scholarly journals Genetic Diversity of Tef [Eragrostis tef (Zucc.)Trotter] as Revealed by Microsatellite Markers

2021 ◽  
Vol 2021 ◽  
pp. 1-9
Author(s):  
Mahilet Tadesse ◽  
Mulugeta Kebede ◽  
Dejene Girma

Genetic variability is the fundamental prerequisite of any crop-breeding program to develop superior cultivars. There are about 350 Eragrostis1 species, of which, tef is the only species cultivated for human consumption. Currently, the Ethiopian Biodiversity Institute (EBI) collected over five thousand tef accessions from different geographical regions, diverse in terms of climate and elevation, which are uncharacterized yet. The objective of this study was to evaluate the genetic diversity among 64 tef accessions using 10 selected polymorphic simple sequence repeats (SSRs) markers. A total of 314 alleles were detected with an average of 14.5 alleles per locus and amplicon size ranged from 90 bp–320 bp. The mean value of polymorphic information content (PIC) was 0.87, appearing polymorphic for all loci. The lowest Fst value (0.05) was recorded among the studied tef populations. The mean value of major allele frequency and the number of effective alleles were 0.33 and 3.32, respectively. The mean value of gene flow (Nm) and Shannon’s information index (I) was 4.74 and 1.65, respectively. The observed (Ho) and expected (He) heterozygosities varied from 0.34 to 0.56 and from 0.58 to 0.76, respectively. The cluster analysis has grouped the 64 tef accessions into three distinct clusters based on their similarity. The PCoA analysis showed that clustering is basing on the geographical origin of accessions. Analysis of molecular variance revealed 56%, 39% and 5% of the total variation due to variation within populations, among individuals and among populations, respectively. Structure bar-plot also inferred three gene pools, but with high level of admixtures. Thus, the present study shows that the identified tef accessions could be of great interest for the initiation of a planned breeding and conservation programs.

2021 ◽  
Vol 34 (2) ◽  
Author(s):  
MUHAMMAD FORHAD ALI ◽  
◽  
MD. RAFIQUL ISLAM SARDER ◽  
MOHAMMAD MATIUR RAHMAN ◽  
MD. FAZLUL AWAL MOLLAH ◽  
...  

Genetic information is essential for conservation and future aquaculture development of the endangered catfish Rita rita (Hamilton, 1822). Two hundred catfish, R. rita, 50 from four rivers, the Old Brahmaputra, Jamuna, Meghna and Kangsa were collected and analysed to evaluate the genetic diversity and population structure using five microsatellite primers (Cba06-KUL, Cba08-KUL, Cba09-KUL, Phy03-KUL and Phy07-KUL). Four of the five amplified loci were found polymorphic (P95) in all the populations and 46 alleles were recorded with 9 to 14 alleles per locus. Differences were observed in the total number of alleles ranging from 41 to 44, effective number of alleles from 29.96 to 37.46, observed heterozygosity from 0.57 to 0.76, Shannon’s information index from 2.09 to 2.30 and polymorphic information content from 0.84 to 0.88 among the four populations. Results exposed the highest levels of genetic diversity in the Meghna population while the lowest in the Kangsa population of R. rita. All the populations were significantly deviated (P < 0.001) from the Hardy-Weinberg equilibrium for all the loci. Nei’s genetic distance between populations ranged 0.007 to 0.017 with low overall genetic difference FST = 0.011 and high gene flow Nm = 24.333, indicating that R. rita populations were not subdivided. This study revealed a high level of gene diversity with deficiency in genetic heterogeneity in all the populations of R. rita, emphasising natural management, conservation and rehabilitation measures of this species.


2021 ◽  
Vol 13 (2) ◽  
pp. 1
Author(s):  
M. K. Khatun ◽  
M. A. Haque ◽  
M. A. Malek ◽  
M. H. Rashid ◽  
S. Islam ◽  
...  

The purpose of the present study was to investigate the genetic diversity and molecular characterization of 50 soybean genotypes in Bangladesh with 20 SSR markers. Genomic DNA was isolated by modified standard cetyl tri-methyl ammonium bromide (CTAB) extraction protocol and alleles were amplified by polymerase chain reaction (PCR). Allele sizes were estimated in comparison with 50 bp DNA ladder. The software NTSYSpc version 2.2 and POPGENE version 1.31 were utilized for molecular data analysis and preparation of dendrogram. Polymorphic Information Content (PIC) values varied from 0.53 (Satt664) to 0.98 (Satt009, Satt330 and Satt522) with the mean value 0.897 and expected heterozygosity varied from 0.4059 (Satt685) to 0.1246 (Satt664) with the mean value 0.244. The dendrogram analysis depicted that the 50 genotypes were grouped in four (4) major clusters. The most diverse genotypes were SBG-1, PM-78-6-3-13, BS-3 and AGS-31, which suggest that the simple sequence repeat (SSR) markers are very efficient for genetic diversity analysis. The similarity matrix revealed the diversity among genotypes. The diverse genetic materials obtained from the present study on genetic diversity of soybean genotypes in Bangladesh may be utilized in the future breeding programme.


2020 ◽  
Vol 70 (2) ◽  
pp. 170-181
Author(s):  
Dimitrijević Vladimir ◽  
Ristanić Marko ◽  
Stanisić Ljubodrag ◽  
Drobnjak Darko ◽  
Urosević Milivoje ◽  
...  

AbstractThe Kangal Shepherd Dog is considered the most common dog breed of Turkish origin. This study investigated variations in ten autosomal microsatellite markers (PEZ01, PEZ03, PEZ05, PEZ06, PEZ08, PEZ12, PEZ20, FHC2010, FHC2054 and FHC2079) for the purposes of genetic diversity assessment of the Kangal breed. In addition, the use of markers was assessed in parentage testing and individual identification within the Kangal breed. The microsatellite markers were typed in 51 Kangal dogs. The total number of alleles in the study population was 69. The mean number of alleles per locus was 6.9, and varied from four (FHC2079) to 12 (PEZ12). The polymorphic information content (PIC) ranged from 0.52 (FHC2079) to 0.87 (PEZ12), with the mean value for all loci of 0.717. Power of exclusion (PE) in 10 microsatellites investigated varied between 0.143 (FHC2054) and 0.472 (PEZ08) per locus. In order to determine the efficiency of using microsatellites for individual identification in the Kangal breed, power of discrimination (PD) and matching probability (MP) were calculated for each microsatellite marker. The panel achieved high combined MP (6.77 × 10-10) and high combined PD value of 99.99999%. The obtained results may contribute to further recognition of the Kangal breed, and confirm that the investigated microsatellites enable a reliable parentage testing and individual identification of the breed.


2014 ◽  
Vol 13 (2) ◽  
pp. 131-141 ◽  
Author(s):  
Beyene Amelework ◽  
Hussien Shimelis ◽  
Pangirayi Tongoona ◽  
Mark Laing ◽  
Fentahun Mengistu

The regions of north-eastern Ethiopia are known for their high levels of sorghum genetic diversity, and for being drought prone. For centuries, sorghum has been developed and maintained by farmers for its adaptation to the marginal and heterogeneous environment of these regions. The objective of this study was to examine the genetic diversity and population structure of 200 sorghum landraces collected from seven lowland districts, using 30 microsatellite markers sampled from all linkage groups of the sorghum genome. Both distance-based and model-based analytical approaches were used to analyse the data. The data analysis revealed that there was a large variation among all the markers under study. The values of polymorphic information content ranged from 0.26 to 0.88, with a mean value of 0.61, reflecting the high discriminating ability of the markers studied. The mean value of total gene diversity was 0.69, which partitioned 86% among the landraces and 14% within the landraces. Gene diversity among the landraces was largely due to the variation among the genotypes within the geographic origins. Landraces sampled from different collection sites appeared to cluster together, indicating the existence of a high level of gene flow among the sites of collection. This indicates that a relatively small, random collection of landraces would capture the bulk of genetic diversity in the target area. A moderately high level of genetic differentiation and a relatively low level of gene flow were observed between sorghum races and maturity groups. Given that the target area is marginal, drought prone and heterogeneous, the study of genetic diversity among sorghum landraces could serve as an important indicator of valuable alleles for drought tolerance in future sorghum improvement programmes.


2017 ◽  
Vol 61 (4) ◽  
pp. 535-542 ◽  
Author(s):  
Tanveer Hussain ◽  
Masroor Ellahi Babar ◽  
Akhtar Ali ◽  
Asif Nadeem ◽  
Zia Ur Rehman ◽  
...  

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.


2019 ◽  
Author(s):  
Alemneh Mideksa Egu ◽  
Kifle Dagne ◽  
Kassahun Tesfaye ◽  
Xuebo Hu

Abstract Background Vernonia (Vernonia galamensis) is a potential novel industrial crop due to high demand to its natural epoxidised oil, which can be used for the manufacturing of polyvinyl chloride, adhesives, and petrochemicals, cosmetic and pharmaceutical products. This study is initiated for the systematic and intensive assessment of V. galamensis accessions genetic diversity through SSR molecular markers to minimize the existing research gaps, and provide a clue for germplasm conservation and further research. Results A total of 150 V. galamensis accessions were analyzed using 20 SSR markers. The markers detected a total of 79 with an average of 3.9 alleles per locus. The mean number of effective alleles was 3.06 and, the mean observed heterozygosity (Ho) was 0.15 across all the 20 markers evaluated. The marker also showed the highest percent of polymorphism that ranged from 0.50 to 0.96 with an average of 0.76. The analysis of molecular variance showed only 11% variation was among populations, 22% among individuals within populations and 67% within individuals. The largest number of migrants per generation was occurred between Derashie and Wollo (Nm=7.37) whereas the lowest values was between East Harerghe and West Harerghe (Nm =1.42). A factor analysis including dendrogram clusters and principal coordinates classified the 150 accessions into 4 groups. However, the Bayesian model based clustering (STRUCTURE) grouped into 3 (K = 3) major gene pools. These analyses showed accessions collected from the same region of origin did not often grouped entirely together within a given major groups. Conclusions Molecular genetic diversity analysis, using SSR markers was the first report in V. galamensis. All the markers used were polymorphic in the population studied. The markers detected the larger number of alleles, higher expected heterozygosity than observed heterozygosity. The markers applied to ten populations, in which East Showa and West Harerghe revealed higher genetic diversity, and can be considered as the hotspots for in-situ conservation of V. galamensis. In addition, the values of SSR markers such as heterozygosity, Shannon‘s index, polymorphic information content and population clusters are an important baseline information for future V. galamensis cultivation, breeding and genetic resource conservation endeavors in Ethiopia.


2021 ◽  
Vol 80 (Suppl 1) ◽  
pp. 1119.1-1119
Author(s):  
L. Nacef ◽  
Y. Besbes ◽  
Y. Mabrouk ◽  
H. Ferjani ◽  
K. Maatallah ◽  
...  

Background:The lipid paradox is termed the decreased cholesterol level in rheumatoid arthritis (RA). Nevertheless, the apolipoprotein levels are usually higher than a healthy person and are predictors of cardiovascular events.Objectives:We aimed to describe lipid abnormalities in RA patients and to look for predictor factors of these changes.Methods:The prospective study was carried out on patients with RA who met the 2010 American College of Rheumatology (ACR)/European League Against Rheumatism (EULAR) classification criteria. These patients were followed in the rheumatology department of the Kassab Institute.We collected the socio-demographic data, biological and immunological parameters.The lipid assessment included: a measurement of total cholesterol (TC), HDL, LDL, and triglycerides (TG). Lipoproteins APOA1 and APOB were measured. All data were collected after patient consent.Results:Of the 47 patients recruited, 78.7% were female. The mean age was 52.5 ±11.06 [32-76]. The average RA progressed from 86.25 ±63 months [5-288] and was erosive in 81.6% of cases. The rheumatoid factor (RF) was positive in 57.8% of patients, and citrullinated antipeptide antibodies (ACPA) were present in 62.2%. Eight patients had a previous CV history.Mean TC was 4.42 ±1.3 [1.2-7.58], mean HDL was 1.38 ±0.73 [0.18-4.10], mean LDL was 2.55 ±1.16 [0.24-5.54]. The mean TG value was 1.28 ±0.6 [0.24-5.54]. TC elevation was found in 9.1% of cases, HDL in 21.3% of cases, LDL in 5.5% of cases, and TG in 16.4% of cases. Mean APOB/APOA1 ratio was 0.67 ±0.18 [0,46-1,11]. LDL elevation was associated to a high DAS28 (p=0.06, r=0.512). APOA1 was associated to a low DAS28 (p=0.04, r=-0.642).The mean value of APO A1 was 1.36 ±0.21 [0.84-1.81], that of APOB was 0.90 ±0.22 [0.58-1.40]. APOA1 values were lower in patients with high-level LDL (p=0.767). The APOB value was associated with lipid disturbance without significant correlation (p=0.291).Conclusion:Lipid test abnormalities can be found in RA patients outside of any known CV risk factors. APOA1 seems to have a protective effect. Screening and treatment of these abnormalities can prevent CV risk.References:[1]Miguel Bernardes and al. Coronary artery calcium score in female rheumatoid arthritis patients: Associations with apolipoproteins and disease biomarkers. Int J Rheum Dis. 2019;00:1–16.[2]Anna So dergren and al. Biomarkers associated with cardiovascular disease in patients with early rheumatoid arthritis. PLOS ONE. August 5, 2019.Disclosure of Interests:None declared


Author(s):  
Workia Ahmed ◽  
Tileye Feyissa ◽  
Kassahun Tesfaye ◽  
Sumaira Farrakh

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.


2009 ◽  
Vol 15 (1) ◽  
pp. 23-28 ◽  
Author(s):  
Katarzyna Kubiak

Genetic diversity ofAvena strigosaSchreb. ecotypes on the basis of isoenzyme markersGenetic diversity was analyzed in 19 ecotypes of the diploid oatA. strigosaoriginating from various geographical regions of the world. Six isoenzyme systems (AAT, ACP, EST, LAP, MDH, PX) were studied and 16 loci were identified. Only two loci (Est4andMdh2) were polymorphic. Ecotypes were characterized by the percentage of polymorphic loci (P=3.3%), the mean number of alleles per locus (A=1.04) and intrapopulation diversity (HS=0.013). Total genetic diversity (HT=0.07) and interpopulation diversity (DST=0.057) were examined as well. The value of the coefficient of gene differentiation (GST=0.821) indicated that diversity among populations was an important contributor to total variability. Genetic similarity betweenA. strigosapopulations was very high (IN=0.94). Cluster analysis did not demonstrate strongly differentiated groups among the ecotypes examined.


2018 ◽  
Vol 7 (1) ◽  
Author(s):  
Filippo Giarratana ◽  
Graziella Ziino ◽  
Valerio D'Andrea ◽  
Antonio Panebianco ◽  
Alessandro Giuffrida

n the last few years, the consumption of fish eggs has increased rapidly, finding widespread use also in mass catering. This increase has involved also those of the Peter’s fish (Zeus faber). Females of this species, by their reproductive characteristics, have highly developed gonads in different periods of the year, making the raw material easy to find. The aim of the present study was to perform a quality assessment of Zeus faber ovaries regularly commercialized for human consumption. A total number of 34 samples, divided in fresh (11) and frozen (23), were processed for microbiological characterization, parasitological and histological evaluations. Fresh and frozen samples have significant (P<0.01) differences in total bacterial charge, with values of 4.75±0.5 Log CFU/g and 3.65±0.7 Log CFU/g respectively. The mean value of Enterobacteriaceae was 2.58±0.7 Log CFU/g in fresh products, while 52.17% (12) of frozen samples reported loads of <1 Log CFU/g. No Salmonella spp. and Listeria monocytogenes were found. Aeromonas spp. was detected in two frozen sample (with loads of 2.2 and <1 Log CFU/g) and in 5 fresh ovaries with value ranged from 1.70 to 3.48 Log CFU/g. Vibrio spp. was found in 4 (36.36%) and 3 (13.04%) of fresh and frozen samples respectively, with loads always <1 Log CFU/g. All 31 Vibrio strains isolated, were identified as Vibrio alginolyticus, and 61.29% (19) of them was positive for the ToxRS factor and 6.45% (2) for ToxR. The 47.06% (16) of total samples showed infestations by larvae of Anisakis Type 1 in the serous and inside the ovary. In this last case, histologically it was found to be free larvae. This study attested satisfactory hygiene conditions for Zeus faber ovaries currently marked for human consumption. The presence of potentially pathogenic strains of V. alginolyticus and Aeromonas spp., but above all the frequent infestation by Anisakis larvae, represent a potentially hazard for the consumer.


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