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Table 3 Counts of markers used for the second round of the linkage analysis

From: Enhancement of Glen Moy x Latham raspberry linkage map using GbS to further understand control of developmental processes leading to fruit ripening

Chromosome

Possible AOxBO nulls

Total No. of markers in JM input file

No. carried to MDS analysis

Mapped markers

Latham (ABxAA)

Moy (AAxAB)

Both (ABxAB +ABxCD)

Null (AOxAB or ABxAO)

Null (AOxBO)

Length (cM)

HMM_mean for MDS order

HMM_mean after swaps

LG1

25

471

331

295

223

33

7 + 1

19

12

114.1

1.48

1.25

LG2

65

737

494

456

286

90

10 + 4

34

32

107.1

1.65

1.42

LG3

21

933

603

557

447

45

9 + 4

39

13

128.2

1.77

1.67

LG4a

79

667

448

435

253

70

25 + 5

39

43

91.5

1.29

1.25

LG5

83

739

509

486

287

66

18 + 8

63

44

85.4

1.42

1.27

LG6

12

514

369

315

284

15

1 + 1

9

5

88.6

1.95

1.52

LG7

16

396

252

243

216

11

0

10

6

100.2

1.93

1.55

  1. HMM_mean denotes the mean number of recombinations inferred using a HMM
  2. a The LG4 map is fitted using LOD2 weighting and 2d MDS, which fitted better than LOD2 weighting and 3d MDS