scholarly journals Genetic diversity and relationships among Chinese Eucommia ulmoides cultivars revealed by sequence-related amplified polymorphism, amplified fragment length polymorphism, and inter-simple sequence repeat markers

2014 ◽  
Vol 13 (4) ◽  
pp. 8704-8713 ◽  
Author(s):  
Y. Li ◽  
S.H. Wang ◽  
Z.Q. Li ◽  
C.F. Jin ◽  
M.H. Liu
Keyword(s):  
Genetic Diversity ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Simple Sequence Repeat ◽  
Fragment Length Polymorphism ◽  
Inter Simple Sequence Repeat ◽  
Eucommia Ulmoides ◽  
Sequence Repeat ◽  
Simple Sequence Repeat Markers ◽  
Simple Sequence

Genetic diversity among Japanese indigenous common buckwheat (Fagopyrum esculentum) cultivars as determined from amplified fragment length polymorphism and simple sequence repeat markers and quantitative agronomic traits

Genome ◽  
2005 ◽  
Vol 48 (3) ◽  
pp. 367-377 ◽  
Author(s):  
Hiroyoshi Iwata ◽  
Kenta Imon ◽  
Yoshihiko Tsumura ◽  
Ryo Ohsawa
Keyword(s):  
Genetic Diversity ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Simple Sequence Repeat ◽  
Allelic Richness ◽  
Fragment Length Polymorphism ◽  
Agronomic Traits ◽  
Sequence Repeat ◽  
Common Buckwheat ◽  
Simple Sequence

We assessed the genetic diversity in Japanese indigenous common buckwheat (Fagopyrum esculentum) cultivars using amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) markers and investigated the relationships between the genetic diversity and agronomic traits. The average expected intracultivar hetero zygosity was 0.303 for AFLP and 0.819 for SSR. The differentiations among agroecotypes, among cultivars within an agroecotype, and among cultivars were small (0.002, 0.024, and 0.026 for SSR and 0.013, 0.013, and 0.026 for AFLP, respectively) but statistically significant from zero except for the SSR differentiation among agroecotypes. In principal coordinates analysis, cultivars within the same agroecotype tended to cluster, indicating that agroecotypes well reflected the genetic relationships among cultivars. In AFLP, the differentiation among the agroecotypes was more distinct than in SSR, and genetic distance showed a moderate correlation with the difference in quantitative traits, indicating that AFLP can resolve the relationships among cultivars with better resolution than SSR. By contrast, SSR may be more sensitive to demographic changes. Four of the five SSR markers showed a significant positive correlation (Kendall's τ = 0.382–0.607) between allelic richness and variation in flowering timing, indicating that cumulative bottleneck events have occurred during the population history, with a decline in the variation of photosensitivity of flowering.Key words: agroecotype, coefficient of gene differentiation, genetic distance, allelic richness, photosensitivity of flowering.

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.

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