Development of CAPS markers and their application in breeding for mango, Mangifera indica L.

To develop cleaved amplified polymorphic sequence (CAPS) markers for the identification of true hybrids in F1 progeny, we cloned sucrose synthase (SS) and sucrose phosphate synthase (SPS) genes from 19 mango cultivars. Through comparison of amino acid sequences in a BLASTX search, cloned SS and SPS genes were found to be homologs of Citrus unshiu CitSUS1 (AB022092) and CitSPS1 (O22060), respectively. Therefore, we designated the SS and SPS genes as MiSUS1 and MiSPS1, respectively. There were 11 genotypes in MiSUS1 and 10 in MiSPS1 sequences. In the MiSUS1 nucleotide sequences, 46 SNPs and 5 in/dels were detected. Twenty-six out of the 46 SNPs mapped on the restriction enzyme recognition sites were successfully converted to 25 CAPS markers. In the MiSPS1 nucleotide sequences, 99 SNPs and 6 in/dels were detected. Thirty out of 99 SNPs and 2 out of 6 in/dels mapped on the recognition sites were also converted to 32 CAPS markers. By using two CAPS markers, SS-2798 and SPS-5745, we identified 37 true hybrids that had different genotypes to ‘Irwin’ from 82 F1 progeny obtained through a cross between ‘Irwin’, the maternal parent, and paternal parents by using flies as pollinators. The method developed here to identify true hybrids is a simple, rapid and highly reliable tool for efficient mango breeding.