Table 1 Candidate SNPs chosen for KASP assays
From: Development of a core SNP arrays based on the KASP method for molecular breeding of rice
Subset | Characters of SNPs | No. of SNPs | No. of assay successfully-designed | No. of core SNPs | Assay design success rate |
|---|---|---|---|---|---|
1 | Subgrouping or quality control related | 61 | 59 | 57 | 96.7 |
2 | Indica/Indica variation related | 64 | 62 | 60 | 96.8 |
3 | SNPs with high polymorphism information content (PIC) | 53 | 52 | 51 | 98.1 |
4 | Functional nucleotide polymorphisms (FNPs) | 21 | 18 | 14 | 85.7 |
5 | Targeting site of cloned genes | 95 | 90 | 86 | 94.7 |
6 | SNPs overlapped gene interval | 173 | 156 | 113 | 90.1 |
7 | Reliable SNP in GWAS | 33 | 32 | 31 | 97.0 |
8 | Gap filling SNP | 96 | 96 | 55 | 100.0 |
| Â | Total | 596 | 565 | 467 | 94.8 |