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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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Growth phenotype of amiRNA lines at 14–16°C and RPP1-like gene expression.(A) Growth phenotype of 5-week old Ler/Kas-2 NIL plants transformed with amiRNAs effective (KB209 and KB212) or not effective (KB228) suppressing incompatibility. (B) Expression of individual RPP1-like Ler genes determined by qRT-PCR in suppressed (compatible) amiRNA KB209 lines (KB209-1, KB209-2, KB209-3), KB212 (KB212-1, KB212-2, KB212-3) and non-suppressed (incompatible) amiRNA lines KB212 (KB212-4, KB212-5), KB228 (KB228-1, KB228-2, KB228-3). Values are relative to Ler and the mean ± SD of three biological replicates each using three technical replicates. cNIL (complemented NIL), NIL (incompatible Ler/Kas-2 near-isogenic line) [23], [31]. Significant differences in gene expression between Ler and other genotypes using Student's t-test are indicated by asterisks: *P<0.05, **P<0.01, ***P<0.005.
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pgen-1004848-g001: Growth phenotype of amiRNA lines at 14–16°C and RPP1-like gene expression.(A) Growth phenotype of 5-week old Ler/Kas-2 NIL plants transformed with amiRNAs effective (KB209 and KB212) or not effective (KB228) suppressing incompatibility. (B) Expression of individual RPP1-like Ler genes determined by qRT-PCR in suppressed (compatible) amiRNA KB209 lines (KB209-1, KB209-2, KB209-3), KB212 (KB212-1, KB212-2, KB212-3) and non-suppressed (incompatible) amiRNA lines KB212 (KB212-4, KB212-5), KB228 (KB228-1, KB228-2, KB228-3). Values are relative to Ler and the mean ± SD of three biological replicates each using three technical replicates. cNIL (complemented NIL), NIL (incompatible Ler/Kas-2 near-isogenic line) [23], [31]. Significant differences in gene expression between Ler and other genotypes using Student's t-test are indicated by asterisks: *P<0.05, **P<0.01, ***P<0.005.

Mentions: Previously, we mapped the Ler locus causing incompatibility with Kas-2 and Kond Central Asian accessions (SRF3 forms) to a large ∼87 kb cluster of RPP1-like genes on chromosome 3 [31]. We also established that HI was suppressed by loss-of-function mutations of the TNL immunity regulator EDS1 or by depletion of the defense signaling hormone salicylic acid (SA), consistent with TNL genes driving HI [31]. To ascertain whether HI is due to one or more RPP1-like Ler genes within the locus, we used artificial microRNA (amiRNA) silencing of an incompatible Ler/Kas-2 near isogenic line (NIL) which contains a Ler introgression spanning the RPP1-like locus in a Kas-2 background [31]. Incompatible NIL plants were transformed with amiRNAs KB209, KB212 and KB228 originally designed against RPP1-like genes in Uk-1 (S1 Table). Of the three amiRNAs used, only KB209 and KB212 have predicted complementarity with RPP1-like Ler genes. Multiple independent NIL lines transformed with amiRNAs KB209, KB212 and KB228 (the latter used as a negative control) were tested for suppression of incompatible phenotypes at 14–16°C. We observed suppression of incompatibility in all NIL plants transformed with amiRNA KB209, and in most KB212 transformants (Fig. 1A). As expected, KB228 did not rescue the incompatible NIL phenotype (Fig. 1A).


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)

Growth phenotype of amiRNA lines at 14–16°C and RPP1-like gene expression.(A) Growth phenotype of 5-week old Ler/Kas-2 NIL plants transformed with amiRNAs effective (KB209 and KB212) or not effective (KB228) suppressing incompatibility. (B) Expression of individual RPP1-like Ler genes determined by qRT-PCR in suppressed (compatible) amiRNA KB209 lines (KB209-1, KB209-2, KB209-3), KB212 (KB212-1, KB212-2, KB212-3) and non-suppressed (incompatible) amiRNA lines KB212 (KB212-4, KB212-5), KB228 (KB228-1, KB228-2, KB228-3). Values are relative to Ler and the mean ± SD of three biological replicates each using three technical replicates. cNIL (complemented NIL), NIL (incompatible Ler/Kas-2 near-isogenic line) [23], [31]. Significant differences in gene expression between Ler and other genotypes 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-g001: Growth phenotype of amiRNA lines at 14–16°C and RPP1-like gene expression.(A) Growth phenotype of 5-week old Ler/Kas-2 NIL plants transformed with amiRNAs effective (KB209 and KB212) or not effective (KB228) suppressing incompatibility. (B) Expression of individual RPP1-like Ler genes determined by qRT-PCR in suppressed (compatible) amiRNA KB209 lines (KB209-1, KB209-2, KB209-3), KB212 (KB212-1, KB212-2, KB212-3) and non-suppressed (incompatible) amiRNA lines KB212 (KB212-4, KB212-5), KB228 (KB228-1, KB228-2, KB228-3). Values are relative to Ler and the mean ± SD of three biological replicates each using three technical replicates. cNIL (complemented NIL), NIL (incompatible Ler/Kas-2 near-isogenic line) [23], [31]. Significant differences in gene expression between Ler and other genotypes using Student's t-test are indicated by asterisks: *P<0.05, **P<0.01, ***P<0.005.
Mentions: Previously, we mapped the Ler locus causing incompatibility with Kas-2 and Kond Central Asian accessions (SRF3 forms) to a large ∼87 kb cluster of RPP1-like genes on chromosome 3 [31]. We also established that HI was suppressed by loss-of-function mutations of the TNL immunity regulator EDS1 or by depletion of the defense signaling hormone salicylic acid (SA), consistent with TNL genes driving HI [31]. To ascertain whether HI is due to one or more RPP1-like Ler genes within the locus, we used artificial microRNA (amiRNA) silencing of an incompatible Ler/Kas-2 near isogenic line (NIL) which contains a Ler introgression spanning the RPP1-like locus in a Kas-2 background [31]. Incompatible NIL plants were transformed with amiRNAs KB209, KB212 and KB228 originally designed against RPP1-like genes in Uk-1 (S1 Table). Of the three amiRNAs used, only KB209 and KB212 have predicted complementarity with RPP1-like Ler genes. Multiple independent NIL lines transformed with amiRNAs KB209, KB212 and KB228 (the latter used as a negative control) were tested for suppression of incompatible phenotypes at 14–16°C. We observed suppression of incompatibility in all NIL plants transformed with amiRNA KB209, and in most KB212 transformants (Fig. 1A). As expected, KB228 did not rescue the incompatible NIL phenotype (Fig. 1A).

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