Characterization and transcriptome analysis of a silent allele of the Unstable factor for orange1 in maize
Open Access
- Author:
- Tan, Qixian
- Graduate Program:
- Agronomy
- Degree:
- Master of Science
- Document Type:
- Master Thesis
- Date of Defense:
- July 20, 2016
- Committee Members:
- Surinder Chopra, Thesis Advisor/Co-Advisor
- Keywords:
- maize
epigenetics
inheritance
transcriptome - Abstract:
- Epigenetic refers to changes in the gene expression or phenotypes that are not associated with changes in the DNA sequence. Epigenetic inheritance of a phenotype can be because of modifications in DNA methylation and/or chromatin structure. To study epigenetic gene regulation, pericarp color1 (p1), gene of maize has been used as a model system. The p1 gene regulates phlobaphenes biosynthesis and has been successfully used as a model for genetic studies because of its obvious pigmentation phenotypes. One of the p1 allelic patterns is white pericarp and red gob glumes conditioned by the P1-wr allele. The Unstable factor for orange 1 (Ufo1) was first described as a modifier of P1-wr expression. In the presence of the dominant mutant Ufo1-1, DNA methylation of P1-wr is reduced, resulting in increased accumulation of phlobaphenes in kernel pericarp, cob glumes and even an ectopic expression in vegetative tissues. In addition, P1-wr; Ufo1-1 plants also show pleiotropic defects of plant growth and development, such as reduced plant height, buggy whip phenotypes with rolled leaves and stunted growth in these plants. The Ufo1 mutant plants are unstable, reverting back to wild type phenotype. Within a population of Ufo1-1 expressing plants (U-E), we identified silent individuals (U-S) that show stable phenotypes resembling wild type P1-wr; ufo1 plants with colorless pericarp, red cob glumes and normal plant height. The first objective of this study is to investigate the inheritance of the silent phenotype of U-S. Genetic experiments have proven that the U-S phenotype is caused by an independent loss-of-function allele of Ufo1-1, namely Ufo1-1S. Also, the formation of Ufo1-1S probably depends on other loci (modifiers) in the genome because of the differences observed in different maize genetic backgrounds. In order to further elucidate global effects of the functional Ufo1-1 allele (Ufo1-1E) and Ufo1-1S, RNA-Seq analysis was performed. Our results indicated that the U-S and wild type transcriptome profile are more similar to each other as compared to the U-E. The KEGG pathway and GO term enrichment assays showed that flavonoid biosynthesis pathway is up regulated in U-E, while it shows no significant difference in U-S and wild type. In addition, the pectinesterase gene expression was upregulated in the presence of Ufo1-1E. Together with the fact that total lignin content is reduced in U-E, we presume that the defects in plant cell wall synthesis are responsible for the Ufo1-1-associated plant growth abnormality.