| Potato(Solanum tuberosum L.)is the world’s most important non-cereal food crop,which feeds 1.3billion people worldwide.Commercial production of potato is dominated by autotetraploid cultivars that are propagated using seed tubers.Reinventing potato from a clonally propagated tetraploid to a true seed-propagated diploid has the potential to significantly accelerate genetic improvement,enabling genome design of a crop that has been highly recalcitrant to the use of molecular breeding and genomics approaches.Potato belongs to the Petota section of the Solanum genus within the Solanaceae family,and the Petota section consists of more than 100 tuber-bearing species,sister to the non-tuber-bearing Etuberosum section and the Lycopersicon section comprising tomato species.Diploid potatoes represent～70% of the wild and landrace potato species,and the vast diversity among them has not been fully characterized nor utilized in previous breeding programs.Furthermore,the impact of the evolution of a clonal reproduction strategy on potato genomes and the evolutionary mechanisms of tuberization are largely unexplored.To date,several potato genome sequences have been released,which have been important resources for genetics and breeding.However,the minor portion of biodiversity in the Petota section,captured by these genomes,is insufficient to obtain a comprehensive understanding of the potato genome to guide breeding.Here,we assembled 44 high-quality diploid potato genomes in combination with Hi Fi sequencing technology.These comprise 20 landraces,four accessions from S.candolleanum(CND)which is considered as the progenitor of cultivated potatoes,and another 20 wild potato species,representative of Solanum section Petota,the tuber-bearing clade.1.The 44 accessions were de novo assembled with an average contig N50 of 22.3 Mb for monoploid assemblies,and the completeness of assemblies was supported by BUSCO with an average score of96.6%,indicating the high-quality of these assemblies.2.We constructed a pan-genome of diploid potato into 51,401 pan-gene clusters,and identified that25.5% were core-genes.The low level of core-/pan-ratio indicates the high level of diversity of diploid potatoes.3.We revealed an uneven distribution of heterozygous intragenomic segments,which can provide target to replace the fragments that can not be homozygous through tranditional selfing.We observed the loss of synteny among the cultivated potato species,indicating the potential impact of tuber-based propagation strategies on potato genomes and give critical insights into hybrid breeding.4.We identified 561,433 high-confidence structural variants and constructed a map of large inversions.5.We observed that the 5.8-Mb inversion located on Chromosome 03 is associated with carotenoid content in tubers,and exhibit reduced recombination around the inversion region in selfed progenies,providing critical insights for improving inbred lines and precluding potential linkage dragThis study will accelerate hybrid potato breeding as well as enrich our understanding of the evolution and biology of potato,as a global staple food crop. |
