Table 2 Distribution of SNPs, minor allele frequency (MAF), heterozygosity, polymorphic information content (PIC) and linkage disequilibrium (LD) on each chromosome in the A and C genomes of 117 accessions of Brassica napus.

From: Identification of resistance loci against new pathotypes of Plasmodiophora brassicae in Brassica napus based on genome-wide association mapping

Genome and Chromosome

Start

End

Total no. seq

SNP

SNP / Kb

MAF

Hetero-zygosity

PIC

Average LD

A genome

A01

2024

23,251,220

23,250

13,062

1.78

0.14

0.08

0.24

0.090

A02

919

24,785,167

24,784

12,455

1.99

0.13

0.08

0.23

0.080

A03

808

29,746,073

29,745

20,541

1.45

0.14

0.07

0.24

0.060

A04

1717

19,141,470

19,140

10,562

1.81

0.14

0.07

0.24

0.090

A05

2697

23,052,978

23,050

14,917

1.55

0.14

0.06

0.24

0.076

A06

2120

24,372,251

24,370

14,696

1.66

0.13

0.06

0.22

0.075

A07

10,938

24,000,655

23,990

14,232

1.69

0.15

0.07

0.24

0.070

A08

1729

18,958,296

18,957

10,281

1.84

0.13

0.07

0.22

0.084

A09

1327

33,857,792

33,857

18,702

1.81

0.12

0.07

0.21

0.010

A10

4083

17,366,872

17,363

12,131

1.43

0.14

0.07

0.23

0.080

Mean

  

23,851

14,158

1.70

0.14

0.07

0.23

0.072

C genome

C01

8039

38,812,658

38,805

17,087

2.27

0.16

0.08

0.27

0.190

C02

1607

46,186,975

46,185

17,662

2.61

0.14

0.09

0.24

0.146

C03

760

60,565,276

60,565

25,136

2.41

0.15

0.09

0.24

0.073

C04

1773

48,929,072

48,927

19,053

2.57

0.14

0.08

0.24

0.140

C05

3386

43,172,068

43,169

16,540

2.61

0.13

0.10

0.22

0.074

C06

1745

37,224,854

37,223

14,761

2.52

0.14

0.09

0.23

0.079

C07

7046

44,766,293

44,760

15,558

2.88

0.13

0.09

0.22

0.083

C08

6385

38,472,912

38,467

16,082

2.39

0.14

0.09

0.23

0.105

C09

1884

48,501,448

48,500

18,295

2.65

0.12

0.09

0.21

0.075

Mean

  

45,178

17,797

2.55

0.14

0.09

0.23

0.107

Overall mean

  

34,514

15,978

2.12

0.14

0.08

0.23

0.088

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