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Table 4 Selected candidate genes mapped in HapMap/GWAS population for anion concentration under phosphate sufficient (+Pi) and deficient (−Pi) treatments

From: QTL and candidate genes associated with leaf anion concentrations in response to phosphate supply in Arabidopsis thaliana

Trait Chr Gene position in kp MAF -log10(P) β deficient β control Description TAIR v10 Genes in LD
PHO 1 AT1G59830 22,022 0.3 4.6 −0.11 −1.16 PROTEIN PHOSPHATASE 2A-1 (PP2A-1). Encodes one of the isoforms of the catalytic subunit of protein phosphatase 2A.  
5 AT5G16440 5370 0.08 4.7 0.53 1.78 ISOPENTENYL DIPHOSPHATE ISOMERASE 1 (IPP1). Encodes a protein with isopentenyl diphosphate:dimethylallyl diphosphate isomerase activity. AT5G16430
PUE 5 AT5G49780 20,232 0.05 5.3 1.06 −2.12 Leucine-rich repeat protein kinase family protein involved in protein phosphorylation. AT5G49810 - AT5G49820 - AT5G49830
5 AT5G60410 24,293 0.08 4.3 −0.76 −1.63 SIZ1, encodes a plant small ubiquitin-like modifier (SUMO) E3 ligase that is a focal controller of Pi starvation-dependent responses. AT5G60440 - AT5G60450
SUL 1 (2) AT1G24030 8503 0.13 4.9 −0.25 −1.50 Protein kinase superfamily protein; functions in: protein serine/threonine kinase activity, protein kinase activity, kinase activity, ATP binding; involved in: protein amino acid phosphorylation. AT1G24040 - AT1G24060
1 AT1G62570 23,171 0.12 4.4 −0.71 0.08 FLAVIN-MONOOXYGENASE GLUCOSINOLATE S-OXYGENASE 4, FMO GS-OX4. Encodes a glucosinolate S-oxygenase that catalyzes the conversion of methylthioalkyl glucosinolates to methylsulfinylalkyl glucosinolates  
3 AT3G46400 17,073 0.14 4.2 0.64 0.67 Leucine-rich repeat protein kinase family protein; functions in: kinase activity; involved in: protein amino acid phosphorylation. AT3G46382
3 AT3G52180 19,351 0.46 4.9 −0.47 0.41 STARCH-EXCESS4 Encodes a plant-specific glucan phosphatase that contains a noncatalytic carbohydrate-binding module as well as a dual specificity protein phosphatase domain AT3G52140 - AT3G52170
5 AT5G10180 3194 0.32 4.8 −0.56 0.10 ARABIDOPSIS SULFATE TRANSPORTER 68, AST68, SULFATE TRANSPORTER 2;1, SULTR2;1. Encodes a low-affinity sulfate transporter expressed in the root cap and central cylinder, where it is induced by sulfur starvation. Expression in the shoot vascular system is not induced by sulfur starvation. AT5G10170 - AT5G10240
5 AT5G57610 23,322 0.17 4.1 0.39 −1.14 Protein kinase superfamily protein. Involved in protein amino acid phosphorylation. AT5G57580
  1. PHO = leaf Pi concentration, PUE = Pi use efficiency,, SUL = leaf sulphate concentration. MAF is the minor allele frequency. -log10(P) indicates the significance level of association. β indicates the phenotypic effect of a SNP in (+Pi) or (−Pi) with positive values indicating a positive effect on the trait value from the Col allele. Chromosome numbers are indicated (Chr.). Numbers between brackets refer to the number of significant SNPs, the SNP positions on each chromosome are given, in kilo base pairs (kb). Both SNP position and description is based on TAIR v.10 (www.arabidopsis.org). Genes found to be in linkage disequilibrium (LD), (LD > 0.3) or within 10 kb on both sides of the significant SNP if no LD is found, are listed