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

Shanshan Yang, Jonathan Fresnedo-Ramírez, Minghui Wang, Linda Cote, Peter Schweitzer, Paola Barba, Elizabeth M. Takacs, Matthew Clark, James Luby, David C. Manns, Gavin Sacks, Anna Katharine Mansfield, Jason Londo, Anne Fennell, David Gadoury, Bruce Reisch, Lance Cadle-Davidson, Qi Sun

Research output: Contribution to journalArticlepeer-review

37 Scopus citations

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 traitassociated 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 o10% 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, lowcost and easily automated analysis.

Original languageEnglish (US)
Article number16002
JournalHorticulture Research
Volume3
DOIs
StatePublished - 2016

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