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Manilkara zapota (L.) P. Royen, commonly known as sapota, a widely adaptable and popular evergreen tree meant for its appetizing fruits in tropics, but lacks genomic resources such as microsatellite markers. To develop the genomic markers for M. zapota, we sequenced the partial genomic DNA using next-generation sequencing technology on the Illumina HiSeq 2500 platform. We analysed a total of 3.33 Gb data that were assembled into 6,396,224 contigs, from which 3591 simple sequence repeats were identified. Among the different type of repeats, mononucleotide repeats (59.1%) were predominant, followed by dinucleotide (28.6%) and trinucleotide repeats (8.2%). Primers were designed for 1285 M. zapota microsatellite regions from which 30 randomly selected primers were standardized and employed for amplification of 53 genotypes. We observed 692 alleles from 30 loci with a polymorphic information content ranging from 0.85 to 0.96, a mean of 0.9118. The probability of identity ranged from 0.002 to 0.043 with a mean of 0.012. Genetic diversity assessed by neighbour-joining and STRUCTURE assignment tests showed an admixed population with three groups. Analysis of molecular variance revealed a significant Fst value of 0.69659, indicating a high genetic differentiation among the 53 genotypes. The microsatellites developed here will be beneficial for assessing the genetic diversity, developing linkage map and also molecular characterization of genotypes. |
