Identification of DNA Markers Linked to Blooming Time in Almond

Document Type: Research Article


1 Department of Horticulture and Landscape Engineering, Faculty of Agriculture, Malayer University, Malayer, Hamedan, Iran

2 Department of Horticulture Science, Faculty of Agriculture, University of Tehran, Karaj, Iran

3 Horticultural Department of Seed and Plant Improvement Institute (SPII), Karaj, Iran

4 Departamento de Mejora Vegetal, CEBAS-CSIC, PO Box 164, E-30100 Espinardo, Murcia, Spain


In this study flowering time and other important morphologic traits were evaluated during two years in F1 almond progenies of seventy two seedlings from cross between the intermediate flowering Italian cultivar ‘Tuono’ and the extra-late blooming Iranian cultivar ‘Shahrood-12’. A modified-bulk segregant analysis in combination with the application of the 140 RAPD primers, 87 nuclear SSR markers spanning the whole almond genome and 5 chloroplast SSR markers, were used to identify molecular markers linked to flowering time. Results showed a quantitative inheritance of this trait in the studied progenies. The seedlings showed a wide range of flowering dates between both progenitors although some of these descendants were earlier in flowering than the early progenitor ‘Tuono’. Results showed that among RAPD markers evaluated, BA-17600,1000, BC-05320, BC-06800, BC-141750, BC-17600, BC-20250, OPC-05850 and OPC-09700,1100 markers were linked to late blooming time. In addition, markers BA-04720, BB-10630,BC-092000, BD-12510andOPC-12350 were linked to early blooming time. Two microsatellite loci (CPPCT008 and EPPCU2584) were also found to be tightly linked to flowering time. After construction the genetic map of population, QTL analysis was performed for blooming time. QTL analysis showed that OPC-09700,1100 and BA-17600,1000, markers were respectively located in 2 and 4 cM distance from one of the late flowering time loci. Also the BA-04720marker was located in 3 cM distances from one of the loci controlling early flowering time. These results are applicable in almond breeding programs for markers assisted strategy. The application of these results to other Prunus species has been also discussed.


Alburquerque N, García-Montiel F, Carrillo A, Burgos L (2008) Chilling and heat requirements of sweet cherry cultivars and the relationship between altitude and the probability of satisfying the chill requirements. Environmental and Experimental Botany. 64, 162–170.

Anderson JL, Seeley SD (1993) Bloom delay in deciduous fruits. Horticultural Reviews. 15, 97–144.

Aranzana MJ, Cosson P, Dirlewanger E, Ascasibar J, Cipriani, G, Arús P, Testolin R, Abbott A, King, GJ  Iezzoni AF (2003) A set of simple-sequence repeat (SSR) markers covering the Prunus genome. Theoretical and Applied Genetics .106, 819–825.

Arús P, Moreno-González J (1993) Marker-assisted selection. InHayward MD, Bosemark NO, Romagosa I (eds) Plant Breeding. Principles and Prospects. Chapman & Hall, London, pp. 314–331.

Asins MJ, Mestre P, García J E, Dicenta F,Carbonell EA (1994) Genotype x environment interaction in QTL analysis of an intervarietal almond cross by means of genetic markers. Theoretical and Applied Genetics. 89, 358–364.

Baird WV, Ballard RE, Rajapakse S, Abbott AG (1996) Progress in Prunus mapping and application of molecular markers to germplasm improvement. HortScience. 31, 1099–1106.

 Ballester JR, Company SI, Arus P, Vicente MC (2001) Genetic mapping of a major gene delaying blooming time in almond. Plant Breeding. 120, 268-270.

Boopathi NM (2013) Genetic Mapping and Marker Assisted Selection: Basics, Practice and Benefits. Springer, New York, USA. pp. 293.

Campoy JA, Martínez-Gómez P, Ruiz D, Rees J, Celton JM (2010a) Developing microsatellite multiplex and megaplex PCR systems for high throughput characterization of breeding progenies and linkage maps spanning the apricot genome. Plant Molecular Biology Reporter. 28, 560–568.

Campoy JA, Martínez-Gómez P, Ruiz D, Rees J, Celton JM (2010b) Inheritance of flowering time in apricot (Prunus armeniaca L.) and analysis of linked quantitative trait loci (QTLs) using simple sequence repeat (SSR) markers. Plant Molecular Biology Reporter. 10, 24-29.

Canli FA (2004) A modified segregant analysis for late blooming in sour cherry. Pakistan Journal of Biological Sciences.7, 1684-1688.

Cantini C, Iezzoni AF, Lamboy WF, Boritzki M, Struss D  (2001) DNA fingerprinting of tetraploid cherry germplasm using SSR. Journal of the American Society for Horticultural Science.126, 205–209.

Certal AC, Almeida RB, Boskovic R, Oliveira MM, Feijo JA (2002) Structural and molecular analysis of self-incompatibility in almond (Prunus dulcis). Sex Plant Reprod. 15, 13-20.

Chen FQ, Prehn D, Hayes PM (1994) Mapping genes for resistance to barley stripe rust. Theoretical and Applied Genetics. 88, 215-219.

Cipriani G, Lot G, Huang WG, Marrazzo MT, Peterlunger E, Testolin R (1999) AC/GT and AG/CT microsatellites repeats in peach (Prunus persica L. Batsch): Isolation, characterization and cross-species amplification in Prunus. Theoretical and Applied Genetics.100, 713–722.

Decousset L, Griffiths S, Dunford RP, Pratchett N, Laurie DA (2000) Development of STS markers closely linked to the Ppd-H1 photoperiod response gene of barley (Hordeum vulgare L.). Theoretical and Applied Genetics.101, 1202-1206.

Dicenta F, Garcia JE, Carbonell E (1993) Heritability of flowering, productivity and maturity in almond. Journal of Horticulture Sciences. 68, 113–120.

Dirlewanger E, Crosson A, Tavaud P, Aranzana MJ, Poizat C, Zanetto A, Arús P, Laigret L (2002) Development of microsatellite markers in peach and their use in genetic diversity analysis in peach and sweet cherry. Theoretical and Applied Genetics.105, 127–138.

Dirlewanger E, Graziano E, Joobeur T, Garriga-Caldré F, Cosson P, Howad W, Arús P (2004) Comparative mapping and marker-assisted selection in Rosaceae fruit crops. Proceedings of the National Academy of Sciences. USA. 101, 9891–9896.

Dong NV, Subudhi PK, Luong PN, Quang VD, Quy TD, Zheng HG, Wang B, Nguyen HT (2000) Molecular mapping of a rice gene conditioning thermo sensitive genetic male sterility using AFLP, RFLP and SSR techniques. Theoretical and Applied Genetics.100, 727-734.

Downey LD, Iezzoni AF (2000) Polymorphic DNA markers in cherry, peach, and sour cherry black cherry are identified using sequences from sweetcherry.Journal of the American Society for Horticultural Science.125, 76–80.

Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin. 19, 11-15.

Grassely C (1978) Observations surl’utilisation d’un mutant d’amandier a´ floraison tardive dans un programme d’hybridation. Ann Amelior Plant. 28, 685–695.

Gupta PK, Balyan HS, Sharma PC, Ramesh B (1996) Microsatellites in plants: A new class of molecular markers. Current Science. 70, 45–54.

 Kester DE, Gradiziel TM (1996) Almonds, in: Janick J., Moore J. N. (Eds.), Fruit Breeding. Vol. 3. Nuts, John Wiley and Sons, New York. pp. 1-97.

Kester DE (1965) Inheritance of time of bloom in certain progenies of almond. The American Society for Horticultural Science. 87, 214–221.

Lander ES, Botstein D (1989) Mapping Mendelian factor underlying quantitative traits using RFLP linkage maps. Genetics. 121, 185-199.

Lander ES, Green P, Abrahamson J, BarlowA, Daly MJ, Lincoln SE, Newburg L (1987) MAPMAKER: An interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics.1, 174–181.

Luby JJ, Shaw DV (2001) Does marker-assisted selection make dollars and sense in a fruit breeding program? Hort Science. 36, 872–879.

Martínez-Gómez P, Sánchez-Pérez R, Rubio M (2012) Clarifying omics concepts, challenges and opportunities for Prunusbreeding in the post-genomic era.Omics A Journal of Integrative Biology. 16, 268-283.

Michelmore R, Paran WI, Kesseli RV (1991) Identification of markers linked to disease-resistance gene by bulked segregant analysis: A rapid method to detect markers in specific genomic regions by using segregation populations. Proceedings of the National Academy of Sciences. 88, 9828-9832.

Miklas PN, Johnson E, Stone V, Beaver JS, Montoya C, Zapata M (1996) Selective mapping of QTL conditioning disease resistance in common bean. Crop Science. 36, 1344-1351.

Mnejia M, Garcia-Mas J, Howard W, Arus P (2005) Development and transportability across Prunus species of 42 polymorphic almond microsatellites. Molecular Ecology Notes. 5, 531-535.

Ohta S, Katsuki T, Tanaka T, HayashiT, Sato YL, Yamamoto T (2005) Genetic variation in flowering cherries (Prunus subgenus Cerasus) characterized by SSR markers. Breeding Science. 55, 415-424.

Rasouli M, Fatahi R, Zamani Z, Imani A, Ebadi A (2011) Evaluation of heritability of some traits, genetic control of blooming time and supplementary pollination in almond. Ph.D. Thesis, Factually of Agriculture, University of Tehran, Tehran, Iran.

Sánchez-Pérez R, Ballester J, Dicenta F, Arús P,Martínez-Gómez P (2006) Comparison of SSR polymorphisms using automated capillary sequencers, and polyacrylamide and agarose gel electrophoresis: Implications for the assessment of genetic diversity and relatedness in almond. Scientia Horticulturae. 108, 310-316.

Sanchez-Perez R, Dicenta F, Gradziel TM, Arus P, Martinez-Gomez P (2004) Application of molecular markers in almond breeding programmes. Nucis - New. 12, 9-12.

Sánchez-Pérez R, Howad W, Dicenta F, Arús P, Martínez-Gómez P (2007) Mapping major genes and quantitative trait loci controlling agronomic traits in almond. Plant Breeding. 126, 310–318.

Socias I Company R (1998) Fruit tree genetics at a turning point: The almond example. Theoretical and Applied Genetics. 96, 588–601.

Sosinski B, Gannavarapu M, Hager LE, Beck LE, King GJ, Ryder CD, Rajapakse S, Baird WV, Ballard RE, Abbott AG (2000) Characterization of microsatellite markers inpeach. (Prunus persica L.) Basch). Theoretical and Applied Genetics. 101, 421–428.

Tabuenca MC (1972) Necessidades de frı´oinvernal en almendro. An Estac Esper Aula Dei. 11, 325–329.

Tautz D (1989) Hypervariability of simple sequences as a general source for polymorphic DNA. Nucleic Acids Research. 17, 6463–6471.

Testolin R, Marrazzo T, Cipriani G, Quarta R, Verde I, Dettori MT, Pancaldi M, Sansavini S (2000) Microsatellite DNA in peach [Prunus persica (L.) Batsch] and its use in fingerprinting and testing the genetic origin of cultivars. Genome. 43, 512–520.

Testolin R, Messina R, Lain O, Marrazo T, Huang G,Cipriani G (2004) Microsatellites isolated in almond from an AC-repeat enriched library. Molecular Ecology Notes. 4, 459–461.

Van Ooijen JW, Voorrips RE (2001) Join Map 3.0, software for the calculation of genetic linkage maps. Plant Research International. B_V, Wageningen.

Vision TJ, Brown DG, Shmoys DB, Durret RT, Tanksley SD (2000). Selective mapping: A strategy for optimizing the construction of high-density linkage maps. Genetics. 155, 407–420.

Warburton ML, Becerra-Velásquez VL, Goffreda JC, Bliss FA (1996) Utility of RAPD markers in identifying genetic linkages to genes of economic interest in peach. Theoretical and Applied Genetics. 93, 920–925.

Yamamoto T, Mochida K, Imai T, Shi YZ, Ogiwara I, Hayashi T (2002) Microsatellite markers in peach [Prunus persica (L.) Batsch] derived from an enriched genomic and cDNA libraries. Molecular Ecology Notes. 2, 298–301.

Yu GX, Wise RP (2000) An anchored AFLP and retrotransposon-based map of diploid Avena.Genome. 43, 736-749.