Identification of two QTLs associated with high fruit acidity in apple using pooled genome sequencing analysis.

Acidity is a critical component determining apple fruit quality. Previous studies reported two major acidity quantitative trait loci (QTLs) on linkage groups (LGs) 16 () and 8 (), respectively, and their homozygous genotypes and usually confer low titratable acidity (TA) (<3.0 mg ml) to apple fruit. However, apples of genotypes - ( and ) or - ( and ) frequently show an acidity range spanning both regular (TA 3.0-10.0 mg ml) and high (TA > 10 mg ml) acidity levels. To date, the genetic control for high-acidity apples remains essentially unknown. In order to map QTLs associated with high acidity, two genomic DNA pools, one for high acidity and the other for regular acidity, were created in an interspecific F population Royal Gala () × PI 613988 () of 191 fruit-bearing progenies. By Illumina paired-end sequencing of the high and regular acidity pools, 1,261,640 single-nucleotide variants (SNVs) commonly present in both pools were detected. Using allele frequency directional difference and density (AFDDD) mapping approach, one region on chromosome 4 and another on chromosome 6 were identified to be putatively associated with high acidity, and were named and , respectively. Trait association analysis of DNA markers independently developed from the and regions confirmed the mapping of and . In the background of , 20.6% of acidity variation could be explained by , 28.5% by and 50.7% by the combination of both. The effects of and in the background of were also significant, but lower. These findings provide important genetic insight into high acidity in apple.