Development and Characterization of Microsatellite Markers, and Genetic Diversity Sapota (Manilkara Zapota (L.) P. Royen)

Abstract Manilkara zapota (L.) P. Royen, commonly known as sapota, a widely adaptable and popular evergreen tree meant for its appetizing fruits in tropics, but lacks genomic resources such as microsatellite markers. To develop the genomic markers for M. zapota, we sequenced the partial genomic DNA using next-generation sequencing technology on the Illumina HiSeq 2500 platform. We analysed a total of 3.33 Gb data that were assembled into 6,396,224 contigs, from which 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 M. zapota microsatellite regions from which 30 randomly selected primers were standardized and employed for amplification of 53 genotypes. We observed 692 alleles from 30 loci with a polymorphic information content ranging from 0.85 to 0.96, 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 an admixed population with three groups. Analysis of molecular variance revealed a significant Fst value of 0.69659, indicating a high genetic differentiation among the 53 genotypes. The microsatellites developed here will be beneficial for assessing the genetic diversity, developing linkage map and also molecular characterization of genotypes.

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

10.21203/rs.3.rs-609051/v1 ◽

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

10.7287/peerj.preprints.2490 ◽

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.

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

Slovenian Veterinary Research ◽

10.26873/svr-1041-2020 ◽

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

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Population structure and genetic diversity using microsatellite markers of four Algerian rabbit populations precludes hybridization with foreign breeds

South Asian Journal of Experimental Biology ◽

10.38150/sajeb.7(5).p191-200 ◽

2018 ◽

Vol 7 (5) ◽

pp. 191-200

Author(s):

Boukabene Fouzia K. ◽

Homrani A. ◽

Ammam A.

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Total Population ◽

Polymorphic Information Content ◽

Pairwise Variation ◽

Black And White ◽

Popula Tions ◽

Hardy Weinberg Equilibrium ◽

Nei's Genetic Distance

The genetic characterization of our native rabbit populations is crucial for their development of genetic improvement and conservation programs. In the current study, fifteen microsatellite markers were used to investigate the genetic diversity and phylogenetic relationship among four Algerian popula-tions of rabbits; White (B), White and grey (G), Black and white (N) and Brown and white (M) in addition to Gabali (EG) and New Zealand White (EN) from Egypt. The microsatellites were INRACCDDV0003, SAT2, SAT3, SAT4, SAT5, SAT7, SAT8, SAT12, SAT13, SOL30, SOL33, SOL44, D3Utr2, D6Utr4 and D7Utr5. 90 animals were studied including 15 rabbits from each population. Results revealed that the average number of alleles per locus was 14.26 and the observed heterozygosity averaged 0.62 and ranging from 0.47 in marker SAT2 to 0.8 in marker, D6Utr4 while the expected heterozygosity averaged 0.72 and ranged from 0.62 in marker SAT2 to 0.77 in marker SOL44. The average polymorphic information content (PIC) was 0.85 and ranged from 0.77 at locus D3Utr2 to 0.93 at locus SOL33. Most loci showed deviations from Hardy-Weinberg Equilibrium with highly significant level. The inbreeding coefficient of the individuals relative to the total population (FIT) was the highest 0.28. The within-population heterozygote deficit (FIS) averaged 0.13. The pairwise variation among the populations (FST) averaged 0.16 and rang-ing from 0.09 for D3Utr2 to 0.27 for SAT2. The highest pairwise Nei’s genetic distance was recorded between G and EG (0.87) and the closest genetic dis-tance for natif population was between M and N (0.33). The smallest pair-wise FST was recorded between G and M (0.059). B, G and M, N populations were clustered together forming admixed mosaic cluster.

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Genetic Diversity Analysis of Five Egyptian Buffalo Populations Using Microsatellite Markers

Journal of Agricultural Science ◽

10.5539/jas.v12n4p271 ◽

2020 ◽

Vol 12 (4) ◽

pp. 271

Author(s):

S. M. Merdan ◽

M. F. El-Zarei ◽

A. A. Ghazy ◽

M. A. Ayoub ◽

Z. M. Al-Shawa ◽

...

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Allelic Richness ◽

Environmental Changes ◽

Polymorphic Information Content ◽

Allelic Diversity ◽

Null Alleles ◽

Indigenous Breed ◽

Egyptian Buffalo

For assessing the genetic diversity and genetic characterization of five Egyptian buffalo populations a total of 12 microsatellite markers were used. The total number of buffaloes sampled was 80, collected at random from five farms in five different governorates; Cairo, Kafr El-Sheikh, Shebeen El-Kom, Menoufia, and Beni Suef. The genetic parameters (allelic diversity, allelic frequencies, observed heterozygosity, unbiased expected heterozygosity, and polymorphic information content) were calculated using three different programs. All used microsatellites were polymorphic and ranged from four alleles (Loci; CSSM029, CSSM036, CSSM038, CSSM043, CSSM046, and ILSTS005) to nine alleles (Loci; BM1818 and CSSM047) with a total of 64 alleles in the whole population. Allelic richness for the whole population ranged between 3.297 (in locus CSSM029) and 6.806 (in locus CSSM047) with overall mean 4.574. Within populations, Kafr El-Sheikh population had the highest average of allelic richness (4.384). This indicates the potential of this population to adapt with environmental changes in future compared with other populations. BMC1013, BM1818, CSSM019, and CSSM047 showed the highest allelic richness. PIC estimates were high and ranged between 0.65 (in locus CSSM029) and 0.92 (in locus CSSM022) with an average of 0.82. Values of Ho were lower than values of HNb for all populations, which denoting depression of heterozygotes in these populations and may be attributable to existence of null alleles and inbreeding. This study as well proves the usefulness of heterologous bovine microsatellite markers in evaluation of the genetic variability in Egyptian buffalo populations due to high polymorphism, informativeness of these markers which can be used to develop future breeding strategies and conservation decisions on our indigenous breed.

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

10.7287/peerj.preprints.2490v1 ◽

2016 ◽

Cited By ~ 1

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

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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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Characterization of genetic diversity of native 'Ancho' chilipopulations of Mexico using microsatellite markers

Chilean journal of agricultural research ◽

10.4067/s0718-58392016000100003 ◽

2016 ◽

Vol 76 (1) ◽

pp. 18-26 ◽

Cited By ~ 5

Author(s):

Rocío Toledo-Aguilar ◽

Higinio López-Sánchez ◽

Amalio Santacruz-Varela ◽

Ernestina Valadez-Moctezuma ◽

Pedro A López ◽

...

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers

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Review: Genetic diversity studies using microsatellite markers and their contribution in supporting sustainable sheep breeding programs

Asian Journal of Agriculture ◽

10.13057/asianjagric/g010109 ◽

2017 ◽

Vol 1 (01) ◽

pp. 46-51

Author(s):

OUMER SHERIFF ◽

KEFYALEW ALEMAYEHU

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Polymorphic Information Content ◽

Domestic Sheep ◽

Breeding Programs ◽

Sheep Breeding ◽

Population Structures ◽

The Mean ◽

Tree Building ◽

Diversity Studies

Sheriff O, Alemayehu K. 2017. Review: Genetic diversity studies using microsatellite markers and their contribution in supporting sustainable sheep breeding programs. Asian J Agric 1: 46-51. Microsatellites have been widely accepted and employed as useful molecular markers for measuring genetic diversity and divergence within and among populations. The various parameters developed so far to measure genetic diversity within and among populations are observed and expected heterozygosities (Ho and He), the mean number of alleles per locus (MNA),polymorphic information content (PIC), genetic distance and phylogenetic or tree building approach.The objective of thisreview was therefore to quantifythe genetic diversity studies of domestic sheep populations using microsatellite markersand their contribution in supporting sustainable sheep breeding programs. From the review, it is possible to see that there was high within population genetic variations in all the studied sheep populations, poor level of population differentiations and high levels of inbreeding. On the other hand, low estimates of hetrozygosities and mean number of alleles and employing only few and weak markers were observed in some of the studies. The gaps observed in the previous genetic diversity studies of the sheep populations may demand further works to reveal more information on the population structures andto start appropriate and sustainable breeding programs.

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

10.7287/peerj.preprints.27027v1 ◽

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.

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