Pool-seq of diverse apple germplasm reveals candidate loci underlying ripening time, phenolic content, and softening

Abstract

Ripening time, softening, and phenolic content are phenotypes of considerable commercial importance in apples. Identifying causal genetic variants controlling these traits not only advances marker-assisted breeding, but it is also an essential step for the application of gene editing technologies in apples. To advance the discovery of genetic variants associated with these phenotypes, we examined allele frequency differences between groups of phenotypically extreme individuals from Canada’s Apple Biodiversity Collection using pooled whole genome sequencing (pool-seq). We sequenced pooled DNA samples to an average read depth of 150x and scanned the genome for allelic differentiation between pools. For each phenotype, we identified >20 million genetic variants and identified numerous candidate genes. We identified loci on chromosomes 3 and 4 associated with ripening time, the former suggesting that regulatory variants upstream of a previously identified transcription factor NAC18.1 may be causal. Our analysis identified candidate regions on chromosomes 4, 8, and 16 associated with phenolic content, and suggested a cluster of UDP-Glycosyltransferase family genes as candidates for polyphenol production. Further, we identified regions on chromosomes 17 and 10 associated with softening and suggest a Long-chain fatty alcohol dehydrogenase family gene as putatively causal.