Persistent whole-chromosome aneuploidy is generally associated with nascent allohexaploid wheat

Abstract

Allopolyploidization has been a driving force in plant evolution. Formation of common wheat (Triticum aestivum L.) represents a classic example of successful speciation via allopolyploidy. Nevertheless, the immediate chromosomal consequences of allopolyploidization in wheat remain largely unexplored. We report here an in-depth investigation on transgenerational chromosomal variation in resynthesized allohexaploid wheats that are identical in genome constitution to common wheat. We deployed sequential FISH, genomic in situ hybridization (GISH), and homeolog-specific pyrosequencing, which enabled unequivocal identification of each of the 21 homologous chromosome pairs in each of >1,000 individual plants from 16 independent lines. We report that whole-chromosome aneuploidy occurred ubiquitously in early generations (from selfed generation S(1) to >S(20)) of wheat allohexaploidy although at highly variable frequencies (20-100%). In contrast, other types of gross structural variations were scant. Aneuploidy included an unexpected hidden type, which had a euploid chromosome number of 2n = 42 but with simultaneous loss and gain of nonhomeologous chromosomes. Of the three constituent subgenomes, B showed the most lability for aneuploidy, followed by A, but the recently added D subgenome was largely stable in most of the studied lines. Chromosome loss and gain were also unequal across the 21 homologous chromosome pairs. Pedigree analysis showed no evidence for progressive karyotype stabilization even with multigenerational selection for euploidy. Profiling of two traits directly related to reproductive fitness showed that although pollen viability was generally reduced by aneuploidy, the adverse effect of aneuploidy on seed-set is dependent on both aneuploidy type and synthetic line.

Fig. 1.

An example of karyotyping of a single plant from the nascent allohexaploid wheat line 960. (A) Karyotype based on FISH using 5S and 45S rDNA probes. Chromosomes 1A, 1B, 1D, 5A, 5B, 5D, and 6B can be identified. (B) The original FISH image used for the karyotype in A. (C) Karyotype based on FISH using two repetitive DNA probes, pSc119.2 and pAS1. All 21 wheat chromosomes can be identified based on these two repeats and the two rDNA probes. (D) The original FISH image used for the karyotype in C. (E) Karyotype based on GISH. The A (green), B (blue), and D (pink) subgenome chromosomes can be distinguished. (F) The original FISH image used for the karyotype in E. (Scale bars, 10 µm.)

Fig. 2.

Chromosome number distribution in five different selfed generations of (A) 960 (S₃, S₄, and S₇–S₉) and (B) AT5 (S₄–S₈). Chromosome numbers were determined based on karyotyping of individual plants. Hidden aneuploids refer to those with a euploid chromosome number (2n = 42) but simultaneous loss and gain of different chromosomes. For each generation, from 26 to 107 randomly selected individuals were karyotyped (SI Materials and Methods). x axis = number of chromosomes and y axis = number of individuals.

Fig. 3.

Examples of the two types (I and II) of “hidden aneuploidy” observed in 960. (A) Karyotype of a type I hidden aneuploid with a 2n chromosome number of 42, but a genomic constitution of 38 + 1 (3A) + 3 (7B). (B) Karyotype of a type II hidden aneuploid with a 2n chromosome number of 42, but a genomic constitution of 38 + 1(1B) + 3(4B). Yellow and red boxes respectively mark the lost and gained chromosomes.

Fig. 4.

Transgenerational chromosome number variation based on karyotyping of a total of 111 individual plants across 11 consecutive selfed-generations (S₀–S₁₀) of 960. A single euploid S₁ plant was selected from a euploid S₀ plant. Then, two euploid S₂ plants and the first two S₂ aneuploid plants (identified as a trisomic 1B plant and a monosomic 4B plant) were selected to produce S₃. In S₃, one euploid plant and the first S₃ aneuploid plant from each S₂ plant were selected (the exact aneuploid karyotypes were shown). From four to nine S₄ plants derived from each of the eight S₃ plants were randomly selected and karyotyped (the exact aneuploid karyotypes were shown). Two independent euploid S₄ plants of different lineages were then used to generate euploidy S₅, S₆, S₇, and S₈ plants sequentially (transgenerational persistent selection for euploidy). Ten randomly selected S₉ plants from each of the two euploid S₈ plants were karyotyped (the exact aneuploid karyotypes were shown). Empty and filled circles denote for euploid and aneuploid plants, respectively, and the exact euploid karyotypes were designated at the bottom.