Exploitation of SSR, SRAP and CAPS-SNP markers for genetic diversity of Citrus germplasm collection

The present study was to assess informativeness and efficiency of three different molecular markers for genetic diversity among 24 Citrus and its relative species. Sixty one SSR, 33 SRAP and 24 CAPS-SNP markers were used to evaluate the level of polymorphism and discriminating capacity. A total of 596, 656 and 135 polymorphic amplicons were observed in SSR, SRAP and CAPS-SNP markers with average polymorphism information content (PIC) of 0.97, 0.98 and 0.89, respectively. High levels of polymorphism were recorded for SSR and SRAP compared with CAPS-SNP markers. The highest correlations (r = 0.930) were obtained between SSR and SRAP markers, whereas SSR and CAPS-SNP were poorly correlated (r = 0.833). Cluster analysis was performed to construct dendrograms using UPGMA. And the dendrogram from SSR data was most congruent with the general dendrogram. These findings provide basis for future efficient use of these molecular markers in the genetic analysis of Citrus and its relatives.

An unweighted pair-group method with arithmetic averages (UPGMA) dendrogram of genetic relationships among 24 genotypes of Citrus and its relative species based on the Dice similarity coefficients obtained using SSR, SRAP and CAPS-SNP combined data.Figure optionsDownload as PowerPoint slideResearch highlights
► A comparative investigation on the performance of SSR, SRAP and CAPS-SNP in the genus Citrus was conducted.
► PIC values were high in both SSR and SRAP compared with that in CAPS-SNP.
► The dendrogram from SSR data was more congruent with the general dendrogram.
► Combining different marker systems was better for diversity study of Citrus and its relatives.