scholarly journals Keragaman Genetik antar Klon Kopi Robusta Lokal Pagar Alam berdasarkan Analisis Marka SSR

2017 ◽  
Vol 4 (3) ◽  
pp. 133
Author(s):  
Syafaruddin Syafaruddin ◽  
Dani Dani ◽  
Marcia Bunga Pabendon
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Binary Data ◽  
Clonal Selection ◽  
Coffea Canephora ◽  
Robusta Coffee ◽  
Long Period ◽  
Ssr Loci ◽  
Biology Laboratory

<em>Robusta coffee (</em>Coffea canephora <em>var. robusta) is the most extensive developed in Indonesia, including Pagar Alam, South Sumatra. In the last few decades, many farmers in Pagar Alam conducted clonal selection and rehabilitation of Robusta coffee trees that generated indigenous clonal populations. This pattern in the long period can damage important alleles and reduce the genetic diversity of indigenous Robusta coffee in farmland. The research aimed to know the genetic diversity among indigenous Robusta coffee clones developed in Pagar Alam based on SSR markers. The study was conducted at Molecular Biology Laboratory, Cereals Research Institute, Maros, from February to April 2017. Molecular characterization of 19 indigenous Robusta coffee clones was conducted using 33 polymorphic SSR markers. The resulting binary data was then analyzed using PowerMarker program to determine polymorphism value (PIC), number and diversity of alleles, and heterozygosity values. The results showed that 33 polymorphic SSR loci produced 134 alleles with an average of 4.06 alleles/locus, whereas PIC values </em><em>ranged from 0.09</em>–<em>0.77 with an average of 0.48. Of the 33 SSR loci, 19 loci (57.58%) exhibited very informative PIC value (&gt; 0.55). Dendrogram generated using NTSYS program divided 19 indigenous Robusta coffee clones into 4 clusters at 0.53 similarity coefficient. KPA41clone was separated in its own cluster, potentially crossed with other clones. Based on genetic distance values &gt;0.55, could arrange 14 combinations of interclonal crosses that potentially increase the genetic variability of indigenous Robusta coffee from Pagar Alam.</em>

scholarly journals Characterization of quince (Cydonia oblonga Mill.) cultivars using SSR markers developed for apple

2009 ◽  
Vol 15 (4) ◽  
Author(s):  
J. Halász ◽  
V. Hoffman ◽  
Z. Szabó ◽  
J. Nyéki ◽  
T. Szabó ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Genetic Bottleneck ◽  
The Self ◽  
Cydonia Oblonga ◽  
Allele Number ◽  
The World ◽  
Ssr Loci ◽  
A Minor

Quince (Cydonia oblongaMill.) is a minor fruit crop, which is primarily used for marmalade, jam and sauce.Very few quince cultivars are known all over the world and in many cases similar names are used for presumably different cultivars. The aim of the present study was to evaluate and characterize the genetic diversity of 36 quince cultivars and selections with SSR markers. Seven out of 8 SSR markers designed from apple sequences could successfully yield amplification also in quince cultivars. Number of alleles per locus ranged from 2 to 3 alleles. These allele numbers are quite low when compared to apple. It is supposed to be the consequence of a genetic bottleneck. In spite of the low allele number per locus, the 36 quince cultivars formed 30 different genotypes. The ratio of homozygosity was low, which might be coupled with the self-(in)compatibility phenotype of quinces. SSR markers proved unable to differentiate putatively closely related cultivars (e.g. ‘Bereczki’ and ‘Bereczki bôtermő’). In general, the level of polymorphism among the tested quince genotypes was much restricted due to the low allele number detected. However, it must be considered that the number of analysed SSR loci is not enough high to estimate the overall heterozygosity of the quince genome. Further experiments are needed and the SSR markers proved to be a reliable and useful tool for such analyses.

scholarly journals Genetic Variability of 15 Robusta Coffee Genotypes Selected by Farmer Based on SSRs Markers

2014 ◽  
Vol 1 (2) ◽  
pp. 87
Author(s):  
Syafaruddin Syafaruddin ◽  
Enny Randriani ◽  
Dani Dani ◽  
Indah Sulistyorini ◽  
M. B. Pabendon
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Coffea Canephora ◽  
Coffee Plantations ◽  
Robusta Coffee ◽  
Allele Number ◽  
Grafting Technique ◽  
Ssrs Markers ◽  
Biology Laboratory ◽  
Research Institute

<p>Robusta coffee (Coffea canephora) has been grown widely in Indonesia, especially in Bengkulu Province. For the last few decades, some farmers have been selected and developed several Robusta clones through plagiotropic shoot grafting technique to replace earlier coffee populations which were derived from seed. Hence, it would reduce the genetic diversity of Robusta coffee at farmer’s field. To understand the genetic variability among 15 Robusta coffee genotypes selected by farmer, it is important to perform molecular analysis. Leaf samples of 15 Robusta coffee genotypes selected by farmer were collected from smallholder Robusta coffee plantations in Bengkulu Province. Genetic diversity analysis was conducted in the Germplasm, Breeding, and Biotechnology Laboratory of Indonesian Industrial and Beverage Crops Research Institute (IIBCRI), and Molecular Biology Laboratory, Indonesian Cereals Research Institute (ICERI). DNA samples were amplified using 34 SSRs markers. The result showed that 23 out of 34 SSRs markers had high polymorphism levels. Allele number per locus ranged from 2-8 with an average of 4 alleles per locus. Dendrogram analysis based on genetic similarity was obtained with score of about 0,44-0,79, and r score = 0,92 (good fit). Based on cluster analysis as well as PCoA analysis, there are three distinct groups of genotypes. Those three groups can be distinguished by specific character of leaf morphotype. Nevertheless, the majority of genotypes were clustered together into the single group. This indicates narrow genetic diversity among Robusta genotypes that selected by farmer.</p><p>Kopi Robusta telah dikembangkan secara luas di Indonesia, khususnya di Provinsi Bengkulu. Beberapa dekade terakhir sebagian petani telah menyeleksi dan mengembangkan beberapa genotipe dengan teknik sambung tunas plagiotrop untuk merehabilitasi populasi kopi Robusta asal biji. Oleh sebab itu, terdapat peluang terjadinya penurunan keragaman genetik kopi Robusta di lahan petani. Analisis molekuler perlu dilakukan untuk mengevaluasi keragaman genetik antar 15 genotipe kopi Robusta hasil seleksi petani. Kegiatan analisis keragaman genetik dilaksanakan di Laboratorium Plasma Nutfah, Pemuliaan, dan Bioteknologi, Balai Penelitian Tanaman Industri dan Penyegar (Balittri), Sukabumi dan Laboratorium Biologi Molekuler, Balai Penelitian Tanaman Serealia (Balitsereal), Maros. DNA diamplifikasi dengan menggunakan 34 marka SSR. Hasil penelitian menunjukkan bahwa 23 dari 34 marka SSR yang digunakan mampu menghasilkan tingkat polimorfisme yang tinggi. Jumlah alel berada pada kisaran 2-8 alel per lokus dengan rata-rata 4 alel per lokus SSR. Analisis dendrogram berdasarkan kemiripan genetik diperoleh dengan skor sekitar 0,44-0,79 dan skor r = 0,92 (good fit). Berdasarkan hasil analisis gerombol dan analisis komponen utama diketahui bahwa terdapat tiga kelompok genotipe. Masing-masing kelompok dapat dibedakan berdasarkan karakter morfotipe daun. Meskipun demikian, sebagian besar genotipe diklasifikasikan ke dalam satu kelompok. Ini menandakan bahwa keragaman genetik klon-klon kopi Robusta hasil seleksi petani cenderung rendah.</p><p>Keywords: Coffea canephora, klon plagiotropik, kehilangan genetik</p>

scholarly journals Keragaman Genetik Klon Kakao Lokal Sulawesi Tenggara Berdasarkan Marka SSR dan Karakter Morfologi

2018 ◽  
Vol 5 (3) ◽  
pp. 95
Author(s):  
Nur Kholilatul Izzah ◽  
Budi Martono ◽  
Baharuddin Baharuddin ◽  
Edi Wardiana
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Genetic Similarity ◽  
Genetic Relationships ◽  
Development Program ◽  
Morphological Characters ◽  
Morphological Characterization ◽  
Biology Laboratory ◽  
High Diversity

<em>Molecular and morphological characterization of cacao clones obtained from exploration in Southeast Sulawesi is very important to know their superiority and genetic relationships. Analysis of genetic diversity using molecular markers is also useful for detecting duplication found among collected clones. The research aimed to determine the genetic diversity of local cacao clones derived from Southeast Sulawesi based on SSR markers and morphological characters. The research was conducted at Cacao Research Sub-Station, Lebojaya Village, Konda Subdistrict, South Konawe Regency, Southeast Sulawesi, and Integrated Laboratory of Indonesian Industrial and Beverage Crops Research Institute Sukabumi, and Molecular Biology Laboratory of Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development Bogor, from April to November 2015. Genetic diversity analysis was performed on 21 cacao clones covering 19 local clones and 2 national varieties using 22 SSR markers. The molecular characterization results showed that 11 markers are polymorphic, and subsequently used to group cacao clones using NTSYS program. The grouping results divided the cacao clones into 4 main groups at 0.46 genetic similarity values. Based on genetic distance values &gt;0.7, 8 combinations of cacao clones can be selected as parental clones with the expectation to increase the effect of heterosis on progeny. On the other hand, result of morphological characterization generally indicated the diversity between the four cacao groups. Based on molecular and morphological characterization, it can be seen that cacao clones derived from Southeast Sulawesi have a high diversity and can be utilized in the development program of new improved varieties.</em>

scholarly journals Molecular Characterization and Similarity Relationships among Flue-Cured Tobacco (Nicotiana tabacum L.) Genotypes Using Simple Sequence Repeat Markers

2012 ◽  
Vol 40 (2) ◽  
pp. 247
Author(s):  
Soheila GHOLIZADEH ◽  
Reza DARVISHZADEH ◽  
Babak ABDOLLAHI MANDOULAKANI ◽  
Iraj BERNOUSI ◽  
Seyed Reza ALAVI ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Genetic ◽  
Genetic Distances ◽  
Similarity Coefficients ◽  
Allele Number ◽  
Nicotiana Tabacum L ◽  
Ssr Loci ◽  
Actual Degree ◽  
Similarity Relationships

Characterization of genetic diversity has long been a major goal in tobacco breeding programs. Information on genetic diversity is essential for a rational use of genetic resources. In the present study, the genetic variation among 72 flue-cured tobacco genotypes was evaluated using microsatellite markers (SSRs). A set of 104 alleles was generated at 30 SSR loci. The mean number of alleles per locus (na) and the effective allele number (ne) were 3.467 and 2.358, respectively. The expected heterozygosity ranged from 0.29 to 0.75 with average of 0.54. Several methods were used to construct the similarity matrices and dendrograms. The co-phenetic correlation coefficient, which is a measure of the correlation between the similarities represented on the dendrograms and the actual degree of similarity, was calculated for each dendrogram. Among the different methods, the highest value (r=0.76368) was observed for the UPGMA created based on Jaccard’s similarity coefficients. The genetic similarity among the tobacco genotypes calculated by using Jaccard’s similarity coefficient ranged from 0.08 to 0.84, suggesting the presence of high molecular genetic variability among the studied tobacco genotypes. Based on UPGMA clustering method all studied flue-cured tobacco genotypes, except for ‘Glustinusa Rasht’, were placed in three distinct groups. We observed an obvious heterotic pattern in the studied flue-cured germplasm corresponding to genetic distances and classification dendrogram, which persuades exploitation of heterosis in flue-cured tobaccos.

scholarly journals Genetic diversity of native and cultivated Ugandan Robusta coffee (Coffea canephora Pierre ex A. Froehner): Climate influences, breeding potential and diversity conservation

PLoS ONE ◽  
2021 ◽  
Vol 16 (2) ◽  
pp. e0245965
Author(s):  
Catherine Kiwuka ◽  
Eva Goudsmit ◽  
Rémi Tournebize ◽  
Sinara Oliveira de Aquino ◽  
Jacob C. Douma ◽  
...  
Keyword(s):  
Climate Change ◽  
Genetic Diversity ◽  
Allelic Variation ◽  
Coffea Canephora ◽  
Ex Situ ◽  
Negative Effects ◽  
Robusta Coffee ◽  
Genetic Diversity And Structure ◽  
Adaptive Diversity ◽  
Southern Central

Wild genetic resources and their ability to adapt to environmental change are critically important in light of the projected climate change, while constituting the foundation of agricultural sustainability. To address the expected negative effects of climate change on Robusta coffee trees (Coffea canephora), collecting missions were conducted to explore its current native distribution in Uganda over a broad climatic range. Wild material from seven forests could thus be collected. We used 19 microsatellite (SSR) markers to assess genetic diversity and structure of this material as well as material from two ex-situ collections and a feral population. The Ugandan C. canephora diversity was then positioned relative to the species’ global diversity structure. Twenty-two climatic variables were used to explore variations in climatic zones across the sampled forests. Overall, Uganda’s native C. canephora diversity differs from other known genetic groups of this species. In northwestern (NW) Uganda, four distinct genetic clusters were distinguished being from Zoka, Budongo, Itwara and Kibale forests A large southern-central (SC) cluster included Malabigambo, Mabira, and Kalangala forest accessions, as well as feral and cultivated accessions, suggesting similarity in genetic origin and strong gene flow between wild and cultivated compartments. We also confirmed the introduction of Congolese varieties into the SC region where most Robusta coffee production takes place. Identified populations occurred in divergent environmental conditions and 12 environmental variables significantly explained 16.3% of the total allelic variation across populations. The substantial genetic variation within and between Ugandan populations with different climatic envelopes might contain adaptive diversity to cope with climate change. The accessions that we collected have substantially enriched the diversity hosted in the Ugandan collections and thus contribute to ex situ conservation of this vital genetic resource. However, there is an urgent need to develop strategies to enhance complementary in-situ conservation of Coffea canephora in native forests in northwestern Uganda.

Analisis Keragaman Genetik 28 Nomor Koleksi Kakao (Theobroma cacao L.) Berdasarkan Marka SSR

2017 ◽  
Vol 4 (1) ◽  
pp. 13 ◽  
Author(s):  
Ilham Nur ardhi Wicaksono ◽  
Rubiyo Rubiyo ◽  
Dewi Sukma ◽  
Sudarsono Sudarsono
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Plant Molecular Biology ◽  
Average Value ◽  
Germplasm Collections ◽  
Ctab Method ◽  
Parental Lines ◽  
Biology Laboratory ◽  
Superior Clones ◽  
Selection Of

<em>Analysis of genetic diversity of cacao germplasm collections using molecular markers has an important role in the assembly of new superior clones. The availability of commercial and superior local clones could increase the success of new superior clones’ assembly. Hence, the genetic diversity analysis of these materials needs to be done. The study was aimed to analyze genetic diversity of 28 cacao collections based on SSR markers that would be useful for selection of parental lines. The research was conducted in the Integrated Laboratory, Indonesian Industrial and Beverage Crops Research Institute, Sukabumi, and Plant Molecular Biology laboratory, Bogor Agricultural University, from November 2015 to May 2016.</em> <em>Analysis of genetic diversity was conducted using 28 cacao clones (13 superior local clones and 15 commercial clones). DNA was extraction using CTAB method, which then amplified by PCR technique using 20 SSR primers. The result showed that all SSR markers used in this study were polymorphic with an average value of PIC was high (57%). Phylogenetic tree constructed using DARwin program version 6.05 is divided into 3 major groups, which placed commercial and superior local clones together in each group. Superior local clones observed herein might have close relationships with commercial clones that have long been cultivated in Indonesia. Furthermore, some cacao clones could potentially be parental lines because they had high genetic distance. The results showed that SSR markers are powerful tools to determine potential parental lines, which is expected to increase the chances of heterosis in their progenies.</em>

KERAGAMAN FENOTIPE DAN GENETIK TIGA VARIETAS KELAPA GENJAH KOPYOR ASAL PATI JAWA TENGAH

2016 ◽  
Vol 21 (1) ◽  
pp. 1 ◽  
Author(s):  
ISMAIL MASKROMO ◽  
ELSJE T. TENDA ◽  
MEITY A. TULALO ◽  
HENGKY NOVARIANTO ◽  
DEWI SUKMA ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Molecular Biology ◽  
Plant Molecular Biology ◽  
Morphological Diversity ◽  
Local Varieties ◽  
Central Java ◽  
Variety Selection ◽  
Ssr Loci ◽  
Biology Laboratory

<p>ABSTRAK<br />Kelapa Genjah kopyor asal Pati, Jawa Tengah merupakan<br />kekayaaan hayati asli Indonesia dengan nilai ekonomi tinggi. Informasi<br />keragaman genetik kelapa kopyor masih terbatas. Data keragaman<br />morfologi dan genetik diperlukan dalam program pemuliaan kelapa<br />kopyor. Penelitian ini mempelajari keragaman tiga varietas kelapa genjah<br />kopyor asal Pati yang telah dilepas berdasarkan karakter morfologi,<br />kuantitas endosperma, dan keragaman alel marka SSR. Penelitian<br />dilakukan di Pati dan di Laboratorium Plant Molecular Biology,<br />Departemen Agronomi dan Hortikultura, IPB. Evaluasi dilakukan terhadap<br />tiga populasi kelapa Genjah kopyor (hijau, coklat, dan kuning) dengan 30<br />tanaman sampel untuk setiap populasi. Rataan data morfologi digunakan<br />untuk menyusun dendogram. Kuantitas endosperma diamati pada satu<br />buah kelapa kopyor per tanaman yang dievaluasi. Karakteristik<br />endosperma dikelompokkan sesuai kategori yang telah ditetapkan. Untuk<br />setiap populasi, analisis marka dengan lima pasang primer SSR dilakukan<br />pada 10 tanaman sampel. Data yang didapat digunakan untuk menentukan<br />keragaman genetik kelapa Genjah kopyor asal Pati. Hasil pengamatan<br />menunjukkan keragaman morfologis dan alel SSR antar tanaman dalam<br />varietasnya (keragaman intra-varietas) rendah. Sebaliknya, keragaman<br />morfologis dan alel SSR antar varietasnya tinggi. Kuantitas endosperma<br />kelapa Genjah kopyor asal Pati bervariasi antara skor 1–6. Keragaman<br />genetik yang rendah dalam varietas dan tinggi antar ketiga varietas (coklat,<br />hijau, dan kuning) memperkuat pelepasan ketiganya sebagai varietas lokal.<br />Selain itu, keragaman genetik antar tanaman dalam varietas yang rendah<br />mendukung penggunaan ketiga varietas lokal sebagai tetua dalam program<br />perakitan varietas kelapa kopyor unggul baru. Tetua yang dipilih dapat<br />diseleksi intra-varietas berdasarkan persentase buah kopyor per tandan<br />dan skor kuantitas endosperma yang tinggi.<br />Kata kunci: Keragaman morfologis, keragaman intra dan antar varietas,<br />kuantitas endosperma</p><p>ABSTRACT<br />Kopyor dwarf coconuts are mutants from Pati, Central Java having<br />high economic values. However, morphological and genetic diversities of<br />this coconut were still limited. Morphological and genetic diversity data<br />are needed for breeding program. The research objectives were to evaluate<br />intra and inter-specific diversity based on morphology, endosperm<br />quantity, and SSR alleles. Field evaluations were conducted in Pati while<br />laboratory activities were at Plant Molecular Biology Laboratory,<br />Department of Agronomy and Horticulture, IPB. Three populations of<br />kopyor dwarf varieties (brown, green, and yellow) were evaluated. Thirty<br />trees were sampled for each population. The average of morphological<br />data were used to construct cluster analysis. Endosperm quantity was<br />scored (0 – 9) based on a single nut sample. Ten palms were analyzed<br />using five SSR loci for each population and used to determine genetic<br />diversity of populations. Results of observations indicated intra-variety<br />morphological and SSR allele variations among kopyor dwarf was low.<br />However, inter-variety variations were high. The endosperm quantity<br />scores among kopyor dwarf coconut ranged from 1–6. The low intra-<br />variety and high inter-variety variations among the three kopyor dwarf<br />coconut supported their release as different local varieties. Moreover, the<br />low intra-variety phenotypic and genotypic diversities among kopyor<br />brown, green, and yellow dwarf coconut support their use as parents for<br />new and superior kopyor coconut variety development in the future. For<br />such purpose, however, it is necessary to conduct intra-variety selection to<br />identify desirable parents based on high kopyor fruit percentage per bunch<br />and for high kopyor endosperm quantity.<br />Key words: Morphological diversity, intra and inter variety diversities,<br />quantity, endosperm</p>

scholarly journals Genetic Differentiation in Moroccan Opuntia ficus-indica Cultivars Using Simple Sequence Repeat (SSR) Markers

2016 ◽  
Vol 8 (3) ◽  
pp. 380-385 ◽  
Author(s):  
Aissam EL FINTI ◽  
Driss TALIBI ◽  
Mouhamed SIDKI ◽  
Abdelhamid E. MOUSADIK
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Ssr Markers ◽  
Opuntia Ficus Indica ◽  
Distance Analysis ◽  
Reference Collection ◽  
Ssr Loci ◽  
Set Up ◽  
Genetic Distance Analysis ◽  
Simple Sequence

Estimation of genetic parameters at SSR loci can be applied for assessing the differences between cultivars or populations, either for variety distinction or the management of genetic resources. In this study, 13 Opuntia ficus-indica cultivars were analyzed using 10 SSR markers selected for studying the genetic diversity among these chosen cultivars. Over the 10 SSR markers, a total of 45 reproducible bands were scored with an average of 4.5 alleles/locus, while the observed heterozygosity (Ho) values of amplified loci ranged from 0.15 (SSR1) to 0.92 (SSR2 and SSR 11). Genetic distance analysis of the 13 cultivars showed a large genetic differentiation (GST = 0.47) and high number of different groups. Most of the accessions were not found to be clustered according to their eco-geographical origin. In addition, each cultivar was characterized by its own multiallelic combination between loci. The results revealed the usefulness of SSR in understanding of genetic diversity in Moroccans Barbary fig cultivars, thus being helpful to set up rational decisions concerning the establishment of a national reference collection.

scholarly journals Characterization of Hemerocallis citrina Transcriptome and Development of EST-SSR Markers for Evaluation of Genetic Diversity and Population Structure of Hemerocallis Collection

2020 ◽  
Vol 11 ◽  
Author(s):  
Sen Li ◽  
Fangfang Ji ◽  
Feifan Hou ◽  
Huliang Cui ◽  
Qingqing Shi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Ssr Markers ◽  
Hemerocallis Citrina

scholarly journals Characterization of genetic diversity in chickpea using SSR markers, Start Codon Targeted Polymorphism (SCoT) and Conserved DNA-Derived Polymorphism (CDDP)

2015 ◽  
Vol 21 (3) ◽  
pp. 365-373 ◽  
Author(s):  
Zahra Hajibarat ◽  
Abbas Saidi ◽  
Zohreh Hajibarat ◽  
Reza Talebi
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Start Codon
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