Potato (Solanum tuberosum L.) is the most important tuber crop worldwide. To accelerate genetic improvement in potato, several projects have been initiated to redomesticate potato from a tuber-propagated, tetraploid crop into a seed-propagated, inbred-line-based diploid crop, which requires a better understanding of the potato genome. Huang Sanwen’s team reported the first haplotype-resolved assembly of a diploid potato. Comparison of the two haplotypes revealed intra-genome diversity, including 22,134 predicted deleterious mutations in annotated genes. In total, 16.6 percent and 30.8percent of allelic genes in homolog haplotypes exhibited diferential expression and methylation between alleles, respectively. Deleterious mutations and diferentially expressed alleles were dispersed throughout both haplotypes, complicating strategies to eradicate deleterious alleles or stack beneficial alleles, via meiotic recombination. This study ofers a holistic view of the genome organization of a clonally propagated diploid species, as well as provides insights into technological evolution in resolving complex genomes.

Tight linkage of two deleterious alleles, white seeding (ws1) and plant architecture (pa1) in repulsion phase