Melon Transcriptome Characterization: Simple Sequence Repeats and Single Nucleotide Polymorphisms Discovery for High Throughput Genotyping across the Species
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Author
Blanca, José Miguel
Cañizares, Joaquín
Ziarsolo, Pello
Esteras, Cristina
Nuez, Fernando
Picó, María Belén
Publication date
2011-07-01ISSN
1940-3372
Abstract
Melon (Cucumis melo L.) ranks among the highest-valued fruit
crops worldwide. Some genomic tools are available for this crop,
including a Sanger transcriptome. We report the generation
of 689,054 C. melo high-quality expressed sequence tags
(ESTs) from two 454 sequencing runs, using normalized and
nonnormalized complementary DNA (cDNA) libraries prepared
from four genotypes belonging to the two C. melo subspecies
and the main commercial types. 454 ESTs were combined with
the Sanger available ESTs and de novo assembled into 53,252
unigenes. Over 63% of the unigenes were functionally annotated
with Gene Ontology (GO) terms and 21% had known orthologs
of Arabidopsis thaliana (L.) Heynh. Annotation distribution
followed similar tendencies than that reported for Arabidopsis
thaliana, suggesting that the dataset represents a fairly complete
melon transcriptome. Furthermore, we identifi ed a set of 3298
unigenes with microsatellite motifs and 14,417 sequences with
single nucleotide variants of which 11,655 single nucleotide
polymorphism met criteria for use with high-throughput genotyping
platforms, and 453 could be detected as cleaved amplifi ed
polymorphic sequence (CAPS). A set of markers were validated,
90% of them being polymorphic in a number of variable C.
melo accessions. This transcriptome provides an invaluable new
tool for biological research, more so when it includes transcripts
not described previously. It is being used for genome annotation
and has provided a large collection of markers that will allow
speeding up the process of breeding new melon varieties.
Document Type
Article
Document version
Published version
Language
English
Subject (CDU)
633 - Field crops and their production
Pages
14
Publisher
Crop Science Society of America
Is part of
The Plant Genome
Citation
Blanca, José Miguel, Joaquín Cañizares, Pello Ziarsolo, Cristina Esteras, Gisela Mir, Fernando Nuez, Jordi Garcia-Mas, and María Belén Picó. 2011. «Melon Transcriptome Characterization: Simple Sequence Repeats And Single Nucleotide Polymorphisms Discovery For High Throughput Genotyping Across The Species». The Plant Genome 4 (2): 118-131. doi: 10.3835/plantgenome2011.01.0003
Program
Genòmica i Biotecnologia
This item appears in the following Collection(s)
- ARTICLES CIENTÍFICS [2650]
Except where otherwise noted, this item's license is described as http://creativecommons.org/licenses/by-nc-nd/4.0/