scholarly journals Genetic diversity of Pongamia pinnata in Bali, Indonesia using Inter Simple Sequence Repeat markers

2019 ◽  
Vol 20 (8) ◽  
Author(s):  
Ni Luh Arpiwi ◽  
I Gusti Ayu Sugi Wahyuni ◽  
I Ketut Muksin
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Simple Sequence Repeat ◽  
Inter Simple Sequence Repeat ◽  
Pongamia Pinnata ◽  
Sequence Repeat ◽  
Binary Matrix ◽  
Simple Sequence Repeat Markers ◽  
Group I ◽  
Simple Sequence

Abstract. Arpiwi NL, Wahyuni IGAS, Muksin IK. 2019. Genetic diversity of Pongamia pinnata in Bali, Indonesia using Inter Simple Sequence Repeat markers. Biodiversitas 20: 2134-2142. Pongamia pinnata (L.) Pierre is a member of family Leguminosae that produces seed oil for biodiesel feedstock. The aim of the present study was to determine genetic diversity of pongamia trees that grow in Bali using Inter Simple Sequence Repeat (ISSR) markers. This study is important to support the breeding program for the improvement of the biodiesel producing species. Leaf samples were taken from 26 pongamia trees grown on northern and southern coastal areas of Bali. Genomic DNA was isolated from fresh leaves sample and was amplified by Polymerase Chain Reaction (PCR) using 9 ISSR primers. The banding patterns of DNA after PCR were scored and tabulated into a binary matrix. Genetic distance was generated by pairwise distance using composite maximum likelihood. A dendrogram was constructed using Unweighted Pair Group Method Arithmetic (UPGMA) method. The binary matrix was further analyzed for Nonmetric Multidimensional Scaling (NMDS) with Primer E V.6 software. DNA concentrations ranged from 98.59-100.55 ng/μL with sufficient quality for PCR. The number of alleles for 9 primers was 43, the number of the polymorphic band was 35, and the number of monomorphic bands was 8. Percentage of polymorphism ranged from 50 to 100%. Cluster analysis of 26 DNA of pongamia trees showed that the trees were grouped into two, namely group I and II. Group I consisted of two trees only, namely Uma Anyar 1 and Penarukan 1. Group II consisted of 24 pongamia trees which were divided into 3 subgroups, namely IIA, IIB, and IIC with close genetic distance. Analysis of NMDS supported cluster analysis that 23 out of 26 pongamia trees had close genetic distance, and possibly they come from a similar source. Genetic diversity of pongamia in Bali needs to be widen possibly by the introduction of new planting materials from across Indonesia or seed procurement from different sources.

scholarly journals Genetic diversity of Panax vietnamensis var. langbianensis populations in Lam Vien plateau - Vietnam detected by inter simple sequence repeat (ISSR) markers

2020 ◽  
Vol 17 (4) ◽  
pp. 651-661
Author(s):  
Le Ngoc Trieu ◽  
Nong Van Duy ◽  
Tran Van Tien
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Simple Sequence Repeat ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Sequence Repeat ◽  
New Variety ◽  
Gene Differentiation ◽  
The Stability ◽  
Simple Sequence

Panax vietnamensis var. langbianensis is a new variety from Lam Vien plateau of Vietnam. In this study, inter simple sequence repeat (ISSR) markers were employed to investigate the genetic diversity and variability of 115 individuals belonging to two naturally distributed populations of this variety, which classified by habitat. Genetic diversity at the taxon level was high (HeT = 0.284 and PPBT = 97.2 %).   The result showed lightly higher genetic diversity in population in Lac Duong region (HeLD= 0.228 and PPBLD = 81.5 %) as compared to those located in Dam Rong region (HeDR= 0.213 and PPBDR = 79.4 %). The interpopulation gene differentiation was high (GST Total = 0.221) with the genetic distance among populations was DLD-DR = 0.191. Gene flow within populations was Nm = 0.8793. In Lac Duong population, the genetic diversity of older group (HeLD O = 0.233; PPBLD O = 77.1%) was higher than of younger group (HeLD Y = 0.214; PPBLD Y = 72.4 %) and the intergroup gene differentiation was GSTDL = 0.0205 with the genetic distance between these two group was DLD O-Y  = 0.0061 showed the risk of reduction in genetic diversity. In Dam Rong population, the genetic diversity of older group (HeDR O = 0.204; PPBDR O = 75.2 %) was equal to younger group (HeDR Y = 0.209; PPBDR Y = 72.7 %) and the intergroup gene differentiation was GSTDR = 0.0304 with the genetic distance between them was DDR O-Y = 0.01393 showed the stability in genetic diversity. Data for genetic diversity and variation from this study can be used to further investigate and protect this variety for conservation and development purposes and for sustainable exploiting and use of these valuable natural resources.

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