Potato dihaploids reveal tetraploid evolutionary patterns of recombination, mutation, and selection

Potato is a globally significant food crop, yet its genetic improvement has been limited by the challenges of clonal propagation and autotetraploidy. To accelerate breeding and facilitate genomic analyses, we developed a panel of 97 dihaploids derived through haploid induction from elite tetraploid cultivars and advanced breeding lines. This panel preserves the haplotype diversity present in commercial U.S. potatoes while providing a simplified genomic background for evolutionary and breeding studies.
We estimated historical recombination rates (ρ = 4Ner) across the genome using short-read sequencing data. Compared to rice, Arabidopsis, soybean, and wheat, potato exhibits remarkably low levels of recombination, with a genome-wide average of 1.42 kb⁻¹. Recombination varied by chromosome and market class, with chromosome 4 consistently showing elevated rates, and chromosome 2 the lowest. A weak but significant negative correlation was observed between recombination rate and nucleotide diversity across genomic intervals.
To characterize allele frequency dynamics, we constructed the derived site frequency spectrum using Nicotiana tabacumand Capsicum annuum as outgroups. The resulting spectrum displayed an abundance of intermediate- and high-frequency derived alleles, indicating a history of allele turnover and retention that may reflect domestication or improvement processes. These frequency patterns provide a context for assessing the distribution of functional variation, including putatively deleterious mutations identified through codon-level predictions and comparative genomics.Together, patterns of recombination, allele frequency spectra, and mutational burden gives a broader view of genetic diversity and constraint in potato, informing both the history of domestication and the design of future breeding populations. By combining these analyses, we aim to support the development of diploid potato varieties that retain valuable haplotypes while reducing genetic load, advancing a breeding strategy that supports long-term genetic improvement.