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Table 4 Barley candidate genes with a high score of converging evidence for a role in QR to Bgh

From: Discovery of genes affecting resistance of barley to adapted and non-adapted powdery mildew fungi

U35-contig no. a CG no. Proposed function (BlastX) Functional category Chr b Position (cM) b Linkage map b Transcript regul. epidermis Transcript regul. leaf Rel. SI (%) c TIGS or OEX Transcr. regul. CNV Colocal Meta- QTL d Ass_SNP_ hapl_ GWAS CE score e
964 1 BAX-Inhibitor1 Cell & death 6H 51.6 Marcel_09_int UP UP 41.9 2 2 1 0 0 5
3589 2 Hv-Lsd1a Cell & death 5H 43.1 BOPA_cons NS NS 49.9 2 0 1 1 1 5
16561 3 Hv-Mlo Cell & death 4H 103.1 BOPA_cons UP UP 13.8 2 2 0 1 0 5
16942 4 Stomatin-like protein (Rnr10) Cell & death 5H 44.2 9K_WGS_BxM UP UP 62.5 1 2 0 1 0 4
11820 5 AP2-EREBP transcription factor Gene expr. 7H 120.4 9K_WGS_BxM UP - 39.0 2 2 0 0 - 4
15932 6 Hv-WRKY2 Gene expr. 7H 126.3 9K_WGS_BxM UP UP 44.6 1 2 0 0 1 4
383 7 Hv-WRKY21 Gene expr. 3H 54.4 BOPA_cons NS DOWN 41.5 2 1 0 1 - 4
4162 8 Hv-WRKY28 Gene expr. 5H 46.5 9K_WGS_BxM UP UP 56.7 2 2 0 0 0 4
43536 9 Hv-WRKY45 Gene expr. 3H 59.3 9K_WGS_BxM UP UP 39.4 2 2 0 1 - 5
2987 10 Os-WRKY68-like Gene expr. 2H 92.3 9K_WGS_BxM UP NS 35.7 2 2 0 0 1 5
2705 11 Pre-mRNA splicing factor PRP38 Gene expr. 7H 33.0 Marcel_09_int UP NS 79.4 1 2 0 1 0 4
16863 12 6-Phosphogluconolactonase 2 Prim. metab. 2H 56.3 BOPA_cons DOWN DOWN 142.9 1 2 0 1 - 4
604 13 Alpha/beta hydrolase Prim. metab. 4H 126.1 Marcel_09_int UP UP 72.2 0 2 0 1 1 4
5070 14 Short chain dehydrogen/reductase Prim. metab. 5H 41.6 9K_WGS_BxM DOWN DOWN 173.9 0 2 1 1 - 4
15523 15 Stearoyl-ACP desaturase Prim. metab. 2H 58.1 9K_WGS_BxM UP UP 78.5 0 2 1 1 - 4
3071 16 ARM repeat protein (Rnr5) Protein 3H 95.4 BOPA_cons UP UP 49.0 2 2 1 0 0 5
17055 17 Nucellin-like aspartic protease Protein 4H 48.5 BOPA_cons UP UP 41.4 1 2 0 1 0 4
19087 18 Subtilisin-like serine proteinase Protein 3H 47.1 9K_WGS_BxM UP UP 137.4 2 2 0 1 - 5
13715 19 Ubiquitin Protein 7H 104.1 9K_WGS_BxM UP NS 427.9 2 2 1 0 - 5
13712 20 Ubiquitin Protein 5H 50.3 BOPA_cons NS NS 270.3 2 0 1 1 - 4
1746 21 4-Coumarate coenzyme A ligase Sec. metab. 6H 59.8 Marcel_09_int UP UP 177.8 2 2 0 0 0 4
14914 22 Caffeic acid 3-O-methyltransferase Sec. metab. 2H 89.9 Marcel_09_int UP UP 42.5 1 2 1 0 0 4
2091 23 Chorismate Synthase Sec. metab. 4H 55.3 9K_WGS_BxM UP UP 72f 2 2 0 1 1 6
14239 24 Phenylalanine ammonia-lyase Sec. metab. 2H 77.1 Marcel_09_int UP UP 95.5 0 2 1 1 - 4
14693 25 Calreticulin 1 or 2g Secr. & CW 2H 151.4 BOPA_cons UP UP 101.9 1 2 0 1 1 5
17745 26 Golgi nucl.-sugar transporter Secr. & CW 4H 65.8 9 K_WGS_BxM UP UP 56.5 2 2 0 0 - 4
6978 27 Hv-CslA11 Secr. & CW 3H 143.0 9 K_WGS_BxM DOWN DOWN 145.9 2 2 0 1 - 5
17157 28 Hv-CslD2 (Rnr6) Secr. & CW 7H 3.8 9 K_WGS_BxM UP UP 216.3 2 2 1 1 0 6
14954 29 Hv-Ger4d (SOD) Secr. & CW 4H 119.8 BOPA_cons UP UP 149.0 2 2 1 1 0 6
16280 30 Hv-Ger5a (SOD) Secr. & CW 5H 97.4 Marcel_09_int UP NS 61.0 2 2 0 0 - 4
14157 31 Hv-Prx40 Secr. & CW 3H 81.2 Marcel_09_int UP UP 184.1 2 2 1 0 0 5
14158 32 Hv-Prx64 Secr. & CW 3H 81.2 Marcel_09_int UP UP 113.7 1 2 0 0 1 4
4293 33 Hv-SNAP34 (Rnr3) Secr. & CW 2H 63.6 Marcel_09_int UP UP 179.8 2 2 0 1 0 5
16316 34 Diacylglycerol kinase Signaling 2H 140.3 BOPA_cons UP UP 40.2 2 2 1 0 0 5
39894 35 Disease resistance protein Hcr2-0B Signaling - - - UP - 122.4 2 2 1 - - 5
1818 36 OPDA reductase Signaling 2H 64.2 BOPA_cons UP UP 68.8 0 2 0 1 1 4
15506 37 Receptor-like kinase (BAK-1) Signaling 3H 142.7 Marcel_09_int UP UP 71.2f 2 2 0 0 0 4
18640 38 Receptor-like kinase (DUF26) Signaling 5H 167.6 9 K_WGS_BxM UP UP 48.2 1 2 0 0 1 4
10720 39 Receptor-like kinase (DUF26) Signaling - - - NS UP 23.3 2 1 1 - - 4
5850 40 Receptor-like kinase (lectin-like) Signaling 5H 46.2 BOPA_cons UP UP 78.2 0 2 1 1 1 5
20697 41 Receptor-like kinase (lectin-like) Signaling 7H 44.4 9 K_WGS_BxM UP UP 45.4 2 2 1 0 - 5
20304 42 Receptor-like kinase (lectin-like) Signaling 2H 59.2 ZIPPER UP UP 60.5 0 2 1 1 - 4
26360 43 Receptor-like kinase (lectin-like) Signaling 5H 46.2 CAPS_BxM UP NS 66.7 0 2 1 1 0 4
39885 44 Receptor-like kinase (LRR) Signaling - - - NS UP 32.6 2 1 1 - - 4
16135 45 Triticum aestivum kinase (TAK) Signaling 3H 6.8 9 K_WGS_BxM NS UP 52.1 2 1 1 0 - 4
16558 46 Glutathione S-transferase Stress 4H 96.6 BOPA_cons COMPL. UP 101.2 0 2 1 1 0 4
1285 47 Sugar transporter (Os-SWEET2a) Transport 1H 18.1 BOPA_cons COMPL. NS 40.8 1 2 0 1 0 4
2230 48 Charged MVB protein 5 Unknown 1H 0.2 9 K_WGS_BxM UP UP 86.7 0 2 1 1 - 4
14824 49 Hv-Ger2a Unknown 2H 44.6 Marcel_09_int DOWN DOWN 58.4f 2 2 0 0 0 4
19741 50 Unknown protein Unknown 7H 23.0 Marcel_09_int UP UP 51.8 2 2 1 1 0 6
1681 51 Unknown protein Unknown 2H 136.2 Marcel_09_int UP UP 66.4 1 2 1 0 1 5
  1. aHarvEST database.
  2. bMap position derived from different mapping populations: 9 K_WGS_BxM, Barke x Morex population for Illumina 9 K SNP chip and WGS contig anchoring by POPSEQ; BOPA_cons, Barley OPA123-2008, consensus map for barley SNP genotyping deposited in GrainGenes database; CAPS_IxF, CAPS marker-based mapping in Igri x Franka DH population (Schweizer lab); Marcel_09_int, Consensus map, Barley, Integrated, Marcel 2009 deposited in GrainGenes database; ZIPPER, gene-order based map position using stringent sequence homology scores between cereal species.
  3. cRelative susceptibility index caused by TIGS or transient over-expression, normalized to corresponding empty-vector controls.
  4. dMap position lying between outmost flanking markers of meta-QTL (consisting of ≥3 overlapping QTL) for resistance to Bgh.
  5. eSum of scores assigned for: (1) TIGS or transient over-expression effect, (2) transcript regulation either in leaf epidermis or entire leaves, (3) significant copy number variation (CNV), (4) meta-QTL co-localization, and (5) SNP or haplotype association with QR to Bgh. More weight (2 CE scores) was assigned to significant TIGS or OEx effects after false-discovery correction (FDR 0.1), and to transcript regulation in the leaf epidermis (versus regulation in entire leaf samples).
  6. fEffect of transient over-expression.
  7. gAlso regulates Ca2+ concentrations and is therefore also involved in signaling.
  8. Ass, marker-trait association of SNP and/or gene haplotype in a candidate-gene approach or by genome-wide association (GWAS) analysis; Chr, chromosome; CE, convergent evidence; cM, centimorgan; CW, cell wall; expr., expression; metab., metabolism; prim, primary; sec., secondary; secr., secretion; SI, susceptibility index.
  9. A more detailed discussion of individual candidate genes can be found in Additional file 6 provided online.