scholarly journals Genetic diversity and differentiation among populations of the pedunculate oak (Quercus robur) at the eastern margin of its range based on a new set of 95 SNP loci

2020 ◽  
Author(s):  
Bernd Degen ◽  
Yulai Yanbaev ◽  
Ruslan Ianbaev ◽  
Svetlana Bakhtina ◽  
Albina Tagirova
Keyword(s):  
Genetic Diversity ◽  
Quercus Robur ◽  
Spatial Genetic Structure ◽  
Allelic Diversity ◽  
Genetic Distances ◽  
Fixation Index ◽  
Pedunculate Oak ◽  
Migration Routes ◽  
Volga River ◽  
Eastern Margin

AbstractThe aim of this study is to determine the genetic variability and differentiation among populations of pedunculate oak (Quercus robur) at the eastern margin of the species distribution range. We applied new set of 95 geographically informative nuclear SNP (single nucleotide polymorphism) loci developed using Double Digest Restriction Site Associated DNA (ddRAD), a new generation DNA sequencing technology. The study area is located in the basins of the Volga River and its two main tributaries, Kama and Belaya. Despite the strong reduction and fragmentation of pedunculate oak forests over the last several centuries and comparatively small sizes of present stands, a relatively similar genetic diversity of seven populations was observed (on average, allelic diversity υа = 1.472–1.603, observed heterozygosity HO = 0.305–0.358, expected heterozygosity HE = 0.272–0.343). The genetic distances between populations vary between 0.102 and 0.170 (on average, d0 = 0.128). We have identified the absence of a spatial genetic structure and the existence of genetically peculiar populations in the territory studied. The genetic distances of Gregorius between populations vary between 0.102 and 0.170 (on average, d0 = 0.128). Genetic differentiation among populations was statistically significant with a mean of the fixation index FST of 0.075. Populations from the Privolzhye Upplands and from northern parts of the study area make the most contribution to overall inter-population differentiation (d0 = 0.137). No significant differences exist among the samples at lowlands along the Volga river (d0 = 0.110). It was concluded that the multiplicity and different ages of local populations and the complexity of migration routes of the pedunculate oak from Pleistocene refugia and secondary Holocene shelters can cause this phenomenon.

scholarly journals Genetic diversity and differentiation of pedunculate (Quercus robur) and sessile (Q. petraea) oaks

2019 ◽  
Vol 31 (6) ◽  
pp. 2445-2452
Author(s):  
Girmantė Jurkšienė ◽  
Oleg Yu. Baranov ◽  
Dmitry I. Kagan ◽  
Olja A. Kovalevič-Razumova ◽  
Virgilijus Baliuckas
Keyword(s):  
Genetic Diversity ◽  
Quercus Robur ◽  
Rapd Markers ◽  
Allelic Diversity ◽  
Pedunculate Oak ◽  
Mixed Stands ◽  
Genotypic Analysis ◽  
Preliminary Study ◽  
Genotypic Structure ◽  
Leaf Morphological Traits

Abstract This study was conducted to determine the parent–offspring genetic structure of the pedunculate oak (Quercus robur L.), sessile oak (Q. petraea [Matt.] Liebl.) and their hybrids. Forty half-sib Quercus families and their maternal trees originating from one tree stand in southern Lithuania were analyzed using SSR and RAPD markers. Based on a preliminary study of leaf morphological traits, the individuals separated into six groups. The studied half-sib oak families were also compared for allelic diversity, including group variations; genotypic structure; genetic diversity; and the degree of genetic subdivision and differentiation. The level of genetic variation and subdivision was lower in the hybrid families than in the families of the parental species. Genotypic analysis of the half-sibling offspring showed the asymmetric nature of interspecific hybridization processes of pedunculate and sessile oaks in mixed stands.

scholarly journals High Genetic Diversity but Absence of Population Structure in Local Chickens of Sri Lanka Inferred by Microsatellite Markers

2021 ◽  
Vol 12 ◽  
Author(s):  
Amali Malshani Samaraweera ◽  
Ranga Liyanage ◽  
Mohamed Nawaz Ibrahim ◽  
Ally Mwai Okeyo ◽  
Jianlin Han ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Sri Lanka ◽  
Microsatellite Markers ◽  
Allelic Diversity ◽  
Genetic Distances ◽  
Population Substructure ◽  
High Genetic Diversity ◽  
Naked Neck ◽  
Local Chicken ◽  
Local Chickens

Local chicken populations belonging to five villages in two geographically separated provinces of Sri Lanka were analyzed using 20 microsatellite markers to determine the genetic diversity of local chickens. Population genetic parameters were estimated separately for five populations based on geographic locations and for eight populations based on phenotypes, such as naked neck, long legged, crested or crown, frizzle feathered, Giriraj, commercial layer, crossbreds, and non-descript chicken. The analysis revealed that there was a high genetic diversity among local chickens with high number of unique alleles, mean number of alleles per locus (MNA), and total number of alleles per locus per population. A total of 185 microsatellite alleles were detected in 192 samples, indicating a high allelic diversity. The MNA ranged from 8.10 (non-descript village chicken) to 3.50 (Giriraj) among phenotypes and from 7.30 (Tabbowa) to 6.50 (Labunoruwa) among village populations. In phenotypic groups, positive inbreeding coefficient (FIS) values indicated the existence of population substructure with evidence of inbreeding. In commercial layers, a high expected heterozygosity He = 0.640 ± 0.042) and a negative FIS were observed. The positive FIS and high He estimates observed in village populations were due to the heterogeneity of samples, owing to free mating facilitated by communal feeding patterns. Highly admixed nature of phenotypes was explained as a result of rearing many phenotypes by households (58%) and interactions of chickens among neighboring households (53%). A weak substructure was evident due to the mating system, which disregarded the phenotypes. Based on genetic distances, crown chickens had the highest distance to other phenotypes, while the highest similarity was observed between non-descript village chickens and naked neck birds. The finding confirms the genetic wealth conserved within the populations as a result of the breeding system commonly practiced by chicken owners. Thus, the existing local chicken populations should be considered as a harbor of gene pool, which can be readily utilized in developing locally adapted and improved chicken breeds in the future.

scholarly journals Assessment of genetic variation in Bapedi sheep using microsatellite markers

2020 ◽  
Vol 50 (2) ◽  
pp. 318-324
Author(s):  
A. Maqhashu ◽  
N.O. Mapholi ◽  
H.A. O’Neill ◽  
K.A. Nephawe ◽  
F.V. Ramukhithi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Microsatellite Markers ◽  
South African ◽  
Agricultural Research ◽  
Germplasm Conservation ◽  
Genetic Distances ◽  
Fixation Index ◽  
Indigenous Sheep ◽  
Agricultural Research Council

This study was conducted to assess genetic variation in Bapedi sheep using 14 microsatellite markers. Blood samples were collected from 174 unrelated Bapedi sheep on six farms in various districts of Limpopo and from the Agricultural Research Council Animal Production Institute (ARC-API) in Gauteng. Genotypes from other South African indigenous sheep, namely Zulu (N = 14), Damara (N = 11), Dorper (N = 8), and Namaqua (N = 11), were included to represent reference populations. The effective number of alleles averaged 5.6 for across the Bapedi flocks and was 4.9 for the reference breeds. Among the Bapedi flocks, the observed heterozygosity (Ho) ranged from 0.56 ± 0.05 to 0.69 ± 0.03 and expected heterozygosity (He) values were between 0.75 ± 0.04 and 0.88 ± 0.01. Thus, there is considerable genetic diversity within the Bapedi sheep populations. However, the fixation index was high, indicating the possibility of inbreeding becoming a problem for these flocks. A neighbour-joining tree was constructed from the estimates of Nei’s genetic distances among flocks. The presence of Bapedi sheep flocks on all of the main branches of the tree along with one of the reference breeds suggests the present-day Bapedi is not an entirely distinct breed and that there are genetic differences between flocks of these South African indigenous sheep. Sustainable breeding and conservation programmes are needed to control inbreeding and to foreclose possible genetic dilution of Bapedi sheep. Keywords: genetic diversity, germplasm conservation, inbreeding, indigenous sheep

scholarly journals Genetic diversity and spatial genetic structure in populations of Orbignya phalerata Mart. under different exploitation intensities in the Brazilian savanna

2015 ◽  
Vol 64 (1-6) ◽  
pp. 201-211 ◽  
Author(s):  
Bruna Ibanes ◽  
A.M. Sebbenn ◽  
V.C.R. Azevedo ◽  
M.A. Moreno ◽  
F.B. Gandara ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Spatial Genetic Structure ◽  
Spatial Distance ◽  
Null Alleles ◽  
Fixation Index ◽  
Genetic Studies ◽  
Expected Heterozygosity ◽  
Adult Trees ◽  
Diversity Structure

Abstract Genetic studies in tropical tree species have found signs of decreased genetic diversity and increased levels of inbreeding and spatial genetic structure (SGS) in fragmented and exploited populations. The aim of this paper was to investigate genetic diversity, structure, and intrapopulation SGS using eight microsatellite loci for three Orbignya phalerata populations that have undergone different intensities of seed harvesting. From each population, we georeferenced and sampled 30 seedlings, 30 juveniles, and 30 adult trees. The total number of alleles over all loci (k), and observed (Ho) and expected heterozygosity (He) presented lower values for the population experiencing more intense fruit harvesting than less heavily exploited populations, suggesting that fruit harvesting may decrease genetic diversity. Null alleles were detected in practically all loci among seedlings, juveniles, and adults in all populations, indicating that the estimates of Ho, He, and fixation index (F) are biased. When corrected for null alleles (FNull), the fixation index decreased for all samples, resulting in significantly higher than zero results for seedlings of all populations, but not for juveniles and adults of all populations. The comparison of FNull values between cohorts in the most heavily exploited population (ESP) suggests that inbred individuals are eliminated between seedling and adult stages. Significant SGS was detected up to 60 m in all populations, which indicates short distance seed dispersal. Genetic differentiation (G’ST) between pairwise populations was related to spatial distance between populations, with the greatest difference between more distant populations.

scholarly journals Genetic diversity of different breeds of Kazakh sheep using microsatellite analysis

2019 ◽  
Vol 62 (1) ◽  
pp. 305-312
Author(s):  
Kairat Dossybayev ◽  
Zarina Orazymbetova ◽  
Aizhan Mussayeva ◽  
Naruya Saitou ◽  
Rakhymbek Zhapbasov ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Microsatellite Loci ◽  
Allelic Diversity ◽  
Genetic Distances ◽  
Sheep Breed ◽  
Expected Heterozygosity ◽  
The Mean ◽  
High Level ◽  
Short Tandem

Abstract. A total of 75 individuals from five sheep populations in Kazakhstan were investigated based on 12 STR (short tandem repeat, also known as microsatellite) markers in order to study their genetic structure and phylogenetic relationship based on genetic distances. These sheep had a high level of genetic diversity. In total, 163 alleles were found in all the populations using 12 microsatellite loci. The mean number of alleles, effective number of alleles, and polymorphism information content (PIC) values per loci were 13.4, 5.9, and 0.78, respectively. Comparing the allelic diversity between the populations, the highest genetic diversity was observed in the Edilbay-1 sheep breed (8.333±0.644), and the lowest parameter was for Kazakh Arkhar-Merino (7.083±0.633). In all populations, there is a deficiency of heterozygosity. The largest genetic diversity was found in loci INRA023 and CSRD247 with 16 alleles, and the smallest polymorphism was noted for the locus D5S2 with 8 alleles. The level of observed heterozygosity was in the range 0.678±0.051 for Kazakh Arkhar-Merino and 0.767±0.047 for Kazakh fat-tailed coarse wool. The expected heterozygosity level range was from 0.702±0.033 for Kazakh Arkhar-Merino to 0.777±0.023 for Edilbay-1. When 12 microsatellite loci are compared, the OarFCB20 locus showed the highest level of genetic variability. Excess of heterozygosity was observed at three loci; MAF065, McM042, and OarFCB20. The highest genetic distance was observed between Kazakh Arkhar-Merino and Edilbay-1, whereas the genetic distance between Edilbay-1 and Edilbay-2 is the smallest using Nei's standard genetic distance. The Edilbay-1 sheep breed possesses the largest genetic diversity among these five populations.

scholarly journals Patterns of genetic variation in leading-edge populations of Quercus robur: genetic patchiness due to family clusters

2020 ◽  
Vol 16 (5) ◽  
Author(s):  
Pekka Vakkari ◽  
Mari Rusanen ◽  
Juha Heikkinen ◽  
Tea Huotari ◽  
Katri Kärkkäinen
Keyword(s):  
Population Structure ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Population Genetic ◽  
Quercus Robur ◽  
Spatial Genetic Structure ◽  
Medium Size ◽  
Pedunculate Oak ◽  
Genetic Structures ◽  
Genetic Patchiness

Abstract The genetic structure of populations at the edge of species distribution is important for species adaptation to environmental changes. Small populations may experience non-random mating and differentiation due to genetic drift but larger populations, too, may have low effective size, e.g., due to the within-population structure. We studied spatial population structure of pedunculate oak, Quercus robur, at the northern edge of the species’ global distribution, where oak populations are experiencing rapid climatic and anthropogenic changes. Using 12 microsatellite markers, we analyzed genetic differentiation of seven small to medium size populations (census sizes 57–305 reproducing trees) and four populations for within-population genetic structures. Genetic differentiation among seven populations was low (Fst = 0.07). We found a strong spatial genetic structure in each of the four populations. Spatial autocorrelation was significant in all populations and its intensity (Sp) was higher than those reported in more southern oak populations. Significant genetic patchiness was revealed by Bayesian structuring and a high amount of spatially aggregated full and half sibs was detected by sibship reconstruction. Meta-analysis of isoenzyme and SSR data extracted from the (GD)2 database suggested northwards decreasing trend in the expected heterozygosity and an effective number of alleles, thus supporting the central-marginal hypothesis in oak populations. We suggest that the fragmented distribution and location of Finnish pedunculate oak populations at the species’ northern margin facilitate the formation of within-population genetic structures. Information on the existence of spatial genetic structures can help conservation managers to design gene conservation activities and to avoid too strong family structures in the sampling of seeds and cuttings for afforestation and tree improvement purposes.

scholarly journals Genetic Diversity and Differentiation of Pedunculate Oak (Quercus robur L.) Populations at the Southern Margin of Its Distribution Range—Implications for Conservation

Diversity ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 371
Author(s):  
Lazar Kesić ◽  
Klára Cseke ◽  
Saša Orlović ◽  
Dejan B. Stojanović ◽  
Saša Kostić ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Quercus Robur ◽  
Allelic Richness ◽  
Distribution Range ◽  
Gene Pools ◽  
Pedunculate Oak ◽  
Rear Edge ◽  
Southern Margin ◽  
Genetic Diversity And Structure

Understanding intraspecific genetic variation is one of the principal requirements for the evaluation of tree species capacity to cope with intensive climatic changes, as well as designing long-term conservation programs. Herein, we evaluated the genetic diversity and genetic structure of seven pedunculate oak (Quercus robur L.) populations, located at the southern margin of its distribution range on the Balkan Peninsula (Serbia). The objective of the study was to propose future in situ conservation measures aimed at protection of pedunculate oak adaptive and neutral genetic diversity at the species rear-edge. Genetic diversity and structure were estimated using twelve highly polymorphic simple sequence repeat (SSR) markers. The mean expected heterozygosity (He) was 0.769, allelic richness (AR) 9.63, and private allelic richness (pAR) 0.79, indicating high genetic diversity in the studied populations. Genetic differentiation among the populations was low (Fst = 0.032). Structure analysis, the unweighted pair group method with arithmetic mean (UPGMA) showed the existence of two gene pools unrelated to the populations’ area of occurrence. Taking into consideration the results of the current study and previous conservation activities on the pedunculate oak in Serbia, as well as the importance of rear-edge populations in the long-term conservation of the species genetic diversity, we suggested establishing three additional gene conservation units for securing long-term sustainability of the species.

scholarly journals Genetic Diversity of Pedunculate Oak (Quercus robur L.) in Clonal Seed Orchards in Croatia, Assessed by Nuclear and Chloroplast Microsatellites

2018 ◽  
Vol 9 (1) ◽  
Author(s):  
Ida Katičić Bogdan ◽  
Davorin Kajba ◽  
Zlatko Šatović ◽  
Silvio Schüler ◽  
Saša Bogdan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Quercus Robur ◽  
Chloroplast Microsatellites ◽  
Pedunculate Oak ◽  
Seed Orchards

scholarly journals Norway maple (Acer platanoides) and pedunculate oak (Quercus robur) demonstrate different patterns of genetic variation within and among populations on the eastern border of distribution ranges

2021 ◽  
Vol 67 (No. 11) ◽  
pp. 522-532
Author(s):  
Artur Akhmetov ◽  
Ruslan Ianbaev ◽  
Svetlana Boronnikova ◽  
Yulai Yanbaev ◽  
Aygul Gabitova ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Differentiation ◽  
Population Genetic ◽  
Quercus Robur ◽  
Distribution Area ◽  
Pedunculate Oak ◽  
Acer Platanoides ◽  
Norway Maple ◽  
Key Species

Norway maple (Acer platanoides L.) is a key species of broadleaved forests whose population genetics is poorly studied using modern genetic tools. We used ISSR analysis to explore genetic diversity and differentiation among 10 Russian populations on the eastern margin of the species range of distribution, and to compare the revealed patterns with the results of our population genetic studies of pedunculate oak (Quercus robur L.). In the first set comparatively high heterozygosity and allelic diversity were found (expected heterozygosity H<sub>E</sub> = 0.160 ± 0.033, number of alleles n<sub>a</sub> = 1.440 ± 0.080, effective number of alleles n<sub>e</sub> = 1.271 ± 0.062) in comparison with strongly fragmented and geographically isolated small maple stands of the second set (H<sub>E</sub> = 0.083 ± 0.011, n<sub>a</sub> = 1.281 ± 0.031, n<sub>e</sub> = 1.136 ± 0.019). A relatively high genetic differentiation among populations was detected (the proportion of the inter-population component of total genetic variation, G<sub>ST</sub> = 0.558 ± 0.038). In the Cis-Urals, local groups of populations that are confined to the northern, middle and southern parts of the Urals were identified. On the contrary, the current significant fragmentation of the pedunculate oak distribution area in the same study area did not lead to any noticeable genetic differentiation among the majority of populations, the values of the population genetic diversity were very similar in different parts of the Southern Urals.

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