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Table 1 Summary statistics for the 251 SNPs analyzed in 12 biomass genes

From: Natural variation in genes potentially involved in plant architecture and adaptation in switchgrass (Panicum virgatum L.)

     

Polymorphism

Nucleotide diversity

Tajima’s test

        

Non Syn

      

Gene

Contig

Chromosome

No. of samples

No. of sites (coding length bp)

Stot

Non Cod

Syn

Con

Non Con

d

πtot × 10-3 (SD × 10-3)

θw × 10-3 (SD ×  10-3)

h

Hd (SD)

D

PHYC

contig03093

Chr09N

353

3224 (2279)

20

7

6

2

5

0.620

1.68 (0.04)

0.87 (0.25)

91

0.963 (0.002)

0.362

TE

contig99597

Chr05K

351

2088 (278)

21

21

0

0

0

1.006

3.43 (0.08)

1.40 (0.31)

84

0.883 (0.010)

0.138

TE

contig04674

Chr05Na

334

2088 (278)

21

20

1

0

0

1.006

3.78 (0.09)

1.58 (0.34)

110

0.959 (0.003)

0.316

VRN3

contig07490

Chr03Na

337

2258 (1771)

12

1

4

2

5

0.531

1.30 (0.05)

0.74 (0.21)

22

0.759 (0.013)

0.723

VRN3

contigl6433

Chr03K

356

2258 (1773)

10

3

1

3

3

0.443

0.95 (0.03)

0.62 (0.19)

30

0.728 (0.016)

0.62

DW3

contig26301

Chr06K

327

2207 (2207)

5

2

0

2

1

0.227

0.56 (0.02)

0.32 (0.14)

10

0.629 (0.018)

1.267

DW3

contigll7938

Chr06N

337

2198 (2198)

4

2

0

1

1

0.182

0.55 (0.02)

0.25 (0.13)

14

0.714 (0.010)

0.793

FLD

contigl02960

Chr07K

346

2329 (1395)

3

2

1

0

0

0.129

0.10 (0.01)

0.18 (0.10)

5

0.207 (0.020)

−0.588

FLD

contig01920

Chr07N

339

2330 (1395)

1

0

0

0

1

0.043

0.15 (0.01)

0.06 (0.06)

2

0.346 (0.017)

1.253

Gl

contigl5400

Chr05K

342

3456 (1185)

20

13

2

1

4

0.608

1.71 (0.06)

0.81 (0.18)

83

0.904 (0.006)

−0.264

Gl

contig01489

Chr05N

312

3464 (1185)

10

7

0

1

2

0.289

1.05 (0.03)

0.40 (0.13)

22

0.757 (0.013)

1.655

FLT

contig09545

Chr07K

365

1826 (195)

17

17

0

0

0

0.931

1.97 (0.05)

1.30 (0.31)

64

0.931 (0.005)

−0.103

FLT

contig08422

Chr07N

339

2181 (195)

21

21

0

0

0

0.963

2.85 (0.04)

1.34 (0.29)

62

0.899 (0.006)

0.63

PHYB

contigl3571

Chr09N

350

3198 (2758)

4

1

0

1

2

0.125

0.55 (0.01)

0.17 (0.09)

7

0.697 (0.009)

3.265**

PHYB

contig21054

Chr09K

342

3194 (2758)

7

6

1

0

0

0.219

0.49 (0.01)

0.30 (0.12)

12

0.666 (0.012)

0.771

HD1

contig03275

Chr04K

306

2220 (1104)

7

2

2

0

3

0.360

0.93 (0.44)

0.44 (0.17)

8

0.776 (0.008)

2.082

HD1

contig05584

Chr04N

363

2140 (1113)

17

17

0

0

0

0.280

1.66 (0.04)

1.11 (0.27)

30

0.901 (0.005)

−0.142

PGM

contigl7299

Chr09K

343

3120 (1634)

8

5

2

0

1

0.256

0.59 (0.36)

0.36 (0.13)

28

0.848 (0.008)

1.27

PGM

contig200892

Chr09Na

315

696 (391)

7

4

3

0

0

1.006

3.3 (0.05)

1.40 (0.53)

13

0.780 (0.007)

1.328

TB1

contig06045

Chr09K

339

2428 (1109)

10

2

5

1

2

0.412

1.42 (0.03)

0.59 (0.21)

38

0.817 (0.010)

1.625

TB1

contig76312

Chr09N

314

2597 (1115)

26

16

5

3

2

1.001

2.53 (0.07)

1.41 (0.37)

84

0.926 (0.005)

0.037

Total

   

51,500 (28313)

251

169

33

17

32

      

Sugenome Nb

  

372

6709 (2884)

106

73

12

9

13

 

1.61 (0.04)

0.65 (0.31)

610

0.99 (0.20)

−0.353

Sugenome Nb

  

372

6709 (2884)

100

67

13

6

10

 

0.31 (0.03)

0.53 (0.11)

637

0.99 (0.10)

−0.269

  1. Stot Total No. of polymorphic sites, Non Cod No. of SNPs in non-coding regions, Syn No. of synonymous SNPs, Con No. of conservative amino acid changes, Non Con No. of non-conservative amino acid changes, d Percentage polymorphism (SNP density), πtot Nucleotide diversity, θw Theta per site from Watterson estimator, D Tajima’s D, h No. of haplotypes, Hd Haplotype diversity, SD Standard deviation
  2. aChromosome and subgenome allocation were corrected according to mapping data (P Qi and KM Devos, unpublished data)
  3. bSubgenome comparisons were limited to overlapping regions
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BMC Ecology and Evolution

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