An enhanced linkage map of the sheep genome comprising more than 1000 loci

Abstract

A medium-density linkage map of the ovine genome has been developed. Marker data for 550 new loci were generated and merged with the previous sheep linkage map. The new map comprises 1093 markers representing 1062 unique loci (941 anonymous loci, 121 genes) and spans 3500 cM (sex-averaged) for the autosomes and 132 cM (female) on the X chromosome. There is an average spacing of 3.4 cM between autosomal loci and 8.3 cM between highly polymorphic [polymorphic information content (PIC) > or = 0.7] autosomal loci. The largest gap between markers is 32.5 cM, and the number of gaps of > 20 cM between loci, or regions where loci are missing from chromosome ends, has been reduced from 40 in the previous map to 6. Five hundred and seventy-three of the loci can be ordered on a framework map with odds of > 1000 : 1. The sheep linkage map contains strong links to both the cattle and goat maps. Five hundred and seventy-two of the loci positioned on the sheep linkage map have also been mapped by linkage analysis in cattle, and 209 of the loci mapped on the sheep linkage map have also been placed on the goat linkage map. Inspection of ruminant linkage maps indicates that the genomic coverage by the current sheep linkage map is comparable to that of the available cattle maps. The sheep map provides a valuable resource to the international sheep, cattle, and goat gene mapping community.

Figure 1

An updated genetic linkage map for the sheep. Loci shown on the main framework map were positioned with odds of >1000 : 1. Loci to the right of the main framework map were significantly linked to the region indicated by the vertical lines, but could not be positioned on the framework at odds of >1000 : 1. All the autosomal linkage maps are sex-averaged and map distances are estimated by use of the Kosambi mapping function. The X chromosome map shows female map distances, whereas the Y chromosome map shows male map distances. (Horizontal arrows) Likely positions of the centromeres for chromosomes 1, 2, and 3. The remaining chromosomes are oriented with the centromeres at the top. Loci present on the second-generation or X chromosome sheep linkage maps that have not been mapped on the IMF are indicated at the bottom of the relevant chromosomes. The species of origin of the marker(s) used to position a locus is indicated by plain text for sheep markers, italics for cattle markers, and underlined for goat markers. Anonymous loci are prefaced by a backslash. Loci are color-coded by the following system: (red) PIC 0.8 or higher, if no PIC, then 11 or more alleles; (orange) PIC between 0.7 and 0.79, if no PIC, then 8–10 alleles; (green) PIC between 0.6 and 0.69, if no PIC, then 6–7 alleles; (blue) PIC between 0.5 and 0.59, if no PIC, then 5 alleles; (purple) PIC between 0.3 and 0.49, if no PIC then 3–4 alleles; (dark grey) PIC below 0.3, if no PIC, then 2 alleles; (light grey) gene in close proximity to a mapped marker that is within, or closer to, another gene. (*) Although there are at least two DQB genes in sheep, the relationship between the ovine DQB PCR products and DQB genes is unresolved (van Oorschot et al. 1994).

Figure 1

An updated genetic linkage map for the sheep. Loci shown on the main framework map were positioned with odds of >1000 : 1. Loci to the right of the main framework map were significantly linked to the region indicated by the vertical lines, but could not be positioned on the framework at odds of >1000 : 1. All the autosomal linkage maps are sex-averaged and map distances are estimated by use of the Kosambi mapping function. The X chromosome map shows female map distances, whereas the Y chromosome map shows male map distances. (Horizontal arrows) Likely positions of the centromeres for chromosomes 1, 2, and 3. The remaining chromosomes are oriented with the centromeres at the top. Loci present on the second-generation or X chromosome sheep linkage maps that have not been mapped on the IMF are indicated at the bottom of the relevant chromosomes. The species of origin of the marker(s) used to position a locus is indicated by plain text for sheep markers, italics for cattle markers, and underlined for goat markers. Anonymous loci are prefaced by a backslash. Loci are color-coded by the following system: (red) PIC 0.8 or higher, if no PIC, then 11 or more alleles; (orange) PIC between 0.7 and 0.79, if no PIC, then 8–10 alleles; (green) PIC between 0.6 and 0.69, if no PIC, then 6–7 alleles; (blue) PIC between 0.5 and 0.59, if no PIC, then 5 alleles; (purple) PIC between 0.3 and 0.49, if no PIC then 3–4 alleles; (dark grey) PIC below 0.3, if no PIC, then 2 alleles; (light grey) gene in close proximity to a mapped marker that is within, or closer to, another gene. (*) Although there are at least two DQB genes in sheep, the relationship between the ovine DQB PCR products and DQB genes is unresolved (van Oorschot et al. 1994).

Figure 1

An updated genetic linkage map for the sheep. Loci shown on the main framework map were positioned with odds of >1000 : 1. Loci to the right of the main framework map were significantly linked to the region indicated by the vertical lines, but could not be positioned on the framework at odds of >1000 : 1. All the autosomal linkage maps are sex-averaged and map distances are estimated by use of the Kosambi mapping function. The X chromosome map shows female map distances, whereas the Y chromosome map shows male map distances. (Horizontal arrows) Likely positions of the centromeres for chromosomes 1, 2, and 3. The remaining chromosomes are oriented with the centromeres at the top. Loci present on the second-generation or X chromosome sheep linkage maps that have not been mapped on the IMF are indicated at the bottom of the relevant chromosomes. The species of origin of the marker(s) used to position a locus is indicated by plain text for sheep markers, italics for cattle markers, and underlined for goat markers. Anonymous loci are prefaced by a backslash. Loci are color-coded by the following system: (red) PIC 0.8 or higher, if no PIC, then 11 or more alleles; (orange) PIC between 0.7 and 0.79, if no PIC, then 8–10 alleles; (green) PIC between 0.6 and 0.69, if no PIC, then 6–7 alleles; (blue) PIC between 0.5 and 0.59, if no PIC, then 5 alleles; (purple) PIC between 0.3 and 0.49, if no PIC then 3–4 alleles; (dark grey) PIC below 0.3, if no PIC, then 2 alleles; (light grey) gene in close proximity to a mapped marker that is within, or closer to, another gene. (*) Although there are at least two DQB genes in sheep, the relationship between the ovine DQB PCR products and DQB genes is unresolved (van Oorschot et al. 1994).

Figure 1

An updated genetic linkage map for the sheep. Loci shown on the main framework map were positioned with odds of >1000 : 1. Loci to the right of the main framework map were significantly linked to the region indicated by the vertical lines, but could not be positioned on the framework at odds of >1000 : 1. All the autosomal linkage maps are sex-averaged and map distances are estimated by use of the Kosambi mapping function. The X chromosome map shows female map distances, whereas the Y chromosome map shows male map distances. (Horizontal arrows) Likely positions of the centromeres for chromosomes 1, 2, and 3. The remaining chromosomes are oriented with the centromeres at the top. Loci present on the second-generation or X chromosome sheep linkage maps that have not been mapped on the IMF are indicated at the bottom of the relevant chromosomes. The species of origin of the marker(s) used to position a locus is indicated by plain text for sheep markers, italics for cattle markers, and underlined for goat markers. Anonymous loci are prefaced by a backslash. Loci are color-coded by the following system: (red) PIC 0.8 or higher, if no PIC, then 11 or more alleles; (orange) PIC between 0.7 and 0.79, if no PIC, then 8–10 alleles; (green) PIC between 0.6 and 0.69, if no PIC, then 6–7 alleles; (blue) PIC between 0.5 and 0.59, if no PIC, then 5 alleles; (purple) PIC between 0.3 and 0.49, if no PIC then 3–4 alleles; (dark grey) PIC below 0.3, if no PIC, then 2 alleles; (light grey) gene in close proximity to a mapped marker that is within, or closer to, another gene. (*) Although there are at least two DQB genes in sheep, the relationship between the ovine DQB PCR products and DQB genes is unresolved (van Oorschot et al. 1994).

Figure 2

Comparisons between positions of loci mapped in sheep on ruminant maps. (Tick marks) Positions of all loci that have been mapped in each species. Dashed and dotted lines are drawn between the same locus on different chromosomes: (dashed) goat–sheep, sheep–MARC97, and MARC97–IBRP97; (dotted) sheep–IBRP97. Lines are drawn only for those loci that have been mapped in sheep. (Although many more links exist between the cattle maps, and additional links can be found when comparing the goat and cattle maps, these are not shown.) The only loci identified by name are those whose relative position differs significantly between maps. All chromosomes are depicted with the centromere at the top except for cattle and goat chromosomes 3, 8, 11, and X for which the order has been inverted. (Box) Region of cattle chromosome 9 that is equivalent to the centomeric portion of sheep and goat chromosomes 14.

Figure 2

Comparisons between positions of loci mapped in sheep on ruminant maps. (Tick marks) Positions of all loci that have been mapped in each species. Dashed and dotted lines are drawn between the same locus on different chromosomes: (dashed) goat–sheep, sheep–MARC97, and MARC97–IBRP97; (dotted) sheep–IBRP97. Lines are drawn only for those loci that have been mapped in sheep. (Although many more links exist between the cattle maps, and additional links can be found when comparing the goat and cattle maps, these are not shown.) The only loci identified by name are those whose relative position differs significantly between maps. All chromosomes are depicted with the centromere at the top except for cattle and goat chromosomes 3, 8, 11, and X for which the order has been inverted. (Box) Region of cattle chromosome 9 that is equivalent to the centomeric portion of sheep and goat chromosomes 14.

Figure 2

Comparisons between positions of loci mapped in sheep on ruminant maps. (Tick marks) Positions of all loci that have been mapped in each species. Dashed and dotted lines are drawn between the same locus on different chromosomes: (dashed) goat–sheep, sheep–MARC97, and MARC97–IBRP97; (dotted) sheep–IBRP97. Lines are drawn only for those loci that have been mapped in sheep. (Although many more links exist between the cattle maps, and additional links can be found when comparing the goat and cattle maps, these are not shown.) The only loci identified by name are those whose relative position differs significantly between maps. All chromosomes are depicted with the centromere at the top except for cattle and goat chromosomes 3, 8, 11, and X for which the order has been inverted. (Box) Region of cattle chromosome 9 that is equivalent to the centomeric portion of sheep and goat chromosomes 14.