A multi-omics framework reveals strawberry flavor genes and their regulatory elements

Area of Science:

• Plant Genetics and Genomics
• Food Science and Technology
• Metabolomics and Biochemistry

Background:

• Consumer food preference is heavily influenced by flavor, making it a key target in plant breeding.
• Identifying genes for volatile organic compounds (VOCs) can accelerate flavor improvement in fruits.
• Polyploidy and heterozygosity in fruit crops pose challenges for flavor gene discovery.

Purpose of the Study:

• To demonstrate a novel framework for uncovering fruit flavor genes and regulatory elements in complex genomes.
• To utilize genomic heterozygosity, transcriptomic intricacy, and metabolomic diversity as assets for gene discovery.
• To advance molecular breeding strategies for enhanced fruit flavor.

Main Methods:

• Generated multi-omics datasets, including an expression quantitative trait loci (eQTL) map from 196 strawberry lines.
• Haplotype-phased genomes and a genome-wide structural variant map were created for a high-flavor strawberry selection.
• Conducted volatile genome-wide association studies (GWAS) on over 300 individuals, integrating regulatory elements and allele-specific expression.

Main Results:

• Successfully linked regulatory elements, structural variants, and GWAS-identified genes to variations in key flavor VOCs.
• Demonstrated the functional role of anthranilate synthase alpha subunit 1 in methyl anthranilate biosynthesis using gene expression assays.
• Identified numerous genes and regulatory elements contributing to flavor compound diversity in strawberry.

Conclusions:

• Developed and validated a robust framework for flavor gene discovery in polyploid fruit crops.
• Showcased how complex genomic traits can be leveraged to accelerate the identification of flavor-associated genes.
• Paved the way for molecular breeding of strawberry cultivars with improved and complex flavor profiles.