Genetic diversity and structure in the northern populations of European hazelnut (Corylus avellana L.)

Genome ◽  
2019 ◽  
Vol 62 (8) ◽  
pp. 537-548
Author(s):  
Pirjo Tanhuanpää ◽  
Maarit Heinonen ◽  
Lidija Bitz ◽  
Veli-Matti Rokka
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Plant Conservation ◽  
Corylus Avellana ◽  
Ice Age ◽  
Genetic Structuring ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates ◽  
Genetic Diversity And Structure ◽  
Corylus Avellana L

European hazelnut (Corylus avellana L.) is a strictly cross-pollinated diploid tree species, which has its northernmost populations in Fennoscandia, and it was one of the first species to recolonize northern Europe after the last ice age. Hazelnut produces edible nuts in Finland but nowadays they are underutilized as food, and currently no breeding programmes exist. In the present study, 300 hazelnut specimens were collected from 20 different locations (= populations) in Finland, and they were genetically analyzed using nine simple sequence repeat (SSR) markers. Most of the genetic diversity existed within populations (83%). According to different genetic analyses (STRUCTURE, principal coordinates analysis, and clustering), a general lack of structure was observed, suggesting extensive gene flow among hazelnuts between 17 investigated populations. However, genetic structuring was clearly observed in three populations: Hakavuori, Mustiala, and Pähkinämäki, which might have become isolated due to geographical barriers that kept them separate, diminishing gene flow from other populations. Studying the diversity of European hazelnut is of great interest for understanding population genetics of a species distributed in its marginal areas in the north, and the results are also valuable for further uses in plant conservation, selection, and possible future breeding actions in Finland.

scholarly journals Genetic Structure and Eco-Geographical Differentiation of Lancea tibetica in the Qinghai-Tibetan Plateau

Genes ◽  
2019 ◽  
Vol 10 (2) ◽  
pp. 97 ◽  
Author(s):  
Xiaofeng Chi ◽  
Faqi Zhang ◽  
Qingbo Gao ◽  
Rui Xing ◽  
Shilong Chen
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Gene Flow ◽  
Tibetan Plateau ◽  
Environmental Changes ◽  
Restricted Gene Flow ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates ◽  
Genetic Diversity And Structure ◽  
Tanggula Mountains

The uplift of the Qinghai-Tibetan Plateau (QTP) had a profound impact on the plant speciation rate and genetic diversity. High genetic diversity ensures that species can survive and adapt in the face of geographical and environmental changes. The Tanggula Mountains, located in the central of the QTP, have unique geographical significance. The aim of this study was to investigate the effect of the Tanggula Mountains as a geographical barrier on plant genetic diversity and structure by using Lancea tibetica. A total of 456 individuals from 31 populations were analyzed using eight pairs of microsatellite makers. The total number of alleles was 55 and the number per locus ranged from 3 to 11 with an average of 6.875. The polymorphism information content (PIC) values ranged from 0.2693 to 0.7761 with an average of 0.4378 indicating that the eight microsatellite makers were efficient for distinguishing genotypes. Furthermore, the observed heterozygosity (Ho), the expected heterozygosity (He), and the Shannon information index (I) were 0.5277, 0.4949, and 0.9394, respectively, which indicated a high level of genetic diversity. We detected high genetic differentiation among all sampling sites and restricted gene flow among populations. Bayesian-based cluster analysis (STRUCTURE), principal coordinates analysis (PCoA), and Neighbor-Joining (NJ) cluster analysis based on microsatellite markers grouped the populations into two clusters: the southern branch and the northern branch. The analysis also detected genetic barriers and restricted gene flow between the two groups separated by the Tanggula Mountains. This study indicates that the geographical isolation of the Tanggula Mountains restricted the genetic connection and the distinct niches on the two sides of the mountains increased the intraspecific divergence of the plants.

scholarly journals Genetic Structure and Eco-Geographical Differentiation of Wild Sheep Fescue (Festuca ovina L.) in Xinjiang, Northwest China

2017 ◽  
Author(s):  
Chenglin Zhang ◽  
Jianbo Zhang ◽  
Yan Fan ◽  
Ming Sun ◽  
Wendan Wu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Abiotic Factors ◽  
Northwest China ◽  
Group Method ◽  
Principal Coordinates Analysis ◽  
High Genetic Diversity ◽  
Festuca Ovina ◽  
Principal Coordinates ◽  
Genetic Diversity And Structure

Glaciation and mountain orogeny have generated new ecologic opportunities for plants, favoring an increase in the speciation rate. Moreover, they also act as corridors or barriers for plant lineages and populations. High genetic diversity ensures that species are able to survive and adapt. Gene flow is one of the most important determinants of the genetic diversity and structure of out-crossed species, and it is easily affected by biotic and abiotic factors. The aim of this study was to characterize the genetic diversity and structure of an alpine species, Festuca ovina L., in Xingjiang, China. A total of 100 individuals from 10 populations were analyzed using six amplified fragment length polymorphism (AFLP) primer pairs. A total of 583 clear bands were generated, of which 392 were polymorphic; thus, the percentage of polymorphic bands (PPB) was 67.24%. The total and average genetic diversities were 0.2722 and 0.2006 (0.1686-0.2225), respectively. The unweighted group method with arithmetic mean (UPGMA) tree, principal coordinates analysis (PCoA) and STRUCTURE analyses revealed that these populations or individuals could be clustered into two groups. The analysis of molecular variance analysis (AMOVA) suggested that most of the genetic variance existed within a population, and the genetic differentiation (Fst) among populations was 20.71%. The Shannon differentiation coefficient (G’st) among populations was 0.2350. Limited gene flow (Nm = 0.9571) was detected across all sampling sites. The Fst and Nm presented at different levels under the genetic barriers due to fragmentation. The population genetic diversity was significant relative to environmental factors such as temperature, altitude and precipitation.

Conservation implications of distinct genetic structuring in the endangered freshwater fish Nannoperca oxleyana (Percichthyidae)

2009 ◽  
Vol 60 (1) ◽  
pp. 34 ◽  
Author(s):  
James T. Knight ◽  
Catherine J. Nock ◽  
Martin S. Elphinstone ◽  
Peter R. Baverstock
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Sand Dunes ◽  
Restricted Gene Flow ◽  
Genetic Structuring ◽  
Conservation Implications ◽  
South Wales ◽  
Haplotypic Diversity ◽  
Genetic Diversity And Structure ◽  
Fragmented Distribution

The maintenance of genetic diversity and gene flow in threatened species is a vital consideration for recovery programs. The endangered Oxleyan pygmy perch Nannoperca oxleyana has a fragmented distribution within coastal freshwater drainages of southern Queensland and northern New South Wales, Australia. In the present study, mitochondrial DNA control region variation was used to assess genetic diversity and structure across the geographical range of this species. Haplotypic diversity was highest in a small NSW subcatchment south of Evans Head (h = 0.594) followed by Marcus Creek in Queensland (h = 0.475). Distinct genetic differentiation was evident among the Queensland localities and the NSW subcatchments, implying restricted gene flow between coastal river systems. One of the nine haplotypes detected was distributed over 83.4% of the species’ range, suggesting historical connectivity among the now fragmented populations. These patterns were concordant with eustatic changes associated with the last glacial maximum. High barrier sand dunes may also act as barriers to gene flow and dispersal between adjacent NSW subcatchments. Conservation efforts should focus on the preservation of genetic diversity by maintaining as many genetically differentiated populations as possible. The relatively diverse populations inhabiting the South Evans Head subcatchment and Marcus Creek require special management consideration.

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

PeerJ ◽  
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.

scholarly journals Morphological and genetic diversity of Senecio vulgaris L. (Asteraceae) in Iran

2021 ◽  
Vol 80 (2) ◽  
Author(s):  
Mostafa Ebadi ◽  
Rosa Eftekharian
Keyword(s):  
Genetic Diversity ◽  
Principal Component ◽  
Morphological Characters ◽  
Mantel Test ◽  
Morphological Data ◽  
Principal Coordinates Analysis ◽  
Cauline Leaf ◽  
Senecio Vulgaris ◽  
Molecular Features ◽  
Principal Coordinates

Senecio vulgaris L., an annual herb belonging to the Asteraceae, is widely distributed in different regions of the world. There is no information on the intraspecific variations of the morphological and molecular features of this species. In the present investigation, we studied the morphological and genetic diversity of 81 accessions of S. vulgaris collected from 10 geographical populations. Eleven inter simple sequence repeat (ISSR) primers were used for the examination of genetic variations among the populations. Analysis of molecular variance (AMOVA) and GST analyses revealed significant differences among the investigated populations. A significant correlation between genetic distance and geographical distance was revealed by the Mantel test. However, reticulation analysis indicated the occurrence of gene flow among most of the populations studied. Principal component analysis (PCA) plot showed that the number of capitula, length of the cauline leaf and plant height were the most variable morphological characters. Principal coordinates analysis (PCoA) plot revealed two groups of populations, according to molecular and morphological data. The results suggested the existence of possible intraspecific taxonomic ranks within this species.

Genetic diversity analysis of the Greek lentil (Lens culinaris) landrace ‘Eglouvis’ using morphological and molecular markers

2018 ◽  
Vol 16 (5) ◽  
pp. 469-477 ◽  
Author(s):  
Georgios F. Tsanakas ◽  
Photini V. Mylona ◽  
Katerina Koura ◽  
Anthoula Gleridou ◽  
Alexios N. Polidoros
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Genetic Variability ◽  
Morphological Analysis ◽  
Phenotypic Variability ◽  
Market Price ◽  
Genetic Distances ◽  
Reaction Products ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates

AbstractThe Greek lentil landrace ‘Eglouvis’ is cultivated continuously at the Lefkada island for more than 400 years. It has great taste, high nutritional value and high market price. In the present study, we used morphological and molecular markers to estimate genetic diversity within the landrace. Morphological analysis was based on characteristics of the seed. Molecular analysis was performed using simple sequence repeat (SSR) molecular markers in a high-resolution melting (HRM) approach. ‘Samos’ and ‘Demetra’, two of the most widely cultivated commercial lentil varieties in Greece, were used for comparisons. Morphological analysis was performed with 584 seeds randomly selected from a lot. Analysis of seed dimensions and colour distributed the samples in different categories and highlighted the phenotypic variability in ‘Eglouvis’ lentil seeds. Genetic variability was estimated from 91 individual DNA samples with 11 SSR markers using HRM analysis. Genotyping was based upon the shape of the melting curves and the difference plots; all polymerase chain reaction products were also run on agarose gels. Genetic distances of individuals and principal coordinates analysis suggested that ‘Eglouvis’ landrace has a unique genetic background that significantly differs from ‘Samos’ and ‘Demetra’ and no overlapping could be detected. Genetic variability within the ‘Eglouvis’ landrace can be considered in targeted breeding programs as a significant phytogenetic resource of lentils in Greece.

Weak genetic structuring suggests historically high genetic connectivity among recently fragmented urban populations of the scincid lizard, Ctenotus fallens

2015 ◽  
Vol 63 (4) ◽  
pp. 279 ◽  
Author(s):  
Josef Krawiec ◽  
Siegfried L. Krauss ◽  
Robert A. Davis ◽  
Peter B. S. Spencer
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Large Population ◽  
Geographic Distance ◽  
Genetic Erosion ◽  
Genetic Connectivity ◽  
Genetic Structuring ◽  
Low Genetic Diversity ◽  
Population Sizes

Populations in fragmented urban remnants may be at risk of genetic erosion as a result of reduced gene flow and elevated levels of inbreeding. This may have serious genetic implications for the long-term viability of remnant populations, in addition to the more immediate pressures caused by urbanisation. The population genetic structure of the generalist skink Ctenotus fallens was examined using nine microsatellite markers within and among natural vegetation remnants within a highly fragmented urban matrix in the Perth metropolitan area in Western Australia. These data were compared with samples from a large unfragmented site on the edge of the urban area. Overall, estimates of genetic diversity and inbreeding within all populations were similar and low. Weak genetic differentiation, and a significant association between geographic and genetic distance, suggests historically strong genetic connectivity that decreases with geographic distance. Due to recent fragmentation, and genetic inertia associated with low genetic diversity and large population sizes, it is not possible from these data to infer current genetic connectivity levels. However, the historically high levels of gene flow that our data suggest indicate that a reduction in contemporary connectivity due to fragmentation in C. fallens is likely to result in negative genetic consequences in the longer term.

Temporal diversity changes among 198 Nordic bread wheat landraces and cultivars detected by retrotransposon-based S-SAP analysis

2008 ◽  
Vol 6 (02) ◽  
pp. 113-125 ◽  
Author(s):  
Shu-Chin Hysing ◽  
Torbjörn Säll ◽  
Hilde Nybom ◽  
Erland Liljeroth ◽  
Arnulf Merker ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Bread Wheat ◽  
Growth Habit ◽  
Gene Diversity ◽  
Pedigree Information ◽  
Principal Coordinates Analysis ◽  
Subsequent Increase ◽  
Principal Coordinates ◽  
Frequent Exchange ◽  
Wheat Landraces

The sequence-specific amplified polymorphism (S-SAP) method was used to genotype 198 Nordic bread wheat landraces and cultivars from the 19th to the 21st centuries. It was shown that theSukkula-9900-LARD retrotransposon primer was highly suitable for resolving closely related wheat materials. Cluster analysis was generally consistent with pedigree information and revealed a clear separation for growth habit but not for countries. A principal coordinates analysis (PCoA) showed a separation into different time periods (before 1910, 1910–1969 and 1970–2003). These results are consistent with the breeding history and pedigree information, indicating that little hybridization has occurred between winter and spring wheat, in contrast to frequent exchange of germplasm between the Nordic countries. Estimates of gene diversity, the PCoA results, and changes in band frequencies across time indicate that plant breeding has led to substantial genetic shifts in Nordic wheat. Diversity was reduced through selections from landraces during the early 20th century, followed by a period of relatively lower genetic diversity, and a subsequent increase and net gains in diversity from the late 1960s onwards through the use of exotic germplasm. Thus, an anticipated loss of overall genetic diversity was found to be negligible, although allele losses have occurred at specific loci.

scholarly journals Pollen-mediated gene flow ensures connectivity among spatially discrete sub-populations of Phalaenopsis pulcherrima, a tropical food-deceptive orchid

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Zhe Zhang ◽  
Stephan W. Gale ◽  
Ji-Hong Li ◽  
Gunter A. Fischer ◽  
Ming-Xun Ren ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Polynomial Regression ◽  
Genetic Erosion ◽  
Population Level ◽  
Hainan Island ◽  
Paternity Analysis ◽  
Genetic Structuring ◽  
Long Distance ◽  
High Genetic Diversity

Abstract Background Gene flow in plants via pollen and seeds is asymmetrical at different geographic scales. Orchid seeds are adapted to long-distance wind dispersal but pollinium transfer is often influenced by pollinator behavior. We combined field studies with an analysis of genetic diversity among 155 physically mapped adults and 1105 F1 seedlings to evaluate the relative contribution of pollen and seed dispersal to overall gene flow among three sub-populations of the food-deceptive orchid Phalaenopsis pulcherrima on Hainan Island, China. Results Phalaenopsis pulcherrima is self-sterile and predominantly outcrossing, resulting in high population-level genetic diversity, but plants are clumped and exhibit fine-scale genetic structuring. Even so, we detected low differentiation among sub-populations, with polynomial regression analysis suggesting gene flow via seed to be more restricted than that via pollen. Paternity analysis confirmed capsules of P. pulcherrima to each be sired by a single pollen donor, probably in part facilitated by post-pollination stigma obfuscation, with a mean pollen flow distance of 272.7 m. Despite limited sampling, we detected no loss of genetic diversity from one generation to the next. Conclusions Outcrossing mediated by deceptive pollination and self-sterility promote high genetic diversity in P. pulcherrima. Long-range pollinia transfer ensures connectivity among sub-populations, offsetting the risk of genetic erosion at local scales.

scholarly journals High-Throughput Genotype, Morphology, and Quality Traits Evaluation for the Assessment of Genetic Diversity of Wheat Landraces from Sicily

Plants ◽  
2019 ◽  
Vol 8 (5) ◽  
pp. 116 ◽  
Author(s):  
Fiore ◽  
Mercati ◽  
Spina ◽  
Blangiforti ◽  
Venora ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Durum Wheat ◽  
Extreme Environments ◽  
Principal Component ◽  
Detailed Knowledge ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates ◽  
Wide Range ◽  
Wheat Landraces ◽  
Durum Wheat Landraces

During the XX Century, the widespread use of modern wheat cultivars drastically reduced the cultivation of ancient landraces, which nowadays are confined to niche cultivation areas. Several durum wheat landraces adapted to the extreme environments of the Mediterranean region, are still being cultivated in Sicily, Italy. Detailed knowledge of the genetic diversity of this germplasm could lay the basis for their efficient management in breeding programs, for a wide-range range of traits. The aim of the present study was to characterize a collection of durum wheat landraces from Sicily, using single nucleotide polymorphisms (SNP) markers, together with agro-morphological, phenological and quality-related traits. Two modern cv. Simeto, Claudio, and the hexaploid landrace, Cuccitta, were used as outgroups. Cluster analysis and Principal Coordinates Analysis (PCoA) allowed us to identify four main clusters across the analyzed germplasm, among which a cluster included only historical and modern varieties. Likewise, structure analysis was able to distinguish the ancient varieties from the others, grouping the entries in seven cryptic genetic clusters. Furthermore, a Principal Component Analysis (PCA) was able to separate the modern testers from the ancient germplasm. This approach was useful to classify and evaluate Sicilian ancient wheat germplasm, supporting their safeguard and providing a genetic fingerprint that is necessary for avoiding commercial frauds to sustaining the economic profits of farmers resorting to landraces cultivation.

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