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. 2015 Apr 29;10(4):e0124215. doi: 10.1371/journal.pone.0124215

Table 4. PUE candidate genes detected based on converging evidence from functional annotation, P-responsiveness based on gene expression profiling and SNP variation in the promoter and coding regions.

Chr. MSU_LOC: MSU_5' MSU_3' MSU_Annotation Pariasca-Tanaka et al. (2010) Zheng et al. (2009) Number of NS-SNPs b Number of P-SNPs c
1 LOC_Os01g13030 7248761 7253629 OsIAA3, Auxin-responsive Aux/IAA gene family member, expressed 0.79** Sa 0.74* S 1 4
LOC_Os01g13060 7264228 7272237 CK1_CaseinKinase_1.1—CK1, expressed 0.53* S NS 1 5
LOC_Os01g13080 7279250 7277720 60S acidic ribosomal protein, putative, expressed 2.16*** S 1.65* R 0 2
LOC_Os01g13090 7280734 7284992 nucleic acid binding protein, putative, expressed NS NS 4 8
LOC_Os01g13150 7324145 7331536 metallo-beta-lactamase family protein, putative, expressed na 1.94* R; 2.99* S 14 16
LOC_Os01g13160 7332691 7338244 expressed protein 0.81** R NS 4 2
LOC_Os01g13170 7339717 7344465 ubiquitin-conjugating enzyme E2, putative, expressed NS NS 6 15
4 LOC_Os04g30110 17790725 17789889 wall-associated receptor kinase 3 precursor, putative, expressed  na 1.24*** S ND ND
11 LOC_Os11g29470 16634045 16631968 expressed protein na na 4 4
LOC_Os11g29490 16642596 16649451 plasma membrane ATPase, putative, expressed NS NS 2 (stop codon) 2
12 LOC_Os12g42970 26659915 26662912 GATA zinc finger domain containing protein, expressed NS 1.86* R ND ND
12 LOC_Os12g43110 26734618 26735291 OsSAUR58, Auxin-responsive SAUR gene family member, expressed NS 1.8* S; 2.6** R ND ND

aValues above 1 indicate up-regulation of the gene under P deficiency.

Asterisks indicate statistical significance, where * P<0.05, ** P<0.01, *** P<0.001, and NS indicates P>0.05.

(S) and (R) refer to shoot and root tissue, respectively. ‘na’ indicates that the data were not available.

bNS-SNP: non-synonymous SNP. Variation based on information taken from RiceVarMap, http://ricevarmap.ncpgr.cn/.

cP-SNP: SNP within a 1 kb upstream promoter region. Variation based on information taken from RiceVarMap, http://ricevarmap.ncpgr.cn/.