Morphometric variation, genetic diversity and allelic polymorphism of an underutilised species Thaumatococcus daniellii population in Southwestern Nigeria

Common bean (Phaseolus vulgaris L.) was introduced in Europe from both Mesoamerican and Andean centers of origin and has been cultivated in central Europe for centuries. The first objective of this study was to evaluate genetic diversity and the population structure of 167 accessions divided into four groups according to geographical origin (Slovenia and Austria) and time periods (historical and present) using 14 simple sequence repeat (SSR) markers. The second objective was to improve our understanding of the pathways of dissemination and the evolution of this species in central Europe. Great allelic polymorphism was detected in all four groups of examined accessions, indicating that Slovene and Austrian bean germplasm in the past possessed significant variation that has been well preserved until today. In factorial correspondence analysis, accessions from different groups clustered together indicating potential gene flow between countries. The uncovered diversity corresponded very well to the two recognized gene pools (Andean and Mesoamerican). The majority of accessions in every single group belonged to the Andean gene pool. Strong predominance of Andean genotypes classifies Slovenia among other Mediterranean countries, like Spain and Italy. The latter appears as a most probable source of first beans in Slovenia and Austria. We assume that in the beginning of the previous century after very tight relationships between Slovenia and Austria loosened, introgression of genotypes from western and northern European countries took place in Austria, which resulted in a very high proportion of Mesoamerican genotypes that we found in the present Austrian germplasm (44%). Several putative hybrids between the Andean and Mesoamerican gene pools were detected in this study. Evolutionary significance, origin, and breeding potential of these recombinants are discussed here.

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Is genetic diversity of Plasmodium falciparum suggestive of malaria endemic zone in West Africa? An attempt to respond by a cross-sectional comparative study between Senegal and Nigeria

10.1101/2020.08.27.20183178 ◽

2020 ◽

Author(s):

Mary Aigbiremo Oboh ◽

Tolla Ndiaye ◽

Khadim Diongue ◽

Yaye D Ndiaye ◽

Mouhamad Sy ◽

...

Keyword(s):

Genetic Diversity ◽

Plasmodium Falciparum ◽

Holistic Approach ◽

Control Measures ◽

Allelic Polymorphism ◽

African Countries ◽

High Genetic Diversity ◽

Cross Sectional ◽

Low Genetic Diversity ◽

Infection Types

Background: Characterization of malaria parasite populations in different endemic settings (from low to high) could be helpful for ascertaining the progress of malaria interventions in endemic settings. The present study aims to compare Plasmodium falciparum parasite population structure between two West African countries with very different level of endemicity using P. falciparum allelic polymorphic markers: msp1 and msp2. Methods: Parasite genomic DNA was extracted from 187 dried blood spot collected from confirmed uncomplicated P. falciparum malaria infected patients in Senegal (94) being at the pre-elimination stage in most part of the country and Nigeria (93) which is still at the control stage. Allelic polymorphism of msp1 and msp2 genes were assessed by nested PCR. Results: In Senegal as well as in Nigeria, K1 and IC3D7 allelic families were the most represented for msp1 and msp2 genes respectively. A higher multiplicity of infection (MOI) was found in both study sites in Senegal (Thies:1.51/2.53; Kedougou:2.2/2.0 for msp 1/2) than from sites in Nigeria (Gbagada: 1.39/1.96; Oredo: 1.35/1.75]). The heterozygosity of msp 1 gene was higher in P. falciparum isolates from Senegal (Thies: 0.62; Kedougou: 0.53) than isolates from Nigeria (Gbagada: 0.55; Oredo: 0.50). In Senegal, K1 alleles were associated with heavy (28) than with moderate (18) infections, in Nigeria however, equal proportions of K1 were observed in both infection types. The IC3D7 subtype allele of the msp 2 family showed high occurrence in heavily infected individuals from both countries (Senegal- 32; Nigeria- 26) than in the moderately infected participants. Conclusion: With the unusual high genetic diversity obtained in low endemic setting in Senegal and low genetic diversity in a high endemic Nigerian setting, multiple holistic approach should be employed in evaluating the actual transmission of a place in order to effectively direct control measures.

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Assessment of Microsatellite Markers (SSRs) For Genetic Diversity in Asparagus Officinalis L. And Allied Species

Bangladesh Journal of Botany ◽

10.3329/bjb.v50i3.55839 ◽

2021 ◽

Vol 50 (3) ◽

pp. 595-602

Author(s):

Muhammad Idrees ◽

Muhammad Irshad ◽

Mitra Lal Pathak ◽

Akash Tariq ◽

Rehan Naeem

Keyword(s):

Genetic Diversity ◽

Genetic Similarity ◽

Clustering Algorithm ◽

Asparagus Officinalis ◽

Allelic Polymorphism ◽

Asparagus Racemosus ◽

Similarity Coefficients ◽

Monophyletic Origin ◽

Genic Ssr ◽

Ssrs Markers

The present study was hypothesized to evaluate a set of SSRs for the assessment of genetic variations in Asparagus officinalis L. and their allied species. Nine genic SSR markers were especially developed for Asparagus genome and employed for DNA profiling studies of Asparagus species. These SSRs markers have revealed the allelic polymorphism ranging from 1.0 to 2.0. Allele frequency was found highest for psbD-trnL (1.0), petB (1.0) and AG7 (1.0), while it was lowest for ZHD1 (0.1). Polymorphism Information content (PIC) was highest for TC7 (0.9) while it was lowest (0.0) for psbD-trnL, petB and AG7 respectively. The genetic similarity coefficients were found to range from 0.42 to 1.0. The UPGMA clustering algorithm based on SSRs data have clustered Asparagus species into 4 groups (I, II, III & IV) indicating Asparagus officinalis (L.) cultivars and allied species in the first clade, while Asparagus officinalis (L.) ‘Gersengum’, Asparagus densiflorus (Kunth) Jessop, and Asparagus racemosus willd. were clustered in separate clades respectively. The present study has endorsed the origin status of Asparagus officinalis and their allied species. A. officinalis cultivars and other allied Asparagus species are clustered in separate clades, and it was revealed that they have monophyletic origin. It was established that SSRs markers could be informative markers for the differentiation of Asparagus officinalis cultivars, and their allied Asparagus species. Bangladesh J. Bot. 50(3): 595-602, 2021 (September)

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Morphometric Variation and Genetic Diversity of the Lesser and Greater Mouse-Eared Bats (Chiroptera: Vespertilionidae) in Thrace and Anatolia

Acta Chiropterologica ◽

10.3161/150811011x624776 ◽

2011 ◽

Vol 13 (2) ◽

pp. 291-298 ◽

Cited By ~ 5

Author(s):

Andrzej Furman ◽

Justyna Bachanek ◽

Tomasz Postawa ◽

Emrah Çoraman

Keyword(s):

Genetic Diversity ◽

Morphometric Variation

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Genetic diversity of pummelo (Citrus grandis Osbeck) and its relatives based on simple sequence repeat markers

Chinese Journal of Agricultural Biotechnology ◽

10.1079/cjb2006102 ◽

2006 ◽

Vol 3 (2) ◽

pp. 119-126 ◽

Cited By ~ 8

Author(s):

Liu Yong ◽

Liu De-Chun ◽

Wu Bo ◽

Sun Zhong-Hai

Keyword(s):

Genetic Diversity ◽

Simple Sequence Repeat ◽

Similarity Coefficient ◽

Group Method ◽

Allelic Polymorphism ◽

Sequence Repeat ◽

Simple Sequence Repeat Markers ◽

Arithmetic Average ◽

Pair Group ◽

Simple Sequence

AbstractGenetic diversity in 122 accessions of pummelo (Citrus grandis Osbeck) and its related varieties was assessed using simple sequence repeat (SSR) markers. Thirty-one pairs of SSR informative primers generated a total of 335 alleles. The average number of alleles per locus was 9.85. The value of allelic polymorphism information content (PIC) ranged from 0.1939 to 0.9073, with an average of 0.7085 per primer. The 122 accessions of pummelo and its related varieties could be clustered into seven groups by the unweighted pair-group method arithmetic average (UPGMA), in which the 110 pummelo accessions could be divided into 18 subgroups at similarity coefficient of 0.712. These subgroups were mainly composed of the Shatian pummelo variety group, the Wendan variety group and many of the hybrid pummelo groups. The classification method can be used in targeting many varieties in order to widen the genetic background of pummelo.

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STUDY OF GENETIC DIVERSITY AND ANALYSIS OF THE DEGREE OF SIMILARITY IN SOME APPLE AND PLUM VARIETIES USING RAPD MARKERS

FRUIT GROWING RESEARCH ◽

10.33045/fgr.v37.2021.03 ◽

2021 ◽

Vol 37 (37) ◽

pp. 19-26

Author(s):

Adina Iancu ◽

◽

Mihai Chivu ◽

Keyword(s):

Genetic Diversity ◽

Genetic Distance ◽

Rapd Markers ◽

The Other ◽

Ex Situ ◽

Allelic Polymorphism ◽

High Genetic Diversity ◽

Ex Situ Collection ◽

Plum Varieties ◽

Degree Of Similarity

Molecular evaluation of germplasm is an important step in breeding programs, and the application of molecular biological techniques has led to important results in terms of both within- and between-species variability of traits. The RAPD technique has been successfully used to reveal allelic polymorphism as well as to measure genetic similarity. In this study, the genetic diversity of 25 genotypes and cultivars for apple species and 26 genotypes and cultivars for plum species was assessed with six RAPD markers. All these cultivars belong to the ex situ collection of apple and the ex situ collection of plum at the Research Institute for Fruit Growing Pitesti. The average number of amplified bands was 19.2 for apple and 17.66 for plum. Statistical analysis of intraspecific allelic polymorphism was expressed using the PIC (Polymorphic Information Content) index, which takes into account the allelic frequency. Two statistical indices were used to quantify genetic diversity: the Shannon index and the Simpson index. The degree of similarity between varieties was analyzed using the NTSYSpc version 2.1. Following RAPD analyses, the allele sizes of the analyzed varieties were within the range quoted in the literature, the genetic profiles of the studied varieties suggesting a medium to high genetic diversity, except for markers OPBC-04 and OPBB-05 for plum species, which expressed a high genetic diversity. Genetic distances calculated based on polymorphism of migrated bands in agarose gel confirmed the known genealogies of the apple and plum varieties studied. Thus, the smallest genetic distance for apple species was found between 'Jonagold' and 'Golden Delicious', 'Pionier' and 'Rustic', 'Jonathan' and 'Idared', 'Wagener Premiat' and 'Granny Smith', 'Remar' and 'Aura', 'Romus 3' and 'Rome Beauty', and the largest between Malus floribunda and the other genotypes studied. In plum, the smallest genetic distance was found between 'Dani' and 'Tita', 'Roman' and 'Tuleu gras', 'Dara' and 'Haganta', 'Romanța' and 'Stanley', 'Anna Spath' and 'Renclod Violet', and the largest between 'Lama', 'Black Diamond' and the other genotypes studied.

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Genetic diversity between and within populations of Handroanthus heptaphyllus (Vell.) Mattos using microsatellite markers

CERNE ◽

10.1590/s0104-77602012000100002 ◽

2012 ◽

Vol 18 (1) ◽

pp. 9-15 ◽

Cited By ~ 2

Author(s):

Neide Tomita Mori ◽

Mario Luiz Teixeira de Moraes ◽

Caroline Midori Morita ◽

Edson Seizo Mori

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Germplasm Collection ◽

Fixation Index ◽

Allelic Polymorphism ◽

Forest Fragments ◽

Germplasm Preservation ◽

The Family ◽

The Mean ◽

Two Populations

Handroanthus heptaphyllus (Vell.) Mattos, popularly known as ipê-roxo, is a species of the family Bignoneaceae much appreciated for its beauty, excellent quality wood which is used for making medicinal products and also in reforestation programs of degraded areas, as well as landscaping and restoration. The aim of this study was to investigate the genetic diversity between and within populations of H. heptaphyllus using microsatellite markers. The 192 seedlings were produced from seeds collected on 30 trees into the two populations of natural forest fragments in Botucatu region, São Paulo, Brazil. Eight microsatellite loci were analyzed, with allelic polymorphism varying from six alleles for locus TAU22 to 14 alleles for loci TAU12, TAU30, and TAU31, with an expected mean number of alleles per locus (Âe) of 4.9. The mean expected heterozygosity(Ĥe) for the two populations was 0.785, the mean observed heterozygosity(Ĥo) was 0.609, and the fixation index (^F) was low between populations, with a mean of 0.222. The gene differentiation between the two populations (Ĝst') was 0.100. We concluded that the higher genetic diversity is within populations; therefore, as far as germplasm collection programs in Botucatu region are concerned, it is recommended that a larger sampling of individuals should be considered within populations, thereby providing good genetic representativeness. The populations have enough genetic diversity to support genetic improvement and germplasm preservation programs.

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Diversity of West African dwarf goat in southwestern Nigeria based on allozyme Markers

Nigerian Journal of Animal Production ◽

10.51791/njap.v45i3.391 ◽

2020 ◽

Vol 45 (3) ◽

Author(s):

O.K. Awobajo ◽

O.H. Osaiyuwu ◽

A.E. Salako ◽

A.O. Odeniyi

Keyword(s):

Genetic Diversity ◽

Allele Frequency ◽

Gene Diversity ◽

Polymorphic Information Content ◽

West African ◽

Southwestern Nigeria ◽

Cellulose Acetate Electrophoresis ◽

West African Dwarf ◽

Goat Population ◽

West African Dwarf Goat

Effective conservation, rational management and inadequate information on genetic diversity are the major challenges in livestock production. Genetic diversity has been used to reveal the extent of differentiation within livestock species. However, information on the use of allozymes in genetic diversity of the West African Dwarf (WAD) goat is insufficient. Therefore, genetic diversity of the WAD goat populations in southwestern Nigeria was investigated in this study. Three protein loci markers were used. Blood (5 mL each) samples were randomly collected from20, 20, 40 and 60 goats from Ondo ,Oyo, Ogun andOsun States respectively. The samples were subjected to cellulose acetate electrophoresis to determine the genetic variants at Haemoglobin (Hb), Carbonic Anhydrase (CA) and Transferrin (Tf) loci. Another set of blood (5 mL) from 20 different individual animals were randomly obtained from each of Ondo, Oyo, Ogun, and Osun States. Allele frequency, observed heterozygosity (H ), Polymorphic Information Content (PIC), F-statistic (F F and F ), gene flow (Nm), gene diversity (D), number of alleles per loci (A ), effective number of allele (AE) Mean Number of Allele (MNA) were generated from the data obtained. Data were analysed using Hardy-Weinberg equilibrium (HWE) at α0.05. The allele frequency ranged between 0.11 (Hb ) and 0.58 (Hb ), 0.17 (CA ) and 0.44 (CA ) and 0.08 (Tf ) to 0.60 (Tf ). Deviation from HWE was not significant in all populations except at Tf locus (0.00). The H ranged from 0.43 to 0.62 andNm and D ranged between 3.68 and 32.40 and 0.34 to 0.50 respectively. TheMNAwas 0.67 butA ranged from 1.52 to 2.00. The allozymes revealed some level of genetic diversity and a genetic differentiation indicative of the amount of genetic differences among individualswithin theWestAfricanDwarf goat population.

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Morphometric and microsatellite-based comparative genetic diversity analysis in Bubalus bubalis from North India

PeerJ ◽

10.7717/peerj.11846 ◽

2021 ◽

Vol 9 ◽

pp. e11846

Author(s):

Vikas Vohra ◽

Narendra Pratap Singh ◽

Supriya Chhotaray ◽

Varinder Singh Raina ◽

Alka Chopra ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Molecular Diversity ◽

Bubalus Bubalis ◽

Breeding Strategy ◽

North India ◽

Genetic Admixture ◽

Advisory Group ◽

Effective Population ◽

Morphometric Variation

To understand the similarities and dissimilarities of a breed structure among different buffalo breeds of North India, it is essential to capture their morphometric variation, genetic diversity, and effective population size. In the present study, diversity among three important breeds, namely, Murrah, Nili-Ravi and Gojri were studied using a parallel approach of morphometric characterization and molecular diversity. Morphology was characterized using 13 biometric traits, and molecular diversity through a panel of 22 microsatellite DNA markers recommended by FAO, Advisory Group on Animal Genetic Diversity, for diversity studies in buffaloes. Canonical discriminate analysis of biometric traits revealed different clusters suggesting distinct genetic entities among the three studied populations. Analysis of molecular variance revealed 81.8% of genetic variance was found within breeds, while 18.2% of the genetic variation was found between breeds. Effective population sizes estimated based on linkage disequilibrium were 142, 75 and 556 in Gojri, Nili-Ravi and Murrah populations, respectively, indicated the presence of sufficient genetic variation and absence of intense selection among three breeds. The Bayesian approach of STRUCTURE analysis (at K = 3) assigned all populations into three clusters with a degree of genetic admixture in the Murrah and Nili-Ravi buffalo populations. Admixture analysis reveals introgression among Murrah and Nili-Ravi breeds while identified the Gojri as unique buffalo germplasm, indicating that there might be a common origin of Murrah and Nili-Ravi buffaloes. The study provides important insights on buffalo breeds of North India that could be utilized in designing an effective breeding strategy, with an appropriate choice of breeds for upgrading local non-descript buffaloes along with conservation of unique germplasm.

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Allelic diversity of MSP1 and MSP2 repeat loci correlate with levels of malaria endemicity in Senegal and Nigerian populations

Malaria Journal ◽

10.1186/s12936-020-03563-4 ◽

2021 ◽

Vol 20 (1) ◽

Author(s):

Mary A. Oboh ◽

Tolla Ndiaye ◽

Khadim Diongue ◽

Yaye D. Ndiaye ◽

Mouhamad Sy ◽

...

Keyword(s):

Genetic Diversity ◽

Allelic Diversity ◽

Surface Protein ◽

Merozoite Surface Protein ◽

Population Diversity ◽

Allelic Polymorphism ◽

Low Genetic Diversity ◽

Study Sites ◽

Infection Types ◽

Parasite Populations

Abstract Background Characterizing the genetic diversity of malaria parasite populations in different endemic settings (from low to high) could be helpful in determining the effectiveness of malaria interventions. This study compared Plasmodium falciparum parasite population diversity from two sites with low (pre-elimination) and high transmission in Senegal and Nigeria, respectively. Methods Parasite genomic DNA was extracted from 187 dried blood spot collected from confirmed uncomplicated P. falciparum malaria infected patients in Senegal (94) and Nigeria (93). Allelic polymorphism at merozoite surface protein 1 (msp1) and merozoite surface protein- 2 (msp2) genes were assessed by nested PCR. Results The most frequent msp1 and msp2 allelic families are the K1 and IC3D7 allelotypes in both Senegal and Nigeria. Multiplicity of infection (MOI) of greater that 1 and thus complex infections was common in both study sites in Senegal (Thies:1.51/2.53; Kedougou:2.2/2.0 for msp1/2) than in Nigeria (Gbagada: 1.39/1.96; Oredo: 1.35/1.75]). The heterozygosity of msp1 gene was higher in P. falciparum isolates from Senegal (Thies: 0.62; Kedougou: 0.53) than isolates from Nigeria (Gbagada: 0.55; Oredo: 0.50). In Senegal, K1 alleles was associated with heavy than with moderate parasite density. Meanwhile, equal proportions of K1 were observed in both heavy and moderate infection types in Nigeria. The IC3D7 subtype allele of the msp2 family was the most frequent in heavily parasitaemic individuals from both countries than in the moderately infected participants. Conclusion The unexpectedly low genetic diversity of infections high endemic Nigerian setting compared to the low endemic settings in Senegal is suggestive of possible epidemic outbreak in Nigeria.

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