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 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.

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 Genetic diversity and interspecific relationships of some Allium species using inter simple sequence repeat markers

2015 ◽  
Vol 22 (2) ◽  
pp. 67-75 ◽  
Author(s):  
Leila Samiei ◽  
Mahnaz Kiani ◽  
Homa Zarghami ◽  
Farshid Memariani ◽  
Mohammad Reza Joharchi
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Gene Diversity ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Group Method ◽  
Sequence Repeat ◽  
Allium Species ◽  
Interspecific Relationships ◽  
Simple Sequence

In this study genetic diversity and interspecific relationships of 11 Allium L. species from Khorassan province of Iran including 32 accessions were investigated by inter simple sequence repeat (ISSR) markers. Nine ISSR primers produced a total of 80 polymorphic markers and revealed high polymorphism among the studied species. The average gene diversity, effective number of alleles and Shannon’s information index were 0.2, 1.28 and 0.3, respectively. Allium kuhsorkhense exhibited the greatest level of variation (He: 0.18), whereas A. stipitatum demonstrated the lowest level of variability (He: 0.05). UPGMA (Unweighted Pair Group Method with Arithmetic mean) analysis showed that Allium accessions have a similarity range of 0.60 to 0.95. Allium scapriscapum composed the most distant group in the dendrogram. The clustered groups of Allium species clearly reflect the recent taxonomic concept of the genus at the subgenus and section levels. The present study showed that the ISSR technique is an effective molecular approach for analyzing genetic diversity and relationship in Allium species.Bangladesh J. Plant Taxon. 22(2): 67-75, 2015 (December)

scholarly journals Simple Sequence Repeat Marker Analysis of Genetic Diversity among Progeny of a Biparental Mapping Population of Sweetpotato

HortScience ◽  
2015 ◽  
Vol 50 (8) ◽  
pp. 1143-1147 ◽  
Author(s):  
Benard Yada ◽  
Gina Brown-Guedira ◽  
Agnes Alajo ◽  
Gorrettie N. Ssemakula ◽  
Robert O.M. Mwanga ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Linkage Analysis ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Polymorphic Information Content ◽  
Genetic Distances ◽  
Sequence Repeat ◽  
Population Improvement ◽  
High Level ◽  
Simple Sequence

Genetic diversity is critical in sweetpotato improvement as it is the source of genes for desired genetic gains. Knowledge of the level of genetic diversity in a segregating family contributes to our understanding of the genetic diversity present in crosses and helps breeders to make selections for population improvement and cultivar release. Simple sequence repeat (SSR) markers have become widely used markers for diversity and linkage analysis in plants. In this study, we screened 405 sweetpotato SSR markers for polymorphism on the parents and progeny of a biparental cross of New Kawogo × Beauregard cultivars. Thereafter, we used the informative markers to analyze the diversity in this population. A total of 250 markers were polymorphic on the parents and selected progeny; of these, 133 were informative and used for diversity analysis. The polymorphic information content (PIC) values of the 133 markers ranged from 0.1 to 0.9 with an average of 0.7, an indication of high level of informativeness. The pairwise genetic distances among the progeny and parents ranged from 0.2 to 0.9, and they were grouped into five main clusters. The 133 SSR primers were informative and are recommended for use in sweetpotato diversity and linkage analysis.

scholarly journals Genetic Diversity of Arabica Coffee (Coffea arabicaL.) in Nicaragua as Estimated by Simple Sequence Repeat Markers

2012 ◽  
Vol 2012 ◽  
pp. 1-11 ◽  
Author(s):  
Mulatu Geleta ◽  
Isabel Herrera ◽  
Arnulfo Monzón ◽  
Tomas Bryngelsson
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Simple Sequence Repeat ◽  
Significant Contribution ◽  
Gene Diversity ◽  
Ex Situ ◽  
Sequence Repeat ◽  
Breeding Programs ◽  
Arabica Coffee ◽  
Simple Sequence

Coffea arabicaL. (arabica coffee), the only tetraploid species in the genusCoffea, represents the majority of the world’s coffee production and has a significant contribution to Nicaragua’s economy. The present paper was conducted to determine the genetic diversity of arabica coffee in Nicaragua for its conservation and breeding values. Twenty-six populations that represent eight varieties in Nicaragua were investigated using simple sequence repeat (SSR) markers. A total of 24 alleles were obtained from the 12 loci investigated across 260 individual plants. The total Nei’s gene diversity (HT) and the within-population gene diversity (HS) were 0.35 and 0.29, respectively, which is comparable with that previously reported from other countries and regions. Among the varieties, the highest diversity was recorded in the variety Catimor. Analysis of variance (AMOVA) revealed that about 87% of the total genetic variation was found within populations and the remaining 13% differentiate the populations (FST=0.13;P<0.001). The variation among the varieties was also significant. The genetic variation in Nicaraguan coffee is significant enough to be used in the breeding programs, and most of this variation can be conserved throughex situconservation of a low number of populations from each variety.

scholarly journals Genetic diversity of mutant napiergrass using Expressed Sequence Tag Simple Sequence Repeat (EST-SSR)

2019 ◽  
Vol 20 (8) ◽  
Author(s):  
Mansyur M Mansyur ◽  
Panca Dewi MH Karti ◽  
Luki Abdullah ◽  
Ali Husni ◽  
Puji Lestari
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Expressed Sequence Tag ◽  
Gene Diversity ◽  
Mutation Breeding ◽  
Sequence Repeat ◽  
Average Value ◽  
Expressed Sequence ◽  
Simple Sequence

Abstract. Mansyur, Karti PMH, Abdullah L, Husni A, Lestari P. 2019. Genetic diversity of mutant napiergrass using Expressed Sequence Tag Simple Sequence Repeat (EST-SSR). Biodiversitas 20: 2403-2409. Napiergrass is one of the tropical grasses which has a very important role in developing ruminant livestock, its productivity is high and its nutritional content is quite good. Plant breeding to produce new varieties that have better productivity continues. One of them is through mutation breeding and in vitro culture. The purpose of this research was to look at the genetic diversity among napiergrasses using the Expressed Sequence Tag Simple Sequence Repeat (EST-SSR). This study used 14 SSR molecular markers. The results showed that mutant DNA of napiergrass can be clearly amplified by all the EST-SSR primers used. The average number of alleles was 4.57, the average frequency of the main allele was 42%, and the average value of gene diversity was 0.66. While the PIC average value was 0.60. There were five markers that were very informative and have PIC values ​​above 0.7, among others, namely ICMP3045, ICMP3018, PSMP2090, PSMP2209, and PSMP2019. Phylogenetic analysis shows that 37 numbers of napiergrass mutants split into two main clusters at a coefficient of 0.56. The first cluster consists of 26 lines while the second cluster consists of 11 mutants. The parent napiergrass is in the first cluster. There are two pairs of mutants that have the same diversity, namely R20-11 with R 20-20-3 and R100-1 with R100-3.

scholarly journals Assessment of genetic diversity in Fusarium wilt tolerant and susceptible oil palm (Elaeis guineensis Jacq) progenies in Nigeria using inter- simple sequence repeat (ISSR) molecular markers

2019 ◽  
Author(s):  
Nnamdi Ifechukwude Chidi ◽  
Adedotun Adeyinka Adekunle ◽  
Temitope Oluwaseun Samuel ◽  
Emmanuel Ifechukwude Eziashi ◽  
David Okeh Igwe
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Oil Palm ◽  
Simple Sequence Repeat ◽  
Elaeis Guineensis ◽  
Gene Diversity ◽  
Inter Simple Sequence Repeat ◽  
Mean Value ◽  
Sequence Repeat ◽  
Simple Sequence

Abstract Background Improving oil palm in Nigeria for food security and subsequent export requires a better understanding of the genetic diversity among oil palm progenies tolerant and susceptible to Fusarium wilt disease. In view of the limitations of the orthodox method used in screening this disease, and the advantages of molecular markers, fourteen (14) Inter-simple sequence repeat (ISSR) DNA markers were applied to evaluate the genetic diversity, population structure and cluster resolutions of alleles responsible for tolerance of 560 Elaeis guineensis Jacq palms representing 8 different progenies distributed across NigeriaResults The amplification product revealed a moderately high level of genetic diversity with a total of 46 alleles identified, resulting in an average of 4.9091 alleles per locus detected between the oil palm progenies. Polymorphic information content (PIC) values varied between 0.3706-0.7861, with a mean value of 0.6829. The genetic diversity values ranged from 0.4063-0.8125 with a mean of 0.7216, while the major allele frequency ranged from 0.2500- 0.7500 with a mean value of 0.3750. Shannon's information index (I), Nei's gene diversity (H), and the effective number of alleles (Ne) had values of 0.6931, 0.5000, and 2.000, respectively. The genetic diversity was highest in progeny 3023, and lowest in progeny 4189. Mean values of the total gene diversity (Ht), gene diversity within the population (Hs) of the progenies, coefficient of gene differentiation among the progenies (Gst) and level of gene flow (Nm) were 0.4899, 0.3520, 0.2815 and 1.2764, respectively. The dendrogram clustered the progenies into six major clusters, while Principal Component Analysis (PCA) grouped the progenies into five clusters. PCA further identified the coordinate positions of tolerant and susceptible alleles of oil palm progeniesConclusion This study confirmed the identification of the coordinate positions of tolerant alleles in the gene loci, which could be exploited by breeders to developing tolerant oil palm seedlings.

scholarly journals Evaluation of Genetic Diversity Among Kongpo Monkshood (Aconitum kongboense L.) Germplasm Accessions Revealed by Inter Simple Sequence Repeat Markers

HortScience ◽  
2015 ◽  
Vol 50 (7) ◽  
pp. 940-943 ◽  
Author(s):  
Fanjuan Meng ◽  
Ruoding Wang ◽  
Mu Peng ◽  
Chao Wang ◽  
Zhongkui Wang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Gene Diversity ◽  
Molecular Data ◽  
Inter Simple Sequence Repeat ◽  
Tibet Plateau ◽  
Polymorphism Analysis ◽  
Sequence Repeat ◽  
The Mean ◽  
Simple Sequence

Inter simple sequence repeat (ISSR) were used to evaluate the genetic diversity of Kongpo Monkshood (Aconitum kongboense L.) in Motuo, Tibet Plateau. From 70 accessions of three populations, 10 out of 100 informative ISSR primers were chosen for polymorphism analysis. Percentage of polymorphic bands was 50% to 66.67% with a mean of 58.42%. The effective number of alleles (Ne) was between 1.545 (population 3) and 1.586 (population 2), and the mean value was 1.564; the Nei’s gene diversity (h) ranged from 0.315 to 0.327 with the average value of 0.320; the value of Shannon’s information index (I) ranged from 0.459 to 0.478, with the mean of 0.469. Based on molecular data, cluster analysis classified the 70 cultivars into three groups. Most accessions were related to the geographical origin and their genetic backgrounds. Bayesian structure and PCoA analysis were consistent with the dendrogram result. Based on the analysis, it will provide a reference for Kongpo Monkshood breeding purposes and contribute to identification, rational exploitation, and conservation of germplasms.

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 Assessment of Genetic Diversity of Niger Plant (Guizotia abyssinica L.) in Moiben Sub County, Kenya, Using Inter Simple Sequence Repeat Markers

2021 ◽  
Vol 8 (1) ◽  
pp. 126-131
Author(s):  
Lynnete Moraa Oimbo
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Gene Diversity ◽  
Distance Matrix ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Guizotia Abyssinica ◽  
Sequence Repeat ◽  
Euclidean Distance Matrix ◽  
Simple Sequence

Niger plant (Guizotia abyssinica), exhibits phenotypic plasticity in different environments. There is need to assess its genetic diversity since guizotia species has a high number of species which may be confused amongst themselves. To achieve this, inter simple sequence repeat (ISSR) markers were used to estimate genetic diversity among 12 wild populations of Niger plant from Moiben sub-county. Total genomic DNA was extracted as per the cetyltrimethylammonium bromide (Ctab) method and subjected to ISSR analysis using 20 primers. None of the primers produced unique banding patterns. ISSR data were used to calculate a squared-euclidean distance matrix. All the twenty primers (100%) gave polymorphic bands thus they were all considered for further analysis. The allele frequency of all the primers was below 0.95 indicating that they were all polymorphic in character. Gene diversity was high ranging from 0.3550 to 0.7337 with a mean value of 0.6302. The ISSR based upgma clustering produced four clusters. Niger plant within Moiben sub-county was found to be genetically diverse though heterozygosity was not noticed. The study recommends further analysis of Niger plant so as to form a basis for further development of the plant.

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