Abstract
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.
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NGS data have been submitted to NCBI with accession ID SRP127995.
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Acknowledgements
Authors acknowledge funding support from ICAR-AICRP on Fruits and ICAR-IIHR, Bengaluru, India.
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This study was funded by ICAR-AICRP on Fruits and ICAR-IIHR, Bengaluru.
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Project was conceptualized by KVR, PP. Sample Preparation, experiments and data analysis were carried out by NSP, KVR, NSP, IP, ARP, RB, AMS, AR and PP. KVR, PP, AR and NSP were involved in discussion of data and MS preparation.
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Sathanandam, P.N., Patil, P., Rekha, A. et al. Development and characterization of microsatellite markers, genetic diversity and population structure analysis in Sapota (Manilkara zapota (L.) P. Royen). Genet Resour Crop Evol 69, 2787–2801 (2022). https://doi.org/10.1007/s10722-022-01399-2
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DOI: https://doi.org/10.1007/s10722-022-01399-2