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

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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Microsatellite based genetic variation among the buffalo breed populations in Pakistan

Journal of Veterinary Research ◽

10.1515/jvetres-2017-0057 ◽

2017 ◽

Vol 61 (4) ◽

pp. 535-542 ◽

Cited By ~ 3

Author(s):

Tanveer Hussain ◽

Masroor Ellahi Babar ◽

Akhtar Ali ◽

Asif Nadeem ◽

Zia Ur Rehman ◽

...

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Polymorphic Information Content ◽

Mean Value ◽

Diversity Analysis ◽

Phenotypic Differentiation ◽

Genetic Diversity Analysis ◽

Expected Heterozygosity ◽

The Mean ◽

Average Gene

AbstractIntroduction: Eight microsatellite loci were used to define genetic diversity among five native water buffalo breeds in Pakistan.Material and Methods: Blood samples (10 mL) from 25 buffaloes of each of the Nili, Ravi, Nili-Ravi, Kundhi, and Azi-Kheli breeds were collected aseptically from the jugular vein into 50 ml Falcon tubes containing 200 μl of 0.5 M EDTA. The phenol-chloroform method was used to extract DNA and the regions were amplified for microsatellite analysis. The eight microsatellite markers ETH10, INRA005, ILSTS029, ILSTS033, ILSTS049, ILSTS052, ETH225, and CSSM66 were analysed.Results: The effective number of alleles across all loci was as usual lower than the observed values with a mean value of 2.52 alleles per locus. The overall allele frequency varied from 0.0041 for alleles B, I, and J over respective loci ILSTS052, INRA005, and ILSTS029 to 0.80 for allele H over locus ILSTS029. The average observed and expected heterozygosity values across all polymorphic loci in all studied buffalo breeds were 0.43 and 0.53, respectively. The overall value for polymorphic information content of considered microsatellite markers was 0.53, suggesting their appropriateness for genetic diversity analysis in buffalo. The mean Fis value was 0.13 and all loci except ILSTS049 were found significantly deviated from HWE, most likely due to non-random breeding. The five buffalo populations were genetically less diverse as indicated by a small mean Fst value (0.07). The average gene flow (Nm) indicative for population migration was calculated as 3.31. Nei’s original measures of genetic distance (Ds) revealed ancient divergence of the Nili and Azi-Kheli breeds (Ds = 0.1747) and recent divergence of the Nili and Ravi breeds (Ds = 0.0374).Conclusion: These estimates of genetic diversity were seen to coincide with phenotypic differentiation among the studied buffalo breeds. The present study reports the first microsatellite marker-based genetic diversity analysis in Pakistani buffalo breeds, and might facilitate similar studies in other livestock breeds of Pakistan.

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Diversity and genetic relatedness among genotypes of Vitis spp. using microsatellite molecular markers

Revista Brasileira de Fruticultura ◽

10.1590/s0100-29452013000300017 ◽

2013 ◽

Vol 35 (3) ◽

pp. 799-808 ◽

Cited By ~ 5

Author(s):

Patrícia Coelho de Souza Leão ◽

Cosme Damião Cruz ◽

Sérgio Yoshimitsu Motoike

Keyword(s):

Genetic Diversity ◽

Cluster Analysis ◽

Molecular Markers ◽

Microsatellite Markers ◽

Information Content ◽

Genetic Relatedness ◽

Polymorphic Information Content ◽

Germplasm Bank ◽

Expected Heterozygosity ◽

Vitis Spp

The purpose of this research was to study the genetic diversity and genetic relatedness of 60 genotypes of grapevines derived from the Germplasm Bank of Embrapa Semiárido, Juazeiro, BA, Brazil. Seven previously characterized microsatellite markers were used: VVS2, VVMD5, VVMD7, VVMD27, VVMD3, ssrVrZAG79 and ssrVrZAG62. The expected heterozygosity (He) and polymorphic information content (PIC) were calculated, and the cluster analysis were processed to generate a dendrogram using the algorithm UPGMA. The He ranged from 81.8% to 88.1%, with a mean of 84.8%. The loci VrZAG79 and VVMD7 were the most informative, with a PIC of 87 and 86%, respectively, while VrZAG62 was the least informative, with a PIC value of 80%. Cluster analysis by UPGMA method allowed separation of the genotypes according to their genealogy and identification of possible parentage for the cultivars 'Dominga', 'Isaura', 'CG 26916', 'CG28467' and 'Roni Redi'.

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

Archives Animal Breeding ◽

10.5194/aab-60-183-2017 ◽

2017 ◽

Vol 60 (3) ◽

pp. 183-189 ◽

Cited By ~ 9

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.

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Genetic Diversity and Population Structure of Cowpea [Vigna unguiculata (L.) Walp.] Germplasm Collected from Togo Based on DArT Markers

Genes ◽

10.3390/genes12091451 ◽

2021 ◽

Vol 12 (9) ◽

pp. 1451

Author(s):

Kodjo M. Gbedevi ◽

Ousmane Boukar ◽

Haruki Ishikawa ◽

Ayodeji Abe ◽

Patrick O. Ongom ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Improvement ◽

Agricultural Research ◽

Polymorphic Information Content ◽

Germplasm Collection ◽

Mean Value ◽

Economic Life ◽

Dart Markers ◽

Crop Genetic Diversity

Crop genetic diversity is a sine qua non for continuous progress in the development of improved varieties, hence the need for germplasm collection, conservation and characterization. Over the years, cowpea has contributed immensely to the nutrition and economic life of the people in Togo. However, the bulk of varieties grown by farmers are landraces due to the absence of any serious genetic improvement activity on cowpea in the country. In this study, the genetic diversity and population structure of 255 cowpea accessions collected from five administrative regions and the agricultural research institute of Togo were assessed using 4600 informative diversity array technology (DArT) markers. Among the regions, the polymorphic information content (PIC) ranged from 0.19 to 0.27 with a mean value of 0.25. The expected heterozygosity (He) varied from 0.22 to 0.34 with a mean value of 0.31, while the observed heterozygosity (Ho) varied from 0.03 to 0.07 with an average of 0.05. The average inbreeding coefficient (FIS) varied from 0.78 to 0.89 with a mean value of 0.83, suggesting that most of the accessions are inbred. Cluster analysis and population structure identified four groups with each comprising accessions from the six different sources. Weak to moderate differentiation was observed among the populations with a genetic differentiation index varying from 0.014 to 0.117. Variation was highest (78%) among accessions within populations and lowest between populations (7%). These results revealed a moderate level of diversity among the Togo cowpea germplasm. The findings of this study constitute a foundation for genetic improvement of cowpea in Togo.

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

Czech Journal of Animal Science ◽

10.17221/62/2019-cjas ◽

2019 ◽

Vol 64 (No. 10) ◽

pp. 411-419 ◽

Cited By ~ 2

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 < 0.05).

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Molecular characterization of some landraces and varieties of Date palm (Phoenix dactylifera L.) from Afar region of Ethiopia using ISSR markers

10.21203/rs.2.10762/v1 ◽

2019 ◽

Author(s):

Meera Indracanti ◽

Dawud Takele Mekonnen ◽

Mesfin Tsegaw

Keyword(s):

Genetic Diversity ◽

Date Palm ◽

Polymorphic Information Content ◽

Phoenix Dactylifera ◽

Issr Markers ◽

Snp Markers ◽

Discrimination Power ◽

Information Index ◽

Phoenix Dactylifera L ◽

Afar Region

Abstract Back ground Date palm (Phoenix dactylifera L.) is one of the oldest fruit trees in hot arid region of the world including North Africa. In some areas of Afar region of Ethiopia, date palm grow as landraces, are in danger due to introduction of improved cultivars. Present study was carried out to fill knowledge gap about molecular diversity of this crop in Afar region. Molecular studies of 5 landraces and 3 introduced cultivars of date palm from Afar region of Ethiopia were tested using 21 randomly selected ISSR primers for amplification and polymorphism detection using genomic DNA. ISSR markers across 8 date palm varieties were scored for their presence (1) or absence (0). Shannon's Information index (I) and polymorphic information content (PIC) were analyzed by popGENE 32 and online PIC calculator respectively. Results 17 out of 21 ISSR markers used for this study produced a total of 557 scorable DNA fragments with average of 33.52 per marker and 61.68, 43.93 and 68.22% polymorphism were obtained within local landraces, introduced varieties and among all samples respectively. The genetic distance among all samples ranged from 0.1402 to 0.5953; and the dendrogram separated date palm varieties into seven clusters. ISSR markers used for this study have high discrimination power and the average values of Shannon's information index and PIC were 0.318 and 0.76 respectively. Conclusion Genetic diversity was observed among all date palms studied in this investigation. To have better understanding on genetic diversity of date palm in the Afar region, further research should be done using SNP markers and landraces should be registered.

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Excess heterozygosity and scarce genetic differentiation in the populations of Phoenix dactylifera L.: human impact or ecological determinants

Plant Genetic Resources ◽

10.1017/s1479262108060905 ◽

2008 ◽

Vol 7 (02) ◽

pp. 95-104 ◽

Cited By ~ 8

Author(s):

Sakina Elshibli ◽

Helena Korpelainen

Keyword(s):

Microsatellite Markers ◽

Date Palm ◽

Isolation By Distance ◽

Phoenix Dactylifera ◽

Mean Value ◽

Mantel Test ◽

Plant Materials ◽

Geographical Distances ◽

Palm Fruits ◽

Excess Heterozygosity

Extensive research has been conducted on the characterization of hundreds of date palm (Phoenix dactyliferaL.) cultivars worldwide. However, the population genetics of date palms has never been studied. In this study, we collected 200 individuals from 19 populations of different geographical locations in Sudan. The collection sites were grouped according to the type of dates (date palm fruits) that dominates in the area. Ten microsatellite markers were used to investigate the genetic diversity within and among populations and the correlation between the genetic and geographical distances. The tested microsatellite markers showed a high level of polymorphism. A total of 261 alleles were detected at the ten loci. The overall mean value of fixation indices equalled − 0.163, which shows the presence of excess heterozygosity. However, the χ2tests conducted for every locus in each population indicated no significant deviation from the Hardy–Weinberg equilibrium. The analyses of molecular variance exhibited that about 95% of the total genetic variation existed within populations, while significant differentiation within the type groups could be detected. Although significant isolation by distance (r2 = 0.552,P < 0.05) was detected by a Mantel test, it seems that the spatial effect has become complicated as a result from the exchange and introduction of different kinds of plant materials by date palm growers and traders, as well as seed dispersal. This complexity was clearly apparent in the weak clustering relationships among most of the tested populations.

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Genetic diversity and population structure of sweet orange [Citrus sinensis (L.) Osbeck] germplasm of India revealed by SSR and InDel markers

10.1101/2022.01.11.475964 ◽

2022 ◽

Author(s):

Prasanth Tej Kumar Jagannadham ◽

Thirugnanavel Anbalagan ◽

Devendra Y Upadhyay ◽

Snehal A. Kamde ◽

Prafulla R. Jalamkar ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Citrus Sinensis ◽

Sweet Orange ◽

Polymorphic Information Content ◽

Citrus Fruit ◽

Molecular Data ◽

Expected Heterozygosity ◽

Indel Markers ◽

Population Structure Analysis

Sweet orange (Citrus sinensis (L.) Osbeck) is an important commercial citrus fruit crop, cultivated in India and across the world. In India most of the cultivated sweet orange species were introduced varieties. In this study, we used two molecular markers, SSR and InDels, to understand the genetic diversity and population structure of seventy-two sweet orange genotypes. Genetic parameters consisted of a total number of alleles, a number of polymorphic alleles (effective alleles); genetic diversity (G.D.), expected heterozygosity (He), and the polymorphic information content (PIC) were calculated based on molecular data. Two dendrograms were constructed based on the InDels and SSR. In both the cases, they formed three major clusters showing various degrees of variations with respect to members of the clusters. Population structure analysis revealed the presence of two distinct subpopulations. Therefore, in order to address various challenges and develop sweet orange varieties with desirable traits, there is a need to broaden the genetic base of sweet orange through the intensive collection in the northeastern region. These results of intraspecific genetic variability of the collections will dictate the path for the sweet orange breeding and conservation programs in India.

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

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.130.4.543 ◽

2005 ◽

Vol 130 (4) ◽

pp. 543-549 ◽

Cited By ~ 56

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.

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