Skip to main content

Table 2 SNPs significantly associated with the four traits, genes of interest and previously reported QTLs in proximity of the significant SNPs. ‘Locus ID’ consists of the trait abbreviation followed by the name of experiment and an ordinal number per trait and experiment. ‘Candidate region’ consists of the chromosome ID followed by the start position and end position of the candidate region (defined by the LD decay distance around the significant SNP). ‘SNP ID’ consists of the ID of the significant SNP followed by the major allele and the minor allele of the significant SNP. ‘P’ is -log10 of the P-value of the significant SNP. ‘R2’ is Phenotypic variance explained by the significant SNP. ‘Allele effect’ is the difference between median trait value of genotypes carrying the major allele and minor allele. ‘Gene of interest’ refers to the gene of interest as in the reference genome Wm82.a2.v1. 'Arabidopsis' is the homolog gene ID and gene name (in parenthesis) from Arabidopsis thaliana. ‘Annotations’ is the gene transcript of the Arabidopsis homolog or its encoding protein retrieved from [65], and the biological function (in parenthesis). ‘Reference’ contains the literature references to the biological functions stated in 'Annotation'. ‘Known QTL’ contains QTL information retrieved from [66] [63] and [62]. The QTLs names are adapted. The original names of QTLs can be found in Additional file 4

From: Genetic control of tolerance to drought stress in soybean

Locus ID

Candidate region

SNP ID

P

R2

Allele effect

Gene of interest

Arabidopsis

Annotation

Reference

Known QTL

CW_SDS_1

Gm03_7027565_7317565

AX-93988673_G_A

4.3

0.05

-0.3

N/A

N/A

N/A

N/A

N/A

CW_SDS_2

Gm03_16874434_17164434

AX-93991327_G_C

4.1

0.02

0.23

N/A

N/A

N/A

N/A

N/A

CW_SDS_3

Gm03_45259915_45549915

AX-93918502_C_A

4.1

0.07

-0.4

Glyma.03G261500

AT2G46820 (PSI-P)

Photosystem I P subunit (photosynthesis)

[67, 68]

PubC 2, PubC 3

      

Glyma.03G261400

AT4G01410 (N/A)

LEA hydroxyproline-rich glycoprotein (lateral root formation)

N/A

N/A

      

Glyma.03G258300

AT3G61830 (ARF18)

Auxin response factor 18 (regulates cell growth and seed weight)

[69]

N/A

CW_SDS_4

Gm05_28547428_28867428

AX-93921335_C_T

5.2

0.06

0.27

N/A

N/A

N/A

N/A

SCN 1

CW_SDS_5

Gm06_14605039_14955039

AX-93923547_T_C

5.8

0.04

-0.18

N/A

N/A

N/A

N/A

PH 1, PH 2

CW_SDS_6

Gm10_7752764_8022764

AX-94072904_A_G

4.2

0.05

-0.3

N/A

N/A

N/A

N/A

PH 3, PH 4

CW_SDS_7

Gm12_268639_738639

AX-94092624_A_G

9.9

0.08

-0.29

Glyma.12G009100

AT5G09680 (RLF)

Reduced lateral root formation (lateral root formation)

[70]

 

CW_SDS_8

Gm13_30347735_30657735

AX-93643614_G_A

4

0.04

0.29

N/A

N/A

N/A

N/A

WUE 1

CW_SDS_9a

Gm15_50341499_50871499

AX-94142375_T_C

4

0.06

-0.38

Glyma.15G269200

AT2G32840

(N/A)

Proline-rich family protein (cell wall integrity and root elongation under drought)

[71]

Cu 1, Cu 2

CW_SDS_9b

Gm15_50369101_50899101

AX-93945641_A_G

4

0.06

-0.38

CW_LDS_1

Gm02_8486923_8816923

AX-93976757_G_A

4.7

0.09

0.62

Glyma.02G094700

AT4G01470 (TIP1-3)

Tonoplast intrinsic protein 1;3 (transmembrane channels for water and small uncharged solutes)

[72]

N/A

      

Glyma.02G094900

AT3G55330 (PPL1)

PsbP-like protein 1 (reapir of PSII damage)

[73]

N/A

      

Glyma.02G097700

AT1G25480 (N/A)

Aluminium activated malate transporter family protein (stomatal opening)

[74]

N/A

CW_LDS_2

Gm06_50717337_51067337

AX-93628808_T_C

4.7

0.14

0.73

Glyma.06G321900

AT1G55670 (PSAG)

Photosystem I subunit G (satbility of photosystem I complex)

[75, 76]

Seedset 1, Seeds

CW_LDS_3

Gm08_47511280_47831280

AX-93761082_G_T

6.1

0.14

1.04

Glyma.08G365700

AT1G67080 (ABA4)

Abscisic acid (aba)-deficient 4 (stress-induced ABA accumulation)

[77]

WUE 2, WUE 3

CW_LDS_4

Gm20_5309031_5709031

AX-93900908_A_C

4.6

0.14

0.76

Glyma.20G037100

AT5G12330 (LRP1)

Lateral root primordium (LRP) protein-related (root development)

[78]

N/A

CW_LDS_5

Gm20_43251405_43651405

AX-93910009_G_T

7.3

0.04

0.6

Glyma.20G197600

AT2G29460 (GSTU4)

Glutathione S-transferase tau 4 (oxidative stress response)

[79, 80]

N/A

LSEN_SDS_1

Gm03_35362990_35652990

AX-93917720_G_A

5.1

0.15

-0.53

Glyma.03G138000

AT5G19450 (CPK8)

Calcium-dependent protein kinase 19 (ABA-mediated stomatal closure and ROS reduction)

[81]

P, Mg, Zn

LSEN_SDS_2

Gm15_49950789_50480789

AX-94142205_C_T

4.9

0.14

-0.43

Glyma.15G266500

AT1G79580 (SMB)

NAC (No Apical Meristem) domain transcriptional regulator superfamily protein (root cap development)

[82, 83]

Cu 1, Cu 2

LSEN_SDS_3

Gm19_2913123_3603123

AX-93886487_C_T

6.8

<0.01

-0.01

Glyma.19G027700

AT5G39360 (EDL2)

EID1-like 2 (ABA signalling and stress respnse)

[84]

SIFC 1

LSEN_LDS_1

Gm02_36400063_36730063

AX-93981961_T_A

6.6

0.14

0.54

Glyma.02G192700

AT5G04870 (CPK1)

Calcium dependent protein kinase 1 (ROS reduction and proline accumulation)

[85]

N/A

      

Glyma.02G193000

AT5G06410

DNAJ heat shock N-terminal domain-containing protein (maintenance of seed shape and size at high ABA; AtDjA3)

[86]

N/A

LSEN_LDS_2

Gm16_25479906_26001906

AX-93852357_C_A

5.6

0.11

-0.6

N/A

N/A

N/A

N/A

N/A

LSEN_LDS_3

Gm16_29164663_29686663

AX-93853705_G_C

4

<0.01

-0.02

N/A

N/A

N/A

N/A

PodShat 1, PodShat 2, qP16*

LSEN_LDS_4a

Gm16_30272259_30794259

AX-93854127_A_T

4

<0.01

-0.14

Glyma.16G145800

AT3G54890 (LHCA1)

Photosystem I light harvesting complex 1 chlorophyll a/b binding protein (electron transport in photosynthesis)

[87]

eChl_T**

LSEN_LDS_4b

Gm16_30395381_30917381

AX-93650691_A_C

4

0.01

0.08

LSEN_LDS_5a

Gm18_48141658_48501658

AX-94178903_C_G

4

0.02

-0.24

Glyma.18G202900, Glyma.18G203500

AT1G09950 (RAS1), AT3G51810 (EM1)

RESPONSE TO ABA AND SALT 1 (Salt and ABA sensitivity), Em-like protein GEA1 (stress induced ABA response through ABI5, ROS reduction)

[88,89,90]

SCN 2, Oil

LSEN_LDS_5b

Gm18_48144745_48504745

AX-94178905_G_A

4

0.02

-0.24

LSEN_LDS_5c

Gm18_48157192_48517192

AX-93655968_A_C

4

0.02

-0.24

LSEN_LDS_5d

Gm18_48205607_48565607

AX-93655972_C_T

4.1

0.02

-0.21

LSEN_LDS_5e

Gm18_48257716_48617716

AX-93881368_A_C

4.1

0.02

-0.21

LSEN_LDS_5f

Gm18_48277688_48637688

AX-93952219_T_C

4.7

0.02

-0.24

LSEN_LDS_5g

Gm18_48322720_48682720

AX-93881396_G_T

4.1

0.02

-0.21

LSEN_LDS_6

Gm19_44805252_45495252

AX-94195039_A_G

7.2

0.12

-0.49

Glyma.19G191700

AT5G03720 (HSFA3)

Heat shock transcription factor A3 (thermotolerance and drought tolerance in combination with DREB2A)

[91, 92]

AMIN, Seedset 2, PH 5, Pods, LeafArea, LeafWidth, StemEnd, Internod, interbrach 1, DTM, DFTM, Lod, Nod, TotalSeed

AGRmax-Yr_SDS_1

Gm05_31841551_32161551

AX-93720346_T_C

7.7

0.1

0.06

Glyma.05G128000

AT1G29930 (LHCB1.3)

Light harvesting chlorophyll a/b binding protein 1 (stomatal movement, drought response)

[93]

N/A

AGRmax-Yr_SDS_2

Gm06_19076651_19426651

AX-93730252_G_T

5.4

0.09

0.05

Glyma.06G204100

AT3G29575 (AFP3)

ABI5 binding protein 3 (negative regulator of ABA signalling)

[94]

WUE 4, WUE 5, interbrach 2, DTF

      

Glyma.06G204400

AT1G74160

LONGIFOLIA protein (cellulose deposition)

[95, 96]

N/A

AGRmax-Yr_SDS_3

Gm17_39250897_39530897

AX-93866910_A_C

7.1

<0.01

0.01

     

AGRmax-Yr_SDS_4

Gm18_54299774_54659774

AX-93883955_T_A

4.6

0.09

-0.04

Glyma.18G259700

AT5G15250 (FTSH6)

FtsH protease 6 (thylakoid membrane biogenesis, PSII repair mechanism)

[97]

SCN 3, Fe

CH-Yr_LDS_1

Gm06_18615861_18965861

AX-93730063_A_G

6.7

0.06

-0.03

Glyma.06G202200

AT1G74310 (HSP101)

Heat shock protein 101 (tolerance to heat sterss)

[98]

PubC 1, PubC 4

CH-Yr_LDS_2

Gm08_15065114_15385114

AX-93754190_C_T

5.1

0.16

0.06

Glyma.08G191300

AT4G33050 (EDA39)

Calmodulin-binding family protein (stomatal opening)

[99]

PUE, SIFC 2

CH-Yr_LDS_3

Gm09_7236144_7576144

AX-94060112_T_C

4.2

0.16

0.05

Glyma.09G071400

AT1G19150 (LHCA6)

Photosystem I light harvesting chlorophyll a/b binding protein 6 (photosynthesis)

[100]

WUE 6

CH-Yr_LDS_4

Gm16_32550790_33072790

AX-93855040_G_A

5.7

0.16

0.06

N/A

N/A

N/A

N/A

BSR

  1. * QTL information from [63]
  2. ** QTL information from [62]