F1-heterozygotes SNP calling concordance

To test the utility and accuracy of the 1k-RiCA to correctly called heterozygous genotypes, a set of 57 F₁ plants derived from six different bi-parental crosses; 8 from IRRI 154 / A69–1 (indica / japonica, with 441 polymorphic SNPs), 14 from A-69-1 / IR 4630-22-2-5-1-3 (japonica / indica, with 280 polymorphic SNPs), 19 from IR 4630-22-2-5-1-3 / CSR 28 (indica / indica, with 105 polymorphic markers), 4 from CSR 28 / MANAW THUKHA (indica / japonica, with 342 polymorphic SNPs), 10 from MANAW THUKHA / IRRI 154 (japonica / indica, with 385 polymorphic SNPs), and 2 from MS11 / A69–1 (japonica / japonica, with 395 polymorphic SNPs) were genotyped along with their parents. For each bi-parental cross, a ‘predicted F₁-genotype’ was generated by combining the SNPs haplotype from each homozygous parent into a genotypic profile of a pseudo-F₁ plant. The ‘predicted F₁-genotype’ was compared with the 1k-RiCA genotypes of each F₁ plant and SNP concordances were estimated by calculating the percentage of exact genotypic calls that are similar between the ‘predicted’ and empirical F₁ genotypes.