Table I. List of candidate genes localized to SNPs.
Candidate genes are those genes containing the SNP and those genes in LD with the SNP associated with a –log10(p) > 4 for ΦPSII measured 1 h after a step-wise increase in irradiance from 100 to 550 µmol m−2 s−1, selected upon a GWAS on 344 Arabidopsis accessions. Chr., Chromosome; Gene, the gene to which the associated SNP localizes (if two genes are indicated, the SNP is mapped between the two genes); SNP Pos., the chromosome position(s) of the SNP(s); MAF, minor allele frequency (the letters in parentheses indicate the Columbia-0 allele [C] or the non-Columbia-0 allele [NC]); −log10(p), the significance level of the associated SNP expressed as –log10(p); Effect Size, the contribution of the Columbia-0 allele of the SNP on ФPSII; Percentage Genetic Variation, the percentage of genetic variation explained by the SNP; Description, the annotation of the gene function as indicated in The Arabidopsis Information Resource (TAIR; www.arabidopsis.org); LD, the genes found to be in LD (r > 0.45) with the indicated SNP.
| Chr. | Gene | SNP Pos. | MAF | −log10(p) | Effect Size | Percentage Genetic Variation | Description | LD |
|---|---|---|---|---|---|---|---|---|
| 1 | AT1G21080/AT1G21090 | 7,384,441 | 0.146 (C) | 4.6 | 0.018 | 9 | DNAJ heat-shock N-terminal domain-containing protein/cupredoxin superfamily protein | AT1G21060 to AT1G21140 |
| 1 | AT1G69770 | 26,249,116 | 0.254 (NC) | 4.3 | −0.014 | 8.1 | Chromomethylase3, involved in methylating cytosine residues at non-CG sites | – |
| 1 | AT1G72560 | 27,329,236 | 0.246 (NC) | 4.6 | 0.014 | 8.1 | PAUSED, a karyopherin | – |
| 1 | AT1G74180 | 27,899,243 | 0.351 (C) | 4.4 | 0.013 | 8.6 | Receptor-like protein14, located in chloroplast | AT1G74190 |
| 1 | AT1G74440 | 27,979,318; 27,981,096 | 0.447 (C); 0.365 (NC) | 5.0; 5.3 | 0.013; 0.013 | 9.0; 9.8 | Unknown protein | – |
| 2 | AT2G26280 | 11,189,311 | 0.196 (NC) | 4.3 | −0.018 | 8.3 | CID7, CTC-interacting domain7, functions in DNA binding and mismatch repair, located in chloroplast | AT2G26290 |
| 3 | AT3G04910 | 1,353,894 | 0.155 (NC) | 4.3 | −0.016 | 8.3 | WNK1, With No Lys Kinase1, Ser/Thr protein kinase, whose transcription is regulated by circadian rhythm | AT3G04880 to AT3G04910 |
| 3 | AT3G05860 | 1,750,265; 1,750,573; 1,750,946; 1,751,042 | 0.175; 0.167; 0.167; 0.211 (C) | 4.2; 4.5; 4.2; 5.4 | 0.016; 0.017; 0.016; 0.016 | 8.3; 9.1; 8.3; 9.8 | MADS box transcription factor family protein | AT3G05790 to AT3G05890 |
| 3 | AT3G22910 | 8,120,853 | 0.307 (NC) | 4.1 | 0.015 | 7.9 | ATPase E1-E2 type family protein/haloacid dehalogenase-like hydrolase family protein | – |
| 3 | AT3G31410 | 12,784,017 | 0.377 (C) | 5.3 | −0.015 | 8.7 | Transposable element | – |
| 3 | AT3G44230 | 15,932,189 | 0.184 (NC) | 4.1 | −0.016 | 6.6 | Unknown protein | – |
| 3 | AT3G54010 | 20,000,766 | 0.289 (NC) | 4.7 | −0.014 | 9.6 | Immunophilin-like protein | AT3G54000 |
| 4 | AT4G11300 | 6,872,903 | 0.480 (C) | 4.2 | 0.014 | 7.6 | Unknown protein | – |
| 4 | AT4G14250 | 8,209,018; 8,209,226 | 0164; 0.187 (C) | 4.9; 5.1 | 0.017; 0.016 | 9.3; 9.1 | Pseudogene | – |
| 4 | AT4G21760 | 11,561,583 | 0.053 (NC) | 4.2 | 0.023 | 6.3 | β-Glucosidase47, involved in carbohydrate metabolic process | AT4G21750 to AT4G21770 |
| 5 | AT5G03760 | 987,180; 987,216; 988,003 | 0.216; 0.272; 0.240 (C) | 4.9; 4.3; 4.4 | 0.014; 0.014; 0.014 | 7.7; 8.5; 8.3 | Cellulose synthase-like A9 | AT5G03750 |
| 5 | AT5G42870 | 17,186,178 | 0.345 (C) | 4.3 | −0.012 | 8 | PAH2, a phosphatidate phosphohydrolase | – |
| 5 | AT5G43390 | 17,424,158 | 0.450 (C) | 4.0 | −0.012 | 8.5 | Uncharacterized conserved protein, located in chloroplast | – |
| 5 | AT5G64960 | 25,956,134 | 0.465 (C) | 4.3 | −0.013 | 9.9 | CDKC2, expression modifies the location of spliceosomal components | AT5G64910 to AT5G65030 |
| 5 | AT5G64980 | 25,963,073 | 0.465 (C) | 4.5 | −0.013 | 9.9 | Unknown protein | |
| 5 | AT5G65000/AT5G65005 | 25,967,700 | 0.354 (NC) | 4.9 | 0.013 | 9.4 | Nucleotide-sugar transporter family protein/polynucleotidyl transferase | |
| 5 | AT5G65010 | 25,968,943 | 0.284 (NC) | 4.2 | 0.014 | 10.1 | ASN2, Asn synthetase2 | |
| 5 | AT5G65030 | 25,975,808 | 0.480 (C) | 4.4 | −0.013 | 10.4 | Unknown protein |