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ARS Home » Northeast Area » Geneva, New York » Grape Genetics Research Unit (GGRU) » Research » Publications at this Location » Publication #324352
Title: A next-generation marker genotyping platform (AmpSeq) in heterozygous crops: a case study for marker assisted selection in grapevine

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

Submitted to: Horticulture Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/25/2016
Publication Date: 2/17/2016
Citation: Yang, S., Fresnedo, J., Wang, M., Cote, L., Bogdanowicz, S., Schweitzer, P., Barba, P., Takacs, E., Clark, M., Luby, J., Manns, D., Sacks, G., Mansfield, A., Londo, J.P., Fennel, 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. Horticulture Research. 3:16002.doi:10.1038/hortres.2016.2.

Interpretive Summary: Plant breeders often use DNA markers to accelerate and improve variety development. DNA markers allow early selection of parents with desirable trait combinations as well as selection of desirable seedlings. Next generation sequencing (NGS) technologies have revolutionized genome-wide DNA marker discovery, but challenges remain in applying these new DNA markers. To bridge the gap between marker discovery and application, this study developed a technology called AmpSeq. Examples of AmpSeq applications are provided for three traits in grapevine: flower sex, disease resistance, and acylated anthocyanins. The AmpSeq platform should be of broad interest due to its accuracy, flexibility, speed, high throughput, low cost, and easily automated analysis.

Technical Abstract: Marker assisted selection (MAS) is often employed in 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) and its derivative technologies have been used for genome-wide molecular marker discovery. To bridge the gap between marker development and MAS implementation, this study developed a novel practical strategy with a semi-automated pipeline that incorporates trait associated SNP marker discovery, low cost genotyping through amplicon sequencing (AmpSeq), and decision making. The results document the development of a MAS package derived from genotyping-by-sequencing (GBS) using three traits (flower sex, disease resistance, and acylated anthocyanins) in grapevine breeding. Several strengths of the AmpSeq platform that make this approach of broad interest in diverse crop species are: accuracy, flexibility, speed, high throughput, low cost, and easily automated analysis.