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Generation and analysis of blueberry transcriptome sequences from leaves, developing fruit, and flower buds from cold
Lisa J Rowland1, Nadim Alkharouf, Omar Darwish
1Genetic Improvement of Fruits and Vegetables Laboratory, USDA-ARS, BARC-West, 10300 Baltimore Ave., Beltsville, MD 20705, USA. Jeannine.Rowland@ars.usda.gov
BMC Plant Biology
|April 5, 2012
Summary
This study developed genomic resources for blueberries, including expressed sequence tags (ESTs) and SSR markers. These resources will aid in understanding cold acclimation and fruit development for improved blueberry genetics.
Area of Science:
- Plant Genomics
- Molecular Biology
- Agricultural Science
Background:
- Blueberries are increasingly consumed due to recognized health benefits, particularly from anthocyanins.
- Limited genomic resources hinder genetic improvement for traits like climatic adaptation and fruit quality.
- Development of expressed sequence tags (ESTs) and molecular markers is crucial for blueberry genetic advancement.
Purpose of the Study:
- To sequence the transcriptome of highbush blueberry (Vaccinium corymbosum) cultivar 'Bluecrop'.
- To identify genes involved in cold acclimation and fruit development.
- To develop SSR markers for genetic mapping studies.
Main Methods:
- Next-generation Roche 454 sequencing of blueberry fruit, flower buds, and leaves.
- Assembly and annotation of transcriptome sequences, including functional mapping to Gene Ontology (GO) terms.
- Identification and characterization of EST-SSR loci, primer design, and testing for amplification and polymorphism.
Main Results:
- Over 600,000 reads assembled into ~15,000 contigs and 124,000 singletons.
- Identified 15,886 blueberry EST-SSR loci, with 7,705 yielding designed primers.
- Tested 100 primer pairs, achieving 68% amplification and 43% polymorphism rates in mapping populations.
Conclusions:
- The generated ESTs are a valuable resource for identifying differentially expressed genes in blueberry development and stress response.
- ESTs have facilitated the development of SSR and EST-PCR markers.
- These markers are actively being used for the construction of genetic linkage maps in blueberry.
