AS  Vol.5 No.5 , April 2014
Low-Cost Strategies for Development of Molecular Markers Linked to Agronomic Traits in Prunus

Evaluation of agronomic traits in Prunus breeding programs is a tedious process because of the long juvenile period of trees, the influence of juvenility and the existence of climatic factors affecting the expression of the trait. For these reasons, marker-assisted selection (MAS) strategies are particularly useful in these cases. The objective of this work is the analysis of alternative low- cost strategies for development of molecular markers linked to agronomic traits in Prunus including the application of modified Bulked segregant analysis (BSA) using Simple sequence repeat (SSRs) markers and the application of Random amplified polymorphism microsatellite (RAMP) markers. First BSA results showed that two SSR loci were found to be tightly linked to flowering time in almond. On the other hand, RAMP analysis has been demonstrated to be a potentially valuable molecular marker for the study of genetic relationships in Prunus. Results showed the dominant nature of these markers with a great abundance and transferability although with a reduced polymorphism. In addition, RAMP application in F1 progenies showed its suitability for molecular characterization and mapping, and later Quantitative trait loci (QTL) or BSA analysis.

Cite this paper: Salazar, J. , Rasouli, M. , Moghaddam, R. , Zamani, Z. , Imani, A. and Martínez-Gómez, P. (2014) Low-Cost Strategies for Development of Molecular Markers Linked to Agronomic Traits in Prunus. Agricultural Sciences, 5, 430-439. doi: 10.4236/as.2014.55044.

[1]   Donmez, A.A. and Yildirimli, S. (2000) Taxonomy of Genus Prunus L. (Rosaceae) in Turkey. Turkish Journal of Botany, 14, 187-202.

[2]   Potter, D. (2012) Basic Information on the Stone Fruit Crops. In: Kole, C. and Abbott, A.G., Eds., Genetics, Genomics and Breeding of Stone Fruits, CRC Press, New York, 1-21.

[3]   Martínez-Gómez, P., Sozzi, G.O., Sánchez-Pérez, R., Rubio, M. and Gradziel, T.M. (2003) New Approach to Prunus Tree Crop Breeding. Journal of Food Agriculture and Environment, 1, 52-63.

[4]   Martínez-Gómez, P., Sánchez-Pérez, R. and Rubio, M. (2012) Clarifying Omics Concepts, Challenges and Opportunities for Prunus Breeding in the Post-Genomic Era. OMICS: Journal of Integrative Biology, 16, 268-283.

[5]   Martínez-Gómez, P., Arulsekar, S., Potter, D. and Gradziel, T.M. (2003) An Extended Inter-Specific Gene Pool Available to Peach and Almond Breeding as Characterized Using Simple Sequence Repeat (SSR) Markers. Euphytica, 131, 313-322.

[6]   Campoy, J.A., Martínez-Gómez, P., Ruiz, D., Rees, J. and Celton, J.M. (2010) 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.

[7]   Wu, K.S., Danneberger, L. and Scolnik, P. (1994) Detection of Microsatellite Polymorphisms without Cloning. Nucleic Acid Research, 22, 3257-3258.

[8]   Provan, J., Thomas, W.T.B., Forster, B.P. and Powel, W. (1999) Copia-SSR: A Simple Marker Technique Which Can Be Used on Total Genomic DNA. Genome, 42, 363-366.

[9]   Cheng, H.Y., Yang, W.C. and Hsiao, Y. (2001) Genetic Diversity and Relationship among Peach Cultivars Based on Random Amplified Microsatellite Polymorphism (RAMP). Botanical Bulletin of the Academia Sinica, 42, 201-206.

[10]   Lihua, Z., Mingyang, L., Guangze, C., Tianchun, P. and Chenghai, S. (2013) Assessment of the Gentic Diversity and Genetic Relationships of Pomegranate (Punica granatum L.) in China Using RAMP Markers. Scientia Horticulturae, 151, 63-67.

[11]   Huang, H.L., Huang, I.Y., Lin, C.Y. and Huang, M.C. (2013) Effective Strategies for Identifying Novel Genetic Markers Based on DNA Polymorphisms. Journal of Molecular Biomarkers & Diagnosis, 5, 1.

[12]   Boopathi, N.M. (2013) Genetic Mapping and Marker Assisted Selection: Basics, Practice and Benefits. Springer, New York, 293 p.

[13]   Michelmore, R.W., Paran, I. and Kesseli, R.V. (1991) Identification of Markers Linked to Disease-Resistance Genes by Bulked Segregant Analysis: A Rapid Method to Detect Markers in Specific Genomic Regions by Using Segregating Populations. Proceedings of the National Academy of Science USA, 88, 9828-9832.

[14]   Warburton, M.L., Becerra-Velasquez, V.L., Goffreda, J.C. and Bliss, F.A. (1996) Utility of RAPD Markers in Identifying Genetic Linkages to Genes of Economic Interest in Peach. Theoretical and Applied Genetics, 93, 920-925.

[15]   Ballester, J., Socias i Company, R., Arús, P. and de Vicente, M.C. (2001) Genetic Mapping of a Major Gene Delaying Blooming Time in Almond. Plant Breeding, 120, 268-270.

[16]   Doyle, J.J. and Doyle, J.L. (1987) A Rapid Isolation Procedure for Small Quantities of Fresh Leaf Tissue. Phytochemistry Bulletin, 19, 11-15.

[17]   Sánchez-Pérez, R., Ballester, J., Dicenta, F., Arús, P. and 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.

[18]   Sánchez-Pérez, R., Howad, W., Dicenta, F., Arús, P. and Martínez-Gómez, P. (2007) Mapping Major Genes and Quantitative Trait Loci Controlling Agronomic Traits in Almond. Plant Breeding, 126, 310-318.

[19]   Dondini, L., Lain, O., Geuna, F., Banfi, R., Gaiotti, F., Tartarini, S., Bassi, D. and Tesolin, R. (2007) Development of a New SSR-Based Linkage Map in Apricot and Analysis of Synteny with Existing Prunus Map. Tree Genetics & Genomes, 3, 239-249.

[20]   Sánchez-Pérez, R., Howad, W., García-Mas, J., Arús, P., Martínez-Gómez, P. and Dicenta, F. (2010) Molecular Markers for Kernel Bitterness in Almond. Tree Genetics & Genomes, 6, 237-247.

[21]   Dirlewanger, E., Crosson, A., Tavaud, P., Aranzana, M.J., Poizat, C., Zanetto, A., Arús, P. and Laigret, L. (2002) Development of Microstellite Markers in Peach and Their Use in Genetic Diversity Analysis in Peach and Sweet Cherry. Theoretical and Applied Genetics, 105, 127-138.

[22]   Mnejja, M., Garcia-Mas, J., Howad, W. and Arús, P. (2005) Development and Transportability across Prunus Species of 42 Polymorphic Almond Microsatellites. Molecular Ecology Notes, 5, 531-535.

[23]   Aranzana, M.J., García-Mas, J., Carbó, J. and Arús, P. (2002) Development and Variability Analysis of Microsatellite Markers in Peach. Plant Breeding, 121, 87-92.

[24]   Howad, W., Yamamoto, T., Dirlewanger, E., Testolin, R., Cosson, P., Cipriani, G., Monforte, A.J., Georgi, L., Abbott, A.G. and Arús, P. (2005) Mapping with a Few Plants: Using Selective Mapping for Microsatellite Saturation of the Prunus Reference Map. Genetics, 171, 1305-1309.

[25]   Yamamoto, T., Mochida, K., Imai, T., Shi, I.Z., Ogiwara, I. and Hayashi, T. (2002) Microsatellite Markers in Peach [Prunus persica (L.) Batsch] Derived from an Enriched Genomic and cDNA Libraries. Molecular Ecology Notes, 2, 298-302.

[26]   Downey, L.D. and Iezzoni, A.F. (2000) Polymorphic DNA Markers in Cherry Are Identified Using Sequences from Sweet Cherry, Peach, and Sour Cherry. Journal of the American Society of Horticultural Science, 125, 76-80.

[27]   Sosinski, B., Gannavarapu, M., Hager, L.E., Beck, L.E., King, G.J., Ryder, C.D., Rajapakse, S., Baird, W.V., Ballard, R.E. and Abbott, A.G. (2000) Characterization of Microsatellite Markers in Peach (Prunus persica (L) Basch). Theoretical and Applied Genetics, 101, 421-428.

[28]   Cantini, C., Iezzoni, A.F., Lamboy, W.L., Boritzki, M. and Struss, D. (2001) DNA Fingerprinting of Tetraploid Cherry Germplasm Using SSR. Journal of the American Society of Horticultural Science, 126, 205-209.

[29]   Testolin, R., Messina, R., Lain, O., Marrazo, T., Huang, G. and Cipriani, G. (2004) Microsatellites Isolated in Almond from an AC-Repeat Enriched Library. Molecular Ecology Notes, 4, 459-461.

[30]   Messina, R., Lain, O., Marrazo, T., Cipriano, G. and Testolin, R. (2004) New Set of Microsatellite Loci Isolated in Apricot. Molecular Ecology Notes, 4, 432-434.

[31]   Cipriani, G., Lot, G., Huang, H.G., Marrazzo, M.T., Peterlunger, E. and Testolin, R. (1999) AC/GT and AG/CT Microsatellite Repeats in Peach (Prunus persica (L) Basch): Isolation, Characterization and Cross-Species Amplification in Prunus. Theoretical and Applied Genetics, 99, 65-72.

[32]   Sánchez-Pérez, R., Ortega, E., Duval, H., Martínez-Gómez, P. and Dicenta, F. (2007) Inheritance and Correlation of Important Agronomic Traits in Almond. Euphytica, 155, 381-391.

[33]   Socias i Company, R., Felipe, A.J. and Gómez-Aparisi, J. (1999) A Major Gene for Flowering Time in Almond. Plant Breeding, 118, 443-448.

[34]   Dicenta, F., García, J.E. and Carbonell, E.A. (1993) Heritability of Flowering, Productivity and Maturity in Almond. Journal of Horticultural Science, 68, 113-120.

[35]   Vargas, F.J. and Romero, M.A. (2001) Blooming Time in Almond Progenies. Options Méditerranéennes, 56, 29-34.

[36]   Colic, S., Rakonjac, V., Zec, G., Nikolic, D. and Fotiric-Aksic, M. (2012) Morphological and Biochemical Evaluation of Selected Almond [Prunus dulcis (Mill.) D.A. Webb] Genotypes in Northern Serbia. Turkish Journal of Agriculture and Forestry, 36, 429-438.

[37]   Kester, D.E., Raddi, P. and Asay, R. (1977) Correlation of Chilling Requirements for Germination, Blooming and Leafing within and among Seedling Populations of Almond. Journal of the American Society of Horticultural Science, 102, 145-148.

[38]   Dicenta, F., García-Gusano, M., Ortega, E. and Martínez-Gómez, P. (2005) The Possibilities of Early Selection of Late-Flowering Almonds as a Function of Seed Germination or Leafing Time of Seedlings. Plant Breeding, 124, 305309.

[39]   Sánchez-Pérez, R., Dicenta, F. and Martínez-Gómez, P. (2012) Inheritance of Chilling and Heat Requirements for Flowering in Almond and QTL Analysis. Tree Genetics & Genomes, 8, 379-389.

[40]   Olukolu, B., Trainin, T., Fan, S., Kole, C., Bielenberg, D., Reighard, G., Abbott, A. and Holland, D. (2009) Genetic Linkage Mapping for Molecular Dissection of Chilling Requirement and Budbreak in Apricot (Prunus armeniaca L.). Genome, 52, 819-828.

[41]   Campoy, J.A., Ruiz, D., Egea, J., Rees, J., Celton, J.M. and Martínez-Gómez, P. (2011) Inheritance of Flowering Time in Apricot (Prunus armeniaca L.) and Analysis of Linked Quantitative Trait Loci (QTLs) Using Simple Sequence Repeat Markers. Plant Molecular Biology Reporter, 29, 404-410.

[42]   Hibrand-Saint Oyant, L., Crespel, L., Rajapakse, S., Zhang, L. and Foucher, F. (2008) Genetic Linkage Maps of Rose Constructed with New Microsatellite Markers and Locating QTL Controlling Flowering. Tree Genetics & Genomes, 4, 11-23.

[43]   Fan, S., Bielenberg, D.G., Zhebentyayeva, T.N., Reighard, G.L., Okie, W.R., Holland, D. and Abbott, A.G. (2010) Mapping Quantitative Trait Loci Associated with Chilling Requirement, Heat Requirement and Bloom Date in Peach (Prunus persica). New Phytology, 185, 917-930.

[44]   Verde, I., Abbott, A.G., Scalabrin, S., Jung, S., Shu, S., Marroni, F., Zhebentyayeva, T., Dettori, M.T., Grimwood, J., Cattanoro, F., Zuccolo, A., Rossini, L., Jenkins, J., Vendramin, E., Meisel, L.A., Decroocq, V., Sosininski, B., Prochnik, S., Mitros, T., Policriti, A., Cipriani, G., Dondini, L., Ficklin, S., Goodstein, D.M., Xuan, P., Del Fabbro, C., Aramini, V., Copeti, D., Barakat, A., Testolin, R., Stella, A., Tartarin, S., Arús, P., Orellana, A., Wells, C., Main, D., Vizzotto, G., Silva, H., Salamani, F., Schmutz, J., Morgante, M. and Rokhsar, D. (2013) The High-Quality Draft of Peach (Prunus persica) Identifies Unique Patterns of Genetic Diversity, Domestication and Genome Evolution. Nature Genetics, 45, 487-494.

[45]   Verde, I., Bassil, N., Scalabrin, S., Gilmore, B., Lawley, C.T., Gasic, K., Micheleti, D., Rosyara, U.R., Cattonaro, F., Vendramin, E., Main, D., Aramini, V., Blas, A.L., Mockler, T.C., Bryant, D.W., Whilelm, L., Troggio, M., Sosinski, B., Aranzana, M.J., Arús, P., Iezzoni, A., Morgante, N. and Peace, C. (2012) Development and Evaluation of a 9K SNP Array for Peach by Internationally Coordinated SNP Detection and Validation in Breeding Germplasm. PLoS ONE, 7, e35668.

[46]   Peace, C., Bassil, N., Main, D., Ficklin, S., Rosyara, U.R., Stegmeir, T., Sebolt, A., Gilmore, B., Mockler, T.C., Bryant, D.W., Whilelm, L. and Iezzoni, A. (2012) Development and Evaluation of a Genome-Wide 6K SNP Array for Diploid Sweet Cherry and Tetraploid Sour Cherry. PLoS ONE, 7, e48305.