Maize SNP Markers


  • Ganal 2011 reported the establishment of a large maize SNP array and its use for diversity analysis and high density linkage mapping. The markers, taken from more than 800,000 SNPs, were selected to be preferentially located in genes and evenly distributed across the genome. A total of 49,585 markers, including 33,417 within 17,520 different genes and 16,168 outside genes. Table.
  • Yan 2010 developed a custom GoldenGate assay containing 1,536 SNPs based on available SNP information for maize and used to genotype two recombinant inbred line (RIL) populations (Zong3 x 87-1, and B73 x By804) and a panel of 154 diverse inbred lines. A total of 975 SNP markers detected polymorphism in at least one of the two mapping populations, with a polymorphic rate of 38.5% in Zong3 x 87-1 and 52.6% in B73 x By804. Table.
  • Jones 2009 mined 1,088 loci sequenced across 60 public inbreds that have been used in maize breeding in North America and Europe and then selected 640 SNPs using generalized marker design criteria that enable utilization with several SNP chemistries. While SNPs were found on average every 43 bases in 1,088 maize gene sequences, SNPs that were amenable to marker design were found on average every 623 bases; representing only 7% of the total SNPs discovered.
  • Using 102,551 maize (Zea mays) EST sequences a total of 14,832 candidate polymorphisms were identified by Jacqueline Batley and group with an SNP redundancy score of two or greater. Segregation of these SNPs with haplotype indicates that candidate SNPs with high redundancy and cosegregation confidence scores are likely to represent true SNPs. This was confirmed by validation of 264 candidate SNPs from 27 loci, with a range of redundancy and co-segregation scores, in four inbred maize lines.
  • Vroh Bi 2006 reported 311 (133 SNP and 178 InDel) loci using 592 unigenes. These 311 markers were mapped on the intermated B73 × Mo17 (IBM) high-resolution mapping population.
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