Multiomics-based dissection of citrus flavonoid metabolism using a Citrus reticulata x Poncirus trifoliata population

Deciphering the genetic basis of plant secondary metabolism will provide useful insights for genetic improvement and enhance our fundamental understanding of plant biological processes. Although citrus plants are among the most important fruit crops worldwide, the genetic basis of secondary metabolism in these plants is largely unknown. Here, we use a high-density linkage map to dissect large-scale flavonoid metabolic traits measured in different tissues (young leaf, old leaf, mature pericarp, and mature pulp) of an F-1 pseudo-testcross citrus population. We detected 80 flavonoids in this population and identified 138 quantitative trait loci (QTLs) for 57 flavonoids in these four tissues. Based on transcriptional profiling and functional annotation, twenty-one candidate genes were identified, and one gene encoding flavanone 3-hydroxylase (F3H) was functionally verified to result in naturally occurring variation in dihydrokaempferol content through genetic variations in its promoter and coding regions. The abundant data resources collected for diverse citrus germplasms here lay the foundation for complete characterization of the citrus flavonoid biosynthetic pathway and will thereby promote efficient utilization of metabolites in citrus quality improvement.

Automated summary

Deciphering the genetic basis of plant secondary metabolism, especially in citrus plants, can provide insights for genetic improvement and enhance our understanding of plant biological processes. By utilizing a high-density linkage map, researchers identified multiple quantitative trait loci (QTLs) for flavonoids in different tissues of a citrus population, shedding light on potential candidate genes involved in flavonoid biosynthesis. Further functional verification of a gene encoding flavanone 3-hydroxylase (F3H) indicated its role in natural variation of dihydrokaempferol content, laying the groundwork for future studies on citrus flavonoid biosynthesis pathway.