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Table 1 Composition of three microsatellite PCR multiplexes developed for Zymoseptoria tritici population genetic studies

From: Development of a rapid multiplex SSR genotyping method to study populations of the fungal plant pathogen Zymoseptoria tritici

Multiplexa

Chrom.

Locusb

Locus in literaturec

Repeat motif of IPO-323d

Primer sequences (5'- > 3')

Fluores-cent dyee

Size range (bp)

Protein IDf

Nag

Neh

Fnai

Gene diversity (H E )j

         

Total pop. (n = 166)

Total pop. (n = 166)

Total pop. (n = 166)

Local pop. (n = 33)

Worldwide pop. (n = 133)

Multiplex 1 (core chromosomes)

1

ST1

GAC0002

(GAC)6

F: AATCGACCCCTTCCTTCAAC

Black

192-222

33894

3

1.4

0.6%

0.305

0.308

    

R: GGGGGAGAGGCATAGTCTTG

        

3

ST3A

AG0003

(AG)15

F: ACTTGGGGAGGTGTTGTGAG

Black

226-258

103950

16

5.8

2.4%

0.785

0.825

    

R: ACGAATTGTTCATTCCAGCG

        

4

ST4

AC0002

(AC)7

F: TGAACATCAACCTCACACGC

Green

182-206

71387

7

2.0

0.0%

0.479

0.504

    

R: AGAAGAGGACGACCCACGAG

        

5

ST5

GGC0001

(GGC)8

F: GATACCAAGGTGGCCAAGG

Green

232-256

104484

6

1.4

0.0%

0.114

0.345

    

R: CACGTTGGGAGTGTCGAAG

        

9

ST9

CT0004

(CT)6

F: CACCTCACTCCTCAATTCCG

Green

336-348

62567

6

1.7

3.0%

0.404

0.413

    

R: GAAAGGTTGGTGTCGTGTCC

        

10

ST10

CAA0003

(CAA)7

F: TCCGTCATCAACAACACCAG

Blue

139-160

62856

6

2.7

0%

0.624

0.631

    

R: TGGCCGTAGAACTGCTGAG

        

13

ST13

AG0009

(AG)10 (GGCA)3

F: GACTCCATTTACCTGTGGCG

Blue

192-200

106529

5

2.4

0%

0.566

0.587

    

R: TGTGAAGGACACGCAAAGAG

        

11

ST11

GCA0002

(GCA)6

F: GTGTGAAACGAAAAGCGGAG

Blue

293-296

-

2

1.1

17.5%

0.071

0.087

    

R: TACTGGGTATCGAGATCGGC

        

Multiplex 2 (core chromosomes)

8

ST8

CT0007

(CT)6

F: TGCAGGGCATTTAATTGAGG

Black

180-188

61457

5

1.6

40.4%

0.322

0.404

    

R: TCCATCCATTTAGGCTCGTC

        

12

ST12

TCC0002

(TCC)6

F: GAATCCACCTCTTCCTTGCC

Black

226-232

111480

3

1.1

5.4%

0.059

0.137

    

R: AGGAGGATATCAAGGCCCAG

        

3

ST3B

CAA0005

(CAA)8

F: AAGAATCCCACCACCCAAAC

Black

263-299

-

10

2.9

0.6%

0.663

0.648

    

R: CACACGGCTCCTTTGACAC

        

6

ST6

TCC0009

(TCC)8

F: TCAATTGCCAATAATTCGGG

Green

161-179

73474

6

1.5

3.6%

0.242

0.342

    

R: AGACGAGGCAGTTGGTTGAG

        

3

ST3C

GCA0003

(GCA)7

F: TCCTATCAACTCCCGAGACG

Green

229-253

108534

5

2.2

1.2%

0.580

0.533

    

R: CCGCACGTAGGAATTTTCAG

        

2

ST2

Chr02-140

(GCT)12

F: ACACCAAAGAAGGATCCACG

Green

338-365

108062

9

2.9

0%

0.439

0.689

    

R: GCCGGAGGTCTATCAGTTTG

        

11

ST1E7

ST1E7

(CGG)3

F: GATCTCGAGCAGGGCGGAAGT

Blue

86-98

-

4

1.5

20.0%

0.204

0.373

    

R: TCACACGCTGGTCTGTGAATC

        

7

ST7

AC0001

(AC)21

F: CACCACACCGTCGTTCAAG

Blue

171-227

105049

15

1.9

0.6%

0.463

0.487

    

R: CGTAAGTTGGTGGAGATGGG

        

Multiplex 3 (accessory chromosomes)

15

ST15

AC0007

(AC)15

F: TGCTCGCAAGACATAAAACG

Black

92-152

106622

15

8.0

16.9%

0.858

0.885

    

R: CTCTTAGCATTGGTCGGTGG

        

21

ST21

GGA0001

(GGA)6

F: GTACGACACGGGCTATGGAG

Black

149-161

111806

5

1.8

32.5%

0.632

0.640

    

R: GGCGATGACGATGAAACC

        

18

ST18

Chr18-007*

(GGA)5

F: AGAGGCAATGGTGGGTGAT

Black

245-272

111768

2

1.2

71.1%

0.411

0.430

    

R: TCCTCCTCGTCCGACAATAC

        

19

ST19

Chr19-031

(TCG)6

F: CTACTGTATTTCCCGGGGGT

Black

351-363

97944

5

2.3

12.6%

0.700

0.631

    

R: ACCCCTCTCTCCTTCTCTCG

        

20

ST20

Chr20-066*

(GAA)22

F: CTCCTCCACATCCATCCAAC

Green

229-289

-

19

13.9

10.8%

0.891

0.914

    

R: GACGGAGGGGGAGAGGTAT

        

16

ST16

Chr16-016

(GAA)6

F: TTCACGGTATCACAGACCCA

Green

496-538

97708

7

1.2

13.3%

0.369

0.364

    

R: GGGTTGTCCAAGCTGTTGTT

        

17

ST17

Chr17-040*

(AGA)5

F: ACAAGAGGCGGAAGACTGAA

Blue

236-239

97821

2

1.0

18.7%

0,367

0.311

    

R: TCATGCGTCGTATTCTTGGA

        

14

ST14

Chr14-023

(TCC)20 (TCG)5

F: CAAACAGCCAGATCCACCTT

Blue

361-529

111734

36

12.1

13.8%

0.898

0.920

    

R: GTCGTGGTCGGAGAGAGAAG

        
  1. aPrimers for the housekeeping gene SOD are added in multiplexes 1 and 3 (green fluorescent dye; 96 bp amplicon; F:CTACCGATGCTCCAGCTGAGA and R:CACCACCCTTGCCATCCA), and primers from the housekeeping gene ILV5 are added in multiplexes 1 and 2 (black fluorescent dye; 108 bp amplicon; F:GCTCTATCGCCATCTTCCAGG and R:TCCTTCTCGAAGGTGGTCTTGT).
  2. bProposed name of microsatellite loci starting with the fungus initials and followed by the chromosome number on which the microsatellite is located (except for ST1E7).
  3. cLoci name found in the literature [20, 22] or in the Additional file 1 (primers for Chr18-007, Chr20-066 and Chr17-040 have been modified from the original design to fit the multiplex range size requirements).
  4. dRepeat motif of IPO-323 as published in [20, 22], with exception of ST7 and ST13, for which the motif was found slightly different after sequencing.
  5. ePrimers were purchased from Sigma Aldrich (France). They are WellRed oligos, licensed by Beckman Coulter (USA), and bearing fluorochromes at their 5’ end: D1: red, D2: black, D3: green, D4: blue.
  6. fIdentity number of the protein corresponding to SSR loci identified within expressed sequences (Filtered Gene Models from Mgraminicolav2 at JGI).
  7. gNumber of alleles identified in the total population (excluding null alleles).
  8. hEffective number of alleles (excluding null alleles).
  9. iFrequency of missing data or null alleles (no amplification) in the total population.
  10. jUnbiased gene diversity H E calculated as the probability that two individuals taken at random have different genotypes (excluding null alleles) [31].
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BMC Research Notes

ISSN: 1756-0500

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