scholarly journals A Simple Sequence Repeat (SSR) Marker Comparison of a Large In- and Ex-situ Potato Landrace Cultivar Collection from Peru Reaffirms the Complementary Nature of both Conservation Strategies

Diversity ◽  
2013 ◽  
Vol 5 (3) ◽  
pp. 505-521 ◽  
Author(s):  
Stef de Haan ◽  
Jorge Núñez ◽  
Merideth Bonierbale ◽  
Marc Ghislain ◽  
Jos van der Maesen
Keyword(s):  
Simple Sequence Repeat ◽  
Ssr Marker ◽  
Ex Situ ◽  
Conservation Strategies ◽  
Sequence Repeat ◽  
Complementary Nature ◽  
Marker Comparison ◽  
Simple Sequence

scholarly journals Genetic Diversity, Population Structure and Relationship of Ethiopian Barley (Hordeum vulgare L.) Landraces as reveled by Simple Sequence Repeat (SSR) Markers

2021 ◽  
Author(s):  
Allo Aman Dido ◽  
B.J.K. Singh ◽  
Ermias Assefa ◽  
M.S.R. Kr ◽  
Dawit Degefu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Diversity Index ◽  
Ex Situ ◽  
Conservation Strategies ◽  
Sequence Repeat ◽  
Genetic Rescue ◽  
Hordeum Vulgare L ◽  
Barley Genotypes ◽  
Simple Sequence

Abstract Characterization of genetic resources maintained at genebanks has important implications for future utilization and collection activities. A total of 49 simple sequence repeat (SSR) or microsatellite markers were used to study genetic diversity and relationships among 376 barley landraces collected from different barley producing parts of Ethiopia and eight cultivars. Overall, 478 alleles with an average of 9.755 alleles per locus were obtained of which 97.07% of the loci were observed to be polymorphic. Nei’s genetic diversity index (h) was 0.654, and the Shannon diversity index (I) was 0.647, indicating that the genetic diversity in barley genotypes studies was moderately high. At the population level, the percentage of polymorphic loci (PPL) averaged 98.37%, h = averaged 0.388, and I = averaged 0.568. The highest level of genetic diversity was observed in the AR population (PPL =100%, h = 0.439, I = 0.624); the lowest was observed in the JM population (PPL = 75.51%, h = 0.291, I =0.430). AMOVA revealed significant genetic differentiation within and between populations (P < 0.001), with 84.21% of the variation occurring within populations and 15.79% occurring among populations. Genetic variation analysis showed a coefficient of gene differentiation of 0.053 and a gene flow value of 4.467 among populations. The 384 barley genotypes were divided into seven genetic clusters according to STRUCTURE, Neighbour joining tree and principal coordinate analysis, correlating significantly with geographic distribution. These results will assist with the formulation of conservation strategies, such as genetic rescue and on-farm in situ and ex situ conservation.

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>

Extent of clonality, genetic diversity and decline in the endangered mallee Eucalyptus imlayensis

2007 ◽  
Vol 55 (5) ◽  
pp. 548 ◽  
Author(s):  
Elizabeth A. James ◽  
Keith L. McDougall
Keyword(s):  
Simple Sequence Repeat ◽  
Ex Situ Conservation ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Lower Number ◽  
Ex Situ ◽  
Sequence Repeat ◽  
Eastern Australia ◽  
Number Of Stems ◽  
Simple Sequence

Eucalyptus imlayensis Crisp & Brooker is a rare mallee known from one location in south-eastern Australia. Discovered in 1977, the population has declined in number and health of stems since 1998. Inter-simple sequence repeat (ISSR) markers were used to assess genetic variation and clonality. Only five multilocus genotypes were distinguished from 27 samples and the proximity of like genotypes within the population is consistent with the population being largely clonal. This means that the species has a much lower number of genetic individuals than is suggested from a census of the number of stems present. The implications of this finding for ex situ conservation of the species are discussed.

scholarly journals Assessment of Genetic Relationship among Male and Female Fig Genotypes Using Simple Sequence Repeat (SSR) Markers

2017 ◽  
Vol 45 (1) ◽  
pp. 172-178
Author(s):  
Sevin TEOMAN ◽  
Meryem IPEK ◽  
Umran ERTURK ◽  
Nesrin Aktepe TANGU ◽  
Erdem DURGUT ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Genetic Relationship ◽  
Simple Sequence Repeat ◽  
Ssr Marker ◽  
Aegean Sea ◽  
Gene Pools ◽  
Sequence Repeat ◽  
Expected Heterozygosity ◽  
Male Tree ◽  
Simple Sequence

Fig (Ficus carica L.) is a traditional crop in Turkey and widely cultivated around the Mediterranean areas. The gynodioecious fig species is present in two sexual forms, i.e. the domesticated fig (female tree) and the caprifig (male tree). Caprifigs are crucial for high quality fig production and breeding while, the studies on assessment of genetic relationship among caprifigs is limited. The aim of this study was to determine genetic diversity among 45 caprifigs and 2 female figs collected from four provinces in Marmara and Aegean Sea Regions of Turkey using simple sequence repeat (SSR) markers. In this work, 24 SSR markers were tested, one was monomorphic and the remaining markers amplified 82 alleles. The number of polymorphic alleles per SSR marker ranged from 2 to 7. The observed heterozygosity (Ho) differed from 0.18 to 0.76 and expected heterozygosity (He) ranged between 0.24 and 0.81. The polymorphism information content (PIC) varied from 0.42 to 0.98. A UPGMA analysis based on Dice similarity matrix clustered fig genotypes into two main groups and similarly, STRUCTURE analysis placed fig genotypes into two different gene pools (K=2). Fig genotypes collected from the same region were not clustered together in a group indicating that the fig genotypes did not cluster on the basis of their collection sites. Our results demonstrated that caprifigs and female figs are not genetically distinct and they clustered together in a group. All fig genotypes had distinct SSR marker profiles suggesting that there were no synonyms or homonyms. These results revealed a high genetic variation among fig genotypes and 23 SSR markers were enough to discriminate all fig genotypes analysed in this study demonstrating that SSR marker system is suitable for genetic analysis in figs.

scholarly journals Genetic Diversity of Arabica Coffee (Coffea arabicaL.) in Nicaragua as Estimated by Simple Sequence Repeat Markers

2012 ◽  
Vol 2012 ◽  
pp. 1-11 ◽  
Author(s):  
Mulatu Geleta ◽  
Isabel Herrera ◽  
Arnulfo Monzón ◽  
Tomas Bryngelsson
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Simple Sequence Repeat ◽  
Significant Contribution ◽  
Gene Diversity ◽  
Ex Situ ◽  
Sequence Repeat ◽  
Breeding Programs ◽  
Arabica Coffee ◽  
Simple Sequence

Coffea arabicaL. (arabica coffee), the only tetraploid species in the genusCoffea, represents the majority of the world’s coffee production and has a significant contribution to Nicaragua’s economy. The present paper was conducted to determine the genetic diversity of arabica coffee in Nicaragua for its conservation and breeding values. Twenty-six populations that represent eight varieties in Nicaragua were investigated using simple sequence repeat (SSR) markers. A total of 24 alleles were obtained from the 12 loci investigated across 260 individual plants. The total Nei’s gene diversity (HT) and the within-population gene diversity (HS) were 0.35 and 0.29, respectively, which is comparable with that previously reported from other countries and regions. Among the varieties, the highest diversity was recorded in the variety Catimor. Analysis of variance (AMOVA) revealed that about 87% of the total genetic variation was found within populations and the remaining 13% differentiate the populations (FST=0.13;P<0.001). The variation among the varieties was also significant. The genetic variation in Nicaraguan coffee is significant enough to be used in the breeding programs, and most of this variation can be conserved throughex situconservation of a low number of populations from each variety.

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