Abstract Detail

Genomics / Proteomics

Lira-Medeiros, Catarina [1], Voloch, Carolina [2], Litt, Amy [3].

Changes in DNA methylation and the domestication of tomato.

Epigenetic modifications are increasingly being shown to play an important role in short- and long-term adaptation of plants in response to changes environmental conditions. Differences in DNA methylation can contribute to genome stability, changes in gene expression, and phenotypic diversity, and this phenotypic diversity can be the target of selection, resulting in adaptive changes. Little is known, however, about the role of epigenetic changes in the domestication process, and the role such changes may play in the suite of traits that characterize domesticated plants. We compared genome-wide DNA methylation patters in two varieties of cultivated tomato (Solanum lycopersicum) in contrast to three accessions of wild tomato (S. pimpinellifolium) using bisulfite sequencing. Sequences were aligned with the reference genome of S. lycopersicum 2.50, and mapping efficiency was high for all libraries. Patterns of cytosine methylation were similar in all accession: 52%, 45% and 3% for CpG, CHG and CHH respectively. Cytosines in the CpG and CHG contexts were highly methylated (95% and 88% respectively) but methylation patterns were not correlated with repeat or centromere regions. Over 700 positions in the genome showed fixed methylation differences between the two cultivated and three wild accessions, with most of these being methylated in the cultivated accessions. We found over 100 of these positions to be in or near genes, including genes predicted to be involved in flower development, fruit development, and ripening, metabolism, histone modification, and other cellular processes. We performed qRT-PCR on 16 genes using breaker-stage fruit tissue to determine if the differences in methylation between wild and cultivated tomato were correlated with differences in expression at that stage. We consistently found greater variability in expression among the wild accessions. Seven genes showed higher expression in wild accessions, one showed higher expression in cultivated, and the rest showed no difference. Most of the differentially expressed genes appear to play roles in metabolic processes, potentially related to the ripening that is occurring at breaker stage. The significance of these results will be discussed in the context of tomato domestication and fruit development.

1 - Jardim Botânico do Rio de Janeiro, Laboratório de Biologia Molecular de Plantas, Rua Pacheco Leão, 915 - sala 402, Rio de Janeiro, RJ, CEP 22460-030, Brazil
2 - Universidade Federal do Rio de Janeiro, Departamento de Genética, Av. Pau-Brasil, 211, lha do Fundão - Cidade Universitária, Rio de Janeiro, RJ, CEP: 21941-590, Brazil
3 - University of California, Riverside, 900 University Avenue, Riverside, CA, 92521, United States

Keywords:
epigenetcs
cytosine methylation
tomato
domestication.

Presentation Type: Oral Paper
Session: 27, Genomics & Proteomics II
Location: 105/Savannah International Trade and Convention Center
Date: Tuesday, August 2nd, 2016
Time: 4:30 PM
Number: 27012
Abstract ID:147
Candidate for Awards:None