Table 2 Candidate genes identified as relevant for adaptation to metalliferous soil in Arabidopsis halleri.

From: Transmembrane transport and stress response genes play an important role in adaptation of Arabidopsis halleri to metalliferous soils

Environmental variable

Gene†

Gene length [bp]

Number of SNPs in gene

Number of associated SNPs

Gene name

Enriched gene pathway

Tajima’s D‡

M_PL22

M_PL27

NM_PL14

NM_PL35

Site-type

AT1G18880

2351

35

2

Nitrate transporter 1.9/NFP2.9

SLC-mediated transmembrane transport

3.13

1.54

2.47

0.91

AT1G47840

2800

78

2

Hexokinase 3

SLC-mediated transmembrane transport

0.89

0.46

1.61

3.14

AT3G15380

3484

80

1

Choline transporter-like 1

SLC-mediated transmembrane transport

1.04

1.80

0.90

2.79

AT3G23550

2385

61

2

Detoxification 18

SLC-mediated transmembrane transport

2.06

1.56

1.56

0.73

AT3G58810

1140

5

4

Metal tolerance protein A2

SLC-mediated transmembrane transport

0.69

−1.08

1.53

0.10

AT4G32510

3254

60

3

HCO3- transporter family

SLC-mediated transmembrane transport

2.39

2.15

0.69

3.03

AT5G52050

1392

35

1

Detoxification efflux carrier 50

SLC-mediated transmembrane transport

1.27

0.66

1.07

2.10

Soil (Cd, K, Mg, Pb, Zn)

AT1G19640

2723

36

1, 1, 1, 1, 1

Jasmonic acid carboxyl methyltransferase

alpha-Linolenic acid metabolism

1.28

−0.49

1.57

0.27

AT2G35690

3158

33

1, 1, 1, 1, 1

Acyl-CoA oxidase 5

alpha-Linolenic acid metabolism

1.03

1.61

1.83

3.12

AT3G57140

2547

29

12, 9, 11, 12, 12

Sugar-dependent 1-like

alpha-Linolenic acid metabolism

2.16

0.36

2.34

0.30

AT4G29010

5898

55

3, 3, 3, 3, 1

Enoyl-CoA hydratase/isomerase family

alpha-Linolenic acid metabolism

1.63

0.47

1.96

1.81

AT5G04040

2649

22

2, 2, 1, 2, 2

Sugar-dependent 1

alpha-Linolenic acid metabolism

1.81

1.13

1.81

2.68

AT5G65110

2654

33

3, 3, 3, 3, 3

Acyl-CoA oxidase 2

alpha-Linolenic acid metabolism

2.01

1.83

1.87

1.58

AT1G21690

2618

100

1, 1, 1, 1, 1

Replication factor C 4

Translesion Synthesis by POLH

−0.97

−0.92

−0.01

1.83

AT2G29070

1686

48

2, 3, 1, 2, 3

Ubiquitin fusion degradation UFD1 family protein

Translesion Synthesis by POLH

1.80

0.83

2.62

1.73

AT3G02920

2293

20

8, 9, 8, 8, 7

Replication protein A, subunit RPA32

Translesion Synthesis by POLH

2.68

2.39

1.42

3.13

AT3G53230

3358

45

2, 2, 2, 2, 1

ATPase, AAA-type, CDC48B protein

Translesion Synthesis by POLH

3.01

0.70

2.89

2.68

AT5G03340

3319

30

1, 1, 1, 1, 1

ATPase, AAA-type, CDC48C protein

Translesion Synthesis by POLH

0.79

1.12

0.91

1.45

AT5G27740

3162

114

3, 5, 3, 5, 5

Replication factor C 3

Translesion Synthesis by POLH

1.21

1.89

2.16

3.67

  1. †Candidate genes with a negative Tajima’s D in at least one metallicolous population are marked in bold.
  2. ‡Negative Tajima’s D values are marked in bold.
  3. All these genes contain SNPs that are associated with Site-type (metalliferous [M] vs non-metalliferous [NM]) or one of the five soil-specific variables and are members of an enriched gene pathway.
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