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Table 2 Overview of results from candidate gene (CG)-association approach using SNPs from GBS or re-sequencing (RS)

From: Genome-wide association mapping in a diverse spring barley collection reveals the presence of QTL hotspots and candidate genes for root and shoot architecture traits at seedling stage

GBS CGs Annotation in BARLEX Alternative names Approach CG status after testing highest –log(p of CG) Corresponding QTL region
HORVU1Hr1G057860 cytokinin oxidase/dehydrogenase 1 AtCKX1 GBS potential 2.3 QTL-1H-3
HORVU1Hr1G080950 Glycogen synthase HvSSIV GBS potential 2.05 QTL-1H-7
HORVU1Hr1G082250 alcohol dehydrogenase 1 Adh2 GBS supported 2.21 QTL-1H-7
HORVU1Hr1G094980 Early flowering 3 HvELF3 GBS potential 3.26 QTL-1H-9
HORVU2Hr1G013400 pseudo-response regulator 7 HvPpd-H1 RS supported 5.34 QTL-2H-3
HORVU2Hr1G036320 WRKY family transcription factor family protein HvSUSIBA2 GBS potential 2.03 QTL-2H-6
HORVU2Hr1G080630 14–3-3-like protein GF14-B HvGID2 GBS potential 3.55 QTL-2H-6
HORVU2Hr1G075240 Thioredoxin superfamily protein TRX-m3 RS supported 5.65 QTL-2H-6
HORVU2Hr1G075240 Thioredoxin superfamily protein TRX-m3 GBS potential 2.73 QTL-2H-6
HORVU2Hr1G085910 Zinc finger protein CONSTANS-LIKE 4 HvCO4 GBS supported 4.21 QTL-2H-7
HORVU2Hr1G097490 expansin B4 HvEXPB1 RS supported 2.63 QTL-2H-10
HORVU2Hr1G097380 pectinesterase 11 PME5 GBS supported 3.71 QTL-2H-10
HORVU2Hr1G103780 protein kinase family protein HERK2 GBS supported 2.73 QTL-2H-11
HORVU3Hr1G075920 Cytokinin dehydrogenase 5 HvCKX5 RS potential 2.27 QTL-3H-4
HORVU3Hr1G085050 WUSCHEL-related homeobox 9 WOX5 RS supported 3.02 QTL-3H-5
HORVU3Hr1G089980 gibberellin 20 oxidase 2 HvGA20ox3 GBS potential 2.51 QTL-3H-6
HORVU3Hr1G094000 Auxin efflux carrier family protein PIN5 RS supported 3.21 QTL-3H-7
HORVU4Hr1G057550 pseudo-response regulator 7 HvPRR73 GBS supported 6.16 QTL-4H-4
HORVU5Hr1G095530 phytochrome C HvPhyC GBS potential 2.15 QTL-5H-2
HORVU6Hr1G058740 cryptochrome 2 HvCry2 GBS supported 2.44 QTL-6H-2
HORVU6Hr1G076110 Auxin efflux carrier family protein| PIN7 GBS supported 5.92 QTL-6H-3
HORVU7Hr1G074690 glyceraldehyde-3-phosphate dehydrogenase C2 GAPC3 GBS potential 2.16 QTL-7H-6
HORVU7Hr1G120030 Delta(24)-sterol reductase HvDIM GBS supported 2.98 QTL-7H-10
HORVU7Hr1G033820 auxin response factor 19 HvARF04 RS supported 3.58 no QTL between QTL-7H-4 and QTL-7H-5
HORVU4Hr1G002880 SEC7-like guanine nucleotide exchange family protein GNOM RS potential 2.02 no QTL, between QTL-4H-1 and QTL-4H-2
HORVU1Hr1G039150 CCT motif family protein HvCMF10 GBS rejected < 2 QTL-1H-3
HORVU1Hr1G093770 Lysine-specific demethylase 5B HvPKDM7–1 GBS rejected < 2 QTL-1H-9
HORVU2Hr1G072750 Protein TERMINAL FLOWER 1 HvCEN RS rejected < 2 QTL-2H-6
HORVU2Hr1G113880 AP2-like ethylene-responsive transcription factor Zeo1/AP2 GBS rejected < 2 QTL-2H-11
HORVU3Hr1G072810 gibberellin 2-oxidase HvGA2ox1 GBS rejected < 2 QTL-3H-3
HORVU3Hr1G090980 gibberellin 20-oxidase 3 sdw1 / denso GBS rejected < 2 QTL-3H-7
HORVU3Hr1G106880 Ankyrin repeat family protein / BTB/POZ domain-containing protein Uniculme4 GBS rejected < 2 QTL-3H-10
HORVU5Hr1G050510 kinesin 4 HvBC12/GGD1 GBS rejected < 2 QTL-5H-2
HORVU5Hr1G026780 Auxin-binding protein ABP1 RS rejected < 2 QTL-5H-2
HORVU6Hr1G056000 CONSTANS-like 3 HvCO5 GBS rejected < 2 QTL-6H-2
HORVU6Hr1G057630 Two-component response regulator-like PRR1 HvPRR1 GBS rejected < 2 QTL-6H-2
HORVU7Hr1G099250 Protein VERNALIZATION INSENSITIVE 3 PRC2 RS rejected < 2 QTL-7H-7
HORVU7Hr1G110470 Auxin efflux carrier family protein PIN2 GBS rejected < 2 QTL-7H-9
HORVU7Hr1G110470 Auxin efflux carrier family protein PIN2 RS rejected < 2 QTL-7H-9
HORVU7Hr1G120520 sucrose synthase 6 HvSuSyII GBS rejected < 2 QTL-7H-10
HORVU7Hr1G120960 callose synthase 1 HvGSL5 GBS rejected < 2 QTL-7H-10
  1. If a SNP showed associations with –log(p)-value> 2, the highest association is presented. The column CG status summarizes the result of testing for associations in comparison to GWAS