scholarly journals Assessment of Microsatellite Markers (SSRs) For Genetic Diversity in Asparagus Officinalis L. And Allied Species

2021 ◽  
Vol 50 (3) ◽  
pp. 595-602
Author(s):  
Muhammad Idrees ◽  
Muhammad Irshad ◽  
Mitra Lal Pathak ◽  
Akash Tariq ◽  
Rehan Naeem
Keyword(s):  
Genetic Diversity ◽  
Genetic Similarity ◽  
Clustering Algorithm ◽  
Asparagus Officinalis ◽  
Allelic Polymorphism ◽  
Asparagus Racemosus ◽  
Similarity Coefficients ◽  
Monophyletic Origin ◽  
Genic Ssr ◽  
Ssrs Markers

The present study was hypothesized to evaluate a set of SSRs for the assessment of genetic variations in Asparagus officinalis L. and their allied species. Nine genic SSR markers were especially developed for Asparagus genome and employed for DNA profiling studies of Asparagus species. These SSRs markers have revealed the allelic polymorphism ranging from 1.0 to 2.0. Allele frequency was found highest for psbD-trnL (1.0), petB (1.0) and AG7 (1.0), while it was lowest for ZHD1 (0.1). Polymorphism Information content (PIC) was highest for TC7 (0.9) while it was lowest (0.0) for psbD-trnL, petB and AG7 respectively. The genetic similarity coefficients were found to range from 0.42 to 1.0. The UPGMA clustering algorithm based on SSRs data have clustered Asparagus species into 4 groups (I, II, III & IV) indicating Asparagus officinalis (L.) cultivars and allied species in the first clade, while Asparagus officinalis (L.) ‘Gersengum’, Asparagus densiflorus (Kunth) Jessop, and Asparagus racemosus willd. were clustered in separate clades respectively. The present study has endorsed the origin status of Asparagus officinalis and their allied species. A. officinalis cultivars and other allied Asparagus species are clustered in separate clades, and it was revealed that they have monophyletic origin. It was established that SSRs markers could be informative markers for the differentiation of Asparagus officinalis cultivars, and their allied Asparagus species. Bangladesh J. Bot. 50(3): 595-602, 2021 (September)

scholarly journals Genetic diversity among 24 clones of robusta coffee in Lampung based on RAPD markers

2021 ◽  
Vol 22 (6) ◽  
Author(s):  
Sri Ramadiana ◽  
Dwi Hapsoro ◽  
Rusdi Evizal ◽  
Kukuh Setiawan ◽  
Agus Karyanto ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Similarity ◽  
Rapd Markers ◽  
Breeding Program ◽  
Similarity Coefficients ◽  
Robusta Coffee ◽  
Genomic Dnas ◽  
Polymerase Chain ◽  
Group Ii ◽  
Group 1

Abstract. Ramadiana S, Hapsoro D, Evizal R, Setiawan K, Karyanto A, Yusnita. 2021. Genetic diversity among 24 clones of robusta coffee in Lampung based on RAPD markers. Biodiversitas 22: 3122-3129. This study aimed to estimate the genetic diversity among 24 clones of Robusta coffee from Lampung, Indonesia, by use of RAPD markers. The clones consisted of 18 local and 6 BP clones. These BP clones were developed from a breeding program of The Indonesian Coffee and Cocoa Research Institute. Genomic DNAs extracted from these clones were subjected to polymerase chain reaction and the amplified products were run using gel electrophoresis. Eleven random primers produced clear, reproducible, scorable bands. Fifty-four of 86 bands showed polymorphism and were used to construct a dendrogram based on UPGMA Jaccard's Similarity Coefficients. The genetic base of the population was narrow (average genetic similarity 68.4%), ranging from 26-93%. The genetic similarity of the local clones was higher than that of BP clones. The clones were clustered into five groups. Group 1 contained one clone (BP 534), while each of Group II-V contained more than one clone. The average genetic similarity of BP 534 to each clone of Group II-V was 41%. The genetic similarity of clones in Group II, III, IV, and V were 55.5%, 43.0%, 81.1%, and 80.1%, respectively. This research should be very useful for selecting parents in a breeding program to produce better clones of Robusta coffee.

scholarly journals Analysis of intra-population variability of bald cypress (Taxodium distichum L. Rich.) in seed stand near Backa Palanka using RAPD markers

Genetika ◽  
2015 ◽  
Vol 47 (2) ◽  
pp. 571-580
Author(s):  
Vladan Popovic ◽  
Aleksandar Lucic ◽  
Danijela Ristic ◽  
Ljubinko Rakonjac ◽  
Sabahudin Hadrovic ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Dna Markers ◽  
Genetic Similarity ◽  
Rapd Markers ◽  
Rapd Analysis ◽  
Genetic Distances ◽  
Similarity Coefficients ◽  
Bald Cypress ◽  
Seed Stand

The analysis of Bald cypress genetic variability at the level of test trees was performed using RAPD (Random Amlified Polymorphic DNA) markers. RAPD analysis was performed on 20 test trees with 13 primers. A total of ten primers gave a clear picture while three primers amplified weakly. 60 is a total number of detected bands obtained by RAPD analysis with 10 selected primers, and the average number of bands is 6. Based on presence/absence of RAPD fragments among all 20 Bald cypress test trees were calculated similarity coefficients by Dice and they range from 0.73 to 1. Based on similarity coefficients was performed the cluster analysis and results were presented as a dendrogram. All 20 test trees were grouped into two sub-clusters. Test trees 1, 4 and 11 were grouped in the first sub-cluster while other test trees were grouped in the second sub-cluster. By analysis of relations within every sub-cluster and sub-sub-cluster the existence of genetic distances between observed test trees can be noticed. The greatest similarity is between test trees 2, 12, 15 and 18. The results of genetic similarity and distance between observed test trees indicate the overwhelming presence of genetic diversity.

scholarly journals Genetic diversity among asexual and sexual progenies of Phytophthora capsici detected with ISSR markers

2021 ◽  
Vol 57 (No. 4) ◽  
pp. 271-278
Author(s):  
Ping Li ◽  
Dong Liu
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Similarity ◽  
Phytophthora Capsici ◽  
Issr Markers ◽  
Similarity Coefficients ◽  
Sexual Progeny ◽  
Sexual Offspring ◽  
Issr Primers

The population structure of Phytophthora capsici among asexual and sexual progenies was analyzed using ISSR. Thirty asexual progenies of one parent and three sexual populations were assayed for genetic diversity using 5 ISSR primers and DNA from 120 offspring of P. capsici was amplified. In total, 71 reproducible ISSR fragments were obtained, of which 100% were polymorphic, revealing high polymorphism among the isolates. Among them, the percentages of polymorphism of sexual and asexual progeny isolates were 100.00 and 77.46%, respectively. Genetic similarity coefficients among all the isolates ranged from 0.54 to 0.73. The sexual offspring population showed much more variability than the asexual offspring population with 76.26% variability attributed to diversity within populations as compared with 23.74% among populations. This research reveals that the sexual progeny population of P. capsici contributes more genetic diversity than that of asexual progeny population.

scholarly journals GENETIC DIVERSITY EEL Anguilla marmorata BY RAPD IN THUA THIEN HUE PROVINCE, VIETNAM

2021 ◽  
Vol 130 (2B) ◽  
Author(s):  
Kiều Thị Huyền ◽  
Hà Thị Huệ ◽  
Nguyễn Quang Linh
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Molecular Marker ◽  
Genetic Similarity ◽  
Economic Value ◽  
Similarity Coefficient ◽  
Similarity Coefficients ◽  
Random Primer ◽  
Anguilla Marmorata ◽  
Random Amplification

Anguilla marmorata is a species with high economic value and increasingly interested by organizations and scientists. So far, many of the eel's biological characteristics remain mysterious, and they are often classified according to morphological features such as pigmentation patches, number of vertebrae, ... It is even difficult to distinguish one individual from another in some species, especially in the larval stage. In this study, the Random amplification of polymorphic DNA (RAPD) molecular marker was used to evaluate the genetic diversity of 48 eels collected in Thua Thien Hue province. Results showed that the genetic diversity of individuals in the Eel population studied is quite high. With 8 random primers via PCR, 77 DNA tapes with 76 polymorphic tapes were obtained, the tape size ranged from 170-2,500 bp, in which primer S10 showed the highest diversity with an average Ho value of 0.563, followed by primer S8 (Ho = 0.558). The lowest diversity was in the OPD5 primer (Ho = 0.300). The OPG17 primer is the primer that produces the most polymorphic tapes (13/13 tapes) and the S3 primer for the least amplified tapes polymorphism (9/10 DNA tapes). The diversity coefficient in each random primer ranged from about 0.300 to 0.563, with an average of 0.433. The genetic variation in the Eel population is random. Genetic variation can be attributed mainly to different eel breeding conditions and origins. Genetic similarity coefficients among the Eels varied from 0.660 to 0.910 and were divided into two main groups in genetic similarity coefficient 0.660.

scholarly journals Study of genetic diversity and molecular variation in natural populations of Pinus armandii subsp. Xuannhaensis L.K. Phan - an endemic species in Son La, Vietnam using ISSR markers

2016 ◽  
Vol 14 (3) ◽  
pp. 441-450 ◽  
Author(s):  
Vũ Đình Duy ◽  
Bùi Thị Tuyết Xuân ◽  
Đỗ Thị Phương Thảo ◽  
Phan Kế Lộc ◽  
Nguyễn Minh Tâm
Keyword(s):  
Genetic Diversity ◽  
Genetic Similarity ◽  
Nature Reserve ◽  
Natural Populations ◽  
Population Level ◽  
Issr Markers ◽  
Similarity Matrix ◽  
Similarity Coefficients ◽  
Analysis Of Molecular Variance ◽  
Narrow Endemic

Pinus armandii subsp. xuannhaensis L.K. Phan is a new five needle pine discovered recently from Xuan Nha Nature Reserve, Son La province. This subspecies is considered as a narrow endemic to Vietnam and is assessed as endangered. In this study, 15 ISSR markers were used to analyze the genetic diversity of this taxon collected in five subpopulations (Tan Xuan, Thac Nuoc, Dinh VTV2, Near VTV2 and Dinh Pomu). Results of the analysis showed 15/15 markers were polymorphic. A total of 51 DNA fragments were amplified, in which 50 fragments were polymorphic (98.04%). Genetic diversity was the highest in Dinh Pomu subpopulation (I = 0.555; h = 0.8; PPB = 68.76%; Ne =1.6 and He = 0.4)) and the lowest in Tan Xuan subpopulation (I = 0.428; h = 0.6; PPB = 57.06%, Ne = 1.215 and He = 0.303). Analysis of molecular variance (AMOVA) results showed that the total level of molecular changes between subpopulations was 7% and between individuals in the same subpopulation was 93%. A constructed dendrogram based on similarity matrix of 71 Pinus armandii subsp. xuannhaensis L.K. Phan samples divided the samples into two main groups with genetic similarity coefficients ranged from 0.53 to 0.96. Results of the molecular analysis showed that Pinus armandii subsp. xuannhaensis L.K. Phan species should be protected at the population level.

scholarly journals Biodiversity of some fig cultivars in Southern Syria

2021 ◽  
pp. 184-191
Author(s):  
Sahara Abo Amin ◽  
Faisal Hamed ◽  
Seba Sarhan ◽  
Nashaat Abo Tafish
Keyword(s):  
Genetic Diversity ◽  
Genetic Similarity ◽  
Significant Contribution ◽  
Mean Value ◽  
Local Fields ◽  
The Mean ◽  
Polymerase Chain ◽  
Ssrs Markers ◽  
Simple Sequence

This research has been conducted in the Biotechnology Laboratory in Damascus University_ Damascus, Syria where the genetic diversity of fourteen cultivars of figs (Ficus carica L.) growing in Swaida governorate which located in the south region of  Syria were investigated using (Simple Sequence Repeats) SSRs technique, where 4 cultivars of them were genotypes scattered in the local fields without any scientific taxonomy and farmers did not classify them properly. Eight pairs of SSRs markers were used depend on their ability to separate between fig cultivars as mentioned in previous studies, six pairs of them gave amplified products in the polymerase chain reaction (PCR), while MFC3 and MFC6 primers did not give any amplification products. A total of 17 alleles were detected at six SSRs loci. The alleles number per locus ranged from 2 to 4 with  an average of 2.83 alleles/locus. The observed heterozygosity (Ho) was 0.33, while the expected heterozygosity (He) was 0.17. The mean value of genetic similarity was 0.69 where fig cultivars has separated into two clusters in Cluster Analysis, which confirms a significant genetic similarity between most of the cultivars. MFC1 and MFC2 loci gave about 0.67 and 0.61 PIC (Polymorphism Information Content) values respectively, which confirms their ability to study the genetic diversity of fig cultivars more than other loci. F1 and F2 cultivars greatly affect the quality of the fruits as paternity traits as Caprifigs. Tammozi cultivar has low values of its genetic similarity with the rest of the cultivars which reflect great difference between it and other cultivars. Generally, the challenges in this study were in characterizing unrecognized fig cultivars in southern Syria to distinguish between them as they were not certified in agriculture ministry in Syria because the lack in studies related to the same topic as these cultivars were not studied before, thus, we managed to make a significant contribution in certifying fig cultivars in Syria using SSR technique.

scholarly journals IRAP and REMAP-based assessment of genetic diversity in chickpea collection from Iran

Genetika ◽  
2014 ◽  
Vol 46 (3) ◽  
pp. 731-744
Author(s):  
Zahra Aghaali ◽  
Morteza Ghadmizadeh ◽  
Babak Abdollahi-Mandoulakani ◽  
Iraj Bernousi
Keyword(s):  
Genetic Diversity ◽  
Genetic Similarity ◽  
Dice Similarity Coefficient ◽  
Similarity Coefficients ◽  
Closely Related Species ◽  
Information Index ◽  
Geographical Distances ◽  
Research Integration ◽  
Clear Differentiation ◽  
Insertional Polymorphism

Retrotransposons (RTN) make a significant contribution to the size, organization and genetic diversity of their host genomes. Several RTN families have been identified in chickpea (Cicer arietinum L.) and other closely related species. In the current research, integration activity and insertional polymorphism of the RTNs CARE1, Tms1Ret1, TPS and LORE were studied in 64 chickpea accessions collected in Iran using inter retrotransposon amplified polymorphism (IRAP) and retrotransposon-microsatellite amplified polymorphism (REMAP) techniques. Results indicated that all RTNs studied, are transpositionally active in chickpea genome and amplified scorable and polymorphic banding pattern. Among the RTN families used, the highest percentage of polymorphic loci (PPL) was produced by TPS family (81.82%). Totally, 129 loci were amplified using 18 IRAP and REMAP primers which 83 (64.34%) were polymorphic. The Dice genetic similarity coefficients among accessions ranged from 0.84 (accessions Tj48 and Ba4) to 0.98 (accessions Ka30 and Urm61), averaging 0.93. The parameters of expected heterozygosity (He), Shannon?s information index (I) and number of effective alleles (Ne) were the highest for Urmia accessions. Cluster analysis based on UPGMA algorithm and Dice similarity coefficient categorized the 64 accessions in 7 main groups. The mean Fst values of all groups except for groups IV and VII, were lower than 0.20, demonstrating no clear differentiation among the groups, no genetic structure of the studied chickpea collection and probably occurrences of gene flow among the origins. In conclusion, although RTN-based markers were able to differentiate the chickpea accessions but the measured relative genetic similarity among accessions were not correlated with geographical distances between places of their origins.

scholarly journals Comparing the effectiveness between issr and ssr markers in assessing genetic diversity of natural populations of Dacrydium elatum in Tay Nguyen, Vietnam

2018 ◽  
Vol 15 (2) ◽  
pp. 293-305
Author(s):  
Trần Thị Liễu ◽  
Vũ Thị Thu Hiền ◽  
Nguyễn Thị Liễu ◽  
Đinh Thị Phòng
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Ssr Markers ◽  
Genetic Similarity ◽  
Natural Populations ◽  
Population Level ◽  
Polymorphic Markers ◽  
Similarity Matrix ◽  
Similarity Coefficients ◽  
Molecular Variance

The two techniques, ISSR (27 markers) and SSR (20 markers), were used to compare the effectiveness and to assess genetic diversity of 70 Dacrydium elatum samples collected in Lam Dong, Kon Tum, Dak Lak, and Gia Lai. The results showed 38/47 polymorphic markers (23/27 ISSR and 15/20 SSR markers) and 180 amplified DNA fragments, in which 85/127 (66.93%) and 46/53 (86.79%) were polymorphic for ISSR and SSR markers, respectively. Generally, the average values among the genetic diversity parameters of the populations for SSR (Hj = 0.213; Ne = 1.566, I = 0.444; He = 0.301; h = 0.228; and PPB = 72.50%) were higher than those for ISSR (Hj = 0.155; Ne = 1.142, I = 0.125; He = 0.083; h = 0.074 and PPB = 25.07%). The correlation coefficient between genetic distance measured with ISSR and combining ISSR + SSR was higher (r = 0.92) than that measured with SSR and combining ISSR + SSR (r = 0.65). There was not much difference in the total level of molecular variance (AMOVA) among populations and among individuals when analyzing ISSR and SSR data separately or combining both data. The three dendrograms constructed based on similarity matrix generated by ISSR, SSR and ISSR + SSR data were similar and they all divided the 70 D. elatum samples into two main groups with genetic similarity coefficients ranged from 74 to 99%, 78.4 to 100% and 76 to 96.6%, respectively. The obtained results indicated D. elatum species should be protected at the population level.

scholarly journals Low Genetic Diversity Indicates the Need to Broaden the Genetic Base of Cultivated Watermelon

HortScience ◽  
2001 ◽  
Vol 36 (6) ◽  
pp. 1096-1101 ◽  
Author(s):  
Amnon Levi ◽  
Claude E. Thomas ◽  
Todd C. Wehner ◽  
Xingping Zhang
Keyword(s):  
Genetic Diversity ◽  
Genetic Similarity ◽  
Citrullus Lanatus ◽  
Plant Introduction ◽  
Group Method ◽  
Similarity Coefficients ◽  
Arithmetic Average ◽  
Pair Group ◽  
Low Genetic Diversity ◽  
Genetic Base

Genetic diversity and relatedness were assessed among 46 American cultivars of watermelon (Citrullus lanatus var. lanatus), and 12 U.S. Plant Introduction accessions (PIs) of Citrullus sp. using 25 randomly amplified polymorphic DNA (RAPD) primers. These primers produced 288 distinct reproducible bands that could be scored with high confidence among cultivars and PIs. Based on the RAPD data, genetic similarity coefficients were calculated and a dendrogram was constructed using the unweighted pair-group method with arithmetic average (UPGMA). The cultivars and C. lanatus var. lanatus PIs differentiated at the level of 92% to 99.6% and 88% to 95% genetic similarity, respectively. In contrast, the C. lanatus var. citroides, and C. colocynthis PIs were more divergent and differentiated at the level of 65% to 82.5% and 70.5% genetic similarity, respectively. The low genetic diversity among watermelon cultivars in this study emphasizes the need to expand the genetic base of cultivated watermelon.

scholarly journals Genetic Diversity within Chinese Watermelon Ecotypes Compared with Germplasm from Other Countries

2012 ◽  
Vol 137 (3) ◽  
pp. 144-151 ◽  
Author(s):  
Yunyan Sheng ◽  
Feishi Luan ◽  
Faxing Zhang ◽  
Angela R. Davis
Keyword(s):  
Genetic Diversity ◽  
Genetic Similarity ◽  
Citrullus Lanatus ◽  
Morphological Characteristics ◽  
Male Flower ◽  
Solid Content ◽  
Soluble Solid Content ◽  
Similarity Coefficients ◽  
Branch Number ◽  
Soluble Solid

Genetic diversity among 95 watermelon (Citrullus lanatus) ecotypes was evaluated and compared with representative Chinese, American, Japanese, and Russian watermelon cultigens, landraces, and a wild watermelon relative (Trichosanthes kirilowii). Open-pollinated, hybrid, and inbred lines were included for most of the ecotypes and are hereafter collectively referred to as cultigens unless an ecotype group is being discussed. Morphological characteristics (including days to flower, female to male flower ratio, branch number, fruit length and diameter ratio, fruit soluble solid content, fruit yield, and simple sequence repeat (SSR) markers were used to estimate genetic diversity. Of 398 watermelon primer pairs tested, 9.5% (38) produced polymerase chain reaction amplicons in watermelon. Of these 38 primer pairs, the average number of polymorphic bands among the 96 cultigens was 2.4, even with 12 primer pairs demonstrating monomorphic banding patterns. Based on the SSR data, the genetic similarity coefficients were calculated and a dendrogram constructed. All cultigens were clustered to six groups. The wild species and landraces formed distant clusters from the cultivated watermelon. The genetic similarity coefficients within the Chinese cultigens ranged from 0.37 to 0.99, but except for a wild relative to watermelon, most cultigens were closely related. The genetic distance among non-Chinese cultigens ranged from 0.67 to 0.91 with an average of 0.88. When combined morphological traits and molecular traits were assessed, Russian and U.S. fruit were more genetically similar to each other than to Chinese and Japanese cultigens. Crossing Russian and/or U.S. cultigens with Chinese or Japanese cultigens should thus improve genetic diversity and introduce new traits for the resulting watermelon cultigens.

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