To meet the challenges in the increasing food demands and diverse breeding targets in plants and animals, molecular markers have been widely used to reveal polymorphism at the DNA level, and these markers have been further applied to identify marker-trait associations, marker-assisted selection, genomic selection, germplasm characterization, etc
(Singh 2015, Xu 2008). The molecular markers like Restriction Fragment Length Polymorphisms (RFLPs)
\cite{Botstein1980}, simple sequence repeats (SSR)
\cite{Tautz1989} have been developed and used for around 40 years ago. However, these platforms have very limited throughput with hundreds of loci on hundreds of lines. Using fluorescence hybridization-based microarray or next-generation sequencing based genotyping platform, the throughput of genotyping increase up to tens of thousands loci on an almost unlimited number of lines. As the development of next-generation sequencing, the most commonly used approaches include restriction-site associated DNA (RAD)
\cite{Miller2007}, genotyping-by-sequencing (GBS)
\cite{Elshire2011} and Specific locus amplified fragment sequencing (SLAF-seq)
\cite{Sun2013}. However, these simplified genome-wide sequencing platforms has a high missing rate and under-calling of heterozygous sites rate in highly diverse and heterozygous species. In the previous study, we have found that the amplicon sequencing (AmpSeq) platform solved the problem of high-missing rate and under-calling of heterozygote site. The remaining problem for the highly diverse and heterozygous species is that the marker transferability. For example, the breeding practice for hardwood in Eucalyptus include species that diverged 2 to 5 Mya
\cite{Grattapaglia2011}, the grape breeding often includes species that diverged around 20 Mya
\cite{Vezzulli2008}, therefore, a universal transāspecies [interspecies? cross-species?] molecular marker panel is highly demanded. In addition, the universal marker panel is very efficient in genotyping non-model organisms that have a well-studied closed related species.