Genetic diversity of primary dihaploid potatoes from US cultivars
Date & Time
Tuesday, July 19, 2022, 9:15 AM
Xiaoxi Meng

As an alternative to the challenges of tetraploid potato breeding, breeders are generating self-fertile inbred diploid breeding lines for inbred hybrid breeding. This could increase the efficiency of potato cultivar development. The first step is to generate dihaploids from various tetraploid parents that span the market classes. These dihaploids will serve as the base for diploid breeding program in the US. Reinventing a crop provides the unique opportunity to understand the founding population and trace the evolution of the crop over time. To that end, and to facilitate imputation and genomic selection, we are re-sequencing 100 promising primary dihaploids with ~20X coverage using Illumina short reads. Thus far we have sequenced 61 primary dihaploids: 22 chip, 23 russet, and 16 red clones. These sequence data will not only support diploid breeding but provide new information about US tetraploid breeding populations and haplotypes as sequencing at this scale is much more feasible in diploids than tetraploids. The first 61 samples exhibit heterozygosity rates of between 0.75 and 1.15%, in line with previous estimates. Notably, this level of diversity is maintained at the population level, with nucleotide diversity (π) between 0.009 and 0.010 for all three market classes. This suggests that the market classes in the US are panmictic populations with minimal inbreeding or population structure within class. Deviations from this may indicate regions of selective constraint. For example, chromosome 10 stands out as a low diversity region for both reds and russets with π below 0.006. These sequences also shed light on haplotype structure within the tetraploid germplasm, the prevalence of deleterious variation, and the way in which introgression shaped the selection of US potato varieties.

Session Type
Parent Session
7/19 - Concurrent Sessions D