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. 2020 Apr 20;21:315. doi: 10.1186/s12864-020-6717-7

Table 5.

List of potential candidate genes and anchoring markers associated with physiological traits

SNP SNP Dataset -log10(p) Effect PVE Alleles Gene-ID Annotation
S1B_4335636 SPAD BLUEA 3.46 1.19 0.17 G/A TraesCS1B01G007900 E3 ubiquitin-protein ligase ORTHRUS 2
BLUEC 3.01 1.20 0.14
S1D_907114 SPAD BLUEA 3.65 1.74 0.18 G/C TraesCS1D01G003300 SNF1-related protein kinase regulatory subunit beta-2
BLUEQ 3.13 2.33 0.14
S1D_907133 SPAD BLUEA 3.65 1.74 0.18 G/C TraesCS1D01G003300 SNF1-related protein kinase regulatory subunit beta-2
BLUEQ 3.13 2.33 0.14
S2D_574118879 SPAD BLUEA 3.98 2.78 0.19 A/G TraesCS2D01G469000 GDSL-like Lipase/Acylhydrolase superfamily protein
BLUEQ 3.09 3.53 0.14
S2D_11171031 SPAD BLUEC 3.48 1.42 0.15 T/C TraesCS2D01G026300 Glutamyl-tRNA (Gln) amidotransferase subunit A
BLUEA 3.07 1.21 0.17
S4A_625244392 SPAD BLUEA 3.35 1.63 0.17 C/T TraesCS4A01G346600 F-box protein
BLUEC 3.22 1.75 0.14
S5D_220760001 SPAD BLUEC 3.34 1.64 0.14 G/A TraesCS5D01G138700 disease resistance protein (TIR-NBS-LRR class) family
BLUEA 3.18 1.46 0.17
S6D_16178496 SPAD BLUEA 3.59 −1.66 0.19 C/T TraesCS6D01G038900 2-oxoglutarate (2OG) and Fe (II)-dependent oxygenase superfamily protein
BLUEC 3.55 −1.81 0.16
S6D_16178499 SPAD BLUEA 3.59 −1.66 0.19 A/T TraesCS6D01G038900 2-oxoglutarate (2OG) and Fe (II)-dependent oxygenase superfamily protein
BLUEC 3.55 −1.81 0.16
S6D_16178505 SPAD BLUEA 3.59 −1.66 0.19 A/C TraesCS6D01G038900 2-oxoglutarate (2OG) and Fe (II)-dependent oxygenase superfamily protein
BLUEC 3.55 −1.81 0.16
S6B_462165779 SPAD BLUEA 4.15 1.34 0.18 C/G TraesCS6B01G257900 Adenosine kinase-like protein
BLUEC 3.19 1.27 0.14
S7A_565347529 SPAD BLUEA 4.54 1.38 0.19 T/G TraesCS7A01G389100 TBC1 domain family member
BLUEQ 4.38 1.98 0.15
S7A_579648980 SPAD BLUEQ 3.63 −1.78 0.15 C/G TraesCS7A01G399700 Telomere repeat-binding factor like-protein
BLUEA 3.48 −1.19 0.17
S1D_262475151 MT BLUEC 3.53 4.15 0.07 T/C TraesCS1D01G190700 Heavy metal transport/detoxification superfamily protein
BLUEA 3.52 4.14 0.10
S3D_590224603 MT BLUEA 4.89 4.60 0.12 T/C TraesCS3D01G501200 Protein kinase
BLUEC 4.80 4.57 0.09
BLUEQ 3.20 4.98 0.12
S3D_590224620 MT BLUEC 3.61 4.21 0.06 G/A TraesCS3D01G501200 Protein kinase
BLUEA 3.12 3.87 0.09
S5B_487440465 MT BLUEQ 3.36 4.36 0.11 A/C TraesCS5B01G302900 Plant/T31B5–30 protein
BLUEA 3.23 3.11 0.09
S5B_509105168 MT BLUEQ 4.25 −6.33 0.14 A/G TraesCS5B01G325000 F-box family protein
BLUEA 3.78 −4.32 0.11
S5B_509105191 MT BLUEQ 4.25 6.33 0.14 T/C TraesCS5B01G325000 F-box family protein
BLUEA 3.78 4.32 0.11
S6B_42215716 MT BLUEC 3.46 6.04 0.07 A/G TraesCS6B01G063500 Peroxidase
BLUEA 3.08 5.64 0.09
S2B_693094464 CT BLUEC 3.83 −0.24 0.10 G/A TraesCS2B01G496300 BTB/POZ and MATH domain-containing protein 2
BLUEA 3.10 −0.16 0.08
S2B_693094466 CT BLUEC 3.83 −0.24 0.10 G/A TraesCS2B01G496300 BTB/POZ and MATH domain-containing protein 2
BLUEA 3.10 −0.16 0.08
S5B_610295429 CT BLUEA 4.41 0.29 0.12 T/G TraesCS5B01G436700 Lipid transfer protein
BLUEQ 4.27 0.34 0.11
S5B_608350950 CT BLUEQ 4.85 −0.34 0.12 C/T TraesCS5B01G433700 Maintenance of telomere capping protein 2
BLUEA 3.19 −0.23 0.09
S5B_621237427 CT BLUEQ 4.37 −0.34 0.11 C/T TraesCS5B01G448700 Mitochondrial transcription termination factor-like
BLUEA 3.22 −0.24 0.10
S5B_606014586 CT BLUEQ 3.37 0.30 0.10 T/C TraesCS5B01G431300 Peptidase M50 family protein
BLUEA 3.03 0.23 0.10
S5B_602833771 CT BLUEA 3.70 −0.24 0.11 C/T TraesCS5B01G426900 DNA topoisomerase
BLUEQ 3.64 −0.28 0.10
S5B_617291841 CT BLUEA 4.79 −0.30 0.13 A/G TraesCS5B01G445300 Endo-1,4-beta-xylanase
BLUEQ 3.51 −0.30 0.10
S5B_643470598 CT BLUEA 3.16 0.18 0.10 G/A TraesCS5B01G470200 Protein phosphatase 2C
BLUEQ 3.07 0.22 0.08
S5B_601343966 CT BLUEA 3.17 −0.24 0.11 C/T TraesCS5B01G425500 Zinc finger CCCH domain-containing protein 16
BLUEQ 3.14 −0.29 0.10
S2B_717098540 NDVIa BLUEC 8.41 −0.02 0.22 C/T TraesCS2B01G522200 SAUR-like auxin-responsive protein family
BLUEA 4.17 −0.01 0.18
S1B_677572998 NDVIg BLUEA 3.48 0.02 0.12 C/G TraesCS1B01G467900 Methyltransferase
BLUEQ 3.32 0.03 0.07
S2D_570960728 NDVIg BLUEQ 3.79 −0.03 0.07 A/C TraesCS2D01G464800 Multidrug resistance protein ABC transporter family protein
BLUEA 3.13 −0.02 0.13
S3A_737114441 NDVIg BLUEQ 3.49 0.02 0.07 T/C TraesCS3A01G519100 rRNA N-glycosidase
BLUEA 3.41 0.02 0.14
S3B_785311773 NDVIg BLUEQ 3.34 0.01 0.07 A/G TraesCS3B01G550500 Myb/SANT-like DNA-binding domain protein
BLUEA 3.01 0.01 0.13
S5B_583295527 NDVIg BLUEC 6.60 0.02 0.12 A/G TraesCS5B01G407600 Myb family transcription factor-like protein
BLUEA 5.00 0.02 0.16
S7B_426882778 NDVIg BLUEQ 3.28 0.03 0.08 A/G TraesCS7B01G226400 RING finger protein 13
BLUEA 3.01 0.02 0.14
S3B_785311769 NDVIa BLUEC 6.02 0.00 0.22 A/G TraesCS3B01G550500 Myb/SANT-like DNA-binding domain protein
NDVIg BLUEQ 3.34 0.01 0.07
NDVIg BLUEA 3.01 0.01 0.13
S7B_701649275 NDVIa BLUEA 5.82 0.00 0.20 C/T TraesCS7B01G434600 FBD-associated F-box protein
NDVIg BLUEA 3.78 0.01 0.15
S3A_699988530 NDVIg BLUEQ 4.46 −0.04 0.12 A/G TraesCS3A01G466000 F-box family protein
BLUEA 3.48 −0.03 0.16
S7D_635578722 NDVIg BLUEC 4.17 0.02 0.11 T/C TraesCS7D01G552700 NBS-LRR disease resistance protein
NDVIa BLUEA 3.49 0.01 0.18
SPAD BLUEQ 3.41 −3.40 0.15
NDVIa BLUEQ 3.34 0.02 0.09
NDVIg BLUEA 3.15 0.03 0.15

SPAD, soil-plant analyses development; MT, cell membrane thermostability; CT, canopy temperature (°C); NDVIa, normalized difference vegetation index at GS65; NDVIg, normalized difference vegetation index at grain filling. BLUEC, BLUEs values derived across Citra; BLUEQ, BLUEs values derived across Quincy, and BLUEA: BLUEs values derived across all environment; PVE, phenotypic variance explained