Genome architecture and tetrasomic inheritance of autotetraploid potato

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

Genome architecture and tetrasomic inheritance of autotetraploid potato

2022

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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