Pan-genome analysis suggests introgression crucial to potato evolution

Tuesday, July 27, 2021
2:25 PM - 2:45 PM

An international collaboration has constructed a potato pan-genome from six US and European tetraploid cultivars. Pan-genome analysis provides the opportunity for insight into the genomic diversity of potato. As part of the project, we explored sequence introgression in the six genome assemblies to identify genetic contributions from 20 wild potato species. We found all 12 chromosomes of all cultivars harbored wild introgressions although number of introgressions varied by cultivar. Furthermore, all 20 wild species were represented in each cultivar. Many of these introgressions were the result of post 1945 introgression breeding for disease resistance. These longer introgressed regions contained a number of annotated R genes and SNPs from the SolSTW array previously identified as the result of introgression breeding. However, the majority of introgressions we observed seem to be the result of much older admixture with sympatric wild species in South America. Most introgressions appeared in multiple genome assemblies, and 6.8% were shared across all six. The haplotype-resolved pseudomolecules of Atlantic and Castle Russet were used to determine dosage for the introgressions. Most introgressions were at least partially homozygous, with only about a quarter appearing in simplex. Introgressions which appeared in all six assemblies were less likely to be in simplex, especially in Atlantic. Twelve of the loci that were introgressed in all six cultivars came from multiple wild species, suggesting selection for introgression in that particular region of the genome. Further evidence for the import of introgressed regions in potato is that both expressed and highly expressed genes were overrepresented in the wild introgression regions, and those genes were enriched for GO terms including ‘cellular response to stress’, ‘response to stimulus’, and ‘hormone transport’. This data suggests that introgression played a major role throughout the history of potato.
Breeding and Genetics