The integration of recombination and physical maps in a large-genome monocot using haploid genome analysis in a trihybrid allium population

Abstract

Integrated mapping in large-genome monocots has been carried out on a limited number of species. Furthermore, integrated maps are difficult to construct for these species due to, among other reasons, the specific plant populations needed. To fill these gaps, Alliums were chosen as target species and a new strategy for constructing suitable populations was developed. This strategy involves the use of trihybrid genotypes in which only one homeolog of a chromosome pair is recombinant due to interspecific recombination. We used genotypes from a trihybrid Allium cepa x (A. roylei x A. fistulosum) population. Recombinant chromosomes 5 and 8 from the interspecific parent were analyzed using genomic in situ hybridization visualization of recombination points and the physical positions of recombination were integrated into AFLP linkage maps of both chromosomes. The integrated maps showed that in Alliums recombination predominantly occurs in the proximal half of chromosome arms and that 57.9% of PstI/MseI markers are located in close proximity to the centromeric region, suggesting the presence of genes in this region. These findings are different from data obtained on cereals, where recombination rate and gene density tends to be higher in distal regions.

Figure 1.—

GISH images of recombinant A. roylei × A. fistulosum (RF) homeologous chromosomes for Allium chromosomes 5 (A) and 8 (B), respectively. Numbers below the GISH pictures indicate a specific CC × RF genotype. The A. roylei segment on a recombinant chromosome appears in green and the A. fistulosum segment in red.

Figure 2.—

The integrated recombination and physical maps for recombinant A. roylei × A. fistulosum (RF), chromosome 5. The recombination and physical maps of the recombinant RF chromosome are split into the recombination and physical maps of A. roylei (left) and the recombination and physical maps of A. fistulosum (right). Horizontal lines on the physical maps indicate sites of recombination between A. roylei and A. fistulosum dividing the chromosome into subregions. The genotype numbers, from which the correspondent recombination sites were obtained, are shown in boldface type. On the recombination maps, markers are indicated as follows: e35m52a-302f means restriction enzyme combination EcoI/MseI, primers e35 and m52; “a” identifies the additional seventh selective base, 302 is the length of the fragment, and “f” or “r” specifies whether a marker is specific for A. roylei or for A. fistulosum. Recombination maps and physical maps are linked to each other by lines connecting observed physical recombination sites and their corresponding genetic sites.

Figure 3.—

The integrated recombination and physical maps for the recombinant A. roylei × A. fistulosum (RF), chromosome 8. See legend to Figure 2.

Figure 4.—

Physical distribution of recombination frequencies along recombinant A. roylei × A. fistulosum (RF), chromosome 5. The frequency of recombination events per physical unit (centimorgans per physical unit) was calculated by dividing the length of a genetic subregion in centimorgans (percentage of recombination) by the length of the corresponding physical subregion in physical units and was plotted at the midpoint of each physical subregion. The arrow indicates the physical position of the centromere. Vertical lines on the chromosome ideogram indicate sites of recombination between A. roylei and A. fistulosum dividing the chromosome into subregions.

Figure 5.—

Physical distribution of recombination frequencies along recombinant A. roylei × A. fistulosum (RF), chromosome 8. See legend to Figure 4.

Figure 6.—

Physical distribution of AFLP markers along recombinant A. roylei × A. fistulosum (RF), chromosome 5. The density of AFLP markers present in each chromosomal subregion is plotted at the midpoint of each subregion. The arrow indicates the physical position of the centromere. Vertical lines on the chromosome ideogram indicate sites of recombination between A. roylei and A. fistulosum dividing the chromosome into subregions.

Figure 7.—

Physical distribution of AFLP markers along recombinant A. roylei × A. fistulosum (RF), chromosome 8. See legend to Figure 6.