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

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

来源：Horticulture Research, 2016, 3(1): 16002.

DOI：10.1038/hortres.2016.2

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 x. 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.

• 出版日期2016-2-17