Date: 2015-03-30

In 2008, a consensus definition of the epigenetic trait, "stably heritable phenotype resulting from changes in a chromosome without alterations in the DNA sequence" was made at a Cold Spring Harbor meeting.

Ref: Berger SL, Kouzarides T, Shiekhattar R, Shilatifard A; Kouzarides; Shiekhattar; Shilatifard (2009). "An operational definition of epigenetics". Genes Dev. 23 (7): 781–3. doi:10.1101/gad.1787609


The ultimate goal for cotton research is to better understand the mechanism of the balancing for optimizing the fiber trait and provide the possible approaches to engineer the crop for better product. By integrating the genomic, genetic and epigenetic studies of cotton, a picture we can draw for cotton fiber research to identity some clues for future study. Here we concentrate the analysis of the genomic redundancy for cotton. Genomic composition is not equal from subgenomes in the allotetraploid cotton. Meanwhile the gene pool from AT and DT genomes is very similar. These features lead a question on how this redundant genome composition affects the cotton fiber traits. From the genomic study, it has been well adopted that the epigenetic regulation plays an important role in gene regulations in the polyploidy. It is not clear yet whether the unbalance genomic composition and the epigenetic regulation over homoeolgs could influent cell differentiation and development.

Cotton fiber cell goes a long developmental stage (30-60 days) and the fiber cell is easy to be collected. These characters make cotton fiber cell a very good model to study the cell differentiation and development regulated by redundant genome. With the next- or third-generation sequencing method and the cotton reference genomic sequences, further study can be explore to test on different perspectives summarized in Figure 4 and the followings:

i.   DNA methylation differences between AT and DT genomes in fiber and non-fiber cells. Small RNA sequencing data show that, the 24nt small RNA abundance in cotton seed is significantly higher than that in leaf tissue {Pang, 2009 #178}. This higher enrichment of 24nt small RNA could be the effect of de nove DNA methylation in endosperm. Some data also show the 24nt small RNA enrichment is also different from fiber cell compared to leaf cell (unpublished data). Furthermore, the cotton fiber cell goes several round of endoreduplication at early stage of development. These observations indicate DNA methylation might be different in fiber cell. This study will give a clear clue about whether DNA methylation could affect cell fate determination.

ii.  Homoeolog expression biases between fiber and non-fiber cells. The intensity of unbalanced gene expression is observed to variant in different tissues. To understand how the homolog expression biased differently in different cell type is to understand from both cis and trans-regulation of genes.

iii. Small RNA mediated gene silencing in fiber and non-fiber cells. As reviewed in this paper, small RNA is the most important component of gene expression regulation in polyploidy. The small RNA mediated MYB2 gene study inspires a wide spectrum of questions about genome widely, can small RNA discriminate homoeologs and buffer the biased homoeolg expression or the other way round. mRNA degradation study will answer this question. On the other hand, it is also of interest to study small RNA mediate chromatin modification and DNA methylation in fiber and non-fiber cells, which are very important mechanism for gene silencing.

iv.  Chromatin modification differences between AT and DT genome or cotton fiber and non-fiber cells. Genomic composition is unbalanced for allotetraploid cotton. AT genome contains more replicated regions than DT on chromosome which implies AT genome is with more DNA and chromatin modifications which drive gene silencing. The chromatin modification study in genome wide can answer the question about the unbalanced gene expression. The particular comparison between fiber and non-fiber cell will answer the question that whether the chromatin modification can affect the cell differentiation.