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Table 1 Nucleotide and haplotype diversity and tests of neutrality for eight high affinity potassium transporter (HKT) family genes from 95 Indian wild rice accessions and 8 cultivated varieties

From: Association of SNP Haplotypes of HKT Family Genes with Salt Tolerance in Indian Wild Rice Germplasm

Candidate gene (Locus ID)

Region

S

Ï€

θω

H

HD

D

D*

F*

HKT1;1

Coding

8

0.00013

0.00084

10

0.217

−2.10133

−3.97252

−3.94393

(LOC_Os04g51820)

Non-coding

3

0.0001

0.00059

4

0.076

−1.48732

−2.01292

−2.16727

All

11

0.00012

0.00076

13

0.084

−2.22874

−4.21517

−4.17222

HKT1;2

Coding

0

0

0

1

0

0

0

0

Non-coding

20

0.00027

0.00135

12

0.387

−2.30631

−4.55086

−4.42942

Chr4:30548314..30545885

All

20

0.00026

0.00131

12

0.387

−2.30631

−4.55086

−4.42942

HKT1;3

Coding

8

0.00019

0.00108

9

0.25

−1.99519

−2.80081

−2.99198

(LOC_Os02g07830)

Non-coding

6

0.00067

0.00137

4

0.164

−1.14077

0.15513

−0.32717

All

14

0.00037

0.00118

10

0.29

−1.88141

−1.8801

−2.24114

HKT1;4

Coding

2

0.00031

0.00091

3

0.128

−1.01249

−1.0804

−1.23948

(LOC_Os04g51830)

Non-coding

42

0.00059

0.00191

19

0.69

−2.1536

−3.07965

−3.2462

All

44

0.00057

0.00182

20

0.692

−2.15775

−3.12193

−3.27713

HKT1;5

Coding

8

0.00025

0.00183

8

0.166

−2.08122

−3.61227

−3.65909

(LOC_Os01g20160)

Non-coding

37

0.0012

0.00322

18

0.571

−1.94371

−2.70539

−2.87895

All

45

0.00094

0.00284

23

0.631

−2.10258

−3.40294

−3.44926

HKT2;1

Coding

5

0.00015

0.00073

5

0.18

−1.66589

−3.23816

−3.20982

(LOC_Os06g48810)

Non-coding

46

0.00042

0.00241

17

0.333

−2.60346

−4.60994

−4.55342

All

51

0.00035

0.00196

18

0.421

−2.61003

−4.91693

−4.76765

HKT2;3

Coding

24

0.00238

0.00353

23

0.891

−0.96284

−1.72038

−1.71118

(LOC_Os01g34850)

Non-coding

4

0.00013

0.00132

3

0.038

−1.77201

−3.90552

−3.78567

All

28

0.00169

0.00284

23

0.891

−1.22676

−2.67757

−2.5308

HKT2;4

Coding

0

0

0

1

0

0

0

0

(LOC_Os06g48800)

Non-coding

4

0.0012

0.00448

5

0.198

−1.44156

−1.48409

−1.72999

All

4

0.0012

0.00448

5

0.198

−1.44156

−1.48409

−1.72999

  1. (S SNP/Indel sites, π nucleotide diversity, θω nucleotide diversity with Watterson’s estimator, H number of haplotypes, HD haplotype diversity, D Tajima’s D statistic, D* Fu and Li’s D* statistic, F*: Fu and Li’s F* statistic.)