Development and characterization of microsatellite markers, genetic diversity and population structure analysis in Sapota (Manilkara zapota (L.) P. Royen)

Manilkara zapota (L.) P. Royen, a widely adapted and popular tree meant for its appetizing fruits in tropics with no genomic resources like microsatellite markers. In order to develop genomic markers primarily for Sapota, the study sequenced partial genomic DNA using next generation sequencing technology on Illumina HiSeq 2500 platform. 3.3 Gb data assembled into 6,396,224 contigs were analysed. From these contigs, 3591 simple sequence repeats were identified. Among these different types of repeats, mononucleotide repeats (59.1%) were predominant followed by dinucleotide (28.6%) and trinucleotide repeats (8.2%). Primers were designed for 1285 microsatellite regions from which randomly selected 30 primers were standardized and employed for amplification in 53 genotypes of Sapota. Six hundred and ninty-two alleles were observed from 30 loci with a polymorphic information content that ranged from 0.85 to 0.96 with a mean of 0.9118. The Probability of Identity ranged from 0.002 to 0.043 with a mean of 0.012. The genetic diversity assessed by neighbour-joining and STRUCTURE assignment tests showed an admixed population with three groups. Analysis of molecular variance revealed a significant F st value of 0.69659 indicating high genetic differentiation among the 53 genotypes. Thus, the developed microsatellites will be advantageous in assessing genetic diversity, developing linkage map, and also molecular characterization of genotypes.

Automated summary

This study developed microsatellite markers for Sapota using next generation sequencing technology. They found a genetically diverse mixed population and demonstrated the importance of the developed microsatellites in assessing genetic diversity and molecular characterization.