Comparative genetic mapping between octoploid and diploid Fragaria species reveals a high level of colinearity between their genomes and the essentially disomic behavior of the cultivated octoploid strawberry

Abstract

Macrosynteny and colinearity between Fragaria (strawberry) species showing extreme levels of ploidy have been studied through comparative genetic mapping between the octoploid cultivated strawberry (F. xananassa) and its diploid relatives. A comprehensive map of the octoploid strawberry, in which almost all linkage groups are ranged into the seven expected homoeologous groups was obtained, thus providing the first reference map for the octoploid Fragaria. High levels of conserved macrosynteny and colinearity were observed between homo(eo)logous linkage groups and between the octoploid homoeologous groups and their corresponding diploid linkage groups. These results reveal that the polyploidization events that took place along the evolution of the Fragaria genus and the more recent juxtaposition of two octoploid strawberry genomes in the cultivated strawberry did not trigger any major chromosomal rearrangements in genomes involved in F. xananassa. They further suggest the existence of a close relationship between the diploid Fragaria genomes. In addition, despite the possible existence of residual levels of polysomic segregation suggested by the observation of large linkage groups in coupling phase only, the prevalence of linkage groups in coupling/repulsion phase clearly demonstrates that the meiotic behavior is mainly disomic in the cultivated strawberry.

Figure 1.—

Parental linkage maps of F. ×ananassa using a F₁ segregating progeny. The linkage groups (LGs) include only markers that segregated in a backcross configuration and were constructed using MapMaker software. A and B show, respectively, the female and male maps. Microsatellites (SSRs) are shown in shaded boxes. Distorted markers are noted with asterisks at the end of their name (*0.01 ≥ P ≥ 0.001 and **P < 0.001). Clusters of distorted markers are visualized by a gray oval on the chromosome bar. The LGs are grouped by homeologous groups (HGs) based on common SSR markers and on anchor markers with the diploid Fragaria genome. The name of each LG includes the number of their HG (I–VII), followed by a letter (a, b, c, or d) to identify arbitrarily groups within the same HG, and a dash with an f or m for LGs of the female or male map, respectively. Linkage groups noted with an asterisk at the end of their name contain exclusively markers segregating in coupling phase. M1 is a linkage group from the male map that has no anchor loci with any other linkage group from this parent.

Figure 1.—

Parental linkage maps of F. ×ananassa using a F₁ segregating progeny. The linkage groups (LGs) include only markers that segregated in a backcross configuration and were constructed using MapMaker software. A and B show, respectively, the female and male maps. Microsatellites (SSRs) are shown in shaded boxes. Distorted markers are noted with asterisks at the end of their name (*0.01 ≥ P ≥ 0.001 and **P < 0.001). Clusters of distorted markers are visualized by a gray oval on the chromosome bar. The LGs are grouped by homeologous groups (HGs) based on common SSR markers and on anchor markers with the diploid Fragaria genome. The name of each LG includes the number of their HG (I–VII), followed by a letter (a, b, c, or d) to identify arbitrarily groups within the same HG, and a dash with an f or m for LGs of the female or male map, respectively. Linkage groups noted with an asterisk at the end of their name contain exclusively markers segregating in coupling phase. M1 is a linkage group from the male map that has no anchor loci with any other linkage group from this parent.

Figure 1.—

Parental linkage maps of F. ×ananassa using a F₁ segregating progeny. The linkage groups (LGs) include only markers that segregated in a backcross configuration and were constructed using MapMaker software. A and B show, respectively, the female and male maps. Microsatellites (SSRs) are shown in shaded boxes. Distorted markers are noted with asterisks at the end of their name (*0.01 ≥ P ≥ 0.001 and **P < 0.001). Clusters of distorted markers are visualized by a gray oval on the chromosome bar. The LGs are grouped by homeologous groups (HGs) based on common SSR markers and on anchor markers with the diploid Fragaria genome. The name of each LG includes the number of their HG (I–VII), followed by a letter (a, b, c, or d) to identify arbitrarily groups within the same HG, and a dash with an f or m for LGs of the female or male map, respectively. Linkage groups noted with an asterisk at the end of their name contain exclusively markers segregating in coupling phase. M1 is a linkage group from the male map that has no anchor loci with any other linkage group from this parent.

Figure 1.—

Parental linkage maps of F. ×ananassa using a F₁ segregating progeny. The linkage groups (LGs) include only markers that segregated in a backcross configuration and were constructed using MapMaker software. A and B show, respectively, the female and male maps. Microsatellites (SSRs) are shown in shaded boxes. Distorted markers are noted with asterisks at the end of their name (*0.01 ≥ P ≥ 0.001 and **P < 0.001). Clusters of distorted markers are visualized by a gray oval on the chromosome bar. The LGs are grouped by homeologous groups (HGs) based on common SSR markers and on anchor markers with the diploid Fragaria genome. The name of each LG includes the number of their HG (I–VII), followed by a letter (a, b, c, or d) to identify arbitrarily groups within the same HG, and a dash with an f or m for LGs of the female or male map, respectively. Linkage groups noted with an asterisk at the end of their name contain exclusively markers segregating in coupling phase. M1 is a linkage group from the male map that has no anchor loci with any other linkage group from this parent.

Figure 2.—

An integrated linkage map of the octoploid F. ×ananassa, based on an F₁ segregating population, and its comparison with the diploid Fragaria F₂ reference map generated from the cross between F. vesca “815” and F. bucharica “601.” Only microsatellite (SSR) and SCAR markers that anchored at least two linkage groups (LGs) are shown. LGs were integrated using JoinMap software. The names of the LGs of the diploid map are those used by Sargent et al. (2006) (from I to VII, chromosome bars shaded). Integrated homoeologous groups (HG) for the octoploid map are notated with the same number (from I to VII) of the corresponding diploid LG. Four pairs of linkage groups identified as homologs were not integrated due to the limited number of anchor common markers and are arranged in a rectangle. Linkage group names for the octoploid consist of the number of the HG to which they belong followed by a letter (a, b, c, or d). The name of the two linkage groups (male and female) that merged to constitute the integrated linkage group is given in parentheses. These groups are named with the same name of the LG followed by a dash and a letter that indicates their origin (f for the female and m for the male maps). An asterisk is added when the LG included only markers in coupling phase.

Figure 2.—

An integrated linkage map of the octoploid F. ×ananassa, based on an F₁ segregating population, and its comparison with the diploid Fragaria F₂ reference map generated from the cross between F. vesca “815” and F. bucharica “601.” Only microsatellite (SSR) and SCAR markers that anchored at least two linkage groups (LGs) are shown. LGs were integrated using JoinMap software. The names of the LGs of the diploid map are those used by Sargent et al. (2006) (from I to VII, chromosome bars shaded). Integrated homoeologous groups (HG) for the octoploid map are notated with the same number (from I to VII) of the corresponding diploid LG. Four pairs of linkage groups identified as homologs were not integrated due to the limited number of anchor common markers and are arranged in a rectangle. Linkage group names for the octoploid consist of the number of the HG to which they belong followed by a letter (a, b, c, or d). The name of the two linkage groups (male and female) that merged to constitute the integrated linkage group is given in parentheses. These groups are named with the same name of the LG followed by a dash and a letter that indicates their origin (f for the female and m for the male maps). An asterisk is added when the LG included only markers in coupling phase.

Figure 2.—

An integrated linkage map of the octoploid F. ×ananassa, based on an F₁ segregating population, and its comparison with the diploid Fragaria F₂ reference map generated from the cross between F. vesca “815” and F. bucharica “601.” Only microsatellite (SSR) and SCAR markers that anchored at least two linkage groups (LGs) are shown. LGs were integrated using JoinMap software. The names of the LGs of the diploid map are those used by Sargent et al. (2006) (from I to VII, chromosome bars shaded). Integrated homoeologous groups (HG) for the octoploid map are notated with the same number (from I to VII) of the corresponding diploid LG. Four pairs of linkage groups identified as homologs were not integrated due to the limited number of anchor common markers and are arranged in a rectangle. Linkage group names for the octoploid consist of the number of the HG to which they belong followed by a letter (a, b, c, or d). The name of the two linkage groups (male and female) that merged to constitute the integrated linkage group is given in parentheses. These groups are named with the same name of the LG followed by a dash and a letter that indicates their origin (f for the female and m for the male maps). An asterisk is added when the LG included only markers in coupling phase.

Figure 2.—

An integrated linkage map of the octoploid F. ×ananassa, based on an F₁ segregating population, and its comparison with the diploid Fragaria F₂ reference map generated from the cross between F. vesca “815” and F. bucharica “601.” Only microsatellite (SSR) and SCAR markers that anchored at least two linkage groups (LGs) are shown. LGs were integrated using JoinMap software. The names of the LGs of the diploid map are those used by Sargent et al. (2006) (from I to VII, chromosome bars shaded). Integrated homoeologous groups (HG) for the octoploid map are notated with the same number (from I to VII) of the corresponding diploid LG. Four pairs of linkage groups identified as homologs were not integrated due to the limited number of anchor common markers and are arranged in a rectangle. Linkage group names for the octoploid consist of the number of the HG to which they belong followed by a letter (a, b, c, or d). The name of the two linkage groups (male and female) that merged to constitute the integrated linkage group is given in parentheses. These groups are named with the same name of the LG followed by a dash and a letter that indicates their origin (f for the female and m for the male maps). An asterisk is added when the LG included only markers in coupling phase.