Genetic mapping and molecular characterization of the self-incompatibility (S) locus in Petunia inflata

The Identification and Analysis of the Self-Incompatibility Pollen Determinant Factor SLF in Lycium barbarum

Self-incompatibility is a widespread genetic mechanism found in flowering plants. It plays a crucial role in preventing inbreeding and promoting outcrossing. The genes that control self-incompatibility in plants are typically determined by the S-locus female determinant factor and the S-locus male determinant factor. In the Solanaceae family, the male determinant factor is often the SLF gene. In this research, we cloned and analyzed 13 S2-LbSLF genes from the L. barbarum genome, which are located on chromosome 2 and close to the physical location of the S-locus female determinant factor S-RNase, covering a region of approximately 90.4 Mb. The amino acid sequence identity of the 13 S2-LbSLFs is 58.46%, and they all possess relatively conserved motifs and typical F-box domains, without introns. A co-linearity analysis revealed that there are no tandemly repeated genes in the S2-LbSLF genes, and that there are two pairs of co-linear genes between S2-LbSLF and the tomato, which also belongs to the Solanaceae family. A phylogenetic analysis indicates that the S2-LbSLF members can be divided into six groups, and it was found that the 13 S2-LbSLFs are clustered with the SLF genes of tobacco and Petunia inflata to varying degrees, potentially serving as pollen determinant factors regulating self-incompatibility in L. barbarum. The results for the gene expression patterns suggest that S2-LbSLF is only expressed in pollen tissue. The results of the yeast two-hybrid assay showed that the C-terminal region of S2-LbSLFs lacking the F-box domain can interact with S-RNase. This study provides theoretical data for further investigation into the functions of S2-LbSLF members, particularly for the identification of pollen determinant factors regulating self-incompatibility in L. barbarum.

Transcriptomic Analysis of Self-Incompatibility in Alfalfa

Alfalfa (Medicago sativa L.) is an important forage crop worldwide, but molecular genetics and breeding research in this species are hindered by its self-incompatibility (SI). Although the mechanisms underlying SI have been extensively studied in other plant families, SI in legumes, including alfalfa, remains poorly understood. Here, we determined that self-pollinated pollen tubes could germinate on the stigma of alfalfa, grow through the style, and reach the ovarian cavity, but the ovules collapsed ~48 h after self-pollination. A transcriptomic analysis of dissected pistils 24 h after self-pollination identified 941 differently expressed genes (DEGs), including 784 upregulated and 157 downregulated genes. A gene ontology (GO) analysis showed that the DEGs were highly enriched in functions associated with the regulation of pollen tube growth and pollen germination. A Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated that pentose and glucuronate interconversion, plant hormone signal transduction, the spliceosome, and ribosomes might play important roles in SI. Our co-expression analysis showed that F-box proteins, serine/threonine protein kinases, calcium-dependent protein kinases (CDPKs), bHLHs, bZIPs, and MYB-related family proteins were likely involved in the SI response. Our study provides a catalog of candidate genes for further study to understand SI in alfalfa and related legumes.

Identification of structural variation and polymorphisms of a sex co-segregating scaffold in spinach

Spinach is a common vegetable, and dioecy is maintained by a pair of XY sex chromosomes. Due to limited genomic resources and its highly repetitive genome, limited studies were conducted to investigate the genomic landscape of the region near sex-determining loci. In this study, we screened the structure variations (SVs) between Y-linked contigs and a 1.78-Mb X scaffold (Super_scaffold 66), which enabled the development of 12 sex co-segregating DNA markers. These markers were tested in one F₁ mapping population and 40 spinach accessions, which comprised 692 individual plants with the strong sex linkage pattern. In addition, we found that Super_scaffold 66 was highly repetitive along with the enriched LTR-RTs insertions and decreased microsatellite distribution compared with the rest genome, which matches extremely low gene density featured by only nine annotated genes. Synteny analysis between Y contigs and Superscaffold_66 revealed a 340-Kb accumulative Y contig (non-continuous) and a 500-Kb X counterpart along with SVs and wide-spread tandem duplications. Among the nine genes, one ABC transporter gene revealed noticeable SVs between Y contig and X counterpart, as an approximate 5-Kb recent Gypsy LTR-RT insertion in the Y-linked allele, but not the X allele. The gene paucity, SVs, and sex-linked polymorphisms attributed to the recombination suppression. We proposed that Super_scaffold 66 is part of the non-recombining region containing the sex determination genes. The spread of 12 sex co-segregating markers from this 1.78 Mb genomic region indicated the existence and expansion of sex determination region during progression of the Y chromosome.

Caspase-like proteases and the phytohormone cytokinin as determinants of S-RNAse-based self-incompatibility-induced PCD in Petunia hybrida L

S-RNAse-based self-incompatibility (SI) in petunia (Petunia hybrida L.) is a self-/non-self-recognition system underlying the pistil rejection of self-pollen. Using different methods, including a TUNEL assay, we have recently shown that programmed cell death (PCD) is a factor of the SI in petunia. Here, we show that the growth of self-incompatible pollen tubes in the style tissues during 4 h after pollination is accompanied by five-sixfold increase in a caspase-like protease (CLP) activity. Exogenous cytokinin (CK) inhibits the pollen tube growth and stimulates the CLP activity in compatible pollen tubes. The actin depolymerization with latrunculin B induces a sharp drop in the CLP activity in self-incompatible pollen tubes and its increase in compatible pollen tubes. Altogether, our results suggest that a CLP is involved in the SI-induced PCD and that CK is a putative activator of the CLP. We assume that CK provokes acidification of the cytosol and thus promotes the activation of a CLP. Thus, our results suggest that CK and CLP are involved in the S-RNAse-based SI-induced PCD in petunia. Potential relations between these components in PCD signaling are discussed.

Inferences on specificity recognition at the Malus×domestica gametophytic self-incompatibility system

In Malus × domestica (Rosaceae) the product of each SFBB gene (the pollen component of the gametophytic self-incompatibility (GSI) system) of a S-haplotype (the combination of pistil and pollen genes that are linked) interacts with a sub-set of non-self S-RNases (the pistil component), but not with the self S-RNase. To understand how the Malus GSI system works, we identified 24 SFBB genes expressed in anthers, and determined their gene sequence in nine M. domestica cultivars. Expression of these SFBBs was not detected in the petal, sepal, filament, receptacle, style, stigma, ovary or young leaf. For all SFBBs (except SFBB15), identical sequences were obtained only in cultivars having the same S-RNase. Linkage with a particular S-RNase was further established using the progeny of three crosses. Such data is needed to understand how other genes not involved in GSI are affected by the S-locus region. To classify SFBBs specificity, the amino acids under positive selection obtained when performing intra-haplotypic analyses were used. Using this information and the previously identified S-RNase positively selected amino acid sites, inferences are made on the S-RNase amino acid properties (hydrophobicity, aromatic, aliphatic, polarity, and size), at these positions, that are critical features for GSI specificity determination.

Evolutionary history of two pollen self-incompatibility factors reveals alternate routes to self-compatibility within Solanum

PREMISE OF THE STUDY

Self-incompatibility (SI) prevents self-fertilization and reduces inbreeding. While SI is common in plants, transitions to self-compatibility (SC) occur frequently. Little is known about the genetic changes and evolutionary steps underlying these shifts.

METHODS

In the Solanaceae, SI is gametophytic, with specificity determined by S-RNases in the pistil and S-locus F-box proteins (SLFs) in pollen. We examined the role of two pollen factors, Cullin1 (CUL1) and SLF-23, in SI → SC transitions in wild tomato species from the Arcanum species group (Solanum arcanum, S. neorickii, and S. chmielewskii). Pollen compatibility was assessed on tester lines that reject pollen lacking functional SLF-23 or CUL1. Complementation tests, gene sequencing, and phylogenetic analyses were used to characterize both functional and nonfunctional alleles.

KEY RESULTS

We found evidence for multiple independent SI → SC transitions. In S. arcanum and S. chmielewskii, SC is caused by loss of pistil S-RNase activity, while in S. neorickii SC is associated with expression of a functional SLF-23 that recognizes the S₉ type S-RNase expressed in its pistils. Interestingly, we found identical deletion mutations in CUL1 exon 7 of S. chmielewskii as previously seen in S. habrochaites.

CONCLUSIONS

Mating system transitions in the Arcanum group have occurred via both pistil loss-of-function and pollen gain-of-function SC mutations. Mutations common to S. chmielewskii and S. habrochaites must have arisen in a common ancestor, possibly to the entire tomato clade, then became fixed in different lineages after loss of pistil-side SI function.

Overcoming self-incompatibility in grasses: a pathway to hybrid breeding

Allogamous grasses exhibit an effective two-locus gametophytic self-incompatibility (SI) system, limiting the range of breeding techniques applicable for cultivar development. Current breeding methods based on populations are characterized by comparably low genetic gains for important traits such as biomass yield. To implement more efficient breeding schemes, the overall understanding of the SI system is crucial as are the mechanisms involved in the breakdown of SI. Self-fertile variants in outcrossing grasses have been studied, and the current level of knowledge includes approximate gene locations, linked molecular markers and first hypotheses on their mode of action. Environmental conditions increasing seed set upon self-pollination have also been described. Even though some strategies were proposed to take advantage of self-fertility, there have, so far, not been changes in the methods applied in cultivar development for allogamous grasses. In this review, we describe the current knowledge about self-fertility in allogamous grasses and outline strategies to incorporate this trait for implementation in synthetic and hybrid breeding schemes.

Comparative De Novo Transcriptome Analysis of Fertilized Ovules in Xanthoceras sorbifolium Uncovered a Pool of Genes Expressed Specifically or Preferentially in the Selfed Ovule That Are Potentially Involved in Late-Acting Self-Incompatibility

Xanthoceras sorbifolium, a tree species endemic to northern China, has high oil content in its seeds and is recognized as an important biodiesel crop. The plant is characterized by late-acting self-incompatibility (LSI). LSI was found to occur in many angiosperm species and plays an important role in reducing inbreeding and its harmful effects, as do gametophytic self-incompatibility (GSI) and sporophytic self-incompatibility (SSI). Molecular mechanisms of conventional GSI and SSI have been well characterized in several families, but no effort has been made to identify the genes involved in the LSI process. The present studies indicated that there were no significant differences in structural and histological features between the self- and cross-pollinated ovules during the early stages of ovule development until 5 days after pollination (DAP). This suggests that 5 DAP is likely to be a turning point for the development of the selfed ovules. Comparative de novo transcriptome analysis of the selfed and crossed ovules at 5 DAP identified 274 genes expressed specifically or preferentially in the selfed ovules. These genes contained a significant proportion of genes predicted to function in the biosynthesis of secondary metabolites, consistent with our histological observations in the fertilized ovules. The genes encoding signal transduction-related components, such as protein kinases and protein phosphatases, are overrepresented in the selfed ovules. X. sorbifolium selfed ovules also specifically or preferentially express many unique transcription factor (TF) genes that could potentially be involved in the novel mechanisms of LSI. We also identified 42 genes significantly up-regulated in the crossed ovules compared to the selfed ovules. The expression of all 16 genes selected from the RNA-seq data was validated using PCR in the selfed and crossed ovules. This study represents the first genome-wide identification of genes expressed in the fertilized ovules of an LSI species. The availability of a pool of specifically or preferentially expressed genes from selfed ovules for X. sorbifolium will be a valuable resource for future genetic analyses of candidate genes involved in the LSI response.

Gene duplication and genetic exchange drive the evolution of S-RNase-based self-incompatibility in Petunia

Self-incompatibility (SI) systems in flowering plants distinguish self- and non-self pollen to prevent inbreeding. While other SI systems rely on the self-recognition between specific male- and female-determinants, the Solanaceae family has a non-self recognition system resulting in the detoxification of female-determinants of S-ribonucleases (S-RNases), expressed in pistils, by multiple male-determinants of S-locus F-box proteins (SLFs), expressed in pollen. It is not known how many SLF components of this non-self recognition system there are in Solanaceae species, or how they evolved. We identified 16-20 SLFs in each S-haplotype in SI Petunia, from a total of 168 SLF sequences using large-scale next-generation sequencing and genomic polymerase chain reaction (PCR) techniques. We predicted the target S-RNases of SLFs by assuming that a particular S-allele must not have a conserved SLF that recognizes its own S-RNase, and validated these predictions by transformation experiments. A simple mathematical model confirmed that 16-20 SLF sequences would be adequate to recognize the vast majority of target S-RNases. We found evidence of gene conversion events, which we suggest are essential to the constitution of a non-self recognition system and also contribute to self-compatible mutations.

Identification of the self-incompatibility locus F-box protein-containing complex in Petunia inflata

The polymorphic S-locus regulating self-incompatibility (SI) in Petunia contains the S-RNase gene and a number of S-locus F-box (SLF) genes. While penetrating the style through the stigma, a pollen tube takes up all S-RNases, but only self S-RNase inhibits pollen tube growth. Recent evidence suggests that SLFs produced by pollen collectively interact with and detoxify non-self S-RNases, but none can interact with self S-RNase. An SLF may be the F-box protein component of an SCF complex (containing Cullin1, Skp1 and Rbx1), which mediates ubiquitination of protein substrates for degradation by the 26S proteasome. However, the precise nature of the complex is unknown. We used pollen extracts of a transgenic plant over-expressing GFP-fused S2-SLF1 (SLF1 of S 2-haplotype) for co-immunoprecipitation (Co-IP) followed by mass spectrometry (MS). We identified PiCUL1-P (a pollen-specific Cullin1), PiSSK1 (a pollen-specific Skp1-like protein) and PiRBX1 (an Rbx1). To validate the results, we raised transgenic plants over-expressing PiSSK1:FLAG:GFP and used pollen extracts for Co-IP-MS. The results confirmed the presence of PiCUL1-P and PiRBX1 in the complex and identified two different SLFs as the F-box protein component. Thus, all but Rbx1 of the complex may have evolved in SI, and all SLFs may be the F-box component of similar complexes.

Proteomics approaches advance our understanding of plant self-incompatibility response

Self-incompatibility (SI) in plants is a genetic mechanism that prevents self-fertilization and promotes out-crossing needed to maintain genetic diversity. SI has been classified into two broad categories: the gametophytic self-incompatibility (GSI) and the sporophytic self-incompatibility (SSI) based on the genetic mechanisms involved in 'self' pollen rejection. Recent proteomic approaches to identify potential candidates involved in SI have shed light onto a number of previously unidentified mechanisms required for SI response. SI proteome research has progressed from the use of isoelectric focusing in early days to the latest third-generation technique of comparative isobaric tag for relative and absolute quantitation (iTRAQ) used in recent times. We will focus on the proteome-based approaches used to study self-incompatibility (GSI and SSI), recent developments in the field of incompatibility research with emphasis on SSI and future prospects of using proteomic approaches to study self-incompatibility.

High-density genetic maps for loci involved in nuclear male sterility (NMS1) and sporophytic self-incompatibility (S-locus) in chicory (Cichorium intybus L., Asteraceae)

High-density genetic maps were constructed for loci involved in nuclear male sterility (NMS1-locus) and sporophytic self-incompatibility (S-locus) in chicory (Cichorium intybus L.). The mapping population consisted of 389 F1' individuals derived from a cross between two plants, K28 (male-sterile) and K59 (pollen-fertile), both heterozygous at the S-locus. This F1' mapping population segregated for both male sterility (MS) and strong self-incompatibility (SI) phenotypes. Phenotyping F1' individuals for MS allowed us to map the NMS1-locus to linkage group (LG) 5, while controlled diallel and factorial crosses to identify compatible/incompatible phenotypes mapped the S-locus to LG2. To increase the density of markers around these loci, bulked segregant analysis was used. Bulks and parental plants K28 and K59 were screened using amplified fragment length polymorphism (AFLP) analysis, with a complete set of 256 primer combinations of EcoRI-ANN and MseI-CNN. A total of 31,000 fragments were generated, of which 2,350 showed polymorphism between K59 and K28. Thirteen AFLP markers were identified close to the NMS1-locus and six in the vicinity of the S-locus. From these AFLP markers, eight were transformed into sequence-characterized amplified region (SCAR) markers and of these five showed co-dominant polymorphism. The chromosomal regions containing the NMS1-locus and the S-locus were each confined to a region of 0.8 cM. In addition, we mapped genes encoding proteins similar to S-receptor kinase, the female determinant of sporophytic SI in the Brasicaceae, and also markers in the vicinity of the putative S-locus of sunflower, but none of these genes or markers mapped close to the chicory S-locus.

Molecular characterization and expression analysis of S1 self-incompatibility locus-linked pollen 3.15 gene in Citrus reticulata

Gametophytic self-incompatibility (GSI) is controlled by a highly polymorphic locus called the S-locus, which is an important factor that can result in seedless fruit in Citrus. The S1 self-incompatibility locus-linked pollen 3.15 gene (S1-3.15 ) belongs to a type of S locus gene. The role of S1-3.15 in the SI reaction of Citrus has not yet been reported. In this study, full-length sequences of cDNA and DNA encoding the S1-3.15 gene, referred to as CrS1-3.15 , were isolated from 'Wuzishatangju' (Self-incompatibility, SI) and 'Shatangju' (Self-compatibility, SC). The predicted amino acid sequences of CrS1-3.15 between 'Wuzishatangju' and 'Shatangju' differ by only three amino acids. Compared to 'Wuzishatangju', three bases were substituted in the genomic DNA of CrS1-3.15 from 'Shatangju'. Southern blot results showed that one copy of CrS1-3.15 existed in the genomic DNA of both 'Wuzishatangju' and 'Shatangju'. The expression level of the CrS1-3.15 gene in the ovaries of 'Shatangju' was approximately 60-fold higher than that in the ovaries of 'Wuzishatangju'. When 'Wuzishatangju' was cross-pollinated, the expression of CrS1-3.15 was upregulated in the ovaries at 3 d, and the highest expression levels were detected in the ovaries at 6 d after cross-pollination of 'Wuzishatangju' × 'Shatangju'. To obtain the CrS1-3.15 protein, the full-length cDNA of CrS1-3.15 genes from 'Wuzishatangju' and 'Shatangju' was successfully expressed in Pichia pastoris. Pollen germination frequency of 'Wuzishatangju' was inhibited significantly with increasing CrS1-3.15 protein concentrations from SI 'Wuzishatangju'.

Inheritance of hetero-diploid pollen S-haplotype in self-compatible tetraploid Chinese cherry (Prunus pseudocerasus Lindl)

The breakdown of self-incompatibility, which could result from the accumulation of non-functional S-haplotypes or competitive interaction between two different functional S-haplotypes, has been studied extensively at the molecular level in tetraploid Rosaceae species. In this study, two tetraploid Chinese cherry (Prunus pseudocerasus) cultivars and one diploid sweet cherry (Prunus avium) cultivar were used to investigate the ploidy of pollen grains and inheritance of pollen-S alleles. Genetic analysis of the S-genotypes of two intercross-pollinated progenies showed that the pollen grains derived from Chinese cherry cultivars were hetero-diploid, and that the two S-haplotypes were made up of every combination of two of the four possible S-haplotypes. Moreover, the distributions of single S-haplotypes expressed in self- and intercross-pollinated progenies were in disequilibrium. The number of individuals of the two different S-haplotypes was unequal in two self-pollinated and two intercross-pollinated progenies. Notably, the number of individuals containing two different S-haplotypes (S₁- and S₅-, S₅- and S₈-, S₁- and S₄-haplotype) was larger than that of other individuals in the two self-pollinated progenies, indicating that some of these hetero-diploid pollen grains may have the capability to inactivate stylar S-RNase inside the pollen tube and grow better into the ovaries.

S genotyping in Japanese plum and sweet cherry by allele-specific hybridization using streptavidin-coated magnetic beads

We report a rapid and reliable method for S genotyping of Rosaceae fruit trees, which would to be useful for successful planting of cross-compatible cultivars in orchards. Japanese plum (Prunus salicina) and sweet cherry (Prunus avium), belonging to the family Rosaceae, possess gametophytic self-incompatibility controlled by a single polymorphic locus containing at least two linked genes, S-RNase and SFB (S-haplotype-specific F-box gene). For successful planting of cross-compatible cultivars of Rosaceae fruit trees in commercial orchards, it is necessary to obtain information on S genotypes of cultivars. Recently, a method of dot-blot analysis utilizing allele-specific oligonucleotides having sequences of SFB-HVa region has been developed for identification of S haplotypes in Japanese plum and sweet cherry. However, dot-blot hybridization requires considerable time and skill for analysis even of a small number of plant samples. Thus, a quick and efficient method for S genotyping was developed in this study. In this method, instead of a nylon membrane used for dot-blot hybridization, streptavidin-coated magnetic beads are used to immobilize PCR products, which are hybridized with allele-specific oligonucleotide probes. Our improved method allowed us to identify 10 S haplotypes (S-a, S-b, S-c, S-d, S-e, S-f, S-h, S-k, S-7 and S-10) of 13 Japanese plum cultivars and 10 S haplotypes (S-1, S-2, S-3, S-4, S-4', S-5, S-6, S-7, S-9 and S-16) of 13 sweet cherry cultivars utilizing SFB or S-RNase gene polymorphism. This method would be suitable for identification of S genotypes of a small number of plant samples.

Identification of a Skp1-like protein interacting with SFB, the pollen S determinant of the gametophytic self-incompatibility in Prunus

Many species in Rosaceae, Solanaceae, and Plantaginaceae exhibit S-RNase-based self-incompatibility (SI). In this system, the pistil and pollen specificities are determined by S-RNase and the S locus F-box protein, respectively. The pollen S determinant F-box protein in Prunus (Rosaceae) is referred to by two different terms, SFB (for S-haplotype-specific F-box protein) and SLF (for S locus F box), whereas it is called SLF in Solanaceae and Plantaginaceae. Prunus SFB is thought to be a molecule indispensable for its cognate S-RNase to exert cytotoxicity and to arrest pollen tube growth in incompatible reactions. Although recent studies have demonstrated the molecular function of SCF(SLF) in the SI reaction of Solanaceae and Plantaginaceae, how SFB participates in the Prunus SI mechanism remains to be elucidated. Here we report the identification of sweet cherry (Prunus avium) SFB (PavSFB)-interacting Skp1-like1 (PavSSK1) using a yeast (Saccharomyces cerevisiae) two-hybrid screening against the pollen cDNA library. Phylogenetic analysis showed that PavSSK1 belongs to the same clade as Antirrhinum hispanicum SLF-interacting Skp1-like1 and Petunia hybrida SLF-interacting Skp1-like1 (PhSSK1). In yeast, PavSSK1 interacted not only with PavSFBs from different S haplotypes and Cullin1-likes (PavCul1s), but also with S-locus F-box-likes. A pull-down assay confirmed the interactions between PavSSK1 and PavSFB and between PavSSK1 and PavCul1s. These results collectively indicate that PavSSK1 could be a functional component of the SCF complex and that PavSFB may function as a component of the SCF complex. We discuss the molecular function of PavSFB in self-/nonself-recognition in the gametophytic SI of Prunus.

Spatial and temporal activity of upstream regulatory regions of rice anther-specific genes in transgenic rice and Arabidopsis

Upstream regulatory regions (URRs) of rice anther-specific genes, namely OSbHLH (coding for basic helix-loop-helix-containing protein) and OSFbox (F-box protein encoding gene), selected from the microarray data have been cloned to control expression of GUS and GFP reporter genes in stably transformed rice. Quantitative real time PCR analysis shows maximum transcript accumulation of these two genes in the meiotic anthers. Analysis of OSbHLH and OSFbox URRs by PLACE database reveal the presence of known pollen-specific cis elements. The URRs of both OSbHLH and OSFbox genes have maximum activity in the meiotic anther stage in rice, but confer constitutive expression in the heterologous dicot system, Arabidopsis, indicative of monocot specificity. Another rice gene (OSIPK; with homology to genes encoding calcium-dependent protein kinases) URR already reported to have anther-specific activity in Arabidopsis and tobacco also confers anther-specific expression in rice and is active in the pollen tubes, suggesting it belongs to the category of late expressed genes. The spatial activity of three URRs has also been analysed by histochemical evaluation of GUS activity in different anther cells/tissues. The activity of OSIPK URR in rice is strongest among the three URRs.

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.

Identification of S-RNase and peroxidase in petunia nectar

Previous SDS PAGE gel analysis of the floral nectars from petunia and tobacco plants revealed significant differences in the protein patterns. Petunia floral nectar was shown to contain a number of RNase activities by in gel RNase activity assay. To identify these proteins in more detail, the bands with RNase activity were excised from gel and subjected to trypsin digestion followed by LC-MS/MS analysis. This analysis revealed that S-RNases accumulate in nectar from Petunia hybrida, where they should carry out a biological function different from self-pollen rejection. In addition, other proteins were identified by the LC-MS/MS analysis. These proteins include a peroxidase, an endochitinase, and a putative fructokinase. Each of these proteins contained a secretory signal sequence that marked them as potential nectar proteins. We developed RT-PCR assays for each of these five proteins and demonstrated that each of these proteins was expressed in the petunia floral nectary. A discussion of the role of these proteins in antimicrobial activity in nectar is presented.

Sex chromosomes in land plants

Sex chromosomes in land plants can evolve as a consequence of close linkage between the two sex determination genes with complementary dominance required to establish stable dioecious populations, and they are found in at least 48 species across 20 families. The sex chromosomes in hepatics, mosses, and gymnosperms are morphologically heteromorphic. In angiosperms, heteromorphic sex chromosomes are found in at least 19 species from 4 families, while homomorphic sex chromosomes occur in 20 species from 13 families. The prevalence of the XY system found in 44 out of 48 species may reflect the predominance of the evolutionary pathway from gynodioecy towards dioecy. All dioecious species have the potential to evolve sex chromosomes, and reversions back from dioecy to various forms of monoecy, gynodioecy, or androdioecy have also occurred. Such reversals may occur especially during the early stages of sex chromosome evolution before the lethality of the YY (or WW) genotype is established.

RNase-based gametophytic self-incompatibility evolution: Questioning the hypothesis of multiple independent recruitments of the S-pollen gene

Multiple independent recruitments of the S-pollen component (always an F-box gene) during RNase-based gametophytic self-incompatibility evolution have recently been suggested. Therefore, different mechanisms could be used to achieve the rejection of incompatible pollen in different plant families. This hypothesis is, however, mainly based on the interpretation of phylogenetic analyses, using a small number of divergent nucleotide sequences. In this work we show, based on a large collection of F-box S-like sequences, that the inferred relationship of F-box S-pollen and F-box S-like sequences is dependent on the sequence alignment software and phylogenetic method used. Thus, at present, it is not possible to address the phylogenetic relationship of F-box S-pollen and S-like sequences from different plant families. In Petunia and Malus/Pyrus the putative S-pollen gene(s) show(s) variability patterns different than expected for an S-pollen gene, raising the question of false identification. Here we show that in Petunia, the unexpected features of the putative S-pollen gene are not incompatible with this gene's being the S-pollen gene. On the other hand, it is very unlikely that the Pyrus SFBB-gamma gene is involved in specificity determination.

High-resolution mapping of the S-locus in Turnera leads to the discovery of three genes tightly associated with the S-alleles

While the breeding system known as distyly has been used as a model system in genetics, and evolutionary biology for over a century, the genes determining this system remain unknown. To positionally clone genes determining distyly, a high-resolution map of the S-locus region of Turnera has been constructed using segregation data from 2,013 backcross progeny. We discovered three putative genes tightly linked with the S-locus. An N-acetyltransferase (TkNACE) flanks the S-locus at 0.35 cM while a sulfotransferase (TkST1) and a non-LTR retroelement (TsRETRO) show complete linkage to the S-locus. An assay of population samples of six species revealed that TsRETRO, initially discovered in diploid Turnera subulata, is also associated with the S-allele in tetraploid T. subulata and diploid Turnera scabra. The sulfotransferase gene shows some level of differential expression in long versus short styles, indicating it might be involved in some aspect of distyly. The complete linkage of TkST1 and TsRETRO to the S-locus suggests that both genes may reside within, or in the immediate vicinity of the S-locus. Chromosome walking has been initiated using one of the genes discovered in the present study to identify the genes determining distyly.

Roles of proteolysis in plant self-incompatibility

Self-incompatibility (SI) is a genetically controlled system adopted by many flowering plants to avoid inbreeding and thus to maintain species diversity. Generally, self-pollen rejection occurs through active pollen and pistil recognition and subsequent signaling responses. So far, three different molecular controls of pollen and pistil recognition have been characterized and are exemplified by three families: the Solanaceae, the Papaveraceae, and the Brassicaceae. With more components involved in these SI systems coming to light, recent studies have provided intriguing insights into the downstream reactions that follow the initial SI signal perception. The process of pollen rejection is closely associated with rapid and effective proteolytic events, including the ubiquitin-proteasome pathway and the vacuolar sorting pathway. Here, we review our current understanding of the roles of proteolysis in SI responses of flowering plants.

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.

RNase-based self-incompatibility: puzzled by pollen S

Many plants have a genetically determined self-incompatibility system in which the rejection of self pollen grains is controlled by alleles of an S locus. A common feature of these S loci is that separate pollen- and style-expressed genes (pollen S and style S, respectively) determine S allele identity. The long-held view has been that pollen S and style S must be a coevolving gene pair in order for allelic recognition to be maintained as new S alleles arise. In at least three plant families, the Solanaceae, Rosaceae, and Plantaginaceae, the style S gene has long been known to encode an extracellular ribonuclease called the S-RNase. Pollen S in these families has more recently been identified and encodes an F-box protein known as either SLF or SFB. In this perspective, we describe the puzzling evolutionary relationship that exists between the SLF/SFB and S-RNase genes and show that in most cases cognate pairs of genes are not coevolving in the expected manner. Because some pollen S genes appear to have arisen much more recently than their style S cognates, we conclude that either some pollen S genes have been falsely identified or that there is a major problem with our understanding of how the S locus evolves.

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.

Genomic consequences of selection on self-incompatibility genes

Frequency-dependent selection at plant self-incompatibility systems is inherent and well understood theoretically. A self-incompatibility locus leads to a strong peak of diversity in the genome, to a unique distribution of diversity across the species and possibly to increased introgression between closely related species. We review recent empirical studies demonstrating these features and relate the empirical findings to theoretical predictions. We show how these features are being exploited in searches for other genes under multi-allelic balancing selection and for inference on recent breakdown of self-incompatibility.

Expression of 10 S-class SLF-like genes in Nicotiana alata pollen and its implications for understanding the pollen factor of the S locus

The S locus of Nicotiana alata encodes a polymorphic series of ribonucleases (S-RNases) that determine the self-incompatibility (SI) phenotype of the style. The pollen product of the S locus (pollen S) in N. alata is unknown, but in species from the related genus Petunia and in self-incompatible members of the Plantaginaceae and Rosaceae, this function has been assigned to an F-box protein known as SLF or SFB. Here we describe the identification of 10 genes (designated DD1-10) encoding SLF-related proteins that are expressed in N. alata pollen. Because our approach to cloning the DD genes was based on sequences of SLFs from other species, we presume that one of the DD genes encodes the N. alata SLF ortholog. Seven of the DD genes were exclusively expressed in pollen and a low level of sequence variation was found in alleles of each DD gene. Mapping studies confirmed that all 10 DD genes were linked to the S locus and that at least three were located in the same chromosomal segment as pollen S. Finally, the different topologies of the phylogenetic trees produced using available SLF-related sequences and those produced using S-RNase sequences suggests that pollen S and the S-RNase have different evolutionary histories.

Comparison of Petunia inflata S-Locus F-box protein (Pi SLF) with Pi SLF like proteins reveals its unique function in S-RNase based self-incompatibility

Petunia inflata possesses S-RNase-based self-incompatibility (SI), which prevents inbreeding and promotes outcrossing. Two polymorphic genes at the S-locus, S-RNase and P. inflata S-locus F-box (Pi SLF), determine the pistil and pollen specificity, respectively. To understand how the interactions between Pi SLF and S-RNase result in SI responses, we identified four Pi SLF-like (Pi SLFL) genes and used them, along with two previously identified Pi SLFLs, for comparative studies with Pi SLF(2). We examined the in vivo functions of three of these Pi SLFLs and found that none functions in SI. These three Pi SLFLs and two other Pi SLFs either failed to interact with S(3)-RNase (a non-self S-RNase for all of them) or interacted much more weakly than did Pi SLF(2) in vitro. We divided Pi SLF(2) into FD1 (for Functional Domain1), FD2, and FD3, each containing one of the Pi SLF-specific regions, and used truncated Pi SLF(2), chimeric proteins between Pi SLF(2) and one of the Pi SLFLs that did not interact with S(3)-RNase, and chimeric proteins between Pi SLF(1) and Pi SLF(2) to address the biochemical roles of these three domains. The results suggest that FD2, conserved among three allelic variants of Pi SLF, plays a major role in the strong interaction with S-RNase; additionally, FD1 and FD3 (each containing one of the two variable regions of Pi SLF) together negatively modulate this interaction, with a greater effect on interactions with self S-RNase than with non-self S-RNases. A model for how an allelic product of Pi SLF determines the fate of its self and non-self S-RNases in the pollen tube is presented.

Meiotic recombination in Turnera (Turneraceae): extreme sexual difference in rates, but no evidence for recombination suppression associated with the distyly (S) locus

To explore the rate of recombination resulting from male vs female meiosis, crosses were performed using distylous Turnera subulata as well as a cross involving the introgression of genes from T. krapovickasii into T. subulata. We assayed four loci on the chromosome bearing the S-locus as well as two loci on each of two other linkage groups. Substantial and consistent dimorphism in recombination rates was found with female meiosis resulting in as much as a approximately 6-fold increase relative to male. Aberrant single locus segregation ratios occurred for some loci, particularly when the male (pollen) parent was heterozygous and the cross involved introgressed genes. The extreme trend of greater recombination resulting from female meiosis was, however, maintained in crosses where no aberrant ratios occurred, indicating that the sex dimorphism in recombination is not the result of aberrant segregation. We also exploited this distylous species and tested whether there is recombination suppression around the S-locus because of an inversion or other chromosome rearrangement(s). We found no significant evidence for recombination suppression.

Self-compatibility of two apricot selections is associated with two pollen-part mutations of different nature

Loss of pollen-S function in Prunus self-compatible mutants has recently been associated with deletions or insertions in S-haplotype-specific F-box (SFB) genes. We have studied two self-compatible cultivars of apricot (Prunus armeniaca), Currot (S(C)S(C)) and Canino (S(2)S(C)), sharing the naturally occurring self-compatible (S(C))-haplotype. Sequence analysis showed that whereas the S(C)-RNase is unaltered, a 358-bp insertion is found in the SFB(C) gene, resulting in the expression of a truncated protein. The alteration of this gene is associated with self-incompatibility (SI) breakdown, supporting previous evidence that points to SFB being the pollen-S gene of the Prunus SI S-locus. On the other hand, PCR analysis of progenies derived from Canino showed that pollen grains carrying the S(2)-haplotype were also able to overcome the incompatibility barrier. However, alterations in the SFB(2) gene or evidence of pollen-S duplications were not detected. A new class of F-box genes encoding a previously uncharacterized protein with high sequence similarity (approximately 62%) to Prunus SFB proteins was identified in this work, but the available data rules them out of producing S-heteroallelic pollen and thus the cause of the pollen-part mutation. These results suggest that cv Canino has an additional mutation, not linked to the S-locus, which causes a loss of pollen-S activity when present in pollen. As a whole, these findings support the proposal that the S-locus products besides other S-locus independent factors are required for gametophytic SI in Prunus.

Maximum-likelihood estimation of rates of recombination within mating-type regions

Features common to many mating-type regions include recombination suppression over large genomic tracts and cosegregation of genes of various functions, not necessarily related to reproduction. Model systems for homomorphic self-incompatibility (SI) in flowering plants share these characteristics. We introduce a method for the exact computation of the joint probability of numbers of neutral mutations segregating at the determinant of mating type and at a linked marker locus. The underlying Markov model incorporates strong balancing selection into a two-locus coalescent. We apply the method to obtain a maximum-likelihood estimate of the rate of recombination between a marker locus, 48A, and S-RNase, the determinant of SI specificity in pistils of Nicotiana alata. Even though the sampled haplotypes show complete allelic linkage disequilibrium and recombinants have never been detected, a highly significant deficiency of synonymous substitutions at 48A compared to S-RNase suggests a history of recombination. Our maximum-likelihood estimate indicates a rate of recombination of perhaps 3 orders of magnitude greater than the rate of synonymous mutation. This approach may facilitate the construction of genetic maps of regions tightly linked to targets of strong balancing selection.

Self-incompatibility in plants

Sexual reproduction in many flowering plants involves self-incompatibility (SI), which is one of the most important systems to prevent inbreeding. In many species, the self-/nonself-recognition of SI is controlled by a single polymorphic locus, the S-locus. Molecular dissection of the S-locus revealed that SI represents not one system, but a collection of divergent mechanisms. Here, we discuss recent advances in the understanding of three distinct SI mechanisms, each controlled by two separate determinant genes at the S-locus. In the Brassicaceae, the determinant genes encode a pollen ligand and its stigmatic receptor kinase; their interaction induces incompatible signaling(s) within the stigma papilla cells. In the Solanaceae-type SI, the determinants are a ribonuclease and an F-box protein, suggesting the involvement of RNA and protein degradation in the system. In the Papaveraceae, the only identified female determinant induces a Ca2+-dependent signaling network that ultimately results in the death of incompatible pollen.

Evolution under tight linkage to mating type

Recent large-scale sequencing studies of mating type loci in a number of organisms offer insight into the origin and evolution of these genomic regions. Extensive tracts containing genes with a wide diversity of functions typically cosegregate with mating type. Cases in which mating type determination entails complementarity between distinct transcription units may descend from systems in which close physical linkage facilitated the coordinated expression and cosegregation of the interacting genes. In response to the particular selection pressures associated with the maintenance of more than one mating type, this nucleus of low recombination may expand over evolutionary time, engulfing neighboring tracts bearing genes with no direct role in reproduction. This scenario is consistent with the present-day structure of some mating type loci, including regulators of homomorphic self-incompatibility in angiosperms (S-loci). Recombination suppression and enforced S-locus heterozygosity accelerate the accumulation of genetic load and promote genetic associations between S-alleles and degenerating genes in cosegregating tracts. This S-allele-specific load may influence the evolution of self-incompatibility systems.

Duplication of the S-locus F-box gene is associated with breakdown of pollen function in an S-haplotype identified in a natural population of self-incompatible Petunia axillaris

We previously identified both self-incompatible and self-compatible plants in a natural population of self-incompatible Petunia axillaris subsp. axillaris, and found that all the self-compatible plants studied carried either SC1- or SC2-haplotype. Genetic crosses showed that SC2 was identical to S17 identified from another natural population of P. axillaris, except that its pollen function was defective, and that the pollen-part mutation in SC2 was tightly linked to the S-locus. Recent identification of the S-locus F-box gene (SLF) as the gene that controls pollen specificity in S-RNase-based self-incompatibility has prompted us to examine the molecular basis of this pollen-part mutation. We cloned and sequenced the S17-allele of SLF of P. axillaris, named PaSLF17, and found that SC2SC2 plants contained extra restriction fragments that hybridized to PaSLF17 in addition to all of those observed in S17S17 plants. Moreover, these additional fragments co-segregated with SC2. We used the SC2-specific restriction fragments as templates to clone an allele of PaSLF by PCR. To determine the identity of this allele, named PaSLFx, primers based on its sequence were used to amplify PaSLF alleles from genomic DNA of 40 S-homozygotes of P. axillaris, S1S1 through S40S40. Sequence comparison revealed that PaSLFx was completely identical with PaSLF19 obtained from S19S19. We conclude that the S-locus of SC2 contained both S17-allele and the duplicated S19-allele of PaSLF. SC2 is the first naturally occurring pollen-part mutation of a solanaceous species that was shown to be associated with duplication of the pollen S. This finding lends support to the proposal, based on studies of irradiation-generated pollen-part mutants of solanaceous species, that duplication, but not deletion, of the pollen S, causes breakdown of pollen function.

Genome-wide analysis of S-Locus F-box-like genes in Arabidopsis thaliana

The Antirrhinum S-locus F-box gene, AhSLF-S2, has been shown to determine the pollen function of S-RNase-mediated self-incompatibility (SI). Its initial identification led to the discovery of a large family of plant-specific F-box proteins, named the SLF (S-Locus F-box) family, including members from species with or without S-RNase SI system. To investigate the evolution and function of its family members in Arabidopsis, we first identified 92 Arabidopsis F-box proteins related to AhSLF-S2, referred to as AtSFL (S-locus F-box-like) in this report. Phylogenetic analyses with family members from several plant species revealed that they could be classified into five subgroups, and the SLF genes appeared to have had a monophyletic origin. Yeast two-hybrid analyses showed that most AtSFL proteins could interact with one or more ASK (Arabidopsis Skp1-like) proteins, a component of the SCF (Skp1/Cullin or CDC53/F-box) complex, suggesting that AtSFLs may function in the process of ubiquitin/26S proteasome-mediated proteolysis. Transcript analysis found that most of AtSFL genes are expressed ubiquitously and only three of them (AtSFL61, 79 and 85) displayed a tissue-specific pattern. In consistent, phenotypic observations for T-DNA insertion lines of 37 AtSFL genes revealed that most of them are functionally redundant, but inactivation of two AtSFL genes (AtSFL 61 and 70) appears to have caused developmental defects in embryo or female gametophyte. Our results show that a diversified expression and functional pattern are associated with AtSFL genes, indicating that they play important roles in various biological processes in Arabidopsis.

Identification of the pollen determinant of S-RNase-mediated self-incompatibility

Many flowering plants have adopted self-incompatibility mechanisms to prevent inbreeding and promote out-crosses. In the Solanaceae, Rosaceae and Scrophulariaceae, two separate genes at the highly polymorphic S-locus control self-incompatibility interactions: the S-RNase gene encodes the pistil determinant and the previously unidentified S-gene encodes the pollen determinant. S-RNases interact with pollen S-allele products to inhibit the growth of self-pollen tubes in the style. Pollen-expressed F-box genes showing allelic sequence polymorphism have recently been identified near to the S-RNase gene in members of the Rosaceae and Scrophulariaceae; but until now have not been directly shown to encode the pollen determinant. Here we report the identification and characterization of PiSLF, an S-locus F-box gene of Petunia inflata (Solanaceae). We show that transformation of S1S1, S1S2 and S2S3 plants with the S2-allele of PiSLF causes breakdown of their pollen function in self-incompatibility. This breakdown of pollen function is consistent with 'competitive interaction', in which pollen carrying two different pollen S-alleles fails to function in self-incompatibility. We conclude that PiSLF encodes the pollen self-incompatibility determinant.

A simple method for computing exact probabilities of mutation numbers

We describe a method for the recursive computation of exact probability distributions for the number of neutral mutations segregating in samples of arbitrary size and configuration. Construction of the recursions requires only characterization of evolutionary changes as a Markov process and determination of one-step transition matrices. We address the pattern of nucleotide diversity at a neutral marker locus linked to a determinant of mating type. Under a reformulation of parameters, the method also applies directly to metapopulation models with island migration among demes. Characterization of complete probability distributions facilitates parameter estimation and hypothesis testing by likelihood- as well as moment-based approaches.