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>

scholarly journals EVALUATION OF GENETIC DIVERSITY IN CACAO COLLECTED FROM KOLAKA, SOUTHEAST SULAWESI, USING SSR MARKERS

2016 ◽  
Vol 16 (2) ◽  
pp. 71
Author(s):  
Rubiyo Rubiyo ◽  
Nur Kholilatul Izzah ◽  
Indah Sulistiyorini ◽  
Cici Tresniawati
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Gel Electrophoresis ◽  
Genetic Similarity ◽  
Similarity Coefficient ◽  
Breeding Program ◽  
New Variety ◽  
Average Value ◽  
The Third ◽  
Ctab Method

Kolaka, which is located in Southeast Sulawesi, has long been known as one of cacao production centers in Indonesia. Therefore, many different cacao germplasms can be found in this region. The study aimed to evaluate genetic diversity and relationships of 12 cacao genotypes collected from Kolaka. Genomic DNA was extracted by using a modified CTAB method. Meanwhile, genetic diversity was analyzed based on 16 SSR markers, which then separated by 6% non-denaturing polyacryl-amide gel electrophoresis. The result showed that all of those markers, 14 markers exhibited polymorphism and subsequently used for data analysis using NTSYS and PowerMarker program. About 70 different alleles were generated from 12 cacao genotypes analyzed with an average of 5 alleles per locus. Average value of polymorphism information content (PIC) resulted in this study was 0.59. The cluster analysis using UPGMA method based on the genetic similarity coefficient revealed that all cacao genotypes were separated into three major groups. The first group consisted of five cacao genotypes, the second one held four cacao genotypes, whereas the third group contained three genotypes. This result indicates that three genotypes that clustered separately from the others could be used as a good clonal candidate for cacao breeding program. The information resulted from this present study would be useful for future cacao breeding program, especially in efforts to release a new variety.

scholarly journals Similarity of 26 New Released Rice Varieties and Rice Parental Hybrids Based on 36 SSR Markers

2014 ◽  
Vol 33 (2) ◽  
pp. 71
Author(s):  
Untung Susanto ◽  
Satoto Satoto ◽  
Nofi A. Rohmah ◽  
Made Jana Mejaya
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Ssr Markers ◽  
Rice Varieties ◽  
Average Value ◽  
Modified Method ◽  
Rice Chromosomes ◽  
Medium Level ◽  
Rice Genotypes ◽  
Parental Lines

More than 200 rice varieties had been released in Indonesia, but the genetic variability among those released varieties was suspected to be relatively low. Molecular markers, especially SSR could be used as a tool to disect the distinctness among rice genotypes, albeit phenotipically similar varieties. The technique could also be used to prove the authenticity of a variety. This research was aimed to obtain DNA fingerprinting data of new released rice varieties and hybrid parental lines using SSR markers. A total of 26 rice genotypes consisted of three upland, ten irrigated, five swampy rice varieties, along with eight hybrid parental lines were used in this experiments. The DNA was extracted from young leaf samples using CTAB modified method and was amplified with 36 SSR markers linked to important rice traits which spread accross the 12 rice chromosomes. The experiment was conducted in Plant Breeding Laboratory of Indonesian Center for Rice Research (ICRR) during 2012. The results showed that PIC value of the genotypes were mostly at medium level of the genetic diversity with the average value of 0.4451. The phylogenetic analysis showed that at the genetic distance of 10%, the genotypes were separated into 9 groups, i.e. Inpago 6, Inpara 5, and BH33d each stood alone while (Inpara 1, Inpara 2 , and Inpara 3); (Inpari 18 and Inpari 19, Inpago 4, Inpago 5, and Inpara 4); (Inpari 11, Inpari 12, Inpari 13, Inpari 14, Inpari 15, Inpari 16, Inpari 17, and Inpari 20); (GMJ6B, B6, and IR79156B); (PK21, BH95E, Bio9, and R14) each belong to one group. The grouping of the genotypes in this study seemed to follow the adaptation type to agro ecosystems. The hybrid parental lines tended to stay in different group from the inbred varieties. The application of these 36 SSR markers was able to distinguish among 26 genotypes rather distinctly.The use of more markers should give more powerful data to distinguish among genotypes.

scholarly journals EVALUATION OF GENETIC DIVERSITY IN CACAO COLLECTED FROM KOLAKA, SOUTHEAST SULAWESI, USING SSR MARKERS

2016 ◽  
Vol 16 (2) ◽  
pp. 71
Author(s):  
Rubiyo Rubiyo ◽  
Nur Kholilatul Izzah ◽  
Indah Sulistiyorini ◽  
Cici Tresniawati
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Gel Electrophoresis ◽  
Genetic Similarity ◽  
Similarity Coefficient ◽  
Breeding Program ◽  
New Variety ◽  
Average Value ◽  
The Third ◽  
Ctab Method

Kolaka, which is located in Southeast Sulawesi, has long been known as one of cacao production centers in Indonesia. Therefore, many different cacao germplasms can be found in this region. The study aimed to evaluate genetic diversity and relationships of 12 cacao genotypes collected from Kolaka. Genomic DNA was extracted by using a modified CTAB method. Meanwhile, genetic diversity was analyzed based on 16 SSR markers, which then separated by 6% non-denaturing polyacryl-amide gel electrophoresis. The result showed that all of those markers, 14 markers exhibited polymorphism and subsequently used for data analysis using NTSYS and PowerMarker program. About 70 different alleles were generated from 12 cacao genotypes analyzed with an average of 5 alleles per locus. Average value of polymorphism information content (PIC) resulted in this study was 0.59. The cluster analysis using UPGMA method based on the genetic similarity coefficient revealed that all cacao genotypes were separated into three major groups. The first group consisted of five cacao genotypes, the second one held four cacao genotypes, whereas the third group contained three genotypes. This result indicates that three genotypes that clustered separately from the others could be used as a good clonal candidate for cacao breeding program. The information resulted from this present study would be useful for future cacao breeding program, especially in efforts to release a new variety.

scholarly journals Diversity Assessment of Some Sesame (Sesamum indicum L.) Genotypes Cultivated in Northern Ghana Using Morphological and Simple Sequence Repeat (SSR) Markers

2019 ◽  
Vol 2019 ◽  
pp. 1-10 ◽  
Author(s):  
Raphael Adu-Gyamfi ◽  
Ruth Prempeh ◽  
Issahaku Zakaria
Keyword(s):  
Genetic Diversity ◽  
Plant Height ◽  
Ssr Markers ◽  
Analysis Of Variance ◽  
Morphological Data ◽  
Northern Ghana ◽  
Land Races ◽  
Diversity Assessment ◽  
Parental Lines ◽  
Number Of Seeds

In Ghana, sesame is cultivated in some districts of northern Ghana. Genotypes cultivated are land races that are low yielding leading to decline in production. There is the need for improvement of these land races to generate high yielding cultivars. Characterization of genetic diversity of the sesame land races will be of great value in assisting in parental lines selection for sesame breeding programmes in Ghana. Twenty-five sesame land races were collected from five districts in northern Ghana noted for sesame cultivation. Seeds collected were planted in three replicates in randomized complete block design and were evaluated for a number of morphological characters. Data collected were subjected to Principal Component Analysis (PCA) and a dendrogram showing similarity between the accessions were drawn. Data on number of capsules per plant, number of seeds per capsule, and plant height at flowering were subjected to analysis of variance using GenStat Discovery Edition 4. Molecular genetic diversity was assessed by using thirty eight SSR markers widely distributed across sesame genome to characterize the materials. Twenty-one out of the 38 primers were polymorphic. Cluster analyses using the Euclidean similarity test and a complete link clustering method were used to make a dendrogram out of the morphological data. Analysis of variance showed that capsule number was significantly different; a range of 54.9 and 146.7 was produced. The number of seeds per capsule varied significantly and the variation between highest and lowest accession in seed production was 33%. Plant height was also significantly different ranging from 60.6 to 94.1 cm. Using morphological traits the accessions clustered into two major groups and two minor groups and variation among accessions were 10-61%. On the other hand, SSR marker-based dendrogram revealed five major and two minor groups. It showed that variation among the accessions was low, 10-20%. Heterozygosity was 0.52, total alleles produced were 410, and average allele per locus was 19.52. Six accessions, C3, C4, S5, W1, W3, and W5 fell in five different clusters in the SSR dendrogram and in six clusters in the morphomolecular based dendrogram. These accessions were noted for high capsule number per plant and seeds number per capsule and are recommended for consideration as potential parental lines for breeding programme for high yield.

Genetic diversity among potato species as revealed by phenotypic resistances and SSR markers

2013 ◽  
Vol 11 (2) ◽  
pp. 131-139 ◽  
Author(s):  
D. Carputo ◽  
D. Alioto ◽  
R. Aversano ◽  
R. Garramone ◽  
V. Miraglia ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Sources Of Resistance ◽  
Wild Potato Species ◽  
Resistance Response ◽  
Potato Species ◽  
Average Value ◽  
Ssr Analysis ◽  
Efficient Breeding ◽  
Resistant Genotypes

The evolutionary diversity of wild potato species makes them excellent materials for improving the narrow genetic basis of the cultivated potato Solanum tuberosum. Understanding their genetic diversity is important not only to choose the best parents for breeding, but also to design proper crossing schemes and selection strategies. The objectives of this study were to determine the resistance response to Ralstonia solanacearum, Potato virus Y and low temperatures of 21 clones of 12 potato species, and to determine their genetic diversity through simple sequence repeat (SSR) markers. Sources of resistance have been found for all the investigated traits, with high resistance variability not only between but also within species. Combined resistances were also identified, with positive implications for efficient breeding. SSR analysis allowed the detection of 12 loci and 46 alleles across all genotypes, with an average value of 3.8 alleles per locus. Both unique and rare alleles useful for marker-assisted selection were found. SSR-based cluster analysis revealed that resistant genotypes were distributed among all clusters, suggesting that genetically different resistant genotypes were identified. The information obtained in this study is discussed from a breeding perspective.

scholarly journals Cross Species/Genera Transferability of SSR Markers, Genetic Diversity and Population Structure Analysis in Gladiolus (Gladiolus × grandiflorus L.) Genotypes

2021 ◽  
Author(s):  
Varun Hiremath ◽  
Kanwar Pal Singh ◽  
Neelu Jain ◽  
Kishan Swaroop ◽  
Pradeep Kumar Jain ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Ssr Markers ◽  
Structure Analysis ◽  
Genetic Relationships ◽  
Crop Improvement ◽  
Test Analysis ◽  
Average Value ◽  
Population Structure Analysis ◽  
Genetic Diversity And Structure

Abstract Genetic diversity and structure analysis using molecular markers is necessary for efficient utilization and sustainable management of gladiolus germplasm. Genetic analysis of gladiolus germplasm using SSR markers is largely missing due to scarce genomic information. In the present investigation, we report 66.66% cross transferability of Gladiolus palustris SSRs whereas 48% of Iris EST-SSRs were cross transferable across the gladiolus genotypes used in the study. A total of 17 highly polymorphic SSRs revealed a total 58 polymorphic loci ranging from two to six in each locus with an average of 3.41 alleles per marker. PIC values ranged from 0.11 to 0.71 with an average value of 0.48. Four SSRs were selectively neutral based on Ewens-Watterson test. Analysis of genetic structure of 84 gladiolus genotypes divided whole germplasm into two subpopulations. 35 genotypes were assigned to subpopulation 1 whereas 37 to subpopulation 2 and rest of the genotypes recorded as admixture. Analysis of molecular variance indicated maximum variance (53.59%) among individuals within subpopulations whereas 36.55% of variation observed among individuals within total population. Least variation (9.86%) was noticed between two subpopulations. Moderate (FST = 0.10) genetic differentiation of two subpopulations was observed. Grouping pattern of population structure was consistent with UPGMA dendrogram based on simple matching dissimilarity coefficient (ranged from 01.6 to 0.89) and PCoA. Genetic relationships assessed among the genotypes of respective clusters assist the breeders in selecting desirable parents for crossing. SSR markers from present study can be utilized for cultivar identification, conservation and sustainable utilization of gladiolus genotypes for crop improvement.

scholarly journals Molecular Diversity Analysis in Boro Rice (Oryza sativa L.) Landraces using SSR Markers

2021 ◽  
pp. 36-48
Author(s):  
Farhana Afrin Vabna ◽  
Mohammad Zahidul Islam ◽  
Md. Ferdous Rezwan Khan Prince ◽  
Md. Ekramul Hoque
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Molecular Diversity ◽  
Genetic Relationships ◽  
Group Method ◽  
Diversity Analysis ◽  
Average Value ◽  
Rice Landraces ◽  
Boro Rice ◽  
Research Institute

Aims: The aim of the study was to determine the genetic diversity of twenty four Boro rice landraces using rice genome specific twelve well known SSR markers. Study Design: Genomic DNA extraction, PCR amplification, Polyacrylamide gel electrophoresis (PAGE) and data analysis-these steps were followed to perform the research work. Data was analysed with the help of following software; POWERMAKER version 3.25, AlphaEaseFC (Alpha Innotech Corporation) version 4.0. UPGMA dendrogram was constructed using MEGA 5.1 software. Place and Duration of Study: The study was conducted at the Genetic Resources and Seed Division (GRSD), Bangladesh Rice Research Institute (BRRI), Joydebpur, Gazipur, Bangladesh during the period of November 2017 to March 2018. Methodology: Simple Sequence Repeat (SSR) markers were used to assay 24 landraces of Boro rice collected from the Gene Bank of Bangladesh Rice Research Institute (BRRI). Results: A total fifty four (54) alleles were detected, out of which forty five (45) polymorphic alleles were identified. The Polymorphic Information Content (PIC) of SSR markers ranged from 0.08 (RM447) to 0.84 (RM206) with an average value of PIC = 0.49. Gene diversity ranges from 0.08 (RM447) to 0.86 (RM206) with an average value of 0.52. The RM206 marker can be considered as the best marker among the studied markers for 24 rice landraces. Dendrogram based on Nei’s genetic distance using Unweighted Pair Group Method of Arithmetic Mean (UPGMA) indicated the segregation of 24 genotypes into three main clusters. Conclusion: The result revealed that SSR markers are very effective tools in the study of genetic diversity and genetic relationships and this result can be conveniently used for further molecular diversity analysis of rice genotypes to identify diverse parent for the development of high yielding variety in rice.

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 SSR Marker-Assisted Management of Parental Germplasm in Sugarcane (Saccharum spp. hybrids) Breeding Programs

Agronomy ◽  
2019 ◽  
Vol 9 (8) ◽  
pp. 449 ◽  
Author(s):  
Jiantao Wu ◽  
Qinnan Wang ◽  
Jing Xie ◽  
Yong-Bao Pan ◽  
Feng Zhou ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Capillary Electrophoresis ◽  
Population Structure ◽  
Ssr Markers ◽  
High Performance ◽  
Breeding Programs ◽  
Saccharum Spp ◽  
Parental Lines ◽  
Assisted Management ◽  
High Performance Capillary Electrophoresis

Sugarcane (Saccharum spp. hybrids) is an important sugar and bioenergy crop with a high aneuploidy, complex genomes and extreme heterozygosity. A good understanding of genetic diversity and population structure among sugarcane parental lines is a prerequisite for sugarcane improvement through breeding. In order to understand genetic characteristics of parental lines used in sugarcane breeding programs in China, 150 of the most popular accessions were analyzed with 21 fluorescence-labeled simple sequence repeats (SSR) markers and high-performance capillary electrophoresis (HPCE). A total of 226 SSR alleles of high-resolution capacity were identified. Among the series obtained from different origins, the YC-series, which contained eight unique alleles, had the highest genetic diversity. Based on the population structure analysis, the principal coordinate analysis (PCoA) and phylogenetic analysis, the 150 accessions were clustered into two distinct sub-populations (Pop1 and Pop2). Pop1 contained the majority of clones introduced to China (including 28/29 CP-series accessions) while accessions native to China clustered in Pop2. The analysis of molecular variance (AMOVA), fixation index (Fst) value and gene flow (Nm) value all indicated the very low genetic differentiation between the two groups. This study illustrated that fluorescence-labeled SSR markers combined with high-performance capillary electrophoresis (HPCE) could be a very useful tool for genotyping of the polyploidy sugarcane. The results provided valuable information for sugarcane breeders to better manage the parental germplasm, choose the best parents to cross, and produce the best progeny to evaluate and select for new cultivar(s).

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