Autoimmune response as a mechanism for a Dobzhansky-Muller-type incompatibility syndrome in plants

Abstract

Epistatic interactions between genes are a major factor in evolution. Hybrid necrosis is an example of a deleterious phenotype caused by epistatic interactions that is observed in many intra- and interspecific plant hybrids. A large number of hybrid necrosis cases share phenotypic similarities, suggesting a common underlying mechanism across a wide range of plant species. Here, we report that approximately 2% of intraspecific crosses in Arabidopsis thaliana yield F1 progeny that express necrosis when grown under conditions typical of their natural habitats. We show that several independent cases result from epistatic interactions that trigger autoimmune-like responses. In at least one case, an allele of an NB-LRR disease resistance gene homolog is both necessary and sufficient for the induction of hybrid necrosis, when combined with a specific allele at a second locus. The A. thaliana cases provide insights into the molecular causes of hybrid necrosis, and serve as a model for further investigation of intra- and interspecific incompatibilities caused by a simple epistatic interaction. Moreover, our finding that plant immune-system genes are involved in hybrid necrosis suggests that selective pressures related to host-pathogen conflict might cause the evolution of gene flow barriers in plants.

Figure 1. Uk-1 × Uk-3 Hybrid Phenotype and QTL Mapping

(A) Uk-1 (left), Uk-1/Uk-3 F₁ hybrid (middle), and Uk-3 (right) plants grown at 16 °C. Scale bar represents 2 cm. (B) QTL mapping using 181 individuals identifies two regions associated with the F₁-like phenotype in F₂ populations. Red line delineates significance threshold (p = 0.05, established by 1,000 permutations); tick marks indicate marker positions. (C) Heat map for two-dimensional genome scan with a two-QTL model for maximum joint lod (upper triangle) and interaction lod (lower triangle) scores. Color-coded scale indicates values for epistatic interaction on the left, and joint lod score on the right.

Figure 2. Identification of DM1 as an AT5G41740/AT5G41750 Allele

(A) Schematic alignment of mapping interval. Genes are indicated with green boxes. Insertions relative to Col-0 are indicated with red triangles, deletions in beige, and duplications in blue. The last two digits of AT5G417XX gene identifiers are given above each line. AT5G41740 and AT5G41750 are NB-LRR genes. Uk-3 has only a single AT5G41740/AT5G41750 gene that is divergent from both Col-0 genes. Parentheses for Uk-1 indicate that these open reading frames are incomplete; asterisk indicates stop codon. Transposons are labeled below each line: MULE (M), copia (C), LINE (L), gypsy (G), and gypsy-associated UlpI protease sequence (U). (B) Uk-1/Uk-3 F₁ hybrids grown at 16 °C, with transgenic sibling constitutively expressing amiRNA targeting AT5G41740/AT5G41750 on the left. (C) T₁ plants carrying a Uk-3 genomic fragment that includes the AT5G41740/AT5G41750 allele. From left to right: Uk-1, Col-0, and Uk-3. Scale bars in (B) and (C) represent 1 cm.

Figure 3. Microarray Analysis of Necrotic Hybrids

(A) Expression profiles of Uk-1, Uk-3, and F₁ hybrids. Genes shown differ significantly between the F₁ and the two parents at 16 °C, but do not differ between the two parents. (B) Profiles of 1,080 genes that are significantly changed in at least one hybrid relative to its parents at 16 °C. Genes induced in hybrids are in green; suppressed genes are in blue. Yellow lines indicate three genes commonly used as markers of pathogen response (PR1, PR2, and PR5; see also Figure S3). In addition to profiles for three hybrids and their parents, regular Uk-1/Uk-3 hybrids (“sick”) are compared with siblings that are phenotypically rescued by a transgene that inactivates DM1. (C) PCA using the same set of 1,080 genes, with hybrids marked red and parents green. B, Bla-1; BH, Bla-1/Hh-0 F₁; H, Hh-0; K, KZ10; KM, KZ10/Mrk-0 F₁; Mi, Mir-0; Mr, Mrk-0; MS, Mir-0/Se-0 F₁; S, Se-0; U, rescued Uk-1/Uk-3 F₁; UU, nontransgenic Uk-1/Uk-3 F₁.

Figure 4. Range of Necrosis Phenotypes in A. thaliana Hybrids

(A) Examples of necrotic hybrids representing three phenotypic classes defined in the text; 6-wk-old vegetative rosettes are shown. Two compatible hybrids, aged 5 wk, are shown in the bottom row for comparison. Scale bar (top right) represents 3 cm. (B) Trypan Blue staining for dead cells in leaves of hybrids and parents. Scale bar (top right) represents 250 μm.

Figure 5. Susceptibility of Hybrids and Parental Accessions to H. parasitica Infection

(A) Number of H. parasitica sporangiophores, scored 5 d (KZ10/Mrk-0, Uk-1/Uk-3, and Se-0/Hh-0) or 6 d (Bla-1/Hh-0) post-infection. H. parasitica strains used are indicated on the bottom. (B) Resistance and disease progression in Mir-0, Se-0, and their F₁ hybrids. Since H. parasitica Noco2 sporulated only weakly on the parents, resistance was assessed by scoring interaction sites (Figure S2). HR sites indicate resistance, free hyphae sites (FH) indicate susceptibility, and trailing necrosis sites (TN) indicate an intermediate response. (C) H. parasitica Emco5 infection of Uk-1, Uk-3, their F₁ hybrid, Col-0, and two Col-0 backcross lines. Col[Uk-1] carries the DM2 region from Uk-1 on Chromosome 3, while Col[Uk-3] carries the DM1 region from Uk-3 on Chromosome 5. Error bars in (A) and (C) indicate 95% confidence interval. All experiments were performed at least twice.