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Table 3 Proposed most likely genes for wax traits by combined GWAS and RNAseq

From: A combination of genome-wide association study and transcriptome analysis in leaf epidermis identifies candidate genes involved in cuticular wax biosynthesis in Brassica napus

SNP Candidate genes in LD interval (number of DEGs) Wax-related DEGs* Log2FCa Arabidopsis orthologs** Gene description
Bn-A01-p6380934 BnaA01g11230D-BnaA01g12160D (6) BnaA01g11780D
BnaA01g11880D
BnaA01g12090D
BnaA01g12130D
3.95
3.64
2.09
−5.46
AT1G14800
AT4G22070
AT4G22270
AT4G22320
Nucleic acid-binding
WRKY31
MEMBRANE RELATED BIGGER1
Golgin family A protein
Bn-A01-p2504370 BnaA01g03740D-BnaA01g36700D (92) BnaA01g03840D N AT4G33030** UDP-Sulfoquinovose Synthase (SQD1)
Bn-A05-p1299570 BnaA05g02080D-BnaA05g36070D (57) BnaA05g02270D 6.12 AT2G41540** NAD-dependent Glycerol-3-Phosphate Dehydrogenase (GPDHc1)
Bn-A05-p2030789 BnaA05g03470D-BnaA05g36470D (47) BnaA05g03540D
BnaA05g03570D
BnaA05g03920D
BnaA05g04000D
−2.47
− 2.19
− 2.59
−3.42
AT2G43770
AT2G43800
AT2G44220
AT2G44450
WD40 repeat-like superfamily protein
FORMIN HOMOLOGY 2
DUF239
BGLU15
Bn-scaff_15798_1-p733219 BnaC04g35190D-BnaC04g36140D (3) BnaC04g35220D
BnaC04g35860D
7.51
−4.97
AT1G13080
AT2G23200
CYP71B2
Protein kinase superfamily protein
Bn-A08-p16793918 BnaA08g17640D-BnaA08g18370D (3) BnaA08g17780D
BnaA08g17990D
BnaA08g18220D
−2.83
2.04
−6.32
AT1G29720
AT1G29330
AT1G28670
Leucine-rich repeat transmembrane protein kinase
ER RETENTION DEFECTIVE 2 (ERD2)
ARAB-1/lipase
Bn-A08-p19244116 BnaA08g22500D- BnaA08g23820D (6) BnaA08g22650D −2.35 AT1G18360** Monoacylglycerol Lipase (MAGL)
Bn-A02-p25285941 BnaA02g32000D-BnaA02g32920D (1) BnaA02g32450D 2.07 AT5G24570 uncharacterized protein
Bn-A05-p19622826 BnaA05g23200D-BnaA05g24000D (2) BnaA05g23670D
BnaA05g23790D
−2.10
−2.60
AT3G15870**
AT3G25110**
Acyl-CoA desaturase-like, FAD5-like Desaturase
Acyl-ACP thioesterase A (FatA)
Bn-scaff_16361_1-p1569363 BnaC08g27100D-BnaC08g29310D (5) BnaC08g27970D
BnaC08g28370D
BnaC08g28510D
−2.09
−6.31
6.77
AT3G57040
AT3G57430
AT1G43760
response regulator 9 (ARR9)
ORGANELLE TRANSCRIPT PROCESSING 84
Unknown
Bn-scaff_18636_1-p11498 BnaA01g13360D-BnaA01g14340D (9) BnaA01g13470D −2.11 AT4G23850** Long-chain acyl-CoA synthetase (LACS4)
Bn-A02-p5516551 BnaA02g05260D-BnaA02g06170D (4) BnaA02g05700D* 4.14 AT5G22500** Alcohol-forming fatty acyl reductase (AlcFAR1)
Bn-A02-p7004091 BnaA02g06800D-BnaA02g34890D (42) BnaA02g15790D
BnaA02g07110D
BnaA02g07120D
BnaA02g27940D
3.02
3.44
3.60
−7.00
AT1G72110**
AT5G59310**
AT5G59310**
AT5G54680
Bifunctional wax ester synthase/DAGAT
Lipid transfer protein type 1 (LTP4)
Lipid transfer protein type 1 (LTP4)
bHLH105
Bn-A05-p4055839 BnaA05g06770D-BnaA05g07650D (3) BnaA05g06830D*
BnaA05g07340D
5.35
−3.75
AT2G37700**
AT2G37090
CER1-like 2
IRX9
Bn-scaff_20270_1-p1172081 BnaA05g30910D-BnaA05g31670D (1) BnaA05g31340D −3.86 AT3G05970** Long-chain acyl-CoA synthetase (LACS6)
Bn-A05-p23445454 BnaA05g31560D-BnaA05g32450D (10) BnaA05g32280D
BnaA05g32300D
BnaA05g32390D
BnaA05g32430D
BnaA05g32400D
BnaA05g32440D
N
N
N
N
−8.36
−9.72
AT3G02990
AT3G03050
AT3G03150
AT3G03200
AT3G03160
AT3G03210
HSFA1E
CSLD3
Unknown
NAC045
Unknown
AXY9
Bn-A07-p6765464 BnaA07g08250D-BnaA07g08960D (7) BnaA07g08340D
BnaA07g08720D
5.12
4.39
AT3G25110**
AT1G27950**
Acyl-ACP thioesterase A (FatA)
Lipid transfer protein type 5 (LTPG1)
Bn-A08-p14906652 BnaA08g13890D-BnaA08g16770D (19) BnaA08g16470D I AT1G47620** Midchain Alkane Hydroxylase (CYP96A8)
Bn-A09-p30763709 BnaA09g40180D-BnaA09g41120D (4) BnaA09g40250D
BnaA09g40500D
N
−4.15
AT5G58470
AT2G26420**
TAF15b
Phosphatidylinositol-Phosphate Kinase type IB
Bn-A09-p32945202 BnaA09g44310D- BnaA09g45200D (1) BnaA09g44740D 4.66 AT1G76690** Oxo-Phytodienoic Acid Reductase
Bn-A10-p4786596 BnaA10g00010D-BnaA10g28040D (50) BnaA10g00380D* −2.18 AT1G01600** Fatty acyl ω-hydroxylase (CYP86A4)
BnaA10g00700D*
BnaA10g02480D*
BnaA10g09300D
BnaA10g25660D*
−2.10
− 2.71
N
4.05
AT1G01120**
AT1G04220**
AT1G08510**
AT5G04530**
Ketoacyl-CoA Synthase (KCS1)
Ketoacyl-CoA Synthase (KCS2/DAISY)
fatty acyl-ACP thioesterases B (FatB)
Ketoacyl-CoA Synthase (KCS19)
Bn-A10-p15096523 BnaA10g21560D-BnaA10g24090D (18) BnaA10g21580D N AT1G50410 CHR28
Bn-A03-p12990610 BnaA03g24640D- BnaA03g25500D (12) BnaA03g24870D
BnaA03g24880D
−4.51
−4.95
AT4G11850**
AT4G11850**
Phospholipase D &gamma
Phospholipase D &gamma
Bn-A03-p18766028 BnaA03g35890D- BnaA03g36690D (2) BnaA03g36540D I AT4G11850** Phospholipase D &gamma
Bn-A06-p600029 BnaA06g00610D- BnaA06g38780D (57) BnaA06g00960D
BnaA06g08550D
BnaA06g08690D
−3.87
4.54
−2.51
AT1G53390**
AT1G13560**
AT1G13640**
ABC Transporter (WBC25/ABCG24)
Diacylglycerol Cholinephosphotransferase (AAPT1)
Phosphatidylinositol-4-Kinase &gamma
Bn-A08-p4273091 BnaA08g04100D- BnaA08g04440D (3) BnaA08g04230D −3.42 AT1G45201** Triacylglycerol lipase (TAGL)
Bn-A07-p1657613 BnaA07g01820D- BnaA07g39090D (31) BnaA07g38540D
BnaA07g36830D*
−3.31
−2.25
AT3G45140**
AT1G24470**
lipoxygenase 2 (LOX2)
Ketoacyl-CoA Reductase (KCR2)
Bn-A04-p14642152 BnaA04g18420D- BnaA04g20360D (3) BnaA04g19180D
BnaA04g19410D*
BnaA04g20360D
−2.76
2.61
4.29
AT2G33150**
AT2G33380**
AT2G34770**
peroxisomal 3-ketoacyl-CoA thiolase (KAT2/FED1)
Caleosin (RD20)
Fatty Acid 2-hydroxylase (FAH1)
Bn-scaff_17369_1-p884077 BnaC01g15540D- BnaC01g18260D (7) BnaC01g17900D −2.23 AT4G25970** phosphatidylserine decarboxylase 3 (PSD3)
Bn-scaff_15918_1-p77704 BnaC02g38670D-BnaC02g39660D (22) BnaC02g39310D
BnaC02g39360D
BnaC02g39080D
BnaC02g38980D
N
N
N
N
AT5G28770
AT5G28650
AT5G49460**
AT5G49300
bZIP63
WRKY74
ATP citrate lyase B subunit (ACLB-2)
GATA16
Bn-scaff_22728_1-p703468 BnaC03g11180D-BnaC03g78270D (16) BnaC03g12050D
BnaC03g72910D
BnaC03g73050D
3.37
−5.35
−2.56
AT5G59320**
AT4G11850**
AT4G11840**
Lipid transfer protein type 1 (LTP3)
Phospholipase D &gamma
Phospholipase D &gamma
Bn-scaff_16888_1-p1834154 BnaC04g00010D-BnaC04g56960D (14) BnaC04g11110D*
BnaC04g24820D
BnaC04g29960D
BnaC04g42410D
BnaC04g45800D
2.15
N
2.57
−4.59
−3.32
AT2G33380**
AT3G56850
AT1G65290**
AT2G31380
AT2G38540**
Caleosin (RD20)
AREB3
Acyl carrier protein (ACP)
salt tolerance homologue
Lipid transfer protein type 1 (LTP1)
Bn-scaff_16485_1-p747170 BnaC06g02420D-BnaC06g43990D (4) BnaC06g14560D
BnaC06g28860D
BnaC06g43050D
BnaC06g43550D
2.21
−2.84
2.21
− 2.20
AT3G53310
AT1G67750
AT1G80080
AT3G25110**
AP2/B3-like TF
Pectate lyase
ATRLP17
Acyl-ACP thioesterase A (FatA)
Bn-scaff_17526_1-p1726345 BnaC09g00720D-BnaC09g02480D (39)
BnaC09g51260D-BnaC09g52120D (2)
BnaC09g01250D
BnaC09g01480D
BnaC09g01910D
BnaC09g01970D
BnaC09g51620D*
N
N
−3.88
−6.39
N
AT3G26935
AT3G27520
AT3G28857
AT3G28920
AT1G57750**
DHHC-type zinc finger family protein
Unknown
bHLH DNA-binding family protein
ZINC FINGER HOMEODOMAIN 9
Midchain alkane hydroxylase (CYP96A15/MAH1)
Bn-scaff_17487_1-p812141 BnaC09g09990D-BnaC09g11020D (19) BnaC09g10340D
BnaC09g10500D
BnaC09g10800D
−3.46
−5.41
N
AT2G20300
AT2G20900**
AT1G62640**
ALE2
diacylglycerol kinase
Ketoacyl-ACP Synthase III (KAS III)
Bn-scaff_20836_1-p125625 BnaC09g15380D-BnaC09g16870D (1) BnaC09g16050D* −2.09 AT1G02205** CER1
  1. a Thresholds for significantly differential expression between high-wax load (HW) and low-wax load (LW) lines were set to false discovery rate (FDR) < 0.001 and fold change ≥4. Positive and negative Log2FC values indicate up and down regulation of gene expression in LW when compared to HW. N indicates not expressed in LW and I indicates not expressed in HW
  2. * indicates the genes annotated in Fatty acid elongation pathway, wax, and cutin and suberin biosynthesis pathway in Fig. 4b, c and d
  3. ** indicates the genes documented in ARALIP plant acyl lipid metabolism website (http://aralip.plantbiology.msu.edu)