Genetic diversity analysis of rice varieties (Oryza sativaL.) based on morphological, pedigree and DNA polymorphism data

2005 ◽  
Vol 3 (3) ◽  
pp. 353-359 ◽  
Author(s):  
Jorge Luis Fuentes ◽  
Maria Teresa Cornide ◽  
Alba Alvarez ◽  
Enrique Suarez ◽  
Ernesto Borges
Keyword(s):  
Genetic Diversity ◽  
Morphological Traits ◽  
Phenotypic Diversity ◽  
Group Method ◽  
Rice Varieties ◽  
Pair Group ◽  
Breeding Programmes ◽  
Genetic Pools ◽  
Diversity Estimates ◽  
Genealogical Information

The diversity within 20 rice varieties used as progenitors in Cuban rice breeding programmes was analysed with respect to agro-morphological traits, pedigree and DNA markers. Eleven agro-morphological traits were scored, and phenotypic (Euclidian) distances between the rice varieties were calculated. Sixty random amplified polymorphism DNA (RAPD) and 115 amplified fragment length polymorphism (AFLP) bands served to determine Dice's distance estimates. Cluster analyses were performed based on genetic distance matrices using the unweighted pair-group method of arithmetical means (UPGMA) as the clustering method. This analysis showed five phenotypic, six genealogical, five RAPD and six AFLP diversity groups. Genetic diversity estimates based on RAPD data, but not on AFLP, efficiently represented the genetic parentage and phenotypic diversity between rice varieties. Combined diversity estimates allowed the identification of 11 different genetic pools and permitted a more effective separation of the progenitor set than those obtained solely by phenotypic and genealogical information. The results of this study stress the necessity to diversify rice parental stocks for further breeding purposes.

scholarly journals Genetic Diversity in Aus Rice Genotypes using ILP Markers

2017 ◽  
Vol 20 (2) ◽  
pp. 13-19
Author(s):  
MA Siddique ◽  
M Khalequzzaman ◽  
MZ Islam ◽  
ESMH Rashid ◽  
MHK Baktiar ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Distance Matrix ◽  
Group Method ◽  
Intron Length Polymorphism ◽  
Arithmetic Average ◽  
Pair Group ◽  
Conservation Genetic ◽  
Breeding Programmes ◽  
Rice Genotypes ◽  
Selection Of

Assessment of genetic diversity is essential for germplasm characterization, utilization and conservation. Genetic diversity of 31 Aus rice genotypes of Bangladesh was assessed using 11 ILP (intron length polymorphism) markers. A total of 28 alleles were detected and the number of alleles per locus varied from 2 (RI01779, RI05751, RI05304, RI03205, RI00299, RI05407) to 4 (RI05559). The PIC values ranged from 0.06 (RI05407) to 0.57 (RI05559) with an average of 0.33. PIC value revealed that RI05559 was the best ILP markers for the studied 31 Aus rice genotypes. The dendrogram from unweighted pair-group method with arithmetic average clustering classified the genotypes into five groups at a coefficient of 0.57. Two dimensional graphical views of Principal Coordinate Analysis (PCoA) revealed that the genotypes Kuchmuch, Kalo dhan, Aus dhan, Sadey aus, Chaina and Dighi bawalia were found far away from the centroid of the cluster and can be seslected as parents for further breeding programmes. Parangi and V3, Adubali and H1-2, Begunbichi and Hashikalmi had closest distance (0.000) in the distance matrix might have same genetic background. This information will be useful for the selection of genetically diversed parents and assist in trait development using genotypes in rice breeding programmes in future. The results provided some useful implications for establishment of sovereignty of Bangladeshi rice gene pool. It was also suggested that ILP markers could be very useful for the genetic study and breeding in rice.Bangladesh Rice j. 2016, 20(2): 13-19

scholarly journals Genetic DiversityAssessment in Ten Aromatic Rice Varieties of Bangladesh

2017 ◽  
Vol 27 (2) ◽  
pp. 217-225 ◽  
Author(s):  
Tahmina Islam ◽  
Shinthia Rahman ◽  
M Imdadul Hoque ◽  
RH Sarker
Keyword(s):  
Genetic Diversity ◽  
Oryza Sativa L ◽  
Group Method ◽  
Aromatic Rice ◽  
Arithmetic Means ◽  
Rice Varieties ◽  
Center Of Origin ◽  
Pair Group ◽  
Relationship Of ◽  
Selection Of

The availability of molecular marker systems allowed estimating the relationships among various taxa. This study was aimed at assessing the genetic diversity among ten aromatic rice (Oryza sativa L.) pools from Bangladesh by means of randomly amplified polymorphic DNA (RAPD) markers. These varieties were evaluated for polymorphisms after amplification with 10 decamer primers. A total of 60 RAPD fragments were generated among the assessed varieties with a polymorphism percentage of 80. Cluster analysis by the unweighted pair group method of arithmetic means (UPGMA) showed that these 10 varieties could be placed into two groups with a similarity ranging from 65 to 86% depicting adjacent association between Rajbhog and Kalijira‐12, whereas Maloti belongs to a separate group maintaining maximum distance from rest of the varieties. The analysis revealed that the intervarietal genetic relationship of several varieties is related to their center of origin. As expected, most of the varieties have a narrow genetic base. The present results could be used for the selection of possible parents to generate a mapping population and utilized by the breeders for assessing the genetic diversity of rice genotypes.Plant Tissue Cult. & Biotech. 27(2): 217-225, 2017 (December)

scholarly journals Assessment of genetic diversity and differentiation among four indigenous Turkish sheep breeds using microsatellites

2020 ◽  
Vol 63 (1) ◽  
pp. 165-172
Author(s):  
Bahar Argun Karsli ◽  
Eymen Demir ◽  
Huseyin Goktug Fidan ◽  
Taki Karsli
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Polymorphic Information Content ◽  
Climatic Conditions ◽  
Group Method ◽  
Sheep Breeds ◽  
Livestock Species ◽  
Pair Group ◽  
Breeding Programmes ◽  
Study Population

Abstract. Conservation and breeding programmes of livestock species depend on determination of genetic diversity. Today in livestock species, microsatellite markers are commonly used to reveal population structure and genetic diversity in both breeds and varieties. In this study, population structure, genetic diversity, and differentiation among four native Turkish sheep breeds including Güney Karaman, Kangal, Norduz, and Karakas were assessed by using 21 microsatellite loci. By genotyping 120 individuals belonging to four sheep breeds, a total of 275 different alleles, 37 of which were private alleles, were observed across all loci. The mean number of alleles per breed ranged from 7.28 (Güney Karaman) to 8.09 (Karakas), while allelic richness ranged from 7.22 (Güney Karaman) to 7.87 (Karakas). Mean observed heterozygosity varied from 0.60 (Kangal) to 0.66 (Norduz and Karakas). The lowest pairwise FST value (0.084) was between Kangal and Karakas populations, while the highest pairwise FST value (0.142) was between Norduz and Karakas populations. Polymorphic information content (PIC) values, ranging from 0.71 (ETH10) to 0.91 (OarFCB304), were highly polymorphic (PIC > 0.5) and informative in studied populations. In the present study, the results of phylogenetic analysis were of importance, since all studied populations have been accepted as Akkaraman varieties till today. However, factorial correspondence and structure analysis, pairwise FST values, and an unweighted pair group method with arithmetic mean analysis (UPGMA) dendrogram revealed that Güney Karaman and Norduz populations have became genetically different from the Akkaraman breed due being raised in different parts of Turkey under different climatic conditions together with their breeding practices. Therefore, we recommend that more comprehensive molecular studies should be conducted to clarify genetic differentiation of Akkaraman sheep varieties.

scholarly journals Genetic Variability in Bangladeshi Aromatic Rice through RAPD Analysis

2014 ◽  
Vol 3 (3) ◽  
pp. 107 ◽  
Author(s):  
Mehfuz Hasan ◽  
Mohammad Sharif Raihan
Keyword(s):  
Genetic Diversity ◽  
Rapd Analysis ◽  
Oryza Sativa L ◽  
Random Amplified Polymorphic Dna ◽  
Group Method ◽  
Aromatic Rice ◽  
Similarity Coefficients ◽  
Rice Varieties ◽  
Pair Group ◽  
Minimum Number

Genetic polymorphism and relationships among 30 commercial varieties of Bangladeshi aromatic rice (Oryza sativa L.) were established using random amplified polymorphic DNA (RAPD) primers. Out of fifty 10-mer RAPD primers screened initially, four were chosen and used in a comparative analysis of different varieties of indigenous Bangladeshi aromatic rice. Of the 33 total RAPD fragments amplified, 7 (21.21%) were found to be shared by individuals of all eight varieties. The remaining 26 fragments were found to be polymorphic (78.79%). Pair-wise estimates of similarity ranged from 0.101 to 0.911. Highest genetic diversity was determined between Radhunipagol and Dubsail varieties (0.911). The amount of genetic diversity within aromatic rice germplasm was quite high as determined by the genetic similarity coefficients between varieties. Genetic similarities obtained from RAPD data were also used to create a cluster diagram. Cluster analysis using an un-weighted pair-group method with arithmetic averages (UPGMA) was used to group the varieties and the 30 aromatic rice varieties were grouped into 6 clusters where cluster I includes the maximum number of varieties (9). Cluster VI includes minimum number of varieties (2). This Study offered a rapid and reliable method for the estimation of variability between different varieties which could be utilized by the breeders for further improvement of the local aromatic rice varieties.

PROFILING OF GUAVA GENOTYPES GROWN IN VIDARBHA CONDITIONS ON THE BASIS OF MORPHOLOGICAL TRAITS

2017 ◽  
Vol 23 (1) ◽  
Author(s):  
R.A. PATIL ◽  
S.G. BHARAD ◽  
S.N. SAWANT
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Morphological Traits ◽  
Considerable Extent ◽  
Fruit Traits ◽  
Breeding Programmes ◽  
Tree Leaf ◽  
Qualitative Characteristics ◽  
Intrapopulation Diversity

Assessment of genetic diversity in the available germplasm is the prerequisite for development of improved genotypes through planned breeding programmes. In the view of this Forty-eight genotypes of seedling origin guava along with 1 check (L-49/Sardar) collected and conserved at germplasm block, Main Garden, Department of Horticulture, Dr. P. D. A. University, Akola were evaluated for genetic variability and diversity based on the qualitative characteristics. The genotypes were evaluated for sixteen morphological traitsviz. tree, leaf, floral and fruit traits. Results Show considerable extent of variability amongst the 49 genotypes in each traits. A sizeable amount of intrapopulation diversity recorded can be used to identify diverse parents which can be utilized in hybridization programmes.

scholarly journals Genetic Diversity Among Some Walnut (Juglans regia L.) Genotypes by SSR Markers

2021 ◽  
Vol 13 (12) ◽  
pp. 6830
Author(s):  
Murat Guney ◽  
Salih Kafkas ◽  
Hakan Keles ◽  
Mozhgan Zarifikhosroshahi ◽  
Muhammet Ali Gundesli ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Plant Genetic Resources ◽  
Juglans Regia ◽  
Genetic Distances ◽  
Mean Value ◽  
Central Anatolia ◽  
Group Method ◽  
Arithmetic Average ◽  
Pair Group ◽  
Principal Coordinates

The food needs for increasing population, climatic changes, urbanization and industrialization, along with the destruction of forests, are the main challenges of modern life. Therefore, it is very important to evaluate plant genetic resources in order to cope with these problems. Therefore, in this study, a set of ninety-one walnut (Juglans regia L.) accessions from Central Anatolia region, composed of seventy-four accessions and eight commercial cultivars from Turkey, and nine international reference cultivars, was analyzed using 45 SSR (Simple Sequence Repeats) markers to reveal the genetic diversity. SSR analysis identified 390 alleles for 91 accessions. The number of alleles per locus ranged from 3 to 19 alleles with a mean value of 9 alleles per locus. Genetic dissimilarity coefficients ranged from 0.03 to 0.68. The highest number of alleles was obtained from CUJRA212 locus (Na = 19). The values of polymorphism information content (PIC) ranged from 0.42 (JRHR222528) to 0.86 (CUJRA212) with a mean PIC value of 0.68. Genetic distances were estimated according to the UPGMA (Unweighted Pair Group Method with Arithmetic Average), Principal Coordinates (PCoA), and the Structure-based clustering. The UPGMA and Structure clustering of the accessions depicted five major clusters supporting the PCoA results. The dendrogram revealed the similarities and dissimilarities among the accessions by identifying five major clusters. Based on this study, SSR analyses indicate that Yozgat province has an important genetic diversity pool and rich genetic variance of walnuts.

scholarly journals Assessment of the Genetic Diversity of Rice Germplasms Characterized by Black-Purple and Red Pericarp Color Using Simple Sequence Repeat Markers

Plants ◽  
2019 ◽  
Vol 8 (11) ◽  
pp. 471
Author(s):  
Jae-Ryoung Park ◽  
Won-Tae Yang ◽  
Yong-Sham Kwon ◽  
Hyeon-Nam Kim ◽  
Kyung-Min Kim ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Germplasm Collection ◽  
Group Method ◽  
Sequence Repeat ◽  
Rice Varieties ◽  
Red Pericarp ◽  
Simple Sequence ◽  
Colored Rice

The assessment of the genetic diversity within germplasm collections can be accomplished using simple sequence repeat (SSR) markers and association mapping techniques. The present study was conducted to evaluate the genetic diversity of a colored rice germplasm collection containing 376 black-purple rice samples and 172 red pericarp samples, conserved by Dong-A University. There were 600 pairs of SSR primers screened against 11 rice varieties. Sixteen informative primer pairs were selected, having high polymorphism information content (PIC) values, which were then used to assess the genetic diversity within the collection. A total of 409 polymorphic amplified fragments were obtained using the 16 SSR markers. The number of alleles per locus ranged from 11 to 47, with an average of 25.6. The average PIC value was 0.913, ranging from 0.855 to 0.964. Four hundred and nine SSR loci were used to calculate Jaccard’s distance coefficients, using the unweighted pair-group method with arithmetic mean cluster analysis. These accessions were separated into several distinctive groups corresponding to their morphology. The results provided valuable information for the colored rice breeding program and showed the importance of protecting germplasm resources and the molecular markers that can be derived from them.

scholarly journals Genetic diversity in table grapes based on RAPD and microsatellite markers

2011 ◽  
Vol 46 (9) ◽  
pp. 1035-1044 ◽  
Author(s):  
Patrícia Coelho de Souza Leão ◽  
Sérgio Yoshimitsu Motoike
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Genetic Relationships ◽  
Similarity Index ◽  
Genetic Distances ◽  
Table Grape ◽  
Group Method ◽  
Molecular Characteristics ◽  
Table Grapes ◽  
Pair Group

The objective of this work was to analyze the genetic diversity of 47 table grape accessions, from the grapevine germplasm bank of Embrapa Semiárido, using 20 RAPD and seven microsatellite markers. Genetic distances between pairs of accessions were obtained based on Jaccard's similarity index for RAPD data and on the arithmetic complement of the weighted index for microsatellite data. The groups were formed according to the Tocher's cluster analysis and to the unweighted pair‑group method with arithmetic mean (UPGMA). The microsatellite markers were more efficient than the RAPD ones in the identification of genetic relationships. Information on the genetic distance, based on molecular characteristics and coupled with the cultivar agronomic performance, allowed for the recommendation of parents for crossings, in order to obtain superior hybrids in segregating populations for the table grape breeding program of Embrapa Semiárido.

AFLP-based assessment of genetic diversity among nine alfalfa germplasms using bulk DNA templates

Genome ◽  
2003 ◽  
Vol 46 (1) ◽  
pp. 51-58 ◽  
Author(s):  
A Segovia-Lerma ◽  
R G Cantrell ◽  
J M Conway ◽  
I M Ray
Keyword(s):  
Genetic Diversity ◽  
Medicago Sativa ◽  
High Throughput ◽  
Genetic Distances ◽  
Group Method ◽  
Aflp Analysis ◽  
Dna Templates ◽  
Arithmetic Average ◽  
Pair Group ◽  
Large Numbers

Improving commercial utilization of perennial Medicago collections requires developing approaches that can rapidly and accurately characterize genetic diversity among large numbers of populations. This study evaluated the potential of using amplified fragment length polymorphism (AFLP) DNA markers, in combination with DNA bulking over multiple genotypes, as a strategy for high-throughput characterization of genetic distances (D) among alfalfa (Medicago sativa L.) accessions. Bulked DNA templates from 30 genotypes within each of nine well-recognized germplasms (African, Chilean, Flemish, Indian, Ladak, Medicago sativa subsp. falcata, Medicago sativa subsp. varia, Peruvian, and Turkistan) were evaluated using 34 primer combinations. A total of 3754 fragments were identified, of which 1541 were polymorphic. The number of polymorphic fragments detected per primer combination ranged from 20 to 85. Pairwise D estimates among the nine germplasms ranged from 0.52 to 1.46 with M. sativa subsp. falcata being the most genetically dissimilar. Unweighted pair-group method arithmetic average (UPGMA) analysis of the marker data produced two main clusters, (i) M. sativa subsp. sativa and M. sativa subsp. varia, and (ii) M. sativa subsp. falcata. Cluster-analysis results and D estimates among the Chilean, Peruvian, Flemish, and M. sativa subsp. varia germplasms supported the hypothesis that Peruvian was more similar to original Spanish introductions into Central and South America than Chilean. Hierarchical arrangement of the nine germplasms was supported by their respective geographic, subspecific, and intersubspecific hybrid origins. Subsets of as few as seven highly informative primer pairs were identified that produced comparable D estimates and similar heirarchical arrangements compared with the complete dataset. The results indicate that use of primer-pair subsets for AFLP analysis of bulk DNA templates could serve as a high-throughput system for accurately characterizing genetic diversity among large numbers of alfalfa populations.Key words: Medicago sativa, DNA bulking, genetic distance.

Characterization of Pyrenophora tritici-repentis in Tunisia and Comparison with a Global Pathogen Population

Plant Disease ◽  
2021 ◽  
Author(s):  
Marwa Laribi ◽  
Alireza Akhavan ◽  
Sarrah M'Barek ◽  
Amor Yahyaoui ◽  
Stephen Ernest Strelkov ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Geographic Origin ◽  
Tan Spot ◽  
Pcr Analysis ◽  
Group Method ◽  
Region Of Origin ◽  
Pyrenophora Tritici Repentis ◽  
Pair Group ◽  
Necrotrophic Effector

Pyrenophora tritici-repentis (Ptr) causes tan spot, an important foliar disease of wheat. A collection of Ptr isolates from Tunisia, located in one of the main secondary centers of diversification of durum wheat, was tested for phenotypic race classification based on virulence on a host differential set, and for the presence of the necrotrophic effector (NE) genes ToxA, ToxB , and toxb by PCR analysis. While races 2, 4, 5, 6, 7, and 8 were identified according to their virulence phenotypes, PCR testing indicated the presence of ‘atypical’ isolates that induced necrosis on the wheat differential ‘Glenlea’, but lacked the expected ToxA gene, suggesting the involvement of other NEs in the Ptr/wheat interaction. Genetic diversity and the Ptr population structure were explored further by examining 59 Tunisian isolates and 35 isolates from Algeria, Azerbaijan, Canada, Iran, and Syria using 24 simple sequence repeat markers. Average genetic diversity, overall gene flow and percentage polymorphic loci were estimated as 0.58, 2.09 and 87%, respectively. Analysis of molecular variance showed that 81% of the genetic variance occurred within populations and 19% between populations. Cluster analysis by the unweighted pair group method indicated that ToxB- isolates grouped together and were distantly related to ToxB+ isolates. Based on Nei’s analysis, the global collection clustered into two distinct groups according to their region of origin. The results suggest that both geographic origin and the host-specificity imposed by different NEs can lead to differentiation among Ptr populations.

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