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.

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

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.

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

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.  

scholarly journals Development of microsatellite markers for the Japanese endemic conifer Thuja standishii and transfer to other East Asian species

2019 ◽  
Author(s):  
James Raymond Peter Worth ◽  
K. S. Chang ◽  
Y.-H. Ha ◽  
Aili Qin
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Microsatellite Loci ◽  
East Asian ◽  
Clonal Reproduction ◽  
Sister Species ◽  
Asian Species ◽  
Expected Heterozygosity ◽  
Polymorphic Microsatellite ◽  
Diversity Structure

Abstract Objective: Design polymorphic microsatellite loci that will be useful for studies of the genetic diversity, structure and reproduction in the Japanese endemic conifer Thuja standishii and test the transferability of these loci to the two other East Asian species, T. sutchuenensis and T. koraiensis . Results: Fifteen loci were developed which displayed 3 to 21 alleles per locus (average = 9.2) among 97 samples from three populations of T. standishii . Observed heterozygosity for all samples varied between 0.33-0.75 (average 0.54) while expected heterozygosity values were higher with an average over the 15 loci of 0.62 (0.37-0.91). Low multi-locus probability of identity values (< 0.00001) indicate that these markers will be effective for identifying individuals derived from clonal reproduction. All 15 loci amplified in 13 samples of T. sutchuenensis , the sister species of T. standishii , with 1 to 11 alleles per locus (average = 4.33) while 13 loci amplified in four samples of the more distantly related T. koraiensis with 1 to 5 alleles per locus (average = 2.15).

scholarly journals Genetic diversity and population structure of four cattle breeds raised in Turkey using microsatellite markers

2019 ◽  
Vol 64 (No. 10) ◽  
pp. 411-419 ◽  
Author(s):  
Eymen Demir ◽  
Murat Soner Balcioğlu
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Microsatellite Markers ◽  
Factorial Correspondence Analysis ◽  
Cattle Breeds ◽  
Expected Heterozygosity ◽  
Bottleneck Analysis ◽  
Holstein Friesian ◽  
Native Cattle ◽  
Marker Level

In the present study, genetic diversity and population structure of Holstein Friesian and three native cattle breeds of Turkey including Turkish Grey Steppe, Eastern Anatolian Red and Anatolian Black were assessed. Totally 120 individuals of 4 breeds were genotyped using 20 microsatellite markers and 204 different alleles, of which 31 were private alleles, were detected. The average observed and expected heterozygosity values were 0.63 and 0.74, respectively. Observed heterozygosity at the marker level ranged from 0.30 (DRBP1) to 0.88 (ILSTS011), while expected heterozygosity ranged from 0.51 (INRABERN172) to 0.88 (SPS113). Inbreeding coefficient values for Turkish Grey Steppe, Eastern Anatolian Red, Anatolian Black and Holstein Friesian were 0.216, 0.202, 0.128 and 0.069, respectively. The lowest pairwise F<sub>ST</sub> value (0.030) was detected between Turkish Grey Steppe and Anatolian Black breeds, while the highest value (0.070) was detected between Turkish Grey Steppe and Holstein Friesian. Results of structure and factorial correspondence analysis revealed that Turkish native cattle breeds and Holstein Friesian were genetically different enough to separate the two breeds. Results of bottleneck analysis indicated heterozygosity deficiency in Turkish Grey Steppe (P &lt; 0.05).

Genetic Diversity of Cambuci (Campomanesia Phaea) Revealed by Microsatellite Markers

2021 ◽  
Author(s):  
Rafael Oliveira Moreira ◽  
Eduardo de Andrade Bressan ◽  
Horst Bremer Neto ◽  
Angelo Pedro Jacomino ◽  
Antonio Figueira ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Microsatellite Markers ◽  
Native Species ◽  
Genetic Parameters ◽  
Genomic Library ◽  
Conservation Strategies ◽  
Paulo State ◽  
Allele Number ◽  
Expected Heterozygosity

Abstract Campomanesia phaea (Myrtaceae), known as cambuci, is a native species from the Brazilian Atlantic Forest with great potential to be developed as a new fruit crop. Microsatellite markers were developed for cambuci to characterize the genetic diversity and to investigate the genetic structure of a group of accessions originally collected at the presumed center of diversity of the species. The work involved the collection of 145 accessions from five regional groups (Juquitiba, Paraibuna, Mogi das Cruzes, Ribeirão Pires, and Salesópolis) in São Paulo state, Brazil. Fourteen loci were identified in an enriched genomic library developed from one of these accessions. Six out of 14 loci revealed to be polymorphic, disclosing 26 alleles. Based on the allele frequencies, the calculated genetic parameters of the five groups indicated an average allele number per loci (A) of 3.83, with the expected heterozygosity (He) of 0.57 and the observed heterozygosity (Ho) of 0.54. The analysis of the genetic structure indicated that most of the genetic diversity is found within each population (HS = 0.57), whereas the genetic diversity among populations was low (GST = 0.19). The genetic diversity parameter of Nei was considered low for the cambuci analyzed populations, with no evidence of inbreeding. Based on Darwin analysis, we chose 18 accessions from the five regional populations to compose a core collection that includes most of the genetic diversity found in this study. Our findings may contribute to define better conservation strategies and genetic breeding approaches for this native species in Brazil.

Genetic relatedness and cultivar identification in a valuable garden species, Hesperantha coccinea ( Schizostylis coccinea)

2009 ◽  
Vol 7 (03) ◽  
pp. 281-290
Author(s):  
Kirsten Wolff ◽  
Sabina Knees ◽  
Suzanne Cubey
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Dna Fingerprinting ◽  
Genetic Relatedness ◽  
Cultivar Identification ◽  
Wild Populations ◽  
Multilocus Genotypes ◽  
Expected Heterozygosity ◽  
Garden Plants ◽  
Garden Plant

DNA fingerprinting using microsatellites is a useful aid in cultivar identification, but has rarely been applied to garden plants. Eleven microsatellite markers were developed for the valuable garden plantHesperanthacoccinea(Schizostylis coccinea), and used to determine relatedness of accessions. Several accessions, described as separate cultivars, appeared to have identical genotypes. Among the 53 accessions tested, there were 34 unique multilocus genotypes. The level of polymorphism detected in the cultivars was high, with on average seven alleles per locus and an average expected heterozygosity of 0.72 across loci. It is clear from the genotypes that a large proportion of the cultivars are closely related to each other. The resulting markers can now be used to generate a complete database of all known cultivars of the species and to detect essentially derived cultivars. As an extension of this study, the markers identified here could also inform us about the genetic diversity in wild populations.

scholarly journals Characterization of Genetic Diversity of Stone Fruit Rootstocks Used in Chile by Means of Microsatellite Markers

2012 ◽  
Vol 137 (5) ◽  
pp. 302-310 ◽  
Author(s):  
María José Arismendi ◽  
Patricio Hinrichsen ◽  
Ruben Almada ◽  
Paula Pimentel ◽  
Manuel Pinto ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Ssr Markers ◽  
Stone Fruit ◽  
Identification System ◽  
Expected Heterozygosity ◽  
Commercially Important ◽  
Taxonomic Groups ◽  
Simple Sequence

Stone fruit (Prunus L.) production in Chile covers ≈43,000 ha and includes a wide variety of soils and climates requiring a large diversity of rootstocks. The most commercially important rootstock cultivars are 26 genotypes from three different taxonomic groups belonging to the subgenera Amygdalus (L.) Benth. Hook. (peach group), Prunus Focke [= Prunophora (Neck.)] Focke (plum group), and Cerasus (Adans.) Focke (cherry group) with eight, seven, and 10 individuals, respectively. To determine their genetic diversity, characterization by microsatellite markers [simple sequence repeat (SSR)] was conducted. Of a total of 20 SSR markers evaluated, 12 generated amplified products that were consistent in the three taxonomic groups. The number of alleles per marker ranged from 18 for PSM-3 to four in CPPCT-002. Clustering analysis, by both traditional hierarchical and model-based approaches, indicate that all genotypes are clustered in their respective taxonomic groups, including the interspecific hybrids. Genetic diversity, measured as the average distances (expected heterozygosity) between individuals in the same cluster, was higher in Cerasus (0.78) followed by Prunus (0.72) and Amygdalus (0.64). Total number of alleles observed was 133, of which 14, 33, and 35 from six, 10, and 10 loci were unique for the peach, plum, and cherry rootstock groups, respectively. Alleles shared among peach/plum, plum/cherry, and peach/cherry rootstock genotypes were 13, 14, and 18 from nine, seven, and seven loci, respectively. Only six alleles from five loci were common to the three taxonomic groups. In addition, to develop a rootstock identification system based on SSR markers, a minimum set of three markers (PMS-3, BPPCT-037, and BPPCT-036) able to differentiate the 26 genotypes was identified. This study is the first step toward establishing a stone fruit rootstock breeding program in Chile.

scholarly journals Transferability and Characterization of Microsatellite Markers from Byrsonima Cydoniifolia A. Juss. (MALPIGHIACEAE) in Seven Related Taxa from Cerrado Biome Reveal Genetic Relationships

2021 ◽  
Author(s):  
Vanessa Bernardes ◽  
Devanir M. Murakami ◽  
Nair Bizão ◽  
Tamara N. Souza ◽  
Marcos J. da Silva ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Genetic Divergence ◽  
High Efficiency ◽  
Population Studies ◽  
Genetic Relationships ◽  
Species Occurrence ◽  
Genetic Population ◽  
Expected Heterozygosity

Abstract Byrsonima Rich. is one of the largest genera of the Malpighiaceae family, with 97 species occurrence in Brazil. In this study, 17 microsatellite markers previously developed and characterized in Byrsonima cydoniifolia A. Juss. were tested for seven related taxa. All species tested here are native to Brazil, and of these species four are endemic. Cross-amplification as successfully optimized with high efficiency for all species. Microsatellite markers panels ranged from 11 (64,8%) transfered markers in B. viminifolia to 6 (35.2%) in B. umbellata. All loci were genotyped for 16 individuals of each species, except for B. viminifolia (14 individuals), then the polymorphic loci were characterized. The total number of alleles per locus across tested species ranged from 5 (B. linearifolia) to 8 (B. subterranea) alleles. B. umbellata showed lower values of observed and expected heterozygosity (Ho = 0.312; He = 0.436) and B. subterranea presented the highest values (Ho = 0.687; He = 0.778). A greater number of microsatellite markers should be developed for B. umbellata, once that the markers set transferred is reasonably informative, due to the greatest genetic divergence between species. The microsatellite marker panels transferred to the species B. intermedia, B. verbascifolia, B. laxiflora, B. subterranea, B. viminifolia and B. linearifolia are very informative, with a high combined probability of exclusion of paternity (Q ≥ 0.976) and the low combined probability of identity (I ≤ 9.91x10− 6), potentially suitable for future genetic-population studies, supporting strategies for maintaining the genetic diversity and for exploration of Byrsonima species as genetic resources.

scholarly journals Microsatellite Markers in Hazelnut: Isolation, Characterization, and Cross-species Amplification

2005 ◽  
Vol 130 (4) ◽  
pp. 543-549 ◽  
Author(s):  
Nahla V. Bassil ◽  
R. Botta ◽  
S.A. Mehlenbacher
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Geographical Origin ◽  
Genome Mapping ◽  
Polymorphic Information Content ◽  
Corylus Avellana ◽  
Expected Heterozygosity ◽  
Gaa Repeats ◽  
Microsatellite Alleles ◽  
Simple Sequence

Three microsatellite-enriched libraries of the european hazelnut (Corylus avellana L.) were constructed: library A for CA repeats, library B for GA repeats, and library C for GAA repeats. Twenty-five primer pairs amplified easy-to-score single loci and were used to investigate polymorphism among 20 C. avellana genotypes and to evaluate cross-species amplification in seven Corylus L. species. Microsatellite alleles were estimated by fluorescent capillary electrophoresis fragment sizing. The number of alleles per locus ranged from 2 to 12 (average = 7.16) in C. avellana and from 5 to 22 overall (average = 13.32). With the exception of CAC-B110, di-nucleotide SSRs were characterized by a relatively large number of alleles per locus (≥5), high average observed and expected heterozygosity (Ho and He > 0.6), and a high mean polymorphic information content (PIC ≥ 0.6) in C. avellana. In contrast, tri-nucleotide microsatellites were more homozygous (Ho = 0.4 on average) and less informative than di-nucleotide simple sequence repeats (SSRs) as indicated by a lower mean number of alleles per locus (4.5), He (0.59), and PIC (0.54). Cross-species amplification in Corylus was demonstrated. These microsatellite markers were highly heterozygous and polymorphic and differentiated among genotypes of C. avellana irrespective of geographical origin. They will aid in fingerprinting genotypes of the european hazelnut and other Corylus species, genome mapping, and genetic diversity assessments.

scholarly journals Assessment of genetic diversity and differentiation of two major camel ecotypes (<i>Camelus dromedarius</i>) in Sudan using microsatellite markers

2015 ◽  
Vol 58 (2) ◽  
pp. 269-275 ◽  
Author(s):  
M. Eltanany ◽  
O. Elfaroug Sidahmed ◽  
O. Distl
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Microsatellite Markers ◽  
Inbreeding Coefficient ◽  
Mean Values ◽  
Significant Differentiation ◽  
Expected Heterozygosity ◽  
Admixed Population ◽  
Relationship Of ◽  
First Time

Abstract. Although Sudan has the second largest camel population in Africa, it has not yet been genetically differentiated. The present study was undertaken to evaluate, for the first time, the genetic diversity and relationship of two major camel ecotypes representing the eastern (Butana) and western (Darfur) regions of Sudan using 12 microsatellite markers. A total of 107 samples of study ecotypes were investigated displaying high mean values of genetic diversity (mean number of alleles: 11.5 ± 1.45; polymorphism information content: 0.67 ± 0.04; observed heterozygosity: 0.69 ± 0.05; expected heterozygosity: 0.72 ± 0.04). The global inbreeding coefficient (FIT = 0.041 ± 0.03, P > 0.05) was attributed to substantial and non-significant within-population inbreeding (FIS = 0.034 ± 0.03) and scarce but highly significant differentiation between ecotypes (FST = 0.008 ± 0.00; P < 0.0001). Multivariate analysis indicated a historical intermixing between different genealogical lineages making up the current admixed gene pool of the geographically divergent ecotypes. Consistent with this, STRUCTURE cluster analysis showed these ecotypes to be one mosaic admixed population. The results showed abundant genetic diversity within Sudanese dromedaries. Our study indicates that the two Sudanese camel ecotypes (Butana and Darfur) appear as an admixture of two geographical branches and do not support the contemporary division of Sudanese dromedaries into their respective socio-ethno-geography.

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