The aim of this study includes: (1) developing a pipeline to design transferable markers using the core genome of the Vitis genus. (2) testing the transferability of these markers using a high-fidelity rhAmpSeq platform, a new technology with improved specificity and the throughput of the original AmpSeq. In this study, we de novo assembled six genomes in the Vitis genus and collected three genomes from the public database, constructed a core genome based on syntenic genome alignment. 2000 markers that span all 19 chromosomes with average distance 200kbp were manufactured and tested in four population that represent the greatest genetic diversity in the US breeding practice. The results in the four populations indicate that the core genome plus rhAmpSeq platform could generate high polymorphic data with a very low missing rate. This pipeline provides an interspecies genotyping method that works for highly diverse and heterozygous species.
Materials and methods
Genomic DNA extraction, library construction and sequencing