With the combination of bisulfite conversion and high-throughput sequencing techniques, it is now possible to generate genome-wide single base resolution maps of cytosine methylation, referred to as whole-genome bisulfite sequencing (WGBS). This has revolutionized the way scientists study epigenetics. Epigenetics is the study of heritable changes in gene expression that occur independently from changes in nucleotide sequence. Before WGBS, methylation could only be determined in small regions at a time or at low resolution, but now it is possible to track single methylation polymorphisms across generations. This technique to experimental and natural populations to understand epigenetic variation and effects of mutations on methylation polymorphisms.
I am specifically interested in the generation, heritability, and stability of spontaneous epialleles both meiotically and mitotically. Epiallele describes a heritable allele that varies in chromatin state. The most interesting, and most rare, of these epialleles are spontaneous epialleles, where the change in chromatin state occurs independent of changes in DNA sequence. Several spontaneous epialleles are known in plants, such as Lcyc gene, which causes altered flower morphology, and colorless non-ripening (CNR) epiallele, which prevents pigmentation in tomatoes. These epialleles have been well studied and documented in the literature, although they offer limited insight into directed applications of directed epimutagenisis and the heritability of epialleles.
This project aims to determine if epialleles are stable across generations and follow Mendelian inheritance, which are requirements for successful introduction into breeding programs.
Previous work from the Schmitz lab with Arabidopsis thaliana mutation accumulation lines revealed the existence of spontaneous epialleles between early and late generation lines.
Using WGBS from successive generations of two MA lines, I determined that approximately 99.998% of methylated regions in the genome are faithfully inherited to the next generation.
For breeding programs, spontaneous epialleles must also be inherited following Mendelian laws.
With a genetic cross between two MA lines, WGBS was obtained for the parents of the cross and 20 F2 individuals.
The parents only had about 40 distinguishing mutations, which required the creation of a novel algorithm to generate a genetic map using only DNA methylation, termed an epigenotype map.
The epigenotype map allowed me to explore the inheritance patterns of differing epialleles between the parents and approximately half of these epialleles showed expected inheritance.