Theoretical and Applied Genetics

, Volume 107, Issue 6, pp 1059–1070 | Cite as

Allele-specific PCR detection of sweet cherry self-incompatibility (S) alleles S1 to S16 using consensus and allele-specific primers

Article

Abstract.

PCR-based identification of all 13 known self-incompatibility (S) alleles of sweet cherry is reported. Two pairs of consensus primers were designed from our previously published cDNA sequences of S 1 to S 6 S-RNases, the stylar components of self-incompatibility, to reveal length variation of the first and the second introns. With the exception of the first intron of S 13 , these also amplified S 7 to S 14 and an allele previously referred to as S x , which we now label S 16 . The genomic PCR products were cloned and sequenced. The partial sequence of S 11 matched that of S 7 and the alleles were shown to have the same functional specificity. Allele-specific primers were designed for S 7 to S 16 , so that allele-specific primers are now available for all 13 S alleles of cherry (S 8 , S 11 and S 15 are duplicates). These can be used to distinguish between S alleles with introns of similar size and to confirm genotypes determined with consensus primers. The reliability of the PCR with allele-specific primers was improved by the inclusion of an internal control. The use of the consensus and allele-specific primers was demonstrated by resolving conflicting genotypes that have been published recently and by determining genotypes of 18 new cherry cultivars. Two new groups are proposed, Group XXIII (S 3 S 16 ), comprising 'Rodmersham Seedling' and 'Strawberry Heart', and Group XXIV (S 6 S 12 ), comprising 'Aida' and 'Flamentiner'. Four new self-compatibility genotypes, S 3 S 3 ′, S 4 S 6 , S 4 S 9 and S 4 S 13 , were found. The potential use of the consensus primers to reveal incompatibility alleles in other cherry species is also demonstrated.

Keywords.

Cherry Consensus and allele-specific primers Prunus avium Self-incompatiblity S-RNase 

Notes

Acknowledgements.

We are grateful to Emma-Jane Lamont (National Fruit Collections, Brogdale, UK), Dr. M. Fischer (BAZ, Dresden, Germany), Dr. R. Andersen (Cornell University, New York, USA), Dr. P. Wiersma and Dr. F. Kappel (Agriculture and Agri-Food Canada, Pacific AgriFood Research Centre, Summerland, Canada), Dr. D. Thompson (Saanich, Canada) and Dr. C. Weeks (USDA/ARS Germplasm Repository Davis, California, USA) for supply of material. Tineke Sonneveld acknowledges receipt of a studentship from the University of Nottingham and Horticulture Research International.

References

  1. Brózik S, Apostol J (2000) In: Brózik S, Kállay Tné (eds) Csonthéjas gyümölcsfajták. Mezögazda Kiadó, BudapestGoogle Scholar
  2. Bošković R, Tobutt KR (1996) Correlation of stylar ribonuclease zymograms with incompatibility alleles in sweet cherry. Euphytica 90:245–250Google Scholar
  3. Bošković R, Tobutt KR (2001) Genotyping cherry cultivars assigned to incompatibility groups, by analysing stylar ribonucleases. Theor Appl Genet 103:475–485Google Scholar
  4. Bošković R, Russell K, Tobutt KR (1997) Inheritance of stylar ribonucleases in cherry progenies, and reassignment of incompatibility alleles to two incompatibility groups. Euphytica 95:221–228CrossRefGoogle Scholar
  5. Bošković R, Tobutt KR, Schmidt H, Sonneveld T (2000) Re-examination of (in)compatibility genotypes of two John Innes self-compatible sweet cherry selections. Theor Appl Genet 101:234–240CrossRefGoogle Scholar
  6. Broothaerts W, Janssens GA, Proost P, Broekaert WF (1995) cDNA cloning and molecular analysis of two self-incompatibility alleles from apple. Plant Mol Biol 27:499–511PubMedGoogle Scholar
  7. Channuntapipat C, Sedgley M, Collins G (2001) Sequences of the cDNAs and genomic DNAs encoding the S 1, S 7, S 8 and S f alleles from almond, Prunus dulcis. Theor Appl Genet 103:1115–1122CrossRefGoogle Scholar
  8. Choi C, Livermore K, Andersen RL (2000) Sweet cherry pollination: recommendation based on compatibility groups and bloom time. J Am Pomological Soc 54:148–152Google Scholar
  9. Coleman CE, Kao T-h (1992) The flanking regions of two Petunia inflate S alleles are heterogeneous and contain repetitive sequences. Plant Mol Biol 18:725–735PubMedGoogle Scholar
  10. Crane MB, Brown AG (1937) Incompatibility and sterility in the sweet cherry, Prunus avium L. J Pomol Hort Sci 15:86–116Google Scholar
  11. Crane MB, Lawrence WJC (1929) Genetical and cytological aspects of incompatibility and sterility in cultivated fruits. J Pomol Hort Sci 7:276–301Google Scholar
  12. Edin M, Lichou J, Saunier R (1997) Les variétés. In: Edin M, Lichou J, Saunier R (eds) Cerise, les variétés et leur conduite. Ctifl, Paris, pp 135–229Google Scholar
  13. Hauck NR, Iezzoni AF, Yamane H, Tao R (2001) Revisiting the S-allele nomenclature in sweet cherry (Prunus avium) using RFLP profiles. J Am Soc Hort Sci 126:654–660Google Scholar
  14. Igic B, Kohn JR (2001) Evolutionary relationships among self-incompatibility RNases. Proc Natl Acad Sci USA 98:13,167–13,171CrossRefGoogle Scholar
  15. Ishimizu T, Inoue K, Shimonaka M, Saito T, Terai O, Norioka S (1999) PCR-based method for identifying the S-genotypes of Japanese pear cultivars. Theor Appl Genet 98:961–967CrossRefGoogle Scholar
  16. Janssens GA, Goderis IJ, Broekaert WF, Broothaerts W (1995) A molecular method for S-allele identification in apple based on allele-specific PCR. Theor Appl Genet 91:691–698Google Scholar
  17. Janssens GA, Van Haute AM, Keulemans J, Broothaerts W, Broekaert FW (1996) PCR analysis of self-incompatibility alleles in apple applied to leaves, seed embryos and in vitro shoots. Acta Hort 484:403–407Google Scholar
  18. Lewis D, Crowe LK (1954) Structure of the incompatibility gene. IV. Types of mutations in Prunus avium L. Heredity 8:357–363Google Scholar
  19. Ma R-C, Oliveira MM (2001) Molecular cloning of the self-incompatibility genes S 1 and S 3 from almond (Prunus dulcis cv Ferragnès). Sex Plant Reprod 14:163–167Google Scholar
  20. Matsumoto S, Kitahara K (2000) Discovery of a new self-incompatibility allele in apple. HortScience 35:1329–1332Google Scholar
  21. Matthews P, Dow KP (1969) Incompatibility groups: sweet cherry (Prunus avium). In: Knight RL (ed), Abstract bibliography of fruit breeding and genetics to 1965, Prunus. Commonwealth Agricultural Bureaux, Farnham Royal, pp 540–544Google Scholar
  22. Matthews P, Lapins K (1967) Self-fertile sweet cherries. Fruit Var Hortic Digest 21:36–37Google Scholar
  23. Matton DP, Mau S-L, Okamoto S, Clarke AE, Newbigin E (1995) The S-locus of Nicotiana alata: genomic organization and sequence analysis of two S-RNase alleles. Plant Mol Biol 28:847–858PubMedGoogle Scholar
  24. Olmstead JW, Ophardt DR, Lang GA (2000) Sweet cherry breeding at Washington State University. Acta Hort 522:103–109Google Scholar
  25. Saba-El-Leil MK, Rivard S, Morse D, Cappadocia M (1994) The S 11 and S 13 self-incompatibility alleles in Solanum chacoense Bitt. are remarkably similar. Plant Mol Biol 24:571–583PubMedGoogle Scholar
  26. Sakurai K, Brown SK, Weeden N (2000) Self-incompatibility alleles of apple cultivars and advanced selections. HortScience 35:116–119Google Scholar
  27. Sansavini S, Lugli S (1997) Tre stelle per la cerasicoltura italiana: 'Early Star', 'Blaze Star', 'LaLa Star'. Rivista di Frutticol 10:68–69Google Scholar
  28. Schmidt H (1999) On the genetics of incompatibility in sweet cherries. Acta Hort 484:233–237Google Scholar
  29. Schmidt H, Wolfram B, Bošković B (1999) Befruchtungsverhältnisse bei Süßkirschen (flower biology in sweet cherries). Erwerbsobstbau 41:42–45Google Scholar
  30. Sonneveld T, Robbins TP, Bošković R, Tobutt KR (2001) Cloning of six cherry self-incompatibility alleles and development of allele-specific PCR detection. Theor Appl Genet 102:1046–1055Google Scholar
  31. Tao R, Yamane H, Sugiura A, Murayama H, Sassa H, Mori H (1999) Molecular typing of S-alleles through identification, characterization and cDNA cloning for S-RNases in sweet cherry. J Am Soc Hort Sci 124:224–233Google Scholar
  32. Tao R, Habu T, Yamane H, Sugiura A, Iwamoto K (2000) Molecular markers for self-compatibility in Japanese apricot (Prunus mume). HortScience 35:1121–1123Google Scholar
  33. Tamura M, Ushijima K, Sassa H, Hirano H, Tao R, Gradziel TM, Dandekar AM (2000) Identification of self-incompatibility genotypes of almond by allele-specific PCR analysis. Theor Appl Genet 101:344–349CrossRefGoogle Scholar
  34. Tobutt KR (2002) 'Penny' – a new cherry variety from HRI-East Malling. The National Fruit Show [Handbook] 2002:40–41Google Scholar
  35. Tobutt KR, Bošković R, Sonneveld T (2001) Cherry (in)compatibility genotypes – harmonization of recent results from UK, Canada, Germany, Japan and USA. Eucarpia Fruit Breed Sect Newslett 5:41–46Google Scholar
  36. Ushijima K, Sassa H, Tao R, Yamane H, Dandekar AM, Gradziel TM, Hirano H (1998) Cloning and characterization of cDNAs encoding S-RNases from almond (Prunus dulcis): primary structural features and sequence diversity of the S-RNases in Rosaceae. Mol Gen Genet 260:261–268PubMedGoogle Scholar
  37. Van Nerum I, Geerts M, Van Haute A, Keulemans J, Broothaerts W (2001) Re-examination of the self-incompatibility genotype of apple cultivars containing putative 'new' S-alleles. Theor Appl Genet 103:584–591Google Scholar
  38. Verdoodt L, Van Haute A, Goderis IJ, De Witte K, Keulemans J, Broothaerts W (1998) Use of the multi-allelic self-incompatibility gene in apple to assess homozygosity in shoots obtained through haploid induction. Theor Appl Genet 96:294–300CrossRefGoogle Scholar
  39. Wiersma PA, Wu Z (1998) A full-length cDNA for phenylalanine ammonia-lyase cloned from ripe sweet cherry fruit (Prunus avium; accession no. AF036948) (PGR98-184). Plant Physiol 118:1102Google Scholar
  40. Wiersma PA, Wu Z, Zhou L, Hampson C, Kappel F (2001) Identification of new self-incompatibility alleles in sweet cherry (Prunus avium L.) and clarification of incompatibility groups by PCR and sequencing analysis. Theor Appl Genet 102:700–708CrossRefGoogle Scholar
  41. Yaegaki H, Shimada T, Moriguchi T, Hayama H, Haji T, Yamaguchi M (2001) Molecular characterization of S-RNase genes and S-genotypes in the Japanese apricot (Prunus mume Sieb. et Zucc.). Sex Plant Reprod 13:251–257Google Scholar
  42. Yamane H, Tao R, Murayama H, Ishiguro M, Abe Y, Soejima J, Sugiura A (2000a) Determining S-genotypes of two sweet cherry (Prunus avium L.) cultivars, 'Takasago (Rockport Bigarreau)' and 'Hinode (Early Purple)'. J Jap Soc Hort Sci 69:29–34Google Scholar
  43. Yamane H, Tao R, Murayama H, Sugiura A (2000b) Determining the S-genotypes of several sweet cherry cultivars based on PCR-RFLP analysis. J Hort Sci Biotechnol 75:562–567Google Scholar

Copyright information

© Springer-Verlag 2003

Authors and Affiliations

  1. 1.Horticulture Research International, East Malling, West Malling, Kent ME19 6BJ, UK
  2. 2.University of Nottingham, Plant Science Division, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK

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