Genomic basis of divergence of modern cultivated potatoes

Abstract Background Modern cultivated potatoes have been bred for distinct market usages such as fresh eating, chip processing and starch manufacturing; however, genomic insights into this differentiation are limited. Results Here, we report a map of genomic variation encompassing ~79 million variants, constructed by genome-wide resequencing of 137 autotetraploid commercial potato varieties or accessions collected worldwide. Population genomic analysis provides evidence for divergence among modern commercial potato varieties and reveal distinct genomic composition in those bred for starch manufacturing industry, which may have been caused by continuous selection of yield-related traits and intensive exploitation of potato wild relatives. We characterize how alien introgression has reshaped the genomes of starch industry potato varieties, implicating an important role of potato wild relatives in genetic determination of yield-related traits as well as possible linkage drag. We further identify previously undiscovered genomic regions underlying agronomically important traits such as tuber bruising, maturity and tuber flesh and skin color. Conclusions These results shed light on the divergence history of modern cultivated potato and provide useful resources for genomics-guided breeding of this globally important staple crop.