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ARS Home » Northeast Area » Geneva, New York » Grape Genetics Research Unit (GGRU) » Research » Publications at this Location » Publication #275818

Title: Genotyping by sequencing in grape - stacks or tassel?

item Baldo, Angela
item Zhong, Gan-Yuan
item Ramming, David
item Yang, Yingzhen

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 12/8/2011
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: Genotyping by sequencing (GBS) is a powerful method for assaying populations of individuals for hundreds of thousands of genetic markers. The optimal strategy employed for data collection and analysis depends on the kind of biological question being asked and the genomic resources already available. We have collected data from a bi-parental population in grape that segregates for berry size and seedlessness. In this talk we will specifically compare the kind of results obtained when using the Stacks and Tassel analysis pipelines on the same dataset. Genotyping each parent multiple times is valuable depending on the scientific question / population structure and the quality of a reference genome can impact the results. For typical QTL mapping a Stacks approach seems to work very well. For genome wide association studies (GWAS) Tassel is more powerful. The potential of combining the approaches will be discussed.