Study of genetic relationship in some Citrus species using EST-SSRs developed by transcriptome sequencing of clementine

Microsatellite markers are important for phylogenetic and gene mapping studies. Several researches developed microsatellite markers (either genomic or transcriptomic) in different Citrus species during recent years. For the first time in this study, Clementine (Citrus clementina) deep transcriptome sequencing data was used for developing Citrus microsatellite markers. Primers were designed for some of these loci and their band patterns were assessed for phylogeny studies in 34 citrus genotypes. Totally 9082 SSRs were identified from 75659 Unigenes obtained from deep transcriptome sequencing of Clementine. Di- and tri- nucleotide repeats had the maximum frequencies respectively. A high number of developed EST-SSRs confirmed Next Generation Sequencing method to be highly efficiencent for molecular marker development. Totally 25 microsatellite loci were selected for primer designing. From these totally 65 alleles obtained with average of 4.25 alleles and 2.53 effective alleles per locus. The average of Polymorphic Information Content (PIC) was 0.48 and the highest PIC observed for ABRII7 and ABRII9. Phylogenetic study for 34 Citrus genotypes was done based on NJ algorithem and Uncorrected P distance. All of genotypes located in 4 groups: Pummelo, Citon, Mandarin and Trifoliate orange. This classification was similar to those obtained by previous studies illustrateed a high efficiency of microsatellite markers developed using deep transcriptome sequencing.