scholarly journals Genetic Diversity Analysis of Jatropha Curcas Provenances Using Randomly Amplified Polymorphic DNA Markers

2011 ◽  
Vol 7 (1) ◽  
pp. 47 ◽  
Author(s):  
Dani Satyawan ◽  
I Made Tasma
Keyword(s):  
Genetic Diversity ◽  
Dna Markers ◽  
Jatropha Curcas ◽  
Group Method ◽  
Diversity Analysis ◽  
Similarity Coefficients ◽  
Improvement Program ◽  
Genetic Diversity Analysis ◽  
Chain Reactions ◽  
Pair Group

<p>Genetic Diversity Analysis of Jatropha Curcas<br />Provenances Using Randomly Amplified Polymorphic<br />DNA Markers. Dani Satyawan and I Made Tasma.<br />Jatropha curcas nuts are rich in oil that is higly suitable for<br />Hak Cipta © 2011, BB-Biogen<br />the production of bio-diesel or to be used directly in<br />modified diesel engines. The objective of this study was to<br />assess the extent of genetic diversity among 50 J. curcas<br />provenances and one accession of J. integerrima using<br />RAPD markers. The fifty J. curcas provenances were<br />collected from ecologically diverse regions of Indonesia, and<br />planted in the Pakuwon Experimental Station (Sukabumi,<br />West Java). Fourteen RAPD primers with 60-80% G+C<br />content were used in this genetic diversity analysis and<br />produced 64 bands with 95.7% polymorphism level. The<br />Polymerase Chain Reactions used to generate the RAPD<br />bands sometimes produced inconsistent and nonreproducible<br />results, necessitating the duplication of each<br />reaction to prevent scoring errors. Sixty one validated bands<br />were subsequently used for genetic diversity analysis using<br />Unweighted Pair Group Method Arithmetic (UPGMA)<br />method and Dice coefficients. It was shown that the<br />similarity coefficients among the provenances ranged from<br />0.2 to 0.98 with an average similarity of 0.75. Dendrogram<br />analysis produced two major groups of provenances, with<br />one outlier from South Lampung. There was no tendency for<br />provenances originated from nearby regions to cluster<br />together in each group, and several provenances showed<br />more similarities with provenances originated from distant<br />regions. This pattern lent credence to reports that Jatropha<br />was introduced to Indonesia around four centuries ago and<br />was mainly spread by humans. Based on the mean<br />similarities among the accessions and their clustering<br />pattern, the genetic diversity of the Jatropha collection<br />appeared to be fairly low. Future additions of genetic<br />materials from more diverse genetic background will be<br />necessary to maintain the current progress of Jatropha<br />improvement program.</p>

scholarly journals Genetic Diversity Analysis of Aluminum-toxicity Tolerant and Sensitive Soybean Genotypes Assessed with Microsattelite Markers

2009 ◽  
Vol 5 (1) ◽  
pp. 1
Author(s):  
I Made Tasma ◽  
Ahmad Warsun
Keyword(s):  
Genetic Diversity ◽  
Numerical Taxonomy ◽  
Aluminum Toxicity ◽  
Group Method ◽  
Diversity Analysis ◽  
Multivariate System ◽  
Genetic Diversity Analysis ◽  
Pair Group ◽  
Soybean Genotypes

<p>Analisis Diversitas Genetik Genotipe Kedelai Toleran dan<br />Peka Keracunan Aluminium Menggunakan Marka Mikrosatelit.<br />I Made Tasma dan Ahmad Warsun. Persilangan<br />dua genotipe kedelai dengan jarak genetik jauh menghasilkan<br />progeni dengan polimorfisme tinggi pada banyak lokus<br />yang memfasilitasi keberhasilan program pemuliaan dan pemetaan<br />karakter agronomi penting kedelai. Tujuan penelitian<br />ini untuk mengetahui diversitas genetik genotipe kedelai<br />toleran dan peka keracunan aluminium (Al), informasi diversitas<br />alel dan tingkat polimorfisme marka SSR dari genotipe<br />kedelai yang diuji, menentukan genotipe dengan jarak genetik<br />jauh sebagai tetua dalam pembentukan populasi pemetaan<br />karakter toleran Al, dan informasi diversitas genetik dalam<br />pemilihan tetua untuk program pemuliaan kedelai toleran<br />keracunan Al. Dua puluh empat genotipe kedelai toleran<br />dan peka keracunan Al dianalisis menggunakan 15 marka<br />SSR. Marka SSR lokasinya menyebar pada 14 kromosom kedelai.<br />Dendrogram dikonstruksi menggunakan Unweighted<br />Pair-Group Method Arithmatic (UPGMA) melalui program<br />Numerical Taxonomy and Multivariate System (NTSYS) versi<br />2.1-pc. Diversitas genetik antara dua genotipe kedelai berkisar<br />antara 2-33,2%. Pada diversitas 33,2% uji klaster UPGMA<br />membagi genotipe menjadi 2 kelompok masing-masing terdiri<br />dari 19 dan 5 genotipe untuk kelompok 1 dan 2. Jumlah<br />alel SSR total 81dengan rata-rata jumlah alel per lokus SSR<br />4,4 dan rata-rata tingkat polimorfisme 0,55. Menggunakan diversitas<br />tertinggi 33,2% dua genotipe paling peka Al (B3293<br />dan B3442) dari kelompok 1 dan dua genotipe paling toleran<br />Al (B3462 dan B3851) dari kelompok 2 dipilih untuk membentuk<br />populasi pemetaan karakter toleran Al. Berdasarkan<br />nilai diversitas genetik tertinggi 33,2% banyak kemungkinan<br />kombinasi persilangan dapat dilakukan antara genotipe<br />toleran Al untuk pemuliaan kedelai toleran Al.</p>

scholarly journals Genetic diversity analysis of thirteen mungbean (Vigna radiata (L.) Wilczek) cultivars using RAPD markers

2013 ◽  
Vol 41 (2) ◽  
pp. 169-175 ◽  
Author(s):  
Sonia Khan Sony ◽  
Md Ahashan Habib ◽  
Mohammad Nurul Islam
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Genetic Distances ◽  
Polymorphic Band ◽  
Group Method ◽  
Diversity Analysis ◽  
Arithmetic Means ◽  
Genetic Diversity Analysis ◽  
Pair Group ◽  
Band Size

Genetic diversity analysis among 13 mungbean cultivars from Bangladesh was performed through polymerase chain reaction (PCR) based random amplification of polymorphic DNA (RAPD). Out of 20 arbitrary decamer oligonucleotide primers used, 10 produced a total of 379 different bands with an average of 37.9 bands per primer. Based on the observed banding pattern all the primers were found to be 100% polymorphic. Band size of the amplicons ranged from 250 - 5000 bp. A total of 10 unique DNA fragments was amplified from the 13 mungbean cultivars genome. The values of pair-wise genetic distances ranged from 0.0700 - 1.0852, indicating the presence of wide genetic diversity. The highest genetic distance (1.0852) was found between cultivar BARI Mung-2 and 6 while the lowest (0.0700) between cultivar BINA Mung-2 and 7. Dendogram based on Nei’s genetic distance using Unweighted Pair Group Method of Arithmetic Means (UPGMA) has segregated the 13 mungbean cultivars into two major clusters. BARI Mung-1, 2, 3, 4 and 5 formed cluster 1 and BARI Mung-6, BINA Mung-1, 2, 7, 6, 4, 5 and 8 have made cluster 2. DOI: http://dx.doi.org/10.3329/bjb.v41i2.13444 Bangladesh J. Bot. 41(2): 169-175, 2012 (December)

Assessment of genetic diversity and differentiation of Elymus nutans indigenous to Qinghai–Tibet Plateau using simple sequence repeats markers

2013 ◽  
Vol 93 (6) ◽  
pp. 1089-1096 ◽  
Author(s):  
Shiyong Chen ◽  
Xinquan Zhang ◽  
Xiao Ma ◽  
Linkai Huang
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeats ◽  
Tibet Plateau ◽  
Group Method ◽  
Similarity Coefficients ◽  
Arithmetic Average ◽  
Pair Group ◽  
Elymus Nutans ◽  
Qinghai Tibet Plateau ◽  
Simple Sequence

Chen, S., Zhang, X., Ma, X. and Huang, L. 2013. Assessment of genetic diversity and differentiation of Elymus nutans indigenous to Qinghai–Tibet Plateau using simple sequence repeats markers. Can. J. Plant Sci. 93: 1089–1096. Elymus nutans Griseb., an important alpine forage grass, is widely distributed in the Qinghai–Tibet Plateau. A total of 50 E. nutans accessions from the eastern Qinghai–Tibet Plateau were analyzed using simple sequence repeats (SSR) markers from wheat and Elymus species. Our results show that a total of 144 reliable bands were generated, of which 132 (91.38%) were found to be polymorphic. Nei-Li's genetic similarity coefficients ranged from 0.515 to 0.870 with an average of 0.719, which shows a high level of genetic diversity and a broad genetic base among accessions. There was a low correlation between genetic distance and geographical distance (r=0.121, P=0.088) in the region, which is consistent with the unweighted pair group method with arithmetic average cluster analysis of accessions. The mountain ridges and river valleys in the eastern Qinghai–Tibet region could serve as genetic barriers for pollinator movement and seed dispersal. The rule of the most genetic diversity at medium altitude of E. nutans in the Qinghai–Tibet Plateau was also validated in the study. The implications of these results for the conservation of E. nutans are discussed.

scholarly journals Genetic Diversity Analysis of Hybrid Rice Parental Lines and Genetic Purity Assessment of Hybrid Seeds of China

2020 ◽  
Vol 12 (5) ◽  
pp. 37
Author(s):  
Haiya Cai ◽  
Yuxia Lu ◽  
Gang Liu ◽  
Shuo Zhang ◽  
Haitao Jia ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Hybrid Rice ◽  
Southern China ◽  
Polymorphic Information Content ◽  
Diversity Analysis ◽  
Japonica Rice ◽  
Similarity Coefficients ◽  
Genetic Purity ◽  
Genetic Diversity Analysis ◽  
Parental Lines

Thirty-five pairs of SSR primers were used for genetic diversity analysis and DNA fingerprinting of 31 hybrid rice core parental lines developed in central- and southern-China using one japonica rice line and three inbred rice lines as the check varieties. The average number of alleles (Na) per SSR locus was 4.02, with a range of two to eight, the effective number of alleles (Ne) was 83.16 with a mean of 2.38, ranging from 1.19 to 4.66. The polymorphic information content (PIC) ranged from 0.16 to 0.79, with an average number of 0.52. The results of the cluster analysis indicated that the check varieties viz., one japonica rice and three inbred rice, were clustered into two groups with similarity coefficients of 0.62 and 0.71 respectively indicating their relatedness. Thirty-one hybrid rice parental lines were clustered into 6 groups according to their different types, pedigrees and regions of development with similarity coefficients of approximately 0.76. The highest genetic similarity coefficient (0.94) was observed between Y58S and C815S, and the lowest (0.63) was observed between Quan9311A and Peiai64S. The purity of one hybrid rice cultivar was tested using characteristic marker and the field test, and it was demonstrated that the purities obtained using the two methods were similar. This research will be helpful for rice breeding, new cultivar registration and seed production.

scholarly journals Genetic diversity of Pleurotus ostreatus (Jacq.) P. Kumm. strains in Java based on random amplified polymorphic DNA markers

2021 ◽  
Vol 22 (6) ◽  
Author(s):  
NURAENI EKOWATI ◽  
ARIS MUMPUNI ◽  
JUNI SAFITRI MULJOWATI ◽  
NUNIEK INA RATNANINGTYAS ◽  
ARDHINI RIN MAHARNING
Keyword(s):  
Genetic Diversity ◽  
Dna Sequences ◽  
Dna Markers ◽  
Pleurotus Ostreatus ◽  
Genetic Similarity ◽  
Random Amplified Polymorphic Dna ◽  
Dna Amplification ◽  
Group Method ◽  
Arithmetic Average ◽  
Pair Group

Abstract. Ekowati N, Mumpuni A, Muljowati JS, Ratnaningtyas NI, Maharning AR. 2021. Genetic diversity of Pleurotus ostreatus (Jacq.) P. Kumm. strains in Java based on Random Amplified Polymorphic DNA markers.  Biodiversitas 22: 3488-3493. Genetic variation in a fungal population can occur due to mutation and recombination, resulting in changes in the nucleotides that encode specific DNA sequences. Strains with a high genetic distance and good production capabilities can be used to develop genetic breeding. This study aimed to investigate genetic relationship among Pleurotus ostreatus strains cultivated in Java (Bogor, Cianjur, Tasikmalaya, Purwokerto, Yogyakarta, Tawangmangu, Malang, and Madiun) based on random amplified polymorphic DNA (RAPD) markers.  The research method consisted of DNA isolation and DNA amplification using six primers, i.e. OPA2, OPA3, OPA4, OPA7, OPA9, and OPA10. DNA band data were analyzed using NTSYSpc21 software to determine the level of genetic similarity, based on the Unweighted Pair Group Method with Arithmetic Average Algorithm (UPGMA). In all, 101 amplified DNA bands were obtained, with sizes ranging from 136 to 2320 bp and 96.0% of the bands were polymorphic. Based on cluster analysis, it shows that three clusters were formed. There were genetic variations and relationships among eight P. ostreatus strains in Java with a genetic similarity varying from 37-98%.

Analysis of genetic diversity in Elytrigia repens germplasm using intersimple sequence repeat (ISSR) markers

Botany ◽  
2012 ◽  
Vol 90 (3) ◽  
pp. 167-174
Author(s):  
Lin Meng ◽  
Xiaoyan Zhang ◽  
Peichun Mao ◽  
Xiaoxia Tian
Keyword(s):  
Genetic Diversity ◽  
Issr Markers ◽  
Group Method ◽  
Sequence Repeat ◽  
Similarity Coefficients ◽  
High Genetic Diversity ◽  
Pair Group ◽  
Elytrigia Repens ◽  
Polymorphic Bands ◽  
Mantel’S Test

The genetic diversity among 30 accessions of Elytrigia repens (L.) Nevski was analyzed using 100 intersimple sequence repeat (ISSR) primers, 12 of which generated distinct amplification products. Out of the 132 repeatable bands detected, 100 bands were polymorphic. The percentage of polymorphic bands was 70.66%, with a mean of 8.33 percentage of polymorphic bands per primer. The ISSR-based genetic similarity coefficients among the 30 accessions ranged from 0.509 to 0.873, revealing high genetic diversity. The 30 E. repens accessions were divided into eight groups based on an unweighted pair-group method with arithmetic mean cluster analysis and a principal components analysis. We found that genetic distance is correlated with geographical distance among the 30 E. repens accessions studied (r = 0.812, p < 0.05) using Mantel’s test. Our results confirm the potential value of genetic diversity preservation for future breeding programs.

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