Molecular and Genetic Analyses of Four Nonfunctional S Haplotype Variants Derived from a Common Ancestral S Haplotype Identified in Sour Cherry (Prunus cerasus L.)

Tetraploid sour cherry (Prunus cerasus) has an S-RNase-based gametophytic self-incompatibility (GSI) system; however, individuals can be either self-incompatible (SI) or self-compatible (SC). Unlike the situation in the Solanaceae, where self-compatibility accompanying polyploidization is often due to the compatibility of heteroallelic pollen, the genotype-dependent loss of SI in sour cherry is due to the compatibility of pollen containing two nonfunctional S haplotypes. Sour cherry individuals with the S₄S₆S_36aS_36b genotype are predicted to be SC, as only pollen containing both nonfunctional S_36a and S_36b haplotypes would be SC. However, we previously found that individuals of this genotype were SI. Here we describe four nonfunctional S₃₆ variants. Our molecular analyses identified a mutation that would confer loss of stylar S function for one of the variants, and two alterations that might cause loss of pollen S function for all four variants. Genetic crosses showed that individuals possessing two nonfunctional S₃₆ haplotypes and two functional S haplotypes have reduced self-fertilization due to a very low frequency of transmission of the one pollen type that would be SC. Our finding that the underlying mechanism limiting successful transmission of genetically compatible gametes does not involve GSI is consistent with our previous genetic model for Prunus in which heteroallelic pollen is incompatible. This provides a unique case in which breakdown of SI does not occur despite the potential to generate SC pollen genotypes.GAMETOPHYTIC self-incompatibility (GSI) is a widespread mechanism in flowering plants that prevents self-fertilization and promotes out-crossing (De Nettancourt 2001). In GSI plants, pollen tube growth is arrested if there is a match between the genes at the S-locus that control pollen and stylar specificity. The gene controlling stylar specificity in the Solanaceae, Rosaceae, and Plantaginaceae is known to encode a ribonuclease (S-RNase) (for a review see McClure 2009), while the gene controlling pollen specificity encodes an F-box protein [S haplotype-specific F-box protein (SFB) or S-locus F-box protein (SLF)] (Lai et al. 2002; Entani et al. 2003; Ushijima et al. 2003; Sijacic et al. 2004). As these two specificity genes are tightly linked and recombination between these two genes has never been observed (Ikeda et al. 2005), these two S-locus specificity genes are collectively termed the S haplotype.Characterization of the S haplotype is most advanced in Prunus (Rosaceae) due to the small physical size of the S haplotype region and the close proximity of the stylar S (S-RNase) and pollen S (SFB) genes (Entani et al. 2003; Ushijima et al. 2003; Yamane et al. 2003b; Ikeda et al. 2005). Within Prunus, sweet cherry (Prunus avium) and sour cherry (P. cerasus) represent a model diploid–tetraploid series that has been used to investigate the effects of polyploidy on GSI. Tetraploid sour cherry is considered to have arisen through hybridization between sweet cherry and tetraploid ground cherry (P. fruticosa) (Olden and Nybom 1968). Like sweet cherry, sour cherry exhibits an S-RNase-based GSI system (Yamane et al. 2001; Hauck et al. 2002; Tobutt et al. 2004) and interspecific crossing studies have demonstrated that sour cherry shares eight sweet cherry S haplotypes: S₁, S₄, S₆, S₉, S₁₂, S₁₃, S₁₄, and S₁₆ (Bošković et al. 2006; Hauck et al. 2006a,b; Tsukamoto et al. 2006, 2008). However, in contrast to sweet cherry, natural sour cherry selections include both self-incompatible (SI) and self-compatible (SC) types. A genetic model demonstrating that the genotype-dependent loss of SI in sour cherry is due to the accumulation of a minimum of two nonfunctional S haploytpes within a single individual was developed and validated (Hauck et al. 2006b). These nonfunctional S haplotypes were characterized as either pollen-part mutants or stylar-part mutants, depending on whether the pollen S or stylar S specificity was disrupted. In Prunus, pollen-part and stylar-part mutants are denoted by a prime symbol “′” or a subscribed “m,” respectively, following the S haplotype number (Tsukamoto et al. 2006). Molecular characterizations of five of the nonfunctional S haplotypes from sour cherry characterized to date support the genetic results because mutations were identified that affected the S-RNase and/or SFB. These changes in coding or regulatory regions included mutations within the S-RNase and/or SFB causing premature stop codons, transposable element insertions within SFB and upstream of the S-RNase, and a 23-bp deletion in a conserved region of the S-RNase (Yamane et al. 2003a; Hauck et al. 2006a; Tsukamoto et al. 2006).According to the genetic model, termed the “one-allele-match model,” sour cherry pollen is rejected if one or both of the functional S haplotypes in the 2x pollen grain match an S haplotype in the style (Hauck et al. 2006b). Therefore, only pollen containing two nonfunctional S haplotypes would be SC; thus, a sour cherry genotype is SC if it has a minimum of two nonfunctional S haplotypes. We previously tested the one-allele-match model using 92 sour cherry selections from four progeny populations (Hauck et al. 2006b). For all the progeny except three, their S genotype correctly predicted whether they were SI or SC. The three progeny individuals that were the exception all had the same genotype: S₄S₆S_aS_d. These individuals were predicted to be SC as the S_a and S_d haplotypes were shown to be nonfunctional in genetic studies and therefore S_aS_d pollen should be SC. However, these progeny were classified as SI on the basis of observations of self-pollen tube growth in the styles. The S_a and S_d haplotypes were originally distinguished on the basis of different RFLP fragment sizes using an S-RNase probe; the HindIII fragment sizes for S_a and S_d differed by ∼200 bp, 6.4-kb and 6.2-kb, respectively (Yamane et al. 2001; Hauck et al. 2002). However, partial S-RNase and SFB sequences from the S_a and S_d haplotypes were identical (N. R. Hauck and A. F. Iezzoni, unpublished results), suggesting that S_a and S_d represented different mutations of the same S haplotype. Therefore, we hypothesized that the SI phenotype of the S₄S₆S_aS_d individuals resulted from complementary pistil S and pollen S mutations in the nonfunctional S_a and S_d haplotypes, thus behaving genetically as one functional S haplotype.We previously reported that heteroallelic sour cherry pollen containing two different functional pollen S haplotypes is incompatible (Hauck et al. 2006b). This finding is counter to the well-documented phenomenon in the Solanaceae where SC accompanying polyploidization is frequently due to the SC of heteroallelic pollen (Lewis 1943; Golz et al. 1999, 2001; Tsukamoto et al. 2005; Xue et al. 2009). Therefore, models explaining the molecular basis of self-recognition in Prunus and the Solanaceae must be consistent with these differing genetic expectations. Recently, Huang et al. (2008) reported competitive interaction in a SC selection of tetraploid P. pseudocerasus, raising the possibility that the SC mechanism between these two tetraploid Prunus species could be different. However, although the data in Huang et al. (2008) are consistent with heteroallelic pollen being SC, homoallelic pollen (e.g., S₁S₁, S₅S₅, or S₇S₇) was not shown to be successful in compatible crosses and unsuccessful in incompatible ones. Therefore, it is possible that the SC in P. pseudocerasus could be caused by mutations in other genes critical for the SI reaction. Because of the importance of these differing genetic expectations for understanding S-RNase-based GSI, we sought to investigate our previously identified exceptions to the one-allele-match model. Specifically, our objective was to test our prior hypothesis that the nonfunctional S_a and S_d haplotypes interact in a complementary manner and therefore behave together genetically as a single functional S haplotype. In this work, the S_a and S_d haplotypes were renamed S_36a and S_36b, respectively, following the order of previously published S haplotypes (Tsukamoto et al. 2008; Vaughan et al. 2008) for reasons explained in the results.