SNP Detection by Using Affymetix Barley 1 Array in Barley

Pei Guo Guo; Rong Hua Li; Nicoló Salvato; Michele Filosi; Yan Shi Xia

doi:10.4028/www.scientific.net/AMR.641-642.803

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HomeAdvanced Materials ResearchAdvanced Materials Research Vols. 641-642SNP Detection by Using Affymetix Barley 1 Array in...

SNP Detection by Using Affymetix Barley 1 Array in Barley

Abstract:

Nowadays the research for discovering SNPs is becoming one of the most important topics to understand the differences between genotypes of the same species. The objective of this study is to discover the SNPs using oligonucleotide microarrays in barley. Two methods are used for the prediction step: one is Robustified Projection Pursuit (RPP) method and another is based on a statistic test between probes of a probeset belonging different genotypes. Following the procedure described above, 124 single feature polymorphisms (SFPs), which can be used for identification of SNPs or insertion/deletions (INDELs), were detected among all genotypes. Sequencing of putative SFP-containing amplicons from the EST region in the genome yielded a validation rate of 85%, indicating the Affymetrix Barley 1 array could provide a satisfactory platform for identification of SNP in barley.

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Periodical:

Advanced Materials Research (Volumes 641-642)

Pages:

803-807

DOI:

https://doi.org/10.4028/www.scientific.net/AMR.641-642.803

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Online since:

January 2013

Authors:

Pei Guo Guo, Rong Hua Li, Nicoló Salvato, Michele Filosi, Yan Shi Xia

Keywords:

Barley 1 Genechip, Robustified Projection Pursuit Method, SNP Detection

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