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Analysis of a plant complex resistance gene locus underlying immune-related hybrid incompatibility and its occurrence in nature.

Alcázar R, von Reth M, Bautor J, Chae E, Weigel D, Koornneef M, Parker JE - PLoS Genet. (2014)

Bottom Line: In a neutral background, expression of most RPP1-like Ler genes, except R3, has no effect on growth or pathogen resistance.Only Gorzów individuals carrying the RPP1-like Ler haplotype are incompatible with Kas-2 and Kond, whereas other RPP1-like alleles in the population are compatible.Therefore, the RPP1-like Ler haplotype has been maintained in genetically different individuals at a single site, allowing exploration of forces shaping the evolution of RPP1-like genes at local and regional population scales.

View Article: PubMed Central - PubMed

Affiliation: Department of Natural Products, Plant Biology and Soil Science, Laboratory of Plant Physiology, Faculty of Pharmacy. University of Barcelona, Barcelona, Spain; Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany; Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany.

ABSTRACT
Mechanisms underlying speciation in plants include detrimental (incompatible) genetic interactions between parental alleles that incur a fitness cost in hybrids. We reported on recessive hybrid incompatibility between an Arabidopsis thaliana strain from Poland, Landsberg erecta (Ler), and many Central Asian A. thaliana strains. The incompatible interaction is determined by a polymorphic cluster of Toll/interleukin-1 receptor-nucleotide binding-leucine rich repeat (TNL) RPP1 (Recognition of Peronospora parasitica1)-like genes in Ler and alleles of the receptor-like kinase Strubbelig Receptor Family 3 (SRF3) in Central Asian strains Kas-2 or Kond, causing temperature-dependent autoimmunity and loss of growth and reproductive fitness. Here, we genetically dissected the RPP1-like Ler locus to determine contributions of individual RPP1-like Ler (R1-R8) genes to the incompatibility. In a neutral background, expression of most RPP1-like Ler genes, except R3, has no effect on growth or pathogen resistance. Incompatibility involves increased R3 expression and engineered R3 overexpression in a neutral background induces dwarfism and sterility. However, no individual RPP1-like Ler gene is sufficient for incompatibility between Ler and Kas-2 or Kond, suggesting that co-action of at least two RPP1-like members underlies this epistatic interaction. We find that the RPP1-like Ler haplotype is frequent and occurs with other Ler RPP1-like alleles in a local population in Gorzów Wielkopolski (Poland). Only Gorzów individuals carrying the RPP1-like Ler haplotype are incompatible with Kas-2 and Kond, whereas other RPP1-like alleles in the population are compatible. Therefore, the RPP1-like Ler haplotype has been maintained in genetically different individuals at a single site, allowing exploration of forces shaping the evolution of RPP1-like genes at local and regional population scales.

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Transgene and PR-1 expression in ColRPP1 lines.Expression of RPP1-like Ler R1, R2, R3, R4, R5, R7 and R8 transgenes (left axis) and PR-1 (right axis) determined in individual homozygous ColRPP1 lines, Ler and NIL plants grown at 14–16°C by qRT-PCR. Values are relative to Ler and the mean ± SD of three biological replicates each using three technical replicates. NIL (incompatible Ler/Kas-2 near-isogenic line [31]). Significant differences in gene expression between Ler and different ColRPP1 lines using Student's t-test are indicated by asterisks: *P<0.05, **P<0.01, ***P<0.005.
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pgen-1004848-g002: Transgene and PR-1 expression in ColRPP1 lines.Expression of RPP1-like Ler R1, R2, R3, R4, R5, R7 and R8 transgenes (left axis) and PR-1 (right axis) determined in individual homozygous ColRPP1 lines, Ler and NIL plants grown at 14–16°C by qRT-PCR. Values are relative to Ler and the mean ± SD of three biological replicates each using three technical replicates. NIL (incompatible Ler/Kas-2 near-isogenic line [31]). Significant differences in gene expression between Ler and different ColRPP1 lines using Student's t-test are indicated by asterisks: *P<0.05, **P<0.01, ***P<0.005.

Mentions: Prolonged activation of defenses bears a fitness cost for the plant [33], [34] and this might shape the genetic composition of Resistance (R) genes in natural populations [13]. We measured the contribution of individual RPP1-like Ler genes to the trade-off between growth and disease resistance by transforming a neutral (compatible) background, accession Col-0, with genomic constructs of each RPP1-like Ler gene under control of its native 5′ and 3′ sequences. These lines are referred to as ColRPP1Ler. We also included RPP1-like Ler R1 and R5 genes, which contain stop codons in their coding sequences (S1 Figure). Expression of the RPP1-like Ler transgenes in Col-0 was detectable and ranged from 0.5 to 5.5-fold their native expression levels in Ler (Fig. 2). Interestingly, ColRPP1Ler R3 lines with higher expression (lines 12, 13 and 27) exhibited dwarfism and sterility at 14–16°C, which were suppressed at 20–22°C (S2 Figure). By contrast, ColRPP1Ler R1, R2, R4, R5, R7 and R8 lines did not show obvious growth defects at 14–16°C regardless of the transgene expression level (Fig. 2 and S3 Figure). Expression of the defense marker gene PR-1 was used to monitor defense activation in the different transgenic lines (Fig. 2). ColRPP1Ler R3 lines with higher transgene expression also exhibited high PR-1 expression. Expression of PR-1 remained low in ColRPP1-like Ler R1, R2, R4, R5, R7 and R8 lines and variation in PR1 transcript levels between lines did not correlate with transgene expression (Fig. 2). Cell death lesions were detected in leaves of the stunted ColRPP1Ler R3 lines at 14–16°C, as observed previously for Ler/Kas-2 incompatible lines [31], but were absent in all other ColRPP1-like Ler R1, R2, R4, R5, R7 and R8 lines grown under the same conditions (S4 Figure).


Analysis of a plant complex resistance gene locus underlying immune-related hybrid incompatibility and its occurrence in nature.

Alcázar R, von Reth M, Bautor J, Chae E, Weigel D, Koornneef M, Parker JE - PLoS Genet. (2014)

Transgene and PR-1 expression in ColRPP1 lines.Expression of RPP1-like Ler R1, R2, R3, R4, R5, R7 and R8 transgenes (left axis) and PR-1 (right axis) determined in individual homozygous ColRPP1 lines, Ler and NIL plants grown at 14–16°C by qRT-PCR. Values are relative to Ler and the mean ± SD of three biological replicates each using three technical replicates. NIL (incompatible Ler/Kas-2 near-isogenic line [31]). Significant differences in gene expression between Ler and different ColRPP1 lines using Student's t-test are indicated by asterisks: *P<0.05, **P<0.01, ***P<0.005.
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Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4263378&req=5

pgen-1004848-g002: Transgene and PR-1 expression in ColRPP1 lines.Expression of RPP1-like Ler R1, R2, R3, R4, R5, R7 and R8 transgenes (left axis) and PR-1 (right axis) determined in individual homozygous ColRPP1 lines, Ler and NIL plants grown at 14–16°C by qRT-PCR. Values are relative to Ler and the mean ± SD of three biological replicates each using three technical replicates. NIL (incompatible Ler/Kas-2 near-isogenic line [31]). Significant differences in gene expression between Ler and different ColRPP1 lines using Student's t-test are indicated by asterisks: *P<0.05, **P<0.01, ***P<0.005.
Mentions: Prolonged activation of defenses bears a fitness cost for the plant [33], [34] and this might shape the genetic composition of Resistance (R) genes in natural populations [13]. We measured the contribution of individual RPP1-like Ler genes to the trade-off between growth and disease resistance by transforming a neutral (compatible) background, accession Col-0, with genomic constructs of each RPP1-like Ler gene under control of its native 5′ and 3′ sequences. These lines are referred to as ColRPP1Ler. We also included RPP1-like Ler R1 and R5 genes, which contain stop codons in their coding sequences (S1 Figure). Expression of the RPP1-like Ler transgenes in Col-0 was detectable and ranged from 0.5 to 5.5-fold their native expression levels in Ler (Fig. 2). Interestingly, ColRPP1Ler R3 lines with higher expression (lines 12, 13 and 27) exhibited dwarfism and sterility at 14–16°C, which were suppressed at 20–22°C (S2 Figure). By contrast, ColRPP1Ler R1, R2, R4, R5, R7 and R8 lines did not show obvious growth defects at 14–16°C regardless of the transgene expression level (Fig. 2 and S3 Figure). Expression of the defense marker gene PR-1 was used to monitor defense activation in the different transgenic lines (Fig. 2). ColRPP1Ler R3 lines with higher transgene expression also exhibited high PR-1 expression. Expression of PR-1 remained low in ColRPP1-like Ler R1, R2, R4, R5, R7 and R8 lines and variation in PR1 transcript levels between lines did not correlate with transgene expression (Fig. 2). Cell death lesions were detected in leaves of the stunted ColRPP1Ler R3 lines at 14–16°C, as observed previously for Ler/Kas-2 incompatible lines [31], but were absent in all other ColRPP1-like Ler R1, R2, R4, R5, R7 and R8 lines grown under the same conditions (S4 Figure).

Bottom Line: In a neutral background, expression of most RPP1-like Ler genes, except R3, has no effect on growth or pathogen resistance.Only Gorzów individuals carrying the RPP1-like Ler haplotype are incompatible with Kas-2 and Kond, whereas other RPP1-like alleles in the population are compatible.Therefore, the RPP1-like Ler haplotype has been maintained in genetically different individuals at a single site, allowing exploration of forces shaping the evolution of RPP1-like genes at local and regional population scales.

View Article: PubMed Central - PubMed

Affiliation: Department of Natural Products, Plant Biology and Soil Science, Laboratory of Plant Physiology, Faculty of Pharmacy. University of Barcelona, Barcelona, Spain; Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany; Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany.

ABSTRACT
Mechanisms underlying speciation in plants include detrimental (incompatible) genetic interactions between parental alleles that incur a fitness cost in hybrids. We reported on recessive hybrid incompatibility between an Arabidopsis thaliana strain from Poland, Landsberg erecta (Ler), and many Central Asian A. thaliana strains. The incompatible interaction is determined by a polymorphic cluster of Toll/interleukin-1 receptor-nucleotide binding-leucine rich repeat (TNL) RPP1 (Recognition of Peronospora parasitica1)-like genes in Ler and alleles of the receptor-like kinase Strubbelig Receptor Family 3 (SRF3) in Central Asian strains Kas-2 or Kond, causing temperature-dependent autoimmunity and loss of growth and reproductive fitness. Here, we genetically dissected the RPP1-like Ler locus to determine contributions of individual RPP1-like Ler (R1-R8) genes to the incompatibility. In a neutral background, expression of most RPP1-like Ler genes, except R3, has no effect on growth or pathogen resistance. Incompatibility involves increased R3 expression and engineered R3 overexpression in a neutral background induces dwarfism and sterility. However, no individual RPP1-like Ler gene is sufficient for incompatibility between Ler and Kas-2 or Kond, suggesting that co-action of at least two RPP1-like members underlies this epistatic interaction. We find that the RPP1-like Ler haplotype is frequent and occurs with other Ler RPP1-like alleles in a local population in Gorzów Wielkopolski (Poland). Only Gorzów individuals carrying the RPP1-like Ler haplotype are incompatible with Kas-2 and Kond, whereas other RPP1-like alleles in the population are compatible. Therefore, the RPP1-like Ler haplotype has been maintained in genetically different individuals at a single site, allowing exploration of forces shaping the evolution of RPP1-like genes at local and regional population scales.

Show MeSH
Related in: MedlinePlus