Extensive chromosomal variation in a recently formed natural allopolyploid species, Tragopogon miscellus (Asteraceae)

Abstract

Polyploidy, or whole genome duplication, has played a major role in the evolution of many eukaryotic lineages. Although the prevalence of polyploidy in plants is well documented, the molecular and cytological consequences are understood largely from newly formed polyploids (neopolyploids) that have been grown experimentally. Classical cytological and molecular cytogenetic studies both have shown that experimental neoallopolyploids often have meiotic irregularities, producing chromosomally variable gametes and progeny; however, little is known about the extent or duration of chromosomal variation in natural neoallopolyploid populations. We report the results of a molecular cytogenetic study on natural populations of a neoallopolyploid, Tragopogon miscellus, which formed multiple times in the past 80 y. Using genomic and fluorescence in situ hybridization, we uncovered massive and repeated patterns of chromosomal variation in all populations. No population was fixed for a particular karyotype; 76% of the individuals showed intergenomic translocations, and 69% were aneuploid for one or more chromosomes. Importantly, 85% of plants exhibiting aneuploidy still had the expected chromosome number, mostly through reciprocal monosomy-trisomy of homeologous chromosomes (1:3 copies) or nullisomy-tetrasomy (0:4 copies). The extensive chromosomal variation still present after ca. 40 generations in this biennial species suggests that substantial and prolonged chromosomal instability might be common in natural populations after whole genome duplication. A protracted period of genome instability in neoallopolyploids may increase opportunities for alterations to genome structure, losses of coding and noncoding DNA, and changes in gene expression.

Fig. 1.

Maps showing T. miscellus collection sites in relation to the northwestern United States. (Upper) The Pacific Ocean (gray) and states of Washington (WA), Oregon (OR), Idaho (ID), and Montana (MT) are indicated; a rectangle shows the area in the enlarged map. (Lower) Locations of collection sites, with major roads shown in gray. The greater Spokane area (shaded gray) includes the city of Spokane (collections 2729 and 2730), and the towns of Veradale (2731), Post Falls (2736) and Coeur d'Alene (2738). Two additional collection sites are indicated: Oakesdale (2872) and Pullman (2785/2875-B). The Washington–Idaho state line is indicated by the dotted line. (Scale bar: 10 mi.)

Fig. 2.

Mitotic karyotype of a T. miscellus plant showing an additive chromosome complement. Metaphase chromosomes (from plant 2875–1-1) were first subjected to FISH (top row) using probes for 35S rDNA (green), a centromeric repeat (TPRMBO; red), and a subtelomeric repeat (TGP7; yellow). The same spread was then reprobed with total genomic DNA (GISH; middle row) of T. dubius (green) and T. pratensis (red); chromosomes were counterstained with DAPI (gray). The lower row shows the same chromosomes with only DAPI staining (blue). Each chromosome is present in two copies (disomic). Examples of chromosomes that are homologs and homeologs are indicated. (Scale bar: 5 μm.)

Fig. 3.

Mitotic karyotype of an additive T. miscellus plant probed with dispersed repetitive DNA. Metaphase chromosomes (from plant 2875-B-5) were first subjected to FISH (upper row) using a mixture of two probes for DNA repeats abundant in only one of the diploid parental genomes, T. pratensis (pra001; red) and T. dubius (dub005; green). In addition, a subtelomeric repeat (TGP7; yellow) present in both subgenomes was included, and DNA was counterstained with DAPI (gray; visible where the probe signal is less intense). The same chromosome spread was then reprobed with total genomic DNA (lower row) of T. dubius (green) and T. pratensis (red). (Scale bar: 5 μm.)

Fig. 4.

Mitotic karyotypes of 10 T. miscellus individuals from Oakesdale, WA. GISH was carried out with total genomic DNA probes of T. dubius (green) and T. pratensis (red). Arrows indicate the positions of translocation breakpoints. Diamond symbols are below aneuploid chromosomes (i.e., those that are not disomic). (Scale bar: 5 μm.)

Fig. 5.

Stacked bar chart showing the number of chromosome losses and gains from GISH karyotypes of seed-grown plants. On the y-axis are the numbers of aneuploid chromosomes observed in the 48 plants grown from seed, which were not chromosomally additive of the parents. Each bar on the x-axis represents one of the six homeologous chromosome groups, A–F, of T. pratensis (magenta) and T. dubius origin (green). Cases of chromosome loss (either monosomy or nullisomy) and gain (either trisomy or tetrasomy) are shown below and above the origin, respectively. The severity of the aneuploidy is indicated by color intensity, with monosomy or trisomy shown by lighter colors and nullisomy or tetrasomy indicated by darker colors.