A high-throughput apple SNP genotyping platform using the GoldenGate™ assay.
EST data generated from 14 apple genotypes were downloaded from NCBI and mapped against a reference EST assembly to identify Single Nucleotide Polymorphisms (SNPs). Mapping of these SNPs was undertaken using 90% of sequence similarity and minimum coverage of four reads at each SNP position. In total, 37,807 SNPs were identified with an average of one SNP every 187 bp from a total of 6888 unique EST contigs. Identified SNPs were checked for flanking sequences of ≥ 60 bp along both sides of SNP alleles for reliable design of a custom high-throughput genotyping assay. A total of 12,299 SNPs, representing 6525 contigs, fit the selected criterion of ≥ 60 bp sequences flanking a SNP position. Of these, 1411 SNPs were validated using four apple genotypes. Based on genotyping assays, it was estimated that 60% of SNPs were valid SNPs, while 26% of SNPs might be derived from paralogous regions.
Department of Natural Resources & Environmental Sciences, University of Illinois, Urbana, IL 61801, USA.
M Awais
MA
Khan
Yuepeng
Y
Han
Youfu Frank
YF
Zhao
Schuyler S
SS
Korban
D002874:Chromosome Mapping; D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D017343:Genes, Plant; D005819:Genetic Markers; D005838:Genotype; D027845:Malus / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide
D005819:Genetic Markers