Defining regions and rearrangements of the Silene latifolia Y chromosome

Abstract

We combine data from published marker genotyping of three sets of S. latifolia Y chromosome deletion mutants with changed sex phenotypes and add genotypes for several new genic markers to refine the deletion map of the Y chromosome and compare it with the X chromosome genetic map. We conclude that the Y chromosome of this species has been derived through multiple rearrangements of the ancestral gene arrangement and that none of the rearrangements so far detected was involved in stopping X-Y recombination. Different Y genotypes may also differ in their gene content and possibly arrangements, suggesting that mapping the Y-linked sex-determining genes will be difficult, even if many further genic markers are obtained. Even in determining the map of Y chromosome markers to discover all the rearrangements, physical mapping by FISH or other experiments will be essential. Future deletion mapping work should ensure that markers are studied in the parents of deletion mutants and should probably include additional deletions that were not ascertained by causing mutant sex phenotypes.

Figure 1.—

Marker genotyping results from the sets of deletion strains from three different initial M0 plants. (A and B) The M and French sets, respectively. (C) The strains of set U. The sizes of the deletions are known only for some of the French strains, and the column with these data is absent from the other diagrams. In all the diagrams, the pseudo-autosomal region is assumed to be at the right end of the markers on the basis of the Yp arm terminal deletion (Lardon et al. 1999) clearly mapping at the other end. The genic marker names are shown in boldface type (and the markers are numbered according to their order in the genetic map of the X chromosome, with the pseudo-autosomal region labeled with number 1 and the most distal marker on the other arm of the X, SlX6a, labeled number 10 in A–C). The positions of the genes whose deletion affects the flower phenotype are shown as wider columns, and their inferred states (deleted or present) are gray. The position of the SlY3 gene is uncertain (see text), but is indicated as on the Yq arm, where it appears to fit best with either set of genotypes. The markers and strains with differences from the data in Zluvova et al. (2005a), in which fewer strains were genotyped, are indicated by boxed cells in the diagrams. Zeros in the column for the SlY6b gene indicate that there is no information in plants from these M0 parents, because the parent plant is deleted for this marker (mutants of set M and the French set; see text). Missing data (markers that were not scored in certain strains) are indicated by open cells (in supplemental Figure 1, the states of these cells are inferred, showing that many of them are consistent with other, probably physically close, markers).

Figure 2.—

Interpretation of the results in Figure 1 and supplemental Figure 1, showing the inversions necessary to account for the deletion data. The shading and numerals indicate X–Y divergence levels (black boxes indicate ∼20% silent-site divergence, and open boxes indicate the PAR, with no divergence). The version shown assumes that SlCypX is on the Xq arm. If it is located on the Xp arm, the pericentric inversion would bring it to a position proximal to the centromere of the Y chromosome, relative to the DD44-Y gene on the Yp arm. Therefore, either DD44-Y should be placed distal to the SlSsY gene (which does not fit the data as well as the position shown, but requires two further strains to have multiple deletions) or a further rearrangement would be necessary to move SlCypY to a more distal position. The right side of the diagram shows the putative alternative arrangement of the Y chromosome in the set of U strains, in which SlY1 is apparently on the Yp arm (see text).