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CC BY V4.0, Open Access
Journal article
A blackberry (Rubus L.) expressed sequence tag library for the development of simple sequence repeat markers
BMC plant biology, Vol.8(1), pp.69-69
2008
Handle:
https://hdl.handle.net/2376/104966
PMCID: PMC2474608
PMID: 18570660
Abstract
Background: The recent development of novel repeat-fruiting types of blackberry (Rubus L.) cultivars, combined with a long history of morphological marker-assisted selection for thornlessness by blackberry breeders, has given rise to increased interest in using molecular markers to facilitate blackberry breeding. Yet no genetic maps, molecular markers, or even sequences exist specifically for cultivated blackberry. The purpose of this study is to begin development of these tools by generating and annotating the first blackberry expressed sequence tag (EST) library, designing primers from the ESTs to amplify regions containing simple sequence repeats (SSR), and testing the usefulness of a subset of the EST-SSRs with two blackberry cultivars.
Results: A cDNA library of 18,432 clones was generated from expanding leaf tissue of the cultivar Merton Thornless, a progenitor of many thornless commercial cultivars. Among the most abundantly expressed of the 3,000 genes annotated were those involved with energy, cell structure, and defense. From individual sequences containing SSRs, 673 primer pairs were designed. Of a randomly chosen set of 33 primer pairs tested with two blackberry cultivars, 10 detected an average of 1.9 polymorphic PCR products.
Conclusion: This rate predicts that this library may yield as many as 940 SSR primer pairs detecting 1,786 polymorphisms. This may be sufficient to generate a genetic map that can be used to associate molecular markers with phenotypic traits, making possible molecular marker-assisted breeding to compliment existing morphological marker-assisted breeding in blackberry.
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Details
- Title
- A blackberry (Rubus L.) expressed sequence tag library for the development of simple sequence repeat markers
- Creators
- Kim S Lewers - USDA-ARS, Beltsville Agricultural Research Center, Genetic Improvement of Fruits and Vegetables Lab, Bldg. 010A, BARC-West, 10300 Baltimore Ave., Beltsville, MD 20705-2350, USAChris A Saski - Clemson University Genomics Institute, 51 New Cherry St., 304 Biosystems Research Complex, Clemson University, Clemson, SC 29634, USABrandon J Cuthbertson - Clemson University Genomics Institute, 51 New Cherry St., 304 Biosystems Research Complex, Clemson University, Clemson, SC 29634, USADavid C Henry - Clemson University Genomics Institute, 51 New Cherry St., 304 Biosystems Research Complex, Clemson University, Clemson, SC 29634, USAMeg E Staton - Clemson University Genomics Institute, 51 New Cherry St., 304 Biosystems Research Complex, Clemson University, Clemson, SC 29634, USADorrie S Main - Clemson University Genomics Institute, 51 New Cherry St., 304 Biosystems Research Complex, Clemson University, Clemson, SC 29634, USAAnik L Dhanaraj - USDA-ARS, Beltsville Agricultural Research Center, Genetic Improvement of Fruits and Vegetables Lab, Bldg. 010A, BARC-West, 10300 Baltimore Ave., Beltsville, MD 20705-2350, USALisa J Rowland - USDA-ARS, Beltsville Agricultural Research Center, Genetic Improvement of Fruits and Vegetables Lab, Bldg. 010A, BARC-West, 10300 Baltimore Ave., Beltsville, MD 20705-2350, USAJeff P Tomkins - Clemson University Genomics Institute, 51 New Cherry St., 304 Biosystems Research Complex, Clemson University, Clemson, SC 29634, USA
- Publication Details
- BMC plant biology, Vol.8(1), pp.69-69
- Academic Unit
- Department of Horticulture
- Publisher
- BioMed Central
- Number of pages
- 8
- Identifiers
- 99900546562701842
- Language
- English
- Resource Type
- Journal article