Parentage assignment using microsatellite DNA typing for the endangered numbat (Myrmecobius fasciatus)

2020 ◽  
Vol 42 (2) ◽  
pp. 240
Author(s):  
Peter B. S. Spencer ◽  
Serina McConnell ◽  
Diana Prada ◽  
J. A. (Tony) Friend
Keyword(s):  
Microsatellite Markers ◽  
Microsatellite Dna ◽  
Dna Typing ◽  
Testing System ◽  
Parentage Assignment ◽  
Informative Marker ◽  
Parentage Testing ◽  
Exclusion Probability ◽  
Expected Heterozygosity

The numbat (Myrmecobius fasciatus) is an endangered and peculiar marsupial with a diet that consists almost exclusively of termites. This study developed a parentage-testing system for numbats using microsatellite markers. Nineteen loci detected 143 alleles, with 4–13 alleles/locus and average expected heterozygosity of 77% (range 0.665–0.855). The total parentage exclusion probability was >0.9999 (given only the genotype of the offspring), >0.9999 for excluding a candidate parent from the parentage of an arbitrary offspring (given the genotype of the offspring and parent) and the probability of identity for full-sibs was 4.6×10–9. Overall, these microsatellites offer a simple and highly informative marker-set for parentage identification in numbats.

scholarly journals Looking for breed differentiating SNP loci and for a SNP set for parentage testing in Mangalica

2013 ◽  
Vol 56 (1) ◽  
pp. 200-207 ◽  
Author(s):  
A. Zsolnai ◽  
G. Tóth ◽  
J. Molnár ◽  
V. Stéger ◽  
F. Marincs ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
Whole Genome ◽  
Parentage Testing ◽  
Exclusion Probability

Abstract. The whole genome of Mangalica animals has been screened on the Illumina porcine chip giving the possibility (1) to replace the previously applied ten microsatellite markers by nine SNP loci to classify the Blond, Swallow-Belly and Red Mangalica individuals into three different breed groups (P>0.95); (2) to propose 54 SNP loci for parentage testing in Mangalica pigs where the exclusion probability is 0.999115 if one parent is known and the probability of identity is 1.54×10-23.

Parentage testing of racing camels (Camelus dromedarius) using microsatellite DNA typing

2010 ◽  
Vol 41 (6) ◽  
pp. 662-665 ◽  
Author(s):  
P. B. S. Spencer ◽  
K. J. Wilson ◽  
A. Tinson
Keyword(s):  
Microsatellite Dna ◽  
Dna Typing ◽  
Camelus Dromedarius ◽  
Parentage Testing

scholarly journals Microsatellite panels suggested for parentage testing in cattle: informativeness revealed in Finnish Ayrshire and Holstein-Friesian populations (Research Note)

1999 ◽  
Vol 8 (3) ◽  
pp. 233-237 ◽  
Author(s):  
P. BREDBACKA ◽  
M.T. KOSKINEN
Keyword(s):  
Microsatellite Markers ◽  
International Society ◽  
Artificial Insemination ◽  
Routine Testing ◽  
Parentage Testing ◽  
Low Level ◽  
Exclusion Probability ◽  
Holstein Friesian ◽  
Core Set ◽  
Parentage Control

Informativeness of eleven microsatellite markers suggested for parentage control in cattle by the International Society for Animal Genetics (ISAG) was studied in Finnish Ayrshire and Holstein-Friesian populations. Calculations were based on a sample of 100 non-sib artificial insemination bulls. Assuming one known parent the nine loci suggested for routine testing exhibited exclusion probabilities of 99.84% in the Ayrshires and 99.91% in the Holstein-Friesians. The addition of markers INRA23 and TGLA53, recommended for further investigations, increased the attained values to 99.94% in Ayrshires and to 99.98% in Holstein-Friesians. The recommended core set of six microsatellites provided a combined exclusion probability of 98.25% in Ayrshires and 99.32% in Holstein-Friesians. Although the combined values were high in general, a relatively low level of polymorphism was detected in some instances.;

scholarly journals GENETIC DIVERSITY OF EGYPTIAN ARABIAN HORSES FROM EL-ZAHRAA STUD BASED ON 14 TKY MICROSATELLITE MARKERS

2021 ◽  
Vol 58 (2) ◽  
Author(s):  
Mary Sargious ◽  
Ragab El-Shawarby ◽  
Mohamed Abo-Salem ◽  
Elham EL-Shewy ◽  
Hanaa Ahmed ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Polymorphic Information Content ◽  
Parentage Assignment ◽  
Expected Heterozygosity ◽  
Bioinformatics Software ◽  
Pcr Products ◽  
Arabian Population ◽  
Genetic Analyzer

The objectives of this study were, firstly, to conduct genetic characterization of Egyptian Arabian horses based on 14 TKY microsatellite markers, secondly, to investigate the powerfulness of these 14 TKY markers for parentage assignment of Arabian horses. A total of 101 horse samples including (Arabian = 71, Thoroughbred = 19 and Nooitgedacht = 11) were analysed by 14 TKY microsatellite markers. The PCR products were electrophoresed on Genetic analyzer 3500 with the aid of Liz standard. The basic measures of the allele’s size and genetic diversity were computed using bioinformatics software. The polymorphism of the TKY markers across the Arabian population showed moderate values for genetic diversity parameters; number of allele (NA) =8.143, effective number of allele (Ne) = 3.694, observed heterozygosity (HO) = 0.599, expected heterozygosity (HE) = 0.691, polymorphic Information Content (PIC) = 0.636 and Inbreeding coefficient (FIS)= 0.128. The combined probability of exclusion (CPE) value of the 14 TKY microsatellite loci of our Arabian horses was 0.9999. The results from current study confirm the applicability and efficiency of TKY microsatellite panel for evaluating the genetic diversity and parentage assignment of Egyptian Arabian horses.Key words: Arabian horses; genetic diversity; microsatellite; TKY markers GENSKA RAZNOVRSTNOST EGIPČANSKIH KONJ ARABSKE PASME IZ KOBILARNE EL-ZAHRAA NA PODLAGI 14 MIKROSATELITSKIH OZNAK TKY Izvleček: Nameni raziskave so bili genetska karakterizacija egipčanskih konj arabske pasme na podlagi 14 mikrosatelitskih označevalecv TKY ter raziskava moči 14 označevalcev TKY za dodelitev staršev arabskih konj. S pomočjo 14 mikrosatelitskih označevalcev TKY je bilo analiziranih 101 vzorcev konj (arabski = 71, čistokrvni = 19 in konji Nooitgedacht = 11). Produkte PCR so analizirali s pomočjo elektroforeze na genskem analizatorju 3500 s pomočjo Liz standarda. Osnovne mere velikosti alela in genske raznovrstnosti so bile izračunane s pomočjo programske opreme za bioinformatiko. Polimorfizem označevalcev TKY v arabski populaciji je pokazal zmerne vrednosti za parametre genske raznolikosti; število alelov (NA) = 8,143, efektivno število alelov (Ne) = 3,694, opazovana heterozigotnost (HO) = 0,599, pričakovana heterozigotnost (HE) = 0,691, polimorfna informacijska vsebina (PIC) = 0,636 in Inbriding koeficient (FIS) = 0,128. Skupna vrednost verjetnosti izključitve (CPE) 14 mikrosatelitskih lokusov TKY njihovih arabskih konj je bila 0,9999. Rezultati te raziskave potrjujejo uporabnost in učinkovitost mikrosatelitske plošče TKY za oceno genetske raznovrstnosti in starševske pripadnosti egipčanskih arabskih konj.Ključne besede: arabski konji; genska raznolikost; mikrosatelit; markerji TKY

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 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.

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