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Molecular and Evolutionary Characterization of Pollen S Determinant (SFB Alleles) in Four Diploid and Hexaploid Plum Species (Prunus spp.)

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Abstract

In more than 60 families of angiosperms, the self- and cross-fertilization is avoided through a complex widespread genetic system called self-incompatibility (SI). One of the major puzzling issues concerning the SI is the evolution of this system in species with complex polyploid genomes. Among plums, one of the first fruits species to attract human interest, polyploid species represent enormous genetic potential, which can be exploited in breeding programs. However, molecular studies in these species are very scarce due to the complexity of their genome. In order to study the SFB gene [the male component of gametophytic self-incompatibility system (GSI)] in plum species, 36 plum accessions belonging to diploid and hexaploid species were used. A total of 19 different alleles were identified; 1 of them was revealed after analyzing sequences. Peptide sequence analysis allowed identifying the five domains features of the SFB gene. Polymorphism analysis showed a subtle difference between domesticated and open pollinated Tunisian accessions and suggested a probable influence of the ploidy level. Divergence analysis between studied sequences showed that a new specificity may appear after 5.3% of divergence at synonymous sites between pairs of sequences in Prunus insititia, 6% in Prunus cerasifera, 8% and 9% in Prunus domestica and Prunus salicina respectively. Furthermore, sites under positive selection, the ones more likely to be responsible for specificity determination, were identified. A positive and significant Pearson correlation was found between the divergence between sequences, divergence time, fixed substitutions (MK test), and PSS number. These results supported the model assuming that functionally distinct proteins have arisen not as a result of chance fixation of neutral variants, but rather as a result of positive Darwinian selection. Further, the role that plays recombination can not be ruled out, since a rate of 0.08 recombination event per polymorphic sites was identified.

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Data Availability

The data sets supporting this article have been uploaded as part of the Supporting Information. The nucleotide sequence data of the SFB gene for Prunus species were deposited in the GeneBank nucleotide sequence databases with the accession numbers KU728959–KU728994.

Abbreviations

Bs:

Bootstrap value

C :

Conservation level between nucleotide sequences

GSI:

Gametophytic self-incompatibility system

K A :

Divergence between alleles at non-synonymous sites

K S :

Divergence between alleles at synonymous sites

MK:

McDonald and Kreitman test

Myr:

Million years

P A :

Polymorphism at non-synonymous sites

P S :

Polymorphism at synonymous sites

PSS:

Positively selected sites

R m :

Minimum number of recombination

R NS :

Rate of new specificity appearance

SFB:

S-haplotype-specific F-box

SI:

Self-incompatibility system

S-RNase:

S-Ribonuclease

T div :

Divergence time

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Acknowledgements

The authors would like to gratefully thank ‘Sodon collection’ (Bou-Selem, Tunisia), Tunisian farmers and the ‘EEAD-CSIC Prunus bank germplasm’ (Zaragoza, Spain) for kindly providing plant material. We gratefully acknowledge V. Guajardo for critical review of the manuscript.

Funding

This research was supported by the Tunisian ‘Ministère de l’Enseignement supérieur et de la Recherche Scientifique’ and the Project PCI ref. AP/038338/11, funded by the ‘Agencia Española de Cooperación Internacional para el Desarrollo-AECID’of the Spanish Ministry of Foreign Affairs and Cooperation.

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Authors and Affiliations

  1. Département de Biologie, Faculté des Sciences de Tunis, Université de Tunis El Manar, Campus Universitaire El Manar, 2092, Tunis, Tunisia

    Donia Abdallah, Ghada Baraket, Sana Ben Mustapha & Amel Salhi Hannachi

  2. Departamento de Pomologı́a, Estación Experimental de Aula Dei, CSIC, Apartado 13034, 50080, Saragossa, Spain

    Marı́a Angeles Moreno

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  1. Donia Abdallah
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  2. Ghada Baraket
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  4. Marı́a Angeles Moreno
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  5. Amel Salhi Hannachi
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Contributions

DA performed the experiments and statistical analyses, developed the genetic analyses and wrote the manuscript. GB provided some plant material, discussed and corrected the content. SBM developed some molecular tests. MAM and ASH offered experimental instructions, supervised and provided editorial advice.

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Correspondence to Amel Salhi Hannachi.

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Abdallah, D., Baraket, G., Ben Mustapha, S. et al. Molecular and Evolutionary Characterization of Pollen S Determinant (SFB Alleles) in Four Diploid and Hexaploid Plum Species (Prunus spp.). Biochem Genet 59, 42–61 (2021). https://doi.org/10.1007/s10528-020-09990-x

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