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. Here, we report a map of genomic variation encompassing ~79 million variants, constructed from genome-wide resequencing of 137 autotetraploid commercial potato varieties or accessions collected worldwide. Population genomic analyses provide evidence for divergence among modern commercial potato varieties and reveal distinct genomic composition of those bred for starch processing industry, which may have been contributed 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. These results shed lights on the divergence history of modern cultivated potato and provide useful resources for genomics-guided breeding of this globally important stable crop.

• Alien introgression
• FST permutation
• GWAS
• Linkage disequilibrium
• Phylogeny
• Population structure
• Principal component
• Read mapping and variant calling
• Selective sweeps highly divergent regions and Tajimas D
• Sweeps overlap QTLs
• Variant filtering

If you find these codes useful or you are insterested in our paper, please cite:

Hongbo Li, Marian Oortwijn, Matthijs Brouwer et al. Genomic basis of divergence of modern cultivated potatoes, 19 February 2024, PREPRINT (Version 1) available at Research Square [https://doi.org/10.21203/rs.3.rs-3968149/v1]

Hongbo Li ([email protected])

Richard G. F. Visser ([email protected])

MIT