Genetic basis for dosage sensitivity in Arabidopsis thaliana

Abstract

Aneuploidy, the relative excess or deficiency of specific chromosome types, results in gene dosage imbalance. Plants can produce viable and fertile aneuploid individuals, while most animal aneuploids are inviable or developmentally abnormal. The swarms of aneuploid progeny produced by Arabidopsis triploids constitute an excellent model to investigate the mechanisms governing dosage sensitivity and aneuploid syndromes. Indeed, genotype alters the frequency of aneuploid types within these swarms. Recombinant inbred lines that were derived from a triploid hybrid segregated into diploid and tetraploid individuals. In these recombinant inbred lines, a single locus, which we call SENSITIVE TO DOSAGE IMBALANCE (SDI), exhibited segregation distortion in the tetraploid subpopulation only. Recent progress in quantitative genotyping now allows molecular karyotyping and genetic analysis of aneuploid populations. In this study, we investigated the causes of the ploidy-specific distortion at SDI. Allele frequency was distorted in the aneuploid swarms produced by the triploid hybrid. We developed a simple quantitative measure for aneuploidy lethality and using this measure demonstrated that distortion was greatest in the aneuploids facing the strongest viability selection. When triploids were crossed to euploids, the progeny, which lack severe aneuploids, exhibited no distortion at SDI. Genetic characterization of SDI in the aneuploid swarm identified a mechanism governing aneuploid survival, perhaps by buffering the effects of dosage imbalance. As such, SDI could increase the likelihood of retaining genomic rearrangements such as segmental duplications. Additionally, in species where triploids are fertile, aneuploid survival would facilitate gene flow between diploid and tetraploid populations via a triploid bridge and prevent polyploid speciation. Our results demonstrate that positional cloning of loci affecting traits in populations containing ploidy and chromosome number variants is now feasible using quantitative genotyping approaches.

Figure 1. Diploid, Tetraploid, and Aneuploid Individuals in the Progeny of a Triploid

The proportions of diploid (light gray), tetraploid (dark gray), and aneuploid (white) individuals represent those observed in the CWW F ₂ population and the Col-0 × Wa-1 RILs [24]. The progressive decline of aneuploidy towards euploidy during the selfing generations is extrapolated.

Figure 2. Analysis of Allele Transmission at SDI in a Tetraploid Population

(A) Generation of the CCWW F ₂ population. (B) Expected (line) and observed (bars) genotype frequencies at the MN1.2 marker in the CCWW F ₂ population. (C) The mean percentage of Wa-1 allele at MN1.2 was significantly higher in the aneuploid than in the euploid individuals (t-test p-value = 0.0396). Standard errors are indicated.

Figure 3. Calculation of the ASI for Each Genome Content Class in the CWW F ₂ Population

Genome content is expressed as multiples of the nuclear genome content of haploid Col-0. (A) The number of individuals in each genome content class observed in the CWW F ₂ population (bars) was compared to the expected numbers based on random assortment of chromosomes at meiosis and absence of selection (line). Euploid classes (diploids and tetraploids) are represented by gray bars, while aneuploid classes are represented by white bars. Inset: the mean percentage of Wa-1 allele at MN1.2 was higher in the aneuploid than in the euploid individuals but the difference was not significant (t-test p-value = 0.382). Individuals with a genome content of 3.0 (black bars) were excluded from this analysis, because it was not possible to determine their exact karyotype and whether they were true triploids or aneuploids with a genome content consistent with 15 chromosomes. (B) ASI values for each genome content class. Negative values indicate that a class is observed more often than expected, while positive values indicate that a class is observed less often than expected.

Figure 4. Biological Relevance of the ASI

(A) For each individual in the CWW F ₂ population, total number of seed (top panel) and percentage of plump seed (bottom panel) were recorded. Data for all individuals in the same genome content class were pooled, and mean values were calculated (bars). Standard errors are indicated. (B) The relationship between ASI and total seed number (top panel) or percentage of plump seed (bottom panel) was estimated by regression analysis. Both regressions were significant, and p-values are indicated.

Figure 5. Relationship between Marker Genotype at MN1.2 and ASI in the CWW F ₂ Population

For each ASI value, the mean percentage of Wa-1 allele (gray dots) and corresponding standard errors (bars) are presented. No standard error could be calculated for classes containing only one individual. A regression curve was calculated using each individual independently, and the regression was significant (p-value < 0.0001, R ² = 0.16).

Figure 6. Different Aneuploid Types Found in the Progeny of Triploids

(A) The different types of individuals expected in the progeny of a selfed triploid depending on their karyotype and on the karyotype of the gametes that produced them. (B) In moderate aneuploids, the difference in number of copies of different chromosome types is maximum 1. In extreme aneuploids, some chromosome types are present in two (or more) additional copies than other chromosome types. (C) In the progeny of a cross between triploid and diploid individuals, only two types of individuals are found: euploids produced by euploid gametes or aneuploids produced from an aneuploid gamete and a euploid gamete.