Skip to main content

Table 3 Crucial stage-specific candidate genes identified by GWAS, WGCNA, and differential expression analysis

From: Genome-wide association study and transcriptome analysis reveal key genes affecting root growth dynamics in rapeseed

Gene ID Cluster Distance to peak SNP (Kb) Type4_10DAT Type4_3EL Type4_5EL Type4_7EL Type5_10DAT Type5_3EL Type5_5EL Type5_7EL Gene_symbol Description
Darkorange
 BnaA05g22690Dc S9 409.40 12.06 2.92 3.27 1.33 1.61 0.88 7.62 0.16
 BnaA08g24120Dc #13 238.10 9.35 4.23 2.85 4.51 1.44 2.90 5.88 6.59 FUT6 Fucosyltransferase 6
White
 BnaA03g43140Db #3 106.11 1.28 1.19 3.24 1.16 0.37 0.03 0.07 0.00 FCAALL.41 Putative glycerol-3-phosphate transporter 4
 BnaA03g47900Db S3 34.26 0.00 0.35 2.79 0.85 0.66 0.41 0.00 0.27
 BnaA09g07790Db S10 107.12 0.66 0.70 2.66 0.99 0.65 0.39 0.27 0.18 DAR3 Protein DA1-related 3
 BnaC08g33940Db #20 118.76 1.64 3.88 12.71 4.35 2.83 0.56 1.69 0.27 REIL2 Cytoplasmic 60S subunit biogenesis factor REI1 homolog 2
Red
 BnaA03g42930Da #3 32.11 2.07 4.87 1.50 2.05 13.84 1.41 0.31 1.28
 BnaA09g07840Da S10 89.43 2.24 3.90 1.15 3.02 12.80 5.08 1.66 1.95 PSBO1 Oxygen-evolving enhancer protein 1–1
 BnaC01g22700Da S19 0.06 3.35 4.12 4.70 5.38 22.74 7.92 4.62 4.68 FD3 Ferredoxin-3
 BnaA03g54270Db #5 252.24 0.39 0.44 0.46 0.41 4.20 1.38 0.63 0.75
 BnaA05g05400Db S6 114.77 22.97 21.13 26.99 30.04 58.49 33.78 26.45 37.25 PRA1B2 PRA1 family protein B2
 BnaA08g24190Db #13 274.89 1.63 2.80 1.19 1.59 10.52 4.34 1.44 1.20
 BnaC02g14450Db #15 92.11 2.23 0.00 0.86 1.19 85.14 0.04 0.55 1.62 AGP22 Arabinogalactan peptide 22
 BnaC03g26110Db S22 59.91 20.84 8.96 13.42 18.16 44.32 19.22 17.27 12.82 F4P13.7 Universal stress protein A-like protein
 BnaA06g37280Dc #11 28.60 5.36 5.99 5.64 4.03 16.82 5.83 4.99 4.92 BPC5 Protein basic pentacysteine5
 BnaA07g02950Dc #12 253.94 1.35 0.72 2.20 4.45 6.65 1.41 2.66 4.18 TIM14-3 Mitochondrial import inner membrane translocase subunit
 BnaA09g07580Dc S10 183.41 2.15 5.44 3.24 3.15 18.16 11.78 2.75 2.20 RALFL34 Protein RALF-like 34
 BnaC02g14330Dc #15 26.80 2.86 31.35 35.15 7.11 102.64 35.21 21.90 7.83
Lightyellow
 BnaA10g23820Db S17 133.94 3.46 7.57 6.16 7.00 7.91 27.73 15.74 10.48 IPK2a Inositol polyphosphate multikinase alpha
  1. aCandidate gene overlapped by WGCNA, GWAS and DEGs
  2. bCandidate gene overlapped by WGCNA and GWAS
  3. cCandidate gene overlapped by GWAS and DEGs