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“Designing an Optimal Amplicon Based Genotyping by Sequencing Panel Sunflower Breeding”

Dr. Farhad Ghavami, the Chief Scientific Officer at Eurofins BioDiagnostics (EBDI), delivered a lecture on “Designing an Optimal Amplicon Based Genotyping by Sequencing Panel Sunflower Breeding” on 16 July 2019 at NIGEB. He has more than 14 years of post-doctoral experience working on plant molecular biology, plant genomics, transcriptomics, quantitative genetics and also molecular breeding. Prior to his current position, Ghavami managed the molecular breeding and genomics technology department for EBDI. Additionally, he has served as a research assistant professor at North Dakota State University, and a senior research associate at the University of Minnesota. He has published more than 25 papers in peer reviewed scientific journals, two book chapters and more than 40 abstracts in different conferences.


He explained that the advent of next-generation sequencing technologies and the ongoing reduction of sequencing costs have made genotyping by sequencing (GBS) a common practice for genotyping in plant and animal breeding.  Among different methods of GBS, amplicon based GBS is an accurate and economical method that can expedite any QTL mapping projects and genomic selection programs.

The first sunflower 10K SNP array was developed thorough a collaboration between Eurofins BioDiagnostics and the National Sunflower Association (NSA).  The array was used on three mapping populations and a consensus map was created consisting of 5,019 SNP and 118 SSR markers distributed on all 17 linkage groups.  Since the development of the chip in 2012, more than 500 varieties were genotyped using the NSA array and the best markers with optimal performance on the array and high minor allele frequency (MAF) were selected to develop a GBS panel. An AgriSeq Panel containing 700 of these markers well distributed on the genome has been created which can help QTL mapping, marker assisted backcrossing, and genomics selection projects in sunflower.