However, TCS17 remained green for the entire life cycle, representing the most common phenotype of cultivated rice (Fig. 1a-e).
The CNVineta workflow, outlined in detail in the online tutorial and Figure 1A, allows for in-depth data mining of a given dataset for associated rare as well as common CNVs for a phenotype of interest.
The identification of common QTLs regulating both the phenotype of interest (pQTLs), and the expression of genes whose transcript levels correlate with the phenotype, provides a strong basis for candidate gene identification (Chesler et al. 2005; Hu et al. 2008; Saba et al. 2006; Tabakoff et al. 2008).
Vast amounts of data, in various forms, are produced for a common goal: to find genetic variants related to a phenotype of interest (e.g., disease status, etc).
A primary method for establishing phenotype-genotype links is through Genome-Wide Association Studies (Gwhich whinterrogategathethe genome in regions of common variability and attempt to statistically associate this variability to the phenotype of interest [ 1].
Indeed, even the phenotype of interest is often controversial, and it is likely that many common disease definitions include diverse underlying pathologies.
In GWAS, a large set of common variants, i.e. SNPs with high minor allele frequencies, is genotyped and tested for genetic association with the phenotype of interest.
Since multiple largely unknown parameters determine a particular phenotype, an inverse strategy to select a phenotype of interest can be useful.
A common approach would be to map a large number of insertion sites in the DNA from a pool of cells enriched for the phenotype of interest, and then argue that certain genes are significant for this phenotype because there are more commonly targeted in this pool than what may be predicted based on random integration.
As the phenotype of interest becomes more narrowly defined, its inheritance becomes increasingly tractable [1], [15].
