scholarly journals Genetic Characterization of Native Donkey (Equus asinus) Populations of Turkey Using Microsatellite Markers

Animals ◽  
2020 ◽  
Vol 10 (6) ◽  
pp. 1093
Author(s):  
Selen Yatkın ◽  
Fulya Özdil ◽  
Emel Özkan Ünal ◽  
Serdar Genç ◽  
Selçuk Kaplan ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
Likelihood Function ◽  
Diversity Index ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Clustering Algorithms ◽  
Structural Features ◽  
Equus Asinus ◽  
Genetic Diversity And Structure

This study presents the first insights to the genetic diversity and structure of the Turkish donkey populations. The primary objectives were to detect the main structural features of Turkish donkeys by microsatellite markers. A panel of 17 microsatellite markers was applied for genotyping 314 donkeys from 16 locations of Turkey. One hundred and forty-two alleles were identified and the number of alleles per locus ranged from 4 to 12. The highest number of alleles was observed in AHT05 (12) and the lowest in ASB02 and HTG06 (4), while ASB17 was monomorphic. The mean HO in the Turkish donkey was estimated to be 0.677, while mean HE was 0.675. The polymorphic information content (PIC) was calculated for each locus and ranged from 0.36 (locus ASB02) to 0.98 (locus AHT05), which has the highest number of alleles per locus in the present study. The average PIC in our populations was 0.696. The average coefficient of gene differentiation (GST) over the 17 loci was 0.020 ± 0.037 (p < 0.01). The GST values for single loci ranged from −0.004 for LEX54 to 0.162 for COR082. Nei’s gene diversity index (Ht) for loci ranged from 0.445 (ASB02) to 0.890 (AHT05), with an average of 0.696. A Bayesian clustering method, the Structure software, was used for clustering algorithms of multi-locus genotypes to identify the population structure and the pattern of admixture within the populations. When the number of ancestral populations varied from K = 1 to 20, the largest change in the log of the likelihood function (ΔK) was when K = 2. The results for K = 2 indicate a clear separation between Clade I (KIR, CAT, KAR, MAR, SAN) and Clade II (MAL, MER, TOK, KAS, KUT, KON, ISP, ANT, MUG, AYD and KAH) populations.

scholarly journals Assessment of Genetic Diversity of Promising Castor Been (Ricinus communis L.) Genotypes in Nigeria

2019 ◽  
Vol 11 (3) ◽  
pp. 467-474
Author(s):  
Bolaji Zuluqurineen SALIHU ◽  
Olamide Ahmed FALUSI ◽  
Adeyinka Olufemi ADEPOJU ◽  
Ibrahim Wasiu AROLU ◽  
Oladipupo Yusuf DAUDU ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Diversity Index ◽  
Gene Diversity ◽  
Ricinus Communis ◽  
Polymorphic Information Content ◽  
Block Design ◽  
Genetic Material ◽  
Morphological Data ◽  
Research Attention ◽  
Ricinus Communis L

Castor oil plant (Ricinus communis L.) is an important oil crop with little research attention in Nigeria. In the present research, extent of genetic diversity among 20 Nigerian castor genotypes was determined using morphological descriptors and molecular markers. The genotypes were laid out on a randomized complete block design with three replicated plots. Molecular genotyping of the genotypes was carried out using genomic Simple Sequence Repeats (SSR). The genotypes revealed high divergence in seed colour, seed shape, seed mottle, seed caruncle and seed sizes. Seedling establishment varied from 70.18% (in Acc. 006) to 93.25% (Acc. 001) with average mean of 81.53%. Raceme length ranged from 15.90 cm to 29.54 cm with population mean of 20.80 cm. The highest seed yield (1222.98 kg/ha) was recorded in Acc. 001 and the least (611.46 kg/ha) was observed in Acc. 006. Seed oil content varied between 32.15% in Acc. 042 and 54.03% in Acc. 006. Agglomerative cluster dendrogram constructed from morphological data showed random distribution of the genotypes into three cluster groups irrespective of the sources/collection points. The genetic diversity based on SSR Marker Analysis revealed high average expected heterozygosity (0.74), Polymorphic information content (0.68), Nei’s gene diversity index (0.72) and Shannon's Information index (1.43). The dendrogram constructed from molecular data grouped the twenty genotypes into three groups at coefficient of 0.34. From these findings, it showed that the twenty genotypes evaluated are divergent in nature and they could serve as good genetic material for castor breeding in Nigeria.

scholarly journals Microsatellite development via next-generation sequencing in Acacia stenophylla (Fabaceae) and Duma florulenta (Polygonaceae): two ecologically important plant species of Australian dryland floodplains

2018 ◽  
Author(s):  
Bruce F Murray ◽  
Michael A Reid ◽  
Shu-Biao Wu
Keyword(s):  
Gene Flow ◽  
Next Generation Sequencing ◽  
Microsatellite Markers ◽  
Information Content ◽  
Polymorphic Information Content ◽  
Extreme Variability ◽  
Polymorphic Microsatellite ◽  
Generation Sequencing ◽  
Semi Arid

Duma florulenta and Acacia stenophylla are two ecologically important but understudied species that naturally occur on the floodplains and riverbanks of Australia’s arid and semi-arid river systems. This paper describes the discovery and characterization of 12 and 13 polymorphic microsatellite markers for D. florulenta and A. stenophylla respectively. The number of alleles per locus for D. florulenta ranged from 2-12 with an average of 6.1. Across all samples, observed and expected heterozygosities ranged from 0.026 to 0.784 and 0.026 to 0.824 respectively and mean polymorphic information content was equal to 0.453. For A. stenophylla, the number of alleles per locus ranged between 2 and 8 with an overall mean of 4.8. Across all samples, observed and expected heterozygosities ranged from 0.029 to 0.650 and 0.029 to 0.761 respectively and mean polymorphic information content was 0.388. The developed suites of 12 and 13 microsatellite markers for D. florulenta and A. stenophylla respectively provide opportunity for novel research into mechanisms of gene flow, dispersal and breeding system and how they operate under the extreme variability these species are exposed to in the environments in which they live.

scholarly journals Molecular characterization of wheat (Triticum aestivum L.) genotypes through SSR markers

2012 ◽  
Vol 37 (3) ◽  
pp. 389-398 ◽  
Author(s):  
S Islam ◽  
MS Haque ◽  
RM Emon ◽  
MM Islam ◽  
SN Begum
Keyword(s):  
Genetic Diversity ◽  
Triticum Aestivum ◽  
Genetic Distance ◽  
Microsatellite Markers ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Allelic Diversity ◽  
Triticum Aestivum L ◽  
Allele Number ◽  
Average Gene

A study was undertaken to examine the genetic diversity of 12 wheat (Triticum aestivum L.) genotypes, using 4 simple sequence repeats (SSRs). A total of 10 alleles were found. Allele number per locus ranged from 2 to 4 with an average of 2.5. The polymorphic information content (PIC) values ranged from 0.2755 to 0.5411 with an average of 0.3839. The average gene diversity over all SSR loci for the 12 wheat genotypes was 0.4688, ranging from 0.3299 to 0.6042. Cluster analysis based on microsatellite allelic diversity discriminated the varieties into different clusters. Genetic diversity was the highest between variety Gourab and Akbar as well as Gourab and BAW-1064, showing a genetic distance value of 0.4697. The genetic distance was lowest between Balaka and Aghrani as well as Triticale and BAW-1036. Positive correlations were found between gene diversity, number of alleles, the allele size range and the types of repeat motif of microsatellite markers. It was found from this study that microsatellite markers could characterize and discriminate all of the genotypes. More primers should be used for saturation of different regions in further studies. Bangladesh J. Agril. Res. 37(3): 389-398, September 2012 DOI: http://dx.doi.org/10.3329/bjar.v37i3.12082

Cross-species amplification and characterization of microsatellite loci in Pinus mugo Turra

Biologia ◽  
2013 ◽  
Vol 68 (4) ◽  
Author(s):  
Konrad Celiński ◽  
Ewa Pawlaczyk ◽  
Aleksandra Wojnicka-Półtorak ◽  
Ewa Chudzińska ◽  
Wiesław Prus-Głowacki
Keyword(s):  
Microsatellite Markers ◽  
Polymorphic Information Content ◽  
Pinus Mugo ◽  
Genetic Studies ◽  
Transfer Rates ◽  
Isolation And Characterization ◽  
Nuclear Microsatellite ◽  
European Mountain ◽  
High Level

AbstractPinus mugo (dwarf mountain pine) is an important component of European mountain ecosystems. However, little is known about the present genetic structure and population differentiation of this species at the DNA level, possibly due to a lack of nuclear microsatellite markers (SSR) developed for Pinus mugo. Therefore in this study we transferred microsatellite markers originally developed for Pinus sylvestris and Pinus taeda to Pinus mugo. This cross-species amplification approach is much faster and less expensive than isolation and characterization of new microsatellite markers. The transfer rates from the source species to Pinus mugo were moderately low (26%). There were no differences in microsatellite repeat motifs between the source species and Pinus mugo. Nuclear microsatellite markers successfully transferred to Pinus mugo can be applied to various genetic studies on this species, due to the high level of their polymorphism and high value of polymorphic information content.

scholarly journals Using microsatellite markers to analyze genetic diversity in 14 sheep types in Iran

2017 ◽  
Vol 60 (3) ◽  
pp. 183-189 ◽  
Author(s):  
Mohammad Taghi Vajed Ebrahimi ◽  
Mohammadreza Mohammadabadi ◽  
Ali Esmailizadeh
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Information Content ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Extraction Procedure ◽  
Shannon Index ◽  
Group Method ◽  
Salting Out ◽  
Pair Group

Abstract. Investigation of genetic relationship among populations has been traditionally based on the analysis of allele frequencies at different loci. The prime objective of this research was to measure the genetic polymorphism of five microsatellite markers (McMA2, BM6444, McMA26, HSC, and OarHH35) and study genetic diversity of 14 sheep types in Iran. Genomic DNA was extracted from blood samples of 565 individuals using an optimized salting-out DNA extraction procedure. The polymerase chain reaction (PCR) was successfully performed with the specific primers. Some locus–population combinations were not at Hardy–Weinberg equilibrium (P < 0. 05). The microsatellite analysis revealed high allelic and gene diversity in all 14 breeds. Pakistani and Arabi breeds showed the highest mean number of alleles (11.8 and 11 respectively), while the highest value for polymorphic information content was observed for the Arabi breed (0.88). A UPGMA (unweighted pair group method with arithmetic mean) dendrogram based on the Nei's standard genetic distance among studied breeds showed a separate cluster for Arabi and Pakistani breeds and another cluster for other breeds. The Shannon index (H0) for McMA2, BM6444, McMA26, HSC, and OarHH35 was 2.31, 2.17, 2.27, 2.04 and 2.18, respectively, and polymorphic information content (PIC) values were 0.88, 0.92, 0.87, 0.84, and 0.86 for McMA2, BM6444, McMA26, HSC, and OarHH35, respectively. The high degree of variability demonstrated within the studied sheep types implies that these populations are rich reservoirs of genetic diversity that must be preserved.

scholarly journals Development and characterization of microsatellite markers for two subspecies of Handroanthus chrysanthus

Rodriguésia ◽  
2021 ◽  
Vol 72 ◽  
Author(s):  
Augusta Yadira Cueva-Agila ◽  
Carlos Manchego ◽  
Cristian Bastidas ◽  
Manuel Curto
Keyword(s):  
Genetic Diversity ◽  
South America ◽  
Genetic Analysis ◽  
Microsatellite Markers ◽  
High Throughput Sequencing ◽  
Biodiversity Loss ◽  
Important Species ◽  
Polymorphic Microsatellites ◽  
Genetic Diversity And Structure

Abstract An understanding of the genetic diversity and structure of plant species is essential in order to comprehend the degree of biodiversity loss and to develop successful restoration programs. Handroanthus is an important genus that presents one of the most valuable timbers of South America. Handroanthus chrysanthus is an important species distributed in Central and South America. Microsatellite markers are not previously developed for this species. Ten microsatellites for Handroanthus chrysanthus developed using high-throughput sequencing are presented here. The usefulness of these microsatellite loci for the genetic analysis of subspecies H. chrysanthus subsp. chrysanthus (distributed in coastal dry forests) and subspecies H. chrysanthus subsp. meridionalis (distributed in premontane moist forests) is analyzed. At least eight polymorphic microsatellites are useful for each subspecies, seven of which can be used in both subspecies.

scholarly journals Development and characterization of novel cross-species tetranucleotide microsatellite markers for sterlet (Acipenser ruthenus) from Chinese sturgeon (Acipenser sinensis)

2019 ◽  
Author(s):  
Yacheng Hu ◽  
Jing Yang ◽  
Xueqing Liu ◽  
Kan Xiao ◽  
Binzhong Wang ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
Polymorphic Information Content ◽  
Diversity Indices ◽  
Chinese Sturgeon ◽  
Acipenser Sinensis ◽  
Management Actions ◽  
Acipenser Ruthenus ◽  
The Mean ◽  
Sterlet Acipenser Ruthenus

Sterlet (Acipenser ruthenus) is an important economic fish because of its nourishing caviar, isinglass and flesh. In order to facilitate the recovery of this species, the full understanding of its population genetic structure is necessary for taking appropriate management actions. However, genetic data on the use of nuclear loci in sterlet is still quite poor because microsatellite markers in sterlet that had been developed appeared to be polyploidy which add difficulties in studying the genetic of the sterlet. In this study, 24 tetranucleotide microsatellite markers were developed in sterlet from 160 microsatellite markers of the endangered Chinese sturgeon (Acipenser sinensis). Ten (ZHX76, ZHX64, Z194, Z217, Z184, Z242, Z250, Z258, Z268 and Z269) of the 24 loci showed disomic patterns while the rest loci showed tetrasomic patterns. In this paper, 24 microsatellite markers were characterized in 16 sterlet individuals and all of them were polymorphic with 2 to 7 alleles per locus. The Hardy-Weinberg departure value (d), polymorphic information content (PIC), the observed heterozygosity (HO), the Shannon-Wiener Diversity Indices (H') and the mean expected heterozygosity (HE) of all 24 polymorphic loci ranged from -0.334 to 0.484, 0.367 to 0.725, 0.438 to 1, 0.659 to 1.695, from 0.466 to 0.777, respectively. The markers described here will help in addressing practical problems such as the study of population genetics, conservation genetics and evolution in the polyploidy derivative nature of sterlet.

scholarly journals Development and characterization of 29 polymorphic microsatellite loci of Megalobrama pellegrini by next-generation sequencing technology and cross-species amplification in related species

2016 ◽  
Author(s):  
Wen Song ◽  
Dongmei Zhu ◽  
Yefeng Lv ◽  
Weimin Wang
Keyword(s):  
Microsatellite Markers ◽  
Microsatellite Loci ◽  
Related Species ◽  
Polymorphic Information Content ◽  
Sequencing Technology ◽  
Next Generation Sequencing Technology ◽  
Expected Heterozygosity ◽  
Polymorphic Microsatellite ◽  
Generation Sequencing

Megalobrama pellegrini is one of the economically important freshwater fish in China. Here, we developed 29 polymorphic microsatellite loci of M. pellegrini. The number of alleles (Na), effective number of alleles (Ne), observed heterozygosity (HO), expected heterozygosity (HE) and polymorphic information content (PIC) ranged from 3 to 11 (mean±SD 5.4828±1.9571), 2.8708 to 9.6257 (mean±SD 5.0865±1.6681), 0.4333 to 0.9333 (mean±SD 0.7874±0.1213), 0.6627 to 0.9113 (mean±SD 0.7946±0.0751) and 0.5785 to 0.8868 (mean±SD 0.7439±0.0950), respectively. Cross-species amplification was successful at most loci for related species such as M. amblycephala, M. hoffmanni, M. skolkovii and Parabramis pekinensis. The transferability rate of the 29 polymorphic microsatellite markers in M. amblycephala, M. hoffmanni, M. skolkovii and P. pekinensis were 96.55%, 86.21%, 86.21% and 75.86%, respectively. These polymorphic microsatellites are not only useful in genetic study and conservation of M. pellegrini, but also an effective tool for identifying the related species. We could use 5 microsatellite markers (HHF-63, HHF-104, HHF-113, HHF-148, HHF-163) to distinguish the 5 species.

scholarly journals Assessing the Genetic Diversity and Population Structure of a Tunisian Melon (Cucumis melo L.) Collection Using Phenotypic Traits and SSR Molecular Markers

Agronomy ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1121
Author(s):  
Hela Chikh-Rouhou ◽  
Najla Mezghani ◽  
Sameh Mnasri ◽  
Neila Mezghani ◽  
Ana Garcés-Claver
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Phenotypic Diversity ◽  
Diversity Index ◽  
Polymorphic Information Content ◽  
Crop Improvement ◽  
Molecular Data ◽  
Mantel Test ◽  
Phenotypic Traits ◽  
Genetic Diversity And Structure

The assessment of genetic diversity and structure of a gene pool is a prerequisite for efficient organization, conservation, and utilization for crop improvement. This study evaluated the genetic diversity and population structure of 24 Tunisian melon accessions, by using 24 phenotypic traits and eight microsatellite (SSR) markers. A considerable phenotypic diversity among accessions was observed for many characters including those related to agronomical performance. All the microsatellites were polymorphic and detected 30 distinct alleles with a moderate (0.43) polymorphic information content. Shannon’s diversity index (0.82) showed a high degree of polymorphism between melon genotypes. The observed heterozygosity (0.10) was less than the expected heterozygosity (0.12), displaying a deficit in heterozygosity because of selection pressure. Molecular clustering and structure analyses based on SSRs separated melon accessions into fivegroups and showed an intermixed genetic structure between landraces and breeding lines belonging to the different botanical groups. Phenotypic clustering separated the accessions into two main clusters belonging to sweet and non-sweet melon; however, a more precise clustering among inodorus, cantalupensis, and reticulatus subgroups was obtained using combined phenotypic–molecular data. The discordance between phenotypic and molecular data was confirmed by a negative correlation (r = −0.16, p = 0.06) as revealed by the Mantel test. Despite these differences, both markers provided important information about the diversity of the melon germplasm, allowing the correct use of these accessions in future breeding programs. Together they provide a powerful tool for future agricultural and conservation tasks.

scholarly journals Development and Characterization of Microsatellite Markers, Genetic Diversity and Population Structure Analysis in Sapota (Manilkara Zapota (L.) P. Royen)

2021 ◽  
Author(s):  
Kundapura Venkataramana Ravishankar ◽  
Pavithra Sathanandam ◽  
Prakash Patil ◽  
Ajitha Rekha ◽  
Iyyamperumal Muthuvel ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Polymorphic Information Content ◽  
Illumina Hiseq ◽  
Next Generation Sequencing Technology ◽  
Manilkara Zapota ◽  
Population Structure Analysis ◽  
Genomic Markers ◽  
Structure Assignment

Abstract Manilkara zapota (L.) P. Royen, a widely adaptable and popular tree meant for its appetizing fruits in tropics with no genomic resources like microsatellite markers. In order to develop genomic markers primarily for sapota, we sequenced partial genomic DNA using next generation sequencing technology on the Illumina HiSeq 2500 platform. We analyzed a total of 3.3 Gb data that were assembled into 6396224 contigs. From these contigs, 3591 simple sequence repeats were identified. Among the different type of repeats mononucleotide repeats (59.1%) were predominant followed by dinucleotide (28.6%) and trinucleotide repeats (8.2%). Primers were designed for 1285 microsatellite regions from which 30 randomly selected primers were standardized and employed for amplification in 53 genotypes of sapota. We observed 692 alleles from 30 loci with a polymorphic information content ranged from 0.85 to 0.96 with a mean of 0.9118. The probability of identity ranged from 0.002 to 0.043 with a mean of 0.012. Genetic diversity assessed by neighbour-joining and STRUCTURE assignment tests showed admixed population with 3 groups. Analysis of molecular variance revealed a significant F st value of 0.69659 indicating high genetic differentiation among the 53 genotypes. The developed microsatellites will be advantageous in assessing genetic diversity, developing linkage map and also molecular characterization of genotypes

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