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Table 5 Trait-marker associations and candidate genes reaching genome-wide or putative significance under optimal models

From: Biomass traits and candidate genes for bioenergy revealed through association genetics in coppiced European Populus nigra (L.)

Trait

SNP

Chromosome

Position (bp)

p value

Candidate gene

Additional information

EB-11

SNP_IGA_6_17929363

6

17,822,770

9.55E−05

POPTR_0006s18990

CNGC17; ATCNGC17; calmodulin binding/cyclic nucleotide binding/ion channel

Height-11

SNP_IGA_7_12319871

7

12,250,804

6.46E−06

POPTR_0007s11900

Unknown protein a

Height-11

SNP_IGA_6_18338146

6

18,228,999

1.30E−05

POPTR_0006s19240

GAE1; UDP-glucuronate 4-epimerase/catalytic+

Height-11

SNP_IGA_15_11900175

15

11,834,554

1.44E−04

POPTR_0015s11190

Unknown protein

EB-12

SNP_IGA_6_8443540

6

8,388,882

9.47E−05

POPTR_0006s11060

ATH9 (thioredoxin H-type 9)

EB-12

SNP_IGA_7_993475

7

987,055

1.54E−04

POPTR_0007s01700

GLX2-4 (glyoxalase 2-4); hydrolase/hydroxyacylglutathione hydrolase/zinc ion binding

Height-12

SNP_IGA_7_12319871

7

12,250,804

4.70E−05

POPTR_0007s11900

Unknown protein#

Height-13

PnCOL2_703

4

9,357,150

3.16E−06

POPTR_0004s10800

COL2 (constans-like 2); transcription factor/zinc ion binding a

SC-13

SNP_IGA_1_44937224

1

44,670,745

1.05E−04

POPTR_0001s44200

ATK3 (ARABIDOPSIS THALIANA KINESIN 3); ATPase/microtubule binding/microtubule motor

SC-13

SNP_IGA_6_7875360

6

7,824,407

1.55E−04

POPTR_0006s10480

FER1; ATFER1; ferric iron binding/iron ion binding

LA-13

SNP_IGA_13_111400

13

110,728

7.83E−05

POPTR_0013s00340

RCI2A (RARE-COLD-INDUCIBLE 2A)#

LA-13

SNP_IGA_8_2418643

8

2,403,351

8.24E−05

POPTR_0008s04290

Unknown protein

SLA-13

SNP_IGA_14_3311885

14

3,293,256

8.14E−05

POPTR_0014s04150/POPTR_0014s04160

Unknown protein/PEX11A (PEROXIN 11A)

SLA-13

SNP_IGA_19_2255781

19

2,244,885

1.53E−04

POPTR_0019s02450

SWIM zinc finger protein-related

SLA-13

SNP_IGA_6_23541394

6

23,399,832

1.73E−04

POPTR_0006s24880

PP2C; protein phosphatase 2C family protein

CA-13

SNP_IGA_6_3818713

6

3,794,879

7.31E−05

POPTR_0006s05370

Unknown protein

CA-13

PnCOL2_69

4

9,356,516

1.14E−04

POPTR_0004s10800

COL2 (constans-like 2); transcription factor/zinc ion binding#

CA-13

SNP_IGA_1_29550802

1

29,371,580

1.20E−04

POPTR_0001s30950

RD21 (responsive to dehydration 21); cysteine-type endopeptidase/cysteine-type peptidase

CA-13

LG_X_35_SNP_325

10

14,394,839

1.51E−04

POPTR_0010s14950

BAS1 (PHYB ACTIVATION TAGGED SUPPRESSOR 1); oxygen binding/steroid hydroxylase

CA-13

LG_X_35_SNP_490

10

14,395,004

1.51E−04

POPTR_0010s14950

As above

CNPL-13

SNP_IGA_13_111400

13

110,728

6.81E−06

POPTR_0013s00340

RCI2A (RARE-COLD-INDUCIBLE 2A) a

CNPL-13

SNP_IGA_6_12938719

6

12,856,743

8.11E−05

POPTR_0006s15470

Bacterial transferase hexapeptide repeat-containing protein

CNPL-13

SNP_IGA_8_2308644

8

2,294,048

1.07E−04

POPTR_0008s04110

AGL62 (Agamous-like 62); DNA binding/transcription factor

CNPL-13

SNP_IGA_6_23601531

6

23,459,494

1.32E−04

POPTR_0006s24980

Unknown protein

CNPL-13

SNP_IGA_10_18449865

10

18,340,999

1.37E−04

POPTR_0010s20920

Immunophilin, putative/FKBP-type peptidyl-prolyl cis–trans isomerase, putative

CNPL-13

SNP_IGA_7_14212007

7

14,130,925

1.72E−04

POPTR_0007s14310

AGL22 (Agamous-like 22); SVP; transcription factor/translation repressor, nucleic acid binding

SD-13

SNP_IGA_6_11135816

6

11,064,511

1.67E−04

POPTR_0006s13890

TES (TETRASPORE); microtubule motor

SI-13

SNP_IGA_6_8990445

6

8,932,413

1.24E−04

POPTR_0006s11720

DML1 (DEMETER-LIKE 1); DNA N-glycosylase/DNA-(apurinic or apyrimidinic site) lyase/protein binding

SP-12

SNP_IGA_1_31674244

1

31,482,266

1.60E−04

POPTR_0001s33290

Zinc finger (DHHC type) family protein

  1. Under optimal models there are 29 SNPs (representing 25 candidate genes) reaching at least the putative significance level (α < 1.76 × 10−4) of which 4 are significant at p < 0.1 (indicated by a +) and three are significant at p < 0.05 (in italic typeface and indicated by a). Genes putatively associated with one trait whilst significantly associated with another at p < 0.05 are indicated by a #