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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)