scholarly journals Genetic Diversity of Seashore Paspalum Revealed with Simple Sequence Repeat Markers

2020 ◽  
Vol 145 (4) ◽  
pp. 228-235
Author(s):  
Qing Shen ◽  
Hua Bian ◽  
Hai-yan Wei ◽  
Li Liao ◽  
Zhi-yong Wang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Ssr Marker ◽  
Diversity Index ◽  
Polymorphic Information Content ◽  
Principal Component ◽  
Sequence Repeat ◽  
Similarity Coefficients ◽  
Seashore Paspalum ◽  
Simple Sequence

Seashore paspalum (Paspalum vaginatum) is an important warm-season turfgrass distributed in tropical and coastal areas. It has excellent resistance to abiotic stresses, such as salinity, drought, and low temperature. However, the research on genetic diversity of local P. vaginatum collections from China is limited. In this study, the genetic diversity among 58 P. vaginatum accessions from four different provinces in China and four cultivars were assessed using simple sequence repeat (SSR) markers. The results indicated that a total of 45 alleles were detected by 19 polymorphic markers, with a range of 2 to 4 and an average of 2.4 alleles per marker. The genetic similarity coefficients between each pair of the 58 P. vaginatum accessions and four cultivars ranged from 0.51 to 1.00, with an average of 0.77. The range of variation of Shannon diversity index of each SSR marker was 0.047 to 1.075, with an average of 0.486. The polymorphic information content of each SSR marker varies from 0.016 to 0.577, with an average of 0.249. The results of cluster analysis and principal component analysis (PCA) showed that 58 P. vaginatum accessions and four cultivars were divided into four groups. These results provide the theoretical basis for the genetic diversity assessments and molecular marker–assisted breeding of P. vaginatum species.

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 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 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 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, Population Structure and Relationship of Ethiopian Barley (Hordeum vulgare L.) Landraces as reveled by Simple Sequence Repeat (SSR) Markers

2021 ◽  
Author(s):  
Allo Aman Dido ◽  
B.J.K. Singh ◽  
Ermias Assefa ◽  
M.S.R. Kr ◽  
Dawit Degefu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Diversity Index ◽  
Ex Situ ◽  
Conservation Strategies ◽  
Sequence Repeat ◽  
Genetic Rescue ◽  
Hordeum Vulgare L ◽  
Barley Genotypes ◽  
Simple Sequence

Abstract Characterization of genetic resources maintained at genebanks has important implications for future utilization and collection activities. A total of 49 simple sequence repeat (SSR) or microsatellite markers were used to study genetic diversity and relationships among 376 barley landraces collected from different barley producing parts of Ethiopia and eight cultivars. Overall, 478 alleles with an average of 9.755 alleles per locus were obtained of which 97.07% of the loci were observed to be polymorphic. Nei’s genetic diversity index (h) was 0.654, and the Shannon diversity index (I) was 0.647, indicating that the genetic diversity in barley genotypes studies was moderately high. At the population level, the percentage of polymorphic loci (PPL) averaged 98.37%, h = averaged 0.388, and I = averaged 0.568. The highest level of genetic diversity was observed in the AR population (PPL =100%, h = 0.439, I = 0.624); the lowest was observed in the JM population (PPL = 75.51%, h = 0.291, I =0.430). AMOVA revealed significant genetic differentiation within and between populations (P < 0.001), with 84.21% of the variation occurring within populations and 15.79% occurring among populations. Genetic variation analysis showed a coefficient of gene differentiation of 0.053 and a gene flow value of 4.467 among populations. The 384 barley genotypes were divided into seven genetic clusters according to STRUCTURE, Neighbour joining tree and principal coordinate analysis, correlating significantly with geographic distribution. These results will assist with the formulation of conservation strategies, such as genetic rescue and on-farm in situ and ex situ conservation.

scholarly journals Genetic Diversity of South African Bottle Gourd [Lagenaria siceraria (Molina) Standl.] Landraces Revealed by Simple Sequence Repeat Markers

HortScience ◽  
2016 ◽  
Vol 51 (2) ◽  
pp. 120-126 ◽  
Author(s):  
Jacob Mashilo ◽  
Hussein Shimelis ◽  
Alfred Odindo ◽  
Beyene Amelework
Keyword(s):  
Genetic Diversity ◽  
South African ◽  
Simple Sequence Repeat ◽  
Polymorphic Information Content ◽  
Bottle Gourd ◽  
Lagenaria Siceraria ◽  
Sequence Repeat ◽  
Dissimilarity Index ◽  
The Mean ◽  
Simple Sequence

Bottle gourd [Lagenaria siceraria (Molina) Standl.] landraces are widely grown in South Africa, and genetic diversity analysis is necessary to identify promising genotypes for breeding or systematic conservation. Sixty-seven diverse bottle gourd landraces were genotyped using 14 selected simple sequence repeat (SSR) markers. The number of alleles detected per marker ranged from 4 to 11, with a total of 86 putative alleles being amplified. Allele sizes ranged from 145 to 330 base pair (bp). Number of effective alleles (Ne) ranged from 1.58 to 6.14 with a mean of 3.10. Allelic richness varied from 3.00 to 8.90 with a mean of 5.23. Expected heterozygosity (He) values ranged from 0.37 to 0.84 with a mean of 0.65. The mean polymorphic information content (PIC) was 0.57. Jaccard’s coefficient of similarity values ranged from 0.00 to 1.00, with a mean of 0.63. Analysis of molecular variance (AMOVA) revealed that 79%, 17%, and 4% of the variation in bottle gourd landraces was attributable to among landraces, within landraces, and between populations, respectively. The study established the existence of considerable genetic diversity among South African bottle gourd landraces. Unique landraces such as BG-4, BG-6, BG-8, BG-9, and BG-15 from cluster I; BG-55, BG-42, BG-57, and BG-58 from cluster II; BG-28, BG-23, BG-29, and BG-34 from cluster III were selected based on their highest dissimilarity index. These could be useful for bottle gourd breeding and systematic conservation.

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.

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