Genus-wide core-genome for Vitis

With the explosion of the genomic data in the past decade, it has been noted that a single genome is insufficient to capture genetic variation of a species. Multiple genomes provide a more comprehensive understanding of complex structural variations, lineage-specific genes, and large-effect variations within a species. Grape (Vitis vinifera subsp. vinifera), which is among the most important horticultural crops in the world belongs to Vitis genus\cite{Jaillon2007}. In this study, we constructed a pan-genome for the Vitis genus, which diverged approximately 20 million years ago. Different from the pan-genome that is constructed for one species or close related species, the core genome for the Vitis genus should smaller than that for a single species due to the elevated genetic distance between the samples we collected. For example, in soybean, 80% genes are present in seven accessions studied\cite{Li2014}.  In rice, 61% of genes are present in 90% of total 62 accessions studied\cite{Zhao2018} . In maize, it has been reported that only 50% percent of genome are in syntenic blocks between B73 and Mo17\cite{Sun2018}.  In the most distantly related accessions we examine (V. rupestris versus V. vinifera), only about 29% of the V. rupestris genome was collinear with the reference genome V. vinifera PN40024. However, our results indicated that the gene regions are conserved in the Vitis genus because 70% of the genes overlap with the core genome. And due to this high conservation in genes, designing universal markers set for the whole Vitis genus is feasible. 

Conclusion

Here we developed a pipeline for genus-wide marker design considering the syntenic core genome and genome-wide polymorphism. Together with the rhAmpSeq platform, this genotyping pipeline can be easily adapted by other taxa for ecological and evolutionary studies, QTL mapping, GWAS and molecular breeding.