Table 3 Candidate genes associated with positive and negative effects on germination and seedling traits under control and drought stress conditions in a global spring barley collection.
Gene HORVU ID | SNP and Position | Annotation | Chr | Traits | Allele +/− | Allele effect | |
|---|---|---|---|---|---|---|---|
Control | |||||||
HORVU.MOREX.r3.1HG0008980.1 | chr1H:21,389,172:C: G | TOX high mobility group box protein | 1 H | G%4d, Gspeed | + | 4.89–13.05 | % |
HORVU.MOREX.r3.1HG0078690.1 | chr1H:482,009,779:C: T | Signal recognition particle 54 kDa | 1 H | G%6d | + | 0.1403 | % |
HORVU.MOREX.r3.1HG0054230.1 | chr1H:362,456,935:A: C | MADS-box transcription factor | 1 H | Seed wt | + | 0.14 | gm |
HORVU.MOREX.r3.1HG0064790.1 | chr1H:425,607,098:G: T | Microtubule associated family protein | 1 H | SL | + | 1.3 | cm |
HORVU.MOREX.r3.2HG0113120.1 | chr2H:43,184,109:G: A | Pentatricopeptide repeat-containing protein | 2 H | G%2d | + | 0.2319 | % |
HORVU.MOREX.r3.4HG0395010.1 | chr4H:523,809,780:C: A | Nuclear pore complex protein NUP133 | 4 H | G%4d, G%6d, G%8d, G%10d, Gspeed | + | 6.74–15.41 | % |
HORVU.MOREX.r3.4HG0395710.1 | chr4H:527,981,433:T: A | Caleosin | 4 H | G%4d, G%8d, G%10d | + | 4.74–5.27 | % |
HORVU.MOREX.r3.4HG0331880.1 | chr4H:1,672,863:C: T | Beta-amylase | 4 H | Gspeed | + | 10.65 | % |
HORVU.MOREX.r3.5HG0426160.1 | chr5H:14,470,056:G: A | Disease resistance protein (NBS-LRR class) | 5 H | G%8d, G%10d | + | 0.0611 | % |
HORVU.MOREX.r3.5HG0463050.1 | chr5H:312,501,130:C: T | 5’-3’ exonuclease family protein | 5 H | G%8d, G%10d | + | 0.0999 | % |
HORVU.MOREX.r3.5HG0463920.1 | chr5H:320,721,391:C: G | LC | 5 H | G%8d, G%10d | + | 0.0448 | % |
HORVU.MOREX.r3.5HG0468940.1 | chr5H:356,510,708:G: A | NAD(P)-binding Rossmann-fold superfamily protein | 5 H | G%8d, G%10d | + | 0.0311 | % |
HORVU.MOREX.r3.5HG0497770.1 | chr5H:496,479,298:G: A | BAG family molecular chaperone regulator-like protein | 5 H | G%8d, G%10d | + | 0.0763 | % |
HORVU.MOREX.r3.5HG0448590.1 | chr5H:150,482,693:T: C | WRKY transcription factor | 5 H | G%4d | + | 0.0505 | % |
HORVU.MOREX.r3.5HG0517230.1 | chr5H:543,063,520:T: C | VQ motif family protein, expressed | 5 H | G%4d | + | 0.0441 | % |
HORVU.MOREX.r3.5HG0430860.1 | chr5H:30,477,592:T: C | Kinase, putative | 5 H | SL | + | 1.03 cm | cm |
HORVU.MOREX.r3.7HG0750970.1 | chr7H:626,568,450:C: T | Protein DETOXIFICATION | 7 H | G%8d, G%10d | + | 9.22 | % |
HORVU.MOREX.r3.1HG0026430.1 | chr1H:113,962,015:C: G | Proline-rich receptor-like kinase, | 1 H | G%6d | − | −15.78 | % |
HORVU.MOREX.r3.1HG0022360.1 | chr1H:83,116,022:A: G | transmembrane protein | 1 H | Seedwt | − | −0.174 | gm |
HORVU.MOREX.r3.1HG0068820.1 | chr1H:445,145,369:G: A | Metacaspase | 1 H | Seedwt | − | −0.093 | gm |
HORVU.MOREX.r3.2HG0096610.1 | chr2H:2,602,324:G: T | StAR-related lipid transfer protein | 2 H | GH%8d, G%10d | − | −13.92 | % |
HORVU.MOREX.r3.2HG0192890.1 | chr2H:606,315,847:T: C | Xyloglucan endotransglucosylase/hydrolase | 2 H | G%4d, G%8d, G%10d | − | −8.26 | % |
HORVU.MOREX.r3.2HG0190170.1 | chr2H:597,869,636:G: A | F-box domain containing protein | 2 H | G%2d | − | −11.67 | % |
HORVU.MOREX.r3.2HG0107400.1 | chr2H:25,328,601:A: G | Kinase family protein | 2 H | G%4d | − | −9.22 | % |
HORVU.MOREX.r3.3HG0221170.1 | chr3H:5,848,191:G: T | F-box like protein | 3 H | SL | − | −1.14 | cm |
HORVU.MOREX.r3.3HG0325670.1 | chr3H:609,276,465:G: A | F-box domain containing protein | 3 H | SL | − | −1.096 | cm |
HORVU.MOREX.r3.3HG0228050.1 | chr3H:18,765,394:A: G | E3 ubiquitin-protein ligase | 3 H | G%6d, G%8d, G%10d, Gspeed | − | −5.69 /− 14.3 | % |
HORVU.MOREX.r3.3HG0297850.1 | chr3H:531,575,910:G: A | Non-specific serine/threonine protein kinase | 3 H | G%4d | − | −5.54 | % |
HORVU.MOREX.r3.4HG0415720.1 | chr4H:602,909,318:G: A | Endoglucanase | 4 H | G%8d, G%10d | − | −12.95 | % |
HORVU.MOREX.r3.4HG0339820.1 | chr4H:27,647,432:A: G | Sugar transporter family protein | 4 H | G%4d | − | −3.34 | % |
HORVU.MOREX.r3.5HG0464370.1 | chr5H:323,072,464:T: C | Vacuolar sorting receptor protein | 5 H | SL | − | −0.94 | gm |
HORVU.MOREX.r3.5HG0509180.1 | chr5H:523,346,728:G: T | Prefoldin subunit 4 | 5 H | G%6d, G%8d, G%10d | − | −15.84 | % |
HORVU.MOREX.r3.5HG0497230.1 | chr5H:494,414,973:T: C | PHD-finger family protein | 5 H | G%4d | − | −10.08 | % |
HORVU.MOREX.r3.5HG0519230.1 | chr5H:547,967,784:G: A | U3 small nucleolar RNA-associated protein 18-like protein | 5 H | G%4d, G%6d, Gspeed | − | −18.06 | % |
HORVU.MOREX.r3.5HG0533230.1 | chr5H:577,482,385:C: G | Pirin-like protein | 5 H | G%8d, G%10d | − | −3.67 | % |
HORVU.MOREX.r3.5HG0535750.1 | chr5H:582,175,268:A: T | Cleavage and polyadenylation specificity factor subunit 3 | 5 H | G%4d, G%8d, G%10d | − | −4.79 | % |
HORVU.MOREX.r3.6HG0628050.1 | chr6H:548,454,590:C: T | Cytosine-specific methyltransferase | 6 H | Seedwt | − | −0.175 | gm |
HORVU.MOREX.r3.6HG0617830.1 | chr6H:518,070,091:G: A | Cyclin-dependent kinase inhibitor | 6 H | G%10d | − | −11.46 | % |
HORVU.MOREX.r3.6HG0555330.1 | chr6H:43,748,789:G: A | BURP domain protein RD22 | 6 H | G%2d | − | −20.42 | % |
HORVU.MOREX.r3.7HG0639100.4 | chr7H:8,170,605:C: G | 6-phosphogluconate dehydrogenase, decarboxylating | 7 H | G%2d, G%4d, G%6d, G%8d, G%10d, Gspeed | − | −10.9/−34.77 | % |
HORVU.MOREX.r3.7HG0743140.1 | chr7H:611,034,910:T: C | Transducin/WD40 repeat protein | 7 H | G%4d, G%6d, GSpeed | − | −7.2/−25.87 | % |
Drought | |||||||
HORVU.MOREX.r3.1HG0082530.1 | chr1H:490,499,372:C: A | Respiratory burst oxidase | 1 H | RL | + | 0.75 | cm |
HORVU.MOREX.r3.2HG0099620.1 | chr2H:10,431,708:A: C | O-methyltransferase family protein | 2 H | G%8d, G%10d | + | 4.57 | % |
HORVU.MOREX.r3.2HG0178520.1 | chr2H:544,530,240:C: G | Endoglucanase | 2 H | RDW | + | 0.05 | gm |
HORVU.MOREX.r3.2HG0205370.1 | chr2H:637,063,406:T: A | Transcription elongation factor Spt5 | 2 H | G%6d, G%8d, G%10d | + | 6.39 | % |
HORVU.MOREX.r3.3HG0234440.1 | chr3H:36,116,907:G: C | Amino acid permease | 3 H | G%2d | + | 7.4 | % |
RL | + | 1.89 | cm | ||||
HORVU.MOREX.r3.3HG0231430.1 | chr3H:26,462,351:C: T | E3 Ubiquitin ligase family protein | 3 H | RL | + | 1.04 | cm |
HORVU.MOREX.r3.5HG0423130.1 | chr5H:7,635,237:G: A | Thaumatin-like protein | 5 H | G%6d, G%8d, G%10, Gspeed | + | 8.8–26.9 | % |
HORVU.MOREX.r3.5HG0481010.1 | chr5H:434,421,304:C: T | Initiation factor 4 F subunit | 5 H | RDW | + | 0.007 | gm |
HORVU.MOREX.r3.6HG0569310.1 | chr6H:117,879,365:G: A | Plant/T31B5-30 protein | 6 H | G%6d | + | 9.41 | % |
HORVU.MOREX.r3.7HG0663860.1 | chr7H:78,057,538:C: T | EF hand calcium-binding protein family | 7 H | RDW | + | 0.001 | gm |
HORVU.MOREX.r3.1HG0004220.1 | chr1H:8,938,031:C: T | Cysteine proteinase | 1 H | Gspeed | − | −7.0 | % |
HORVU.MOREX.r3.2HG0185030.1 | chr2H:572,536,278:T: C | Multiprotein-bridging factor | 2 H | Seedwt | − | −0.105 | gm |
HORVU.MOREX.r3.2HG0107400.1 | chr2H:25,328,604:T: C | Kinase family protein | 2 H | RDW | − | −0.013 | gm |
HORVU.MOREX.r3.2HG0207520.1 | chr2H:641,742,088:G: A | Wound-responsive family protein | 2 H | RDW | − | −0.006 | gm |
HORVU.MOREX.r3.2HG0189740.2 | chr2H:596,332,379:G: A | Acetylglutamate kinase-like protein | 2 H | RDW | − | −0.006 | gm |
HORVU.MOREX.r3.3HG0294370.1 | chr3H:513,961,348:T: C | Methyl esterase | 3 H | RL | − | −0.68 | cm |
HORVU.MOREX.r3.3HG0286190.1 | chr3H:469,908,093:C: T | Protodermal factor 1 | 3 H | G%2d | − | −5.08 | % |
HORVU.MOREX.r3.3HG0303390.1 | chr3H:552,642,883:G: A | Dirigent protein 17 | 3 H | G%2d | − | −4.37 | % |
HORVU.MOREX.r3.3HG0307390.1 | chr3H:564,672,872:A: C | 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase | 3 H | RDW | − | −0.012 | gm |
HORVU.MOREX.r3.3HG0249600.1 | chr3H:141,885,554:G: A | Reticulon-like protein | 3 H | RDW | − | −0.006 | gm |
HORVU.MOREX.r3.4HG0406060.1 | chr4H:572,733,912:G: T | Agmatine coumaroyltransferase-2 | 4 H | G%6d | − | −13.08 | % |
HORVU.MOREX.r3.4HG0415570.1 | chr4H:602,417,124:G: A | Cortical cell-delineating protein | 4 H | RDW | − | −0.001 | gm |
HORVU.MOREX.r3.5HG0495430.1 | chr5H:490,757,115:G: A | Beta-glucosidase | 5 H | SL | − | −1.33 | cm |
HORVU.MOREX.r3.5HG0487790.1 | chr5H:467,410,034:C: T | Cyclin family protein | 5 H | RL | − | −1.1 | cm |
HORVU.MOREX.r3.5HG0432280.1 | chr5H:36,660,118:A: G | Kinase interacting (KIP1-like) family protein | 5 H | G%2d | − | −2.52 | % |
HORVU.MOREX.r3.5HG0505720.1 | chr5H:516,564,134:T: C | Receptor-like protein kinase | 5 H | G%2d | − | −7.02 | % |
HORVU.MOREX.r3.5HG0533710.1 | chr5H:578,375,767:G: C | Dehydrogenase/reductase | 5 H | RDW | − | −0.005 | gm |
HORVU.MOREX.r3.6HG0633710.1 | chr6H:560,514,671:C: G | LysM receptor-like kinase | 6 H | G%10d | − | −11.99 | % |
HORVU.MOREX.r3.6HG0541280.1 | chr6H:7,962,039:G: A | Mitochondrial transcription termination factor-like | 6 H | G%2d | − | −2.73 | % |
HORVU.MOREX.r3.6HG0610180.1 | chr6H:480,310,319:G: C | DUF506 family protein | 6 H | G%6d | − | −14.16 | % |
HORVU.MOREX.r3.7HG0744530.1 | chr7H:613,938,048:G: A | disease resistance protein (TIR-NBS-LRR class) | 7 H | RDW | − | −0.005 | gm |
HORVU.MOREX.r3.7HG0748160.1 | chr7H:620,907,100:C: T | receptor kinase 1 | 7 H | G%6d | − | −4.39 | % |
HORVU.MOREX.r3.7HG0641760.1 | chr7H:13,838,812:T: A | K + uptake permease 9 | 7 H | RDW | − | −0.001 | gm |
