DNA Marker Analysis Reveals Genomic Diversity and Putative QTL Associated with Drupe Traits in Phyllanthus emblica L.

Abstract

Phyllanthus emblica L.(V. Nelli) is an important constituent of indigenous medicine and a commercially important fresh fruit species. The genomic diversity of the P. emblica germplasm in Sri Lanka has not been studied in detail. Therefore, the present study was conducted to molecularly characterize the P. emblica germplasm in Sri Lanka. Young tender leaves from 66 trees of P. emblica were collected from various parts of the country for DNA assessment. Genomic DNA was extracted using DNeasy Plant mini kit. Six microsatellite (SSR) markers and one SCAR marker developed for P. emblica were used in the PCR amplification. The PCR products were size separated by using 6% denaturing polyacrylamide gel electrophoresis. A binary scoring matrix was constructed on presence and absence of alleles in each single locus and a dendrogram based on genetic similarities was constructed. For each allele, allele frequency, heterozygosity and polymorphic information content were calculated. Cluster analysis was conducted based on marker data and association analysis was carried out to detect putative QTL associated with drupe traits. The dendrogram based on seven DNA marker alleles, showed two major clusters at 14.67% molecular similarity coefficient. A total of 51 alleles were detected in the sampled P. emblica germplasm with the six SSR markers and the SCAR marker used. Out of the six SSR markers, four were polymorphic, one was monomorphic and the other one did not produce clear bands. Heterozygosity of the tested markers ranged from 0.44. to 0.89. Allele at 176 bp of the marker Phyll112 showed a significant association (P<0.001 and P<0.0001) with commercially important traits such as drupe height, width, weight and mesocarp thickness. The P. emblica germplasm has a higher variation in Sri Lanka and this diversity can be used to develop genetically superior varieties in the future and also to dissect underlying molecular genetic mechanisms of drupe development.Ceylon Journal of Science (Bio. Sci.) 43 (2): 31-46, 2014