Cloning and characterization of genomic DNA sequences of four self-incompatibility alleles in sweet cherry ( Prunus avium L.)

A New One-Tube Reaction Assay for the Universal Determination of Sweet Cherry (Prunus avium L.) Self-(In)Compatible MGST- and S-Alleles Using Capillary Fragment Analysis

The sweet cherry plant (Prunus avium L.) is primarily self-incompatible, with so-called S-alleles responsible for the inability of flowers to be pollinated not only by their own pollen grains but also by pollen from other cherries having the same S-alleles. This characteristic has wide-ranging impacts on commercial growing, harvesting, and breeding. However, mutations in S-alleles as well as changes in the expression of M locus-encoded glutathione-S-transferase (MGST) can lead to complete or partial self-compatibility, simplifying orchard management and reducing possible crop losses. Knowledge of S-alleles is important for growers and breeders, but current determination methods are challenging, requiring several PCR runs. Here we present a system for the identification of multiple S-alleles and MGST promoter variants in one-tube PCR, with subsequent fragment analysis on a capillary genetic analyzer. The assay was shown to unequivocally determine three MGST alleles, 14 self-incompatible S-alleles, and all three known self-compatible S-alleles (S3', S4', S5') in 55 combinations tested, and thus it is especially suitable for routine S-allele diagnostics and molecular marker-assisted breeding for self-compatible sweet cherries. In addition, we identified a previously unknown S-allele in the 'Techlovicka´ genotype (S54) and a new variant of the MGST promoter with an 8-bp deletion in the ´Kronio´ cultivar.

Identification and Molecular Analysis of Putative Self-Incompatibility Ribonuclease Alleles in an Extreme Polyploid Species, Prunus laurocerasus L

Cherry laurel (Prunus laurocerasus L.) is an extreme polyploid (2n = 22x) species of the Rosaceae family where gametophytic self-incompatibility (GSI) prevents inbreeding. This study was carried out to identify the S-ribonuclease alleles (S-RNases) of P. laurocerasus using PCR amplification of the first and second intron region of the S-RNase gene, cloning and sequencing. A total of 23 putative S-RNase alleles (S ₁-S ₂₀, S _{5 m}, S _{13 m}, and S _{18 m}) were sequenced from the second (C2) to the fifth conserved region (C5), and they shared significant homology to other Prunus S-RNases. The length of the sequenced amplicons ranged from 505 to 1,544 bp, and similar sizes prevented the proper discrimination of some alleles based on PCR analysis. We have found three putatively non-functional alleles (S _{5 m}, S _{18 m}, and S ₉) coding for truncated proteins. Although firm conclusions cannot be drawn, our data seem to support that heteroallelic pollen cannot induce self-compatibility in this polyploid Prunus species. The identities in the deduced amino acid sequences between the P. laurocerasus and other Prunus S-RNases ranged between 44 and 100%, without a discontinuity gap separating the identity percentages of trans-specific and more distantly related alleles. The phylogenetic position, the identities in nucleotide sequences of the second intron and in deduced amino acid sequences found one or more trans-specific alleles for all but S ₁₀, S ₁₄, S ₁₈, and S ₂₀ cherry laurel RNases. The analysis of mutational frequencies in trans-specific allele pairs indicated the region RC4-C5 accepts the most amino acid replacements and hence it may contribute to allele-specificity. Our results form the basis of future studies to confirm the existence and function of the GSI system in this extreme polyploid species and the alleles identified will be also useful for phylogenetic studies of Prunus S-RNases as the number of S-RNase sequences was limited in the Racemose group of Prunus (where P. laurocerasus belongs to).

A new dual-specific incompatibility allele revealed by absence of glycosylation in the conserved C2 site of a Solanum chacoense S-RNase

The stylar determinant of gametophytic self-incompatibility (GSI) in Solanaceae, Rosaceae, and Plantaginaceae is an S-RNase encoded by a multiallelic S-locus. The primary structure of S-RNases shows five conserved (C) and two hypervariable (HV) regions, the latter forming a domain implicated in S-haplotype-specific recognition of the pollen determinant to SI. All S-RNases are glycosylated at a conserved site in the C2 region, although previous studies have shown that N-linked glycans at this position are not required for S-haplotype-specific recognition and pollen rejection. Here the incompatibility phenotype of three constructs derived from an originally monoglycosylated S11-RNase of Solanum chacoense, that were designed to explore the role of the HV domain in determining pollen recognition and the role of the N-linked glycan in the C2 region, is reported. In one series of experiments, a second glycosylation site was introduced in the HVa region to test for inhibition of pollen-specific recognition. This modification does not impede pollen rejection, although analysis shows incomplete glycosylation at the new site in the HVa region. A second construct, designed to permit complete glycosylation at the HVa site by suppression of the conserved site in the C2 region, did increase the degree of site occupancy, but, again, glycosylation was incomplete. Plants expressing this construct rejected S 11 pollen and, surprisingly, also rejected S 13 pollen, thus displaying an unusual dual specificity phenotype. This construct differs from the first by the absence of the conserved C2 glycosylation site, and thus the dual specificity is observed only in the absence of the C2 glycan. A third construct, completely lacking glycosylation sites, conferred an ability to reject only S 11 pollen, disproving the hypothesis that lack of a conserved glycan would confer a universal pollen rejection phenotype to the plant.

Cloning and expression analysis of S-RNase homologous gene in Citrus reticulata Blanco cv. Wuzishatangju

S-RNase-based self-incompatibility is the most widespread form of genetically controlled mate selection in plants and that S-RNase controls pollination specificity in the pistils. 'Wuzishatangju' (Citrus reticulata Blanco), a nature bud mutant from a self-compatible (SC) cultivar 'Shatangju', displays gametophytic self-incompatibility (GSI). In this study, full-length sequences of cDNA and DNA of the S-RNase homologous gene were obtained from 'Wuzishatangju' and 'Shatangju'. There was no difference in ORF sequences of the S-RNase cDNA between 'Wuzishatangju' and 'Shatangju'. However, 13, 9 and 6 consecutive bases were missing in 'Wuzishatangju' cDNA 5' UTR, 3' UTR and genomic DNA, respectively. Tissue-specific expression of the S-RNase gene was detected using semi-quantitative RT-PCR and quantitative real-time PCR. The expression level of the S-RNase gene in styles of 'Wuzishatangju' was approximately 10- and 5-fold higher than that in leaves and pollen, respectively. When 'Wuzishatangju' was self-pollinated, the expression of S-RNase in pistils peaked at 3 days, which was approximately 10-fold higher than that at 4h and 7 days, while in cross-pollination of 'Wuzishatangju' x 'Shatangju' the expression was very weak at 3 days. Results from a Southern blot showed that two copies of the S-RNase gene existed in genomic DNA of both 'Wuzishatangju' and 'Shatangju'.

Self-compatibility of 'Katy' apricot (Prunus armeniaca L.) is associated with pollen-part mutations

Apricot (Prunus armeniaca L.) cultivars originated in China display a typical S-RNase-based gametophytic self-incompatibility (GSI). 'Katy', a natural self-compatible cultivar belonging to the European ecotype group, was used as a useful material for breeding new cultivars with high frequency of self-compatibility by hybridizing with Chinese native cultivars. In this work, the pollen-S genes (S-haplotype-specific F-box gene, or SFB gene) of 'Katy' were first identified as SFB₁ and SFB (8), and the S-genotype was determined as S₁ S₈. Genetic analysis of 'Katy' progenies under controlled pollination revealed that the stylar S₁-RNase and S₈-RNase have a normal function in rejecting wild-type pollen with the same S-haplotype, while the pollen grains carrying either the SFB₁ or the SFB₈ gene are both able to overcome the incompatibility barrier. However, the observed segregation ratios of the S-genotype did not fit the expected ratios under the assumption that the pollen-part mutations are linked to the S-locus. Moreover, alterations in the SFB₁ and SFB₈ genes and pollen-S duplications were not detected. These results indicated that the breakdown of SI in 'Katy' occurred in pollen, and other factors not linked to the S-locus, which caused a loss of pollen S-activity. These findings support a hypothesis that modifying factors other than the S-locus are required for GSI in apricot.

Genetic and molecular characterization of three novel S-haplotypes in sour cherry (Prunus cerasus L.)

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, S(33) and S(34), that are presumed to be contributed by the P. fruticosa species parent, the complete S-RNase and SFB sequences of a third S-haplotype, S(35), plus the presence of two previously identified sweet cherry S-haplotypes, S(14) and S(16) are described here. Genetic segregation data demonstrated that the S(16)-, S(33)-, S(34)-, and S(35)-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.

Primary molecular features of self-incompatible and self-compatible F(1) seedling from apricot (Prunus armeniaca L.) Katy x Xinshiji

Expression of the S-RNase genes in the self-compatible (SC) apricot (Prunus armeniaca L.) cultivar Katy, the self-incompatible (SI) cultivar Xinshiji and their F(1) seedling was examined in this study. Three S-genotypes, S(9)Sc (Sc, self-compatibility S-gene absent from the style), S(8)S(9), and S(8)S(10), were obtained. Seedlings with S-RNase that migrated as a single band in gel electrophoresis were SC, despite high transcript abundance, and those with S-RNase that migrated as two bands were SI with high transcript abundance or SC with low transcript expression. S(8)-RNase was induced in SI cultivars only 24 h after self-pollination, indicating post-transcriptional regulation of S(8)-RNase in SI apricots. A Proteomic study showed that 35 protein spots were synthesized differently between SC and SI pistils. Fifteen of the 35 protein spots were identified; nine proteins, including receptor protein kinase-like protein, reversibly glycosylated polypeptide-2, and isoflavone reductase-like protein, were detected only in the SC pistils; while nine proteins, including actin 7, a putative serine/threonine kinase, and S-RNase, were detected only in the SI pistils. A mitochondrial NAD-dependent malate dehydrogenase and a probable elongation factor G were up-regulated, while heat shock cognate 70 was down-regulated in the SC pistils compared to those in the SI pistils. The results suggest that the proteins responsible for self-compatibility and self-incompatibility may be different.

Detection and transcript expression of S-RNase gene associated with self-incompatibility in apricot (Prunus armeniaca L.)

The identity and expression of S-RNase genotypes in the self-compatible (SC) apricot cultivar 'Katy' and the self-incompatible (SI) cultivar 'Xinshiji' were examined. We used allele specific polymerase chain reaction (AS-PCR) and designated the alleles in 'Katy' and 'Xinshiji' as S(8)Sc and S(9)S(10), respectively. The S-RNase gene was expressed in style at the balloon stage in both genotypes. Using real-time fluorescence quantification RT-PCR technology (FQRT-PCR), spatio-temporal expression patterns of S-RNase gene between 'Katy' and 'Xinshiji' were compared. The results revealed that the expression of the S-RNase gene in 'Katy' and 'Xinshiji' were different. The transcript abundance was distinctly diverse at the key stage (i.e., at 24 h after self-pollination) in both genotypes, and was greater in 'Xinshiji' (SI) than 'Katy' (SC). In addition, the abundance of the S-RNase transcript was higher in upper-half of style than in the lower-half of style or in the ovary. In the SI cultivar 'Xinshiji', the expression of S-RNase reminded a relatively high level after cross-pollination, but it dropped continuously after self-pollination and un-pollination.

Molecular characterization of three non-functional S-haplotypes in sour cherry (Prunus cerasus)

Tetraploid sour cherry (Prunus cerasus) exhibits a genotype-dependent loss of gametophytic self-incompatibility that is caused by the accumulation of non-functional S-haplotypes with disrupted pistil component (stylar-S) and/or pollen component (pollen-S) function. Genetic studies using diverse sour cherry germplasm identified non-functional S-haplotypes for which an equivalent wild-type S-haplotype was present in sweet cherry (Prunus avium), a diploid progenitor of sour cherry. In all cases, the non-functional S-haplotype resulted from mutations affecting the stylar component S-RNase or Prunus pollen component S-haplotype-specific F-box protein (SFB). This study determines the molecular bases of three of these S-haplotypes that confer unilateral incompatibility, two stylar-part mutants (S(6m2) and S(13m)) and one pollen-part mutant (S(13)'). Compared to their wild-type alleles, S(6m2)-RNase has a 1 bp deletion, S(13m) -RNase has a 23 bp deletion and SFB(13)' has a 1 bp substitution that lead to premature stop codons. Transcripts were identified for these three alleles, S(6m2)-RNase, S(13m)-RNase, and SFB(13)', however, these transcripts presumably result in altered proteins with a resulting loss of activity. Our characterization of natural pollen-part and stylar-part mutants in sour cherry along with other natural S-haplotype mutants identified in Prunus supports the view that loss of pollen specificity and stylar rejection evolve independently and are caused by structural alterations affecting the S-haplotype. The prevalence of non-functional S-haplotypes in sour cherry but not in sweet cherry (a diploid) suggests that polyploidization and gene duplication were indirectly responsible for the dysfunction of some S-haplotypes and the emergence of self-compatibility in sour cherry. This resembles the specific mode of evolution in yeast where accelerated evolution occurred to one member of the duplicated gene pair.

Determining self-incompatibility genotypes in Belgian wild cherries

ABSTRACT The self-incompatibility (S) genotypes of a collection of 65 Belgian accessions of wild cherry, selected within two populations and planted in a seed orchard, were determined using polymerase chain reaction (PCR) methods. Initially, DNA extracts were amplified with consensus primers that amplify across the second intron of the S-ribonuclease gene which shows considerable length polymorphism. The provisional genotypes deduced were checked with the appropriate allele-specific primers for the known alleles S(1) to S(16). Putative new alleles were subjected to PCR with consensus primers amplifying across the first intron. Six new alleles, S(17) to S(22), were thus indicated on the basis of the estimated lengths of the first and second intron PCR products. Examples of these alleles were partially sequenced and were indeed mutually distinct and different from the known alleles. The incompatibility genotypes of all 65 accessions were determined and one triploid individual was found. Seventeen alleles were detected in all. Allele frequencies differed between samples and the expected total number of alleles in the underlying populations was estimated. The wild cherry populations differed significantly with respect to allelic frequencies from sweet cherry cultivars; alleles S(4) and S(5), which are moderately frequent in sweet cherry, were absent from the wild cherry accessions. The knowledge of the S genotypes will be useful for studying the gene flow within the seed orchard and these approaches should also be informative in wild populations.

Accumulation of nonfunctional S-haplotypes results in the breakdown of gametophytic self-incompatibility in tetraploid Prunus

The transition from self-incompatibility (SI) to self-compatibility (SC) is regarded as one of the most prevalent transitions in Angiosperm evolution, having profound impacts on the genetic structure of populations. Yet, the identity and function of mutations that result in the breakdown of SI in nature are not well understood. This work provides the first detailed genetic description of the breakdown of S-RNase-mediated gametophytic self-incompatibility (GSI) in a polyploid species that exhibits genotype-dependent loss of SI. Genetic analyses of six natural sour cherry (Rosaceae, Prunus cerasus) selections identified seven independent, nonfunctional S-haplotypes with disrupted pistil component (stylar-S) and/or pollen component (pollen-S) function. A genetic model demonstrating that the breakdown of SI in sour cherry is due to the accumulation of a minimum of two nonfunctional S-haplotypes within a single individual is developed and validated. Our finding that sour cherry is SI when only one nonfunctional S-haplotype is present has significant evolutionary implications since nonfunctional S-haplotypes would be maintained in the population without causing an abrupt shift to SC. Furthermore, we demonstrate that heteroallelic sour cherry pollen is self-incompatible, which is counter to the well-documented phenomenon in the Solanaceae where SC accompanying polyploidization is frequently due to the SC of heteroallelic pollen.

Analysis of the S-locus structure in Prunus armeniaca L. Identification of S-haplotype specific S-RNase and F-box genes

The gametophytic self-incompatibility (GSI) system in Rosaceae has been proposed to be controlled by two genes located in the S -locusan S-RNase and a recently described pollen expressed S -haplotype specific F-box gene (SFB). However, in apricot (Prunus armeniaca L.) these genes had not been identified yet. We have sequenced 21 kb in total of the S -locus region in 3 different apricot S -haplotypes. These fragments contain genes homologous to the S-RNase and F-box genes found in other Prunus species, preserving their basic gene structure features and defined amino acid domains. The physical distance between the F-box and the S-RNase genes was determined exactly in the S2-haplotype (2.9 kb) and inferred approximately in the S 1-haplotype (< 49 kb) confirming that these genes are linked. Sequence analysis of the 5' flanking regions indicates the presence of a conserved region upstream of the putative TATA box in the S-RNase gene. The three identified S-RNase alleles (S1, S2 and S4) had a high allelic sequence diversity (75.3 amino acid identity), and the apricot F-box allelic variants (SFB1, SFB2 and SFB4) were also highly haplotype-specific (79.4 amino acid identity). Organ specific-expression was also studied, revealing that S1- and S2-RNases are expressed in style tissues, but not in pollen or leaves. In contrast, SFB1 and SFB2 are only expressed in pollen, but not in styles or leaves. Taken together, these results support these genes as candidates for the pistil and pollen S-determinants of GSI in apricot.