Comparative values of SSRs, SNPs and InDels for citrus genetic diversity analysis

SSRs have long been considered as almost ideal markers for genetic diversity analysis. With the increasingavailability of sequencing data, SNPs and InDels become major classes of codominant markers with genomewide coverage. We have analyzed the respective values of SSRs, InDels, and SNPs for intra and interspecificCitrus genetic diversity analysis. Moreover, we have compared the diversity structure revealed by markersmined in a single heterozygous genotype (the clementine) and markers mined in a large interspecific survey. A random set of 25 markers was selected for each marker class to genotype 48 citrus accessions. SSRs werethe most polymorphic markers at the intraspecific level allowing complete varietal differentiation within basictaxa (Citrus reticulata, Citrus maxima, Citrus medica). However, SSRs gave the lowest values for interspecificdifferentiation, followed by SNPs and InDels, that displayed low intraspecific variability but high interspecificdifferentiation. A clear effect of the discovery panel was observed for SNPs and InDels. The ascertainmentbiases associated with the clementine heterozygosity mining resulted mainly in an over estimation of withinC. reticulata diversity and an underestimation of the interspecific differentiation. Therefore SSRs are veryuseful for intraspecific structure analysis while SNPs and InDels mined in large discovery panel will be morepowerful to decipher the interspecific mosaic structure of secondary cultivated species.