Genetic diversity in Tunisian castor genotypes (Ricinus communis L.) detected using RAPD markers

Castor (Ricinus communis L.) is a plant that is commercially very important to the world. It is produced in about 30 countries lying in the tropical belt of the world. It is an important plant for production of industrial oil. Assessment of genetic diversity of a crop species is a prerequisite to its improvement; hence it is important to identify the genetic diversity of castor genetic resources for development of improved cultivars. The present study is focused on estimation of genetic distance between 56 Tunisian castor genotypes, based on 18 RAPD markers. Seeds of castor were obtained from the University of Carthage, National Institute of Research in Rural Engineering, Waters and Forests (INRGREF), Regional Station of Gabès, Tunisia. The ricin genotypes were obtained from 12 regions of Tunisia. The efficacy of the RAPD technique in this study is further supported by the obtained PIC values of the primers used in the analysis. PCR amplification of DNA using 18 primers for RAPD analysis produced 145 DNA fragments that could be scored in all 56 genotypes of Tunisian castor. The number of amplified fragments varied from 3 (OPE-07) to 13 (SIGMA-D-01), and the amplicon size ranged from 100 to 1500 bp. Of the 145 amplified bands, 145 were polymorphic, with an average of 8.11 polymorphic bands per primer. The lowest values of polymorphic information content were recorded for RLZ 9 (0.618) and the the highest PIC values were detected for OPD-08 (0.846) with an average of 0.761. A dendrogram was constructed from a genetic distance matrix based on profiles of the 18 RAPD primers using the unweighted pair-group method with the arithmetic average (UPGMA). According to analysis, the collection of 56 Tunisian castor genotypes were clustered into five main clusters. Genetically the closest were four genotypes from cluster 1 (BT-1 – S-5 and K-1 – N-3). Knowledge of the genetic diversity of castor can be used in future breeding programs for increased oil production to meet the ever increasing demand of castor oil for industrial uses as well as for biodiesel production.

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Evaluation of Genetic Diversity in Castor (Ricinus communis L.) using RAPD Markes

Advanced Materials Research ◽

10.4028/www.scientific.net/amr.343-344.981 ◽

2011 ◽

Vol 343-344 ◽

pp. 981-987

Author(s):

Feng Juan Li ◽

Chang Lu Wang ◽

Dong He ◽

Ya Qiong Liu ◽

Mian Hua Chen ◽

...

Keyword(s):

Genetic Diversity ◽

Phylogenetic Tree ◽

Genetic Distance ◽

Oil Content ◽

Rapd Markers ◽

Rapd Analysis ◽

Ricinus Communis ◽

Major Group ◽

Ricinus Communis L ◽

Polymorphic Bands

RAPD markers are used to study the genetic diversity of the main planting on 37 castor varieties widely cultivated in china according to the oil content and other characteristic of different castor varieties. Genetic distance of 37 Chinese castor varieties is studied by RAPD markers analysis. RAPD analysis shows that a total of 122 bands are amplified from random primers of 20 S series, including 71 polymorphic bands with polymorphic rate of 58.20%. 37 castor beans are divided into four major groups in the phylogenetic tree. One castor germplasm is included in1, 2, 3 groups respectively, and two sub-groups are included in the 4 major group.

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Optimal use of SSR markers for varietal identification of upland cotton

Pesquisa Agropecuária Brasileira ◽

10.1590/s0100-204x2015000700007 ◽

2015 ◽

Vol 50 (7) ◽

pp. 571-581 ◽

Cited By ~ 1

Author(s):

Guilherme da Silva Pereira ◽

Ana Luíza Ramos Cazé ◽

Michelle Garcia da Silva ◽

Vanessa Cavalcante Almeida ◽

Fernanda Oliveira da Cunha Magalhães ◽

...

Keyword(s):

Genetic Distance ◽

Ssr Markers ◽

Polymorphic Information Content ◽

Group Method ◽

Discrimination Power ◽

Arithmetic Average ◽

Pair Group ◽

Varietal Identification ◽

The World ◽

The Mean

Abstract: The objective of this work was to identify polymorphic simple sequence repeat (SSR) markers for varietal identification of cotton and evaluation of the genetic distance among the varieties. Initially, 92 SSR markers were genotyped in 20 Brazilian cotton cultivars. Of this total, 38 loci were polymorphic, two of which were amplified by one primer pair; the mean number of alleles per locus was 2.2. The values of polymorphic information content (PIC) and discrimination power (DP) were, on average, 0.374 and 0.433, respectively. The mean genetic distance was 0.397 (minimum of 0.092 and maximum of 0.641). A panel of 96 varieties originating from different regions of the world was assessed by 21 polymorphic loci derived from 17 selected primer pairs. Among these varieties, the mean genetic distance was 0.387 (minimum of 0 and maximum of 0.786). The dendrograms generated by the unweighted pair group method with arithmetic average (UPGMA) did not reflect the regions of Brazil (20 genotypes) or around the world (96 genotypes), where the varieties or lines were selected. Bootstrap resampling shows that genotype identification is viable with 19 loci. The polymorphic markers evaluated are useful to perform varietal identification in a large panel of cotton varieties and may be applied in studies of the species diversity.

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Assessment of Genetic Diversity of Promising Castor Been (Ricinus communis L.) Genotypes in Nigeria

Notulae Scientia Biologicae ◽

10.15835/nsb11310346 ◽

2019 ◽

Vol 11 (3) ◽

pp. 467-474

Author(s):

Bolaji Zuluqurineen SALIHU ◽

Olamide Ahmed FALUSI ◽

Adeyinka Olufemi ADEPOJU ◽

Ibrahim Wasiu AROLU ◽

Oladipupo Yusuf DAUDU ◽

...

Keyword(s):

Genetic Diversity ◽

Diversity Index ◽

Gene Diversity ◽

Ricinus Communis ◽

Polymorphic Information Content ◽

Block Design ◽

Genetic Material ◽

Morphological Data ◽

Research Attention ◽

Ricinus Communis L

Castor oil plant (Ricinus communis L.) is an important oil crop with little research attention in Nigeria. In the present research, extent of genetic diversity among 20 Nigerian castor genotypes was determined using morphological descriptors and molecular markers. The genotypes were laid out on a randomized complete block design with three replicated plots. Molecular genotyping of the genotypes was carried out using genomic Simple Sequence Repeats (SSR). The genotypes revealed high divergence in seed colour, seed shape, seed mottle, seed caruncle and seed sizes. Seedling establishment varied from 70.18% (in Acc. 006) to 93.25% (Acc. 001) with average mean of 81.53%. Raceme length ranged from 15.90 cm to 29.54 cm with population mean of 20.80 cm. The highest seed yield (1222.98 kg/ha) was recorded in Acc. 001 and the least (611.46 kg/ha) was observed in Acc. 006. Seed oil content varied between 32.15% in Acc. 042 and 54.03% in Acc. 006. Agglomerative cluster dendrogram constructed from morphological data showed random distribution of the genotypes into three cluster groups irrespective of the sources/collection points. The genetic diversity based on SSR Marker Analysis revealed high average expected heterozygosity (0.74), Polymorphic information content (0.68), Nei’s gene diversity index (0.72) and Shannon's Information index (1.43). The dendrogram constructed from molecular data grouped the twenty genotypes into three groups at coefficient of 0.34. From these findings, it showed that the twenty genotypes evaluated are divergent in nature and they could serve as good genetic material for castor breeding in Nigeria.

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Evaluation of Genetic Diversity among Persian Fig Cultivars by Morphological Traits and RAPD Markers

HortScience ◽

10.21273/hortsci11306-16 ◽

2018 ◽

Vol 53 (5) ◽

pp. 613-619 ◽

Cited By ~ 1

Author(s):

Ghazal Baziar ◽

Moslem Jafari ◽

Mansoureh Sadat Sharifi Noori ◽

Samira Samarfard

Keyword(s):

Genetic Diversity ◽

Rapd Markers ◽

Polymorphic Information Content ◽

Random Amplified Polymorphic Dna ◽

Hierarchical Cluster ◽

Fruit Trees ◽

Group Method ◽

Fars Province ◽

Pair Group

Ficus carica L. is one of the most ancient fruit trees cultivated in Persia (Iran). The conservation and characterization of fig genetic resources is essential for sustainable fig production and food security. Given these considerations, this study characterizes the genetic variability of 21 edible F. carica cultivars in the Fars Province using random amplified polymorphic DNA (RAPD) markers. The collected cultivars were also characterized for their morphological features. A total of 16 RAPD primers produced 229 reproducible bands, of which, 170 loci (74.43%) were polymorphic with an average polymorphic information content (PIC) value of 0.899. Genetic analysis using an unweighted pair-group method with arithmetic averaging (UPGMA) revealed genetic structure and relationships among the local germplasms. The dendrogram resulting from UPGMA hierarchical cluster analysis separated the fig cultivars into five groups. These results demonstrate that analysis of molecular variance allows for the partitioning of genetic variation between fig groups and illustrates greater variation within fig groups and subgroups. RAPD-based classification often corresponded with the morphological similarities and differences of the collected fig cultivars. This study suggests that RAPD markers are suitable for analysis of diversity and cultivars’ fingerprinting. Accordingly, understanding of the genetic diversity and population structure of F. carica in Iran may provide insight into the conservation and management of this species.

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Genetic diversity analysis in Brassica varieties through RAPD markers

Bangladesh Journal of Agricultural Research ◽

10.3329/bjar.v34i3.3976 ◽

1970 ◽

Vol 34 (3) ◽

pp. 493-503 ◽

Cited By ~ 5

Author(s):

KK Ghosh ◽

ME Haque ◽

S Parvin ◽

F Akhter ◽

MM Rahim

Keyword(s):

Genetic Diversity ◽

Genetic Distance ◽

Rapd Markers ◽

Gene Diversity ◽

Random Amplified Polymorphic Dna ◽

Arithmetic Mean ◽

Polymorphic Band ◽

Group Method ◽

Polymorphic Loci ◽

Pair Group

This investigation was aimed at exploring the genetic diversity and relationship among nine Brassica varieties, namely BARI Sharisha-12, Agrani, Sampad, BINA Sharisha-4, BINA Sharisha-5, BARI Sharisha-13, Daulot, Rai-5, Alboglabra using Random Amplified Polymorphic DNA (RAPD) markers. In total, 59 reproducible DNA bands were generated by four arbitrary selected primers of which 58 (98.03%) bands were proved to be polymorphic. These bands ranged from 212 to 30686 bp in size. The highest proportion of polymorphic loci and gene diversity values were 37.29% and 0.1373, respectively, for BARI Sharisha-12 and the lowest proportion of polymorphic loci and gene diversity values were 8.47% and 0.0318, 8.47% and 0.0382 for BINA Sharisha-4 and Rai-5, respectively. A dendrogram was constructed using unweighted pair group method of arithmetic mean (UPGMA). The result of cluster analysis indicated that the 9 accessions were capable of being classified into 2 major groups. One group consists of BARI Sharisha-12, Agrani, Sampad, Daulot, Rai-5, Alboglabra. where Daulot and Rai-5 showed the lowest genetic distance of 0.049. And another group contains BINA Sharisha-4, BINA Sharisha-5, and BARI Sharisha-1 3, where BINA Sharisha-5 and BARI sharisha-13 showed genetic distance of 0.071. Key Words: RAPD, Brassica, genetic distance, polymorphic band. DOI: 10.3329/bjar.v34i3.3976 Bangladesh J. Agril. Res. 34(3) : 493-5032, September 2009

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Performance of salinity tolerance of F3 rice lines of BRRI dhan 29 × PBRC (STL-20) using RAPD markers

Research in Agriculture Livestock and Fisheries ◽

10.3329/ralf.v6i2.43040 ◽

2019 ◽

Vol 6 (2) ◽

pp. 215-225

Author(s):

Nazmul Islam Mazumder ◽

Tania Sultana ◽

Prtitish Chandra Paul ◽

Dinesh Chandra Roy ◽

Deboprio Roy Sushmoy ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Distance ◽

Salinity Tolerance ◽

Rapd Markers ◽

Random Amplified Polymorphic Dna ◽

Susceptible Variety ◽

Group Method ◽

Arithmetic Means ◽

Pair Group ◽

Tolerant Line

Twenty six rice lines of PBRC (salt tolerant line-20) × BRRI dhan-29 were used to evaluate salinity tolerance at the seedling stage and tested for salt tolerance using RAPD markers. Salinity screening was done using hydrophonic system at the greenhouse following IRRI standard protocol. Among the studied line, ten were moderately salinity tolerant, nine susceptible and rest of the lines highly susceptible. For assessing genetic diversity and relationship of F3 rice lines including two parents were tested against PCR-based Random Amplified Polymorphic DNA (RAPD) technique using three arbitrary decamer primers; OPA02, OPC01, and OPC12. Selected three primers generated a total of 14 bands. Out of 14 bands, 12 bands (86.67%) were polymorphic and 2 bands (13.33%) were monomorphic. The Unweighted Pair Group Method of Arithmetic Means (UPGMA) dendrogram constructed from Nei’s (1972) genetic distance produced 2 main clusters of the 28 rice genotypes. Most of the moderately tolerant lines and PBRC (STL-20) (tolerant variety) were grouped in same cluster due to lower genetic distance, while maximum susceptible along with BRRI dhan29 (susceptible variety) showed higher genetic distance with PBRC (STL-20) and moderately tolerant lines. This result indicates that the lines which formed grouped together, they are less diversed. On the other hand the lines remain in different clusters or different groups, are much diversed. Thus RAPD perform a potentially simple, rapid and reliable method to evaluate genetic diversity and molecular characterization as well. Res. Agric., Livest. Fish.6(2): 215-225, August 2019

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Genetic Diversity of Castor Bean (Ricinus communis L.) Revealed by ISSR and RAPD Markers

Agronomy ◽

10.3390/agronomy11030457 ◽

2021 ◽

Vol 11 (3) ◽

pp. 457

Author(s):

HyokChol Kim ◽

Pei Lei ◽

Aizhi Wang ◽

Shuo Liu ◽

Yong Zhao ◽

...

Keyword(s):

Genetic Diversity ◽

Castor Bean ◽

Genetic Similarity ◽

Rapd Markers ◽

Ricinus Communis ◽

Similarity Coefficient ◽

Morphological Data ◽

Oilseed Crop ◽

Ricinus Communis L ◽

Polymorphic Bands

Castor (Ricinus communis L.), known as castor oil plant or castor bean, is a non-edible oilseed crop. In the present study, the genetic diversity among 54 samples (3 wild and 51 cultivated) collected worldwide was evaluated using inter-simple sequence repeats (ISSRs) and random amplified polymorphic DNA (RAPD) markers. A total of 9 ISSR primers produced 83 high-resolution bands with 61 (74.53%) as polymorphic. The percentage of polymorphic bands per primer and the genetic similarity coefficient ranged from 54.55% (UBC-836) to 100% (UBC-808) and from 0.74 to 0.96, respectively. A total of 11 out of 20 RAPD primers amplified unique polymorphic products with an average percentage of polymorphic bands of 60.98% (56 polymorphic bands out of a total of 90 bands obtained). The percentage of polymorphic bands per primer ranged from 25% (OPA-02 and B7) to 90.91% (B21) with the genetic similarity coefficient ranging from 0.73 to 0.98. The unweighted pair group method with arithmetic averages (UPGMA) dendrogram using two molecular markers divided 54 castor genotypes into three groups. Furthermore, based on morphological data, all 54 castor varieties were grouped into three main clusters. The genetic diversity analysis based on two molecular makers showed that most varieties from China were closely related to each other with three varieties (GUANGDONGwild, ZHEJIANGWild, and HANNANWild) belonging to a wild group separated from most of the cultivated castor samples from China, India, France, and Jordan. These results suggested that the cultivated castor contains a narrow genetic base. Accordingly, we recommend that wild castor genetic resources be introduced for breeding novel castor varieties. Furthermore, the Vietnam, Malaysia, Indonesia, and Nigeria accessions were clustered into the same group. The results of principal coordinate analysis (PCoA) and UPGMA cluster analysis were consistent with each other. The findings of this study are important for future breeding studies of castor.

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Assessment of genetic diversity of different tomato genotypes using RAPD markers

Progressive Agriculture ◽

10.3329/pa.v29i4.41341 ◽

2019 ◽

Vol 29 (4) ◽

pp. 276-283

Author(s):

M Paul ◽

SR Saha

Keyword(s):

Genetic Diversity ◽

Genetic Distance ◽

Rapd Markers ◽

Random Amplified Polymorphic Dna ◽

Group Method ◽

Breeding Programs ◽

Pair Group ◽

Information Indices ◽

Tomato Breeding ◽

Tomato Genotypes

The present investigation was carried out for assessment of genetic diversity among the 28 tomato genotypes though three random amplified polymorphic DNA (RAPD) markers. A total of 15 distinct DNA fragments ranging form 100-1000 bp were amplified by using three selected primers of which 5.00 polymorphic bands per primer and over all polymorphic loci was 100 percent. The extent of genetic diversity among these genotypes was computed through parameters of genetic diversity and Shanon’s information indices. The highest genetic distance was observed among the accession Cl-3d-0-99 (V93) vs. F1 (G X V12), F1 (G X V17), F1 (G X V29) and Durch fuegel (G) vs. F1 (G X V17) and F1 (G X V93) vs. F1 (G X V12), F1 (G X V17), while the lowest genetic distance was observed among the accessions Fut. Wed Abrid (V94) vs. Sunlight pole (V67) and F1 (V67 X VG) vs. F1 (V17 X VG), F1 (V93 X VG) and F1 (V93 X V17) vs. F1 (V17 X VG), F1 (V67 X VG), F1 (V93 X VG). The Unweighted Pair Group Method of Arithmetic Mean (UPGMA) dendrogram based on Nei’s genetic distance divided the genotypes into two main clusters: A & B. Cluster ‘A’ consists of 19 accessions and cluster ‘B’ consists of 9 accessions. The information generated from this study could be useful in gene mapping and marker assisted breeding for future tomato breeding programs. Progressive Agriculture 29 (4): 276-283, 2018

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Molecular Diversity Analysis in Potato (Solanum tuberosum L.) through RAPD Markers

SAARC Journal of Agriculture ◽

10.3329/sja.v11i2.18405 ◽

2014 ◽

Vol 11 (2) ◽

pp. 95-102 ◽

Cited By ~ 4

Author(s):

ME Hoque ◽

H Huq ◽

NJ Moon

Keyword(s):

Genetic Diversity ◽

Genetic Distance ◽

Rapd Markers ◽

Molecular Diversity ◽

Solanum Tuberosum L ◽

Random Amplified Polymorphic Dna ◽

Group Method ◽

Leaf Sample ◽

Dna Profile ◽

Potato Varieties

Random Amplified Polymorphic DNA (RAPD) markers were used to study the molecular diversity of 12 popular potato varieties in Bangladesh. DNA was extracted from tender leaf sample for PCR amplification. The PCR amplified DNA profile was visualized on 2% agarose gel, staining with ethidium bromide. Eight RAPD primers were used to evaluate the genetic diversity of potato varieties. Some total of 36 DNA fragments were amplified and out of them 24 were polymorphic. Those primers generated 61.53% of polymorphic DNA band. The primer OPX 04 produced highest (9) number of DNA band and out of 9 amplicon 6 were polymorphic. Lowest number of amplification was observed in the primer OPA-17 and it was only 3. The highest Neis genetic distance (0.9701) was noticed between the variety Granola and Provinto. The highest (0.8205) number of genetic identity/similarity was observed between the varieties Cardinal and Diamant. The unweighted pair group method of arithmetic mean (UPGMA) dendrogram based on Neis genetic distance revealed that the 12 varieties followed into two main clusters. The present finding showed that there was high level of genetic diversity among the varieties which can be used for parental selection in potato breeding program. DOI: http://dx.doi.org/10.3329/sja.v11i2.18405 SAARC J. Agri., 11(2): 95-102 (2013)

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GENETIC DIVERSITY AMONG AND WITHIN BRAVE BEAN (Capparis flexuosa L.) POPULATIONS ASSESSED USING RAPD MARKERS

Revista Caatinga ◽

10.1590/1983-21252019v32n109rc ◽

2019 ◽

Vol 32 (1) ◽

pp. 81-91

Author(s):

Jorge Xavier de Almeida Neto ◽

Mailson Monteiro do Rêgo ◽

Elizanilda Ramalho do Rêgo ◽

Ana Paula Gomes da Silva

Keyword(s):

Genetic Diversity ◽

Rapd Markers ◽

Polymorphic Information Content ◽

Random Amplified Polymorphic Dna ◽

Group Method ◽

Jaccard Similarity ◽

Cophenetic Correlation ◽

Pair Group ◽

Cophenetic Correlation Coefficient ◽

Bean Leaves

ABSTRACT Brave bean (Capparis flexuosa L.) is a Caatinga species that is used as forage, mainly during the dry season when some plant species lose their leaves. The aim of this study was to assess genetic diversity within and among brave bean populations using Random Amplified Polymorphic DNA (RAPD) markers. Brave bean leaves were collected from 30 accessions in the following municipalities of Paraíba state, Brazil: Barra de Santa Rosa (BSR), Cuité (C), São João do Cariri (SJC), Damião (D), Baraúna (B), and Picuí (P). DNA extraction followed the standard methodology of CTAB with modifications. RAPD analyses were carried out using 18 primers, and polymorphism of the amplified DNA fragments was visualized using agarose gel electrophoresis. Data were used to calculate Jaccard Similarity Coefficient values, which were then used to group samples with the Unweighted Pair Group Method with Arithmetic Mean. Cophenetic Correlation Coefficient, Stress, and Distortion Coefficient values were also calculated from these analyses. Band polymorphism was generated with 14 primers, but the sampled populations showed low numbers of polymorphic loci (27 in BSR, 18 in C, 7 in SJC, 9 in D, and 0 in B and P). The highest polymorphic information content was found in samples from the BSR (9 groups), C (22 groups), SJC (7 groups), and D (6 groups) municipalities. In the interpopulation analysis, 34 groups were formed, the matrices of which showed high cophenetic correlations (0.95 to 0.98), but low stress (12.9 to 17.45%) and distortion (3.05%). Therefore, results showed that there was genetic variability both among and within brave bean populations.

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