Pisum Genetics   

Volume 25

1993

Research Reports

pages 5-12

On the pea linkage map

Ellis, T.H.N., Hellens, R.P., Turner, L., Lee, C,

Domoney, C. and  Welham, T.

John Innes Institute

Colney Lane, Norwich  NR4 7UH ,  UK

In the previous issue of Pisum Genetics (2), comments were made concerning difficulties in the interpretation of an RFLP map (1) of pea presented from this laboratory. The main problem concerns 'consistency' of the linkage map and leaves unresolved the question of whether patterns of linkage association are generally conserved within this species. We emphasised the variability in the linkage associations which we observed, and this was the main general biological point we wished to make. However, this emphasis may have detracted from the more specialist aim of developing a workable linkage map for pea. The purpose of this article is to simplify this process.

Here we present an update (Fig. 1) of the linkage map derived from one of our pea recombinant inbred populations (JI281 x JI399). This map is redrawn (from ref. 1) with the addition of a few extra markers, and some small alterations to the local order of a few markers. Details of all the markers are given in Table 1. In addition to these minor changes, the map as drawn has some major differences which are itemised below.

1.                The presumed translocation involving groups 1 and 4 has been broken into its constituent parts, and is not drawn as a single group. In addition, three markers have been removed and placed next to a glutamine synthase gene on group 6. This alteration removes one association 'between linkage groups' discussed in ref. 1.

2.       The linkage segment including Gty was previously part of group 5 (1) and is now drawn as a separate linkage group and is assigned to group 6 in agreement with the conventional map position of Gty (5) and because of a loose association between the two parts of group 6.

3.       Markers near a on group 1 and those near to the locus detected by cDNA 2a on group 7 have been reordered in recognition of the association between DR 18 and markers on group 1 near a and markers on group 7. This 1/7 association was discussed briefly in Ellis et al. (1) and will be discussed more fully elsewhere.

4.       The linkage segment from hst3/3 to cDNA 40/1 is assigned to group 4 on account of the association between cDNA 136 and other markers from this segment in another cross. In the JI15 x JI61 recombinant inbred population the markers linked to cDNA 136 include a Gs and Cab locus.

5.    Classical markers known from other recombinant inbred populations to be tightly linked to RFLPs placed on this map are given an approximate location to the left of their respective groups.

6.    The thick lines designate linkages supported by a LOD score greater than or equal to 3.0. The thin lines are linkages with less support presented previously (1).

  

The relationship between this map and the standard genetic map [Weeden and Wolko (5) and the Linkage Map Committee (3)] can be established for each of the major linkage segments of Fig. 1 because each of these segments carries one or more markers placed on the standard map. Markers which can be used to relate Fig. 1 to the standard map are listed in Table 1. The agreement is reasonably good with the notable exception of group 7. This difference is discussed in Ellis et al. (1) and below in conjunction with glutamine synthase genes.

The Gs/Lhb/sym2 association on this map is in agreement with Weeden et al. (4), but this Gs marker (called Gse in ref. 4) does not appear to correspond to any of the four Gs loci on the standard map (5). The association between a Gs and Cab gene on group 4 of this map may be a confirmation of the Gs-n1 (=GS341)/Cab association of the standard map. The former shows an association with rDNAl and the latter with Rrn2. This may imply that our previous tentative suggestion that rDNAl corresponds to Rrn1 was unfounded; the direct connection between rDNAl and le has been broken in this redrawn map, in part due to the relocation of the markers mentioned in item 1) above. The linkage data on which this connection was based can be found in ref. 1. The uppermost linkage segment in the group 4 as drawn in Fig. 1 may therefore correspond to group 7 of the standard map (5). The associations between linkage segments are not shown on this map, but the data corresponding to these and especially in relation to the differences between the two versions of the linkage map from this one cross can be found in Ellis et al. (1).

Fig. 1 shows an RFLP map derived largely from the analysis of the recombinant inbred population JI281 x JI399 as discussed in the text. Marker names are as in ref. 1, with the following exceptions. The markers detected with a glutamine synthase gene probe are written as Gs/x where they were previously written as GST-10/x; this is to avoid confusion with glutathione-S-transferase. The glycine decarboxylase genes are designated gdc rather than by the plasmid names pST. Similarly, Adh genes are designated Adh/x where they were previously designated pPSR 546/x. The lipoxygenase genes are designated Lox9/x, corresponding to pPE 923/x, and Lox10 corresponding to pPE1036a. The markers designated 0.9 MI/x have been shown to correspond to Cab genes and are designated Cab/x. The rDNA locus referred to as rDNAl was previously designated by the probe name cDB107. The marker Fs was previously regarded as F. These alterations have been made to facilitate comparison to the map of Weeden and Wolko (5).

Table 1. Explanation of marker names in Fig. 1.

Marker (Fig. 1)

Marker (in 5)

Comments

Group 1 (upper)

 

 

1.

gr-14

 

glutathione reductase

2.

LgJ

Lg-J

B-type legumin gene cluster. NOT Lg2 of Matta

3.

LgJ/2

 

and Gatehouse (see 1) LgJ/2 is adjacent seq.

4.

cDNA 260

 

 

5.

a

a

lacking anthocyanin

6.

pCD 72

 

vicilin

7.

cDNA 150/2

 

 

8.

gr-16/9

 

 

9.

cDNA 125/5

 

 

10.

cDNA 24

 

 

11.

CDNA56/1

 

 

12.

cDNA 39

 

 

13.

CDS/1

 

 

14.

gdcP

 

glycine decarboxylase, previously pST P

Group 1 (lower)

 

 

15.

DR 11

 

copia-like element

16.

cDNA 148/2

 

 

17.

Gs/3

 

Glutamine synthase

18.

gdcH

 

glycine decarboxylase, previously pST H

19.

Chs-2/2

 

The major chalcone synthase gene cluster with

20.

Chs-2/3

 

recombination within the Chs gene cluster.

21.

i

i

green cotyledons

22.

P7

 

seed polypeptide

23.

cDNA 76

 

 

24.

Lox9/1

linked to af

lipoxygenase, previously pPE 923/1

25.

cDNA 206

 

 

26.

c41

 

tandem repeat in situ marker

27.

SHMT

 

serine hydroxymethyl transferase

28.

cDNA 150/1

 

 

29.

DR 9

 

copia-like element

30.

cDNA 125/8

 

 

31.

CDNA40/8

 

 

32.

CDS/3

 

 

33.

CDS/2

 

 

34.

Gs/1

? Gse

glutamine synthase       } Sym2 associated

35.

lhb/1

 

leghaemoglobin            } Sym2 associated

36.

cDNA 164

 

 

37.

cDNA 44

 

 

38.

cDNA 40/3

 

 

39.

cDNA 267

 

 

40.

cDNA 186

 

 

41.

Adh/3

 

Alcohol dehydrogenase

Group 2

 

 

42.

DR 16

 

copia-like element

43.

CD126/2

 

 

44.

Cvc

Cvc

Convicilin

45.

cDNA 40/5

 

 

46.

cDNA 75

 

 

47.

lhb/3

 

leghaemoglobin

48.

D15B/2

 

 

49.

DR 6

 

copia-like element

50.

cDNA 243

 

 

51.

D15B/1

 

 

52.

cDNA 125/10

 

 

53.

cDNA 148/3

 

 

54.

cDNA 194/2

 

 

55.

DR 12

 

copia-like element

56.

DR 13

 

copia-like element

Group 3

 

 

57.

cDNA 34

 

 

58.

cDNA 125/1

 

 

59.

cDNA 23

 

 

60.

Vc-3

 

Vicilin

61.

5sr-7

 

5S rRNA related sequence

62.

5sr-4

 

5S rRNA related sequence

63.

5S/2

 

5S rRNA gene cluster

64.

cDNA 40/2

 

 

65.

cDNA 67a

 

 

66.

cDNA 137

linked to st

 

67.

cDNA 40/7

 

 

68.

Chs-2/1

 

Chalcone synthase gene responsive to a

69.

cDNA 194/1

 

 

70.

DR 14

 

copia-like element

71.

Adh/1

 

Alcohol dehydrogenase (major signal)

72.

gr-16/7

 

 

73.

gr-16/2

 

 

74.

cDNA 331

 

 

75.

DR 10

 

copia-like element

76.

DR 4

 

copia-like element

77.

Vc-5

 

 

78.

cDNA 53

 

 

79.

CD 126/1

 

 

80.

LT18

 

legumin gene related sequence

81.

rb

rb

wrinkled seed

Group 4 (top)

 

 

82.

Gs/4

? Gs-n1

glutamine synthase

83.

Cab/1

? Cab

chlorophyll a/b binding protein related sequence

84.

cDNA 119

 

 

85.

cDNA 38a

 

 

86.

cDNA 228

 

 

87.

rDNAl

Rrn1 or Rrn2

large rRNA gene cluster

88.

CD7/3

 

 

89.

gr-16/5

 

 

90.

gr-16/1

 

 

91.

gr-16/3

 

 

92.

gr-16/4

 

 

Group 4 (middle)

 

 

93.

pAt-T4/6

 

telomere related sequence

94.

le

le

short intemodes

95.

Lox10

Lox

lipoxygenase

96.

DR 1

 

copia-like element

Group 4 (bottom)

 

 

97.

hst3/3

 

Histone H3 related DNA sequence

98.

cDNA 136

 

 

99.

cDNA 125/2

 

 

100.

gr-16/8

 

 

101.

cDNA 56/2

 

 

102.

cDNA 148/1

 

 

103.

DR 2,

 

copia-like element

104.

DR 7,

 

copia-like element

105.

DR 8

 

copia-like element

106.

cDNA 40/1

 

 

Group 5 (top)

 

 

107.

pAt-T4/2

 

telomere related sequence

108.

pAt-T4/l

 

telomere related sequence

Group 5 (bottom)

 

 

109.

rbcS/1

RbcS

RUBP carboxylase

110.

hst3/l

 

Histone H3 related DNA sequence

111.

Fs

Fs

violet speckles on testa

112.

5sr-2

 

5S rRNA related sequence

113.

5S/1

linked to ce

5S gene cluster

114.

5sr-6

 

 

115.

5sr-l

 

 

116.

5sr-5

 

 

117.

5sr-10

 

 

118.

Adh/4

 

Alcohol dehydrogenasc

119.

cDNA 231

linked to gp

 

120.

ti/b

linked to gp

trypsin inhibitor

121.

Vc-2

linked to gp

vicilin

122.

cDNA 373

 

 

123.

cDNA 204/1

 

 

124.

Adh/2

 

Alcohol dehydrogenase

125.

cDNA 204/4

 

 

126.

cDNA 148/6

 

 

Group 6 (upper)

 

 

127.

cDNA 40/6

 

 

128.

cDNA 324

 

 

129.

pCD7/5&6

 

previously 2 markers

130.

cDNA 48a

 

 

131.

cDNA 289/2

 

 

132.

5S/3

linked to Pl

5S gene cluster

133.

5sr-3

 

5S rRNA related sequence

Group 6 (lower)

 

 

134.

cDNA 204/3

 

 

135.

Gty

Gty

gritty testa

136.

CDNA40/4

 

 

137.

cDNA 204/2

 

 

138.

Cab/2

 

chlorophyll a/b binding protein related sequence

139.

rbcS/2

 

RUBP carboxylase

140.

cDNA 133

 

 

141.

Gs/2

 

glutamine synthase

142.

cDNA 41

 

 

143.

cDNA 148/5

 

 

144.

pAt-T4/5

 

telomere related sequence

Group 7 (upper)

 

 

145.

T4

 

microsatellite adjacent to telomere sequence

146.

pAt-T4/8

 

telomere related sequence

147.

Lox9/2

 

lipoxygenase

148.

Lox9/3

 

lipoxygenase

149.

DR 19

 

copia-like element

150.

DR 20

 

copia-like element

151.

DR 18

 

copia-like element

152.

cDNA 200

 

 

153.

cDNA 2a

linked to r

 

154.

DR 26

 

copia-like element

155.

lhb/4

 

leghaemoglobin

156.

cDNA 189a

 

 

157.

cDNA 280

linked to r

 

158.

cDNA 189a

 

 

159.

cDNA 286

 

 

160.

Lg-1

Lg-1

A-type legumin

161.

DR 3

 

copia-like element

162.

cDNA 148/4

 

 

Group 7 (lower)

 

 

163.

rDNA2/B

Rrn1 or Rrn2

large ribosomal RNA gene cluster,

164.

rDNA2/H

Rrn1 or Rrn2

recombination within the array

165.

gdcT

 

glycine decarboxylase, previously pST T

166.

cDNA 289/1

 

 

167.

gdcL

 

glycine decarboxylase, previously pST L

168.

cDNA 125/11

 

 

pCD7/5 and pCD7/6 could be mapped as two markers, but all the lines carrying the JI399 allele of 7/6 carry the JI399 allele of 7/5. This and the relatedness of the DNA sequences has led us to treat this probe as detecting a single marker for the purposes of the present map. This is essentially the pCD7/5 marker of ref 1. T. Bisseling pers. comm.

This map is an attempt to make sense of the patterns of segregation of markers in a recombinant inbred population. The difficulties in relating this map to the standard map should not be taken to imply that either is wrong. Some of the difficulties are probably a consequence of working with different data sets, but the more interesting possibility that the difficulties arise from the variability of the pea genome seem well worth further study. Furthermore, the segregation data for recombinant inbred populations can be built upon with additional molecular markers and with the analysis of phenotypic traits. The population from which this map was derived (and our other recombinant inbred populations) are sets of multiply marked genetic stocks, with attendant and interrelated segregation data. At present, the JI281 x JI399 recombinant inbred population is at the F12 generation. This population is generally available for further genetic analysis, subject only to limitations of seed number and import or export controls.

1.             Ellis, T.H.N., Turner, L., Hellens, R.P., Lee, D., Harker, C.L., Enard, C,
Domoney, C. and Davies, D.R. 1992. Genetics 130:649-663.

2.        Weeden, N.F. 1992. Pisum Genetics 24:91.

3.        Weeden, N.F., Ambrose, M. and Swiecicki, W.K. 1991. Pisum Genetics 23:
Cover.

4.         Weeden, N.F., Kneen, B.E. and LaRue, T.A. 1990. In: Nitrogen Fixation:
Achievements and Objectives, Eds P.M. Gresshoff, J. Roth, G. Stacey and
W.E. Newton, Chapman and Hall, New York, pp. 323-330.

5.         Weeden, N.F. and Wolko, B. 1990. In: Genetic Maps, 5th edition, Ed. S.J.
O'Brien,  Cold  Spring  Harbor Press,  Cold Spring Harbor,  N.Y., pp. 6 .106-6.112.