Advertisement

Genotyping Tools for the Octoploid Strawberry

  • Robert Vickerstaff
Chapter
Part of the Compendium of Plant Genomes book series (CPG)

Abstract

Genotyping is the process of determining which set of alleles an individual has at a set of loci in its genome. An expanding set of techniques have become available for genotyping the cultivated, octoploid strawberry, beginning in the early 2000s. Despite the complexity of an allopolyploid genome, it has never the less proven possible to obtain reliable genotypic data from strawberry. With the decreasing cost of sequencing and other related technologies, more genotyping methods will continue to be developed and are likely to become integrated into research and breeding programs, even following the expected release of a comprehensive genome sequence in the near future. This chapter explores a range of genotyping techniques and covers the additional procedures sometimes required to make them function for the cultivated strawberry, providing a detailed look at genetic mapping as a key use of genotyping data.

Keywords

Fragaria × ananassa Genetic mapping Target capture Microarray Genotyping-by-sequencing 

Bibliography

  1. Bassil NV et al (2015) Development and preliminary evaluation of a 90 K Axiom® SNP array for the allo-octoploid cultivated strawberry Fragaria × ananassa. BMC Genom 16(1):155. Available at: http://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-015-1310-1. Accessed 12 Apr 2016
  2. Cartwright DA et al (2007) Genetic mapping in the presence of genotyping errors. Genetics 176(4):2521–2527. Available at: http://www.genetics.org/content/176/4/2521.abstract. Accessed 17 May 2016CrossRefPubMedPubMedCentralGoogle Scholar
  3. Catchen J et al (2013) Stacks: an analysis tool set for population genomics. Mol Ecol 22(11):3124–3140. Available at: http://doi.wiley.com/10.1111/mec.12354. Accessed 8 July 2013CrossRefPubMedPubMedCentralGoogle Scholar
  4. Davik J et al (2015) A ddRAD based linkage map of the cultivated Strawberry, Fragaria × ananassa. PLoS ONE 10(9)CrossRefPubMedPubMedCentralGoogle Scholar
  5. Elshire RJ et al (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE 6(5):e19379. Available at: http://dx.doi.org/10.1371/journal.pone.0019379. Accessed 7 Oct 2013CrossRefPubMedPubMedCentralGoogle Scholar
  6. Grattapaglia D, Sederoff R (1994) Genetic linkage maps of Eucalyptus grandis and Eucalyptus urophylla using a pseudo-testcross: mapping strategy and RAPD markers. Genetics 137(4):1121–1137. Available at: http://www.genetics.org/content/137/4/1121. Accessed 17 May 2016
  7. Isobe SN et al (2013) Construction of an integrated high density simple sequence repeat linkage map in cultivated strawberry (Fragaria × ananassa) and its applicability. DNA Res 20(1):79–92. Available at: http://dnaresearch.oxfordjournals.org/content/20/1/79. Accessed 28 June 2014CrossRefPubMedPubMedCentralGoogle Scholar
  8. Jaccoud D et al (2001) Diversity arrays: a solid state technology for sequence information independent genotyping. Nucleic Acids Res 29(4):e25–e25. Available at: http://nar.oxfordjournals.org/content/29/4/e25. Accessed 17 July 2013CrossRefGoogle Scholar
  9. James CM et al (2003) Isolation and characterization of polymorphic microsatellites in diploid strawberry (Fragaria vesca L.) for mapping, diversity studies and clone identification. Mol Ecol Notes 3(2):171–173CrossRefGoogle Scholar
  10. Kim C et al (2016) Application of genotyping by sequencing technology to a variety of crop breeding programs. Plant Sci 242:14–22CrossRefPubMedGoogle Scholar
  11. Lander ES et al (1987) MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1(2):174–181CrossRefPubMedPubMedCentralGoogle Scholar
  12. Lerceteau-Köhler E et al (2003) Characterization of mixed disomic and polysomic inheritance in the octoploid strawberry (Fragaria × ananassa) using AFLP mapping. Theor Appl Genet 107(4):619–628CrossRefPubMedGoogle Scholar
  13. Li H. et al (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25(16):2078–2079. Available at: http://bioinformatics.oxfordjournals.org/content/25/16/2078. Accessed 19 Sept 2013CrossRefPubMedPubMedCentralGoogle Scholar
  14. Li H (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv:1303.3997 [q-bio]. Available at: http://arxiv.org/abs/1303.3997. Accessed 23 July 2014
  15. Maliepaard C (2000) Genetic mapping in a full-sib family of apple. Wageningen Agricultural UniversityGoogle Scholar
  16. Margarido GRA, Souza AP, Garcia AaF (2007) OneMap: software for genetic mapping in outcrossing species. Hereditas 144(3):78–79. Available at: http://onlinelibrary.wiley.com/doi/10.1111/j.2007.0018-0661.02000.x/abstract. Accessed 2 Feb 2015CrossRefPubMedGoogle Scholar
  17. Monfort A et al (2006) A new set of polymorphic simple sequence repeat (SSR) markers from a wild strawberry (Fragaria vesca) are transferable to other diploid Fragaria species and to Fragaria × ananassa. Mol Ecol Notes 6(1):197–200CrossRefGoogle Scholar
  18. Peterson BK et al (2012) Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS ONE 7(5)CrossRefPubMedPubMedCentralGoogle Scholar
  19. Rastas P et al (2013) Lep-MAP: fast and accurate linkage map construction for large SNP datasets. Bioinformatics 29(24):3128–3134. Available at: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4433499&tool=pmcentrez&rendertype=abstract. Accessed 17 May 2016CrossRefPubMedPubMedCentralGoogle Scholar
  20. Rousseau-Gueutin M et al (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(4):2045–2060CrossRefPubMedPubMedCentralGoogle Scholar
  21. Sánchez-Sevilla JF et al (2015) Diversity arrays technology (DArT) marker platforms for diversity analysis and linkage mapping in a complex crop, the octoploid cultivated strawberry (Fragaria × ananassa) L. Lukens, ed. PLOS ONE 10(12):p.e0144960. Available at: http://dx.plos.org/10.1371/journal.pone.0144960 Accessed 26 May 2016CrossRefPubMedPubMedCentralGoogle Scholar
  22. Sansaloni C et al (2011) Diversity arrays technology (DArT) and next-generation sequencing combined: genome-wide, high throughput, highly informative genotyping for molecular breeding of Eucalyptus. BMC Proc 5(Suppl 7):P54. Available at: http://www.biomedcentral.com/1753-6561/5/S7/P54CrossRefPubMedCentralGoogle Scholar
  23. Sargent DJ et al (2006) An enhanced microsatellite map of diploid Fragaria. Theor Appl Genet 112(7):1349–1359. Available at: http://link.springer.com/article/10.1007/s00122-006-0237-y. Accessed 2 Apr 2015CrossRefPubMedGoogle Scholar
  24. Sargent DJ et al (2008) The development of a bin mapping population and the selective mapping of 103 markers in the diploid Fragaria reference map. Genome 51(2):120–127CrossRefPubMedGoogle Scholar
  25. Sargent DJ et al (2009) A genetic linkage map of the cultivated strawberry (Fragaria × ananassa) and its comparison to the diploid fragaria reference map. Mol Breeding 24(3):293–303CrossRefGoogle Scholar
  26. Sargent DJ et al (2012) A microsatellite linkage map for the cultivated strawberry (Fragaria × ananassa) suggests extensive regions of homozygosity in the genome that may have resulted from breeding and selection. Theor Appl Genet 124(7):1229–1240CrossRefPubMedGoogle Scholar
  27. Sargent DJ et al (2015) HaploSNP affinities and linkage map positions illuminate subgenome composition in the octoploid, cultivated strawberry (Fragaria × ananassa). Plant Sci 242:140–150CrossRefPubMedGoogle Scholar
  28. Shulaev V et al (2011) The genome of woodland strawberry (Fragaria vesca). Nat Genet 43(2):109–116. Available at: http://www.nature.com/ng/journal/v43/n2/full/ng.740.html. Accessed 3 June 2014
  29. Tennessen JA et al (2013) Targeted sequence capture provides insight into genome structure and genetics of male sterility in a gynodioecious diploid strawberry, Fragaria vesca ssp. bracteata (Rosaceae). G3: Genes|Genomes|Genetics 3(8):1341–1351. Available at: http://www.g3journal.org/content/3/8/1341. Accessed 16 Feb 2015
  30. Tennessen JA et al (2014) Evolutionary origins and dynamics of octoploid strawberry subgenomes revealed by dense targeted capture linkage maps. Genome Biol Evol 6(12):3295–3313. Available at: http://gbe.oxfordjournals.org/content/6/12/3295. Accessed 2 Feb 2015CrossRefPubMedPubMedCentralGoogle Scholar
  31. van Dijk T et al (2012) Microsatellite allele dose and configuration establishment (MADCE): an integrated approach for genetic studies in allopolyploids. BMC Plant Biol 12(1):25. Available at: http://bmcplantbiol.biomedcentral.com/articles/10.1186/1471-2229-12-25CrossRefPubMedPubMedCentralGoogle Scholar
  32. van Dijk T et al (2014) Genomic rearrangements and signatures of breeding in the allo-octoploid strawberry as revealed through an allele dose based SSR linkage map. BMC Plant Biol 14(1):55. Available at: http://bmcplantbiol.biomedcentral.com/articles/10.1186/1471-2229-14-55. Accessed 26 May 2016CrossRefPubMedPubMedCentralGoogle Scholar
  33. van Ooijen JW (2011) Multipoint maximum likelihood mapping in a full-sib family of an outbreeding species. Genet Res 93(5):343–349. Available at: http://www.ncbi.nlm.nih.gov/pubmed/21878144. Accessed 23 Apr 2016
  34. van Ooijen JW, Jansen J (2013) Genetic mapping in experimental populations. Cambridge University Press. Available at: https://books.google.co.uk/books?id=MfskAAAAQBAJ
  35. Vos P et al (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23(21):4407–4414CrossRefPubMedPubMedCentralGoogle Scholar
  36. Wu KK et al (1992) The detection and estimation of linkage in polyploids using single-dose restriction fragments. Theor Appl Genet 83(3):294–300. Available at: http://link.springer.com/article/10.1007/BF00224274. Accessed 2 Apr 2015
  37. Wu Y et al (2008) Efficient and accurate construction of genetic linkage maps from the minimum spanning tree of a graph. PLoS Genetics 4(10). Available at: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2556103/. Accessed 22 July 2014CrossRefPubMedPubMedCentralGoogle Scholar
  38. Zorrilla-Fontanesi Y, Cabeza A, Domínguez P, Medina JJ, Valpuesta V, Denoyes-Rothan B, Sánchez-Sevilla J.F et al (2011) Quantitative trait loci and underlying candidate genes controlling agronomical and fruit quality traits in octoploid strawberry (Fragaria × ananassa). Theor Appl Genet 123(5):755–778. Available at: http://link.springer.com/article/10.1007/s00122-011-1624-6. Accessed 29 Dec 2015CrossRefPubMedGoogle Scholar

Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  1. 1.NIAB EMREast MallingUK

Personalised recommendations