scholarly journals Analysis of Genetic Diversity of Myrtle (Myrtus Communis L.) by Using SSR Technique

2021 ◽  
Vol 923 (1) ◽  
pp. 012011
Author(s):  
Alyaa Muayad Adham ◽  
Saleh Shehab Sabah ◽  
Mohammed Radwan Mahmoud ◽  
Omar Farouk Fahel
Keyword(s):  
Genetic Diversity ◽  
Ssr Marker ◽  
Molecular Size ◽  
Similarity Coefficient ◽  
Sea Surface ◽  
Dice Coefficient ◽  
Humid Climate ◽  
Minimum Number ◽  
Partial Degradation ◽  
Simple Sequence

Abstract This research carried out to compare some of the individuals of Myrtle from bushes in different environmental sites (Lattakia, Safita, Qusul Maaf, northern Aleppo and at different altitudes from the sea surface). The genetic diversity of 19 genotypes was tested using simple sequence repeats (SSRs) technique with 10 primers. The results of DNA extraction showed a high molecular size fragment as a band at the top of each lane, additionally to a partial degradation. At the end DNA concentration, integrity and purity were enough for SSR marker. Genetic variations were detected by SSR marker with similarity coefficient ranged between 0.08 – 0.89 based on Dice coefficient. Total of 27 alleles were scored from 19 genotypes, and the number of alleles was ranged between 2 (myrcom8 and 9) and 4 (myrcom2 and 6). The calculated value of polymorphism information content (PIC) was ≤ 0.5. Nineteen genotypes were distributed on three main clusters, two of them II and III included minimum number of genotypes from humid climate sites, while the majority of genotypes was distributed on cluster I in mixed manner.

scholarly journals ANALISIS KERAGAMAN GENETIK PLASMA NUTFAH KAKAO (Theobroma cacaoL.) BERDASARKANMARKA SSR / Analysis of Genetic Variability Germplasm of Cacao (Theobroma cacaoL.)Basedon SSR Marker

2020 ◽  
Vol 17 (4) ◽  
pp. 156
Author(s):  
Surti Kurniasih ◽  
Rubiyo Rubiyo ◽  
Asep Setiawan ◽  
Agus Purwantara ◽  
Sudarsono Sudarsono
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Ssr Markers ◽  
Theobroma Cacao ◽  
Simple Sequence Repeat ◽  
Ssr Marker ◽  
Gene Diversity ◽  
Sequence Repeat ◽  
Theobroma Cacao L ◽  
Simple Sequence

<p>Microsatellite or simple sequence repeat (SSR) markers have proven to be an excellent tool for cultivar identification, pedigree analysis, and genetic distance evaluations among organisms. The objectives of this research were to characterize cacao collection of Indonesian Coffee and Cacao Research Institute (ICCRI) and to analyze their genetic diversity using SSR markers. In this research, 39 SSR primer pairs were used to amplify genomic DNA of 29 cacao clones. Amplified SSR fragments for each primer pair were scored as individual band and used to determine genetic distance among evaluated cacao clones. Results of the experiment indicated that all SSR primer pairs evaluated were able to produce SSR markers for 29 cacao clones. The results also indicated that 34 out of 39 microsatellite loci evaluated were polymorphic, while 5 others were monomorphic. The total number of observed alleles among 29 clones was 132. Number of alleles per locus ranged from 4-8, with an average of 5.5 alelles per locus. Results of data analysis indicated that the PIC value was 0.665, the observed heterozigosity (Ho) was 0.651, and the gene diversity (He) was 0.720. The PIC, Ho, and He values were considered high. Genetic distances were evaluated using NTSys version 2.1 and dendrogram was constructed. Results of analysis indicated that 12 cacao clones evaluated were clustered in the first group with diversity coefficient of &lt; 3.75. Nine cacao clones were in the second group but with the same value of diversity coefficient (&lt;7.50). The rest of the cacao clones were in the third group with diversity coefficient of&gt;7.50. Based on those finding, all SSR primer pairs evaluated could be used to analyze cacao genome and be useful for genetic diversity analysis of cacao germplasm. The SSR marker analysis in ICCRI cacao collections resulted in high PIC, high observed heterozygosity, and high genetic diversity.</p><p>Key words: Theobroma cacao L, microsatelite, molecular marker, genetic diversity, heterozygosity</p><p> </p><p><strong>Abstrak</strong></p><p>Marka mikrosatelit atau sekuens sederhana berulang (simple sequence repeat = SSR) terbukti merupakan alat yang bagus untuk identifikasi kultivar, analisis pedigree, dan evaluasi jarak genetik berbagai organisme. Penelitian ini bertujuan untuk:1) karakterisasi kakao koleksi Pusat penelitian Kopi dan Kakao Indonesia menggunakan marka SSR dan 2) analisis keragaman genetik klon-klon kakao koleksi dengan menggunakan marka SSR. Dalam penelitian ini, 39 pasangan primer SSR telah digunakan untuk amplifikasi DNA genomik dari 29 klon kakao. Skoring pita SSR hasil amplifikasi menggunakan masing-masing pasangan primer dilakukan secara terpisah dan digunakan untuk menentukan jarak genetik di antara klon kakao yang dievaluasi. Hasil percobaan menunjukkan bahwa semua pasangan primer SSR yang digunakan mampu menghasilkan pita DNA hasil amplifikasi (marka SSR) untuk 29 klon kakao yang diuji. Hasil penelitian juga menunjukkan bahwa 34 dari 39 lokus SSR yang dianalisis bersifat polimorfik sedangkan lima primer yang lain bersifat monomorfik. Dari 29 klon kakao yang dievaluasi, telah berhasil diamplifikasi sebanyak 132 alel, dengan kisaran antara 4-8 alel/lokus. Rataan jumlah alel per lokus sebanyak 5,50. Hasil analisis data yang dilakukan juga menunjukkan nilai PIC untuk marka SSR yang digunakan sebesar 0,665. Untuk populasi klon kakao yang dievaluasi, diperoleh nilai rataan heterosigositas pengamatan (Ho) sebesar 0,651 dan rataan diversitas gen (He) sebesar 0,720. Nilai PIC Ho dan He yang didapat tergolong tinggi. Berdasarkan analisis keragaman dengan menggunakan program NTSys, diperoleh hasil 12 klon kakao berada dalam grup pertama (koefisien keragaman&lt;3,75) dan9 klon berada dalam grup kedua, dengan koefisien keragaman &lt; 7,50. Sedangkan klon-klon lainnya mempunyai koefisien keragaman &gt; 7,50. Berdasarkan hasil penelitian dan analisis data disimpulkan bahwa marka SSR dapat digunakan untuk menganalisis keragaman genetik plasma nutfah kakao. Tingkat polimorfisme yang dihasilkan marka SSR relatif tinggi. Tingkat heterosigositas plasma nutfah kakao koleksi Puslit Kopi dan Kakao Indonesiarelatif tinggi, dan keragaman genetiknyacukup tinggi.</p><p>Kata kunci : Theobroma cacao L, mikrosatelit, marka molekuler, keragaman genetik, heterosigositas</p>

scholarly journals  Genetic diversity of Czech apple cultivars inferred from microsatellite markers analysis

2012 ◽  
Vol 39 (No. 4) ◽  
pp. 149-157 ◽  
Author(s):  
J. Patzak ◽  
F. Paprštein ◽  
A. Henychová ◽  
J. Sedlák
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Simple Sequence Repeat ◽  
Cultivar Identification ◽  
Genetic Relationships ◽  
Similarity Coefficient ◽  
Collection Management ◽  
Apple Cultivars ◽  
Repeat Primer ◽  
Simple Sequence

Genetic diversity and genetic relationships of Czech apple cultivars were evaluated. Trees of 33&nbsp;Czech apple cultivars and 97 reference foreign cultivars were analysed using the set of 10 SSR (simple sequence repeat) primer pairs. The total of 89 polymorphic alleles were amplified, while the number of alleles per locus ranged from 4 to 14. The SSR dendrogram, based on the Jaccard&rsquo;s similarity coefficient, divided apple cultivars into three major groups: Cox&rsquo;s Orange Pippin, McIntosh and Golden Delicious ancestries. The clustering highly depended on pedigree and origin of apple cultivars. Spontaneous mutated cultivars were identical with their progenitors. We proved that microsatellite markers were useful for evaluation of genetic resources, collection management and cultivar identification. &nbsp;

Genetic diversity of oil-tea camellia germplasms revealed by ISSR analysis

2015 ◽  
Vol 08 (05) ◽  
pp. 1550070 ◽  
Author(s):  
Lan-Ying Zhou ◽  
Xiang-Nan Wang ◽  
Li-Ping Wang ◽  
Yong-Zhong Chen ◽  
Xiao-Cheng Jiang
Keyword(s):  
Genetic Diversity ◽  
Reaction System ◽  
Inter Simple Sequence Repeat ◽  
Genetic Distances ◽  
Similarity Coefficient ◽  
Hunan Province ◽  
Information Index ◽  
Group I ◽  
Issr Pcr ◽  
Simple Sequence

Genetic diversity of 51 oil-tea camellia germplasms was analyzed using the optimized inter-simple sequence repeat (ISSR)–PCR reaction system with 22 primers screened from a set of 100 ISSR primers. The results showed that 493 discernible loci with distinct electrophoretic bands were obtained, of which, 478 loci (96.78%) were polymorphic. This indicated that oil-tea germplasms possess abundant genetic diversities. By clustering analysis performed using softwares of NTSYS 2.10 and Winboot, 51 oil-tea germplasms were divided into two groups: Group I had 48 lines of Camellia oleifera Abel, while Group II had three C. oleifera Abel related species and their similarity coefficient was 0.62. Group I was further divided into Group I-1 and Group I-2, and their similarity coefficient (Gs) was 0.634. All members of Group I-1 originated from Hunan Province, while Group I-2 included the rest of Hunan lines and those originated from other regions of China. Analyzed by software POPGENE 1.32, the Shannon's information index (I*) of genetic polymorphism was 0.3852, the genetic diversity among different region populations (Ht) was 0.2537, the genetic diversity within populations (Hs) was 0.15545, the differentiation coefficient of genetic diversity among populations (Gst) was 0.3967, and the gene flow among populations (Nm*) was 0.8262. The Nei's genetic distances between the Hunan population and the populations originated from other regions of China implied that geographic isolation strongly influenced genetic differentiation among populations. Meanwhile, seedling rootstock grafting and high grafting for tree crown produced genetic variations among clonal offsprings.

scholarly journals Genetic Diversity of Vitis davidii Accessions Revealed Using Microsatellite and Sequence-related Amplified Polymorphism Markers

HortScience ◽  
2018 ◽  
Vol 53 (3) ◽  
pp. 283-287
Author(s):  
Xiu Cai Fan ◽  
Hai Sheng Sun ◽  
Ying Zhang ◽  
Jian Fu Jiang ◽  
Min Li ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Genetic Similarity ◽  
Similarity Coefficient ◽  
Srap Markers ◽  
Average Percentage ◽  
Allele Number ◽  
Ssr Primers ◽  
Vitis Davidii ◽  
Simple Sequence

In this study, simple sequence repeat (SSR) and sequence-related amplified polymorphism (SRAP) markers were used to analyze the genetic diversity of 48 wild Vitis davidii accessions. A total of 78 distinct alleles were amplified by 11 SSR primers, and the average allele number was 8.8. The average observed heterozygosity (Ho) and expected heterozygosity (He) values were 0.785 and 0.814, respectively. The effective allele numbers ranged from 3.92 to 9.61. The average polymorphism information content (PIC) was 0.798. Twelve of 169 SRAP primer combinations were selected for SRAP analysis. A total of 188 bands were produced, and the average was 15.7 bands per primer combination; the average percentage of polymorphic bands was 84.0%. The average PIC was 0.76. The results of the clustering analysis based on SSR markers showed that the 48 wild V. davidii accessions could be classified into five main clusters and had a genetic similarity coefficient level of 0.68. The dendrogram obtained from the SRAP data showed that 48 wild V. davidii accessions could be classified into five main clusters and had a genetic similarity coefficient of 0.72. SSR and SRAP markers differentiated all accessions studied including those with a similar pedigree. We speculated on the origin of Ciputao 0941♀, Ciputao 0940♂, and Fu’an-ci-01 using SSR markers and used both SSR and SRAP markers to resolve homonymy. The result will be valuable for further management and protection of V. davidii germplasm resources.

scholarly journals Genetic Diversity of Local Maize Germplasm of Tana Toraja South Sulawesi Using SSR (Simple Sequence Repeat) Markers

2018 ◽  
Vol 2 (3) ◽  
pp. 144
Author(s):  
Ramlah Ramlah ◽  
Isna Rasdianah Aziz ◽  
Cut Muthiadin ◽  
Mashuri Masri ◽  
Muhammad Khalifah Mustami ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Simple Sequence Repeat ◽  
Genetic Similarity ◽  
Agricultural Research ◽  
Similarity Coefficient ◽  
Sequence Repeat ◽  
Maize Germplasm ◽  
South Sulawesi ◽  
Simple Sequence

Plant genetic diversity is an emerging variation in a crop group caused by its genetic factors. Local corn germplasm as a source of plant genes that are able to adapt to the local environment. The purpose of this research is to obtain information on genetic variation of Tana Toraja local maize germ plasm using SSR (Simple Sequence Repeat) marker. This research was conducted at Balitsereal Molecular Biology Laboratory, Agricultural Research Agency in Maros Regency, South Sulawesi. A total of 4 local maize populations were analyzed by laboratory experimental method with observation with NTSYS pc 2.1 program. The results showed that the average number of alleles was 3.72 alleles per locus and the polymorphism rate of 0.53 with the genetic similarity coefficient was in the range of 0.47 to 0.85. 2 main clusters formed in the genetic similarity coefficient 0.47. Klaster I is Local DallePondan and Local Purple. Klaster II is Local Bebo and Kandora. The genetic distance is in the range of 0.15 to 0.74 with an average genetic distance of 0.46. From the data obtained shows that the 4th germplasm of the population of Tana Toraja Local maize diteleti has a very informative level of genetic diversity. Genetic diversity of local maize germplasm of Tana Toraja, can be used as a source of genes in the assembly of improved varieties in the future.

scholarly journals Analysis of genetic diversity among different tomato genotypes using ISSR DNA marker

Genetika ◽  
2017 ◽  
Vol 49 (1) ◽  
pp. 31-42
Author(s):  
Saida Sharifova ◽  
Sabina Mehdiyeva ◽  
Mehraj Abbasov
Keyword(s):  
Genetic Diversity ◽  
Dna Marker ◽  
Diversity Index ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Similarity Coefficient ◽  
Variation Analysis ◽  
A Value ◽  
Polymorphic Bands ◽  
Simple Sequence

Inter simple sequence repeat (ISSR) markers were used for variation analysis among 41 tomato accessions. A total of 50 scorable bands were obtained, where 32 were polymorphic, representing 63.3% of all the amplified loci. Polymorphism percentage ranged from 50 to 90% and an average number of polymorphic bands of 4.0 were observed. An average genetic diversity index was 0.61. Primer UBC860 and UBC825 generated the greatest diversity index with a value of 0.89 and 0.85 respectively. The smallest diversity identified by primer UBC808, with an index of 0.34. The genetic similarity among studied genotypes ranged from 0.52 to 0.98. The cluster analysis based on Jaccard?s similarity coefficient divided genotypes into 6 distinct clusters on a value of 0.74. The lowest genetic distance was found between ?Gronastiy? and ?AG1224? (0.52), ?Orange? and ?AG1224? (0.54), and ?Evgeniya? and ?AG1224? (0.55) accessions. The highest similarity of 0.98 was determined between ?Zafar? and ?Azerbaijan-94?, ?Khachmaz-1? and ?Azerbaijan-94?, ?Khachmaz-1? and ?Severyanka?, and ?Shakar? and ?Absheron-1? accessions.

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