In the following pages, linkage group (LG) names ... · lg02-c500(a)a) lg02-r(a) chr02 (a) 0 5 10...
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In the following pages, linkage group (LG) names containing “-SNP511” contain markers from the map reported by Maughan et al. (2012); LG names containing “-c500” contain markers from the Atlas × Carina Red population; and LG names containing “-R” contain RNA-Seq makers from the Kurmi × 0654 map. LGs from the integrated map are designated with “Chr” in the name. WWW.NATURE.COM/NATURE | 1
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Transcript of In the following pages, linkage group (LG) names ... · lg02-c500(a)a) lg02-r(a) chr02 (a) 0 5 10...
In the following pages, linkage group (LG) names containing “-SNP511” contain markers from the map
reported by Maughan et al. (2012); LG names containing “-c500” contain markers from the Atlas ×
Carina Red population; and LG names containing “-R” contain RNA-Seq makers from the Kurmi × 0654
map. LGs from the integrated map are designated with “Chr” in the name.
WWW.NATURE.COM/NATURE | 1
Chr01: Links at identity level between the genetic maps of the three segregating populations and the integrated map.
LG01+29-SNP511(B) Chr01(B) LG01-c500 LG01-R(B) Chr01(B)0
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WWW.NATURE.COM/NATURE | 2
Chr01: Links between markers in the genetic maps of the three segregating populations within the same 1 Mb bin (0-999,999 nt and so on) showing the concordance of order of marker positions. Links of the same 1 Mb bin are linked within a linkage group with arcs of the same color and links between linkage groups use the same color.
LG01+29-SNP511(B) LG01-c500 LG01-R(B) LG01+29-SNP511(B)0
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WWW.NATURE.COM/NATURE | 3
Chr01: Links between markers in the genetic maps of the three segregating populations within same scaffold of the assembly showing the concordance of order of scaffold positions (each scaffold has a separate color which color is used to indicated links within linkage groups with arcs of the same color as links between linkage groups).
LG01+29-SNP511(B) LG01-c500 LG01-R(B) LG01+29-SNP511(B)0
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WWW.NATURE.COM/NATURE | 4
Chr02: Links at identity level between the genetic maps of the three segregating populations and the integrated map.
LG02-SNP511(A) Chr02A) LG02-c500(A) LG02-R(A) Chr02(A)0
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WWW.NATURE.COM/NATURE | 5
Chr02: Links between markers in the genetic maps of the three segregating populations within the same 1 Mb bin (0-999,999 nt and so on) showing the concordance of order of marker positions. Links of the same 1 Mb bin are linked within a linkage group with arcs of the same color and links between linkage groups use the same color.
LG02-SNP511(A) LG02-c500(A) LG02-R(A) LG02-SNP511(A)0
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WWW.NATURE.COM/NATURE | 6
Chr02: Links between markers in the genetic maps of the three segregating populations within same scaffold of the assembly showing the concordance of order of scaffold positions (each scaffold has a separate color which color is used to indicated links within linkage groups with arcs of the same color as links between linkage groups).
LG02-SNP511(A) LG02-c500(A) LG02-R(A) LG02-SNP511(A)0
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WWW.NATURE.COM/NATURE | 7
Chr03: Links at identity level between the genetic maps of the three segregating populations and the integrated map.
LG03-SNP511(B) Chr03(B) LG03-c500(B) LG03-R(B) Chr03(B)0
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WWW.NATURE.COM/NATURE | 8
Chr03: Links between markers in the genetic maps of the three segregating populations within the same 1 Mb bin (0-999,999 nt and so on) showing the concordance of order of marker positions. Links of the same 1 Mb bin are linked within a linkage group with arcs of the same color and links between linkage groups use the same color.
LG03-SNP511(B) LG03-c500(B) LG03-R(B) LG03-SNP511(B)0
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WWW.NATURE.COM/NATURE | 9
Chr03: Links between markers in the genetic maps of the three segregating populations within same scaffold of the assembly showing the concordance of order of scaffold positions (each scaffold has a separate color which color is used to indicated links within linkage groups with arcs of the same color as links between linkage groups).
LG03-SNP511(B) LG03-c500(B) LG03-R(B) LG03-SNP511(B)0
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WWW.NATURE.COM/NATURE | 10
Chr04: Links at identity level between the genetic maps of the three segregating populations and the integrated map.
LG04-SNP511(A) Chr04(A) LG04-17B-c500(A) LG04-R(A) Chr04(A)0
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WWW.NATURE.COM/NATURE | 11
Chr04: Links between markers in the genetic maps of the three segregating populations within the same 1 Mb bin (0-999,999 nt and so on) showing the concordance of order of marker positions. Links of the same 1 Mb bin are linked within a linkage group with arcs of the same color and links between linkage groups use the same color.
LG04-SNP511(A) LG04-17B-c500(A) LG04-R(A) LG04-SNP511(A)0
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WWW.NATURE.COM/NATURE | 12
Chr04: Links between markers in the genetic maps of the three segregating populations within the same 1 Mbase bin (0-999,999 nt and so on) showing the concordance of order of marker positions.Links of the same 1 Mbase bin are linked within a linkage group with arcs of the same color and links between linkage groups use the same color.
LG04-SNP511(A) LG04-17B-c500(A) LG04-R(A) LG04-SNP511(A)0
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WWW.NATURE.COM/NATURE | 13
Chr05: Links at identity level between the genetic maps of the three segregating populations and the integrated map.
LG05-29-SNP511(B) Chr05(B) LG05-29-c500(B) LG05-29-R(B) Chr05(B)0
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WWW.NATURE.COM/NATURE | 14
Chr05: Links between markers in the genetic maps of the three segregating populations within the same 1 Mb bin (0-999,999 nt and so on) showing the concordance of order of marker positions. Links of the same 1 Mb bin are linked within a linkage group with arcs of the same color and links between linkage groups use the same color.
LG05-29-SNP511(B) LG05-29-c500(B) LG05-29-R(B) LG05-29-SNP511(B)0
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WWW.NATURE.COM/NATURE | 15
Chr05: Links between markers in the genetic maps of the three segregating populations within the same 1 Mbase bin (0-999,999 nt and so on) showing the concordance of order of marker positions.Links of the same 1 Mbase bin are linked within a linkage group with arcs of the same color and links between linkage groups use the same color.
LG05-29-SNP511(B) LG05-29-c500(B) LG05-29-R(B) LG05-29-SNP511(B)0
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WWW.NATURE.COM/NATURE | 16
Chr06: Links at identity level between the genetic maps of the three segregating populations and the integrated map.
LG06-SNP511(B) Chr06(B) LG06-c500(B) LG06-R19-22-24 Chr06(B)0
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WWW.NATURE.COM/NATURE | 17
Chr06: Links between markers in the genetic maps of the three segregating populations within the same 1 Mb bin (0-999,999 nt and so on) showing the concordance of order of marker positions. Links of the same 1 Mb bin are linked within a linkage group with arcs of the same color and links between linkage groups use the same color.
LG06-SNP511(B) LG06-c500(B) LG06-R19-22-24 LG06-SNP511(B)0
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WWW.NATURE.COM/NATURE | 18
Chr06: Links between markers in the genetic maps of the three segregating populations within the same 1 Mbase bin (0-999,999 nt and so on) showing the concordance of order of marker positions.Links of the same 1 Mbase bin are linked within a linkage group with arcs of the same color and links between linkage groups use the same color.
LG06-SNP511(B) LG06-c500(B) LG06-R19-22-24 LG06-SNP511(B)0
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WWW.NATURE.COM/NATURE | 19
Chr07: Links at identity level between the genetic maps of the three segregating populations and the integrated map.
LG07-09-20-SNP511(A) Chr07(A) LG07-09-20-24-c500(A) LG07-R(A) Chr07(A)0
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WWW.NATURE.COM/NATURE | 20
Chr07: Links between markers in the genetic maps of the three segregating populations within the same 1 Mb bin (0-999,999 nt and so on) showing the concordance of order of marker positions. Links of the same 1 Mb bin are linked within a linkage group with arcs of the same color and links between linkage groups use the same color.
LG07-09-20-SNP511(A) LG07-09-20-24-c500(A) LG07-R(A) LG07-09-20-SNP511(A)0
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WWW.NATURE.COM/NATURE | 21
Chr07: Links between markers in the genetic maps of the three segregating populations within the same 1 Mbase bin (0-999,999 nt and so on) showing the concordance of order of marker positions.Links of the same 1 Mbase bin are linked within a linkage group with arcs of the same color and links between linkage groups use the same color.
LG07-09-20-SNP511(A) LG07-09-20-24-c500(A) LG07-R(A) LG07-09-20-SNP511(A)0
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WWW.NATURE.COM/NATURE | 22
Chr08: Links at identity level between the genetic maps of the three segregating populations and the integrated map. Because the distance of the distal part of LG08-SNP511 in the RNAseq-map to the rest of the RNAsec-map is rather long (30 cM) and the SNP511 and c500-map have good concordance, for this Chr group, the c500-map was taken as reference for positions of anchor markers.
LG08-SNP511(A) Chr08(A) LG08-c500(A) LG08-R(A) Chr08(A)0
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WWW.NATURE.COM/NATURE | 23
Chr08: Links between markers in the genetic maps of the three segregating populations within the same 1 Mb bin (0-999,999 nt and so on) showing the concordance of order of marker positions. Links of the same 1 Mb bin are linked within a linkage group with arcs of the same color and links between linkage groups use the same color.
LG08-SNP511(A) LG08-R(A) LG08-c500(A) LG08-SNP511(A)0
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WWW.NATURE.COM/NATURE | 24
Chr08: Links between markers in the genetic maps of the three segregating populations within same scaffold of the assembly showing the concordance of order of scaffold positions (each scaffold has a separate color which color is used to indicated links within linkage groups with arcs of the same color as links between linkage groups).
LG08-SNP511(A) LG08-R(A) LG08-c500(A) LG08-SNP511(A)0
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WWW.NATURE.COM/NATURE | 25
Chr09: Links at identity level between the genetic maps of the three segregating populations and the integrated map. No markers found in the SNP511 map on this Chr.
LG10B-c500(B) Chr09(B) LG10B-R(B)0
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WWW.NATURE.COM/NATURE | 26
Chr09: Links between markers in the genetic maps of the three segregating populations within the same 1 Mb bin (0-999,999 nt and so on) showing the concordance of order of marker positions. Links of the same 1 Mb bin are linked within a linkage group with arcs of the same color and links between linkage groups use the same color.
LG10B-c500(B) LG10B-R(B)0
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WWW.NATURE.COM/NATURE | 27
Chr09: Links between markers in the genetic maps of the three segregating populations within same scaffold of the assembly showing the concordance of order of scaffold positions (each scaffold has a separate color which color is used to indicated links within linkage groups with arcs of the same color as links between linkage groups). For comparison, the Chr10 (B-subgenome)) has been shown next to the LG going into Chr09(B-subgenome). Only one marker links Chr10(A) with Chr09(subgenome B), and this was the reason for the initial naming of the LG in the Atlas x Carina Red cross (c500-map)and RNAseq-map as LG10B. Chr1.
LG10B-c500(B) LG10B-R(B)0
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WWW.NATURE.COM/NATURE | 28
Chr10: Links at identity level between the genetic maps of the three segregating populations and the integrated map.
LG10-SNP511(A) Chr10(A) LG10-c500(A) LG10-R(A) Chr10(A)0
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WWW.NATURE.COM/NATURE | 29
Chr10: Links between markers in the genetic maps of the three segregating populations within the same 1 Mb bin (0-999,999 nt and so on) showing the concordance of order of marker positions. Links of the same 1 Mb bin are linked within a linkage group with arcs of the same color and links between linkage groups use the same color.
LG10-SNP511(A) LG10-c500(A) LG10-R(A) LG10-SNP511(A)0
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WWW.NATURE.COM/NATURE | 30
Chr10: Links between markers in the genetic maps of the three segregating populations within same scaffold of the assembly showing the concordance of order of scaffold positions (each scaffold has a separate color which color is used to indicated links within linkage groups with arcs of the same color as links between linkage groups).
LG10-SNP511(A) LG10-c500(A) LG10-R(A) LG10-SNP511(A)0
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WWW.NATURE.COM/NATURE | 31
Chr11: Links at identity level between the genetic maps of the three segregating populations and the integrated map.
LG11-20-28-SNP511 chrom11(B) LG11-c500(B) LG11-R(B) Chr11(B)0
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WWW.NATURE.COM/NATURE | 32
Chr11: Links between markers in the genetic maps of the three segregating populations within the same 1 Mb bin (0-999,999 nt and so on) showing the concordance of order of marker positions.
LG11-20-28-SNP511 LG11-c500(B) LG11-R(B)0
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WWW.NATURE.COM/NATURE | 33
Chr11: Links between markers in the genetic maps of the three segregating populations within the scaffold of the assembly showing the concordance of order of scaffold positions.
LG11-20-28-SNP511 LG11-c500(B) LG11-R(B)0
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WWW.NATURE.COM/NATURE | 34
Chr12: Links at identity level between the genetic maps of the three segregating populations and the integrated map.
LG26-29-20-12-SNP511 Chr12(A) LG12-20-26-c500(A) LG12-R(A/B) Chr12(A)0
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WWW.NATURE.COM/NATURE | 35
Chr12: Links between markers in the genetic maps of the three segregating populations within the same 1 Mb bin (0-999,999 nt and so on) showing the concordance of order of marker positions.
LG26-29-20-12-SNP511 LG12-20-26-c500(A) LG12-R(A/B) LG26-29-20-12-SNP5110
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WWW.NATURE.COM/NATURE | 36
Chr12: Links between markers in the genetic maps of the three segregating populations within scaffolds of the assembly showing the concordance of order of scaffold positions.
LG26-29-20-12-SNP511 LG12-20-26-c500(A) LG12-R(A/B) LG26-29-20-12-SNP5110
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WWW.NATURE.COM/NATURE | 37
Chr13: Links at identity level between the genetic maps of the three segregating populations and the integrated map.
LG13-SNP511(A) Chr13(A) LG13-c500(A) LG13-R(A) Chr13(A)0
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WWW.NATURE.COM/NATURE | 38
Chr13: Links between markers in the genetic maps of the three segregating populations within the same 1 Mb bin (0-999,999 nt and so on) showing the concordance of order of marker positions.
LG13-SNP511(A) LG13-c500(A) LG13-R(A) LG13-SNP511(A)0
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WWW.NATURE.COM/NATURE | 39
Chr13: Links between markers in the genetic maps of the three segregating populations within the scaffold of the assembly showing the concordance of order of scaffold positions. Distal end of LG13-R is located on LG8-SNP511; this might be a Chrosomal translocation. In the integrated map this has been placed in Chr08, because there is a link of this distal to LG08-R and also a strong link in LG8-SNP511.
LG13-SNP511(A) LG13-c500(A) LG13-R(A) LG13-SNP50
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WWW.NATURE.COM/NATURE | 40
Chr14: Links at identity level between the genetic maps of the three segregating populations and the integrated map.
LG14-20-27-SNP511(A) Chr14(A) LG14-c500(A) LG14-20-27-R9 Chr14(A)0
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WWW.NATURE.COM/NATURE | 41
Chr14: Links between markers in the genetic maps of the three segregating populations within the same 1 Mb bin (0-999,999 nt and so on) showing the concordance of order of marker positions.
LG14-20-27-SNP511(A) LG14-c500(A) LG14-20-27-R9 LG14-20-270
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WWW.NATURE.COM/NATURE | 42
Chr14: Links between markers in the genetic maps of the three segregating populations within the scaffold of the assembly showing the concordance of order of scaffold positions.
LG14-20-27-SNP511(A) LG14-c500(A) LG14-20-27-R9 LG14-20-27-SNP5110
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WWW.NATURE.COM/NATURE | 43
Chr15: Links at identity level between the genetic maps of the three segregating populations and the integrated map.
LG15-SNP511(A) Chr15(A) LG15-20B-LG15-21-c500(A) LG15-R(A) Chr15(A,U,B)0
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WWW.NATURE.COM/NATURE | 44
Chr15: Links between markers in the genetic maps of the three segregating populations within the same 1 Mb bin (0-999,999 nt and so on) showing the concordance of order of marker positions.
LG15-SNP511(A) LG15-20B-LG15-21-c500(A) LG15-R(A) LG15-SNP511(A)0
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150
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Chr15: Links between markers in the genetic maps of the three segregating populations within the scaffold of the assembly showing the concordance of order of scaffold positions.
LG15-SNP511(A) LG15-20B-LG15-21-c500(A) LG15-R(A) LG15-SNP511(A)0
5
10
15
20
25
30
35
40
45
50
55
60
65
70
75
80
85
90
95
100
105
110
115
120
125
130
135
140
145
150
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Chr16: Links at identity level between the genetic maps of the three segregating populations and the integrated map.
LG16-SNP511(B) Chr16(B) LG16-c500(B) LG16-R15 Chr16(B)0
5
10
15
20
25
30
35
40
45
50
55
60
65
70
75
80
85
90
95
100
105
110
115
120
125
130
135
140
145
150
155
160
WWW.NATURE.COM/NATURE | 47
Chr16: Links between markers in the genetic maps of the three segregating populations within the same 1 Mb bin (0-999,999 nt and so on) showing the concordance of order of marker positions.
LG16-SNP511(B) LG16-c500(B) LG16-R15 LG16-SNP511(B)0
5
10
15
20
25
30
35
40
45
50
55
60
65
70
75
80
85
90
95
100
105
110
115
120
125
130
135
140
145
150
155
160
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Chr16: Links between markers in the genetic maps of the three segregating populations within the scaffold of the assembly showing the concordance of order of scaffold positions.
LG16-SNP511(B) LG16-c500(B) LG16-R15 LG16-SNP511(B)0
5
10
15
20
25
30
35
40
45
50
55
60
65
70
75
80
85
90
95
100
105
110
115
120
125
130
135
140
145
150
155
160
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Chr17: Links at identity level between the genetic maps of the three segregating populations and the integrated map
LG17-SNP511(B) Chr17(B) LG17-c500(B) LG17-R(B) Chr17(B)0
5
10
15
20
25
30
35
40
45
50
55
60
65
70
75
80
85
90
95
100
105
110
115
120
125
130
135
140
145
150
WWW.NATURE.COM/NATURE | 50
Chr17: Links between markers in the genetic maps of the three segregating populations within the same 1 Mb bin (0-999,999 nt and so on) showing the concordance of order of marker positions.
LG17-SNP511(B) LG17-c500(B) LG17-R(B)0
5
10
15
20
25
30
35
40
45
50
55
60
65
70
75
80
85
90
95
100
105
110
115
120
125
130
135
140
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Chr17: Links between markers in the genetic maps of the three segregating populations within the scaffold of the assembly showing the concordance of order of scaffold positions.
LG17-SNP511(B) LG17-c500(B) LG17-R(B)0
5
10
15
20
25
30
35
40
45
50
55
60
65
70
75
80
85
90
95
100
105
110
115
120
125
130
135
140
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Chr18: Links at identity level between the genetic maps of the three segregating populations and the integrated map.
LG18-SNP511(B) LG18-new1-c500(B) Chr18(B) LG18-R(B)0
5
10
15
20
25
30
35
40
45
50
55
60
65
70
75
80
85
90
WWW.NATURE.COM/NATURE | 53
Chr18: Links between markers in the genetic maps of the three segregating populations within the same 1 Mb bin (0-999,999 nt and so on) showing the concordance of order of marker positions.
LG18-SNP511(B) LG18-new1-c500(B) LG18-R(B)0
5
10
15
20
25
30
35
40
45
50
55
60
65
70
75
80
85
90
WWW.NATURE.COM/NATURE | 54
Chr18: Links between markers in the genetic maps of the three segregating populations within the scaffold of the assembly showing the concordance of order of scaffold positions.
LG18-SNP511(B) LG18-new1-c500(B) LG18-R(B)0
5
10
15
20
25
30
35
40
45
50
55
60
65
70
75
80
85
90
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