Geographical description and molecular characterization of genetic structure and diversity using a 6K SNP array in Turkish oat germplasm

Cultivated oat (Avena sativa L. and Avena byzantina Koch) is native to Turkey, a secondary center of oat diversity. Oat breeding has received less attention relative to other cereals. In this work, the diversity of oat landraces collected from different regions of Turkey as well as obtained from different gene banks was investigated using 3293 high quality SNP markers. Expected heterozygosity (Hs), observed heterozygosity (Ho), inbreeding coefficient (Fis), and overall genetic diversity (Ht) of the oat gene pool were 0.22, 0.01, 0.96, and 0.38, respectively. The value of the genetic differentiation (Fst) metric for genetic structure was 0.41 and indicated that kinship was more of a determinant for population structure than the geographical provenance. The populations from different geographical regions shared a great proportion of genetic diversity. Clustering using model-based STRUCTURE, principal coordinates (PCoA), and neighbour-joining (NJ) algorithms were mostly comparable except for five discrepantly clustered accessions in NJ and PCoA relative to STRUCTURE, which can be attributed to the relatively reduced resolution power in the NJ and PCoA approaches. SNP markers partitioned all oat accessions into four main groups (A, B, C, and D) with 10 unclassified accessions. Some landraces were identical based on genetic distance and can represent duplications in gene banks. The data presented in this work represent the initial results on genetic diversity as investigated in Turkish oat, and are an important resource for systematicians, geneticists, and breeders interested in Turkish oat germplasm. These results are expected to open new opportunities for further studies in oat genomics and cultivar development.

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Analysis of the Genetic Structure and Diversity of Upland Cotton Groups in Different Planting Areas Based on SNP Markers

10.1101/2021.06.11.448075 ◽

2021 ◽

Author(s):

Zeliang Zhang ◽

Junduo Wang ◽

Zhaolong Gong ◽

Yajun Liang ◽

Xiantao Ai ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Gossypium Hirsutum ◽

Diversity Index ◽

Principal Component ◽

Snp Markers ◽

High Genetic Diversity ◽

Origin And Evolution ◽

Population Structure Analysis ◽

Genetic Structure And Diversity

Genetic diversity, kinship and population genetic structure analyses of Gossypium hirsutum germplasm can provide a better understanding of the origin and evolution of G. hirsutum biodiversity. In this study, 1313331 SNP molecular markers were used to construct a phylogenetic tree of each sample using MEGAX, to perform population structure analysis by ADMIXTURE software and principal component analysis (PCA) by EIGENSOFT software, and to estimate relatedness using SPAGeDi. ADMIXTURE software divided the experimental cotton population into 16 subgroups, and the Gossypium hirsutum samples could be roughly clustered according to source place, but there were some overlapping characteristics among samples. The experimental cotton population was divided into six groups according to source to calculate the genetic diversity index (H), and the obtained value (0.306) was close to that for germplasm collected by others in China. Cluster 4 had a relatively high genetic diversity level (0.390). The degrees of genetic differentiation within the experimental cotton population groups were low (the population differentiation indexes ranged from 0.02368 to 0.10664). The genetic distance among cotton accessions varied from 0.000332651 to 0.562664014, with an average of 0.25240429. The results of this study may provide a basis for mining elite alleles and using them for subsequent association analysis.

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Genotyping of Two Mediterranean Trout Populations in Central-Southern Italy for Conservation Purposes Using a Rainbow-Trout-Derived SNP Array

Animals ◽

10.3390/ani11061803 ◽

2021 ◽

Vol 11 (6) ◽

pp. 1803

Author(s):

Valentino Palombo ◽

Elena De Zio ◽

Giovanna Salvatore ◽

Stefano Esposito ◽

Nicolaia Iaffaldano ◽

...

Keyword(s):

Rainbow Trout ◽

Genetic Structure ◽

Fishery Management ◽

Snp Array ◽

Fine Scale ◽

Principal Coordinates Analysis ◽

Data Set ◽

Management Actions ◽

Principal Coordinates ◽

Mediterranean Trout

Mediterranean trout is a freshwater fish of particular interest with economic significance for fishery management, aquaculture and conservation biology. Unfortunately, native trout populations’ abundance is significantly threatened by anthropogenic disturbance. The introduction of commercial hatchery strains for recreation activities has compromised the genetic integrity status of native populations. This work assessed the fine-scale genetic structure of Mediterranean trout in the two main rivers of Molise region (Italy) to support conservation actions. In total, 288 specimens were caught in 28 different sites (14 per basins) and genotyped using the Affymetrix 57 K rainbow-trout-derived SNP array. Population differentiation was analyzed using pairwise weighted FST and overall F-statistic estimated by locus-by-locus analysis of molecular variance. Furthermore, an SNP data set was processed through principal coordinates analysis, discriminant analysis of principal components and admixture Bayesian clustering analysis. Firstly, our results demonstrated that rainbow trout SNP array can be successfully used for Mediterranean trout genotyping. In fact, despite an overwhelming number of loci that resulted as monomorphic in our populations, it must be emphasized that the resulted number of polymorphic loci (i.e., ~900 SNPs) has been sufficient to reveal a fine-scale genetic structure in the investigated populations, which is useful in supporting conservation and management actions. In particular, our findings allowed us to select candidate sites for the collection of adults, needed for the production of genetically pure juvenile trout, and sites to carry out the eradication of alien trout and successive re-introduction of native trout.

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Revelation of genetic diversity and structure of wild Elymus excelsus (Poaceae: Triticeae) collection from western China by SSR markers

PeerJ ◽

10.7717/peerj.8038 ◽

2019 ◽

Vol 7 ◽

pp. e8038

Author(s):

Yanli Xiong ◽

Wenhui Liu ◽

Yi Xiong ◽

Qingqing Yu ◽

Xiao Ma ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Western China ◽

Tibet Plateau ◽

Group Method ◽

Breeding Strategies ◽

Population Genetic Differentiation ◽

Principal Coordinates ◽

Geographical Regions ◽

Genetic Diversity And Structure

Hosting unique and important plant germplasms, the Qinghai-Tibet Plateau (QTP), as the third pole of the world, and Xinjiang, located in the centre of the Eurasian continent, are major distribution areas of perennial Triticeae grasses, especially the widespread Elymus species. Elymus excelsus Turcz. ex Griseb, a perennial forage grass with strong tolerance to environmental stresses, such as drought, cold and soil impoverishment, can be appropriately used for grassland establishment due to its high seed production. To provide basic information for collection, breeding strategies and utilization of E. excelsus germplasm, microsatellite markers (SSR) were employed in the present study to determine the genetic variation and population structure of 25 wild accessions of E. excelsus from Xinjiang (XJC) and the QTP, including Sichuan (SCC) and Gansu (GSC) of western China. Based on the 159 polymorphic bands amplified by 35 primer pairs developed from three related species, the average values of the polymorphic information content (PIC), marker index (MI), resolving power (Rp), Nei’s genetic diversity (H) and Shannon’s diversity index (I) of each pair of primers were 0.289, 1.348, 1.897, 0.301 and 0.459, respectively, validating that these SSR markers can also be used for the evaluation of genetic diversity of E. excelsus germplasms, and demonstrating the superior versatility of EST-SSR vs. G-SSR. We found a relatively moderate differentiation (Fst = 0.151) among the XJC, SCC and GSC geo-groups, and it is worth noting that, the intra-group genetic diversity of the SCC group (He = 0.197) was greater than that of the GSC (He = 0.176) and XJC (He = 0.148) groups. Both the Unweighted Pair Group Method with Arithmetic (UPGMA) clustering and principal coordinates analysis (PCoA) divided the 25 accessions into three groups, whereas the Bayesian STRUCTURE analysis suggested that E. excelsus accessions fell into four main clusters. Besides, this study suggested that geographical distance and environmental variables (annual mean precipitation and average precipitation in growing seasons), especially for QTP accessions, should be combined to explain the population genetic differentiation among the divergent geographical regions. These data provided comprehensive information about these valuable E. excelsus germplasm resources for the protection and collection of germplasms and for breeding strategies in areas of Xinjiang and QTP in western China.

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Spectrum of genetic diversity and networks of clonal organisms

Journal of The Royal Society Interface ◽

10.1098/rsif.2007.0230 ◽

2007 ◽

Vol 4 (17) ◽

pp. 1093-1102 ◽

Cited By ~ 56

Author(s):

Alejandro F Rozenfeld ◽

Sophie Arnaud-Haond ◽

Emilio Hernández-García ◽

Víctor M Eguíluz ◽

Manuel A Matías ◽

...

Keyword(s):

Genetic Diversity ◽

Population Genetics ◽

Genetic Structure ◽

Small World ◽

Clonal Plants ◽

Posidonia Oceanica ◽

Genetic Distances ◽

Wide Range ◽

Clonal Organisms ◽

Genetic Structure And Diversity

Clonal reproduction characterizes a wide range of species including clonal plants in terrestrial and aquatic ecosystems, and clonal microbes such as bacteria and parasitic protozoa, with a key role in human health and ecosystem processes. Clonal organisms present a particular challenge in population genetics because, in addition to the possible existence of replicates of the same genotype in a given sample, some of the hypotheses and concepts underlying classical population genetics models are irreconcilable with clonality. The genetic structure and diversity of clonal populations were examined using a combination of new tools to analyse microsatellite data in the marine angiosperm Posidonia oceanica . These tools were based on examination of the frequency distribution of the genetic distance among ramets, termed the spectrum of genetic diversity (GDS), and of networks built on the basis of pairwise genetic distances among genets. Clonal growth and outcrossing are apparently dominant processes, whereas selfing and somatic mutations appear to be marginal, and the contribution of immigration seems to play a small role in adding genetic diversity to populations. The properties and topology of networks based on genetic distances showed a ‘small-world’ topology, characterized by a high degree of connectivity among nodes, and a substantial amount of substructure, revealing organization in subfamilies of closely related individuals. The combination of GDS and network tools proposed here helped in dissecting the influence of various evolutionary processes in shaping the intra-population genetic structure of the clonal organism investigated; these therefore represent promising analytical tools in population genetics.

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Genetic structure and diversity of the endangered growling grass frog in a rapidly urbanizing region

Royal Society Open Science ◽

10.1098/rsos.140255 ◽

2015 ◽

Vol 2 (8) ◽

pp. 140255 ◽

Cited By ~ 7

Author(s):

Claire C. Keely ◽

Joshua M. Hale ◽

Geoffrey W. Heard ◽

Kirsten M. Parris ◽

Joanna Sumner ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Dna Sequences ◽

Nuclear Dna ◽

Urban Expansion ◽

Nuclear Gene ◽

Management Approach ◽

Natural Habitats ◽

High Genetic Diversity ◽

Genetic Structure And Diversity

Two pervasive and fundamental impacts of urbanization are the loss and fragmentation of natural habitats. From a genetic perspective, these impacts manifest as reduced genetic diversity and ultimately reduced genetic viability. The growling grass frog ( Litoria raniformis ) is listed as vulnerable to extinction in Australia, and endangered in the state of Victoria. Remaining populations of this species in and around the city of Melbourne are threatened by habitat loss, degradation and fragmentation due to urban expansion. We used mitochondrial DNA (mtDNA) and microsatellites to study the genetic structure and diversity of L. raniformis across Melbourne's urban fringe, and also screened four nuclear gene regions (POMC, RAG-1, Rhod and CRYBA1). The mtDNA and nuclear DNA sequences revealed low levels of genetic diversity throughout remnant populations of L. raniformis . However, one of the four regions studied, Cardinia, exhibited relatively high genetic diversity and several unique haplotypes, suggesting this region should be recognized as a separate Management Unit. We discuss the implications of these results for the conservation of L. raniformis in urbanizing landscapes, particularly the potential risks and benefits of translocation, which remains a contentious management approach for this species.

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Genetic structure and diversity of a collection of Brassica rapa subsp. rapa L. revealed by simple sequence repeat markers

The Journal of Agricultural Science ◽

10.1017/s002185961100013x ◽

2011 ◽

Vol 149 (5) ◽

pp. 617-624 ◽

Cited By ~ 9

Author(s):

P. SOENGAS ◽

M. E. CARTEA ◽

M. FRANCISCO ◽

M. LEMA ◽

P. VELASCO

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Brassica Rapa ◽

Genetic Relationships ◽

Population Level ◽

Research Centre ◽

Breeding Programmes ◽

Western Spain ◽

Genetic Structure And Diversity ◽

Simple Sequence

SUMMARYBrassica rapa subsp. rapa L. includes three different crops: turnips (roots), turnip greens (leaves) and turnip tops (inflorescences). A collection of B. rapa subsp. rapa from north-western Spain is currently kept at ‘Misión Biológica de Galicia’ (a research centre of the Consejo Superior de Investigaciones Científicas (CSIC), Spain). This collection has been characterized based on morphological and agronomical traits. A better understanding of the genetic diversity present in the collection is necessary in order to optimize its use and maintenance. The objectives of the present work were to assess the genetic diversity present in the B. rapa subsp. rapa collection, to establish genetic relationships among populations and to study the genetic structure of the collection. Eighty populations were analysed based on 18 simple sequence repeats (SSRs). Populations showed a broad range of genetic diversity, thus offering good potential for further genetic improvement. Most of the variability was found within the population level, probably due to high rates of allogamy, to migration and/or interchange of seed among local growers. Populations showed a low level of differentiation, grouping in just one cluster, and therefore they can be considered as samples of a highly variable metapopulation that can be used for B. rapa breeding programmes.

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Assessment of Genetic Diversity and Population Structure of Tunisian Barley Accessions (Hordeum vulgare L.) Using SSR Markers

Acta Agrobotanica ◽

10.5586/aa.7343 ◽

2020 ◽

Vol 73 (4) ◽

Author(s):

Salem Marzougui ◽

Mohamed Kharrat ◽

Mongi Ben Younes

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Polymorphic Information Content ◽

Hordeum Vulgare L ◽

Software Analysis ◽

Average Value ◽

Allele Number ◽

Cultivar Development ◽

Principal Coordinates ◽

Ssr Loci

In barley breeding programs, information about genetic dissimilarity and population structure is very important for genetic diversity conservation and new cultivar development. This study aimed to evaluate the genetic variation in Tunisian barley accessions (Hordeum vulgare L.) based on simple sequence repeat (SSR). A total of 89 alleles were detected at 26 SSR loci. The allele number per locus ranged from two to five, with an average of 3.4 alleles per locus detected from 32 barley accessions, and the average value of polymorphic information content was 0.45. A cluster analysis based on genetic similarity was performed, and the 32 barley resources were classified into five groups. Principal coordinates (PCoA) explained 12.5% and 9.3% of the total variation, and the PCoA was largely consistent with the results of cluster separation of STRUCTURE software analysis. The analysis of genetic diversity in barley collection will facilitate cultivar development and effective use of genetic resources.

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Genetic structure and diversity among individuals of Copaifera langsdorffii Desf. from Mato Grosso, Brazilian Amazon, using ISSR markers

Research Society and Development ◽

10.33448/rsd-v10i16.23025 ◽

2021 ◽

Vol 10 (16) ◽

pp. e187101623025

Author(s):

Daniele Paula Maltezo ◽

Julliane Dutra Medeiros ◽

Ana Aparecida Bandini Rossi

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Genetic Variability ◽

Polymorphic Information Content ◽

Issr Markers ◽

Group Method ◽

Mato Grosso ◽

Copaifera Langsdorffii ◽

Genetic Structure And Diversity ◽

Issr Primers

The Amazon is the largest tropical forest in the world and is home to around 20% of all the biodiversity on the planet, among the species present in the Amazon is Copaifera langsdorffii, exploited mainly for the extraction of oil-resin and wood, often in ways incorrect, which can cause the loss of genetic variability. The aim of this study was to evaluate the genetic structure and diversity among individuals of C. langsdorffii located in Mato Grosso, Brazil, using ISSR markers. We sampled leaves from 27 adult individuals of C. langsdorffii, whose total genomic DNA was extracted. A total of 12 ISSR primers were used for the molecular characterization of the individuals. A grouping analysis was performed using the unweighted pair group method, Bayesian analysis and characterized by the genetic diversity. The genetic diversity among and within the groups was demonstrated by the AMOVA. As a result, 106 fragments were amplified and 98.11% were polymorphic. The polymorphic information content of each primer ranged from 0.45 to 0.81. The dendrogram showed the formation of 4 distinct groups. The greatest genetic variability is found within the groups and not between them. The percentage of polymorphism, genetic dissimilarity values and genetic diversity indexes indicate that there is high genetic variability among Copaifera langsdorffii individuals, suggesting that ISSR primers were efficient in detecting polymorphism in this species and that the individuals have potential for compose programs aimed at the preservation of the species and the ability to integrate germplasm banks.

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Genetic diversity and population structure analysis of bambara groundnut (Vigna subterrenea L) landraces using DArT SNP markers

PLoS ONE ◽

10.1371/journal.pone.0253600 ◽

2021 ◽

Vol 16 (7) ◽

pp. e0253600

Author(s):

Charles U. Uba ◽

Happiness O. Oselebe ◽

Abush A. Tesfaye ◽

Wosene G. Abtew

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

West Africa ◽

East Africa ◽

Unknown Origin ◽

Snp Markers ◽

Bambara Groundnut ◽

Conservation Strategy ◽

Population Structure Analysis ◽

Geographical Regions

Understanding the genetic structure and diversity of crops facilitates progress in plant breeding. A collection of 270 bambara groundnut (Vigna subterrenea L) landraces sourced from different geographical regions (Nigeria/Cameroon, West, Central, Southern and East Africa) and unknown origin (sourced from United Kingdom) was used to assess genetic diversity, relationship and population structure using DArT SNP markers. The major allele frequency ranged from 0.57 for unknown origin to 0.91 for West Africa region. The total gene diversity (0.482) and Shannon diversity index (0.787) was higher in West African accessions. The genetic distance between pairs of regions varied from 0.002 to 0.028 with higher similarity between Nigeria/Cameroon-West Africa accessions and East-Southern Africa accessions. The analysis of molecular variance (AMOVA) revealed 89% of genetic variation within population, 8% among regions and 3% among population. The genetic relatedness among the collections was evaluated using neighbor joining tree analysis, which grouped all the geographic regions into three major clusters. Three major subgroups of bambara groundnut were identified using the ADMIXTURE model program and confirmed by discriminant analysis of principal components (DAPC). These subgroups were West Africa, Nigeria/Cameroon and unknown origin that gave rise to sub-population one, and Central Africa was sub-population two, while Southern and East Africa were sub-population three. In general, the results of all the different analytical methods used in this study confirmed the existence of high level of diversity among the germplasm used in this study that might be utilized for future genetic improvement of bambara groundnut. The finding also provides new insight on the population structure of African bambara groundnut germplasm which will help in conservation strategy and management of the crop.

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Assessing the genetic diversity of cowpea [Vigna unguiculata (L.) Walp.] germplasm collections using phenotypic traits and SNP markers

BMC Genetics ◽

10.1186/s12863-020-00914-7 ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Nelia Nkhoma ◽

Hussein Shimelis ◽

Mark D. Laing ◽

Admire Shayanowako ◽

Isack Mathew

Keyword(s):

Genetic Diversity ◽

Grain Yield ◽

Vigna Unguiculata ◽

Polymorphic Information Content ◽

Snp Markers ◽

Phenotypic Traits ◽

Environment Interaction ◽

Lattice Design ◽

Cultivar Development ◽

Parental Lines

Abstract Background Productivity of cowpea [Vigna unguiculata (L.) Walp] in sub-Sahara Africa is curtailed by a lack of farmer-preferred and improved cultivars and modern production technologies. The objectives of the study were to determine the extent of genetic diversity present among a collection of cowpea accessions from Zambia and Malawi using phenotypic traits and single nucleotide polymorphism (SNP) markers and, to select distinct and complementary parental lines for cultivar development. One hundred cowpea genotypes were evaluated for agronomic traits in two selected sites in Zambia, using a 10 × 10 alpha lattice design with two replications. Ninety-four of the test genotypes were profiled with 14,116 SNP markers. Results Number of pods plant− 1 (NPP), pod length (PDL), and number of seeds pod− 1 (NSP), were significantly (p < 0.05) affected by genotype × environment interaction effects. Genotypes such as CP411, CP421, CP645, CP732, Chimponongo, and MS1–8–1-4 exhibited higher grain yield of > 1200 kg/ha with excellent performance in yield components such as NSP, PDL, HSW and GYD. Grain yield had significant (p < 0.05) associations with NPP (r = 0.50), NSP (r = 0.46) and PDL (r = 0.42) useful for simultaneous selection for yield improvement in cowpea. The SNP markers revealed gene diversity and polymorphic information content of 0.22 and 0.17, respectively, showing that the tested cowpea accessions were genetically diverse. Test genotypes were classified into four genetic groups irrespective of source of collection allowing selection and subsequent crosses to develop breeding populations for cultivar development. Conclusions Genotypes Bubebe, CP411, CP421, CP645, Chimponogo and MS1–8–1-4 were identified to be the most genetically divergent and high yielding making them ideal parental lines for breeding. This study provided a baseline information and identified promising cowpea genetic resources for effective breeding and systematic conservation.

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