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 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 a Natural Population of Akebia trifoliata (Thunb.) Koidz and Extraction of a Core Collection Using Simple Sequence Repeat Markers

2021 ◽  
Vol 12 ◽  
Author(s):  
Yicheng Zhong ◽  
Yue Wang ◽  
Zhimin Sun ◽  
Juan Niu ◽  
Yaliang Shi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Simple Sequence Repeat ◽  
Core Collection ◽  
Polymorphic Information Content ◽  
Germplasm Conservation ◽  
Sequence Repeat ◽  
Information Index ◽  
Molecular Identity ◽  
Simple Sequence

Understand genetic diversity and genetic structure of germplasm is premise of germplasm conservation and utilization. And core collection can reduce the cost and difficulty of germplasm conservation. Akebia trifoliata (Thunb.) Koidz is an important medicinal, fruit and oil crop, particularly in China. In this study, 28 simple sequence repeat (SSR) markers were used to assess the genetic diversity and genetic structure of 955 A. trifoliata germplasms, determine their molecular identity and extract a core collection. The genetic diversity of the 955 germplasms was moderately polymorphic. The average number of alleles (Na), observed heterozygosity (HO), expected heterozygosity (HE), Shannon’s information index (I∗), and polymorphic information content (PIC) were 3.71, 0.24, 0.46, 0.81, and 0.41, respectively. Four subpopulations were identified, indicating a weak genetic structure. A 955 germplasms could be completely distinguished by the characters of s28, s25, s74, s89, s68, s30, s13, s100, s72, s77, and s3. And each germplasm’s molecular identity was made up of eleven characters. The core collection was composed of 164 germplasms (17.2% of 955 total germplasms in the population) and diversity parameters differed significantly from those of a random core collection. These results have implications for germplasm conservation. At the same time, based on the results, the 955 germplasm could be better used and managed.

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 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 ANALYSIS OF GENETIC DIVERSITY IN TWELVE CULTIVARS OF PEA BASED ON MORPHOLOGICAL AND SIMPLE SEQUENCE REPEAT MARKERS

2018 ◽  
Vol 19 (2) ◽  
pp. 57
Author(s):  
Brijesh Kumar Singh ◽  
Monoj Sutradhar ◽  
Amit Kumar Singh ◽  
Ajay Kumar Singh ◽  
Rajendra Prakash Vyas
Keyword(s):  
Genetic Diversity ◽  
Total Variation ◽  
Simple Sequence Repeat ◽  
Diversity Index ◽  
Polymorphic Information Content ◽  
Resolving Power ◽  
Sequence Repeat ◽  
Simple Sequence Repeat Markers ◽  
Simple Sequence ◽  
Number Of Seeds

<p class="abstrakinggris"><span class="judul"><span>Pea</span></span><span class="judul"><em><span>(Pisum sativum </span></em></span><span class="judul"><span>L<em>.)</em></span></span><span class="judul"><span>is the second most important legume crop worldwide after chickpea</span></span><span class="judul"><span> (</span></span><span class="judul"><em><span>Cicer arietinum </span></em></span><span class="judul"><span>L</span></span><span class="judul"><span>.) </span></span><span class="judul"><span>and valuable resources for their genetic improvement. This study aimed to analyze genetic diversity of pea cultivars through morphological and molecular markers. The present investigation was carried out with 12 pea cultivars using 28 simple sequence repeat markers. A total of 60 polymorphic bands with an average of 2.31 bands per primer were obtained. The polymorphic information content, diversity index and resolving power were ranged from 0.50 to 0.33, 0.61 to 0.86 and 0.44 to 1.0 with an average of 0.46, 0.73 and 0.76, respectively. The 12 pea cultivars were grouped into 3 clusters obtained from cluster analysis with a Jaccardd’s similarity coefficient range of 0.47-0.78, indicating the sufficient genetic divergence among these cultivars of pea. The principal component analysis showed that first three principal components explained 86.97% of the total variation, suggesting the contribution of quantitative traits in genetic variability. The contribution of 32.59% for number of seeds per plant, stem circumference, number of pods per plant and number of seeds per pod in the PC1 leads to the conclusion that these traits contribute more to the total variation observed in the 12 pea cultivars and would make a good parental stock material. Overall, this SSR analysis complements morphological characters of initial selection of these pea germplasms for future breeding program.</span></span></p>

scholarly journals Simple Sequence Repeat Markers Reveal Genetic Diversity Within and among Landrace Collections of Citron and Dessert Watermelon from South Africa

2016 ◽  
Vol 141 (6) ◽  
pp. 598-608 ◽  
Author(s):  
Jacob Mashilo ◽  
Hussein Shimelis ◽  
Alfred Odindo ◽  
Beyene Amelework
Keyword(s):  
South Africa ◽  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Polymorphic Information Content ◽  
Citrullus Lanatus ◽  
Sequence Repeat ◽  
Simple Sequence Repeat Markers ◽  
The Mean ◽  
Two Populations ◽  
Simple Sequence

Genetic diversity analysis is fundamental for effective breeding and genetic conservation. The objective of this study was to determine the genetic diversity present among dessert watermelon (Citrullus lanatus var. lanatus) and citron watermelon (C. lanatus var. citroides) landraces widely grown in South Africa and to select genetically diverse and complimentary genotypes for strategic breeding or conservation. Thirty-one dessert watermelon and 34 citron watermelon landraces were genotyped using 10 polymorphic simple sequence repeat markers. The number of alleles detected per marker ranged from 2 to 23 alleles, with a mean of 13.5 alleles. A total of 135 putative alleles were amplified from sampled watermelon populations. Number of effective alleles ranged from 1.99 to 10.88 alleles with a mean of 5.83 alleles. The mean observed and expected heterozygosity were 0.50 and 0.79, respectively. The mean polymorphic information content was 0.79. Cluster and principal coordinate analyses grouped the two watermelon populations into two separate clusters. The two populations were genetically differentiated with low gene flow, suggesting the presence of high genetic differences between the two populations. Overall, the study established the existence of considerable genetic diversity among South African grown dessert and citron watermelon landraces. Unique dessert watermelon landraces such as SWM-39, SWM-24, SWM-01, SWM-40, SWM-18, SWM-36, and SWM-26; and citron watermelon genotypes including WWM-24, WWM-37, WWM-28, WWM-34, WWM-02, WWM-22, WWM-50, and WWM-36 were selected based on their high dissimilarity index. These could be useful for breeding and systematic conservation.

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.

Assessment of molecular genetic diversity and population structure of sesame (Sesamum indicum L.) core collection accessions using simple sequence repeat markers

2013 ◽  
Vol 12 (1) ◽  
pp. 112-119 ◽  
Author(s):  
Jong-Hyun Park ◽  
Sundan Suresh ◽  
Gyu-Taek Cho ◽  
Nag-Gor Choi ◽  
Hyung-Jin Baek ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Simple Sequence Repeat ◽  
Core Collection ◽  
Sesamum Indicum ◽  
Group Method ◽  
Sequence Repeat ◽  
Simple Sequence Repeat Markers ◽  
The Core ◽  
Simple Sequence

Sesame (Sesamum indicum L.) is one of the oldest oil crops and is widely cultivated in Asia and Africa. The aim of this study was to assess the genetic diversity, phylogenetic relationships and population structure of 277 sesame core collection accessions collected from 15 countries in four different continents. A total of 158 alleles were detected among the sesame accessions, with the number varying from 3 to 25 alleles per locus and an average of 11.3. Polymorphism information content values ranged from 0.34 to 0.84, with an average of 0.568. These values indicated a high genetic diversity at 14 loci both among and within the populations. Of these, 44 genotype-specific alleles were identified in 12 of the 14 polymorphic simple sequence repeat markers. The core collection preserved a much higher level of genetic variation. Therefore, 10.1% was selected as the best sampling percentage from the whole collection when constructing the core collection. The 277 core collection accessions formed four robust clusters in the unweighted pair group method and the arithmetic averages (UPGMA) dendrogram, although the clustering did not indicate any clear division among the sesame accessions based on their geographical locations. Similar patterns were obtained using model-based structure analysis and country-based dendrograms, as some accessions situated geographically far apart were grouped together in the same cluster. The results of these analyses will increase our understanding of the genotype-specific alleles, genetic diversity and population structure of core collections, and the information can be used for the development of a future breeding strategy to improve sesame yield.

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