Genome architecture and tetrasomic inheritance of autotetraploid potato
2022
Bao, Zhigui | Li, Canhui | Li, Guangcun | Wang, Pei | Peng, Zhen | Cheng, Lin | Li, Hongbo | Zhang, Zhiyang | Li, Yuying | Huang, Wu | Ye, Mingwang | Dong, Daofeng | Cheng, Zhukuan | VanderZaag, Peter | Jacobsen, Evert | Bachem, Christian W.B. | Dong, Suomeng | Zhang, Chunzhi | Huang, Sanwen | Zhou, Qian
Potato (Solanum tuberosum) is the most consumed non-cereal food crop. Most commercial potato cultivars are autotetraploids with highly heterozygous genomes, severely hampering genetic analyses and improvement. By leveraging the state-of-the-art sequencing technologies and polyploid graph binning, we achieved a chromosome-scale, haplotype-resolved genome assembly of a cultivated potato, Cooperation-88 (C88). Intra-haplotype comparative analyses revealed extensive sequence and expression differences in this tetraploid genome. We identified haplotype-specific pericentromeres on chromosomes, suggesting a distinct evolutionary trajectory of potato homologous centromeres. Furthermore, we detected double reduction events that are unevenly distributed on haplotypes in 1021 of 1034 selfing progeny, a feature of autopolyploid inheritance. By distinguishing maternal and paternal haplotype sets in C88, we simulated the origin of heterosis in cultivated tetraploid with a survey of 3110 tetra-allelic loci with deleterious mutations, which were masked in the heterozygous condition by two parents. This study provides insights into the genomic architecture of autopolyploids and will guide their breeding.
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