title: A next-generation marker genotyping platform (AmpSeq) in heterozygous crops: a case study for marker-assisted selection in grapevine.
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 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 single nucleotide polymorphism 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 using three traits (flower sex, disease resistance and acylated anthocyanins) in grapevine breeding. The vast majority of sequence reads (⩾99%) were from the targeted regions. Across 380 individuals and up to 31 amplicons sequenced in each lane of MiSeq data, most amplicons (83 to 87%) had <10% missing data, and read depth had a median of 220-244×. Several strengths of the AmpSeq platform that make this approach of broad interest in diverse crop species include accuracy, flexibility, speed, high-throughput, low-cost and easily automated analysis.
authors.affiliation: Horticulture Section, School of Integrative Plant Science, Cornell University , Geneva, NY 14456, USA.
authors.forename: Shanshan
authors.initials: S
authors.lastname: Yang
authors.affiliation: Bioinformatics Facility, Cornell University , Ithaca, NY 14853, USA.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Fresnedo-Ramírez
authors.affiliation: Bioinformatics Facility, Cornell University , Ithaca, NY 14853, USA.
authors.forename: Minghui
authors.initials: M
authors.lastname: Wang
authors.affiliation: Institute of Biotechnology, Cornell University , Ithaca, NY 14853, USA.
authors.forename: Linda
authors.initials: L
authors.lastname: Cote
authors.affiliation: Institute of Biotechnology, Cornell University , Ithaca, NY 14853, USA.
authors.forename: Peter
authors.initials: P
authors.lastname: Schweitzer
authors.affiliation: Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University , Ithaca, NY 14853, USA.
authors.forename: Paola
authors.initials: P
authors.lastname: Barba
authors.affiliation: Horticulture Section, School of Integrative Plant Science, Cornell University , Geneva, NY 14456, USA.
authors.forename: Elizabeth M
authors.initials: EM
authors.lastname: Takacs
authors.affiliation: Department of Horticultural Science, University of Minnesota , St Paul, MN 55108, USA.
authors.forename: Matthew
authors.initials: M
authors.lastname: Clark
authors.affiliation: Department of Horticultural Science, University of Minnesota , St Paul, MN 55108, USA.
authors.forename: James
authors.initials: J
authors.lastname: Luby
authors.affiliation: Department of Food Science, Cornell University , Geneva, NY 14456, USA.
authors.forename: David C
authors.initials: DC
authors.lastname: Manns
authors.affiliation: Department of Food Science, Cornell University , Ithaca, NY 14853, USA.
authors.forename: Gavin
authors.initials: G
authors.lastname: Sacks
authors.affiliation: Department of Food Science, Cornell University , Geneva, NY 14456, USA.
authors.forename: Anna Katharine
authors.initials: AK
authors.lastname: Mansfield
authors.affiliation: USDA-ARS Grape Genetics Research Unit , Geneva, NY 14456, USA.
authors.forename: Jason
authors.initials: J
authors.lastname: Londo
authors.affiliation: Plant Science Department, South Dakota State University , Brookings, SD 57007, USA.
authors.forename: Anne
authors.initials: A
authors.lastname: Fennell
authors.affiliation: Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University , Geneva, NY 14456, USA.
authors.forename: David
authors.initials: D
authors.lastname: Gadoury
authors.affiliation: Horticulture Section, School of Integrative Plant Science, Cornell University , Geneva, NY 14456, USA.
authors.forename: Bruce
authors.initials: B
authors.lastname: Reisch
authors.affiliation: USDA-ARS Grape Genetics Research Unit , Geneva, NY 14456, USA.
authors.forename: Lance
authors.initials: L
authors.lastname: Cadle-Davidson
authors.affiliation: Bioinformatics Facility, Cornell University , Ithaca, NY 14853, USA.
authors.forename: Qi
authors.initials: Q
authors.lastname: Sun