And this problem is more evident in the highly diverse and heterozygous species. The transferability drops to 2.3% when transferring the marker between species in the
Vitis genus
(Vezzulli 2008). The same issue has been reported in cattle
\cite{Michelizzi2010,wu2013genome}, only 2% of markers are polymorphic when applying the panel designed for cattle to water buffalo (diverged ~12MYA). Miller et al discovered a pattern of the retention of polymorphisms using a series of species that share a common ancestor, and they found that the retention of polymorphisms follows an exponential decay as the divergence time increase. The polymorphisms decreased to only 5% when examined in a species that diverged 5 Mya
\cite{Miller2012}. 3) Variable genetic position or different physical position due to fast linkage disequilibrium decay and large structural variations in the genome. For example, for the same sex-related QTL, the significant markers are different in the four populations studied
(Yang 2016).
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.