Genetic Diversity and Molecular Characterization of Worldwide Prairie Grass (Bromus catharticus Vahl) Accessions Using SRAP Markers

Prairie grass (Bromus catharticus Vahl) is an important grass species that could be used in the production systems of certified seed and high-quality forage for grazing ruminants. In the present research, a sequence-related amplified polymorphism (SRAP) marker was employed to detect the genetic variability and structure of 80 prairie grass accessions from all over the world. Altogether, 460 reliable bands were amplified from 47 SRAP primer pairs with 345 (75%) polymorphic bands. The average values of discrimination power (DP) and polymorphic information content (PIC) were 0.753 and 0.317, respectively. Both the UPGMA clustering and PCoA analyses grouped the 80 accessions into five clusters, whereas the STRUCTURE analysis showed that 80 prairie grass accessions possessed three genetic memberships (K = 3). The results of the Mantel test showed that the distance matrix has a moderately positive correlation between the morphological and molecular data sets (r = 0.524). A poor genetic differentiation (Fst = 0.045) was discovered among the six geo-groups of accessions. Besides, the highest intragroup genetic diversity was found in the North America group (He = 0.335). This study provides a genetic structure and diversity case for prairie grass, and supplies new clues for the study and utilization of prairie grass.

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Assessing the Genetic Diversity and Population Structure of a Tunisian Melon (Cucumis melo L.) Collection Using Phenotypic Traits and SSR Molecular Markers

Agronomy ◽

10.3390/agronomy11061121 ◽

2021 ◽

Vol 11 (6) ◽

pp. 1121

Author(s):

Hela Chikh-Rouhou ◽

Najla Mezghani ◽

Sameh Mnasri ◽

Neila Mezghani ◽

Ana Garcés-Claver

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Phenotypic Diversity ◽

Diversity Index ◽

Polymorphic Information Content ◽

Crop Improvement ◽

Molecular Data ◽

Mantel Test ◽

Phenotypic Traits ◽

Genetic Diversity And Structure

The assessment of genetic diversity and structure of a gene pool is a prerequisite for efficient organization, conservation, and utilization for crop improvement. This study evaluated the genetic diversity and population structure of 24 Tunisian melon accessions, by using 24 phenotypic traits and eight microsatellite (SSR) markers. A considerable phenotypic diversity among accessions was observed for many characters including those related to agronomical performance. All the microsatellites were polymorphic and detected 30 distinct alleles with a moderate (0.43) polymorphic information content. Shannon’s diversity index (0.82) showed a high degree of polymorphism between melon genotypes. The observed heterozygosity (0.10) was less than the expected heterozygosity (0.12), displaying a deficit in heterozygosity because of selection pressure. Molecular clustering and structure analyses based on SSRs separated melon accessions into fivegroups and showed an intermixed genetic structure between landraces and breeding lines belonging to the different botanical groups. Phenotypic clustering separated the accessions into two main clusters belonging to sweet and non-sweet melon; however, a more precise clustering among inodorus, cantalupensis, and reticulatus subgroups was obtained using combined phenotypic–molecular data. The discordance between phenotypic and molecular data was confirmed by a negative correlation (r = −0.16, p = 0.06) as revealed by the Mantel test. Despite these differences, both markers provided important information about the diversity of the melon germplasm, allowing the correct use of these accessions in future breeding programs. Together they provide a powerful tool for future agricultural and conservation tasks.

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Morphologic and molecular assessments of cucumber (Cucumis sativus L.) landraces

Notulae Botanicae Horti Agrobotanici Cluj-Napoca ◽

10.15835/nbha48211932 ◽

2020 ◽

Vol 48 (2) ◽

pp. 604-614

Author(s):

Esra CEBECI ◽

Volkan GOZEN ◽

Levent KESKIN ◽

Aytul YILDIRIM

Keyword(s):

Genetic Diversity ◽

Cucumis Sativus ◽

Polymorphic Marker ◽

Morphological Data ◽

Group Method ◽

Srap Marker ◽

Discrimination Power ◽

Cucumis Sativus L ◽

Pair Group ◽

Morphologic Data

In this study, 90 locally grown cucumber (Cucumis sativus L.) landraces were collected and morphologically characterized using 20 descriptors derived from UPOV (International Union for the Protection of New Varieties of Plants). Genetic diversity and relationships of the genotypes were revealed using 20 sequence-related amplified polymorphism (SRAP) marker combinations. The discrimination power of each polymorphic marker (estimated by the polymorphism information content) ranged from 0.15 to 0.99 with an average of 0.73. Dice's similarity coefficient ranged between 0.00-1.00. The cluster analysis that was conducted using the unweighted pair group method of arithmetic averages (UPGMA) for both molecular and morphologic data showed that all of the genotypes fell into two main groups and many subdivisions. According to morphological data, fruit length, diameter and weight of the genotypes were determined between 6.5 - 32.5 cm, 25 - 52 mm and, 28 - 625 g respectively. It is clear from the results, a moderate level of genetic diversity, which has the potential for broadening the genetic base, was observed among the Turkish cucumber landraces.

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Species relationship and genetic diversity in some Iranian Lamium L. species using ISSR markers

Biodiversitas Journal of Biological Diversity ◽

10.13057/biodiv/d200724 ◽

2019 ◽

Vol 20 (7) ◽

Author(s):

FATEMEH AZIMISHAD ◽

MASOUD SHEIDAI ◽

SAYED MEHDI TALEBI ◽

ZAHRA NOORMOHAMMADI

Keyword(s):

Genetic Diversity ◽

High Efficiency ◽

Isolation By Distance ◽

Leaf Shape ◽

Morphological Characteristics ◽

Molecular Data ◽

Issr Markers ◽

Mantel Test ◽

Species Relationships ◽

Species Relationship

Abstract. Azimishad F, Sheidai M, Talebi SM, Noormohammadi Z. 2019. Species relationship and genetic diversity in some Iranian Lamium L. species using ISSR markers. Biodiversitas 20: 1963-1972. Lamium is a widespread and taxonomically complex genus of Lamiaceae which comprises of 16-38 species. This genus is represented in Iran by nine species. In the present study, we used morphological and molecular (ISSR, Cp DNA, and nrITS) data to evaluate species relationships, genetic diversity and population genetic structure of the genus. 27 morphological characteristics, including 13 qualitative and 14 quantitative, and ten ISSR markers were used for morphological and genetical evaluation of 73 accessions from eight taxa. In general, species relationships obtained from morphological and molecular data were largely congruent. In the morphological study, characteristics like the life form, leaf shape, absence/existence of bracts and shape of corolla, were distinctive traits and we did not encounter intermediate forms. Our findings indicated a very high efficiency of the ISSR markers in the identification and delimitation of Lamium species. These results confirmed the placement of L. galeobdolon in the genus Lamium and segregation of L. purpureum and L. garganicum in section Lamium. AMOVA analysis revealed that the species of this genus are genetically differentiated. Nm analysis showed very low value of gene flow among the studied species and mantel test indicated isolation by distance occurred among them.

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Morphological Characterization and Genetic Diversity Analysis of a Tunisian Durum Wheat (Triticum Turgidum Var. Durum) Collection

10.21203/rs.3.rs-51248/v1 ◽

2020 ◽

Author(s):

Maroua Ouaja ◽

Bochra Amina Bahri ◽

Lamia Aouini ◽

Sahbi Ferjaoui ◽

Maher Medini ◽

...

Keyword(s):

Genetic Diversity ◽

Durum Wheat ◽

Gene Diversity ◽

Polymorphic Information Content ◽

Morphological Characterization ◽

Genetic Variations ◽

Mantel Test ◽

Ex Situ ◽

The South ◽

Population Structure Analysis

Abstract Background: Tunisia is a center of genetic diversity of durum wheat and has a large number of abandoned old local landraces. An accurate investigation and characterization of the morphological and genetic features of these landraces would allow their rehabilitation and use for practical and beneficial purposes. In this context, a collection of 304 local accessions of durum wheat, collected from five regions and three climatic zones of central and southern Tunisia, was studied. Results: Morphological characterization was carried out using 12 spike-related traits and rendered a mean Shannon-Weaver Index (H') of 0.80 indicating the presence of a high level of polymorphism among accessions. Based on these traits 11 local landraces, namely Mahmoudi, Azizi, Jneh Khotifa, Mekki, Biskri, Taganrog, Biada, Badri, Richi, Roussia and Souri were identified. Spike length (H’=0.98) and shape (H’=0.86) with grains size (H’=0.94), form (H’=0.87) and color (H’=0.86) were the most polymorphic morphological traits. The genetic diversity was assessed using 10 SSR markers, with a polymorphic information content (PIC) of 0.69. Levels of genetic diversity were generally high, with a Shannon's Information Index (I) of 0.62 and a gene diversity (He) of 0.35. In addition, population structure analysis distinguished 11 genetic groups resulted from STRUCTURE and Mantel test showed a significant correlation between genetic and morphological distances. Analysis of molecular variance (AMOVA) showed high genetic variations within regions (81%) and wheat subpopulations (41%) showing a considerable amount of admixture between landraces realized by farmers; as well as a moderate (19%) and high (59%) genetic variations among regions and wheat subpopulations, indicating practices of selection pressure conducted by farmers. The Mahmoudi landrace showed spike densities significantly different between the center to the south of Tunisia; notably loose spikes with open glumes in the south and compact ones in the center, which may represent an adaptation form for tolerance to high temperature. Conclusion: Overall, this study highlights the genetic richness of local resources for better in situ or ex situ conservation and for their subsequent use in plant breeding programs.

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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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Magnitude of the genetic base of commercial popcorn and in recommendation in Brazil

Cropp Breeding and Applied Biotechnology ◽

10.1590/s1984-70332010000400002 ◽

2010 ◽

Vol 10 (4) ◽

pp. 289-297 ◽

Cited By ~ 7

Author(s):

Thiago Otávio Mendes de Paula ◽

Leandro Simões Azeredo Gonçalves ◽

Antonio Teixeira do Amaral Júnior ◽

Érica Cristina de Oliveira ◽

Vanessa Quitete Ribeiro da Silva ◽

...

Keyword(s):

Genetic Diversity ◽

Agronomic Traits ◽

Group Formation ◽

Distance Matrix ◽

Molecular Data ◽

Issr Markers ◽

Private Institutions ◽

Final Test ◽

Breeding Programs ◽

Public And Private

The purpose of this study was to quantify the genetic diversity among popcorn genotypes on the market and in the final test phase, suitable for three environments in Brazil, based on 11 agronomic traits and ISSR markers. In the environment Campos dos Goytacazes a more reliable group formation was observed than in the other environments. The molecular data indicated the presence of cultivars recommended in the same group, as in the case of UFVM2 Barão de Viçosa, IAC 125, Zélia and Jade. This result is an appeal to the few popcorn breeders in Brazil to pay particular attention to increase the genetic diversity among breeding programs conducted by public and private institutions in the country. There was virtually no correlation between the distance matrix obtained by the ISSR marker and the matrices obtained by the agronomic data.

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Implementation of a limited set of SSR markers for screening of genetic variability in Latvian and Swedish sour cherry (Prunus cerasus L.) genetic resources collections

Proceedings of the Latvian Academy of Sciences Section B Natural Exact and Applied Sciences ◽

10.2478/v10046-011-0014-4 ◽

2011 ◽

Vol 65 (1-2) ◽

pp. 21-28

Author(s):

Gunārs Lācis ◽

Isaak Rashal ◽

Viktor Trajkovski

Keyword(s):

Genetic Diversity ◽

Genetic Variability ◽

Genetic Resources ◽

Ssr Markers ◽

Genetic Similarity ◽

Polymorphic Information Content ◽

Sour Cherry ◽

Prunus Cerasus ◽

Discrimination Power ◽

Ssr Loci

Implementation of a limited set of SSR markers for screening of genetic variability in Latvian and Swedish sour cherry (Prunus cerasusL.) genetic resources collectionsForty-one sour cherry (Prunus cerasusL.) accessions were evaluated using three SSR markers to characterise genetic diversity in the sour cherry genetic resource collections at the Latvia State Institute of Fruit-Growing (LIFG), Dobele, Latvia and the Division of Horticultural Genetics and Plant Breeding at Balsgård, Department of Crop Sciences, Swedish University of Agricultural Sciences (SLU-Balsgård), Sweden, and to test the usability and reliability of a small set of SSR markers for preliminary characterisation of sour cherry germplasm collections. The SSR loci were highly polymorphic with 7-14 alleles per locus. Heterozygosity and Polymorphic Information Content values ranged from 0.750 to 1.000 and 0.748-0.899, respectively, while discrimination power per locus varied from 0.716 to 0.965. Five to thirty genotypes were found in the sour cherry collections for the three tested SSR loci. The combined discrimination power of all loci was effectively 0.994 and 0.999 for the LIFG and SLU-Balsgård collections, respectively. The SSRs used were able to uniquely identify all accessions in the analysed genetic resources collections. The genotype data allowed estimation of genetic diversity and genetic characterisation of accessions in the collections. Genetic similarity analysis showed higher genetic similarity among the Baltic and Scandinavian sour cherry varieties, than between Baltic and Eastern European varieties.

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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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Assessment of genetic structure and diversity of Erodium (Geranaiceae) species

Genetika ◽

10.2298/gensr2102507l ◽

2021 ◽

Vol 53 (2) ◽

pp. 507-520

Author(s):

Lejing Lin ◽

Li Lin ◽

Abdul Waheed

Keyword(s):

Genetic Diversity ◽

Isolation By Distance ◽

Pcr Amplification ◽

Molecular Data ◽

Mantel Test ◽

Test Results ◽

Species Characteristics ◽

Polymerase Chain ◽

Morphological And Molecular Data ◽

Genetic Structure And Diversity

Erodium Aiton (Geraniaceae) with 75 species is distributed in all continents except Antarctic. Its main diversification center is Mediterranean region with 62 species. The genetic diversity was assessed through Sequence-related amplified polymorphism. To uncover genetic diversity and species characteristics in Erodium species, were studied through a combination of morphological and molecular data. 70 individuals related to seven Erodium were collected in 7 provinces. A total of 96 (Number of total loci) (NTL) DNA bands were produced through polymerase chain reaction amplifications (PCR) amplification of seven Erodium species. These bands were produced with the combinations of six selective primers. The total number of amplified fragments ranged from 10 to 25. The genetic similarities between seven species are estimated from 0.70 to 0.85. Clustering results showed two major clusters. This study also detected a significant signature of isolation by distance (Mantel test results). Present results showed that sequence-related amplified polymorphism have the potential to identify and decipher genetic affinity in Erodium species. Current results have implications in biodiversity and conservation programs. Besides this, present results could pave the way for selecting suitable ecotypes for forage and pasture purposes in Iran.

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Genetic diversity of natural populations of Taxus wallichiana var. mairei

10.21203/rs.3.rs-392442/v1 ◽

2021 ◽

Author(s):

Qianqian Luo ◽

Fengqing Li ◽

Longhua Yu ◽

Liyun Wang ◽

Gangbiao Xu ◽

...

Keyword(s):

Genetic Diversity ◽

Diversity Index ◽

Polymorphic Information Content ◽

Natural Populations ◽

Mantel Test ◽

Jiangxi Province ◽

Timber Species ◽

Endangered Tree ◽

Endangered Tree Species ◽

Taxus Wallichiana

Abstract Maire yew (Taxus wallichiana var. mairei (Lemée H. Léveillé.) L. K. Fu et Nan Li) is a rare and endangered tree species, and it is also a precious timber species in China. We used 13 microsatellites to assess the genetic diversity and differentiation of 665 Maire yew samples from 18 natural populations. A total of 291 alleles were detected. The average number of alleles (Na=22.39), expected heterozygosity (He=0.74), polymorphic information content (PIC = 0.86) and Shannon diversity index (I = 1.66) of the loci indicated a high level of genetic diversity in natural Maire yew populations. Moreover, gene flow was more active among populations (Nm=1.62) than within populations. Among the 18 populations, the Xinfeng population in Jiangxi Province has the highest genetic diversity. Although each of the studied populations should be protected from further deforestation and agricultural expansion, the Xinfeng population deserves the highest conservation priority. The results based on analysis of molecular variance showed that genetic variation occurred mainly within populations (84.90%; P < 0.001), which indicated that the degree of genetic differentiation of the natural populations of Maire yew was low. Based on UPGMA, the 18 populations were categorized into 4 groups. A Mantel test showed that there was no significant correlation between standard genetic distance and geographical distance or altitude differences among the populations. The genetic clustering results also indicated that the genetic relationship followed a north to south clustered trend. The information presented here forms the basis for the development of genetic guidelines for appropriate conservation programs.

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