Functional Analysis of Singleton and Gene Families Table 2. Summary of Screen for Phenotypes Associated with 20 Candidate Genes Showing at least 8-Fold Induction in the Light. No homo No homo NF6834/ albino ND7057/ dwarf 1-deoxy-D-xylulose 5-phosphate reductoisomerase T-DNA Locus_IDa (Gene ID b) Annotation Unique genes screened Os01g01710 (U1) Os01g40710 (U2) Expressed protein Os01g71190 (U3) Psb28 Os02g57030 (U4) Expressed protein Os03g04470 (U5) Expressed protein Os03g06230 (U6) Expressed protein Os03g19760 (U7) HAD-superfamily hydrolase Os03g47610 (U8) ThiC Os04g37619 (U10) Zeaxanthin epoxidase Os07g46460 (U11) Ferredoxin-dependent glutamate synthase Os08g40160 (U12) Thylakoid lumen protein Predominant gene family members screened Os01g08460 (P1-1) TMS membrane family protein Os01g45274 (P2-1) Carbonic anhydrase Os03g37830 (P4-1) Potassium uptake protein Os03g52840 (P5-1) Serine hydroxylmethyl transferase Os05g47540 (P6-1) Phosphoethanolamine N-methyltransferase Os06g04510 (P7-1) Enolase 1 Os07g32880 (P8-1) ATP synthase gamma chain Os08g36480 (P9-1) Nitrate reductase 1 Os12g08810 (P13-1) VTC2 aTIGR Locus identifiers. bGene identifiers used in Figure 2, Figure 3, Figure 4, Figure 5, Figure S3, Figure S4, Figure S5, and Figure S7. cName of line with T-DNA or Tos17 insertion in the candidate gene [21]. (In most cases, two independent lines, and therefore two independent alleles, were selected for characterization.) dResults of tests for co-segregation of insertion and phenotype. O, a co-segregating line; X, a non co-segregating line; ND, co-segregation not determined due to issues involving somaclonal variation or problems with designed primers; No homo, there were no homozygous progenies; and LS, less seeds due to the very low fertility. eNA, not analyzed because homozygous progenies were not available for screening or seeds were not available due to the very low fertility. doi:10.1371/journal.pgen.1000164.t002 PLoS Genetics | www.plosgenetics.org 7 August 2008 | Volume 4 | Issue 8 | e1000164 Linec 1B-14224 1C-03301 3A-00098 3A-08586 4A-00716 1C-06727 2A-50128 4A-50119 1A-09123 3A-03564 1B-01520 4A-00253 1B-01342 1C-06809 1A-08723 1A-17021 3A-16669 4A-50669 1D-02443 3A-01082 2B-20208 2B-20162 2B-00356 1B-20710 2B-60065 3C-00294 2C-10006 2D-40669 1D-03944 3A-60218 3A-07919 4A-00172 3A-02083 3A-12320 2A-10285 3D-01688 2D-10946 4A-50280 3A-14221 3A-50953 Phenotypee Cod albino albino pale green pale green pale green pale green albino albino dwarf dwarf pale green pale green dwarf dwarf albino albino albino slender pale green pale green pale green dwarf pale green Semi-dwarf Semi-dwarf oxidative stress oxidative stress O O LS ND O LS O O O ND X X X X O O O O ND ND ND ND O O X X O LS ND LS X X ND O O No homo No Homo No homo Tos17 Linec/phenotype ND6028/ dwarf ND7938/semi_dwarf ND1302/ semi_dwarf NC2658/ albino NC3521/ albino NC6571 /albino ND4332 / albino NF2004 / hard leaf