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

Abstract

Marand et al. use a high-resolution recombination map to dissect the genetic components of yield in diploid potato. Regions of recalcitrant heterozygosity in the inbred parent co-localized with elevated recombination rates, signatures of selection, and tissue-specific gene expression... 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 pseudotestcross 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 (QTL) underpinning yield, average tuber weight, and tubers produced per plant in a population exhibiting a striking 332% average midparent-value heterosis. Nearly 80% of yield-associated QTL were epistatic, and contained between 0 and 44 annotated genes. We found that approximately one-half of epistatic QTL 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 QTL 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 QTL, exposing several promising candidate genes for future investigation.

The origin and widespread occurrence of Sli-based self-compatibility in potato

“…Therefore, it seems that the lethal allele described above has recombined from Sli and is not a limitation to reach homozygosity in this region. This is in agreement with Marand et al (2019) who did not identify recalcitrant heterozygosity in the distal end of M6 chromosome 12.…”

QTL detection in a pedigreed breeding population of diploid potato

“…In diploid potato, further insight should be gained by extending QTL detection to include dominance effects, given the prevalence of inbreeding depression. Furthermore, dense marker sets can increase the mapping resolution and allow the study of residual heterozygosity, unravelling further the genetic architecture of yield as reported by Marand et al (2019).…”

Understanding Genetic Load in Potato for Hybrid Diploid Breeding

“…Subsequent generations of inbreeding are required to gain better understanding of the trade-offs between increasing homozygosity and decreasing vigor and fertility. Recently, Marand et al (2019) have illustrated this trade-off in M6 clone, by showing that after six generations of inbreeding, extensive regions of recalcitrant heterozygosity remain. The ultimate goal of boosting potato breeding with the power of the fixation of genetic gains is so important that much more research in this field is highly justified.…”