Genetic diversity analysis of rambutan (Nephelium lappaceum L.) accessions using molecular markers
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Date
2023-09-12
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Department of fruit science, College of agriculture ,Vellayani
Abstract
Rambutan (Nephelium lappaceum L.) holds great potential in Kerala being a tropical region. It belongs to the Sapindaceae family, which consists of numerous trees and shrubs, comprising over 125 genera and more than 1000 species that are found across the tropics and warm regions. These plants are adaptable to various soil types, ranging from heavy soils in low-lying areas to hilly soils in upland regions. The origin of rambutan can be traced back to Southeast Asia, specifically Indonesia and Malaysia. Rambutan cultivation is rapidly expanding along India's western coast, particularly in the districts of Pathanamthitta, Kottayam, and Thrissur of Kerala. Even though morphological characterization and diversity studies of the collections from various localities in Kerala have been carried out, the genetic diversity analysis using molecular markers has not yet been conducted. Hence, the current research titled "Genetic diversity analysis of rambutan (Nephelium lappaceum L.) accessions using molecular markers" was conducted at the Regional Agricultural Research Station Kumarakom and at the Department of Fruit Science, College of Vellayani between 2020 and 2022. The main objective of this study was to assess the diversity of twenty rambutan accessions using SSR and ISSR molecular markers collected from the districts of Kottayam, Pathanamthitta, and Thrissur. DNA isolation was performed using the CTAB method (Doyle and Doyle,1987) with minor modifications. A pre-washing with sorbitol buffer was done to improve the DNA quality. The DNA samples showed UV absorbance ratios (A260/A280) between 1.80 and 1.95 indicating their purity. The initial primer screening was conducted with thirty ISSR and sixteen SSR primers. Based on their ability to yield reproducible and distinct banding patterns, eleven ISSR and five SSR primers were selected for subsequent analysis. The ISSR primers used in the study exhibited a polymorphism percentage ranging from 55.56% (ISSR 10 ) to 100% (ISSR-1 and UBC 828), with an average value of 79.44%. On the other hand, the selected SSR primers displayed a 100% polymorphism percentage. The Polymorphic Information Content (PIC) values ranged from 0.12 (UBC-819) to 0.41 (ISSR-23) for ISSR markers and from 0.60 (NlaSSR 7) to 0.72 (NlaSSR 23) for SSR markers. PIC is an indication of the informativeness of the primers. The Marker index (MI) which measures the utility of the primers ranged between 0.36 (UBC 819) to 2.88 (UBC 825) for ISSR markers and it varied between 1.80(NlaSSR 7) to 2.88 (NlaSSR 23) for SSR markers. The diversity analysis of rambutan accessions was performed using the NTSYS-Pc software. In the UPGMA (Unweighted Pair Group Method with Arithmetic Mean) cluster analysis based on ISSR data, the rambutan accessions were divided into two distinct clusters at a similarity coefficient of 0.61 with 10 accessions in each cluster. The Col.03 and Col.53 were found to be closely related with a similarity of 71%. In the SSR data-based cluster analysis, the rambutan accessions were divided into two major clusters at a similarity coefficient of 0.70. Cluster I comprised a total of eight rambutan accessions and Cluster II included the remaining twelve genotypes. The highest similarity of 67% was observed between Col.87 and Col.97, Col. 81 and Col.86, Col.04 and Col.52, and Col.48 and Col.15. In the combined SSR-ISSR cluster analysis, at a similarity coefficient of 0.62, the rambutan accessions were divided into two clusters, showing a similar dendrogram pattern as observed in the ISSR data-based dendrogram. The Principal Coordinate Analysis (PCoA) also revealed a similar pattern of distribution of the accessions as recorded in cluster analysis.The results of the present study revealed that the accessions studied had genetic diversity ranging from 61% to 70% under different marker systems. The accessions from the same area have shown a closer genetic distance, suggesting that dispersal from related parents may have occurred. In future crop improvement programmes for this exotic crop, existing germplasm from different locations of the state and molecular analysis employing more markers can be exploited. Identification of markers associated with economically important trails will be useful for marker assisted breeding programmes. The current study on genetic diversity using molecular markers is the first of its type in Kerala and hence can be considered as a basic information for future related works.