Functional Analysis of Singleton and Gene Families Figure 3. Functional Analyses of Unique Genes and Gene Family Members Predominantly Expressed in the Light by Using T-DNA Insertional Mutants. (A) Co-segregating phenotypes observed in knockout lines affecting 6 unique genes. (B) Co-segregating phenotypes observed in knockout lines affecting 4 gene family members predominantly expressed in the light. Green arrows indicate mutant phenotypes that co- segregated with T-DNA insertions in the candidate gene (gene designations are given in parentheses). All primers used for genotyping are described in Table S5. The phenotype analyses for 20 light-inducible genes are detailed in Table 8. doi:10.1371/journal.pgen.1000164.g003 The endogenous retrotransposon Tos17 has been shown to be an efficient insertional mutagen in rice and phenotypes of some 50,000 M2 generation insertion lines carrying Tos17 insertions have been reported [21]. We used the available Tos17 phenotypic data to assess the functions of some of our candidate genes. Phenotypes similar to those identified in the T-DNA insertional mutants for Os01g71190 (Psb28), Os03g47610 (Dxr), and Os04g37619 (Aba1) have also been observed for the corresponding Tos17 insertional mutant lines (Table 2; [21,37]). We could not identify mutant phenotypes for the other unique genes containing T-DNA insertional mutations that we analyzed. We assume that phenotypes associated with two genes, PLoS Genetics | www.plosgenetics.org 6 August 2008 | Volume 4 | Issue 8 | e1000164