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Population structure and core collection construction of apricot (Prunus armeniaca L.) in North Africa based on microsatellite markers

Published online by Cambridge University Press:  31 July 2015

Hedia Bourguiba ,
Mohamed-Amine Batnini ,
Lamia Krichen ,
Neila Trifi-Farah  and
Jean-Marc Audergon
Hedia Bourguiba*
Affiliation:
LR99ES12, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Faculté des Sciences de Tunis, Université Tunis El Manar, Campus Universitaire Tunis-El Manar, 2072Tunis, Tunisie
Mohamed-Amine Batnini
Affiliation:
LR99ES12, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Faculté des Sciences de Tunis, Université Tunis El Manar, Campus Universitaire Tunis-El Manar, 2072Tunis, Tunisie
Lamia Krichen
Affiliation:
LR99ES12, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Faculté des Sciences de Tunis, Université Tunis El Manar, Campus Universitaire Tunis-El Manar, 2072Tunis, Tunisie
Neila Trifi-Farah
Affiliation:
LR99ES12, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Faculté des Sciences de Tunis, Université Tunis El Manar, Campus Universitaire Tunis-El Manar, 2072Tunis, Tunisie
Jean-Marc Audergon
Affiliation:
INRA Centre PACA, UR 1052 GAFL, Domaine St Maurice, Allée des Chênes, CS 60094, 84143Montfavet Cedex, France
*
*Corresponding author. E-mail: [email protected]
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Abstract

North Africa enclosed original apricot genetic resources with the cohabitation of grafting and seed-propagated accessions. In this study, we assessed the genetic diversity and population structure of 183 apricot accessions using 24 microsatellite markers distributed evenly in the Prunus genome. A total of 192 alleles and a high level of gene diversity (0.593) were detected among the whole panel. Genetic structure analysis revealed the presence of four genetic clusters. We also found that both geographical origin and mode of propagation are important factors structuring genetic diversity in apricot species. Results confirmed the presence of gene exchange between the northern and southern countries of the Mediterranean Basin. Subsequently, a core collection of 98 accessions based on M (maximization) strategy showing 99.47% of allele retention ratio was constructed. No significant differences for Shannon's information index and Nei's diversity index were observed between the core and entire collections. Our results provide an effective aid for future germplasm preservation and conservation strategies as well as genetic association studies development in relation to phenotypic data.

Keywords

core collectiongenetic diversitymicrosatellite markersPrunus armeniaca L
Type
Research Article
Information
Plant Genetic Resources , Volume 15 , Issue 1 , February 2017 , pp. 21 - 28
Copyright
Copyright © NIAB 2015 

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References

Amalraj, VA, Balakrishnan, R, Jebadhas, AW and Balasundaram, N (2006) Constituting a core collection of Saccharum spontaneum L. and comparison of three stratified random sampling procedures. Genetic Resources and Crop Evolution 53: 1563–1572.CrossRefGoogle Scholar
Aranzana, MJ, Garcia-Màs, J, Carbo, J and Arús, P (2002) Development and variability analysis of microsatellite markers in peach. Plant Breeding 121: 87–92.Google Scholar
Aranzana, MJ, Pineda, A, Cosson, P, Dirlewanger, E, Ascasibar, J, Cipriani, G, Ryder, CD, Testolin, R, Abbott, A, King, GJ, Iezzoni, AF and Arùs, P (2003) A set of simple-sequence repeat (SSR) markers covering the Prunus genome. Theoretical and Applied Genetics 106: 819–825.Google Scholar
Bailey, CH and Hough, LF (1975) Apricots. In: Janick, J and Moore, JN (eds) Advances in Fruit Breeding. West Lafayette, Indiana: Purdue University Press, pp. 367–383.Google Scholar
Belaj, A, Dominguez-García, MC, Atienza, SG, Urdíroz, NM, De la Rosa, R, Satovic, Z, Martín, A, Kilian, A, Trujillo, I, Valpuesta, V and Del Río, C (2012) Developing a core collection of olive (Olea europaea L.) based on molecular markers (DArTs, SSRs, SNPs) and agronomic traits. Tree Genetics & Genomes 8: 365–378.CrossRefGoogle Scholar
Bourguiba, H, Khadari, B, Krichen, L, Trifi-Farah, N, Santoni, S and Audergon, JM (2010) Grafting versus seed propagated apricot populations: two main gene pools in Tunisia evidenced by SSR markers and model-based Bayesian clustering. Genetica 138: 1023–1032.CrossRefGoogle ScholarPubMed
Bourguiba, H, Audergon, JM, Krichen, L, Trifi-Farah, N, Mamouni, A, Trabelsi, S, D'Onofrio, C, Asma, BM, Santoni, S and Khadari, B (2012) Loss of genetic diversity as a signature of apricot domestication and diffusion into the Mediterranean Basin. BMC Plant Biology 12: 49. doi:10.1186/1471-2229-12-49.Google Scholar
Brown, AHD (1989) Core collections: a practical approach to genetic resources management. Genome 31: 818–824.Google Scholar
Cipriani, G, Lot, G, Huang, WG, Marrazzo, MT, Peterlunger, E and Testolin, R (1999) AC/GT and AG/CT microsatellite repeats in peach (Prunus persica L. Batsch): isolation, characterization and cross-species amplification in Prunus . Theoretical and Applied Genetics 99: 65–72.CrossRefGoogle Scholar
Crossa-Raynaud, P (1960) Problèmes d'arboriculture fruitière en Tunisie. Annales de l'Institut National de la Recherche Agronomique en Tunisie 33: 39–63.Google Scholar
Dirlewanger, E, Cosson, P, Tavaud, M, Aranzana, MJ, Poizat, C, Zanetto, A, Arús, P and Laigret, F (2002) Development of microsatellite markers in peach [Prunus persica (L.) Batsch] and their use in genetic diversity analysis in peach and sweet cherry (Prunus avium L.). Theoretical and Applied Genetics 105: 127–138.Google Scholar
Evanno, G, Regnaut, S and Goudet, J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology 14: 2611–2620.CrossRefGoogle ScholarPubMed
Franco, G, Crossa, J, Warburton, M and Taba, S (2006) Sampling strategies for conserving maize diversity when forming core subsets using genetic markers. Crop Science 46: 854–864.Google Scholar
Frankel, OH (1984) Genetic perspectives of germplasm conservation. In: Arber, W, Limensee, K, Peacock, WJ and Starlinger, P (eds) Genetic Manipulation: Impact on Man and Society. Cambridge: Cambridge University Press, pp. 161–171.Google Scholar
Frankel, OH and Brown, AHD (1984) Plant genetic resources today: a critical appraisal. Crop genetic resources. In: Holden, JHW and Williams, JT (eds) Conservation and Evaluation. London: Georges Allen & Unwin Ltd, pp. 249–257.Google Scholar
Hagen, LS, Chaib, J, Fady, B, Decroocq, V, Bouchet, JP, Lambert, P and Audergon, JM (2004) Genomic and cDNA microsatellites from apricot (Prunus armeniaca L.). Molecular Ecology Notes 4: 742–745.Google Scholar
Hu, J, Wang, P, Su, Y, Wang, R, Li, Q and Sun, K (2014) Microsatellite diversity, population structure, and core collection formation in melon germplasm. Plant Molecular Biology Reporter. doi 10. 1007/s11105-014-0757-6.Google Scholar
Joobeur, T, Viruel, MA, de Vicente, MC, Jauregui, B, Ballester, J, Dettori, MT, Verde, I, Truco, MJ, Messeguer, R, Batlle, I, Quarta, R, Dirlewanger, E and Arús, P (1998) Construction of a saturated linkage map for Prunus using an almond × peach F2 progeny. Theoretical and Applied Genetics 97: 1034–1041.CrossRefGoogle Scholar
Khadari, B, Krichen, L, Lambert, P, Marrakchi, M and Audergon, JM (2006) Genetic structure in Tunisian apricot populations multiplicated by grafting: a signature of bottleneck effects and ancient propagation by seedlings. Genetic Resources and Crop Evolution 53: 811–819.Google Scholar
Kim, KW, Chung, HK, Cho, GT, Ma, KH, Chandrabalan, D, Gwag, JG, Kim, TS, Cho, EG and Park, YJ (2007) PowerCore: a program applying the advanced M strategy with a heuristic search for establishing core sets. Bioinformatics 23: 2155–2162.Google Scholar
Krichen, L, Trifi-Farah, N, Marrakchi, M and Audergon, JM (2009) Evolution of the current apricot variability in Tunisia – comparison with previously described cultivars. Acta Horticulturae 814: 113–119.Google Scholar
Krichen, L, Bourguiba, H, Audergon, JM and Trifi-Farah, N (2010) Comparative analysis of genetic diversity in Tunisian apricot germplasm using AFLP and SSR markers. Scientia Horticulturae 127: 54–63.Google Scholar
Pritchard, JK, Stephens, M and Donnelly, P (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945–959.Google Scholar
Raji, R, Jannatizadeh, A, Fattahi, R and Esfahlani, MA (2014) Investigation of variability of apricot (Prunus armeniaca L.) using morphological traits and microsatellite markers. Scientia Horticulturae 176: 225–231.CrossRefGoogle Scholar
Rao, ES, Kadirvel, P, Symonds, RC, Geethnajali, S and Ebert, AW (2011) Using SSR markers to map genetic diversity and population structure of Solanum pimpinellifolium for development of a core collection. Plant Genetic Resources 10: 38–48.Google Scholar
Schoen, DJ and Brown, AHD (1993) Conservation of allelic richness in wild crop relatives is aided by assessment of genetic markers. Proceedings of the National Academy of Sciences of the United States of America 90: 10623–10627.Google Scholar
Song, Y, Fan, L, Chen, H, Zhang, M, Ma, Q, Zhang, S and Wu, J (2014) Identifying genetic diversity and a preliminary core collection of Pyrus pyrifolia cultivars by a genome-wide set of SSR markers. Scientia Horticulturae 167: 5–16.Google Scholar
Testolin, R, Marrazzo, T, Cipriani, G, Quarta, R, Verde, I, Dettori, MT, Pancaldi, M and 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.CrossRefGoogle ScholarPubMed
Vavilov, NI (1992) Origin and Geography of Cultivated Plants (tr.L.storr-best). Cambridge: CUP.Google Scholar
Yamamoto, T, Mochida, K, Imai, T, Shi, YZ, Ogiwara, T and Hayashi, T (2002) Microsatellite markers in peach [Prunus persica (L.) Batsch] derived from an enriched genomic and cDNA libraries. Molecular Ecology Notes 2: 298–301.Google Scholar
Yeh, FC and Boyle, TJB (1997) Population genetic analysis of codominant and dominant markers and quantitative traits. Belgian Journal of Botany 129: 157.Google Scholar
Yilmaza, KU, Paydas-Kargib, S, Doganb, Y and Kafkasb, S (2012) Genetic diversity analysis based on ISSR, RAPD and SSR among Turkish Apricot Germplasms in Iran Caucasian eco-geographical group. Scientia Horticulturae 138: 138–143.Google Scholar
Zhang, QP, Liu, DC, Liu, S, Liu, N, Wei, X, Zhang, AM and Liu, WS (2014) Genetic diversity and relationships of common apricot (Prunus armeniaca L.) in China based on simple sequence repeat (SSR) markers. Genetic Resources and Crop Evolution 61: 357–368.Google Scholar
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