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ARS Home » Northeast Area » Geneva, New York » Grape Genetics Research Unit (GGRU) » Research » Publications at this Location » Publication #325991

Research Project: Improving Fruit Quality, Disease Resistance, and Tolerance to Abiotic Stress in Grape

Location: Grape Genetics Research Unit (GGRU)

Title: A next-generation marker genotyping platform (AmpSeq) in heterozygous crops: A case study for marker assisted selection in grapevine

item YANG, SHANSHAN - Cornell University - New York
item FRESNEDO, JONATHAN - Cornell University - New York
item WANG, MINGHUI - Cornell University - New York
item COTE, LINDA - Cornell University - New York
item SCHWEITZER, PETER - Cornell University - New York
item BARBA, PAOLA - Cornell University - New York
item TAKACS, ELIZABETH - Cornell University - New York
item CLARK, MATT - University Of Minnesota
item LUBY, JIM - University Of Minnesota
item MANNS, DAVID - Cornell University - New York
item SACKS, GAVIN - Cornell University - New York
item MANSFIELD, ANNA KATHERINE - Cornell University - New York
item Londo, Jason
item FENNELL, ANNE - South Dakota State University
item GADOURY, DAVID - Cornell University - New York
item REISCH, BRUCE - Cornell University - New York
item Cadle-Davidson, Lance
item SUN, QI - Cornell University - New York

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 10/31/2015
Publication Date: 1/1/2016
Publication URL:
Citation: Yang, S., Fresnedo, J., Wang, M., Cote, L., Schweitzer, P., Barba, P., Takacs, E., Clark, M., Luby, J., Manns, D., Sacks, G., Mansfield, A., Londo, J.P., Fennell, A., Gadoury, D., Reisch, B., Cadle Davidson, L.E., Sun, Q. 2016. A Next-Generation Marker Genotyping Platform (AmpSeq) in Heterozygous Crops: A Case Study for Marker Assisted Selection in Grapevine. Plant and Animal Genome Conference.

Interpretive Summary:

Technical Abstract: Marker assisted selection (MAS) has become widely used in perennial crop breeding programs to accelerate and enhance cultivar development via selection during the juvenile phase and parental selection prior to crossing. Next generation sequencing (NGS) has been widely used for whole genome molecular marker discovery, but it also offers a potential opportunity for tailored molecular marker development with high-throughput and low per-sample cost. This study presents a novel and efficient MAS strategy for molecular marker development incorporating a semi-automated primer design pipeline based on amplicon sequencing (AmpSeq). The results document the development of an MAS package using three relevant traits (flower sex, disease resistance, and modified anthocyanins) in grapevine breeding. Here we discuss several strengths of the amplicon sequencing platform that make this approach of broad interest in diverse crop species: accuracy, flexibility, high throughput, low cost, easily automated analysis, and rapid results.