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Title:   Author  item
                                            YANG, SHANSHAN - Cornell Universityitem
                                            FRESNEDO, JONATHAN - Cornell Universityitem
                                            WANG, MINGHUI - Cornell Universityitem
                                            COTE, LINDA - Cornell Universityitem
                                            BOGDANOWICZ, STEVEN - Cornell Universityitem
                                            SCHWEITZER, PETER - Cornell Universityitem
                                            BARBA, PAOLA - Cornell Universityitem
                                            TAKACS, ELIZABETH - Cornell Universityitem
                                            CLARK, MATTHEW - University Of Minnesotaitem
                                            LUBY, JIM - University Of Minnesotaitem
                                            MANNS, DAVID - Cornell Universityitem
                                            SACKS, GAVIN - Cornell Universityitem
                                            MANSFIELD, ANNA KATHARINE - Cornell Universityitem
                                            Londo, Jasonitem
                                            FENNEL, ANNE - South Dakota State Universityitem
                                            GADOURY, DAVID - Cornell Universityitem
                                            REISCH, BRUCE - Cornell Universityitem
                                            Cadle-Davidson, Lanceitem
                                            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.


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