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Nucleotide sequence polymorphism in the RFL-PPR genes of potato

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Abstract

Cytoplasmic male sterility (CMS) is widely used for hybrid seed production in cultivated Solanaceae species. However, there is very limited information about CMS-Rf genetic systems in potato (Solanum tuberosum). Studying the CMS-Rf systems in potato is both of theoretical and practical significance due to the emergence of a new revolutionary strategy of reinventing potato as a diploid inbred line-based crop to develop \(\hbox {F}_{{1}}\) hybrid seed potato breeding (Lindhout et al.2011; Jansky et al.2016). To search for potato Rf gene candidates, the comparative genetic approach was applied. Based on similarity to petunia Rf-PPR592 gene, 38 fragments were identified in five loci of the whole-genome nucleotide sequence of the accession DM 1-3 516 R44 S. tuberosum Phureja group (https://blast.ncbi.nlm.nih.gov/Blast.cgi). The putative encoded mitochondrial proteins have 589–597 amino acid residues, similar to RF-PPR proteins of petunia and chili pepper and contain 14 or 15 PPR motifs. Primers have been developed flanking the most variable 782–865 bp regions of the selected loci, and polymorphism of the cloned fragments has been investigated in a subset of nine potato genotypes. The amplified fragments included seven or eight PPR motifs and lacked introns. The SNP frequencies ranged from 7.0 to 19.8% depending on the locus, while the ratio of nonsynonymous to synonymous substitutions varied between 0.9 and 2.1. Positions 1, 3 and 6 were the most variable in the studied PPR motifs. Our results demonstrated that the analysed sequences belong to the RFL-PPR gene subfamily and may be considered as Rf gene candidates in potato.

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Acknowledgements

This work was supported by the grant of Russian Science Foundation (project no. 16-16-04125).

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Authors and Affiliations

  1. Federal Research Centre, The N. I. Vavilov All-Russian Institute of Plant Genetic Resources, Saint Petersburg, 190000, Russia

    Irina N. Anisimova, Natalia V. Alpatieva, Yulia I. Karabitsina & Tatjana A. Gavrilenko

  2. Saint Petersburg State University, Saint Petersburg, 199034, Russia

    Tatjana A. Gavrilenko

Authors
  1. Irina N. Anisimova
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  2. Natalia V. Alpatieva
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  3. Yulia I. Karabitsina
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  4. Tatjana A. Gavrilenko
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Correspondence to Tatjana A. Gavrilenko.

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Corresponding editor: R. S. Sangwan

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Anisimova, I.N., Alpatieva, N.V., Karabitsina, Y.I. et al. Nucleotide sequence polymorphism in the RFL-PPR genes of potato. J Genet 98, 87 (2019). https://doi.org/10.1007/s12041-019-1130-1

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