Genetic Diversity of Duabanga moluccana Blume from Two Provenances in West Nusa Tenggara Revealed by Microsatellite markers

Duabanga moluccana Blume, locally known as Rajumas, is a tree species that suitable for building materials, pulp, and plywood. The information about genetic diversity is required for the conserving of this species. Here, we elucidated the genetic diversity of D. moluccana from two provenances in West Nusa Tenggara, Indonesia. Four microsatellite markers successfully amplified 12 randomly selected samples and produced polymorphic DNA bands. Those primers were DMAG10, DMAG09, DMACAG01 and DMTCAC11. High genetic diversity was detected in the populations with 0.54 of mean expected heterozygosity (He). The genetic variation among individuals was 100%, whereas there were no genetic variations among populations and within individuals

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Regional Polymorphism Assessment of Myanmar ‘Sein Ta Lone’ Mango (Mangifera indica Linn) from Sintgaing Township Based on Microsatellite Markers

Horticultural Biotechnology Research ◽

10.25081/hbr.2019.v5.5447 ◽

1970 ◽

pp. 17-22

Author(s):

May Sandar Kyaing ◽

Sein Sandar May Phyo

Keyword(s):

Genetic Diversity ◽

Cluster Analysis ◽

Genetic Variation ◽

Microsatellite Markers ◽

Mangifera Indica ◽

Germplasm Management ◽

Upgma Dendrogram ◽

Expected Heterozygosity ◽

Upgma Cluster Analysis ◽

Relationship Of

This study was conducted to explore the genetic diversity and relationship of Sein Ta Lone mango cultivars among 20 commercial orchards in Sintgaing Township, Mandalay region. Nine microsatellite (SSR) markers were used to detect genetic polymorphism in a range from (3 to 6) alleles with (4.33) alleles per marker in average. Six out of nine microsatellite markers gave the PIC values of greater than (0.5). Among them, SSR36 held the highest PIC values of (0.691) while MiSHRS39 and MN85 possessed the least PIC values of (0.368) and (0.387) respectively. The genetic diversity was expressed as unbiased expected heterozygosity (UHe) value with an average of (0.561). The genetic relationship was revealed by (UPGMA) dendrogram in a range of (0.69 to 1.00). Based on UPGMA cluster analysis, three main clusters were classified among three different locations. This study was intended to help cultivar characterization and conservation for proper germplasm management with the estimation of genetic variation and relationship in the existing population of Sein Ta Lone mangoes in Sintgaing Township by microsatellite markers.

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Genetic Diversity and Population Structure Analysis of Dalbergia Odorifera Germplasm and Development of a Core Collection Using Microsatellite Markers

Genes ◽

10.3390/genes10040281 ◽

2019 ◽

Vol 10 (4) ◽

pp. 281 ◽

Cited By ~ 5

Author(s):

Fu-Mei Liu ◽

Ning-Nan Zhang ◽

Xiao-Jin Liu ◽

Zeng-Jiang Yang ◽

Hong-Yan Jia ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Microsatellite Markers ◽

Genetic Resources ◽

Tree Species ◽

Core Collection ◽

Southern China ◽

Breeding Programs ◽

Expected Heterozygosity ◽

Dalbergia Odorifera

Dalbergia odorifera T. Chen (Fabaceae) is a woody tree species indigenous to Hainan Island in China. Due to its high medicinal and commercial value, this tree species has been planted over 3500 ha2 in southern China. There is an urgent need for improvement of the D. odorifera germplasm, however, limited information on germplasm collection, conservation, and assessment of genetic resources is available. Therefore, we have built a database of 251 individuals collected across the whole of southern China, which included 42 wild trees and 210 cultivated trees, with the following objectives. (1) Evaluate genetic diversity and population structure of the database using 19 microsatellite markers and (2) develop a core collection for improvement and breeding programs. Totally, the 19 microsatellite markers harbored 77 alleles across the database with the polymorphic information content (PIC) ranging from 0.03 to 0.66. Medium genetic diversity level was inferred by Nei’s gene diversity (0.38), Shannon’s information index (0.65), and observed (0.33) and expected heterozygosity (0.38). Structure analysis showed that four was the optimum cluster size using the model-based Bayesian procedure, and the 251 D. odorifera individuals were grouped into five populations including four pure ones (RP1-4) and one mixed one (MIX) based on their maximum membership coefficients. Among these populations, the expected heterozygosity varied from 0.30 (RP3) to 0.38 (RP4). Analysis of molecular variance (AMOVA) showed 11% genetic variation existed among populations, and moderate population differentiation was inferred by the matrix of pairwise Fst (genetic differentiation among populations), which was in the range of 0.031 to 0.095. Moreover, a core collection of 31 D. odorifera individuals including six wild and 25 cultivated trees was developed, which was only 12.4% of the database but conserved the whole genetic diversity. The results of this study provided additional insight into the genetic structure of the large D. odorifera germplasm, and the core collection will be useful for the efficient and sustainable utilization of genetic resources, as well as efficient improvement in breeding programs.

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Changes in Genetic Diversity and Demographic History of Jankowski’s Bunting (Emberiza Jankowskii), as Revealed by Mitochondrial DNA and Microsatellite Markers

10.21203/rs.3.rs-265651/v1 ◽

2021 ◽

Author(s):

Long Huang ◽

Guochen Feng ◽

Dan Li ◽

Weiping Shang ◽

Lishi Zhang ◽

...

Keyword(s):

Genetic Diversity ◽

Mitochondrial Dna ◽

Genetic Variation ◽

Microsatellite Markers ◽

Population Size ◽

Demographic History ◽

Effective Population ◽

High Genetic Diversity ◽

History Of ◽

Eastern Inner Mongolia

Abstract The genetic variation and distribution of a population depend largely on the demographic history. For instance, populations that have recently experienced shrinkage usually have a lower genetic diversity. However, some endangered species with a narrow distribution have a high genetic diversity resulting from large historical population sizes and long generation times. In addition, very recent population bottlenecks may not be reflected in the population’s genetic information. In this study, we used a mitochondrial DNA marker and 15 microsatellite markers to reveal the genetic diversity, recent changes, inbreeding, and demographic history of a Jankowski’s bunting (Emberiza jankowskii) population in eastern Inner Mongolia. The results show that the genetic diversity of the population remained at a relatively stable and high level until recently. Severe population shrinkage did not result in a considerable lack of genetic variation because of the large historical population size and relatively short periods of human disturbance. In addition, introgression and gene flow among populations compensate for the loss of genetic variation to some extent. Considering the current small effective population size and the existence of inbreeding, we recommend that habitat protection be continued to maximize the genetic diversity of the Jankowski’s bunting population.

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Genetic diversity and population structure of date palms (Phoenix dactylifera L.) in Ethiopia using microsatellite markers

Journal of Genetic Engineering and Biotechnology ◽

10.1186/s43141-021-00168-5 ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Workia Ahmed ◽

Tileye Feyissa ◽

Kassahun Tesfaye ◽

Sumaira Farrakh

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Microsatellite Markers ◽

Information Content ◽

Date Palm ◽

Polymorphic Information Content ◽

Phoenix Dactylifera ◽

Mean Value ◽

Date Palms ◽

Expected Heterozygosity

Abstract Background Date palm tree (Phoenix dactylifera L.) is a perennial monocotyledonous plant belonging to the Arecaceae family, a special plant with extraordinary nature that gives eminent contributions in agricultural sustainability and huge socio-economic value in many countries of the world including Ethiopia. Evaluation of genetic diversity across date palms at DNA level is very important for breeding and conservation. The result of this study could help to design for genetic improvement and develop germplasm introduction programmes of date palms mainly in Ethiopia. Results In this study, 124 date palm genotypes were collected, and 10 polymorphic microsatellite markers were used. Among 10 microsatellites, MPdCIR085 and MPdCIR093 loci showed the highest value of observed and expected heterozygosity, maximum number of alleles, and highest polymorphic information content values. A total of 112 number of alleles were found, and the mean number of major allele frequency was 0.26, with numbers ranging from 0.155 (MPdCIR085) to 0.374 (MPdCIR016); effective number of alleles with a mean value of 6.61, private alleles ranged from 0.0 to 0.65; observed heterozygosity ranged from 0.355 to 0.726; expected heterozygosity varied from 0.669 to 0.906, polymorphic information content with a mean value of 0.809; fixation index individuals relative to subpopulations ranged from 0.028 for locus MPdCIR032 to 0.548 for locus MPdCIR025, while subpopulations relative to total population value ranged from − 0.007 (MPdCIR070) to 0.891 (MPdCIR015). All nine accesstions, neighbour-joining clustering analysis, based on dissimilarity coefficient values were grouped into five major categories; in population STRUCTURE analysis at highest K value, three groups were formed, whereas DAPC separated date palm genotypes into eight clusters using the first two linear discriminants. Principal coordinate analysis was explained, with a 17.33% total of variation in all populations. Generally, the result of this study revealed the presence of allele variations and high heterozygosity (> 0.7) in date palm genotypes. Conclusions Microsatellites (SSR) are one of the most preferable molecular markers for the study of genetic diversity and population structure of plants. In this study, we found the presence of genetic variations of date palm genotypes in Ethiopia; therefore, these genetic variations of date palms is important for crop improvement and conservation programmes; also, it will be used as sources of information to national and international genbanks.

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

Animals ◽

10.3390/ani11082193 ◽

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.

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Genetic analysis of silver-fir populations in the Beskids

Acta Societatis Botanicorum Poloniae ◽

10.5586/asbp.2003.015 ◽

2011 ◽

Vol 72 (2) ◽

pp. 115-119 ◽

Cited By ~ 3

Author(s):

Leon Mejnartowicz

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Genetic Analysis ◽

Abies Alba ◽

Genetic Distances ◽

Silver Fir ◽

Geographical Distance ◽

Polymorphic Loci ◽

Expected Heterozygosity ◽

Rare Alleles

Twenty-eight isozymic loci were studied in the Beskid Mts., in four populations of common silver-fir (Abies alba): one in Beskid Makowski (BM) and three populations in Beskid Sądecki (BS). Their genetic variation and diversity were analyzed, and Nei's genetic distances between the populations were calculated. The results show that the geographical distance between the BM population and the three BS populations is reflected in genetic distances. The BM population is clearly distinct from the others. It has the lowest genetic diversity (I = 0.42), percentage of polymorphic loci (%PoL = 64.29) and number of rare alleles (NoRa = 5). Besides, the BM population has the highest observed heterozygosity (Ho = 0.291), which exceeds the expected heterozygosity (He = 0.254), estimated on the basis of the Hardy-Weinberg Principle. On the contrary, BS populations are in the state of equilibrium, which is manifested, in similar values of He = 0.262 and Ho = 0.264.

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High Genetic Diversity but Absence of Population Structure in Local Chickens of Sri Lanka Inferred by Microsatellite Markers

Frontiers in Genetics ◽

10.3389/fgene.2021.723706 ◽

2021 ◽

Vol 12 ◽

Author(s):

Amali Malshani Samaraweera ◽

Ranga Liyanage ◽

Mohamed Nawaz Ibrahim ◽

Ally Mwai Okeyo ◽

Jianlin Han ◽

...

Keyword(s):

Genetic Diversity ◽

Sri Lanka ◽

Microsatellite Markers ◽

Allelic Diversity ◽

Genetic Distances ◽

Population Substructure ◽

High Genetic Diversity ◽

Naked Neck ◽

Local Chicken ◽

Local Chickens

Local chicken populations belonging to five villages in two geographically separated provinces of Sri Lanka were analyzed using 20 microsatellite markers to determine the genetic diversity of local chickens. Population genetic parameters were estimated separately for five populations based on geographic locations and for eight populations based on phenotypes, such as naked neck, long legged, crested or crown, frizzle feathered, Giriraj, commercial layer, crossbreds, and non-descript chicken. The analysis revealed that there was a high genetic diversity among local chickens with high number of unique alleles, mean number of alleles per locus (MNA), and total number of alleles per locus per population. A total of 185 microsatellite alleles were detected in 192 samples, indicating a high allelic diversity. The MNA ranged from 8.10 (non-descript village chicken) to 3.50 (Giriraj) among phenotypes and from 7.30 (Tabbowa) to 6.50 (Labunoruwa) among village populations. In phenotypic groups, positive inbreeding coefficient (FIS) values indicated the existence of population substructure with evidence of inbreeding. In commercial layers, a high expected heterozygosity He = 0.640 ± 0.042) and a negative FIS were observed. The positive FIS and high He estimates observed in village populations were due to the heterogeneity of samples, owing to free mating facilitated by communal feeding patterns. Highly admixed nature of phenotypes was explained as a result of rearing many phenotypes by households (58%) and interactions of chickens among neighboring households (53%). A weak substructure was evident due to the mating system, which disregarded the phenotypes. Based on genetic distances, crown chickens had the highest distance to other phenotypes, while the highest similarity was observed between non-descript village chickens and naked neck birds. The finding confirms the genetic wealth conserved within the populations as a result of the breeding system commonly practiced by chicken owners. Thus, the existing local chicken populations should be considered as a harbor of gene pool, which can be readily utilized in developing locally adapted and improved chicken breeds in the future.

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Genetic Diversity and Structure of Latvian Tilia cordata Populations

Proceedings of the Latvian Academy of Sciences. Section B. Natural, Exact, and Applied Sciences. ◽

10.2478/prolas-2021-0039 ◽

2021 ◽

Vol 75 (4) ◽

pp. 261-267

Author(s):

Dainis Edgars Ruņģis ◽

Baiba Krivmane

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Vegetative Reproduction ◽

Growth Conditions ◽

Climatic Conditions ◽

Tilia Cordata ◽

High Genetic Diversity ◽

Genetic Diversity And Structure ◽

Broadleaf Tree ◽

Broadleaf Species

Abstract Changing climatic conditions are transforming the ecological and silvicultural roles of broadleaf tree species in northern Europe. Small-leaved lime (Tilia cordata Mill.) is distributed throughout most of Europe, and is a common broadleaf species in Latvia. This species can tolerate a broad range of environmental and ecological conditions, including temperature, water availability, and soil types. The aim of this study was to assess the genetic diversity and differentiation of Latvian T. cordata populations using nuclear microsatellite markers developed for Tilia platyphyllos. After testing of 15 microsatellite markers, Latvian T. cordata samples were genotyped at 14 micro-satellite loci. Latvian T. cordata populations had high genetic diversity, and were not overly isolated from each other, with moderate gene flow between populations. No highly differentiated populations were identified. Vegetative reproduction was identified in most analysed populations, and almost one-third of analysed individuals are of clonal origin. T. cordata has high timber production potential under the current climatic and growth conditions in Latvia, and therefore this species has potential for use in forestry, as well as playing a significant role in maintaining biodiversity and other ecosystem services.

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Genetic variation analysis of superior cotton varieties of Gossypium hirsutum through microsatellite markers

International Journal of Plant Biology ◽

10.4081/pb.2017.6996 ◽

2017 ◽

Vol 8 (1) ◽

Author(s):

Dede Nuraida ◽

Yusuf Abdurrajak ◽

Moh Amin ◽

Utami S. Hastutik

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Gossypium Hirsutum ◽

Microsatellite Markers ◽

Size Range ◽

Allele Frequencies ◽

Variation Analysis ◽

Ctab Method

This study was conducted in order to obtain information on genetic variation in populations rated as superior cotton (Gossypium hirsutum L.) varieties in Balittas Malang, Indonesia. The samples used 10 varieties of cotton Kanesia series and 2 other superior varieties that are LRA 5166 and ISA 205A. Indicators of genetic diversity are the number of alleles per locus, allele frequencies, and heterozygosity values. DNA was isolated from the leaves of 3- week-old seedlings using the CTAB method. Amplification was performed using 5 SSRs primer pairs of the JESPR series. The results showed five microsatellite loci, yielding 12 alleles with a size range of 80–500 bp, with an average number of alleles per locus of 4.60. The average values of heterozygosity of the five loci was high, at 0.71. Based on the number of alleles, allele frequencies and heterozygosity values, the genetic variation sampled in the superior cotton varieties studied here is quite high.

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