PMID- 31034726 OWN - NLM STAT- MEDLINE VI - 99 IP - 5 TI - Genetic, epigenetic and genomic effects on variation of gene expression among grape varieties. PG - 895-909 CI - © 2019 The Authors The Plant Journal © 2019 John Wiley & Sons Ltd. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Plant J JT - The Plant journal : for cell and molecular biology JID - 9207397 IS - 1365-313X (Electronic) LID - 10.1111/tpj.14370 [doi] FAU - Magris, Gabriele AU - Magris G AUID- ORCID: 0000-0003-0801-0089 AD - Department of Agricultural Food, Environmental and Animal Sciences, University of Udine, Udine, I-33100, Italy. AD - Istituto di Genomica Applicata, Udine, I-33100, Italy. FAU - Di Gaspero, Gabriele AU - Di Gaspero G AUID- ORCID: 0000-0001-5810-2163 AD - Istituto di Genomica Applicata, Udine, I-33100, Italy. FAU - Marroni, Fabio AU - Marroni F AUID- ORCID: 0000-0002-1556-5907 AD - Department of Agricultural Food, Environmental and Animal Sciences, University of Udine, Udine, I-33100, Italy. AD - Istituto di Genomica Applicata, Udine, I-33100, Italy. FAU - Zenoni, Sara AU - Zenoni S AUID- ORCID: 0000-0002-0496-8161 AD - Department of Biotechnology, University of Verona, Verona, I-37034, Italy. FAU - Tornielli, Giovanni Battista AU - Tornielli GB AUID- ORCID: 0000-0001-5027-0269 AD - Department of Biotechnology, University of Verona, Verona, I-37034, Italy. FAU - Celii, Mirko AU - Celii M AD - Department of Agricultural Food, Environmental and Animal Sciences, University of Udine, Udine, I-33100, Italy. AD - Istituto di Genomica Applicata, Udine, I-33100, Italy. FAU - De Paoli, Emanuele AU - De Paoli E AUID- ORCID: 0000-0003-3646-7692 AD - Department of Agricultural Food, Environmental and Animal Sciences, University of Udine, Udine, I-33100, Italy. FAU - Pezzotti, Mario AU - Pezzotti M AUID- ORCID: 0000-0002-7430-6147 AD - Department of Biotechnology, University of Verona, Verona, I-37034, Italy. FAU - Conte, Federica AU - Conte F AD - Institute for Systems Analysis and Computer Science Antonio Ruberti, National Research Council, Rome, I-00185, Italy. AD - SysBio Centre for Systems Biology, Rome, I-00185, Italy. FAU - Paci, Paola AU - Paci P AUID- ORCID: 0000-0002-9393-2047 AD - Institute for Systems Analysis and Computer Science Antonio Ruberti, National Research Council, Rome, I-00185, Italy. AD - SysBio Centre for Systems Biology, Rome, I-00185, Italy. FAU - Morgante, Michele AU - Morgante M AUID- ORCID: 0000-0003-2591-2156 AD - Department of Agricultural Food, Environmental and Animal Sciences, University of Udine, Udine, I-33100, Italy. AD - Istituto di Genomica Applicata, Udine, I-33100, Italy. IS - 0960-7412 (Linking) SB - IM MH - Chromosomes, Plant/genetics MH - *Epigenesis, Genetic MH - Fruit/genetics MH - *Gene Expression Regulation, Plant MH - Gene Regulatory Networks MH - Genes, Plant/*genetics MH - *Genetic Variation MH - *Genomics MH - Haplotypes MH - Heterozygote MH - Metabolic Networks and Pathways/genetics MH - Polymorphism, Single Nucleotide MH - Sequence Analysis, DNA MH - Vitis/classification/*genetics OTO - NOTNLM OT - * Vitis vinifera OT - *chromosomal location OT - *gene body methylation OT - *grapevine OT - *haplotype sharing OT - *purifying selection OT - *regulatory variation DCOM- 20200629 LR - 20200629 DP - 201909 DEP - 20190607 AB - 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 single-nucleotide polymorphism (SNP) genotyping; (ii) analyse gene expression through RNA-seq in four stages of berry development; and (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 was 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 mean expression level, and with positive associations 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. OPEN RESEARCH BADGES: This article has earned an Open Data Badge for making publicly available the digitally-shareable data necessary to reproduce the reported results. The data is available at https://www.ncbi.nlm.nih.gov/bioproject/PRJNA385116; https://www.ncbi.nlm.nih.gov/bioproject/PRJNA392287; https://www.ncbi.nlm.nih.gov/bioproject/PRJNA373967 (released upon publication); https://www.ncbi.nlm.nih.gov/bioproject/PRJNA490160 (released upon publication); https://www.ncbi.nlm.nih.gov/bioproject/PRJNA265039; https://www.ncbi.nlm.nih.gov/bioproject/PRJNA265040.