JXB Advance Access published online on July 9, 2008
Journal of Experimental Botany, doi:10.1093/jxb/ern172
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© 2008 The Author(s).
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
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RESEARCH PAPER |
Genetic and molecular characterization of three novel S-haplotypes in sour cherry (Prunus cerasus L.)
1Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
2Department of Plant Sciences, University of California, Davis, CA 95616–8780, USA
3Laboratory of Pomology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
4Instituto de Biologia Molecular e Celular, University of Porto, 4150–180 Porto, Portugal
To whom correspondence should be addressed. E-mail: iezzoni{at}msu.edu
Received 20 March 2008; Revised 22 May 2008 Accepted 27 May 2008
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Abstract |
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Tetraploid sour cherry (Prunus cerasus L.) exhibits gametophytic self-incompatibility (GSI) whereby the specificity of self-pollen rejection is controlled by alleles of the stylar and pollen specificity genes, S-RNase and SFB (S haplotype-specific F-box protein gene), respectively. As sour cherry selections can be either self-compatible (SC) or self-incompatible (SI), polyploidy per se does not result in SC. Instead the genotype-dependent loss of SI in sour cherry is due to the accumulation of non-functional S-haplotypes. The presence of two or more non-functional S-haplotypes within sour cherry 2x pollen renders that pollen SC. Two new S-haplotypes from sour cherry, S33 and S34, that are presumed to be contributed by the P. fruticosa species parent, the complete S-RNase and SFB sequences of a third S-haplotype, S35, plus the presence of two previously identified sweet cherry S-haplotypes, S14 and S16 are described here. Genetic segregation data demonstrated that the S16-, S33-, S34-, and S35-haplotypes present in sour cherry are fully functional. This result is consistent with our previous finding that ‘hetero-allelic’ pollen is incompatible in sour cherry. Phylogenetic analyses of the SFB and S-RNase sequences from available Prunus species reveal that the relationships among S-haplotypes show no correspondence to known organismal relationships at any taxonomic level within Prunus, indicating that polymorphisms at the S-locus have been maintained throughout the evolution of the genus. Furthermore, the phylogenetic relationships among SFB sequences are generally incongruent with those among S-RNase sequences for the same S-haplotypes. Hypotheses compatible with these results are discussed.
Key words: Prunus cerasus, self-incompatibility, SFB, S-RNase
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Introduction |
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Gametophytic self-incompatibility (GSI) is a common genetic mechanism that promotes outcrossing in flowering plants (de Nettancourt, 2001). In GSI, self-incompatibility (SI) is determined by a single multi-allelic locus, called the S-locus, which contains a minimum of two genes, one (stylar-S) controlling stylar specificity and the other (pollen-S) controlling pollen specificity of the SI reaction. The stylar-S gene in three plant families, the Solanaceae, Plantaginaceae, and Rosaceae encodes a ribonuclease (S-RNase; Anderson et al., 1986; McClure et al., 1989; Sassa et al., 1992; Xue et al., 1996), which is expressed in the pistil and specifically degrades the RNA of incompatible pollen (McClure et al., 1990). The pollen-S gene encodes an F-box protein named S-locus F-box protein (SLF) in Antirrhinum (Lai et al., 2002), Petunia inflata (Sijacic et al., 2004), and Prunus mume (Entani et al., 2003), or S haplotype-specific F-box protein (SFB) in Prunus dulcis, P. mume, P. avium, P. spinosa, and P. cerasus (Ushijima et al., 2003; Yamane et al., 2003b; Ikeda et al., 2004a; Nunes et al., 2006). Despite having similar or even identical names in Solanaceae and Prunus the pollen gene is not orthologous (Wheeler and Newbigin, 2007).
Within Prunus (Rosaceae), cherry represents a natural diploid–tetraploid series with the tetraploid sour cherry (P. cerasus) arising through hybridization between sweet cherry (P. avium) and the 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), however, in contrast to sweet cherry, natural sour cherry selections include both SI and self-compatible (SC) types (Redalen, 1984; Lansari and Iezzoni, 1990). This genotype-dependent loss of SI in sour cherry indicates that genetic changes, and not polyploidy per se, cause the breakdown of SI. The genetic switch from SI to SC in sour cherry results from the accumulation of non-functional S-haplotypes according to the ‘one-allele-match model’ (Hauck et al., 2006b). In this model, the match between a functional pollen-S in the 2x pollen and its cognate functional S-RNase in the style, results in an incompatible reaction. A similar reaction would occur regardless of whether the pollen contained a single functional pollen-S gene or two different pollen-S genes. The absence of any functional match results in a compatible reaction. Thus for successful self-fertilization, the 2x pollen must contain two non-functional S-haplotypes. Recently, Huang et al. (2008) reported competitive interaction in a SC selection of tetraploid Prunus 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) is consistent with hetero-allelic pollen being SC, homo-allelic pollen (e.g. S1S1, S5S5, or S7S7) was not shown to be successful in a compatible cross and unsuccessful in an incompatible cross. Therefore, it is possible that the SC in P. pseudocerasus could be caused by mutations in other genes critical for the SI reaction.
Six S-haplotypes present in sweet cherry (S1, S4, S6, S9, S12, and S13) have been shown to be present in sour cherry as well. However, three of these S-haplotypes (S1, S6, and S13) also have non-functional variants in sour cherry that have lost pollen and/or stylar function (Yamane et al., 2003a; Hauck et al., 2006a, b; Tsukamoto et al., 2006). Loss of function in these non-functional S-haplotypes was due to structural alterations of the S-RNase, SFB or S-RNase upstream sequences. Sour cherry also possesses S-haplotypes (S26, S36a, S36b, S36b2, and S36b3) that were presumably derived from the other species parent, P. fruticosa, as these S-haplotypes have not been identified in sweet cherry (Hauck et al., 2006b; T Tsukamoto et al., unpublished data). The extensive sour cherry germplasm collection at Michigan State University (Iezzoni, 2005) provides an excellent resource for the identification of previously undiscovered S-haplotypes for which information about their functionality would aid in the breeding of SC types. Therefore a germplasm survey was undertaken to search for novel S-haplotypes in sour cherry and to determine the functionality of these S-haplotypes. Here two new S-haplotypes identified in sour cherry are described that are presumed to be contributed by the P. fruticosa species parent. The first complete S-RNase and SFB sequences for a third S-haplotype that was previously identified in sour cherry are also reported. Furthermore, genetic segregation data presented demonstrates that all three of these sour cherry S-haplotypes are fully functional. In addition, the S14- and S16-haplotypes have been identified in sour cherry. Phylogenetic analyses of S-RNase and SFB sequences are used to investigate patterns of evolution of S-haplotypes in Prunus.
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Materials and methods |
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Plant material
One sweet cherry cultivar ‘Hedelfingen’ (S3S5) and 17 sour cherry cultivars were used: ‘Cigány 59’, ‘Crisana’, ‘Englaise Timpurii’, ‘Erdi Botermo’, ‘Erdi Jubileum’, ‘Erdi Nagygyumolcsu’, ‘Meteor’, ‘Montmorency’, ‘Pandy 38’, ‘Pandy 114’, ‘Rheinische Schattenmorelle’, ‘Surefire’, ‘Tamaris’, ‘Tarina’, ‘Tschernokorka’, ‘Újfehértói f
rt
s’, and ‘MSU III 18 (12)’. These cultivars were grown at the Michigan State University Clarksville Horticultural Experimental Station, Clarksville, MI, USA and a commercial orchard in Suttons Bay, MI, USA. To determine the inheritance of the S-haplotypes, self-pollinated progeny of ‘Meteor’, ‘Montmorency’ and ‘Tamaris’ plus cross-pollinated progeny between ‘Újfehértói frts’x‘Surefire’ were obtained.
DNA isolation
Young unfolded leaves were collected in the spring, frozen in liquid nitrogen, lyophilized, and stored at –20 °C. Genomic DNA was isolated from lyophilized leaves according to the method of Ikeda et al. (2004b). Extracted leaf DNA was treated with RNase A (Roche, Mannheim, Germany). To genotype the self-pollinated progeny of ‘Meteor’, ‘Montmorency’, and ‘Tamaris’, DNA was extracted from mature seed from which the testa was removed using the procedure of Hauck et al. (2006b). Extracted seed DNA was treated with RNase A (Roche).
PCR amplification
Total DNA was isolated from the cherry selections and used as template DNA for PCR. PCR procedures were identical to those used by Tao et al. (1999). The S-RNase gene specific primer set, Pru-C2 and PCE-R (Tao et al., 1999; Yamane et al., 2001) that correspond to the previously identified C2 and C3 conserved regions (Ushijima et al., 1998), respectively, were used. This primer pair can differentiate among most S-RNase alleles based on polymorphisms in the length of the second intron in the Prunus S-RNase. However, this primer pair cannot amplify S35-RNase. EM-PC2consFD and EM-PC5consRD (Sutherland et al., 2004) were used to amplify S35-RNase. In addition, the primer pair of Pru-C2 and PCE-R cannot differentiate S36a from S36b, S36b2 and S36b3. Instead, these variants of the S36-haplotype were differentiated using the following primer pairs for detection of the S36a-haplotype [PcS36ab-F (5'-GCTAGCCAACCACTTTTACG-3’) and PcS36a-spR (5'-GAAACCCACATGATACAAACTG-3’)] and detection of the S36b-, S36b2-, and S36b3-haplotypes [PcS36ab-F and PcS36b-spR (5'-ATACATTGTAGGCCAGTCTGTG-3’)]. PCR products were run on 2% agarose gels and the DNA bands were visualized by ethidium bromide staining. Furthermore, PCR products were purified using the QIAquick Gel Extraction Kit (Qiagen, Hilden, Germany), ligated into the pGEM-T Easy vector (Promega, Madison, WI, USA), and transformed Escherichia coli JM109 (Promega). Plasmid DNA was prepared using Wizard Plus Minipreps DNA Purification Kit (Promega) and their sequences were determined as described below.
Construction and screening of genomic libraries
Fosmid libraries were constructed using the Copy Control Fosmid library production kit (Epicentre Technologies, Madison, WI, USA). Fosmid libraries from ‘Meteor’, ‘Montmorency’, and ‘Tamaris’ were constructed to clone the S-RNase and SFB alleles from the S-haplotypes being investigated. The fosmid libraries were screened at 60 °C with a mixture of DIG-dUTP-labelled S6-RNase and SFB6 probes, as previously described (Ushijima et al., 2001). The DIG-labelled S6-RNase and SFB6 probes were obtained by PCR-labelling using the PCR DIG Probe Synthesis Kit (Roche) with Pru-C2 and PCE-R primers (Tao et al., 1999; Yamane et al., 2001), and SFB-C1F (Ikeda et al., 2004a) and SFB-C4R primers (Yamane et al., 2003c). Fosmid DNAs from positive clones were prepared using the Wizard Plus Minipreps DNA Purification Kit (Promega). The S-haplotype of each positive fosmid clone was determined by PCR with the S-RNase consensus primer pair (Pru-C2 and PCE-R). Positive clones were also analysed by PCR with the SFB consensus primer pair (SFB-C1F and SFB-C2R) (Ikeda et al., 2004a) to check if the clone has SFB. S-RNase and SFB allele-specific primer pairs were also used to identify the S-haplotypes. For the S35-haplotype in ‘Montmorency’ (S6S13mS35S36a), positive clones were obtained by using a DIG-dUTP-labelled S35-RNase probe. Then more positive clones obtained by hybridization with a mixture of DIG-dUTP-labelled SFB6 and SFB36a probes were subjected to PCR with the SFB consensus primer (SFB-C1F and SFB-C2R) to confirm that the clones contain SFB. Then positive clones were analysed by PCR with SFB allele-specific (SFB6, SFB13, and SFB36a/SFB36b) primer pairs: PaSFB6-F and PaSFB6-R (Ikeda et al., 2005), DdeS13-F (Tsukamoto et al., 2008) and SFB13-spR (Tsukamoto et al., 2006), and PcSFB36ab-F (5'-GGCGGTCGATCCTGATGAC-3') and PcSFB36ab-R (5'-TGTCCGATAACAGCTCCGG-3'), respectively. The positive clones from which a fragment could be amplified with the primer pair SFB-C1F and SFB-C2R, but not amplified with SFB6-, SFB13-, and SFB36a/SFB36b-specific primers, were determined to contain SFB35 and one positive clone was sequenced.
DNA sequencing
DNA sequencing was carried out by using ABI PRISM 3100 Genetic Analyser at the Michigan State University Research Technology Support Facility. The plasmid clones were sequenced by using SP6 and T7 primers. The fosmid clones were sequenced by primer walking using Pru-T2, Pru-C2, Pru-C2R, PCE-F, PCE-R, Pru-C4R, and Pru-C5 (Tao et al., 1999; Yamane et al., 2001; Tsukamoto et al., 2006) for S-RNase, and SFB-C1F, SFB-C2R, SFB-C5F, and FB3R (Ikeda et al., 2005) for SFB. The EM-PC5consRD primer (Sutherland et al., 2004) was also used to sequence S35-RNase.
Phylogenetic and variability analysis
For phylogenetic analyses, available nucleotide sequences for S-RNase and SFB from Prunus armeniaca, P. avium, P. cerasus, P. domestica, P. dulcis, P. mume, P. salicina, P. spinosa, and P. tenella S-haplotypes were assembled (see Fig. 7). Only sequences whose predicted amino acid sequences covered at least 75% of the average length of available complete sequences of S-RNase (227 amino acids) and SFB (375 aminio acids) from the two cherry species (P. avium and P. cerasus) were included. Nucleotide sequences were translated into deduced amino acid sequences using DAMBE (Xia and Xie, 2001); the amino acid sequences were then aligned using ClustalX (Thompson et al., 1997) and adjusted manually. Finally, nucleotide sequences were aligned to the amino acid alignments with DAMBE. Analyses of DNA variability were performed using DnaSP 4.1 (Rozas et al., 2003). Phylogenetic analyses of the aligned amino acid and nucleotide sequences based on maximum parsimony were implemented in PAUP* (Swofford, 2002) with heuristic searches using the TBR branch-swapping algorithm and 1000 random taxon addition replicates and maxtrees allowed automatic increases as necessary. Relative support for clades was assessed using 1000 bootstrap replicates with 10 random taxon addition replicates per bootstrap replicate and maxtrees set at 100.
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Several approaches were used to test for significant incongruence between the topologies of phylogenetic trees supported by the SFB and S-RNase data sets, respectively, and all of these approaches were used for both the amino acid and the nucleotide sequences for each gene. First, a combined data set was constructed including only the 49 haplotypes for which sequences of both determinants were available. The partition homogeneity test, implemented in PAUP* with 1000 test replicates and heuristic searches using the TBR branch-swapping algorithm and 10 random taxon addition replicates per test replicate with maxtrees set to 100, was used to test for significant conflict between the S-RNase and SFB partitions within each data set. Second, each partition was analysed separately and all of the most parsimonious trees were saved to a single tree file. The Kishino-Hasegawa (K-H), Templeton, and winning-sites tests were implemented in PAUP* to test whether or not the topologies produced by the two data partitions were significantly different. Third, because bootstrap analyses showed that many relationships were only weakly supported by each of the two data partitions, constraint trees were constructed in which only groups supported with bootstrap values of 80% or more by each of the data partitions were resolved. Four such constraint trees were constructed; one each for SFB and S-RNase for the combined amino acid data set and one each for SFB and S-RNase for the combined nucleotide data set. Each data partition was analysed without constraints and the best trees were saved to a file. Then each data partition was analysed under the constraint corresponding to the well-supported groups from the other partition and the best trees were saved to the same file. The K-H, Templeton, and winning-sites tests were implemented in PAUP* to test whether or not the constrained trees were significantly longer than the unconstrained trees. In order to test whether or not the phylogenetic relationships among SFB and S-RNase alleles were significantly different from the phylogenetic relationships among species of Prunus based on other evidence, each data set was re-analysed with various topological constraints enforced (see Results). For each data set, all of the most parsimonious trees (MPT) from unconstrained and constrained analyses were saved to a single tree file. The K-H, Templeton, and winning-sites tests were implemented in PAUP* to test whether or not the constrained trees were significantly longer than the unconstrained trees.
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Identification and cloning of novel S-haplotype genes (S-RNase and SFB) from sour cherry
Genomic PCR with the S-RNase consensus primer pair Pru-C2 and PCE-R (Tao et al., 1999; Yamane et al., 2001) revealed three amplification products not previously characterized in three sour cherry cultivars (Fig. 1A). Fragments of
480 bp, 420 bp, and 850 bp were identified in ‘Englaise Timpurii’, ‘Meteor’, and ‘Tamaris’, respectively.
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The nucleotide sequence of the 481 bp S-RNase PCR product from ‘Englaise Timpurii’ revealed high similarity (99.6%) with the P. avium S14-RNase partial sequence (GenBank accession no. AJ635277 [GenBank] ; Sonneveld et al., 2003) and the P. avium S23-RNase complete sequence (GenBank accession no. AY259114 [GenBank] ; Wünsch and Hormaza, 2004; the two sequences are identical). The ‘Englaise Timpurii’ 481 bp S-RNase nucleotide sequence differed from the P. avium S14-/S23-RNase by only two base pairs within the second intron (data not shown). Therefore, the 481 bp PCR S-RNase product from ‘Englaise Timpurii’ was considered to be the S14-RNase, as the P. avium S14- and S23-RNases likely code the same specificity.
BlastN of the 424 bp partial nucleotide sequence of the S-RNase PCR product from ‘Meteor’ revealed high homology (98.3%) with the partial S10-RNase of Japanese apricot (P. mume) sequence (GenBank accession no. DQ011150 [GenBank] ; sequence upstream of the C2 conserved region and downstream of the RC4 conserved region is lacking). This novel S-haplotype was named S33 to follow the previously named functional cherry S-haplotypes (S1 to S7, S9, S10, S12 to S14, S16 to S32) (for a review see Vaughan et al., 2008).
Two S33 clones were obtained by screening a ‘Meteor’ fosmid library. Both clones contained the S-haplotype genes, S33-RNase and SFB33, and the complete nucleotide sequences of the S33-RNase (GenBank accession no. EU054325) and SFB33 (GenBank accession no. EU054328) were obtained by sequencing the genes from these two clones. The predicted amino acid sequence of the S33-RNase consisted of 238 residues and was aligned with that of functional S-RNases present in sour cherry (Fig. 2). When the nucleotide sequences of the coding regions of the sour cherry S33-RNase and P. mume S10-RNase were compared, there were four synonymous and one non-synonymous differences. In the second intron, there were four nucleotide differences plus two indels (148 bp and 1 bp long, respectively; see Supplementary Fig. 1 at JXB online).
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SFB33 consisted of 376 amino acid residues that exhibited the characteristic F-box and variability patterns of previously identified SFBs (Fig. 3). S33-RNase and SFB33 specific primer pairs were designed (Table 1) that amplified the allele specific fragments of 819 bp and 860 bp, respectively (Fig. 4A, B).
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BlastN with the 868 bp partial nucleotide sequence of the S-RNase PCR product from ‘Tamaris’ revealed high homology with the S1-RNase obtained from sweet cherry (GenBank accession no. AB031815 [GenBank] ), the P. tenella S8-RNase (GenBank accession no. DQ983367 [GenBank] ), and partial sequences of the P. dulcis S11-RNase (GenBank accession no. AM231660 [GenBank] ) and the P. domestica S5-RNase (GenBank accession no. AM746946 [GenBank] ). This novel S-haplotype was named S34 (Fig. 5; Table 2). Sour cherry S34-RNase falls in this previously described group of S-RNases where the sweet cherry S1-RNase was found to be identical to the P. tenella S8-RNase and to differ from the P. dulcis S11-RNase by just one amino acid (
urbanovski et al., 2007).
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One S34 clone was obtained by screening a ‘Tamaris’ fosmid library. This clone contained both of the S34-RNase and SFB34 permitting the complete nucleotide sequencing of the S34-RNase (GenBank accession no. EU054326) and SFB34 (GenBank accession no. EU054329). The predicted amino acid sequence of S34-RNase consisted of 226 residues and was aligned with that of functional S-RNases obtained from sour cherry cultivars (Fig. 2). A comparison of the S34-RNase with a partial sequence of the P. domestica S5-RNase (PdoS5-RNase lacks 30 and 27 amino acids at the N- and C-terminals, respectively) revealed high homology (97%) and only five amino acid differences (Fig. 5). When PcS34-RNase was compared with P. avium S1-RNase, 15 amino acid differences were identified (Fig. 5). Nevertheless, the sweet cherry S1-RNase specific primer pair (Sonneveld et al., 2001) amplified a product for the S34-RNase. However, the amplification product from the S34-RNase was the expected size of
850 bp instead of 615 bp as for the P. avium S1-RNase (data not shown). The second intron of the S34-RNase is 238 bp longer than that of the P. avium S1-RNase (GenBank accession nos AB031815
[GenBank]
and AB028153
[GenBank]
; see Supplementary Fig. 2 at JXB online). SFB34 was composed of 376 amino acid residues that exhibited the characteristic variability patterns of previously identified SFBs (Fig. 3). Due to the high homology of the S34-RNase with the P. avium S1-RNase, an alignment was performed with their respective SFBs. The predicted amino acid sequence of P. cerasus SFB34 was aligned with three cherry SFB1 sequences: (i) the P. cerasus SFB1 obtained from ‘Pandy 114’ (GenBank accession no. DQ827715 [GenBank] ), (ii) the P. avium SFB1 cloned from ‘Skeena’ (GenBank accession no. AY805048 [GenBank] ), and (iii) the P. avium SFB1 sequence obtained from ‘Seneca’ (GenBank accession no. AB111518 [GenBank] ) and P. dulcis SFB11, and P. tenella SFB8 (Fig. 6). The P. cerasus ‘Pandy 114’ SFB1 and P. avium cv. ‘Skeena’ SFB1 sequences are identical, however the ‘Skeena’ sequence is not complete as 10 amino acid residues at the C-terminal are not determined. The amino acid sequence of the ‘Seneca’ SFB1 is slightly different from that of SFB1 of ‘Pandy 114’ and ‘Skeena’ (Fig. 6). Unlike their S-RNases, the predicted amino acid sequences for the sour cherry SFB34 and SFB1 differed by 69 amino acids (Fig. 6) and shared only 81.6% identity (Table 2). Similarly, the amino acid sequence of the P. cerasus SFB34 had only 81.0% homology with that of the identical P. tenella SFB8 and P. dulcis SFB11. By comparison, the P. cerasus SFB34 and the partial sequence of the P. domestica SFB5 (GenBank accession number. AM746955 [GenBank] ; PdoSFB5 is lacking 12 and 33 amino acid residues at the N- and C-terminals, respectively) differed at 15 amino acid residues (95.5% homology), compared with 69 different residues between SFB34 and SFB1 (Fig. 6).
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To compare the S34- and S1-haplotypes further, a partial sequence of the intergenic region between S-RNase and SFB of P. cerasus S34 was obtained. However, the intergenic sequence for the S34-haplotype was extremely divergent compared with that from the P. avium S1, P. dulcis S11, and P. tenella S8 and did not permit a conclusive alignment (see Supplementary Fig. 3 at JXB online).
To aid in the confirmation of the S34-haplotype in future germplasm surveys, S34-RNase and SFB34 specific primer pairs were designed (Table 1) that amplified allele specific fragments of expected size (898 bp and 714 bp, respectively) (Fig. 4C, D). The S1-RNase specific primer pair (Sonneveld et al., 2001) amplified fragments for the S1-RNase (615 bp) and S34-RNase (850 bp) (data not shown), but the S34-RNase specific primer pair only amplified a product from the S34-RNase, not the S1-RNase (Fig. 4C).
To identify all the S-haplotypes in ‘Tamaris’, genomic PCR was performed with all available S-RNase specific primer pairs. A fragment of 680 bp was amplified with the S16-RNase specific primer pair (Sonneveld et al., 2003). A comparison of the nucleotide sequence from the S16-RNase PCR product from ‘Tamaris’ with the P. avium S16-RNase revealed only one base pair difference in the second intron. Therefore ‘Tamaris’ was considered to have the S16-haplotype.
Identification and cloning of the S35-RNase and SFB35
Previously an S-haplotype survey in sour cherry cultivars was carried out using RFLP analysis, and S-RNase based PCR was also carried out using the consensus S-RNase gene-specific primer set, Pru-C2 and PCE-R (Tao et al., 1999; Yamane et al., 2001). Using these two approaches, only three different S-haplotypes were characterized in many cultivars, including the landrace sour cherry cultivar ‘Pandy’ (syn. ‘Köröser’, ‘Crisana’) and ‘Montmorency’. Yet, genetic studies with many of these cultivars led to the conclusion that none of the three S-haplotypes identified in each cultivar was present in a double dose (Hauck et al., 2006b). For example, the cultivar ‘Újfehértói frts’ has the S-haplotypes S1', S4, and S36b of which S1' and S36b are non-functional. Therefore, it is possible that ‘Újfehértói frts’ could contain two copies for either of these two non-functional S-haplotypes. However, our genetic segregation data was consistent in rejecting this hypothesis (Hauck et al., 2006a, b). Therefore, it is postulated that these cultivars contained a fourth allele and termed it Snull as it was not possible to resolve this fourth allele on a Southern blot with either S-RNase or SFB probes.
Bo
kovi
et al. (2006) reported the presence of a different S-RNase, SD, in ‘Köröser’, ‘Montmorency’, and ‘Bruine Waalse’ using a different S-RNase consensus primer pair (EM-PC2consFD and EM-PC5consRD). Therefore, this alternate primer pair was used to test the possibility that SD might be the Snull allele. Using this primer pair, a 530 bp amplification product was amplified in eight selections (‘Crisana’, ‘Erdi Botermo’, ‘Montmorency’, ‘Pandy 38’, ‘Pandy 114’, ‘Surefire’, ‘Tschernokorka’, and ‘Újfehértói frts’; Fig. 1B), that had a similar size to the SD-RNase (Bokovi et al., 2006). The 527 bp S-RNase PCR products amplified with the EM-PC2consFD and EM-PC5consRD primers from ‘Crisana’, ‘Pandy 114’, and ‘Újfehértói frts’ were cloned and sequenced and the nucleotide sequences were identical. Unfortunately, these nucleotide sequences could not be compared with that of SD-RNase since the latter is not available in GenBank. Nevertheless, a comparison using the amino acid sequence available in Fig. 2 of Bokovi et al. (2006) revealed that our sequence differed from SD-RNase in two regions (see Supplementary Fig. 4 at JXB online). One region is just before the first intron. The SD-RNase has two additional glycine residues not present in our S-RNase sequence. The other region is the RHV region just after the second intron. The reasons for these discrepancies are not known. However, as the validity of our full length S-RNase sequences were verified multiple times from fosmid clones from three different genotypes (see below), and genetically verified in inheritance studies (see below), it has been tentatively postulated that our sequence indeed represents the previously identified SD-haplotype. This S-haplotype is named S35.
To clone the S35-RNase and SFB35, a fosmid library of ‘Montmorency’ (S6S13mS35S36a) was first screened using a probe of DIG-dUTP-labelled with a 527 bp S35-RNase fragment amplified by EM-PC2consFD and EM-PC5consRD from ‘Crisana’. Sixteen positive clones were obtained. Among them, two clones (Mon37 and Mon46) were shown to contain the S35-RNase since an 530 bp fragment was amplified by PCR with the S-RNase consensus primer pair (EM-PC2consFD and EM-PC5consRD) but no fragment was obtained with the other S-RNase consensus primer pair (Pru-C2 and PCE-R). Unfortunately these two clones did not contain the SFB35 since the SFB band was not amplified by PCR with the SFB consensus primer pair (SFB-C1F and SFB-C2R). Next the ‘Montmorency’ fosmid library was screened again with a mixture of DIG-dUTP-labelled SFB6 and SFB36a probes at lower stringency (55 °C) and obtained 25 positive clones. Among them, six clones (Mon64, Mon71, Mon74, Mon76, Mon122, and Mon132) were considered to contain the novel SFB since these six clones amplified a SFB fragment by PCR with the SFB consensus primer (SFB-C1F and SFB-C2R) but not with allele specific primer pairs for SFB6, SFB13, and SFB36a/SFB36b. This novel SFB was named SFB35. These six clones were also analysed by PCR with the S-RNase primer pair EM-PC2consFD and EM-PC5consRD, but no fragment was amplified from any of the six clones. Therefore these six clones were considered to contain SFB35 but not to contain S35-RNase. This suggests that the intergenic distance between the S35-RNase and SFB35 is larger than that observed in the majority of cherry S-haplotypes (380 bp to 38 kb) identified to date (Ikeda et al., 2005) as the average insert size of our fosmid clones was 40 kb. Mon37 and Mon64 were sequenced to determine the complete nucleotide sequences of the S35-RNase (GenBank accession no. EU054327) and SFB35 (GenBank accession no. EU054330), respectively. The S35-RNase, which consists of 232 amino acid residues (Fig. 2), is very different from other S-RNases identified in cherry. The second intron of S35-RNase is extremely short, consisting of only 82 bp (see Supplementary Fig. 4 at JXB online). The S-RNase consensus primer pair (Pru-C2 and PCE-R) could not amplify S35-RNase because the Pru-C2 primer was designed based on the amino acid sequence LWPSNYSN and the S35-RNase has LWPSNYSK. The PCE-R primer was designed based on the amino acid sequence EXEWNK, but the deduced amino acid sequence for S35-RNase is GREWNK.
SFB35 is composed of 371 amino acid residues that exhibited the characteristic variability patterns of previously identified SFBs (Fig. 3). Using these sequences, S35-RNase and SFB35 specific primers were designed (Table 1). The S35-RNase specific primer pair amplified a fragment of the expected size (435 bp) in all eight selections from which the 527 bp PCR product was amplified with the EM-PC2consFD and EM-PC5consRD primer pair (Fig. 4E). The SFB35 specific primer pair also amplified fragments of the expected size (557 bp) in all eight selections that had a 527 bp fragment following amplification using the EM-PC2consFD and EM-PC5consRD primer pair (Fig. 4F). It was further confirmed that the 560 bp fragment was amplified by the SFB35 specific primer pair in all six fosmid clones (Mon64, Mon71, Mon74, Mon76, Mon122, and Mon132) (data not shown).
S-haplotype functionality
The functionality of the S-haplotypes identified in sour cherry was tested using populations derived from self- and cross-pollination. In the parents of these populations the S-haplotype being tested would segregate in both the eggs and pollen grains in an expected 1:1 ratio assuming that these gametes are viable and equally probable of occurring in a successful gamete. Therefore, if the S-haplotype is functional in the style and pollen, the pollen that contains that S-haplotype would be incompatible and the ratio of that S-haplotype would be 1:1 to represent its expected ratio in the eggs. However, if the S-haplotype being tested has lost either pollen or stylar function, the pollen carrying that S-haplotype would be compatible and that S-haplotype would be expected to be present in the progeny in a 3:1 ratio representing the additional contribution of the pollen S-haplotype. Using this strategy, multiple functional and non-functional S-haplotypes were previously identified in sour cherry (Hauck et al., 2006b).
To determine if the S33-haplotype in ‘Meteor’ was fully functional, the self-pollinated progeny of ‘Meteor’ were genotyped for their S-haplotypes. The progeny segregation ratio for S33 fit the expected 1:1 ratio and rejected the 3:1 ratio indicating that S33 is a functional S-haplotype (Table 3). Self-pollinated progeny of ‘Tamaris’ also segregated according to a 1:1 rejecting the 3:1 ratio for the S34-haplotype indicating that this S-haplotype is functional (Table 3). As ‘Tamaris’ is the first report of the presence of the sweet cherry S16-haplotype in sour cherry, the functionality of this S-haplotype was also tested. S16 segregated according to a 1:1 ratio indicating that the S16-haplotype is also functional.
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S35 was identified in several cultivars with diverse geographic origin; therefore, three different cultivars with diverse origins were used to test the functionality of S35. Segregation of S35 in the self-pollinated progeny of ‘Montmorency’ fit a 1:1 ratio and rejected the 3:1 ratio indicating that S35 is a functional S-haplotype in this cultivar (Table 3). As S35 is also present in ‘Újfehértói f
rts’ and ‘Surefire’ it allowed us to test whether the S35 containing pollen from ‘Surefire’ is compatible in ‘Újfehértói frts’ styles. The segregation of S35 in the progeny from this cross segregated according to the 1:1 ratio, rejecting the 3:1 ratio confirming that S35 is a functional S-haplotype.
‘Montmorency’, ‘Újfehértói frts’, and ‘Surefire’ had previously been determined to have the Snull-haplotype as our genetic data predicted the presence of a fourth S-haplotype (Hauck et al., 2006b). To test the hypothesis that Snull is the newly identified S35, the progeny from self-pollinated ‘Montmorency’ and ‘Újfehértói frts’x‘Surefire’ were S-genotyped with the addition of the S35. In all cases S35 co-segregated with the previous prediction of Snull (data not presented) confirming that S35 is the fourth S-haplotype in these selections.
Phylogenetic analyses
Phylogenetic analyses of amino acid and nucleotide sequences of S-RNase and SFB sequences from eight species of Prunus (Fig. 7) produced trees in which the closest relatives of many alleles were alleles from other species. This pattern, first reported for Solanaceae species, was named trans-specific evolution by Richman et al. (1996). In Prunus this pattern has been described before (see references in Vieira et al., 2008), but in contrast with the observation made for the Solanaceae species, in this genus trans-specific evolution cannot be taken as evidence for the very old age of alleles (Vieira et al., 2008). Although this pattern has been known for more than a decade, no proper phylogenetic analyses have so far been performed to show conclusively that this pattern is not simply due to lack of phylogenetic resolution. In Prunus, bootstrap support values are generally weak. Nevertheless, in no case were all the alleles of any one gene from any one species supported as monophyletic.
Phylogenetic analyses of nucleotide sequences of both S-RNase and SFB data resolved the P. cerasus S35 along with the P. dulcis Sa as highly divergent from the remaining S-haplotypes (Fig. 7). Therefore, S35 was identified as not only divergent from other cherry S-haplotypes but also divergent from other Prunus S-haplotypes. For the P. cerasus S33 and P. cerasus S34, as well as for the alleles from several other S-haplotypes, the resolved relationships were different in the two data sets (Fig. 7). All data sets strongly supported the sister relationship between P. cerasus S34 and P. domestica S5. Both the amino acid and the nucleotide sequence data resolved the S-RNases of the last two haplotypes as sister to a clade including the P. avium S1-RNase, the P. dulcis S11-RNase, and the P. tenella S8-RNase. The SFB data did not, however, show this relationship, and the position of P. cerasus SFB34 plus P. domestica SFB5 was very weakly supported. The P. cerasus S33-RNase was weakly supported as sister to P. mume S1-RNase and P. spinosa S10-RNase; however, P. cerasus SFB33 was resolved, again with very weak support, as sister to the clade of P. avium SFB3, P. cerasus SFB34, and P. domestica SFB5. The relationships resolved by the amino acid sequence data for both genes (not shown) differed in some details from those resolved by the nucleotide sequence data, especially for the more weakly supported relationships.
Results of the Partition Homogeneity test revealed strong differences in phylogenetic signal between the S-RNase and the SFB nucleotide data sets as well as between the amino acid data sets for the two genes (P=0.001 for all tests). Tests were carried out for significant differences in the tree topologies between the S-RNase and SFB data for both nucleotides and amino acids using the Templeton, K–H, and