Assessment of Genetic Diversity and Relationship of the Two Sanga Type Cattle of Botswana Based on Microsatellite Markers

Abstract The study was performed to evaluate genetic variation on two Sanga type cattle found in Botswana; Tswana and Tuli using twelve microsatellite markers. All amplified loci were polymorphic with 75 and 77 alleles genotyped in the Tswana and Tuli populations, respectively. The total number of alleles per locus ranged from 2 (BM1818) to 10 (TGLA227) with total mean of 6.25 for Tswana and 6.43 for Tuli population. Almost all the markers showed high polymorphic information content (PIC) apart from BM1818 (0.375) and INTRA23 (0.393) which were moderately informative in Tswana population. Most of the markers were in Hardy-Weinberg equilibrium except for CSSRM60 and CSSM66 loci in Tswana population and ETH10, ETH225 and CSSM66 loci in Tuli population. A total of 103 unique alleles were genotyped across the two breeds with 49-shared, and 26 and 28 were unique to Tswana and Tuli populations, respectively. The expected heterozygosity (He) values were higher than the observed heterozygosity (Ho) in both populations; Tswana (He=0.7895±0.033 vs Ho=0.631±0.091) and Tuli (He=0.8123±0.033 vs Ho=0.556±0.021). The inbreeding coefficient was 0.200±0.002 and 0.332±0.001 in Tswana and Tuli populations, respectively. Analysis of molecular variance revealed 6.8% of the total genetic variation corresponding to differences between the two breeds and 93.2% within populations. The genetic identity between the two breeds was 56% and there were similar levels of multilocus heterozygosity and allelic diversity in the two breeds. The use of Tswana and Tuli breeds in a crossbreeding program is likely to result in minimal heterosis and therefore not recommended.

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

Archives Animal Breeding ◽

10.5194/aab-58-269-2015 ◽

2015 ◽

Vol 58 (2) ◽

pp. 269-275 ◽

Cited By ~ 6

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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Evaluation of Genetic Diversity and Structure of Turkish Water Buffalo Population by Using 20 Microsatellite Markers

Animals ◽

10.3390/ani11041067 ◽

2021 ◽

Vol 11 (4) ◽

pp. 1067

Author(s):

Emel Özkan Ünal ◽

Raziye Işık ◽

Ayşe Şen ◽

Elif Geyik Kuş ◽

Mehmet İhsan Soysal

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Water Buffalo ◽

Polymorphic Information Content ◽

Breeding Strategy ◽

Weinberg Equilibrium ◽

Expected Heterozygosity ◽

Genetic Diversity And Structure ◽

Hardy Weinberg Equilibrium ◽

The Mean

The present study was aimed to investigate the genetic diversity among 17 Turkish water buffalo populations. A total of 837 individuals from 17 provincial populations were genotyped, using 20 microsatellites markers. The microsatellite markers analyzed were highly polymorphic with a mean number of alleles of (7.28) ranging from 6 (ILSTS005) to 17 (ETH003). The mean observed and expected heterozygosity values across all polymorphic loci in all studied buffalo populations were 0.61 and 0.70, respectively. Observed heterozygosity varied from 0.55 (Bursa (BUR)) to 0.70 (Muş (MUS)). It was lower than expected heterozygosity in most of the populations indicating a deviation from Hardy–Weinberg equilibrium. The overall value for the polymorphic information content of noted microsatellite loci was 0.655, indicating their suitability for genetic diversity analysis in buffalo. The mean FIS value was 0.091 and all loci were observed significantly deviated from Hardy–Weinberg Equilibrium (HWE), most likely based on non-random breeding. The 17 buffalo populations were genetically less diverse as indicated by a small mean FST value (0.032 ± 0.018). The analysis of molecular variance (AMOVA) analysis indicated that about 2% of the total genetic diversity was clarified by population distinctions and 88 percent corresponded to differences among individuals. The information produced by this study can be used to establish a base of national conservation and breeding strategy of water buffalo population in Turkey.

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

Bangladesh Journal of Agricultural Research ◽

10.3329/bjar.v37i3.12082 ◽

2012 ◽

Vol 37 (3) ◽

pp. 389-398 ◽

Cited By ~ 3

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

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Isolation and Characterization of Microsatellite Loci for the Ornamental Plant Primula obconica Hance (Primulaceae)

HortScience ◽

10.21273/hortsci.45.2.314 ◽

2010 ◽

Vol 45 (2) ◽

pp. 314-315 ◽

Cited By ~ 2

Author(s):

Hai-fei Yan ◽

Xue-jun Ge ◽

Chi-ming Hu ◽

Gang Hao

Keyword(s):

Genetic Variation ◽

Genetic Structure ◽

Microsatellite Markers ◽

Microsatellite Loci ◽

Ornamental Plant ◽

Microsatellite Variation ◽

Isolation And Characterization ◽

Expected Heterozygosity ◽

Fiasco Protocol

Nine microsatellite loci were isolated from Primula obconica using the FIASCO protocol. We used 30 individuals from three populations for the assessment of microsatellite variation. Seven loci were detected with microsatellite polymorphism. The number of alleles per locus ranged from three to seven. The average observed heterozygosity and expected heterozygosity ranged from 0.167 to 0.6 and from 0.409 to 0.653, respectively. These microsatellite markers will be useful to assess the genetic variation and genetic structure of P. obconica.

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Cross-amplification and Characterization of Polymorphic Microsatellite Markers From Acacia (Senegalia) mellifera and Acacia brevispica to Acacia senegal (L.) Willd.

Silvae Genetica ◽

10.1515/sg-2010-0040 ◽

2010 ◽

Vol 59 (1-6) ◽

pp. 285-288 ◽

Cited By ~ 1

Author(s):

Stephen F. Omondi ◽

O. G. Dangasuk ◽

D. W. Odee ◽

S. Cavers ◽

D. P. Khasa

Keyword(s):

Microsatellite Markers ◽

Allelic Diversity ◽

Breeding Systems ◽

Acacia Senegal ◽

Cross Amplification ◽

Expected Heterozygosity ◽

Potential Source ◽

Polymorphic Microsatellite ◽

Acacia Mellifera

Abstract Seven polymorphic microsatellite markers isolated from Acacia brevispica and Acacia mellifera were successfully cross-amplified in Acacia senegal. The loci were surveyed for polymorphism using 30 samples. Allelic diversity ranged from 4 (Ame02, Ab06 and Ab18) to 13 (Ab26) per locus. The expected heterozygosity (HE) ranged from 0.543 (Ame02) to 0.868 (Ab26) while observed heterozygosity (HO) ranged from 0.516 (Ame05) to 0.800 (Ame03). Cross-amplification of these loci represents a potential source of co-dominant markers and will be useful in the study of genetic diversity, structure, gene flow and breeding systems of this important Acacia species.

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Molecular evaluations of thirty one clones of poplar based on RAPD and SSR molecular markers

Genetika ◽

10.2298/gensr1403985s ◽

2014 ◽

Vol 46 (3) ◽

pp. 985-1001 ◽

Cited By ~ 1

Author(s):

M.K. Singh ◽

N.B. Singh ◽

S. Thakur ◽

P.K. Naik

Keyword(s):

Genetic Variation ◽

Molecular Markers ◽

Selective Breeding ◽

Analysis Of Molecular Variance ◽

Ssr Primers ◽

The World ◽

The Mean ◽

Relationship Of ◽

Management And Conservation ◽

Selective Breeding Programme

Poplar is an important tree species valued all over the world for its wood importance. Despite limited knowledge of the levels of genetic diversity and relatedness, their cultivation as a source of plywood is widespread. In order to facilitate reasoned scientific decisions on its management and conservation and prepare for selective breeding programme, genetic analysis of 31 genotypes was performed using RAPD and SSR molecular markers. Twenty six RAPD primers and 14 SSR primers amplified a total of 236 and 85 scoreable bands of which 86.44% and 86.02% were polymorphic. The mean coefficient of gene differentiation (Gst) was 0.388 and 0.341 indicating that 61.2% and 65.9% of the genetic variation resided within the populations. Analysis of molecular variance (AMOVA) indicated that majority of genetic variation (94.6% using RAPD and 89% using SSR) occurred among genotypes, while the variation between the three groups (categorized as tall, medium and small plants height) was 5.4% (using RAPD and 11% (using SSR). The dendrogram obtained from NJ and STRUCTURE analysis revealed splitting of genotypes into four clusters with clear distinction between short, medium and tall height genotypes, indicated that genetic differentiations measure with respect to RAPD and SSR. However, both the markers were equally useful in providing some understanding about the genetic relationship of different genotypes of poplar that are important in the conservation and exploitation of poplar genetic resources.

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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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Development of microsatellite markers for the critically endangered conifer Glyptostrobus pensilis (Cupressaceae) using transcriptome data

Silvae Genetica ◽

10.2478/sg-2019-0007 ◽

2019 ◽

Vol 68 (1) ◽

pp. 41-44 ◽

Cited By ~ 1

Author(s):

Xin-Yu Li ◽

Xue-Ying Lin ◽

Markus Ruhsam ◽

Lu Chen ◽

Xing-Tong Wu ◽

...

Keyword(s):

Microsatellite Markers ◽

Related Species ◽

Population Genetic ◽

Critically Endangered ◽

Transcriptome Data ◽

Genetic Studies ◽

Chinese Populations ◽

Expected Heterozygosity ◽

Ssr Loci ◽

Hardy Weinberg Equilibrium

Abstract Glyptostrobus pensilis (Cupressaceae) is a critically endangered conifer which occurs in China, Laos, and Vietnam where it is only known from a few populations. Here we aim to develop microsatellite markers which can be used to study the genetic variation within this species. Using transcriptome data we tested 170 SSR loci for polymorphism in 16 samples. Twenty-three loci were polymorphic and selected for the genetic analysis of 83 individuals from three Chinese populations. The number of alleles per locus and population ranged from one to eight, the observed and expected heterozygosity from Ho = 0.00-1.00 and He = 0.00-0.83, respectively. Fifteen loci deviated from Hardy-Weinberg equilibrium in at least one of the three populations. The majority of loci could also be successfully amplified in four related species, namely Cryptomeria fortunei, Taxodium distichum, Taxodium ascendens and Cunninghamia lanceolata. These developed microsatellites are suitable for population genetic studies of Glyptostrobus pensilis and related species.

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