Dr. Ashrafi to Breed Blueberries Through Stronger Genomic Data

Dr. Ashrafi, Blueberry Plant Breeding through genomic markers

The use of molecular markers in blueberry breeding has been hampered by inadequate DNA markers and structured populations. Did you know that there are only two genetic maps for blueberry with ~265 conventional molecular markers on them, and limited genomics data available in databases?

Hamid Ashrafi, assistant professor in blueberry breeding, is passionate to use his expertise to breed for higher quality blueberries. He received his B.S. in agronomy and plant breeding from the University of Technology, Esfahan, Iran, and M.S. in plant breeding from Azad University, Tehran, Iran.  Hamid received his Ph.D. in genetics from the Pennsylvania State University in August 2007 where he was working on tomato breeding and genetics under the supervision of Dr. Majid R. Foolad.

He moved to University of California-Davis in early 2008, where he started to work with Drs. Allen Van Deynze and Richard Michelmore as a post-doctoral scholar. Analyzing Affymetrix microarray GeneChips® data, he was able to generate ultra-saturated genetic maps of pepper and lettuce with more than 16,000 and 11,000 markers, respectively.

In July 2010, Hamid Ashrafi was promoted to a senior scientist position in bioinformatics when he took the lead to work on next generation sequencing data analysis. Initially, working on transcriptome sequencing and later on re-sequencing 22 pepper lines and cultivars, he developed more than 1.5 million SNP markers for pepper. In collaboration with Dr. Doil Choi at Seoul National University, he was a part of a pepper genome sequencing project which was published in Nature Genetics in 2014.

During Dr. Ashrafi’s tenure as a postdoc and a research scientist, he has also collaborated with Drs. David Stelly at Texas A&M University, Phillip Simon and Michael Havey both at University of Wisconsin. In collaboration with Dr. Stelly, he generated thousands of putative SNP markers for diploid and allotetraploid cotton germplasms and became a part of the team who sequenced diploid cotton sequence at Joint Genome Institute, the results of which were published in Nature in 2012. In collaboration with Dr. Simon, he worked on transcriptome analysis of carrot germplasms and carrot genome sequencing.

Over the past several years, he has collaborated with more than 10 seed companies on various projects including sequencing different vegetable crops such as spinach and re-sequencing genome of 12 melon cultivars. He has also developed a pipeline to generate millions of SNP markers for melon, eggplant, spinach, pepper, cotton and many other crops. Ashrafi recently left that position to join the Department of Horticultural Science at NC State.

Under his supervision five seniors were trained in bioinformatics and defended their final projects, most of whom have attended to graduate school. He has also been an instructor of a biannual workshop in “Breeding with Genomics” at UC-Davis. Hamid is interested in plant breeding and genetics, with special interests in molecular breeding through marker assisted selection, genetic mapping, QTL analysis, association mapping, bioinformatics and statistical genomics. His office is located at 234 Kilgore hall and can be reached by phone (919) 515-1216 or email: hamidashrafi@ncsu.edu