Genomic Characterization of the Fruity Aroma Gene, FaFAD1, Reveals a Gene Dosage Effect on γ-Decalactone Production in Strawberry (Fragaria × ananassa)

Abstract

Strawberries produce numerous volatile compounds that contribute to the unique flavors of fruits. Among the many volatiles, γ-decalactone (γ-D) has the greatest contribution to the characteristic fruity aroma in strawberry fruit. The presence or absence of γ-D is controlled by a single locus, <i>FaFAD1</i>. However, this locus has not yet been systematically characterized in the octoploid strawberry genome. It has also been reported that the volatile content greatly varies among the strawberry varieties possessing <i>FaFAD1</i>, suggesting that another genetic factor could be responsible for the different levels of γ-D in fruit. In this study, we explored the genomic structure of <i>FaFAD1</i> and determined the allele dosage of <i>FaFAD1</i> that regulates variations of γ-D production in cultivated octoploid strawberry. The genome-wide association studies confirmed the major locus <i>FaFAD1</i> that regulates the γ-D production in cultivated strawberry. With the hybrid capture-based next-generation sequencing analysis, a major presence-absence variation of <i>FaFAD1</i> was discovered among γ-D producers and non-producers. To explore the genomic structure of <i>FaFAD1</i> in the octoploid strawberry, three bacterial artificial chromosome (BAC) libraries were developed. A deletion of 8,262 bp was consistently found in the <i>FaFAD1</i> region of γ-D non-producing varieties. With the newly developed InDel-based codominant marker genotyping, along with γ-D metabolite profiling data, we revealed the impact of gene dosage effect for the production of γ-D in the octoploid strawberry varieties. Altogether, this study provides systematic information of the prominent role of <i>FaFAD1</i> presence and absence polymorphism in producing γ-D and proposes that both alleles of <i>FaFAD1</i> are required to produce the highest content of fruity aroma in strawberry fruit.