Genus-wide core-genome for Vitis
As the explosion of the genomic data in the past decade, it has been noted that a single genome is insufficient to capture genetic variance of one species. Multiple genomes provide a comprehensive understanding of complex structural variations, lineage specific genes and large effect variations within one species . In this study, we constructed a pan-genome for the whole Vitis genus, which diverged approxinately 20 million years ago. Different from the pan-genome that constructed for one specie or close related specie, we expect the core genome for the Vitis genus is smaller than that in one species due to the elevated genetic distance between the samples we collected. For example, In soybean, 80% genes are present in all seven accessions \cite{Li2014}. In rice , 61% of genes are present in 90% of total 62 collections\cite{Zhao2018}. In maize, it has been reported that only 50% percent of genome are in syntenic blockes between B73 and Mo17 \cite{Sun2018}. In the most distant related species in Vitis genus we examine (between V. rupestris and V.vinifera), only about 29% of the genome are collinear with the reference genome PN40024. However, our result indicates that the gene regions are conserved in the Vitis genus because 70% of the genes are overlapped 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 clades/genus for ecology and evolutionary study, QTL mapping, GWAS and molecular breeding.