Self-compatibility in peach [ Prunus persica (L.) Batsch]: patterns of diversity surrounding the S-locus and analysis of SFB alleles

Abstract

Self-incompatibility (SI) to self-compatibility (SC) transition is one of the most frequent and prevalent evolutionary shifts in flowering plants. Prunus L. (Rosaceae) is a genus of over 200 species most of which exhibit a Gametophytic SI system. Peach [Prunus persica (L.) Batsch; 2n = 16] is one of the few exceptions in the genus known to be a fully self-compatible species. However, the evolutionary process of the complete and irreversible loss of SI in peach is not well understood and, in order to fill that gap, in this study 24 peach accessions were analyzed. Pollen tube growth was controlled in self-pollinated flowers to verify their self-compatible phenotypes. The linkage disequilibrium association between alleles at the S-locus and linked markers at the end of the sixth linkage group was not significant (P > 0.05), except with the closest markers suggesting the absence of a signature of negative frequency dependent selection at the S-locus. Analysis of SFB1 and SFB2 protein sequences allowed identifying the absence of some variable and hypervariable domains and the presence of additional α-helices at the C-termini. Molecular and evolutionary analysis of SFB nucleotide sequences showed a signature of purifying selection in SFB2, while the SFB1 seemed to evolve neutrally. Thus, our results show that the SFB2 allele diversified after P. persica and P. dulcis (almond) divergence, a period which is characterized by an important bottleneck, while SFB1 diversified at a transition time between the bottleneck and population expansion.

Keywords: Evolutionary biology; Self incompatability.

Fig. 1. Pollen grain germination and pollen tube growth.

a The flowers of each genotype were collected at the balloon stage, b the pollen grain germination was successful at the surface of stigma in self-pollinated flowers, c pollen tube growth was arrested at the style of self-incompatible plum “Cidre” used as reference, and d the pollen tubes reached the base of the style in peach and self-compatible plum “Bedri” used as reference. Stig Surf surface of stigma. Pol T Germ pollen tube germination. Sty style. P pollen tube. B Sty base of style. Scale bars = 50 µm

Fig. 2. Linkage disequilibrium extent at the end of the sixth LG.

a Schematic representation of the sixth chromosome in Prunus, b genetic position of the tested loci mapped in the Prunus-TE-F2 linkage map (http://www.rosaceae.org/peach/genome), c heatmap representing the distribution of P values per pairs of the ten tested loci. *: significance of P value

Fig. 3. Example of SFB allele amplification in 13 peach samples with PsSFB-F1 and PsSFB-R1.

L: 1 KB ladder. R1, R2, and R3: Plum samples used as control with previously known S-genotypes. R1 Fortune, R2 Santa Rosa, R3 Beauty. Kha Kharfi, Mes Meski, Bar Bargou, Kar Khoukh Arbi, Bou Boutabgaya, Amb Amber, Ess Essifi, NP Negra Palmera, RM Rojo Mollar, VNZ Venezolano, AM Amarillo Melocoton, RR Rubby Rich, SL Spring Lady

Fig. 4. Peptide sequences alignment of peach studied genotypes, two SFB1 and SFB2 reference sequences retrieved from Genebank and 11 Japanese plum SFB sequences.

F-box and (hyper) variables regions V1, V2, Hva, and HVb are boxed. The amino acid sequences of SFBs were aligned using Clustal X

Fig. 5

Secondary protein structures predictions of consensus SFB1 sequence (a) SFB2 sequence(b), SFBk (c), and SFBa (d). The figures showed the distribution of the β-strands (E), coils and α-helices along the four proteins. Structures were done on the website: http://bioinf.cs.ucl.ac.uk/psipred

Fig. 6. Evolutionary relationships between the SFBp alleles and their ancestral copies.

a UPGMA tree: the optimal tree with the sum of branch length = 1.16720195 is shown. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (500 replicates) are shown next to the branches. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the Poisson correction method and are in the units of the number of amino acid substitutions per site. The analysis involved 28 amino acid sequences. There were a total of 374 positions in the final dataset. b Minimum spanning network: the network was constructed using the median joining algorithm. The estimated number of mutations of the shortest tree = 651. The total number of taxa = 28. The total number of haplotypes is 26