Potato dihaploids uncover diverse alleles to facilitate diploid potato breeding

Abstract

Commercial potato in North America is a clonal autotetraploid crop, which complicates breeding. Efforts are underway to convert potato to a diploid inbred-hybrid crop that is amenable to additional breeding strategies and allows breeders to more quickly respond to demands for crop improvement. With the goal of preserving haplotypes developed over the last 200 years of selection, diploid potato breeding in the US started with the creation of diploids from tetraploid commercial varieties and advanced breeding lines through prickle pollination. This is an effective but slow method which presents a barrier to entry for individual breeding programs. Therefore, we developed 97 publicly available dihaploids (diploids from prickle pollination of tetraploids) as a resource for diploid breeding in the U.S. These clones contain the majority of alleles in the US breeding population for three market classes: chips, russets, and fresh market reds. To facilitate genomic informed breeding, all clones have been resequenced using short read sequencing technology, and we have developed de novo assemblies based on PacBio HiFi long reads for 20 individuals. As an illustration of how these data will be used in breeding, we explored the maturity locus (StCDF1) and identified 15 different alleles. The majority of dihaploids were heterozygous for early and late alleles, resulting in intermediate maturity. Beyond informing breeding, this data facilitates investigations into potato genomics. The dihaploid population is both highly heterozygous and incredibly diverse on a population level. In particular, there is extensive structural diversity, including copy number variation, segregating within the population. This contrasts with a relatively low genome-wide historical recombination rate ({rho}). Taken together, these findings indicate that potato is highly diverse, with much of that diversity found within long linkage blocks.