Assignment of SNP allelic configuration in polyploids using Competitive Allele-Specific PCR: application to triploid citrus progenies

Abstract

Estimation of DNA allele doses in polyploid genotypes is essential to assign the allelic configuration for the different types of heterozygosity for parents and segregating progenies. It is of special interest in citrus with the implementation of extensive triploid breeding programs to develop new seedless varieties. Single nucleotide polymorphisms (SNPs) are becoming the most important class of molecular markers and we have tested the potential 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 proportions to test the accuracy of the technique for quantitative analysis. All analyzed 7 SNPs provided clear clustering related with allele doses. DNA mixes at intermediary proportions revealed high correlation coefficients between observed and expected data (mean = 0.9796; sd = 0.0094). For all SNPs, separated cluster analyses and ANOVA from mixed DNA data formed all expected homogeneous groups, with correct assignation for practically all samples. Moreover, two triploid populations were easily genotyped and results were in agreement with expected segregations. KASPar technology is a routine and a cost-effective technique to assess the allele doses at the DNA level, which is especially interesting in citrus triploid breeding programs. Moreover, it could be also used to correlate genomic and transcriptomic doses in allele specific expression analyses. (Résumé d'auteur