scholarly journals Estimation of Genetic Diversity among Canola Accessions using Simple Sequence Repeat Markers

2021 ◽  
Vol 8 (4) ◽  
pp. 86-94
Author(s):  
Jaleel Ahmad ◽  
Muhammad Baber ◽  
Wajid Nazeer ◽  
Sana Hamdullah ◽  
Aleena Ahmad Somroo
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Gene Diversity ◽  
Molecular Genetic ◽  
Genetic Distances ◽  
Genetic Studies ◽  
Molecular Genetic Basis ◽  
Ssr Primers ◽  
Minimum Genetic Distance ◽  
Simple Sequence

Genetic studies through molecular markers proved important to find out the genetic diversity of canola. In this study, 50 lines of canola were used to find the polymorphism using 15 SSR primers and investigated the genetic diversity, PIC values, frequency-based genetic distance, and allelic frequencies. Mean gene diversity, frequency-based genetic distance, and PIC values were 0.8777, 0.233 and 0.8666, respectively for the canola lines. A good range of genetic diversity was found among studied canola lines with value 85.91% polymorphism. Maximum and minimum genetic distances among 50 lines were 1 and 0.26, respectively. Accessions ACC-26068, ACC-24241, ACC-24244, ACC-24233, ACC-24423 and ACC-24224 have maximum genetic distance. Accessions ACC-24879 and ACC-24169 had minimum genetic distance i.e., 0.26. Dendrogram based on genetic distances showed four main clusters that were further dividing into several sub-clusters. The primers utilized in the present study, were valuable to identify different accessions of canola to find the variability present. This variability will be helpful to initiate the breeding program with their molecular genetic basis.

scholarly journals GENETIC DIVERSITY OF HONEYBEE (APIS MELLIFERA ADANSONII) IN IJEBU ENVIRONAS REVEALED BY SIMPLE SEQUENCE REPEAT (SSR) MARKERS

2020 ◽  
Vol 10 ◽  
pp. 77
Author(s):  
Mistura Temitope Adeleke ◽  
Oladunni Nimota Adekunle ◽  
Folarin Ojo Owagboriaye ◽  
Adebola Olayemi Odeseye ◽  
Kemi Sarah Oyedele ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Apis Mellifera ◽  
Simple Sequence Repeat ◽  
Gene Diversity ◽  
Genetic Distances ◽  
Sequence Repeat ◽  
Ogun State ◽  
Ssr Primers ◽  
Apis Mellifera Adansonii ◽  
Simple Sequence

Honeybee Apis mellifera adansonii, dominant honey producing species in Nigeria was subjected to genetic variability studies using Simple Sequence Repeat (SSR) in other to provide the baseline data in Nigeria. Nine (9) Simple Sequence Repeats (SSR) primers were used to assess the genetic diversity in Two (2) worker bees each collected from 22 colonies found in the four apiaries in Ijebu environs of Ogun State. Data collected were subjected to analysis and results showed that six (6) out of nine primers produced 80 reproducible, polymorphic bands while the remaining three (3) were monomorphic. Gene diversity (H ) in total population and magnitude of differentiation among T populations (FST) was 0.430 and 0.340, respectively. Analysis of Molecular Variance (AMOVA) partitioned the total genetic variation as 70% within, 30% among populations. The cluster analysis showed that Ipari-Oke 3 and Odo-Epo 1-8 populations diverged from others which showed they are closer in genetic distances while Ipari-Oke 1 and Odo-Epo 2-5 were newly observed subcluster which represents another subspecies. In conclusion, genetic variations existed amongst the honey worker bees populations in Ogun State.

scholarly journals ANALISIS KERAGAMAN GENETIK PLASMA NUTFAH KAKAO (Theobroma cacaoL.) BERDASARKANMARKA SSR / Analysis of Genetic Variability Germplasm of Cacao (Theobroma cacaoL.)Basedon SSR Marker

2020 ◽  
Vol 17 (4) ◽  
pp. 156
Author(s):  
Surti Kurniasih ◽  
Rubiyo Rubiyo ◽  
Asep Setiawan ◽  
Agus Purwantara ◽  
Sudarsono Sudarsono
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Ssr Markers ◽  
Theobroma Cacao ◽  
Simple Sequence Repeat ◽  
Ssr Marker ◽  
Gene Diversity ◽  
Sequence Repeat ◽  
Theobroma Cacao L ◽  
Simple Sequence

<p>Microsatellite or simple sequence repeat (SSR) markers have proven to be an excellent tool for cultivar identification, pedigree analysis, and genetic distance evaluations among organisms. The objectives of this research were to characterize cacao collection of Indonesian Coffee and Cacao Research Institute (ICCRI) and to analyze their genetic diversity using SSR markers. In this research, 39 SSR primer pairs were used to amplify genomic DNA of 29 cacao clones. Amplified SSR fragments for each primer pair were scored as individual band and used to determine genetic distance among evaluated cacao clones. Results of the experiment indicated that all SSR primer pairs evaluated were able to produce SSR markers for 29 cacao clones. The results also indicated that 34 out of 39 microsatellite loci evaluated were polymorphic, while 5 others were monomorphic. The total number of observed alleles among 29 clones was 132. Number of alleles per locus ranged from 4-8, with an average of 5.5 alelles per locus. Results of data analysis indicated that the PIC value was 0.665, the observed heterozigosity (Ho) was 0.651, and the gene diversity (He) was 0.720. The PIC, Ho, and He values were considered high. Genetic distances were evaluated using NTSys version 2.1 and dendrogram was constructed. Results of analysis indicated that 12 cacao clones evaluated were clustered in the first group with diversity coefficient of &lt; 3.75. Nine cacao clones were in the second group but with the same value of diversity coefficient (&lt;7.50). The rest of the cacao clones were in the third group with diversity coefficient of&gt;7.50. Based on those finding, all SSR primer pairs evaluated could be used to analyze cacao genome and be useful for genetic diversity analysis of cacao germplasm. The SSR marker analysis in ICCRI cacao collections resulted in high PIC, high observed heterozygosity, and high genetic diversity.</p><p>Key words: Theobroma cacao L, microsatelite, molecular marker, genetic diversity, heterozygosity</p><p> </p><p><strong>Abstrak</strong></p><p>Marka mikrosatelit atau sekuens sederhana berulang (simple sequence repeat = SSR) terbukti merupakan alat yang bagus untuk identifikasi kultivar, analisis pedigree, dan evaluasi jarak genetik berbagai organisme. Penelitian ini bertujuan untuk:1) karakterisasi kakao koleksi Pusat penelitian Kopi dan Kakao Indonesia menggunakan marka SSR dan 2) analisis keragaman genetik klon-klon kakao koleksi dengan menggunakan marka SSR. Dalam penelitian ini, 39 pasangan primer SSR telah digunakan untuk amplifikasi DNA genomik dari 29 klon kakao. Skoring pita SSR hasil amplifikasi menggunakan masing-masing pasangan primer dilakukan secara terpisah dan digunakan untuk menentukan jarak genetik di antara klon kakao yang dievaluasi. Hasil percobaan menunjukkan bahwa semua pasangan primer SSR yang digunakan mampu menghasilkan pita DNA hasil amplifikasi (marka SSR) untuk 29 klon kakao yang diuji. Hasil penelitian juga menunjukkan bahwa 34 dari 39 lokus SSR yang dianalisis bersifat polimorfik sedangkan lima primer yang lain bersifat monomorfik. Dari 29 klon kakao yang dievaluasi, telah berhasil diamplifikasi sebanyak 132 alel, dengan kisaran antara 4-8 alel/lokus. Rataan jumlah alel per lokus sebanyak 5,50. Hasil analisis data yang dilakukan juga menunjukkan nilai PIC untuk marka SSR yang digunakan sebesar 0,665. Untuk populasi klon kakao yang dievaluasi, diperoleh nilai rataan heterosigositas pengamatan (Ho) sebesar 0,651 dan rataan diversitas gen (He) sebesar 0,720. Nilai PIC Ho dan He yang didapat tergolong tinggi. Berdasarkan analisis keragaman dengan menggunakan program NTSys, diperoleh hasil 12 klon kakao berada dalam grup pertama (koefisien keragaman&lt;3,75) dan9 klon berada dalam grup kedua, dengan koefisien keragaman &lt; 7,50. Sedangkan klon-klon lainnya mempunyai koefisien keragaman &gt; 7,50. Berdasarkan hasil penelitian dan analisis data disimpulkan bahwa marka SSR dapat digunakan untuk menganalisis keragaman genetik plasma nutfah kakao. Tingkat polimorfisme yang dihasilkan marka SSR relatif tinggi. Tingkat heterosigositas plasma nutfah kakao koleksi Puslit Kopi dan Kakao Indonesiarelatif tinggi, dan keragaman genetiknyacukup tinggi.</p><p>Kata kunci : Theobroma cacao L, mikrosatelit, marka molekuler, keragaman genetik, heterosigositas</p>

scholarly journals Efficiency of different PCR-based marker systems for assessment of Iris pumila genetic diversity

Biologia ◽  
2013 ◽  
Vol 68 (4) ◽  
Author(s):  
Olena Bublyk ◽  
Igor Andreev ◽  
Ruslan Kalendar ◽  
Kateryna Spiridonova ◽  
Viktor Kunakh
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Gene Diversity ◽  
Issr Markers ◽  
Genetic Distances ◽  
Resolving Power ◽  
Abiotic Stress Response ◽  
Genetic Population ◽  
Iris Pumila ◽  
Polymorphic Bands

AbstractWe investigated informativeness and effectiveness of different marker types (ISSR, IRAP, REMAP, RGAP and LP-PCR that employ primers based on the conservative sequences of abiotic stress response genes) to study genetic diversity of Iris pumila L. By the number of amplicons per primer, number of polymorphic amplicons per primer and resolving power index (Rp), ISSR-markers were the most efficient followed by LP-PCR-markers. In order of decreasing value of indicators of genetic diversity “the percentage of polymorphic bands”, and “the average Jaccardś genetic distance between plants”, marker systems may be arranged as follows: ISSR > RAPD > LP-PC > RGAP ≈ IRAP. For ISSR-markers, the percentage of polymorphic bands was 1.3–1.7 times higher than for the others, and the average genetic distance was 1.2–1.3 times higher. Different marker systems were ranked by the value of Neiś gene diversity and the Shannonś index as follows: ISSR > RAPD ≈ LP-PCR > RGAP ≈ IRAP, with the highest and the lowest values differing 1.4 times. Genetic population structure was investigated with program Structure 2.3. The data of all marker systems suggest that all genomes under study belonged to one population. The PCoA and cluster analyses based on genetic distances showed distinctions in clustering generated from different markers data and summarized data, as well as the lack of strong clusters. Mantel test revealed significant positive correlation between the matrices of genetic distances generated by the data of almost all marker systems. The strongest correlation was found between RGAP- and IRAP-markers (r = 0.452, p = 0.01) and between RGAP and ISSR (r = 0.430, p = 0.01). ISSR, RAPD and LP-PCR proved to be more effective for the study of I. pumila genetic diversity, nevertheless, joint use of different marker systems will provide a more comprehensive assessment of variation in different genomic regions.

scholarly journals Impact of different numbers of microsatellite markers on population genetic results using SLAF-seq data for Rhododendron species

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Huaying Wang ◽  
Baiming Yang ◽  
Huan Wang ◽  
Hongxing Xiao
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Population Genetic ◽  
Nuclear Markers ◽  
Genetic Studies ◽  
Population Genetic Diversity ◽  
Polymorphic Microsatellites ◽  
Ssr Primers ◽  
The Impact ◽  
Simple Sequence

AbstractMicrosatellites (simple sequence repeats, SSRs) are co-dominant nuclear markers that are widely used in population genetic studies. Population genetic parameters from different studies might be significantly influenced by differences in marker number. In our study, 265 sequences with polymorphic microsatellites were obtained from SLAF-seq data. Then, subpopulations containing different numbers (5, 6, 7,…, 15, 20, 25, 30, 35, 40) of markers were genotyped 10 times to investigate the impact of marker numbers on population genetic diversity results. Our results show that genotyping with less than 11 or 12 microsatellite markers lead to significant deviations in the population genetic diversity or genetic structure results. In order to provide markers for population genetic and conservation studies for Rhododendron, 26 SSR primers were designed and validated in three species.

scholarly journals Molecular Genetic Variability of Spigelia marilandica and S. gentianoides

2015 ◽  
Vol 140 (2) ◽  
pp. 120-128
Author(s):  
Amanda J. Hershberger ◽  
Tracie M. Jenkins ◽  
Carol Robacker
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Variability ◽  
Gene Diversity ◽  
Molecular Genetic ◽  
Genetic Distances ◽  
Population Variation ◽  
Group Method ◽  
Polymorphism Analysis ◽  
Two Samples

Despite the ecologic and ornamental potential of southeastern U.S. native Spigelia, little is known about the intraspecific or the interpopulation genetic variation. The southeastern U.S. native Spigelia habitat is becoming more and more fragmented as a result of human activity, making it imperative to gain an understanding of natural genetic variation among and within species and populations for the purpose of obtaining variability for plant breeding and preserve the genetic variability in Spigelia. Therefore, the objective of this study was to use amplified fragment length polymorphism analysis to determine interspecific and intraspecific genetic variation and to evaluate gene flow. Thirteen populations of two species of native Spigelia, S. marilandica (SM), S. gentianoides var. gentianoides (SGG), and S. gentianoides var. alabamensis (SGA), were analyzed using four primer pairs that amplified a total of 269 bands. Based on analysis of molecular variance and estimates of Nei’s coefficients of gene diversity (percentage of polymorphic loci, average genetic diversity within populations, average genetic diversity within species, and proportion of species genetic diversity attributed to among population variation), the majority of variation found in Spigelia occurs within populations. Both among-species and among-population variation was low, likely the effect of common ancestry as well as relatively frequent introgression among individuals (and populations) of Spigelia. When all individuals were evaluated using Nei’s unbiased genetic distances and viewed as a unweighted pair group method with arithmetic mean phenogram, three main groups were shown, one with two samples of SGG from one population, one with 13 individuals from both SGG populations used in this study, and one with all of the SM, SGA, and remaining SGG individuals. Further evaluation using STRUCTURE software showed introgression between populations and species, although all allele clusters have not entirely introgressed into all populations. The significance of these results is discussed in relation to breeding in Spigelia.

scholarly journals Keragaman Genetik Inbrida Jagung QPM dan Provit-A Berdasarkan Marka SSRs (Simple Sequence Repeats)

2016 ◽  
Vol 35 (2) ◽  
pp. 133
Author(s):  
Nining Nurini Andayani ◽  
M. Yasin H.G ◽  
Marcia B. Pabendon
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Simple Sequence Repeats ◽  
Genetic Similarity ◽  
Genetic Distances ◽  
Large Variability ◽  
Maize Germplasm ◽  
High Level ◽  
Biology Laboratory ◽  
Simple Sequence

Information on genetic diversity of QPM and Provit-A maize germplasm is important to support breeding program, in order to form a high yielding maize hybrid. Simple sequence repeats (SSR) have been extensively utilized as genetic markers to study the genetic diversity, cultivar identification, and gene mapping. The objectives of this research were to investigate the genetic diversity and to obtain information the genetic relationship among 20 maize accessions using 29 SSRs. The research was carried out at the Moleculer Biology Laboratory of Indonesian Cereals Research Institute (ICERI) in Maros, South Sulawesi. Twenty nine polymorphic primers that covered the 10 maize chromosomes were used to fingerprint the genotype of the lines, detecting 83 allels, with an average allel number of 3 allels per locus, ranging from 2 to 6 alleles per locus. The results indicated that polymorphism information content (PIC) ranged from 0.10 (nc133 and phi072) to 0.74 (phi064) with the average of 0.45. Genetic distance based on genetic similarity estimate ranged from 0.39 to 0.92. The high level of PIC values and wide genetic distances indicated the large variability among maize germplasm. Cluster analysis divided the 20 maize accessions into three groups. Coefficient cofenetic value (r) was 0.85 indicated a good fit based on the genetic similarity value. As many as 30 inbred heterotic recombinants were derived by incorporating 20 QPM and Provit-A with genetic distance of ≤0.65. The SSRs proved to be reliable and is practical technique for revealing the relationship among specialty maize genotypes.

scholarly journals Selection of a core collection of Prunus sibirica L. germplasm by a stepwise clustering method using simple sequence repeat markers

PLoS ONE ◽  
2021 ◽  
Vol 16 (11) ◽  
pp. e0260097
Author(s):  
Yongqiang Sun ◽  
Shengjun Dong ◽  
Quangang Liu ◽  
Jianhua Chen ◽  
Jingjing Pan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Core Collection ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Northern China ◽  
Genetic Distances ◽  
Germplasm Resources ◽  
Sequence Repeat ◽  
Simple Sequence

Prunus sibirica is an economically important tree species that occurs in arid and semi-arid regions of northern China. For this species, creation of a core collection is critical for future ecological and evolutionary studies, efficient economic utilization, and development and management of the broader collection of its germplasm resources. In this study, we sampled 158 accessions of P. sibirica from Russia and China using 30 pair of simple sequence repeat molecular markers and 30 different schemes to identify candidate core collections. The 30 schemes were based on combinations of two different sampling strategies, three genetic distances, and five different sample sizes of the complete germplasm resource. We determined the optimal core collection from among the 30 results based on maximization of genetic diversity among groups according to Number of observed alleles (Na), Number of effective alleles (Ne), Shannon’s information index (I), Polymorphic information content (PIC), Nei gene diversity (H) and compared to the initial collection of 158 accessions. We found that the optimal core collection resulted from preferred sampling at 25% with Nei & Li genetic distance these ratios of Na, Ne, I, PIC and H to the complete 158 germplasm resources were 73.0%, 113%, 102%, 100% and 103%, respectively, indicating that the core collection comprised a robust representation of genetic diversity in P. sibirica. The proposed core collection will be valuable for future molecular breeding of this species and management of its germplasm resources.

Molecular Characterization and Genetic Diversity Study in F3 Population of Rice

2013 ◽  
Vol 20 (1-2) ◽  
pp. 1-8
Author(s):  
MM Rahman ◽  
L Rahman ◽  
SN Begum ◽  
F Nur
Keyword(s):  
Genetic Distance ◽  
Gene Diversity ◽  
Random Amplified Polymorphic Dna ◽  
Molecular Genetic ◽  
Molecular Genetic Analysis ◽  
Polymorphic Loci ◽  
Rice Genotypes ◽  
High Level ◽  
Genetic Diversity Study ◽  
Diversity Study

Random Amplified Polymorphic DNA (RAPD) assay was initiated for molecular genetic analysis among 13 F3 rice lines and their parents. Four out of 15 decamer random primers were used to amplify genomic DNA and the primers yielded a total of 41 RAPD markers of which 37 were considered as polymorphic with a mean of 9.25 bands per primer. The percentage of polymorphic loci was 90.24. The highest percentage of polymorphic loci (14.63) and gene diversity (0.0714) was observed in 05-6 F3 line and the lowest polymorphic loci (0.00) and gene diversity (0.00) was found in 05-12 and 05-15 F3 lines. So, relatively high level of genetic variation was found in 05-6 F3 line and it was genetically more diverse compared to others. The average co-efficient of gene differentiation (GST) and gene flow (Nm) values across all the loci were 0.8689 and 0.0755, respectively. The UPGMA dendrogram based on the Nei’s genetic distance differentiated the rice genotypes into two main clusters: PNR-519, 05-19, 05-14, 05-12 and 05-17 grouped in cluster 1. On the other hand, Baradhan, 05-9, 05-13, 05-11, 05-5, 05-6, 05-1, 05-4, 05-15 and 05-25 were grouped in cluster 2. The highest genetic distance (0.586) was found between 05-4 and 05-17 F3 lines and they remain in different cluster.DOI: http://dx.doi.org/10.3329/pa.v20i1-2.16839 Progress. Agric. 20(1 & 2): 1 – 8, 2009

Ampelographic characterization of white grapevine cul-tivars (Vitis vinifera L.) grown in Palestine

2015 ◽  
Vol 3 (1) ◽  
pp. 1-11
Author(s):  
Rezq Basheer-Salimia
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Germplasm Conservation ◽  
Genetic Distances ◽  
Vitis Vinifera L ◽  
Similarity Matrix ◽  
Breeding Programs ◽  
Local Varieties ◽  
Synonymies And Homonymies

Abstract: In Palestine, grape culture consists of ecotypes and cultivars (also called local varieties), for which a large number of homonymous and synonymous designations exist as well as misnaming of cultivars. The present study is the first report using detailed ampelographic characterizations (39 informative traits) to assess genetic diversity and detect similarities among sixteen accessions collected from putative diverse grape genotypes In general, 30 descriptors presented highly and satisfactory divergent genotypes, whereas the remaining traits showed no or very little ampelographic variation. Based on the similarity matrix and the resulting dendrogram of these ampelographic data, distinguishable genotypes as well as some cases of synonymies and homonymies clearly exist. A synonymy case seemed to be in four genotypes including Jandali-Mfarad, Jan-dali-Mrazraz, Jandali, and Hamadani-Mattar, which indeed showed genetic distances of less than 0.5, sug-gesting their relatedness, and the possibility that they are the same genotype, but with different names. In addition, homonym cases also occur in the following pairs of “Marawi’s, Hamadani’s, and Zaini’s genotypes, in which each pair seems to be two distinctive genotypes. Finally, among the 16 examined genotypes, the Zaini-Baladi genotype tended to show the highest genetic distance values from the others and thus could be potentially incorporated into any further local or regional breeding programs as well as germplasm conservation.

ISSR Marker Based Genetic Diversity in Morinda Spp. For Its Enhanced Collection, Conservation and Utilization

2021 ◽  
Author(s):  
Lalit Arya ◽  
Ramya Kossery Narayanan ◽  
Anjali Kak ◽  
Chitra Devi Pandey ◽  
Manjusha Verma ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Diversity ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Morinda Citrifolia ◽  
Species Differentiation ◽  
Information Index ◽  
Upgma Cluster Analysis ◽  
Simple Sequence

Abstract Morinda (Rubiaceae) is considerably recognized for its multiple uses viz. food, medicine, dyes, firewood, tools, oil, bio-sorbent etc. The molecular characterization of such an important plant would be very useful for its multifarious enhanced utilization. In the present study, 31 Morinda genotypes belonging to two different species Morinda citrifolia and Morinda tomentosa collected from different regions of India were investigated using Inter Simple Sequence Repeat (ISSR) markers. Fifteen ISSR primers generated 176 bands with an average of 11.7 bands per primer, of which (90.34%) were polymorphic. The percentage of polymorphic bands, mean Nei’s gene diversity, mean Shannon’s information index in Morinda tomentosa and Morinda citrifolia was [(69.89%, 30.68%); (0.21 ± 0.19, 0.12 ± 0.20); (0.32 ± 0.27 0.17 ± 0.28)] respectively, revealing higher polymorphism and genetic diversity in Morinda tomentosa compared to Morinda citrifolia. Structure, and UPGMA cluster analysis placed the genotypes into well-defined separate clusters belonging to two species Morinda tomentosa and Morinda citrifolia revealing the utility of ISSR markers in species differentiation. Distinct ecotypes within a particular species could also be inferred emphasizing the collection and conservation of Morinda genotypes from different regions, in order to capture the overall diversity of respective species. Further higher diversity of M. tomentosa must be advanced for its utilization in nutraceutical, nutritional and other nonfood purposes.

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