Genetic, epigenetic and genomic effects on variation of gene expression among grape varieties

The transcriptional regulatory structure of plant genomes is still relatively unexplored and little is known about factors that influence expression variation in plants. We used a genetic system consisting of 10 heterozygous grape varieties with high consanguinity and high haplotypic diversity to: (i) identify regions of haplotype sharing through whole genome resequencing and SNP genotyping; (ii) analyse gene expression through RNA-seq in four stages of berry development; (iii) associate gene expression variation with genetic and epigenetic properties. We found that haplotype sharing in and around genes was positively correlated with similarity in expression and negatively correlated with the fraction of differentially expressed genes. Genetic and epigenetic properties of the gene and the surrounding region showed significant effects on the extent of expression variation, with negative associations for the level of gene body methylation and the mean expression level and positive ones for nucleotide diversity, structural diversity and ratio of non-synonymous to synonymous nucleotide diversity. We also observed a spatial dependency of covariation of gene expression among varieties. These results highlight relevant roles for cis-acting factors, selective constraints and epigenetic features of the gene and the regional context in which the gene is located in the determination of expression variation. This article is protected by copyright. All rights reserved.