High-throughput SNP genotyping with the GoldenGate assay in maize uri icon

abstract

  • Single nucleotide polymorphisms (SNPs) are abundant and evenly distributed throughout the genomes of most plant species. They have become an ideal marker system for genetic research in many crops. Several high throughput platforms have been developed that allow rapid and simultaneous genotyping of up to a million SNP markers. In this study, a custom GoldenGate assay containing 1,536 SNPs was developed based on public 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. Over 90% of the SNPs were successfully scored in the diversity panel and the two RIL populations, with a genotyping error rate of less than 2%. 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. The polymorphic SNPs in B73 x By804 have been integrated with previously mapped simple sequence repeat markers to construct a high-density linkage map containing 662 markers with a total length of 1,673.7 cM and an average of 2.53 cM between two markers. The minor allelic frequency (MAF) was distributed evenly across 10 continued classes from 0.05 to 0.5, and about 16% of the SNP markers had a MAF below 10% in the diversity panel. Polymorphism rates for individual SNP markers in pair-wise comparisons of genotypes tested ranged from 0.3 to 63.8% with an average of 36.3%. Most SNPs used in this GoldenGate assay appear to be equally useful for diversity analysis, marker-trait association studies, and marker-aided breeding.
  • Single nucleotide polymorphisms (SNPs) are abundant and evenly distributed throughout the genomes of most plant species. They have become an ideal marker system for genetic research in many crops. Several high throughput platforms have been developed that allow rapid and simultaneous genotyping of up to a million SNP markers. In this study, acustom GoldenGate assay containing 1,536 SNPs was developed based on public 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. Over 90% of the SNPs were successfully scored in the diversity panel and the two RIL populations, with agenotyping error rate of less than 2%. 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. The polymorphic SNPs in B73 x By804 have been integrated with previously mapped simple sequence repeat markers to construct a high-densitylinkage map containing 662 markers with a total length of 1,673.7 cM and an average of 2.53 cM between two markers. The minor allelic frequency (MAF) was distributed evenly across 10 continued classes from 0.05 to 0.5, and about 16% of the SNP markers had a MAF below 10% in the diversity panel. Polymorphism rates for individual SNP markers in pair-wise comparisons of genotypes tested ranged from 0.3 to 63.8% with an average of 36.3%. Most SNPs used in this GoldenGate assay appear to be equally useful for diversity analysis, marker-trait association studies, and marker-aided breeding
  • Single nucleotide polymorphisms (SNPs) are abundant and evenly distributed, and they have become an ideal marker system for genetic research in many organisms. Several high throughput platforms have been developed that allow genotyping thousands to a million markers in parallel. In this study, a custom GoldenGate assay containing 1536 SNPs was developed based on public SNP information for maize and used to genotype two recombinant inbred line (RIL) populations (Zong3x87-1 and B73xBy804) and a diversity panel consisting of 154 inbred lines. After scoring, 92% (1414/1536) and 91% (1393/1536) of the SNPs were successfully identified (called) in the diversity panel and two RIL populations respectively, with a genotyping error rate of less than 2%. Of the 1393 successfully called SNPs, 975 SNPs were polymorphic in at least one of the two mapping populations with a polymorphism rate of 38.5% in Zong3x87-1 and 52.6% in B73xBy804. The identified polymorphic SNPs were integrated with previously mapped SSR markers to construct two high-density linkage maps. Alleles with a low frequency were distributed evenly in the 10 continued classes from 0.05 to 0.5 and about 16% of the SNPs had a minor allelic frequency (MAF) of less than 10% in the diversity panel. Polymorphism rates ranged from 0.3% to 63.8% in any two given lines with an average of 36.3%. Because most of the SNPs in the present GoldenGate assay were not present in the low frequency classes, they can be used for QTL mapping, diversity analysis, marker-trait association studies, and marker assisted breeding. The high success rate for SNP calling also implies that the GoldenGate assay platform can be used with diverse maize germplasm. Issues for successful utilization of the GoldenGate assay in maize genomic research are discussed

publication date

  • 2010
  • 2010
  • 2010
  • 2010