Sequence analysis of the Petunia inflata S-locus region containing 17 S-Locus F-Box genes and the S-RNase gene involved in self-incompatibility

Self-incompatibility in Petunia is controlled by the polymorphic S-locus, which contains S-RNase encoding the pistil determinant and 16-20 S-locus F-box (SLF) genes collectively encoding the pollen determinant. Here we sequenced and assembled approximately 3.1 Mb of the S₂ -haplotype of the S-locus in Petunia inflata using bacterial artificial chromosome clones collectively containing all 17 SLF genes, SLFLike1, and S-RNase. Two SLF pseudogenes and 28 potential protein-coding genes were identified, 20 of which were also found at the S-loci of both the S_6a -haplotype of P. inflata and the S_N -haplotype of self-compatible Petunia axillaris, but not in the S-locus remnants of self-compatible potato (Solanum tuberosum) and tomato (Solanum lycopersicum). Comparative analyses of S-locus sequences of these three S-haplotypes revealed potential genetic exchange in the flanking regions of SLF genes, resulting in highly similar flanking regions between different types of SLF and between alleles of the same type of SLF of different S-haplotypes. The high degree of sequence similarity in the flanking regions could often be explained by the presence of similar long terminal repeat retroelements, which were enriched at the S-loci of all three S-haplotypes and in the flanking regions of all S-locus genes examined. We also found evidence of the association of transposable elements with SLF pseudogenes. Based on the hypothesis that SLF genes were derived by retrotransposition, we identified 10 F-box genes as putative SLF parent genes. Our results shed light on the importance of non-coding sequences in the evolution of the S-locus, and on possible evolutionary mechanisms of generation, proliferation, and deletion of SLF genes.

Compatibility and incompatibility in S-RNase-based systems

BACKGROUND

S-RNase-based self-incompatibility (SI) occurs in the Solanaceae, Rosaceae and Plantaginaceae. In all three families, compatibility is controlled by a polymorphic S-locus encoding at least two genes. S-RNases determine the specificity of pollen rejection in the pistil, and S-locus F-box proteins fulfill this function in pollen. S-RNases are thought to function as S-specific cytotoxins as well as recognition proteins. Thus, incompatibility results from the cytotoxic activity of S-RNase, while compatible pollen tubes evade S-RNase cytotoxicity.

SCOPE

The S-specificity determinants are known, but many questions remain. In this review, the genetics of SI are introduced and the characteristics of S-RNases and pollen F-box proteins are briefly described. A variety of modifier genes also required for SI are also reviewed. Mutations affecting compatibility in pollen are especially important for defining models of compatibility and incompatibility. In Solanaceae, pollen-side mutations causing breakdown in SI have been attributed to the heteroallelic pollen effect, but a mutation in Solanum chacoense may be an exception. This has been interpreted to mean that pollen incompatibility is the default condition unless the S-locus F-box protein confers resistance to S-RNase. In Prunus, however, S-locus F-box protein gene mutations clearly cause compatibility.

CONCLUSIONS

Two alternative mechanisms have been proposed to explain compatibility and incompatibility: compatibility is explained either as a result of either degradation of non-self S-RNase or by its compartmentalization so that it does not have access to the pollen tube cytoplasm. These models are not necessarily mutually exclusive, but each makes different predictions about whether pollen compatibility or incompatibility is the default. As more factors required for SI are identified and characterized, it will be possible to determine the role each process plays in S-RNase-based SI.

S-RNase-based self-incompatibility in Petunia inflata

BACKGROUND

For the Solanaceae-type self-incompatibility, also possessed by Rosaceae and Plantaginaceae, the specificity of self/non-self interactions between pollen and pistil is controlled by two polymorphic genes at the S-locus: the S-locus F-box gene (SLF or SFB) controls pollen specificity and the S-RNase gene controls pistil specificity.

SCOPE

This review focuses on the work from the authors' laboratory using Petunia inflata (Solanaceae) as a model. Here, recent results on the identification and functional studies of S-RNase and SLF are summarized and a protein-degradation model is proposed to explain the biochemical mechanism for specific rejection of self-pollen tubes by the pistil.

CONCLUSIONS

The protein-degradation model invokes specific degradation of non-self S-RNases in the pollen tube mediated by an SLF, and can explain compatible versus incompatible pollination and the phenomenon of competitive interaction, where SI breaks down in pollen carrying two different S-alleles. In Solanaceae, Plantaginaceae and subfamily Maloideae of Rosaceae, there also exist multiple S-locus-linked SLF/SFB-like genes that potentially function as the pollen S-gene. To date, only three such genes, all in P. inflata, have been examined, and they do not function as the pollen S-gene in the S-genotype backgrounds tested. Interestingly, subfamily Prunoideae of Rosaceae appears to possess only a single SLF/SFB gene, and competitive interaction, observed in Solanaceae, Plantaginaceae and subfamily Maloideae, has not been observed. Thus, although the cytotoxic function of S-RNase is an integral part of SI in Solanaceae, Plantaginaceae and Rosaceae, the function of SLF/SFB may have diverged. This highlights the complexity of the S-RNase-based SI mechanism. The review concludes by discussing some key experiments that will further advance our understanding of this self/non-self discrimination mechanism.

Molecular and genetic characterization of the S locus in Hordeum bulbosum L., a wild self-incompatible species related to cultivated barley

Gametophytic self-incompatibility (GSI) in the grasses is controlled by a distinct two-locus genetic system governed by the multiallelic loci S and Z. We have employed diploid Hordeum bulbosum as a model species for identifying the self-incompatibility (SI) genes and for elucidating the molecular mechanisms of the two-locus SI system in the grasses. In this study, we attempted to identify S haplotype-specific cDNAs expressed in pistils and anthers at the flowering stage in H. bulbosum, using the AFLP-based mRNA fingerprinting (AMF, also called cDNA-AFLP) technique. We used the AMF-derived DNA clones as markers for fine mapping of the S locus, and found that the locus resided in a chromosomal region displaying remarkable suppression of recombination, encompassing a large physical region. Furthermore, we identified three AMF-derived markers displaying complete linkage to the S locus, although they showed no significant homology with genes of known functions. Two of these markers showed expression patterns that were specific to the reproductive organs (pistil or anther), suggesting that they could be potential candidates for the S gene.

Biochemical models for S-RNase-based self-incompatibility

S-RNase-based self-incompatibility (SI) is a genetically determined self/non-self-recognition process employed by many flowering plant species to prevent inbreeding and promote outcrosses. For the Plantaginaceae, Rosaceae and Solanaceae, it is now known that S-RNase and S-locus F-box (two multiple allelic genes at the S-locus) determine the female and male specificity, respectively, during SI interactions. However, how allelic products of these two genes interact inside pollen tubes to result in specific growth inhibition of self-pollen tubes remains to be investigated. Here, we review all the previously proposed biochemical models and discuss whether their predictions are consistent with all SI phenomena, including competitive interaction where SI breaks down in pollen that carries two different pollen S-alleles. We also discuss these models in light of the recent findings of compartmentalization of S-RNases in both incompatible and compatible pollen tubes. Lastly, we summarize the results from our recent biochemical studies of PiSLF (Petunia inflata SLF) and S-RNase, and present a new model for the biochemical mechanism of SI in the Solanaceae. The tenet of this model is that a PiSLF preferentially interacts with its non-self S-RNases in the cytoplasm of a pollen tube to result in the assembly of an E3-like complex, which then mediates ubiquitination and degradation of non-self S-RNases through the ubiquitin-26S proteasome pathway. This model can explain all SI phenomena and, at the same time, has raised new questions for further study.

Construction and application of a bacterial artificial chromosome (BAC) library of Prunus armeniaca L. for the identification of clones linked to the self-incompatibility locus

To facilitate gene discovery in the Rosaceae, a bacterial artificial chromosome (BAC) library was constructed using high-molecular-weight (HMW) DNA from apricot leaves (Prunus armeniaca L.). The library contains 101,376 clones (264, 384-well plates) with an average insert size of 64 kb, equivalent to 22-fold genome coverage. In the first application of this library, high-density filters were screened for self-incompatibility genes using apricot DNA probes. Eight positive BAC clones were detected and fingerprinted to determine clone relationships and assemble contigs. These results demonstrate the suitability of this library for gene identification and physical mapping of the apricot genome.

Genealogy-dependent variation in viability among self-incompatibility genotypes

Many hermaphroditic plants avoid self-fertilization by rejecting pollen that express genetically determined specificities in common with the pistil. The S-locus, comprising the determinants of pistil and pollen specificity, typically shows extremely high polymorphism, with dozens to hundreds of specificities maintained within species. This article explores a conjecture, motivated by empirical findings, that the expression of recessive deleterious factors at sites closely linked to the S-locus may cause greater declines in the viability of zygotes constituted from more closely related S-alleles. Diffusion approximation models incorporating variation in viability among S-locus genotypes and antagonistic interactions between a new specificity and its immediate parent specificity are constructed and analyzed. Results indicate that variation in viability tends to reduce the number of specificities maintained in a population at stochastic steady state, and that genealogy-based antagonism reduces the rate of bifurcation of S-allele lineages. These effects may account for some of the unusual features observed in empirical studies of S-allele genealogies.

S-RNase-mediated self-incompatibility

The Solanaceae, Rosaceae, and Scrophulariaceae families all possess an RNase-mediated self-incompatibility mechanism through which their pistils can recognize and reject self-pollen to prevent inbreeding. The highly polymorphic S-locus controls the self-incompatibility interaction, and the S-locus of the Solanaceae has been shown to be a multi-gene complex in excess of 1.3 Mb. To date, the function of only one of the S-locus genes, the S-RNase gene, has been determined. This article reviews the current status of the search for the pollen S-gene and the current models for how S-haplotype specific inhibition of pollen tubes can be accomplished by S-RNases.

Molecular mechanisms underlying the breakdown of gametophytic self-incompatibility

The breakdown of self-incompatibility has occurred repeatedly throughout the evolution of flowering plants and has profound impacts on the genetic structure of populations. Recent advances in understanding of the molecular basis of self-incompatibility have provided insights into the mechanisms of its loss in natural populations, especially in the tomato family, the Solanaceae. In the Solanaceae, the gene that controls self-incompatibility in the style codes for a ribonuclease that causes the degradation of RNA in pollen tubes bearing an allele at the S-locus that matches either of the two alleles held by the maternal plant. The pollen component of the S-locus has yet to be identified. Loss of self-incompatibility can be attributed to three types of causes: duplication of the S-locus, mutations that cause loss of S-RNase activity, and mutations that do not cause loss of S-RNase activity. Duplication of the S-locus has been well studied in radiation-induced mutants but may be a relatively rare cause of the breakdown of self-incompatibility in nature. Point mutations within the S-locus that disrupt the production of S-RNase have been documented in natural populations. There are also a number of mutants in which S-RNase production is unimpaired, yet self-incompatibility is disrupted. The identity and function of these mutations is not well understood. Careful work on a handful of model organisms will enable population biologists to better understand the breakdown of self-incompatibility in nature.

Molecular recognition and response in pollen and pistil interactions

Many bisexual flowering plants possess a reproductive strategy called self-incompatibility (SI) that enables the female tissue (the pistil) to reject self but accept non-self pollen for fertilization. Three different SI mechanisms are discussed, each controlled by two separate, highly polymorphic genes at the S-locus. For the Solanaceae and Papaveraceae types, the genes controlling female function in SI, the S-RNase gene and the S-gene, respectively, have been identified. For the Brassicaceae type, the gene controlling male function, SCR/SP11, and the gene controlling female function, SRK, have been identified. The S-RNase based mechanism involves degradation of RNA of self-pollen tubes; the S-protein based mechanism involves a signal transduction cascade in pollen, including a transient rise in [Ca(2+)]i and subsequent protein phosphorylation/dephosphorylation; and the SRK (a receptor kinase) based mechanism involves interaction of a pollen ligand, SCR/SP11, with SRK, followed by a signal transduction cascade in the stigmatic surface cell.