Document Type
Article
Publication Date
2-2016
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.
Publication Title
Horticulture Research
Volume
3
Issue
Article number: 16002
Format
application/pdf
DOI of Published Version
10.1038/hortres.2016.2
Publisher
Springer Nature Limited
Recommended Citation
Yang, S., Fresnedo-Ramírez, J., Wang, M. et al. A next-generation marker genotyping platform (AmpSeq) in heterozygous crops: a case study for marker-assisted selection in grapevine. Hortic Res 3, 16002 (2016) doi:10.1038/hortres.2016.2
Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 International License.
Comments
Supplemental Information for this article can be found on the Horticulture Research website (http://www.nature.com/hortres).