scholarly journals Genetic diversity and relationship of Hunan province of China local tree peonies based on SSR markers

2019 ◽  
Vol 18 (4) ◽  
pp. 213-223
Author(s):  
Min-Huan Zhang ◽  
Xiao-Ling Jin ◽  
Ya-Feng Wen ◽  
Shouyun Shen ◽  
Wen Xing ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Shannon Index ◽  
Ornamental Plant ◽  
Hunan Province ◽  
Fixation Index ◽  
Tree Peony ◽  
The World ◽  
Relationship Of ◽  
Simple Sequence

Paeonia sect. Moutan is a wide known ornamental plant in the world. The objective of this study was to provide the theoretical basis for scientific preservation and utilization of tree peony resources of Hunan province of China. Simple sequence repeat (SSR) markers were applied to reveal the genetic diversity and relationship of 21 tree peony resources and 45 domestic and foreign tree peony cultivars. Clear bands, the size of which ranged from 115 bp to 379 bp, were detected with 14 primers. In total, 90 alleles were detected and the number of alleles detected with one primer varied between 5 and 13; the number of effective alleles ranged from 1.183 to 2.070; the polymorphism ratio of each locus was 100%. The observed heterozygosity, which ranged from 0.120 to 0.851 with an average of 0.532, was larger than the expected one, which ranged from 0.090 to 0.470 with an average of 0.300. Shannon index ranged from 0.137 to 0.695 and fixation index ranged from −0.332 to −0.869. The results show abundant genetic diversity in tree peony of Hunan province and SSR markers distinguishing homonymous tree peony resources successfully.

Genetic diversity of Symplocos paniculata of Hunan province revealed by inter-simple sequence repeat (ISSR)

2019 ◽  
Vol 51 (5) ◽  
Author(s):  
Huifang Cao ◽  
Qiang Lin ◽  
Peiwang Li ◽  
Jingzhen Chen ◽  
Changzhu Li ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Inter Simple Sequence Repeat ◽  
Hunan Province ◽  
Sequence Repeat ◽  
Simple Sequence

scholarly journals Assessment of the Genetic Diversity of Rice Germplasms Characterized by Black-Purple and Red Pericarp Color Using Simple Sequence Repeat Markers

Plants ◽  
2019 ◽  
Vol 8 (11) ◽  
pp. 471
Author(s):  
Jae-Ryoung Park ◽  
Won-Tae Yang ◽  
Yong-Sham Kwon ◽  
Hyeon-Nam Kim ◽  
Kyung-Min Kim ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Germplasm Collection ◽  
Group Method ◽  
Sequence Repeat ◽  
Rice Varieties ◽  
Red Pericarp ◽  
Simple Sequence ◽  
Colored Rice

The assessment of the genetic diversity within germplasm collections can be accomplished using simple sequence repeat (SSR) markers and association mapping techniques. The present study was conducted to evaluate the genetic diversity of a colored rice germplasm collection containing 376 black-purple rice samples and 172 red pericarp samples, conserved by Dong-A University. There were 600 pairs of SSR primers screened against 11 rice varieties. Sixteen informative primer pairs were selected, having high polymorphism information content (PIC) values, which were then used to assess the genetic diversity within the collection. A total of 409 polymorphic amplified fragments were obtained using the 16 SSR markers. The number of alleles per locus ranged from 11 to 47, with an average of 25.6. The average PIC value was 0.913, ranging from 0.855 to 0.964. Four hundred and nine SSR loci were used to calculate Jaccard’s distance coefficients, using the unweighted pair-group method with arithmetic mean cluster analysis. These accessions were separated into several distinctive groups corresponding to their morphology. The results provided valuable information for the colored rice breeding program and showed the importance of protecting germplasm resources and the molecular markers that can be derived from them.

scholarly journals The new use of Sorghum bicolor-derived SSR markers to evaluate genetic diversity in 17 Australian Sorghum species

2005 ◽  
Vol 3 (1) ◽  
pp. 19-28 ◽  
Author(s):  
Sally L. Dillon ◽  
Peter K. Lawrence ◽  
Robert J. Henry
Keyword(s):  
Genetic Diversity ◽  
Sorghum Bicolor ◽  
Ssr Markers ◽  
Diversity Indices ◽  
Basic Knowledge ◽  
Apparent Lack ◽  
Breeding Programmes ◽  
Diversity Studies ◽  
Potential Use ◽  
Simple Sequence

The Sorghum genus is extremely diverse both morphologically and geographically, however, relatively few of the 25 recognized species have been evaluated genetically. The apparent lack of basic knowledge pertaining to the levels of genetic diversity both within and between the 17 Australian wild species is a major obstacle to both their effective conservation and potential use in breeding programmes. Twelve Sorghum bicolor-derived simple sequence repeat (SSR) markers were evaluated for cross-species amplification in all 25 Sorghum species. The SSR markers were highly polymorphic, with diversity indices ranging from 0.59 to 0.99 with mean of 0.91. Five markers combined were able to differentiate 24 of the 25 Sorghum species, with intra-species polymorphism apparent. Sorghum bicolor-derived SSRs have proven to be an efficient source of markers for genetic diversity studies of the relatively poorly characterized Australian indigenous Sorghum species.

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 Cross-Genera Transferability of Microsatellite Markers and Phylogenetic Assessment of Three Salsola Species from Western Kazakhstan

2020 ◽  
Vol 74 (5) ◽  
pp. 325-334
Author(s):  
Shyryn Almerekova ◽  
Nasima Favarisova ◽  
Yerlan Turuspekov ◽  
Saule Abugalieva
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Sand Dunes ◽  
Haplotype Network ◽  
Internal Transcribed Spacers ◽  
Western Kazakhstan ◽  
Desert Zone ◽  
Environmental Importance ◽  
Simple Sequence

Abstract Salsola arbuscula Pall., Salsola arbusculiformis Drob. and Salsola chiwensis M. Pop. have great environmental importance as they can stabilise sand dunes and therefore are useful for desert zone landscaping. The genetic diversity and phylogenetic relationships of populations of these species collected in Western Kazakhstan were analysed using internal transcribed spacers (ITS) and simple sequence repeat (SSR) markers. The ITS sequences of species were aligned with sequences of 37 Salsola species from the NCBI. ITS analysis clustered the samples into two major groups and eight sections. The phylogenetic tree and haplotype network relationships confirmed the polyphyletic origin of Salsola and allowed taxonomic reassessment for the studied species. A set of SSR markers originally developed from genera Agriophyllum, Haloxylon, and Beta was tested for their variability in Salsola species. Twenty-six tested SSR markers were selected for their transferability scores, and 13 of them were suitable for study of genetic diversity in populations of three Salsola species. It was concluded that polymorphic SSR markers were efficient in the separation of the studied Salsola species and could be effectively used in studies related to the genetic variation in the genus.

Genetic diversity among silkworm (Bombyx mori L., Lep., Bombycidae) germplasms revealed by microsatellites

Genome ◽  
2005 ◽  
Vol 48 (5) ◽  
pp. 802-810 ◽  
Author(s):  
Muwang Li ◽  
Li Shen ◽  
Anying Xu ◽  
Xuexia Miao ◽  
Chengxiang Hou ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Bombyx Mori ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Genetic Relationships ◽  
Group Method ◽  
Sequence Repeat ◽  
Bombyx Mori L ◽  
Simple Sequence ◽  
Silkworm Bombyx Mori

To determine genetic relationships among strains of silkworm, Bombyx mori L., 31 strains with different origins, number of generations per year, number of molts per generation, and morphological characters were studied using simple sequence repeat (SSR) markers. Twenty-six primer pairs flanking microsatellite sequences in the silkworm genome were assayed. All were polymorphic and unambiguously separated silkworm strains from each other. A total of 188 alleles were detected with a mean value of 7.2 alleles/locus (range 2–17). The average heterozygosity value for each SSR locus ranged from 0 to 0.60, and the highest one was 0.96 (Fl0516 in 4013). The mean polymorphism index content (PIC) was 0.66 (range 0.12–0.89). Unweighted pair group method with arithmetic means (UPGMA) cluster analysis of Nei's genetic distance grouped silkworm strains based on their origin. Seven major ecotypic silkworm groups were analyzed. Principal components analysis (PCA) for SSR data support their UPGMA clustering. The results indicated that SSR markers are an efficient tool for fingerprinting cultivars and conducting genetic-diversity studies in the silkworm.Key words: silkworm, Bombyx mori L., microsatellites, simple sequence repeat (SSR), genetic diversity.

scholarly journals Analysis of genetic diversity and population structure in Asparagus species using SSR markers

2020 ◽  
Vol 18 (1) ◽  
Author(s):  
Manish Kapoor ◽  
Pooja Mawal ◽  
Vikas Sharma ◽  
Raghbir Chand Gupta
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Mean Value ◽  
Discrete Groups ◽  
Base Pairs ◽  
High Genetic Diversity ◽  
Pharmaceutical Industries ◽  
Improvement Programs ◽  
Northwest India ◽  
Simple Sequence

Abstract Background Various Asparagus species constitute the significant vegetable and medicinal genetic resource throughout the world. Asparagus species serve as important commodity of food and pharmaceutical industries in India. A diverse collection of Asparagus species from different localities of Northwest India was investigated for its genetic diversity using simple sequence repeat (SSR) markers. Results Polymorphic SSR markers revealed high genetic diversity. Primer SSR-15 amplified maximum of 8 fragments while 3 primers, namely, SSR-43, SSR-63, and AGA1 amplified minimum of 3 fragments. Collectively, 122 alleles were amplified in a range between 3 and 8 with an average of 5 alleles per marker. The size of the amplified alleles ranged between 90 and 680 base pairs. Polymorphism information content (PIC) value varied from a highest value of 0.499 in primer AGA1 to a lowest value of 0.231 in primer SSR-63 with a mean value of 0.376 showing considerable SSR polymorphism. Dendrogram developed on the basis of Jaccard’s similarity coefficient and neighbor-joining tree segregated all the studied Asparagus species into two discrete groups. Structure analysis based on Bayesian clustering allocated different accessions to two independent clusters and exhibited low level of individual admixture. Conclusions The genetic diversity analysis showed a conservative genetic background for maximum species of asparagus. Only Accessions of Asparagus adscendens were split into two diverse clusters suggesting a wide genetic base of this species as compared to other species. Overall genetic diversity was high, and this germplasm of Asparagus can be used in future improvement programs. The findings of current research on Asparagus germplasm can make a momentous contribution to initiatives of interbreeding, conservation, and improvement of Asparagus in future.

Genetic diversity of oil-tea camellia germplasms revealed by ISSR analysis

2015 ◽  
Vol 08 (05) ◽  
pp. 1550070 ◽  
Author(s):  
Lan-Ying Zhou ◽  
Xiang-Nan Wang ◽  
Li-Ping Wang ◽  
Yong-Zhong Chen ◽  
Xiao-Cheng Jiang
Keyword(s):  
Genetic Diversity ◽  
Reaction System ◽  
Inter Simple Sequence Repeat ◽  
Genetic Distances ◽  
Similarity Coefficient ◽  
Hunan Province ◽  
Information Index ◽  
Group I ◽  
Issr Pcr ◽  
Simple Sequence

Genetic diversity of 51 oil-tea camellia germplasms was analyzed using the optimized inter-simple sequence repeat (ISSR)–PCR reaction system with 22 primers screened from a set of 100 ISSR primers. The results showed that 493 discernible loci with distinct electrophoretic bands were obtained, of which, 478 loci (96.78%) were polymorphic. This indicated that oil-tea germplasms possess abundant genetic diversities. By clustering analysis performed using softwares of NTSYS 2.10 and Winboot, 51 oil-tea germplasms were divided into two groups: Group I had 48 lines of Camellia oleifera Abel, while Group II had three C. oleifera Abel related species and their similarity coefficient was 0.62. Group I was further divided into Group I-1 and Group I-2, and their similarity coefficient (Gs) was 0.634. All members of Group I-1 originated from Hunan Province, while Group I-2 included the rest of Hunan lines and those originated from other regions of China. Analyzed by software POPGENE 1.32, the Shannon's information index (I*) of genetic polymorphism was 0.3852, the genetic diversity among different region populations (Ht) was 0.2537, the genetic diversity within populations (Hs) was 0.15545, the differentiation coefficient of genetic diversity among populations (Gst) was 0.3967, and the gene flow among populations (Nm*) was 0.8262. The Nei's genetic distances between the Hunan population and the populations originated from other regions of China implied that geographic isolation strongly influenced genetic differentiation among populations. Meanwhile, seedling rootstock grafting and high grafting for tree crown produced genetic variations among clonal offsprings.

scholarly journals Genetic Diversity of Vitis davidii Accessions Revealed Using Microsatellite and Sequence-related Amplified Polymorphism Markers

HortScience ◽  
2018 ◽  
Vol 53 (3) ◽  
pp. 283-287
Author(s):  
Xiu Cai Fan ◽  
Hai Sheng Sun ◽  
Ying Zhang ◽  
Jian Fu Jiang ◽  
Min Li ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Genetic Similarity ◽  
Similarity Coefficient ◽  
Srap Markers ◽  
Average Percentage ◽  
Allele Number ◽  
Ssr Primers ◽  
Vitis Davidii ◽  
Simple Sequence

In this study, simple sequence repeat (SSR) and sequence-related amplified polymorphism (SRAP) markers were used to analyze the genetic diversity of 48 wild Vitis davidii accessions. A total of 78 distinct alleles were amplified by 11 SSR primers, and the average allele number was 8.8. The average observed heterozygosity (Ho) and expected heterozygosity (He) values were 0.785 and 0.814, respectively. The effective allele numbers ranged from 3.92 to 9.61. The average polymorphism information content (PIC) was 0.798. Twelve of 169 SRAP primer combinations were selected for SRAP analysis. A total of 188 bands were produced, and the average was 15.7 bands per primer combination; the average percentage of polymorphic bands was 84.0%. The average PIC was 0.76. The results of the clustering analysis based on SSR markers showed that the 48 wild V. davidii accessions could be classified into five main clusters and had a genetic similarity coefficient level of 0.68. The dendrogram obtained from the SRAP data showed that 48 wild V. davidii accessions could be classified into five main clusters and had a genetic similarity coefficient of 0.72. SSR and SRAP markers differentiated all accessions studied including those with a similar pedigree. We speculated on the origin of Ciputao 0941♀, Ciputao 0940♂, and Fu’an-ci-01 using SSR markers and used both SSR and SRAP markers to resolve homonymy. The result will be valuable for further management and protection of V. davidii germplasm resources.

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