Table II. Candidate loci associated with responses to the combination of salt and Pi starvation identified with GWAS.
The candidate genes were selected based on LOD score [−log10(α × P value)] and different thresholds of minor allele frequency (MAF) of the SNP associated with the RSA phenotype. For loci containing SNPs in LD with an associated marker, the SNP initially associated with the RSA trait is indicated with an asterisk.
| Locus | Chromosome | Marker | Position | LOD | Phenotype | MAF | Gene | Gene Description | Remarks |
|---|---|---|---|---|---|---|---|---|---|
| 1 | 1 | m13374 | 7,841,617 | 6.85 | aLRL | 0.01 | AT1G22210 | TPPC, TREHALOSE-6-PHOSPHATE PHOSPHATASE C | Specific for responses to double stress |
| LRL/MRL | |||||||||
| 2 | m22386 | 12,461,353 | 5.86 | LRL | 0.1 | AT1G34210 | SERK2, SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASE2 | ||
| m22387 | 12,461,560 | 6.50 | 0.1 | ||||||
| m22389 | 12,461,977 | 6.07 | 0.1 | ||||||
| m22392 | 12,462,722 | 6.07 | 0.1 | ||||||
| m22399 | 12,464,518 | 6.02 | 0.1 | ||||||
| m22400 | 12,464,689 | 6.02 | 0.1 | AT1G34220 | IST1-LIKE1, ISTL1 | ||||
| m22403 | 12,465,407 | 6.02 | 0.1 | ||||||
| m22415 | 12,470,273 | 6.46 | 0.1 | AT1G34240 | hAT-like transposase family | ||||
| m22422 | 12,472,127 | 6.27 | 0.1 | AT1G34245 | EPF2, EPIDERMAL PATTERNING FACTOR2 | ||||
| 3 | 2 | m64345 | 8,047,170 | 6.12 | MRPL | 0.1 | AT2G18540 | mIC-like cupins superfamily protein; functions in nutrient reservoir activity | |
| 5.96 | MRVL | 0.1 | |||||||
| 4 | m64548 | 8,152,277 | 6.14 | LRL | 0.01 | ||||
| m64560 | 8,155,450 | 6.01 | 0.01 | AT2G18820 | Non-LTR retrotransposon family (LINE) | ||||
| m64583 | 8,166,012 | 6.85 | 0.01 | ||||||
| 5 | m64591 | 8,169,986 | 5.89 | LRL | 0.05 | AT2G18876 | Encodes a microtubule-associated protein | ||
| 6 | m64600 | 8,177,544 | 5.71 | LRL | 0.01 | AT2G18880 | VEL2, VERNALIZATION5/VIN3-LIKE2 | ||
| 7 | m68418 | 10,952,801 | 7.16 | MRVL | 0.1 | AT2G25710 | HCS1, HOLOCARBOXYLASE SYNTHASE1 | ||
| 6.97 | MRPL | 0.1 | |||||||
| 8 | m78909 | 18,487,046 | 5.64 | aLRL | 0.1 | AT2G44830 | Protein kinase superfamily protein | ||
| 9 | 3 | m82851 | 1,350,879 | 6.12 | LRL | 0.01 | AT3G04903 | Encodes a defensin-like (DEFL) family protein | |
| 10 | 4 | ml38169 | 7,153,336 | 5.86 | LRL | 0.1 | AT4G11900 | S-Locus lectin protein kinase family protein | |
| 11 | 5 | At5G11280 | Unknown | Common for responses to double stress, salt, and Pi starvation | |||||
| At5G11290 | Encodes a plant protein of unknown function | ||||||||
| At5G11300 | CYCA2;2, MITOTIC-LIKE CYCLIN3B from Arabidopsis | ||||||||
| At5GU310 | SOAR1, SUPPRESSOR OF THE ABAR OVEREXPRESSOR1; negative regulator of ABA signaling | ||||||||
| At5G11320 | AtYUC4, YUC4, YUCCA4 | ||||||||
| At5G 11330 | FAD/NAD(P)-binding oxidoreductase family protein | ||||||||
| At5G11340 | Acyl-CoA N-acyltransferases (NAT) superfamily protein | ||||||||
| At5G11350 | DNase l-like superfamily protein | ||||||||
| At5G11360 | lnterleukin-1 receptor-associated kinase4 protein | ||||||||
| At5G11370 | FBD/Leu-rich repeat domain-containing protein | ||||||||
| At5G11380 | 1-DEOXY-d-XYLULOSE 5-PHOSPHATE (DXP) SYNTHASE3 | ||||||||
| At5G11390 | WIT1, WPP DOMAIN-INTERACTING PROTEIN1 | ||||||||
| At5G 11400 | Protein kinase superfamily protein | ||||||||
| At5G11410 | Protein kinase superfamily protein | ||||||||
| At5G11412 | RNA-binding (RRM/RBD/RNP motifs) family protein | ||||||||
| At5G11420 | Unknown | ||||||||
| ml67447 | 3,649,667 | 6.97 | MRPL | 0.01 | At5G11430* | SPOC domain/transcription elongation factor S-ll protein | |||
| 6.42 | MRVL | ||||||||
| AT5G28210 | mRNA-capping enzyme family protein | Specific for responses to double stress | |||||||
| ml81370 | 10,180,694 | 5.99 | aLRL/MRL | 0.01 | AT5G28220* | Protein prenylyltransferase superfamily protein | |||
| 12 | AT5G28232 | Mutator-like transposase family | |||||||
| AT5G28235 | Ulpl protease family protein | ||||||||
| AT5G28240 | Similar to Ulpl protease family protein | ||||||||
| AT5G28263 | Mutator-like transposase family |