Development and bin mapping of strawberry genic-SSRs in diploid Fragaria and their transferability across the Rosoideae subfamily
- 432 Downloads
Cultivated strawberry (Fragaria × ananassa) together with other economically important genera such as Rosa (roses) and Rubus (raspberry and blackberry) belongs to the subfamily Rosoideae. There is increasing interest in the development of transferable markers to allow genome comparisons within the Rosaceae family. In this report, 122 new genic microsatellite (SSR) markers have been developed from cultivated strawberry and its diploid ancestor Fragaria vesca. More than 77% of the sequences from which the markers were developed show significant homology to known or predicted proteins and more than 92% were polymorphic among strawberry cultivars, representing valuable markers in transcribed regions of the genome. Sixty-three SSRs were polymorphic in the diploid Fragaria reference population and were bin-mapped together with another five previously reported but unmapped markers. In total, 72 loci were distributed across the seven linkage groups. In addition, the transferability of 174 Fragaria SSRs to the related Rosa and Rubus genera was investigated, ranging from 28.7% for genic-SSRs in rose to 16.1% for genomic-SSRs in raspberry. Among these markers, 33 and 16 were both localized in the diploid Fragaria reference map and cross-amplified in rose and raspberry, respectively. These results indicate that transferability of SSRs across the Rosoideae subfamily is limited. However, we have identified a set of Fragaria markers, polymorphic in the diploid reference population, which cross-amplified in both Rosa and Rubus, which represents a valuable tool for comparative mapping and genetic diversity analyses within the Rosoideae subfamily.
KeywordsComparative mapping Synteny Strawberry Rose Raspberry Rosoideae
This work was supported by grants RTA2008-00029-00-00 (INIA, partly funded by FEDER, European Union), AGR-03230 (CICE, Junta de Andalucía) and BIO2007-67509-C02-01 (MEC). The IFAPA Fragaria germplasm collection is funded by grant RFP2008-00009-00-00 (INIA). At CRAG, this work was supported with funds of the Spanish Ministry of Science and Innovation, project RTA2007-00063-00-00 (INIA). Y.Z-F. was supported by a fellowship and I.A. by a contract from INIA. We are gratefull to E. Cruz-Rus for obtaining the genomic sequence of GaLUR.
The experiments of this study comply with the current laws of Spain.
Conflict of interest
The authors declare that they have no conflict of interest.
- Akiyama Y, Yamamoto Y, Ohmido N, Oshima M, Fukui K (2001) Estimation of the nuclear DNA content of strawberries (Fragaria ssp.) compared with Arabidopsis thaliana by using dual-stem flow cytometry. Cytologia 66:431–436Google Scholar
- Benbouza H, Jacquemin J, Baudoin JP, Mergeai G (2006) Optimization of a reliable, fast, cheap and sensitive silver staining method to detect SSR markers in polyacrylamide gels. Biotechnol Agron Soc Environ 10:77–81Google Scholar
- Cheng FS, Brown SK, Weeden NF (1997) A DNA extraction protocol from various tissues in woody species. Hortscience 32:921–922Google Scholar
- Davis TM, Yu H (1997) A linkage map of the diploid strawberry, Fragaria vesca. J Hered 88:215–221Google Scholar
- Davis TM, DiMeglio LM, Yang RH, Styan SMN, Lewers KS (2006) Assessment of SSR marker transfer from the cultivated strawberry to diploid strawberry species: Functionality, linkage group assignment, and use in diversity analysis. J Am Soc Hort Sci 131:506–512Google Scholar
- Davis T, Denoyes-Rothan B, Lecerteau-Köhler E (2007) Strawberry. In: Kole C (ed) Genome mapping and molecular breeding in plants: fruits and nuts. Springer, Berlin, pp 189–206Google Scholar
- Doyle JJ, Doyle JL (1990) Isolation of plant DNA from fresh tissue. Focus 12:13–15Google Scholar
- Gil-Ariza DJ, Amaya I, Botella MA, Blanco JM, Caballero JL, Lopez-Aranda JM, Valpuesta V, Sanchez-Sevilla JF (2006) EST-derived polymorphic microsatellites from cultivated strawberry (Fragaria × ananassa) are useful for diversity studies and varietal identification among Fragaria species. Mol Ecol Notes 6:1195–1197CrossRefGoogle Scholar
- Gil-Ariza D, Amaya I, Lopez-Aranda JM, Botella MA, Valpuesta V, Sanchez-Sevilla JF (2009) Impact of plant breeding on the genetic diversity of cultivated strawberry as revealed by expressed sequence tag-derived simple sequence repeat markers. J Am Soc Hort Sci 134:337–347Google Scholar
- Hadonou M, Sargent D, Walden R, Simpson D (2004) Characterisation of Fragaria vesca single sequence repeats (SSR) markers. Proceedings of the Euro Berry Symposium–Cost 836 Final Worskhop, pp 99–102Google Scholar
- Hokanson SC, Maas J (2001) Strawberry biotechnology. Plant Breed Rev 21:139–180Google Scholar
- Jennings DL (1988) Raspberries and blackberries: their breeding, diseases and growth. Academic, LondonGoogle Scholar
- Lerceteau-Kohler E, Moing F, Gurin G, Renaud C, Courlit S, Camy D, Praud K, Parisy V, Bellec F, Maucourt M, Rolin D, Roudeillac P, Denoyes-Rothan B (2004) QTL analysis for fruit quality traits in octoploid strawberry (Fragaria × ananassa). Proceedings of the XIth Eucarpia Symposium on Fruit Breeding and Genetics, Vols 1 and 2:331–335Google Scholar
- Lewers KS, Styan SMN, Hokanson SC, Bassil NV (2005) Strawberry GenBank-derived and genomic simple sequence repeat (SSR) markers and their utility with strawberry, blackberry, and red and black raspberry. J Am Soc Hort Sci 130:102–115Google Scholar
- Rousseau-Gueutin M, Lerceteau-Kohler E, Barrot L, Sargent DJ, Monfort A, Simpson D, Arus P, Guerin G, Denoyes-Rothan B (2008) Comparative genetic mapping between octoploid and diploid Fragaria species reveals a high level of colinearity between their genomes and the essentially disomic behavior of the cultivated octoploid strawberry. Genetics 179:2045–2060CrossRefPubMedGoogle Scholar
- Rousseau-Gueutin M, Gaston A, Ainouche A, Ainouche ML, Olbricht K, Staudt G, Richard L, Denoyes-Rothan B (2009) Tracking the evolutionary history of polyploidy in Fragaria L. (strawberry): new insights from phylogenetic analyses of low-copy nuclear genes. Mol Phylogenet Evol 51:515–530CrossRefPubMedGoogle Scholar
- Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. Meth Mol Biol 132:365–386Google Scholar
- Sargent DJ, Marchese A, Simpson DW, Howad W, Fernandez-Fernandez F, Monfort A, Arus P, Evans KM, Tobutt KR (2009b) Development of “universal” gene-specific markers from Malus spp. cDNA sequences, their mapping and use in synteny studies within Rosaceae. Tree Genet Genome 5:133–145CrossRefGoogle Scholar
- Silfverberg-Dilworth E, Matasci CL, Van de Weg WE, Van Kaauwen MPW, Walser M, Kodde LP, Soglio V, Gianfranceschi L, Durel CE, Costa F, Yamamoto T, Koller B, Gessler C, Patocchi A (2006) Microsatellite markers spanning the apple (Malus × domestica Borkh.) genome. Tree Genet Genome 2:202–224CrossRefGoogle Scholar
- Bombarely A, Merchante C-, Csukasi F, Cruz-Rus E, Caballero JL, Medina-Escobar N, Botella MA, Muñoz-Blanco J, Valpuesta V, Sanchez-Sevilla JF (submitted) Generation and analysis of ESTs from strawberry (Fragaria × ananassa) fruits and evaluation of their utility in genetic and molecular studies. BMC GenomicsGoogle Scholar
- Yamamoto T, Kirnura T, Saito T, Kotobuki K, Matsuta N, Liebhard R, Gessler C, van de Weg WE, Hayashi T (2004) Genetic linkage maps of Japanese and European pears aligned to the apple consensus map. Proceedings of the XIth Eucarpia Symposium on Fruit Breeding and Genetics, Vols 1 and 2: 51–56Google Scholar