Analyses of genetic diversity and drupe size QTLs in 𝘗𝘩𝘺𝘭𝘭𝘢𝘯𝘵𝘩𝘶𝘴 𝘦𝘮𝘣𝘭𝘪𝘤𝘢 𝘓. using DNA markers

Abstract

𝘗𝘩𝘺𝘭𝘭𝘢𝘯𝘵𝘩𝘶𝘴 𝘦𝘮𝘣𝘭𝘪𝘤𝘢 𝘓. (V. Nelli) is a medicinally and commercially important fresh fruit species. Yet it remains as an underutilized fruit crop to date. There is a significant diversity in this germplasm in relation to drupe traits which can be exploited to breed superior cultivars. However, the genomic diversity of 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 were collected from 66 trees of 𝘗. 𝘦𝘮𝘣𝘭𝘪𝘤𝘢 from various parts of Kandy, Kurunegala and Anuradhapura districts of Sri Lanka. Genomic DNA was extracted using QiaGen DNeasy Plant mini kit. Six microsatellite markers and one SACR marker developed for 𝘗. 𝘦𝘮𝘣𝘭𝘪𝘤𝘢 were used for PCR amplification of the sampled 𝘗. 𝘦𝘮𝘣𝘭𝘪𝘤𝘢 germplasm. The PCR products of the DNA samples of 66 𝘗. 𝘦𝘮𝘣𝘭𝘪𝘤𝘢 trees were then size separated by using 6 % denaturing polyacrylamide gel electrophoresis. Different alleles for each marker were visually identified in base pairs and a binary scoring matrix was built for all the markers. For each allele, allele frequency, heterozygosity and polymorphic information content were calculated. Cluster analysis was conducted based on marker data and association analysis was done to detect putative QTLs associated with drupe traits.

The dendrogram based on seven DNA marker alleles, showed three major clusters at 46.39 % genetic similarity coefficient without showing any biasness based on sampling location. A total of 51 alleles were detected for the sampled 𝘗. 𝘦𝘮𝘣𝘭𝘪𝘤𝘢 germplasm for the six microsatellite markers and SCAR marker tested. Out of the six microsatellite markers, four were polymorphic and one was monomorphic. Heterozygosity of the tested markers ranged from 0.89 to 0.44. Out of those markers highest significant association (𝘗 < 0.001 and 𝘗 < 0.0001) with commercially important traits drupe height, width, weight and mesocarp thickness was shown by the marker 𝘗𝘩𝘺𝘭𝘭 112, alleles 175 bp, 176 bp and 178 bp. 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. The putative QTLs can be used for marker assisted selection in breeding and for molecular screening of seedlings for drupe traits of commercial importance.