Development and validation of DNA markers for predicting polymethoxyflavone accumulation in citrus

Polymethoxyflavone (PMF), which is known to have multiple health functional components, such as anti-cancer and anti-Alzheimer’s disease effects, is abundant in the limited species of citrus.
When we breed for PMF accumulation, the long juvenile period of the citrus prevents the effective selection of target traits.
DNA markers can predict traits based on DNA polymorphism information, allowing selection for superior traits to be efficient regardless of the juvenile period.
However, DNA markers that predict PMF accumulation have not yet been reported.
Therefore, in this study we developed two types of DNA markers based on single-nucleotide polymorphism (SNP) using the high resolution melting (HRM) and cleaved amplified polymorphic sequence (CAPS) methods.
We report that they can be used to predict PMF accumulation in 134 citrus accessions.
The HRM marker targets a SNP in scaffold 3_10054492 and amplifies a fragment of approximately 71 bp containing the target SNP. The PMF accumulation can be predicted by discriminating homozygosity and heterozygosity according to the shape of melting peaks obtained by heat denaturation of the fragments.
The CAPS marker amplifies a fragment of approximately 260 bp in the flavanone 3-hydroxylase-like gene, Ciclev10023305m, present in scaffold_3, and only the citrus accessions with specific fragment indicating accumulation can be identified because it is digested into two fragments of approximately 160 and 100 bp by BamHI. This study provides two DNA markers that can predict PMF accumulation and will be useful for breeding of citrus for high accumulation of PMF, a health functional component.

XV International Citrus Congress

T. Yamashita, T. Kubo, Y. Matsumoto, N. Kotoda

marker-assisted selection, SNP, flavonoids, HRM, CAPS

https://doi.org/10.17660/ActaHortic.2026.1448.24