Gazel M Gaddafi
Genetic diversity analysis of rambutan (Nephelium lappaceum L.) accessions using molecular markers - Vellayani Department of fruit science, College of agriculture 2023 - 82p.
MSc
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.
(Nephelium
Fruit science
Nephelium lappaceum L
Deoxyribonucleic acid
634.1 / GAZ/GE PG
Genetic diversity analysis of rambutan (Nephelium lappaceum L.) accessions using molecular markers - Vellayani Department of fruit science, College of agriculture 2023 - 82p.
MSc
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.
(Nephelium
Fruit science
Nephelium lappaceum L
Deoxyribonucleic acid
634.1 / GAZ/GE PG