The emerging complexity of self-incompatibility (S-) loci

 A complex picture of S-loci is beginning to emerge from recent studies of the S-locus of RNase-based gametophytic self-incompatibility displayed by the Rosaceae, Solanaceae, and Scrophulariaceae, and of the S-locus of the type of sporophytic self-incompatibility displayed by the Brassicaceae. It now appears that not only do these S-loci contain two separate genes, one controlling pollen function and the other controlling pistil function in self-incompatibility interactions, but also many other genes whose functions are largely unknown. The implications of these recent findings for the study of the mechanisms of self-incompatibililty interactions and evolution of the self-incompatibility systems are discussed. Received: 7 January 1999 / Revision accepted: 13 January 1999     

Structure and expression of AtS1, an Arabidopsis thaliana gene homologous to the S-locus related genes of Brassica

Summary Genetic and molecular analysis of the self-incompatibility locus (S-locus) of the crucifer Brassica has led to the characterization of a multigene family involved in pollen-stigma interactions. While the crucifer Arabidopsis thaliana does not have a self-incompatibility system, S-related sequences were detected in this species by cross-hybridization with Brassica DNA probes. In this paper, we show that an A. thaliana S-related sequence, designated AtS1, is expressed specifically in flower buds. Sequence analysis suggests that AtS1 encodes a secreted glycoprotein that is most similar to the Brassica S-locus related protein SLR1. As has been proposed for SLR1, this gene may be involved in determining some fundamental aspect of pollen-stigma interactions during pollination. The molecular and genetic advantages of the Arabidopsis system will provide many avenues for testing this hypothesis.     

Physical distances between S-locus genes in various S haplotypes of Brassica rapa and B. oleracea

In Brassica, self-incompatibility genes SLG (for S-locus glycoprotein) and SRK (for S-receptor kinase) are located in the S-locus complex region with several other S-linked genes. The S locus is a highly polymorphic region: polymorphism has been observed not only in sequences of SLG and SRK but also in the location of the S-locus genes. In order to compare the physical location of the S-locus genes in various S haplotypes, we used six class-I S haplotypes of B. rapa and seven class-I S haplotypes of B. oleracea in this study. DNA gel blot analysis using pulsed-field gel electrophoresis (PFGE) showed that the physical distances between SLG and SRK in B. rapa are significantly shorter than those in B. oleracea and that the sizes of MluI and BssHII fragments harboring SLG and SRK are less variable within B. rapa than within B. oleracea. We concluded that several large genomic fragments might have been inserted into the S-locus region of B. oleracea after allelic differentiation of S-locus genes. Received: 20 September 1999 / Accepted: 8 October 1999     

Molecular Determinants and Mechanisms of Gametophytic Self-Incompatibility in Fruit Trees of Rosaceae

Self-incompatibility is an important genetic mechanism that prevents inbreeding and promotes genetic polymorphism and heterosis in flowering plants. Many fruit species in the Rosaceae, including apple, pear, plum, apricot, sweet cherry, Japanese apricot, and almond, exhibit typical gametophytic self-incompatibility (GSI) controlled by an apparently single multi-allelic locus. This locus encodes at least two components from both the pollen and the pistil, and controls recognition of self- and non-self pollen. Recently, the GSI system has been investigated at the molecular and cellular levels in Rosaceae, and findings have provided some important insights as to how these two genes interact within pollen tubes that lead to specific inhibition of germination and/or growth of self-pollen tubes. In this review, molecular features of S-determinants of both pistil and pollen, identification of S-alleles, mechanisms of self-incompatibility break-down, and evolution of S-alleles are presented. Moreover, hypothetical signal transduction models in a self-incompatible system in Rosaceae are proposed based on recent findings that indicate that several signal factors are involved in GSI responses.     

Isolation and <Emphasis Type="Italic">S</Emphasis>-genotyping application of <Emphasis Type="Italic">S</Emphasis>-allelic polymorphic <Emphasis Type="Italic">MdSLFB</Emphasis>s in apple (<Emphasis Type="Italic">Malus domestica</Emphasis> Borkh.)

Apple (Malus domestica Borkh.) possesses gametophytic self-incompatibility (GSI) which is controlled by S-RNase in the pistil as well as a pollen S-determinant that has not been well characterized. The identification of S-locus F-box brother (SFBB) genes, which are good candidates for the pollen S-determinant in apple and pear, indicated the presence of multiple S-allelic polymorphic F-box genes at the S-locus. In apple, two SFBB gene groups have been described, while there are at least three groups in pear. In this report, we identified five MdSLFB (S-RNase-linked F-box) genes from four different S-genotypes of apple. These genes showed pollen- and S-allele-specific expression with a high polymorphism among S-alleles. The phylogenetic tree suggested that some of them belong to SFBBα or β groups as described previously, while others appear to be different from SFBBs. In particular, the presence of MdSLFB3 and MdSLFB9 suggested that there are more S-allelic polymorphic F-box gene groups in the S-locus besides α and β. Based on the sequence polymorphism of MdSLFBs, we developed an S-genotyping system for apple cultivars. In addition, we isolated twelve MdSLFB-like genes, which showed pollen-specific expression without S-allelic polymorphism.     

<Emphasis Type="Italic">S</Emphasis>-Allele characterization in self-incompatible pear (<Emphasis Type="Italic">Pyrus communis</Emphasis> L.)

Gametophytic self-incompatibility, a natural mechanism occurring in pear and other fruit-tree species, is usually controlled by the S-locus with allelic variants ( S1, S2, Sn). Recently, biochemical and molecular tools have determined the S-genotype of cultivars in various species. The present study determined the S-locus composition of ten European pear cultivars via S-PCR molecular assay, thereby obviating time-consuming fieldwork whose results are often ambiguous because of environmental effects. To verify the S-PCR assay, two putative S-allele DNA fragments of Japanese pear were isolated; their sequences proved to be identical to those reported in the databank. Six S-allele fragments of European pear were then sequenced. While field data confirmed the molecular results, fully and half-compatible field crosses were not distinguishable.     

Expression level of the SLG gene is not correlated with the self-incompatibility phenotype in the class II S haplotypes of Brassica oleracea

In Brassica, the S-locus glycoprotein (SLG) gene has been strongly implicated in the self-incompatibility reaction. Several alleles of this locus have been sequenced, and accordingly grouped as class I (corresponding to dominant S-alleles) and class II (recessive). We recently showed that a self-compatible (Sc) line of Brassica oleracea expressed a class II-like SLG (SLG-Sc) gene. Here, we report that the SLG-Sc glycoprotein is electrophoretically and immunochemically very similar to the recessive SLG-S15 glycoprotein, and is similarly expressed in stigmatic papillae. Moreover, by seed yield analysis, we observe that both alleles are associated with a self-compatibility response, in contrast with the other known recessive S haplotypes (S2 and S5). By genomic DNA blot analysis, we show the existence of molecular homologies between the Sc and S15 haplotypes, but demonstrate that they are not identical. On the other hand, we also report that the S2 haplotype expresses very low amounts of SLG glycoproteins, although it exhibits a self-incompatible phenotype. These results strongly question the precise role of the SLG gene in the molecular mechanisms that control the self-incompatibility reaction of Brassica.     

Determination of partial genomic sequences and development of a CAPS system of the S-RNase gene for the identification of 22 S haplotypes of apple (Malus × domestica Borkh.)

Information about self-incompatibility (S) genotypes of apple cultivars is important for the selection of pollen donors for fruit production and breeding. Although S genotyping systems using S haplotype-specific PCR of S-RNase, the pistil S gene, are useful, they are sometimes associated with false-positive/negative problems and are unable to identify new S haplotypes. The CAPS (cleaved amplified polymorphic sequences) system is expected to overcome these problems, however, the genomic sequences needed to establish this system are not available for many S-RNases. Here, we determined partial genomic sequences of eight S-RNases, and used the information to design new primer and to select 17 restriction enzymes for the discrimination of 22 S-RNases by CAPS. Using the system, the S genotypes of three cultivars were determined. The genomic sequence-based CAPS system would be useful for S genotyping and analyzing new S haplotypes of apple.     

Self-incompatibility in Petunia inflata: isolation and characterization of cDNAs encoding three S-allele-associated proteins

Summary We have identified three alleles of the S-locus controlling self-incompatibility and their associated pistil proteins in Petunia inflata, a species that displays monofactorial gametophytic self-incompatibility. These S-allele-associated proteins (S-proteins) are pistil specific, and their levels are developmentally regulated. The amino-terminal sequences determined for the three S-proteins are highly conserved and show considerable homology to those of S-proteins from Petunia hybrida, Nicotiana alata and Lycopersicon peruvianum, three other species of the Solanaceae that also exhibit gametophytic self-incompatibility. cDNA clones encoding the three S-proteins were isolated and sequenced. Comparison of their deduced amino acid sequences reveals an average homology of 75.6%, with conserved and variable residue interspersed throughout the protein. Of the 137 conserved residues, 53 are also conserved in the N. alata S-proteins studies so far; of the 64 variable residues, 29 were identified as hypervariable based on calculation of the Similarity Index. There is only one hypervariable region of significant length, and it consists of eight consecutive hypervariable residues. This region correspond approximately to the hypervariable region HV2 identified in N. alata S-proteins. Of the two classes of N. alata S-proteins previously identified, one class exhibits greater homology to the three P. inflata S-proteins reported here than to the other class of N. alata S-proteins.     

Insights Gained From 50 Years of Studying the Evolution of Self-Compatibility in <Emphasis Type="Italic">Leavenworthia</Emphasis> (Brassicaceae)

The shift from outcrossing to selfing is one of the most common evolutionary trends in plants, and there is intense interest in why this is so. The genus Leavenworthia has been the focus of research on this question for half of a century, with particular attention paid to the evolution of self-compatibility from self-incompatibility. In this review, we discuss the last 50 years of research concerning this evolutionary transition in Leavenworthia. Selfing appears to have evolved independently at minimum three times within this genus of eight species. Work on the ecological basis of mating system evolution in Leavenworthia has clarified that selection among individuals is likely a major force behind the recurrent evolution of selfing. Although inadequate pollination is appreciated as a factor favoring selfing, definitive ecological mechanisms that act to favor selfing are still not known and future work on the efficacy of pollinating bees and the effects of climate change is needed. Recent research has likely identified the SRK ortholog at the S-locus controlling self-incompatibility in Leavenworthia alabamica. Analyses of S-locus variation have revealed substantial S-allele diversity in outcrossing populations, with the recurrent fixation of mutations at the S-locus permitting the parallel evolution of selfing in this species. Although we appreciate some of the factors that may explain the evolution of selfing in this group, there is less known about the mechanisms underlying the widespread maintenance of outcrossing at the population and species levels. Studies in Leavenworthia have revealed that genetic diversity is lost over the long-term within selfing populations and leads to elevated population subdivision, but work is needed to determine why these genetic consequences of selfing cause lineages to become evolutionary dead ends.     

Molecular Characterization and Evolution of Self-Incompatibility Genes in Arabidopsis thaliana: The Case of the Sc Haplotype

The switch from an outcrossing mode of mating enforced by self-incompatibility to self-fertility in the Arabidopsis thaliana lineage was associated with mutations that inactivated one or both of the two genes that comprise the self-incompatibility (SI) specificity-determining S-locus haplotype, the S-locus receptor kinase (SRK) and the S-locus cysteine-rich (SCR) genes, as well as unlinked modifier loci required for SI. All analyzed A. thaliana S-locus haplotypes belong to the SA, SB, or SC haplotypic groups. Of these three, the SC haplotype is the least well characterized. Its SRKC gene can encode a complete open-reading frame, although no functional data are available, while its SCRC sequences have not been isolated. As a result, it is not known what mutations were associated with inactivation of this haplotype. Here, we report on our analysis of the Lz-0 accession and the characterization of its highly rearranged SC haplotype. We describe the isolation of its SCRC gene as well as the subsequent isolation of SCRC sequences from other SC-containing accessions and from the A. lyrata S36 haplotype, which is the functional equivalent of the A. thaliana SC haplotype. By performing transformation experiments using chimeric SRK and SCR genes constructed with SC- and S36-derived sequences, we show that the SRKC and SCRC genes of Lz-0 and at least a few other SC-containing accessions are nonfunctional, despite SCRC encoding a functional full-length protein. We identify the probable mutations that caused the inactivation of these genes and discuss our results in the context of mechanisms of S-locus inactivation in A. thaliana.     

Breakdown of self-incompatibility in a natural population of Petunia axillaris (Solanaceae) in Uruguay containing both self-incompatible and self-compatible plants

 Many members of the Solanaceae display a type of gametophytic self-incompatibility which is controlled by a single multiallelic locus, called the S-locus. From our previous survey of more than 100 natural populations of Petunia axillaris (a solanaceous species) in Uruguay, we had found that the majority of the populations of subspecies axillaris were comprised of virtually all self-incompatible individuals. The rest were ”mixed populations” which contained mostly self-incompatible and some self-compatible individuals. In this study, we examined the self-incompatibility behavior and determined the S-genotypes of 33 plants raised from seeds obtained from one such mixed population, designated U1. We found that 30 of the 33 plants (designated U1–1 through U1–33) were self-incompatible and a total of 18 different S-alleles were represented. To determine the S-genotypes of the three self-compatible plants (U1–2, U1–16, and U1–22) and the possible causes for the breakdown of their self-incompatibility, we carried out reciprocal crosses between each of them and each of the 18 S-homozygotes (S ₁ S ₁ through S ₁₈ S ₁₈ ) obtained from bud-selfed progeny of 14 of the 30 self-incompatible plants. For U1–2 and U1–16, we also carried out additional crosses with U1–25 (with S ₁ S ₁₃ genotype) and an S ₁₃ S ₁₅ plant (obtained from a cross between an S ₁₃ -homozygote and an S ₁₅ -homozygote), respectively. Based on all the pollination results and analysis of the production of S-RNases, products of S-alleles in the pistil, we determined the S-genotypes of U1–2, U1–16, and U1–22, and propose that the breakdown of self-incompatibility in these three plants is caused by suppression of the production of S₁₃-RNase from the S ₁₃ -allele they all carry. We have termed this phenomenon ”stylar-part suppression of an S-allele” or SPS. Received: 25 September 1998 / Revision accepted: 22 December 1998     

Identification of S-locus linked PCR fragments in rye (Secale cereale L.) by denaturing gradient gel electrophoresis

Rye inbred lines segregating at the S-locus and homozygous at the Z-locus were investigated by PCR with primers derived from Brassica SLG-sequences. After denaturing gradient gel electrophoresis (DGGE), a 280 bp PCR-fragment displays a polymorphism perfectly correlated to the underlying S-genotypes. This is the first report on S-related DNA polymorphism in a bifactorial self-incompatibility system of the Poaceae.     

Genetic mapping of AFLP/AMF-derived DNA markers in the vicinity of the self-incompatibility locus in<Emphasis Type="Italic"> Ipomoea trifida</Emphasis>

Sporophytic self-incompatibility of diploid Ipomoea trifida is controlled by a single multiallelic locus, the S-locus. To make a fine linkage map around the S-locus, AFLP (amplified restriction fragment length polymorphism) and AMF (AFLP-based mRNA fingerprinting) analyses were performed using bulked genomic DNA and mRNA, respectively, from several plants of each S-haplotype in a segregating population. Putative S-haplotype-specific fragments were obtained and subjected to RFLP analysis of genomic DNA to confirm genetic linkage to the S-locus. Eight DNA markers co-segregating with the S-haplotype were identified and mapped in close proximity to the S-locus. One of them, AAM-68, was the most tightly linked to the S-locus, because no recombinants were detected in the 873 plants of the segregating population analyzed. The S-locus region was defined to be within 1.25 cM in the linkage map. These markers are useful for positional cloning of the S-locus genes in Ipomoea.