Time flies! As we have already entered into a new year, it is time to think how to put the best foot forward in the new year. I have three projects in mind.
First, I want to explore the factors that impact gene expression profiles. When it comes to studies on gene expression, expression breadth and expression specificity are the two main subjects. What are the driving forces behind expression breadth and specificity? Are there convergent pattern of expression breadth and specificity across different species? Are expression breadth and specificity related to gene duplication, thus giving rise to dosage effect?
Second, I want to dissect complex traits using both SNPs and copy number variations (CNVs). Structure variations have been rarely used for dissecting quantitative traits in forest trees, yet it seems they exerted a similar impact on quantitative traits as nucleotide substitution variation. It would be interesting to employ both SNP and CNV variation in GWAS and see whether it can increase the test power.
Third, I want to compare the repeated sequences in different tree species. Repeated DNA have been called junk DNA historically, which has been proved wrong as evidences have shown repeated DNA may function as regulatory elements influencing coding genes expression. Gymnosperm trees differ from their angiosperm counterparts in the large size genome. Their repeats-filled genome evaded from downsizing by selection. Do the repeats between gymnosperm and angiosperm trees differ in type, distribution, and functional role? I think this would be one important aspect to explain the species radiation in flowering species.