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!


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)

Recent Updates

June 8, 2014, Congrats to Dr. Swanson who graduated from the ISKF Instructor Trainee Program today. He is now one of the few officially Licensed Instructors, Examiners, and Judges in the ISKF.

May 18, 2014, Say goodbye to Noe, Kelsey, Shennel, and Alyssia who are graduating from Salve today. Thank you for all the hard work you put in!

April 26-27, 2014, Congrats to Shennel and Noe for their excellent talks at the 53rd Annual Northeast Algal Society Symposium. (Hosted by Salve Regina University). Big shoutout to the Swanson lab for helping with the organization of that meeting.

April 16, 2014. Dr. Swanson finally "earned his Ph.D." with a presentation and paper entitled "The five principals of Shotokan Karate and their linkage to the jitsu vs. do of karate training" at the American Philosophical Association annual conference in San Diego.

March 22, 2014. Thank you to all lab members for representing at this years SRYou day! It was a huge success!

March 8-9, 2014, Nice representation at NURDS! go Kelsey, Steph, and Noe

Jan 11-15, 2014, Go Stephanie, Kelsey, and Noe Presenting at the Plant and Animal Genome Conference in San Diego!

Jan 12, 2014 - Dr. Swanson was voted to be the New President of the US Rosaceae Genetics, Genomic and Breeding committee.

December 6, 2013, Dr. Swanson did a talk and other members of the lab presented at BioNess at Roger Williams University! Go Team!

November 17, 2013, Congrats to Dr. Swanson for passing his Godan (5th dan) examination under Okazaki and Yaguchi Sensei's.

August 14-16, 2013, Nice job Stephanie, Kelsey, and Tia in presenting your work at the IDEA Regional meeting at the University of Delaware in Newark DE.

August 2, 2013 - Thanks to Kelsey, Stephanie, Matt, Noe, Rhiannon, and Ally for presenting their work so well at this years 5th annual RI Research day at URI!

May 1, 2013 - Dr. Swanson was honored at the annual Salve Student affairs dinner with the freshman advocate award. It is an award voted on by the entire freshman class!

April 30, 2013 - Special congrats to Alexis Gallipoli for presenting an excellent senior thesis!

April 20, 2013 - Nice job Matt Breeseman for presenting his work at the 20013 NEAC meeting in Mystic this weekend.

March 29, 2013 - Dr. Swanson did a talk on the effects of Gallic Acid on human stomach cancer cells at the University of Rhode Island.

March 22, 2013 - Congrats to all of the students in the Swanson lab for representing us so well at SRYou day this year!

March 18, 2013 - Congrats to Noe and Matt for being awarded a SURF fellowship to continue their work on Algal Bloom genomics for the summer!

Mar 2013 - Dr. Swanson was featured in the Spring issue of Newport Life Magazine for his Algal research with Carol Thornber.

Mar 2, 2013 - Several students from the Swanson lab went to the NURDS conference at the University of New England to present their research! Nice job!!!

Feb 23, 2013 - Brian Dalagerie, Madeine Berry, and Wayne Bainter took part in the ECCKU Collegiate Karate Camp and Tournament held in Williamsport PA. Congrats to Brian who reached the finals for Kata and took third in Kumite, and well done to Madeline who place third in Kata and got first in Kumite!!!

Jan 12, 2013 - Dr. Swanson was voted to be the New Vice President of the US Rosaceae Genetics, Genomic and Breeding committee.

Jan 11-16, 2013 - Dr. Swanson, Kelsey Stafstorm, and Shennel Gelin went to the Plant and Animal Genome conference in San Diego to present their data. This was a great place to showcase their work on Algal Genomic and Galic Acid work! Both Kelsey and Shennel held their own in a conference full of PhDs, Post-doc's and Grad students. Nice Job!

December 9, 2012 - Thanks to Sensei Joe Faracchio for coming to Salve Regina and conducting our semesterly seminar and test. The first one hosted by Salve. Was attended by UMass and Brown. Nice showing by the Salve students!

December 4, 2012 - Dr. Swanson along with several colleagues had their manuscript "Saturated linkage map construction in Rubus idaeus using genotyping by sequencing and genome-independent imputation" accepted by BMC Genomics. Extra special kudos to Jud Ward the lead author!

October 20, 2012 - Congrats to the SRU Students who competed at the UMass collegiate Karate Tournament. One first, two seconds and a third!

August 4, 2012 - Dr. Swanson presented a talk at the annual ASHS conference in Miami Florida.

July 27, 2012 - Congrats to Drs. Swanson, Dussourd and Ms Ganong for geting their paper entitled "Girdling by notodontid caterpillars: Distribution and occurrence" published in Plant anthropoid interactions.

July 26, 2012. - Six Salve students presented five posters showcasing their work at the SURF Undergraduate Symposium at URI. Well done to this great group, that hard work this summer paid off!

May 9, 2012 - The lab was notified by RI STAC of its success in obtaining funding for the project "Climate-driven impacts on the formation and persistence of macroalgal blooms: Bringing Ulva bloom biology into the genomics era". This is collaboration with Dr. Carol Thornber (URI)

May 8, 2012 - Congratulations to Jessica Fite, Dr. Swanson's last M.S. student at UCA in successfully defending her thesis. All of those talks over Skype were worth while eh?

May 5, 2012 - The lab was notified of its success in being funded by RI INBRE for the project entitled "The Physiological Role of Plant Phenolics in Plant and Mammalian Growth". This is a collaboration with Drs. Marie Chow (UAMS), and Steve Moss (Brown) as mentors to Dr. Swanson

May, 2012 - Congratulations to Dr. Swanson's to Dr. Swanson's Lab seniors, Adam Barragan and Amy Canino. You both did great on your thesis presentations. Best of luck for the future!

April 26, 2012 - Congrats to the members of the Salve Karate club for passing their kyu exams under Sensei Robin Rielly (8th Dan) at UMass. Well done guys!!!

March 26-29, 2012 - Mice job to the 12 Salve students who presented lessons DNA fingerprinting at Barrington high school.

March 23, 2012 - Congrats to the Swanson lab for presenting six posters at the annual SRYou day. Posters covered a wide range of topics from tissue culture to karate injury rates, from science education to gene hunting.

February 11, 2012 - The Salve Karate club competed as a university for the first time at an East Coast Collegiate Karate Union Event hosted by Penn College in Williamsport PA. Salve had two students representing us, Colin Dudley and Christina Musser. Both represented well and Colin received third place in the Beginner Mens fighting (Kumite) division. It was a well represented tournament university wise and I am proud of both of them.

Jan 16-18, 2012 - Dr. Swanson presented a talk to the North American Raspberry and Blackberry growers annual meeting in Sandusky OH, about the importance of molecular tools to the industry.

January 14, 2012 - Dr. Swanson was told that he has been elected to serve as secretary for the US Rosaceae Genetics, Genomic and Breeding committee.