loci analysis, and will be essential to speed up the process of breeding new and better adapted squash varieties.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute for the Conservation and Breeding of Agricultural Biodiversity, Universidad Politécnica de Valencia (COMAV-UPV), Camino de Vera s/n, 46022 Valencia, Spain.

ABSTRACT

Background: Cucurbita pepo belongs to the Cucurbitaceae family. The "Zucchini" types rank among the highest-valued vegetables worldwide, and other C. pepo and related Cucurbita spp., are food staples and rich sources of fat and vitamins. A broad range of genomic tools are today available for other cucurbits that have become models for the study of different metabolic processes. However, these tools are still lacking in the Cucurbita genus, thus limiting gene discovery and the process of breeding.

Results: We report the generation of a total of 512,751 C. pepo EST sequences, using 454 GS FLX Titanium technology. ESTs were obtained from normalized cDNA libraries (root, leaves, and flower tissue) prepared using two varieties with contrasting phenotypes for plant, flowering and fruit traits, representing the two C. pepo subspecies: subsp. pepo cv. Zucchini and subsp. ovifera cv Scallop. De novo assembling was performed to generate a collection of 49,610 Cucurbita unigenes (average length of 626 bp) that represent the first transcriptome of the species. Over 60% of the unigenes were functionally annotated and assigned to one or more Gene Ontology terms. The distributions of Cucurbita unigenes followed similar tendencies than that reported for Arabidopsis or melon, suggesting that the dataset may represent the whole Cucurbita transcriptome. About 34% unigenes were detected to have known orthologs of Arabidopsis or melon, including genes potentially involved in disease resistance, flowering and fruit quality. Furthermore, a set of 1,882 unigenes with SSR motifs and 9,043 high confidence SNPs between Zucchini and Scallop were identified, of which 3,538 SNPs met criteria for use with high throughput genotyping platforms, and 144 could be detected as CAPS. A set of markers were validated, being 80% of them polymorphic in a set of variable C. pepo and C. moschata accessions.

Conclusion: We present the first broad survey of gene sequences and allelic variation in C. pepo, where limited prior genomic information existed. The transcriptome provides an invaluable new tool for biological research. The developed molecular markers are the basis for future genetic linkage and quantitative trait loci analysis, and will be essential to speed up the process of breeding new and better adapted squash varieties.

Show MeSH
Related in: MedlinePlus