scholarly journals Genetic Diversity of the Endangered Dalbergia odorifera Revealed by SSR Markers

Forests ◽  
2019 ◽  
Vol 10 (3) ◽  
pp. 225 ◽  
Author(s):  
Fumei Liu ◽  
Zhou Hong ◽  
Daping Xu ◽  
Hongyan Jia ◽  
Ningnan Zhang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Basis ◽  
Gene Diversity ◽  
Hainan Island ◽  
Deciduous Tree ◽  
Neighbor Joining ◽  
Expected Heterozygosity ◽  
Dalbergia Odorifera ◽  
Simple Sequence

Dalbergia odorifera T. Chen (Fabaceae) is a semi-deciduous tree species indigenous to Hainan Island in China. Due to its precious heartwood “Hualimu (Chinese)” and Chinese medicinal components “Jiangxiang”, D. odorifera is seriously threatened of long-term overexploitation and has been listed on the IUCN (International Union for Conservation of Nature’s) red list since 1998. Therefore, the elucidation of its genetic diversity is imperative for conservation and breeding purposes. In this study, we evaluated the genetic diversity of 42 wild D. odorifera trees from seven populations covering its whole native distribution. In total, 19 SSR (simple sequence repeat) markers harbored 54 alleles across the 42 samples, and the medium genetic diversity level was inferred by Nei’s gene diversity (0.36), observed (0.28) and expected heterozygosity (0.37). Among the seven wild populations, the expected heterozygosity (He) varied from 0.31 (HNQS) to 0.40 (HNCJ). The analysis of molecular variance (AMOVA) showed that only 3% genetic variation existed among populations. Moderate population differentiations among the investigated populations were indicated by pairwise Fst (0.042–0.115). Structure analysis suggested two clusters for the 42 samples. Moreover, the seven populations were clearly distinguished into two clusters from both the principal coordinate analysis (PCoA) and neighbor-joining (NJ) analysis. Populations from Haikou city (HNHK), Baisha autonomous county (HNBS), Ledong autonomous county (HNLD), and Dongfang city (HNDF) comprised cluster I, while cluster II comprised the populations from Wenchang city and Sansha city (HNQS), Changjiang autonomous county (HNCJ), and Wuzhisan city (HNWZS). The findings of this study provide a preliminary genetic basis for the conservation, management, and restoration of this endemic species.

Genetic diversity and population structure of pencil yam (Vigna lanceolata) (Phaseoleae, Fabaceae), a wild herbaceous legume endemic to Australia, revealed by microsatellite markers

Botany ◽  
2015 ◽  
Vol 93 (3) ◽  
pp. 183-191 ◽  
Author(s):  
Phakchana Nubankoh ◽  
Sarocha Pimtong ◽  
Prakit Somta ◽  
Sujinna Dachapak ◽  
Peerasak Srinives
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Gene Diversity ◽  
Taxonomic Revision ◽  
Neighbor Joining ◽  
Complex Species ◽  
Vigna Species ◽  
Vigna Umbellata ◽  
Its Gene ◽  
Simple Sequence

Pencil yam (Vigna lanceolata Benth.) (Phaseoleae, Fabaceae) is a herbaceous legume endemic to Australia. A previous morphological study suggested that pencil yam is a complex species of two or more related taxa with seven distinct morphological types (morphotypes) and, thus, taxonomic revision is necessary. In this study, we assessed genetic diversity and determined the genetic structure of a pencil yam collection of 62 accessions from seven morphotypes using 18 microsatellite (simple sequence repeat) markers with the aim to provide information for taxonomic study. In total, 138 alleles were detected with a mean of 7.67 alleles per locus. Polymorphism information content per marker varied between 0.06 and 0.90 with a mean of 0.61, while the overall gene diversity was 0.62. Bayesian clustering, principal coordinate, and neighbor-joining analyses consistently revealed that these accessions are grouped into two subpopulations with difference in number of alleles, allelic richness, and gene diversity. The population structure was not related to either morphotype or geographical origin. Gene diversity of V. lanceolata was higher than that of wild Vigna radiata (L.) Wilczek and wild Vigna umbellata (Thunb.) Ohwi & Ohashi, comparable with that of wild Vigna mungo (L.) Hepper, Vigna exilis Tateishi & Maxted, and Vigna grandiflora (Prain) Tateishi & Maxted, and lower than that of wild Vigna angularis (Willd.) Ohwi & Ohashi. These results indicated that the taxonomy of V. lanceolata should be revised and that its gene diversity was moderate compared with the other wild Vigna species.

scholarly journals Microsatellite-Based Genetic Structure and Hybrid Detection in Alpacas Bred in Poland

Animals ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 2193
Author(s):  
Angelika Podbielska ◽  
Katarzyna Piórkowska ◽  
Tomasz Szmatoła
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
First Generation ◽  
Expected Heterozygosity ◽  
Hybrid Detection ◽  
Average Coefficient ◽  
Mixed Origin ◽  
Generation Hybrid

This study aimed to characterize the population structure and genetic diversity of alpacas maintained in Poland using 17 microsatellite markers recommended by the International Society for Animal Genetics. The classification of llamas, alpacas, and hybrids of both based on phenotype is often difficult due to long-term admixture. Our results showed that microsatellite markers can distinguish alpacas from llamas and provide information about the level of admixture of one species in another. Alpacas admixed with llamas constituted 8.8% of the tested individuals, with the first-generation hybrid displaying only 7.4% of llama admixture. The results showed that Poland hosts a high alpaca genetic diversity as a consequence of their mixed origin. More than 200 different alleles were identified and the average observed heterozygosity and expected heterozygosity values were 0.745 and 0.768, respectively, the average coefficient of inbreeding was 0.034, and the average polymorphism information content value was 0.741. The probability of exclusion for one parent was estimated at 0.99995 and for two parents at 0.99999.

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.

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)

Genetic diversity and population structure of Vigna exilis and Vigna grandiflora (Phaseoleae, Fabaceae) from Thailand based on microsatellite variation

Botany ◽  
2013 ◽  
Vol 91 (10) ◽  
pp. 653-661 ◽  
Author(s):  
Anochar Kaewwongwal ◽  
Arunee Jetsadu ◽  
Prakit Somta ◽  
Sompong Chankaew ◽  
Peerasak Srinives
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Allelic Richness ◽  
Gene Diversity ◽  
In Situ Conservation ◽  
Natural Populations ◽  
Microsatellite Variation ◽  
Genetic Clusters ◽  
Simple Sequence

The objective of this research was to determine the genetic diversity and population structure of natural populations of two rare wild species of Asian Vigna (Phaseoleae, Fabaceae), Vigna exilis Tateishi & Maxted and Vigna grandiflora (Prain) Tateishi & Maxted, from Thailand. Employing 21 simple sequence repeat markers, 107 and 85 individuals from seven and five natural populations of V. exilis and V. grandiflora, respectively, were analyzed. In total, the markers detected 196 alleles for V. exilis and 219 alleles for V. grandiflora. Vigna exilis populations showed lower average values in number of alleles, allelic richness, observed heterozygosity, gene diversity, and outcrossing rate than V. grandiflora populations, namely 58.00% versus 114.60%, 51.96% versus 74.80%, 0.02% versus 0.18%, 0.40% versus 0.66%, and 3.24% versus 17.41%, respectively. Pairwise FST among populations demonstrated that V. exilis was much more differentiated than V. grandiflora. Analysis of molecular variance revealed that 41.83% and 15.06% of total variation resided among the populations of V. exilis and V. grandiflora, respectively. Seven and two genetic clusters were detected for V. grandiflora and V. exilis by STRUCTURE analysis. Our findings suggest that different strategies are required for in situ conservation of the two species. All V. exilis populations, or as many as possible, should be conserved to protect genetic resources of this species, while a few V. grandiflora populations can capture the majority of its genetic variation.

Molecular characterization of almond accessions from the island of La Palma (Canary Islands, Spain) using SSR markers

2014 ◽  
Vol 12 (3) ◽  
pp. 323-329 ◽  
Author(s):  
Guillermo Padilla ◽  
Rafel Socias i Company ◽  
Amando Ordás
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Average Value ◽  
La Palma ◽  
Expected Heterozygosity ◽  
Commercial Cultivars ◽  
Soft Shell ◽  
Genetic Profiles ◽  
Simple Sequence

In this study, 15 simple sequence repeat (SSR) markers were used for genetic diversity analysis of 45 almond accessions, which included 25 local cultivars from La Palma Island and three other commercial cultivars. A total of 110 amplification fragments were produced, with an average value of 7.9 alleles per locus. Twelve of the SSR markers can be considered as highly informative, with values of expected heterozygosity and power of discrimination above 0.5 and 0.8, respectively. Due to cases of synonymy and homonymy, 37 different genetic profiles were obtained, with the homonymy of the soft-shell varieties known as ‘Mollar’ being the most significant. Cluster analysis identified four groups within the accessions. One of these groups exclusively consisted of the two commercial cultivars ‘Guara’ and ‘Ferraduel’. The other commercial cultivar used in the study, ‘Desmayo Largueta’, was in a cluster with three cultivars from the same locality. The analysis of molecular variance revealed that the within-localities component accounts for most of the total variation, suggesting that La Palma almond cultivars did not originate independently in different parts of the island. The results of the study reveal the genetic singularity of La Palma almond cultivars and the genetic diversity among them.

Evaluation of genetic diversity of Rubus hyrcanus using Inter Simple Sequence Repeat (ISSR) and morphological markers

Biologia ◽  
2015 ◽  
Vol 70 (3) ◽  
Author(s):  
Ehsan Sedighi ◽  
Mehdi Rahimmalek
Keyword(s):  
Genetic Diversity ◽  
Caspian Sea ◽  
Gene Diversity ◽  
Inter Simple Sequence Repeat ◽  
Morphological Markers ◽  
The Caspian Sea ◽  
Geographical Regions ◽  
North Eastern ◽  
North Western ◽  
Simple Sequence

AbstractRubus hyrcanus is considered as an important wild blackberry species scattered around the Caspian Sea. In this research, ISSR and morphological markers were used to assess genetic diversity in several populations of R. hyrcanus from various geographical regions of Caspian Sea in Iran. Twenty-five populations of R. hyrcanus from three regions (North- Western (NW), North- Eastern (NE) and Central (C)) and one population from R. discolor were applied in this research. Ten primers were used to amplify bands out of which 157 (77.13%) were polymorphic. Cluster and Principle coordinate analyses (PCoA) showed the higher similarity of NE and NW populations. Analysis of molecular variance (AMOVA) revealed that the differences among three collection regions only accounted for 28.09% of the total variation, whereas differences among populations within groups were 66.03%. Analyses among three regions showed that the minimum gene diversity over loci was observed in NW (0.16) and NE (0.17), while the highest one was found in C (0.238) region. Furthermore, narrow genetic base and relatively high genetic differentiation obtained for studied R. hyrcanus genotypes. The results of morphological analysis in most cases corresponded to those obtained through molecular analyses.

scholarly journals Genetic and species-level biodiversity patterns are linked by demography and ecological opportunity

2020 ◽  
Author(s):  
Chloé Schmidt ◽  
Stéphane Dray ◽  
Colin J. Garroway
Keyword(s):  
Genetic Diversity ◽  
Species Richness ◽  
Gene Diversity ◽  
Spatial Scales ◽  
Ecological Opportunity ◽  
Biogeographic Patterns ◽  
Genome Wide ◽  
Diversity Gradients ◽  
Low Levels

AbstractSpecies richness and genetic diversity are the two most fundamental products of evolution. Both are important conservation targets—species richness contributes to ecosystem functioning and human wellbeing, while genetic diversity allows those species to respond to changes in their environment and persist in the long-term. Biogeographic patterns of species richness are well-described, but we know little about patterns of genome-wide genetic diversity at similar spatial scales. Further, despite considerable attention to latitudinal trends in species richness, we still do not have a solid empirical understanding of the various processes that produce them, how they interact, or how they affect genetic diversity. Here we show that genome-wide genetic diversity and species richness share spatial structure, however, species richness hotspots tend to harbor low levels of within-species genetic variation. A single model encompassing eco-evolutionary processes related to environmental energy availability, niche availability, and proximity to humans explained 75% of variation in gene diversity and 90% of the variation in species richness. Our empirical model of both levels of biodiversity supports theory and demonstrates the importance of carrying capacity and ecological opportunity at individual and species levels for generating continent-wide genetic and species diversity gradients.

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