Development of a dense SNP-based linkage map of an apple rootstock progeny using the Malus Infinium whole genome genotyping array
Antanaviciute, L., Fernandez-Fernandez, F., Jansen, J., Banchi, E., Evans, K. M., Viola, R., Velasco, R., Dunwell, J. M., Troggio, M. and Sargent, D. J. (2012) Development of a dense SNP-based linkage map of an apple rootstock progeny using the Malus Infinium whole genome genotyping array. BMC Genomics, 13. 203. ISSN 1471-2164
To link to this article DOI: 10.1186/1471-2164-13-203
Background A whole-genome genotyping array has previously been developed for Malus using SNP data from 28 Malus genotypes. This array offers the prospect of high throughput genotyping and linkage map development for any given Malus progeny. To test the applicability of the array for mapping in diverse Malus genotypes, we applied the array to the construction of a SNPbased linkage map of an apple rootstock progeny. Results Of the 7,867 Malus SNP markers on the array, 1,823 (23.2 %) were heterozygous in one of the two parents of the progeny, 1,007 (12.8 %) were heterozygous in both parental genotypes, whilst just 2.8 % of the 921 Pyrus SNPs were heterozygous. A linkage map spanning 1,282.2 cM was produced comprising 2,272 SNP markers, 306 SSR markers and the S-locus. The length of the M432 linkage map was increased by 52.7 cM with the addition of the SNP markers, whilst marker density increased from 3.8 cM/marker to 0.5 cM/marker. Just three regions in excess of 10 cM remain where no markers were mapped. We compared the positions of the mapped SNP markers on the M432 map with their predicted positions on the ‘Golden Delicious’ genome sequence. A total of 311 markers (13.7 % of all mapped markers) mapped to positions that conflicted with their predicted positions on the ‘Golden Delicious’ pseudo-chromosomes, indicating the presence of paralogous genomic regions or misassignments of genome sequence contigs during the assembly and anchoring of the genome sequence. Conclusions We incorporated data for the 2,272 SNP markers onto the map of the M432 progeny and have presented the most complete and saturated map of the full 17 linkage groups of M. pumila to date. The data were generated rapidly in a high-throughput semi-automated pipeline, permitting significant savings in time and cost over linkage map construction using microsatellites. The application of the array will permit linkage maps to be developed for QTL analyses in a cost-effective manner, and the identification of SNPs that have been assigned erroneous positions on the ‘Golden Delicious’ reference sequence will assist in the continued improvement of the genome sequence assembly for that variety.
1. Velasco R, Zharkikh A, Affourtit J, Dhingra A, Cestaro A, Kalyanaraman A, Fontana P, Bhatnagar SK, Troggio M, Pruss D, et al: The genome of the domesticated apple (Malus x domestica Borkh.). Nat Genet 2010, 42:833–839. 2. Zharkikh A, Troggio M, Pruss D, Cestaro A, Eldrdge G, Pindo M, Mitchell JT, Vezzulli S, Bhatnagar S, Fontana P, et al: Sequencing and assembly of highly heterozygous genome of Vitis vinifera L. cv Pinot Noir: Problems and solutions. J Biotechnol 2008, 136:38–43. 3. Huo NX, Garvin DF, You FM, McMahon S, Luo MC, Gu YQ, Lazo GR, Vogel JP: Comparison of a high-density genetic linkage map to genome features in the model grass Brachypodium distachyon. Theor Appl Genet 2011, 123:455–464. 4. Pindo M, Vezzulli S, Coppola G, Cartwright DA, Zharkikh A, Velasco R, Troggio M: SNP high-throughput screening in grapevine using the SNPlex (TM) genotyping system. BMC Plant Biol 2008, 8:12. 5. Micheletti D, Troggio M, Zharkikh A, Costa F, Malnoy M, Velasco R, Salvi S: Genetic diversity of the genus Malus and implications for linkage mapping with SNPs. Tree Genet Genomes 2011, 7:857–868. 6. Iezzoni A, Weebadde C, Luby J, Yue CY, Weg Evd, Fazio G, Main D, Peace CP, Bassil NV, McFerson J: RosBREED: Enabling marker-assisted breeding in Rosaceae. In Acta Horticulturae. Edited by Bassil NV, Martin R. 2010:389–394. 7. Chagné D, Crowhurst R, Troggio M, Davey MW, Gilmore B, Lawley C, Vanderzande S, Hellens RP, Kumar S, Cestaro A, Velasco R, Main D, Rees DJG, Iezzoni A, Mockler T, Wilhelm L, Van de Weg E, Gardiner SE, Bassil N, Peace C: Genome-wide SNP detection, validation, and development of an 8 K SNP array for apple. PLoS One 2012, 7:e31745. 8. Evans KM, Fernandez-Fernandez F, Govan CL, Clarke JB, Tobutt KR: Development of a new apple rootstock framework map. In Acta Horticulturae. Edited by Robinson TL.: ; 2011:69–74. 9. Fernández-Fernández F, Antanaviciute L, van Dyk MM, Tobutt KR, Evans KM, Rees DJG, Dunwell JM, Sargent DJ: A genetic linkage map of an apple rootstock progeny anchored to the Malus genome sequence. Tree Genet Genomes (online first) 2012, doi:10.1007/s11295-012-0478-7. 10. Franke L, de Kovel CGE, Aulchenko YS, Trynka G, Zhernakova A, Hunt KA, Blauw HM, van den Berg LH, Ophoff R, Deloukas P, van Heel DA, Wijmenga C: Detection, imputation, and association analysis of small deletions and null alleles on oligonucleotide arrays. Am J Hum Genet 2008, 82:1316–1333. 11. Sanzol J: Dating and functional characterization of duplicated genes in the apple (Malus domestica Borkh.) by analyzing EST data. BMC Plant Biol 2010, 10:87. 12. Jung S, Cestaro A, Troggio M, Main D, Zheng P, Cho I, Folta KM, Sosinski B, Abbott AG, Celton JM, Arús P, Shulaev V, Verde I, Morgante M, Rokhsar DS, Velasco R, Sargent DJ: Whole genome comparisons of Fragaria, Prunus and Malus reveal different modes of evolution between Rosaceous subfamilies. BMC Genomics 2012, 13:129. 13. Bošković R, Tobutt KR: Correlation of stylar ribonuclease isoenzymes with incompatibility alleles in apple. Euphytica 1999, 107:29–43. 14. Maliepaard C, Alston FH, van Arkel G, Brown LM, Chevreau E, Dunemann F, Evans KM, Gardiner S, Guilford P, van Heusden AW, et al: Aligning male and female linkage maps of apple (Malus pumila Mill.) using multi-allelic markers. Theor Appl Genet 1998, 97:60–73. 15. Rockman MV, Kruglyak L: Recombinational landscape and population genomics of Caenorhabditis elegans. PLoS Genet 2009, 5:e1000419. 16. Tian ZX, Rizzon C, Du JC, Zhu LC, Bennetzen JL, Jackson SA, Gaut BS, Ma JX: Do genetic recombination and gene density shape the pattern of DNA elimination in rice long terminal repeat retrotransposons? Genome Res 2009, 19:2221–2230. 17. Barendse W, Armitage SM, Kossarek LM, Shalom A, Kirkpatrick BW, Ryan AM, Clayton D, Li L, Neibergs HL, Zhang N, et al: A genetic-linkage map of the bovine genome. Nat Genet 1994, 6:227–235. 18. Wegmann D, Kessner DE, Veeramah KR, Mathias RA, Nicolae DL, Yanek LR, Sun YV, Torgerson DG, Rafaels N, Mosley T, et al: Recombination rates in admixed individuals identified by ancestry-based inference. Nat Genet 2011, 43:847–853. 19. Jung S, Staton M, Lee T, Blenda A, Svancara R, Abbott A, Main D: GDR (Genome Database for Rosaceae): integrated web-database for Rosaceae genomics and genetics data. Nucleic Acids Res 2008, 36(Database issue):D1034–D1040. 20. Payne RW, Harding SA, Murray DA, Soutar DM, Baird DB, Glaser AI, Welham SJ, Gilmour AR, Thompson R, Webster R: GenStat® Release 14 Reference Manual. Hemel Hempstead, UK: VSN International; 2012. 21. Jansen J: Construction of linkage maps in full-sib families of diploid outbreeding species by minimizing the number of recombinations in hidden inheritance vectors. Genetics 2005, 170:2013–2025. 22. Lander ES, Green P: Construction of multilocus genetic linkage maps in humans. Proc Natl Acad Sci U S A 1987, 84:2363–2367. 23. Voorrips RE: MapChart: Software for the graphical presentation of linkage maps and QTLs. J Hered 2002, 93:77–78.
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