Characterizing genome-wide changes associated with inbreeding tolerance in cranberry: insights into homozygosity and heterozygosity

The American cranberry ( Vaccinium macrocarpon ) is an important native North American fruit. Cranberry is a self-fertile woody perennial. As part of an ongoing breeding and genetics program, inbred lines have been developed to help understand the effects of inbreeding in cranberries and to develop near-homozygous lines. Self-pollination can lead to a phenomenon known as inbreeding depression. As the effects propagate through generations, the loss of genetic diversity in offspring can cause reduced vigor, size of fruit and vegetative organs, and overall fitness. Our early observations suggested that different cranberry cultivars might vary in their expression of inbreeding depression. Here, we investigate genomic and phenotypic patterns potentially associated with inbreeding tolerance across multiple selfing cycles, or generations, of four cranberry cultivars: Ben Lear, Stevens, Wilcox, and Pilgrim, which we generated over a period of 27 years. Using genotyping by sequencing data from individuals across each generation, we assessed the offspring for genetic heterogeneity and observed phenotypic signs of inbreeding depression. We quantified contiguous runs of heterozygosity (ROHet) and homozygosity (ROHom) throughout the cranberry genome and show that from early generations, heterozygosity decreases, and homozygosity increases rapidly, correlating with an increase in genomic inbreeding levels. However, the cultivars were remarkably tolerant of inbreeding from a phenotypic standpoint. We also identified candidate genes in regions of maintained heterozygosity, such as those functioning in metabolism and stress responses, whose potential role in inbreeding tolerance warrants further functional validation. Notably, we identified a conserved ROHet in chromosome 11 of Ben Lear containing eight genes. Altogether, this is the first study to present a public repository of cranberry sequencing data from multiple cultivar generations and identification of candidate genes based on ROHet and ROHom trends across consecutive inbred generations of V. macrocarpon .