# A haplotype-resolved chromatin landscape connects cis-regulatory variants to trait variation in Citrus

## TL;DR

This study explores how genetic and epigenetic changes in citrus genomes affect gene expression and fruit traits using a phased genome assembly.

## Contribution

The paper introduces a haplotype-resolved chromatin landscape linking cis-regulatory variants to phenotypic variation in citrus.

## Key findings

- 30% of allele-specific expression variation is linked to haplotype-associated chromatin factors.
- Structural variants in promoters, including transposon sequences, are associated with allele-specific expression.
- Trait-associated variants are enriched in open chromatin regions, with a retrotransposon insertion linked to reduced fruit size.

## Abstract

Genetic and epigenetic perturbation of cis-regulatory sequences can shift patterns of gene expression and result in novel phenotypes. Phased genome assemblies now enable the local dissection of linkages between cis-regulatory sequences, including their epigenetic state, and allele-specific gene expression to further characterize gene regulation and resulting phenotypes in heterozygous genomes.

We assembled a locally phased genome for a mandarin hybrid named ‘Fairchild’ to explore the molecular signatures of allele-specific gene expression. With local genome phasing, genes with allele-specific expression were paired with haplotype-specific chromatin states, including levels of chromatin accessibility, histone modifications, and DNA methylation. We found that 30% of variation in allele-specific expression could be attributed to haplotype associated factors, with allelic levels of chromatin accessibility and three histone modifications in gene bodies having the most influence. Structural variants in promoter regions were also associated with allele-specific expression, including specific enrichments of hAT and MULE-MuDR DNA transposon sequences. Integration of haplotype-resolved genetic and epigenetic landscapes with high-throughput phenotypic analysis of fruit traits in a panel of 154 accessions with mandarin and pummelo ancestry revealed that trait-associated variants were enriched in regions of open chromatin. Mining of trait-associated variants uncovered a Gypsy retrotransposon insertion in a gene that regulates potassium transport and may contribute to the reduction in fruit size that is observed in mandarins.

​​Using a locally phased assembly of a heterozygous cultivar of citrus, we dissected the interplay between genetic variants and molecular phenotypes to reveal cis-regulatory sequences with potential functional effects on phenotypes relevant for genetic improvement.

The online version contains supplementary material available at 10.1186/s12864-025-12137-0.