Residual Heterozygosity and Epistatic Interactions Underlie the Complex Genetic Architecture of Yield in Diploid Potato.

Deconvolution of the genetic architecture underlying yield is critical for understanding bases of genetic gain in species of agronomic importance. To dissect the genetic components of yield in potato, we adopted a reference-based recombination map composed of four segregating alleles from an interspecific pseudo-testcross F1 potato population (n=90). Approximately 1.5 million short nucleotide variants were utilized during map construction, resulting in unprecedented resolution for an F1 population; estimated by a median bin length of 146-kb, and 11 genes per bin. Regression models uncovered 14 quantitative trait loci (QTLs) underpinning yield, average tuber weight, and tubers produced per plant in a population exhibiting a striking 332% average mid-parent value heterosis. Nearly 80% of yield-associated QTLs were epistatic andcontained between 0 and 44 annotated genes. We found that approximately half of epistatic QTLs overlap regions of residual heterozygosity identified in the inbred parental parent (M6). Genomic regions recalcitrant to inbreeding were associated with an increased density of genes, many of which demonstrated signatures of selection and floral tissue-specificity. Dissection of the genome-wide additive and dominance values for yield and yield components indicated a widespread prevalence of dominance contributions in this population, enriched at QTLs and regions of residual heterozygosity. Finally, the effects of short nucleotide variants and patterns of gene expression were determined for all genes underlying yield-associated QTLs, exposing several promising candidate genes for future investigation.