Assignment of SNP allelic configuration in polyploids using Competitive Allele-Specific PCR: applica

Estimation of DNA allele doses in polyploid genotypes is essential to assign the allelic configuration for thedifferent types of heterozygosity for parents and segregating progenies. It is of special interest in citrus with theimplementation of extensive triploid breeding programs to develop new seedless varieties. Single nucleotidepolymorphisms (SNPs) are becoming the most important class of molecular markers and we have tested thepotential of KASPar technology (based on competitive allele-specific PCR) to infer allele doses of SNP markers in polyploid citrus. DNAs from haploids Citrus clementina and Citrus maxima were mixed at different proportionsto test the accuracy of the technique for quantitative analysis. All analyzed 7 SNPs provided clear clusteringrelated with allele doses. DNA mixes at intermediary proportions revealed high correlation coefficients betweenobserved and expected data (mean = 0.9796; sd = 0.0094). For all SNPs, separated cluster analyses and ANOVAfrom mixed DNA data formed all expected homogeneous groups, with correct assignation for practicallyall samples. Moreover, two triploid populations were easily genotyped and results were in agreement withexpected segregations. KASPar technology is a routine and a cost-effective technique to assess the allele dosesat the DNA level, which is especially interesting in citrus triploid breeding programs. Moreover, it could be alsoused to correlate genomic and transcriptomic doses in allele specific expression analyses.