Identification of self-incompatibility alleles in some of Yazd province almond ‎genotypes by using PCR method‏ ‏

Document Type : Full Paper


1 M.Sc. Student, Faculty of Agriculture, Zabol University, Zabol, Iran

2 Associate Professor, Faculty of Agriculture and Natural Resources, Yazd University, Yazd, Iran

3 Associate Professor, Faculty of Agriculture, Zabol University, Zabol, Iran

4 Associate Professor, Temperate Fruits Research Center, Horticultural Science Research Institute(HSRI), Agricultural Research, ‎Education and Extension Organization (AREEO), Karaj, Iran


One of the problems in almond production is self-incompatibility in this plant, which is considered as an important point of breeding. Self-incompatibility causes non-uniformity of harvesting time as well as some of garden management and pollination problems. Most cultivars of almonds have gametophytic self-incompatibility that is controlled by a multi-allelic gene locus. The fertilization inhibitor factor in this phenomenon, pollen tube growth stops in the middle of the style. The purpose of this research was identification and determination of the self-compatible genotype in the Yazd this investigation better genotypes of almond were collected and after DNA extraction was done, in order to detect S alleles in different almond and some hybrid genotypes, the specific primer pairs, including AS1II-AmyC5R, ConF-ConR and Cebador2-Cebador8, were used in the polymerase chain reaction. In polymerase chain reaction, using the AS1II-AmyC5R and Cebador2-Cebador8 primers, the Sf allele with the size of 1200 base pairs was detected. Using the ConF-ConR pair of primer, the S1, S2, S3, S10, S11, S23, and S31 alleles were detected in the self-incompatible samples. Using AS1II-AmyC5R pair of primer, the known alleles of S3, Sf, S2, S1, S5, S10 S11 S23, and S13 were detected. The other bands obtained from the PCR were related to the known self-in-compatibility alleles that might be considered as new alleles.  According to the obtained results, S1, S2, S3, and S11alleles had the highest frequency and S5, S23, S10, S13and S31alleles respectively had the lowest frequency.


  1. Alonso, J. M. Socias i Company, R. (2005). Identification of the S3 self-incompatibile allele in almond by specific primers. Journal of Agricultural Research, 3, 296-303.
  2. Channuntapipat, C., Sedgley, M. & Collins, G. (2001). Sequences of the cDNAs and genomic DNAs encoding the S1, S7, S8, and Sf alleles from almond, Prunus dulcisTheoretical and Applied Genetics103(6-7), 1115-1122.
  3. Channuntapipat, C., Wirthensohn, M., Ramesh, S. A., Batlle, I., Arús, P., Sedgley, M. & Collins, G. (2003). Identification of incompatibility genotypes in almond (Prunus dulcis Mill.) using specific primers based on the introns of the S‐alleles. Plant Breeding122(2), 164-168.
  4. Ebadi, A., Kamali, K., Moghaddam, M. R. F., Naghavi, M. R., Imani, A. & Ofoghi, H. (2011). Determination of self-compatible almond genotypes obtained from controlled crosses and identification of S-alleles in some foreign cultivars and genotypes by PCR. Seed and Plant Improvement Journal, 27(1), 57-67. (in Farsi)
  5. Fallah, M., Rasouli, M., Sharafi ,Y. & Imani, A.(2016)Study of pollen compatibility relationships among some selected promising almond cultivars and genotypes. Iranian Journal of Horticulture Sciences, 47(3),457-467. (in Farsi).
  6. Gómez, E. M., Buti, M., Sargent, D. J., Dicenta, F. & Ortega, E. (2019). Transcriptomic analysis of pollen-pistil interactions in almond (Prunus dulcis) identifies candidate genes for components of gametophytic self-incompatibility. Tree Genetics & Genomes, 15(53), 1-13.
  7. Gepts, P. & Clegg, M. T. (1989). Genetic diversity in pearl millet (Pennisetum glaucum [L.] R. Br.) at the DNA sequence level. Journal of Heredity80(3), 203-208.
  8. Gradziel, T. M. & Kester, D. E. (1996). Genetic improvements. Almond production manual, 70-75.
  9. Gradziel, T. M. (2016). Self-compatibility sources and sources of variation in advanced almond introgression lines. Options Méditerranéenes, Series A, 119, 43-47.
  10. Halasz, J., Fodor, A., Hegedus, A. & Pedryc, A. (2008). Identification of a new self-incompatibility allele (S31) in a Hungarian almond cultivar and its reliable detection. Scientia Horticulturae, 116(4), 448-451.
  11. Hamzaoui, A. E., Oukabli, A. & Moumni, M. (2015). Identification of self-incompatibility S alleles in Moroccan almond (Prunus dulcis Miller) germplasm using PCR. The Journal of Horticultural Science and Biotechnology, 90(3), 337-343.
  12. Imani, A. (2000). Almond breeding, Agricultural Extension and Education, Tehran. (in Farsi).
  13. Kamali, K. (2008). An investigation of classical and molecular methods in almond breeding program to produce self-compatible genotypes. Ph.D. Thesis, University of Tehran, Tehran, Iran. (in Farsi).
  14. Kamali, K., Ebadi, A., Fatahi Moghadam, R. Naghavi, M.R. & Imani, A. (2009). Heritability of Sf allele in almond progenies with PCR method. Iranian Journal of Horticulture Sciences, 40, 61-68. (in Farsi)
  15. Kodad, O., Socias, I., Company, R. & Alonso, J.M. (2015). Unilateral recognition of the Sf allele in almond. Scientia Horticulturae, 1, 1-6.
  16. Ma, R. C. & Oliveira, M. M. (2001). Molecular cloning of the self-incompatibility genes S1and S3 from almond (Prunus dulcis cv. Ferragnès). Sexual Plant Reproduction14(3), 163-167.
  17. Momenpour, A., Ebadi, A. & Imani, A. (2012 )Determination of self and cross compatible genotypes obtained from almond breeding program. Iranian Journal of Horticulture Sciences, 43(4), 447-461. (in Farsi)
  18. Mousavi, A., Babadaei, R., Fatahi, M. R., Zamani, Z., Dicenta, F. & Ortega, E. (2014). Self incompatibility in the Iranian almond cultivar ‘Mamaei’ using pollen tube growth, fruit set and PCR technique. Journal of Nuts, 5(2), 1-10.
  19. Mousavi, A., Fatahi, R., Zamani, Z., Imani, A., Dicenta, F. & Ortega, E. (2014). Genetic variation and frequency of S- alleles in Iranian almond cultivars. Acta Horticulture, 1028, 45-48.
  20. Mousavi, A., Fatahi, R., Zamani, Z., Imani, A., Ortega, E. & Dicenta, F. (2011). Identification of self- incompatibility (S-) genotypes of Iranian almond genotypes and cultivars using PCR. Iranian Journal of Horticultureal Sciences, 42(2), 169-183. (in Farsi)
  21. Mousavi, A., Fatahi, R., Zamani, Z., Imani, A., Dicenta, F. & Ortega, E. (2011). Identification of self- incompatibility genotypes in Iranian almond cultivars. Acta Horticulture, 912, 303-311.
  22. Mousavi, A., Fatahi, R., Zamani, Z., Imani, A., Ortega, E. & Dicenta, F. (2014). Identification of new S- alleles in Iranian almond cultivars using cloning and sequencing. Seed and Plant Improvement Journal, 30, 651-668. (in Farsi).
  23. Ortega, E. & Dicenta, F. (2003). Inheritance of self-compatibility in almond: breeding strategies to assure self-compatibility in the progeny. Theoretical and Applied Genetics106(5), 904-911.
  24. Rahemi, A., Fatahi, R., Ebadi, A., Taghavi, T., Hassani, D., Thomas Gradziel, T. & Chaparro, J. (2010). Genetic variation of S-alleles in wild almonds and their related Prunus species. Australian Journal of Crop Science 4(8), 648-659.
  25. Rasouli, M. (2017). The Study of morphological traits and identification of self-incompatibility alleles in almond cultivars and genotypes. Journal of Nuts, 8(2), 137-150.
  26. Sanchez-PR´., Dicenta, F. & Mart´ınez-G´omez, P. (2004). Identification of S-alleles in almond using PCR. Euphytica, 138, 263-269.
  27. Herrera, S., Rodrigo, J., Hormaza, J. I. & Lora, J. (2018). Identification of self-incompatibility alleles by specific PCR analysis and S-RNase sequencing in apricot. International Journal of Molecular Sciences, 19(11), 3612.
  28. Sergio, C., Stefano, L.M., Gaetano, D., Guiyou, L., Francesco, S. & Alessandra, G. (2015). Analysis of S‐allele genetic diversity in sicilian almond germplasm comparing different molecular methods. Plant Breeding, 134(6),713-718.
  29. Sheikh-Alian, A., Vezvaei, A., Ebadi, A., Fatahi-Moghadam, M. R. & Sarkhosh, A. (2010). Determination and identification of self-incompatibility alleles in selective Iranian and foreign almond (Prunus dulcis M.) cultivars by PCR method. Iranian Journal of Horticultural Sciences, 41(3), 247-252. (in Farsi)
  30. Tamura, M., Ushijima, K., Sassa, H., Hirano, H., Tao, R., Gradziel, T. M. & Dandekar, A. M. (2000). Identification of self-incompatibility genotypes of almond by allele-specific PCR analysis. Theoretical and Applied Genetics101(3), 344-349.
  31. Valizadeh, B., Ershadi, A. & Gholami, M. (2008). Identification of self-incompatibility alleles in some Iranian and foreign almond (Prunus dulcis M.) cultivars using PCR. Iranian Journal of Horticultural science and Technology, 8(4), 249-258. (in Farsi)
  32. Zeinalabedini, M., Khayamnekue, M., Imani, F. & Majidian, P. (2012). Identification of self-compatibility and self-incompatibility genotypes in almond and some Prunus species using molecular markers. Iranian Journal of Seed and Plant Improvement, 28(1), 227-238. (in Farsi).