Abstract
The advent of Next-Generation sequencing-by-synthesis technologies has fuelled SNP discovery, genotyping, and screening of populations in myriad ways for many species, including various plant species. One technique widely applied to screening a large number of SNP markers over a large number of samples is the Illumina Infinium™ assay.
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References
The Potato Genome Sequencing Consortium (2011) Genome sequence and analysis of the tuber crop potato. Nature 475:189–195
Chagné D, Crowhurst RN, Troggio M et al (2012) Genome-wide SNP detection, validation, and development of an 8 k SNP array for apple. PLoS One 7:e31745
Syvanen AC (2005) Toward genome-wide SNP genotyping. Nat Genet 37:S5–S10
Myles S, Boyko AR, Owens CL et al (2011) Genetic structure and domestication history of the grape. Proc Natl Acad Sci U S A 108:3530–3535
Myles S, Chia J-M, Hurwitz B et al (2010) Rapid genomic characterization of the genus Vitis. PLoS One 5:e8219
Kumar S, Chagné D, Bink MCAM et al (2012) Genomic selection for fruit quality traits in apple (Malus x domestica Borkh.). PLoS One 7:e36674
Antanaviciute L, Fernandez-Fernandez F, Jansen J et al (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
Bachlava E, Taylor CA, Tang S et al (2012) SNP discovery and development of a high-density genotyping array for Sunflower. PLoS One 7:e29814
Bowers JE, Bachlava E, Brunick RL et al (2012) Development of a 10,000 locus genetic map of the sunflower genome based on multiple crosses. G3-Genes Genomes. Genetics 2:721–729
Hamilton JP, Hansey CN, Whitty BR et al (2011) Single nucleotide polymorphism discovery in elite north american potato germplasm. BMC Genomics 12:302
Felcher KJ, Coombs JJ, Massa AN et al (2012) Integration of two diploid potato linkage maps with the potato genome sequence. PLoS One 7:e36347
Matukumalli LK, Lawley CT, Schnabel RD et al (2009) Development and characterization of a high density SNP genotyping assay for cattle. PLoS One 4:e5350
Peace C, Bassil N, Main D et al (2012) Development and evaluation of a genome-wide 6K SNP array for diploid sweet cherry and tetraploid sour cherry. PLoS One 7:e48305
Thomson MJ, Zhao K, Wright M et al (2012) High-throughput single nucleotide polymorphism genotyping for breeding applications in rice using the BeadXpress platform. Mol Breed 29:875–886
Verde I, Bassil N, Scalabrin S et al (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
Sim S-C, Durstewitz G, Plieske J et al (2012) Development of a large SNP genotyping array and generation of high-density genetic maps in tomato. PLoS One 7:e40563
Velasco R, Zharkikh A, Affourtit J et al (2010) The genome of the domesticated apple (Malus x domestica Borkh.). Nat Genet 42:833–839
Marco-Sola S, Sammeth M, Guigo R, Ribeca P (2012) The GEM mapper: fast, accurate and versatile alignment by filtration. Nat Methods 9:1185–1188
Homer N, Merriman B, Nelson SF (2009) BFAST: an alignment tool for large scale genome resequencing. PLoS One 4:A95–A106
Li H, Handsaker B, Wysoker A et al (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25:2078–2079
Danecek P, Auton A, Abecasis G et al (2011) The variant call format and VCFtools. Bioinformatics 27:2156–2158
Li R, Li Y, Kristiansen K, Wang J (2008) SOAP: short oligonucleotide alignment program. Bioinformatics 24:713–714
Ganal MW, Durstewiz G, Polley A et al (2011) A large maize (Zea mays L.) SNP genotyping array: development and germplasm genotyping, and genetic mapping to compare with the B73 reference genome. PLoS One 6:e28334
Teo YY, Inouye M, Small KS et al (2007) A genotype calling algorithm for the Illumina BeadArray platform. Bioinformatics 23:2741–2746
Giannoulatou E, Yau C, Colella S et al (2008) GenoSNP: a variational Bayes within-sample SNP genotyping algorithm that does not require a reference population. Bioinformatics 24:2209–2214
Carvalho B, Bengtsson H, Speed TP, Irizarry RA (2007) Exploration, normalization, and genotype calls of high-density oligonucleotide SNP array data. Biostatistics 8:485–499
Ritchie ME, Carvalho BS, Hetrick KN et al (2009) R/Bioconductor software for Illumina's Infinium™ whole-genome genotyping BeadChips. Bioinformatics 25:2621–2623
Ankerst M, Breunig MM, Kriegel HP, Sander J (1999) OPTICS: ordering points to identify the clustering structure. ACM SIGMOD international conference on management of data. ACM Press, New York, pp 49–60
Douches D, Coombs J, Merk HL (2012) How to develop SNP-based tetraploid maps for Potato. http://www.extension.org/pages/63187/how-to-develop-snp-based-tetraploid-maps-for-potato. Webinar. Accessed 8 April 2013
Voorrips RE, Gort G, Vosman B (2011) Genotype calling in tetraploid species from bi-allelic marker data using mixture models. BMC Bioinformatics 12:172
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Chagné, D., Bianco, L., Lawley, C., Micheletti, D., Jacobs, J.M.E. (2015). Methods for the Design, Implementation, and Analysis of Illumina Infinium™ SNP Assays in Plants. In: Batley, J. (eds) Plant Genotyping. Methods in Molecular Biology, vol 1245. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-1966-6_21
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DOI: https://doi.org/10.1007/978-1-4939-1966-6_21
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