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

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.

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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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