Molecular Tools for Rubus

Genomic Resource Building in Blackberry

This is a project I am involved with in collaboration with Dr. Bob Skirvin, Dr. Ray Ming, and Daniel Weber (Ph.D. candidate) at the University of Illinois, Urbana-Champaign.   We are creating the first blackberry molecular map.  This is a great project since the population we are using is tetraploid.  In 2014 this Map was completed and we are currently preparing it for publication.

We also are working towards developing other marker tools for Blackberry such as a project in collaboration with Dr. John Clark at the University of Arkansas, Fayetteville.  We worked to develop a set of DNA fingerprinting markers that can be used to identify particular blackberry varieties.

Sequencing of the Raspberry Genome

In collaboration with Drs. Josh Udall, Mark Clement, Mr. Jared Ward (Bingham Young University), and Drs. Courtney Weber, and Jud Ward (Cornell University), we are in the process of sequencing the ‘Heritage’ Genome.  This has also resulted in a high density GBS map for ‘Heritage’.

Development of Transgenic Blackberry

Transgenic Blackberry Callus

This project is in collaboration with Dr. Kevin Folta at the University of Florida, Gainesville.  We have been working towards establishing the first transgenic lines in Blackberry.  Folta is a world leader in small berry transformation methodologies (Strawberry) and to this end I sent a UCA undergraduate student, Nadine Gates, to work in his lab during the Summer of 2008 (NABGA grant and EPSCoR) and again in the Summer of 2009 (INBRE Summer grant).  Upon coming back was successful in creating callus tissues and regenerating shoots from that tissue.  We have also generated transgenic callus and bud tissues, the first ever created in Blackberry!

References

Ward JA, Bhangoo J, Fernández-Fernández F, Moore P, Swanson JD, Viola R, Velasco R, Bassil N, Weber CA, Sargent DJ, (2013) Saturated linkage map construction in Rubus idaeus using genotyping by sequencing and genome-independent imputation, BMC Genomics, 14:2. doi:10.1 186/1471-2164-14-2

Swanson, JD, Spencer, N., Dostie, K. (Submitted) A refined set of primers to fingerprint blackberry cultivars. Journal of ASHS

Swanson, J-D, Weber, C., Finn, C. E., Fernández-Fernández, F., Sargent, D., Carlson, J.E., Graham, J. (2011) Breeding, Genetics and Genomics of Rubus, Genetics, Genomics and Breeding in Fruit and Vegetable Crops- Berries, Springer

Ward, J.A., Price, J.C., Clement, M., Schatz, M., Weber C.A. Swanson, J.D., Bodily, P., Lewers, K.S., Fernandez, F., Burns, P.D., Velasco, R., Sargent, D., Udall, J. (2012) A draft assembly and analysis of the highly heterozygous diploid red raspberry genome (Rubus idaeus cv. Heritage) Plant and Animal Genome Meeting XX, San Diego, CA. Jan 14-18, 2012

Price, J. C., Ward, J. A., Clement, M. J., Weber, C. A., Lewers, K. S., Swanson, J. D., Hagen, W., Haynes, B., Udall, J. A. (2011) Whole genome sequencing of the highly heterozygous diploid red raspberry, Rubus Idaeus cv. Heritage. Plant and Animal Genome Meeting XIX, San Diego, CA. Jan 15-19, 2011

Spencer, N (2011) The use of Molecular Markers in Blackberry: Fingerprinting Blackberry cultivars and the identification of a potential gene involved with prickle development. M.S. Thesis, University of Central Arkansas, Conway AR (Defended Aug 8, 2011)

Spencer, N.**,  Rodriguez, C.*, Swanson, JD (2011) Fingerprinting and Diversity Analysis of Selected Blackberry Cultivars Using Microsatellite Markers. Plant and Animal Genome Meeting XIX, San Diego, CA. Jan 15-19, 2011

Swanson, J-D (2010) The Development Of Prickles: A model system to build genomic resources for Rubus. Plant and Animal Genome Meeting XVIII, San Diego, CA. Jan 9-13, 2010

Gates, N. (2009) The Creation of Transgenic Blackberry and the Ethical Dilemmas Surrounding Genetically Modified Crops. B.S. Honors Thesis, UCA, Conway, AR (Defended Dec 11, 2009)