scholarly journals Evaluation of genetic diversity and DNA fingerprinting of 19 standard reference rice varieties using SSR markers

2020 ◽  
Vol 16 (4) ◽  
pp. 603-609
Author(s):  
Tran Long ◽  
Luu Minh Cuc ◽  
Nguyen Quang Sang ◽  
Pham Xuan Hoi
Keyword(s):  
Genetic Diversity ◽  
Dna Fingerprinting ◽  
Genetic Similarity ◽  
Similarity Coefficient ◽  
International Union ◽  
Rice Varieties ◽  
Reference Marker ◽  
High Uniformity ◽  
New Varieties ◽  
Group 2

Molecular markers are advanced-tools for identifying new varieties at DNA levels. According to the International Union for the Protection of New Varieties ofPlants,  new breeded varieties need to be tested for the Distinctness, Uniformity and Stability (DUS), before being recognized as the new ones. Traditional DUS criteria based on 62 - 65 morphological and biochemical characteristics, which evaluated on comparison of new varieties with 19 standard reference varieties for traits of interest.  Study on the genotypic polymorphism of 19 standard reference rice varieties provides genotypic information of these varieties for the evaluation of new rice varieties based on genotyping analysis.  The reference marker set (30 markers) was used to evaluate the genetic diversity and DNA fingerprinting of 19 standard reference rice varieties. The results showed the similarity coefficient of 19 varieties varied from 0.04 to 0.548. At the genetic similarity coefficient of 0.1, the 19 rice varieties divided into two main groups. Group one included 3 varieties: DH1, DH5, DH13. Group 2 included the remaining 16 varieties. Inside group two, phylogenetic tree divided into two main branches at the genetic similarity coefficient of 0.3. Branch 1 includes 5 varieties including DH2, DH6, DH10, DH11 and DH7. The 11 remaining varieties were in the branch 2. The most closely varieties were DH6 and DH10 with the genetic similarity coefficient of 0.548. This study shows that, the standard reference varieties have high uniformity and high genotypic polymorphism, could used for testing new varieties based on genotyping by DNA fingerprinting combining with phenotype.

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 Genetic diversity in different populations of sloths assessed by DNA fingerprinting

2002 ◽  
Vol 62 (3) ◽  
pp. 503-508 ◽  
Author(s):  
N. MORAES ◽  
J. S. MORGANTE ◽  
C. Y. MIYAKI
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Dna Fingerprinting ◽  
Genetic Similarity ◽  
Similarity Indices ◽  
Different Populations ◽  
Related Individuals ◽  
Low Levels ◽  
Dna Profiles ◽  
Two Populations

In this study we analyzed a population of Bradypus torquatus with individuals originally distributed in different localities of Bahia, and two populations of B. variegatus with individuals from Bahia and São Paulo States. Using the DNA fingerprinting method, we assessed the genetic variability within and between populations. Analysis of the DNA profiles revealed genetic similarity indices ranging from 0.34 ± 0.07 to 0.87 ± 0.04. Similar low levels of genetic variability were found only in isolated mammalian populations or among related individuals. This study presents the first analyses of genetic diversity in sloth populations.

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.

Improved Livelihoods, Genetic Diversity and Farmer Participation: A Strategy for Rice Breeding in Rainfed Areas of India

1988 ◽  
Vol 24 (3) ◽  
pp. 311-320 ◽  
Author(s):  
D. M. Maurya ◽  
A. Bottrall ◽  
J. Farrington
Keyword(s):  
Genetic Diversity ◽  
Plant Breeding ◽  
Alternative Strategy ◽  
Central Feature ◽  
Rice Breeding ◽  
Farmer Participation ◽  
Rice Varieties ◽  
New Varieties ◽  
On Farm ◽  
Traditional Rice

SUMMARYThe present structure of plant breeding and seed multiplication in India is highly centralized. Furthermore, only a small number of new varieties is officially released each year. The system therefore appears inappropriate for the requirements of the large proportion of Indian farmers located in risk-prone and highly diverse environments. An alternative strategy is described whose central feature is close matching of the characteristics of farmers' traditional rice varieties with those of advanced breeders' lines. A selection from these lines is then distributed in small quantities for on-farm trials managed by farmers themselves. If the success of these initial efforts is to be sustained, a more decentralized approach to breeding and multiplication will be necessary.

Genetic diversity in four cabbage populations based on UPOV and IPGRI description forms and allozyme variation

2001 ◽  
Vol 136 (3) ◽  
pp. 309-318 ◽  
Author(s):  
T. V. KOUTSOS ◽  
M. KOUTSIKA-SOTIRIOU
Keyword(s):  
Genetic Diversity ◽  
Principal Component Analysis ◽  
Plant Genetic Resources ◽  
Principal Component ◽  
Allozyme Variation ◽  
Gene Frequencies ◽  
International Union ◽  
New Varieties ◽  
International Plant ◽  
Physiological Characters

Morphophysiological characters, designated as descriptors by the International Union for the Protection of New Varieties of Plants (UPOV) and the International Plant Genetic Resources Institute (IPGRI), and allozyme variation were used to study genetic diversity among four cabbage (Brassica oleracea L. var. capitata L.) open pollinated (OP) populations. The morphological and physiological characters, and gene frequencies among OP populations were analysed by using cluster (CA) and principal component analysis (PCA). Both methods gave the same clustering of OP populations. The relationships found among OP populations by analysing UPOV descriptors (30 characters) and IPGRI descriptors (30+14 characters) were similar. The relationships among OP populations obtained from gene frequencies were not similar to those obtained from morphophysiological characters, but two of the four OP populations were clustered together by both categories of data. The biggest correlation between the relationships among OP populations obtained from morphophysiological characters and those obtained from gene frequencies was r = −0·44 and r =−0·38 given by PCA and CA respectively. The importance of each character or allele with respect to the relationships among OP populations were also detected by PCA.

scholarly journals GENETIC DIVERSITY AMONG NATURAL POPULATIONS OF Keteleeria evelyniana Mast. IN CENTRAL HIGLANDS OF VIETNAM USING SSR MARKERS

2018 ◽  
Vol 56 (3) ◽  
pp. 275
Author(s):  
Tran Thi Lieu ◽  
Dinh Thi Phong ◽  
Vu Thi Thu Hien
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Similarity ◽  
Natural Populations ◽  
Similarity Coefficient ◽  
Similarity Matrix ◽  
Analysis Of Molecular Variance ◽  
Molecular Variance ◽  
Private Alleles ◽  
Softwood Species

Keteleeria evelyniana Mast. is a big softwood species with high economic values. Therefore, the number of these trees are rapidly decreasing due to rampant exploitation as well as its habitat loss and recently, the species is considered vulnerablein Vietnam. In this study, we assessed the genetic variation among seventy K. evelyniana samples of three natural populations in Lam Dong, Dak Lak and Kon Tum using 16 microsatellite markers. The results showed that thirteen markers were polymorphic. A total 39 DNA fragments were amplified, among them, thirty – five were polymorphic (accounting for 89.74%). Among studied populations, the level of genetic diversity at Lam Dong (Na = 2.063; Ne = 1.730; Ap = 0.375; I = 0.558; Ho = 0.459 and He = 0.367) was the highest. Analysis of molecular variance (AMOVA) showed that the total level of molecular changes between populations was 34.65% and between individuals in the same population was 65.35%. Private alleles (Ap) and inbreeding values (Fis) of K. evelyniana species were founded of all three populations in Lam Dong, Dak Lak and Kon Tum (0.375 and -0.234; 0.188 and -0.065; 0.063 and -0.047, respectively). The gene flow (Nm) also occurred among the K. evelyniana populations with the average of Nm = 5.423. A dendrogram (UPGMA) constructed based on the similarity matrix of 70 K. evelyniana samples divided into two main groups with their genetic similarity coefficient ranged from 76.5% (Ke26 and Ke44) to 99% (Ke23 and Ke25). The obtained results indicated the importance of conserving the genetic resources of K. evelyniana species in Tay Nguyen.

scholarly journals Assessment of RAPD Markers to Analyse the Genetic Diversity among Sunflower (Helianthus annuus L.) Genotypes

2018 ◽  
Vol 6 (1) ◽  
pp. 107 ◽  
Author(s):  
Ali Raza ◽  
Haseeb Shaukat ◽  
Qasim Ali ◽  
Madiha Habib
Keyword(s):  
Genetic Diversity ◽  
Genetic Similarity ◽  
Rapd Markers ◽  
Polymorphic Information Content ◽  
Random Amplified Polymorphic Dna ◽  
Future Studies ◽  
Group 2 ◽  
Maximum Similarity ◽  
Sunflower Genome ◽  
Group 1

Genetic diversity estimation among different species is an important tool for genetic improvement to maximize the yield, desirable quality, wider adaptation, pest and insect resistance that ultimately boosting traditional plant breeding methods. The most efficient way of diversity estimation is application of molecular markers. In this study, twenty random amplified polymorphic DNA (RAPD) primers were utilized to estimate the genetic diversity between ten sunflower genotypes. Overall 227 bands were amplified by 20 primers with an average of 11.35 bands per primer. RAPD data showed 86.34% polymorophic bands and 13.65% of monomorophic bands. Genetic similarity was ranged from 50.22% to 87.22%. The lowest similarity (50.22%) was observed between FH-352 and FH-359 and the maximum similarity 87.22% was observed between A-23 and G-46. Polymorphic information content (PIC) values were varying from 0.05 to 0.12 with a mean of 0.09. Cluster analysis based on RAPD results displayed two major distinct groups 1 and 2. Group-2 contains FH-352 which was the most diverse genotype, while group-1 consists of few sub groups with all other genotypes. Ample diversity was found in all the genotypes. Present study reveals novel information about sunflower genome which can be used in future studies for sunflower improvement.

scholarly journals Identifikasi Molekuler dan Analisis Kekerabatan Aksesi Nenas Menggunakan Marka RAPD Menunjang Perakitan Varietas Unggul Baru

2019 ◽  
Vol 28 (1) ◽  
pp. 1
Author(s):  
Sri Hadiati ◽  
Riry Prihatini ◽  
Ellina Mansyah
Keyword(s):  
Molecular Identification ◽  
Genetic Similarity ◽  
Rapd Marker ◽  
Computer Software ◽  
Similarity Coefficient ◽  
Ananas Comosus ◽  
Similarity Coefficients ◽  
Tropical Fruit ◽  
New Varieties ◽  
Polymorphism Level

<p><strong>(</strong><em><strong>Molecular Identification and Relationships Among Several Pineapple Accessions Using RAPD Marker to Support the Assembling New Varieties</strong></em><strong>)</strong></p><p>Produksi dan produktivitas nenas dapat ditingkatkan antara lain melalui penggunaan varietas unggul. Dalam perakitan varietas, dibutuhkan informasi hubungan kekerabatan antartetuanya agar diperoleh efek heterosis yang tinggi melalui kegiatan identifikasi secara molekuler. Penelitian bertujuan (1) mengetahui tingkat polimorfisme primer yang digunakan,(2) mengidentifikasi fragmen DNA spesifik yang membedakan individu atau kelompok individu nenas, dan (3) mengetahui hubungan kekerabatan antarspesies dan aksesi nenas. Penelitian dilaksanakan mulai bulan Mei–Desember 2014 di Laboratorium Uji Mutu Benih dan Molekuler Balai Penelitian Tanaman Buah Tropika. Sampel yang digunakan sebanyak 19 aksesi dari empat spesies nenas (Ananas comosus, A. bracteatus, A. lucidus, dan A. nanus). Sebanyak 20 marka rapid amplified polymorphism DNA (RAPD) digunakan dalam analisis. Data diskor secara biner kemudian dianalisis menggunakan program NTSYSpc 2,1x. Hasil analisis menunjukkan bahwa polimorfisme 20 primer yang diuji berkisar 33–100% dengan rata-rata 87%. Primer dengan tingkat polimorfisme 100%, yaitu RAPD3, OPA13, OPAV3, OPC12, OPC16, dan OPY15. Kelompok Cayenne dicirikan oleh marka RAPD1 ukuran1.000 base-pair (bp) dan OPAV3 700 bp. Kelompok Queen dapat diidentifikasikan oleh marka RAPD3 ukuran 700 bp, kelompok Spanish dengan marka RAPD2 dan RAPD3 ukuran 1.500 bp. Analisis kluster menunjukkan bahwa 19 aksesi yang diuji terpisah menjadi enam kelompok pada koefisien kesamaan genetik 0,75, yaitu kelompok Queen, Cayenne, Spanish, A. bracteatus, A. lucidus, dan A. nanus. Aksesi yang diuji mempunyai keragaman genetik yang luas dengan koefisien kesamaan genetik berkisar 0,41–0,85. Aksesi yang mempunyai kesamaan genetik tertinggi, yaitu antara N-73 dengan BB (0,85) dan terkecil, yaitu antara N-94 (A. nanus) dengan N-18 (Green Spanish) sebesar 0,41. Implikasi hasil penelitian adalah aksesi yang mempunyai kesamaan genetik tinggi salah satunya dapat dieliminasi untuk efisiensi dalam pengelolaan plasma nutfah, sedangkan aksesi-aksesi yang memiliki kesamaan genetik kecil, baik digunakan sebagai tetua persilangan agar diperoleh variabilitas genetik yang luas dan efek heterosis yang tinggi.</p><p><strong>Keywords</strong></p><p><em>Ananas</em> spp.; Identifikasi; Karakterisasi; Kekerabatan genetik; Molekuler.</p><p><strong>Abstract</strong></p><p>Pineapple production and productivity can increased by the use of superior variety. Pertaining to variety assembling, the relationship information among parents are needed to gain heterosis effect through molecular identification activity. This research was aimed to (1) determine the level of polymorphism primers used, (2) identify specific DNA fragments which discrete individual or group of pineapple, and (3) reveal genetic relationship among pineapple species and accessions. The experiment was conducted on May to December 2014 in Seeds Quality Testing and Molecular Laboratory of Indonesian Tropical Fruit Research Institute. Nineteen accessions from four species (Ananas comosus, A. brachteatus, A. lucidus, and A. nanus) of pineapple were used as samples. Twenty rapid amplified polymorphism DNA (RAPD) markers were used on molecular analysis. The data were scored binary and then they were analyzed using NTSYSpc 2.1x computer software. The analysis showed that the 20 primers had 33–100%  polymorphic with 87% in average. Primers with 100% polymorphism level were RAPD3, OPA13, OPAV3, OPC12, OPC16, and OPY15. Cayenne group could be denoted with RAPD1 and OPAV3 markers by 1,000 base-pairs (bp) and 700 bp band, respectively. Meanwhile the Queen group can be identified by 700 bp band  RAPD3 marker. The Spanish group can be specified by1,500 bp band RAPD2 and RAPD3 markers. Based on cluster analysis the 19  accessions were separated  into six groups with 0.75 genetic similarity coefficient i.e., Queen, Cayenne, Spanish, A. bracteatus, A. lucidus, and A. nanus. These accessions had a wide genetic diversity with 0.41 to (0.85) genetic similarity coefficients. The highest genetic similarity coefficient (0.85) was determined between N-73 and BB, whereas the lowest value down to 0.41 was indicated on N-94 (A. nanus) and N-18 (Green Spanish). The implications of this research are that one of two accessions that have high genetic similarities can be eliminated for efficiency in the management of germplasm. While accessions which  have little genetic similarity are both used as crosses parent in order to obtain wide genetic variability and high heterosis effects.</p>

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.

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