scholarly journals Genetic assessment of three Fagaceae species in forest restoration trials

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6958 ◽  
Author(s):  
Patcharawadee Thongkumkoon ◽  
Siriwadee Chomdej ◽  
Jatupol Kampuansai ◽  
Waranee Pradit ◽  
Pimubon Waikham ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Tree Species ◽  
Forest Restoration ◽  
Second Generation ◽  
Fixation Index ◽  
Seed Sample ◽  
Sample Collection ◽  
Entire Genome ◽  
Collection Method ◽  
Adult Trees

Restoring isolated patches of forest ecosystems in degraded landscapes could potentially lead to genetic loss and inbreeding. Therefore, this study determined the occurrence of genetic diversity among the tree species Castanopsis tribuloides, C. calathiformis, and Lithocarpus polystachyus all of which were proven previously to be effective native tree species in the restoration of upland evergreen forests in northern Thailand when using the seed sample collection method. We tested our hypothesis as to whether the genetic diversity of a plant population that had been planted from the seeds of 4–6 adult trees would be lower and whether incidences of fixation index (Fis) would be higher among the second generation seedlings of these three Fagaceae species in isolated forest restoration trial plots. Microsatellite primers were selected from the entire genome sequence of C. tribuloides and the genetic sequences of C. tribuloides, L. polystachyus, and C. calathiformis were analyzed. Our results indicated a high degree of genetic diversity (He) in C. tribuloides (0.736) and C. calathiformis (0.481); however, a low level of genetic diversity was observed in L. polystachyus (0.281) within the restored forest. The fixation index for the second generation of L. polystachyus and C. calathiformis in the restored forest showed evidence of inbreeding. These results imply the efficiency of the seed sample collection method and verify that it does not reduce the level of genetic diversity in C. tribuloides and C. calathiformis. However, it may result in incidences of an inbreeding phenomena, suggesting the need to increase the number of adult trees used at the seed collection stage.

scholarly journals Genetic diversity of Anadenanthera colubrina Vell. (Brenan) var cebil, a tree species from the South American subtropical forest as revealed by cpSSR markers

2011 ◽  
Vol 60 (1-6) ◽  
pp. 123-132 ◽  
Author(s):  
M. E. Barrandeguy ◽  
M.V. García ◽  
C. F. Argüelles ◽  
G. D. L. Cervigni
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Tree Species ◽  
Evolutionary Dynamics ◽  
Pairwise Comparison ◽  
Fixation Index ◽  
Haplotypic Diversity ◽  
Adult Trees ◽  
Minimum Spanning Network ◽  
Subdivided Populations

Abstract Anadenanthera colubrina var cebil is a tree species native to the Upper Parana Atlantic Forest where human activities have severely impacted causing deep fragmentation. Microsatellites are not available in this species. Therefore, the first objective of this study was to generate chloroplast simple sequence repeats (cpSSR) by cross-species transfer. Understanding the evolutionary dynamics of subdivided populations is an important matter. In this way, a first approach to the characterization of the haplotypic diversity within and between populations as well as the genetic structure of native Argentinean populations were the main goals of this study. Twenty four individuals from two populations of the Misiones province were studied and four cpSSR loci were tested. Two of them exhibited polymorphic patterns leading to the identification of 11 cpDNA haplotypes with high mean genetic diversity (GD=0.73). The minimum spanning network defined three clear groups which can be assigned to at least three subpopulations. AMOVA indicated that the total variance showed the highest percentage of variation (48%) within subpopulations with a fixation index (FST) statistically significant (FST=0.520; p<0.05). Brown’s two loci component analysis indicated that substructure population is present. Jost’s differentiation global index (Dest) was 0.049 while Dest pairwise comparison reflected a certain level of genetic structure. The high diversity level detected in the adult trees of A. colubrina var cebil from the populations under study could be due to recent human influence. In this way, the reduction in population size caused a reduction in the number of trees leading to surviving trees showing the historical diversity of the populations analyzed.

scholarly journals Evaluation of the genetic diversity of selected Fagus sylvatica L. populations in the Czech Republic using nuclear microsatellites

2017 ◽  
Vol 63 (No. 2) ◽  
pp. 53-61 ◽  
Author(s):  
Cvrčková Helena ◽  
Máchová Pavlína ◽  
Poláková Lucie ◽  
Trčková Olga
Keyword(s):  
Genetic Diversity ◽  
Czech Republic ◽  
Microsatellite Markers ◽  
Fagus Sylvatica ◽  
Tree Species ◽  
European Beech ◽  
Fixation Index ◽  
Detailed Knowledge ◽  
The Czech Republic ◽  
Adult Trees

Fagus sylvatica Linnaeus (European beech), the ecologically and economically most important broadleaved tree species in the Czech Republic, was strongly reduced in the past. Today there are efforts to increase the proportion of beech to ensure optimal forest tree species composition. When extensively reintroducing beech, it is important to acquire more detailed knowledge of genetic diversity. Thirteen important beech populations in different stands in the territory of the Czech Republic were genotyped using 12 polymorphic nuclear microsatellite markers. The genotypic data from adult trees imply genetic differences between the populations. The estimated genetic diversity expressed as Shannon’s information index ranged from 1.73 to 1.92. Thirteen beech populations showed excess homozygotes, as indicated by positive fixation index (F) values (F = 0.005–0.115). The pairwise F<sub>ST</sub> values indicated low genetic differentiation between the 13 Czech beech populations, because they were greater than zero, that means they confirmed the presence of population structuring in Czech European beech. Not significant linear correlations were observed between genetic and geographic distances of the 13 beech populations studied on the basis of microsatellite markers. Twelve microsatellite markers were verified as highly polymorphic and suitable for genotyping of European beech populations.

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 Inventory of native and mother trees in Key Biodiversity Areas of Cebu Island, Philippines for species selection in local reforestation programs

2021 ◽  
Vol 22 (11) ◽  
Author(s):  
Edgardo P. Lillo ◽  
ARCHIEBALD B. MALAKI ◽  
STEVE MICHAEL T. ALCAZAR ◽  
RAAMAH ROSALES ◽  
BERNARDO R. REDOBLADO ◽  
...  
Keyword(s):  
Tree Species ◽  
Native Species ◽  
Forest Restoration ◽  
Habitat Preferences ◽  
Forest Degradation ◽  
Species Selection ◽  
Adult Trees ◽  
Native Tree ◽  
Native Tree Species ◽  
Planting Materials

Abstract. Lillo EP, Malaki AB, Alcazar SMT, Rosales R, Redoblado BR, Diaz JLB, Pantinople EM, Buot Jr. IE. 2021. Inventory of native and mother trees in Key Biodiversity Areas of Cebu Island, Philippines for species selection in local reforestation programs. Biodiversitas 22: 4740-4749. Forest restoration is the counterforce of deforestation and forest degradation. Yet, despite promoting natural recovery after forest harvest, afforestation and reforestation efforts, tropical forest ecosystems still experience a poor ratio of forest loss to forest gain. The study assessed the native tree species and potential mother trees in different Cebu Island Key Biodiversity Areas (KBAs) as well as their distribution and habitat preferences which can be used in local reforestation programs. A vegetation survey was conducted in three KBAs in Cebu Island, namely Nug-as forest, Mount Lantoy and Mount Capayas to inventory all native species. Assessment based on the phenotypic characteristics of adult trees was also conducted for indicating mother trees. This study in Cebu Island KBAs recorded a total of 292 species, categorized into 125 families and 203 genera, which can be classified into native trees (210), vines and lianas (18), shrub (37), and herbs (27). Out of the 292 species, 214 were recorded in Nug-as forest, 172 in Mount Lantoy, and 145 in Mount Capayas. Of the 210 native tree species, Nug-as forest had 145 species, Mount Lantoy 131 species, and Mount Capayas 109 species. A total of 241 mother trees were identified in the three KBAs, corresponding to 77 species in which Nug-as forest had 143 trees correspond to 52 species, Mount Lantoy had 68 trees correspond to 29 species, and Mount Capayas had 31 trees correspond to 6 species. Such native tree species are recommended for reforestation programs as planting materials that could reduce the risks of failure due to its high adaptability to the environment.

scholarly journals Genetic diversity and population structure of ridge gourd (Luffa acutangula) accessions in a Thailand collection using SNP markers

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Grimar Abdiel Perez ◽  
Pumipat Tongyoo ◽  
Julapark Chunwongse ◽  
Hans de Jong ◽  
Anucha Wongpraneekul ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Germplasm Collection ◽  
Snp Markers ◽  
Fixation Index ◽  
Breeding Programs ◽  
Total Fixation ◽  
Unrooted Phylogenetic Tree ◽  
Luffa Acutangula ◽  
Selection Of

AbstractThis study explored a germplasm collection consisting of 112 Luffa acutangula (ridge gourd) accessions, mainly from Thailand. A total of 2834 SNPs were used to establish population structure and underlying genetic diversity while exploring the fruit characteristics together with genetic information which would help in the selection of parental lines for a breeding program. The study found that the average polymorphism information content value of 0.288 which indicates a moderate genetic diversity for this L. acutangula germplasm. STRUCTURE analysis (ΔK at K = 6) allowed us to group the accessions into six subpopulations that corresponded well with the unrooted phylogenetic tree and principal coordinate analyses. When plotted, the STRUCTURE bars to the area of collection, we observed an admixed genotype from surrounding accessions and a geneflow confirmed by the value of FST = 0.137. AMOVA based on STRUCTURE clustering showed a low 12.83% variation between subpopulations that correspond well with the negative inbreeding coefficient value (FIS =  − 0.092) and low total fixation index (FIT = 0.057). There were distinguishing fruit shapes and length characteristics in specific accessions for each subpopulation. The genetic diversity and different fruit shapes in the L. acutangula germplasm could benefit the ridge gourd breeding programs to meet the demands and needs of consumers, farmers, and vegetable exporters such as increasing the yield of fruit by the fruit width but not by the fruit length to solve the problem of fruit breakage during exportation.

scholarly journals Stand Stability of Pure and Mixed-Eucalyptus Forests of Different Tree Species in a Typhoon-Prone Area

Forests ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 458
Author(s):  
Haiyan Deng ◽  
Linlin Shen ◽  
Jiaqi Yang ◽  
Xiaoyong Mo
Keyword(s):  
Tree Species ◽  
Forest Restoration ◽  
Large Scale ◽  
Stand Structure ◽  
Pinus Elliottii ◽  
Stem Form ◽  
Tree Species Composition ◽  
Eucalyptus Plantation ◽  
Mixed Plantation ◽  
Preservation Rate

Background and Objectives: The stable stand structure of mixed plantations is the basis of giving full play to forest ecological function and benefit. However, the monocultural Eucalyptus plantations with large-scale and successive planting that caused ecological problems such as reduced species diversity and loss of soil nutrients have presented to be unstable and vulnerable, especially in typhoon-prone areas. The objective of this study was to evaluate the nonspatial structure difference and the stand stability of pure and mixed-Eucalyptus forests, to find out the best mixed pattern of Eucalyptus forests with the most stability in typhoon-prone areas. Materials and Methods: In this study, we randomly investigated eight plots of 30 m × 30 m in pure and mixed-Eucalyptus (Eucalyptus urophylla S. T. Blake × E. grandis W. Hill) plantations of different tree species (Neolamarckia cadamba (Roxb.) Bosser, Acacia mangium Willd., and Pinus elliottii var. Elliottii Engelm. × P. caribaea Morelet) on growth status, characterized and compared the distribution of nonspatial structure of the monoculture and mixtures, and evaluated the stand quality and stability from eight indexes of the nonspatial structure, including preservation rate, stand density, height, diameter, stem form, degree of stem inclination, tree-species composition, and age structure. Results: Eucalyptus surviving in the mixed plantation of Eucalyptus and A. mangium (EA) and in the mixed plantation of Eucalyptus and P. elliottii × P. caribaea (EP) were 5.0% and 7.6% greater than those in pure Eucalyptus plantation (EE), respectively, while only the stand preservation rate of EA was greater (+2.9%) than that of the pure Eucalyptus plantation. The proportions of all mixtures in the height class greater than 7 m were fewer than that of EE. The proportions of EA and mixed plantation of Eucalyptus and N. cadamba (EN) in the diameter class greater than 7 m were 10.6% and 7.8%, respectively, more than that of EE. EN had the highest ratio of branching visibly (41.0%), EA had the highest ratio of inclined stems (8.1%), and EP had the most straight and complete stem form (68.7%). The stand stability of the mixed plantation of Eucalyptus and A. mangium presented to be optimal, as its subordinate function value (0.76) and state value (ω = 0.61) of real stand were the largest. Conclusions: A. mangium is a superior tree species to mix with Eucalyptus for a more stable stand structure in the early growth stage to approach an evident and immense stability and resistance, which is of great significance for the forest restoration of Eucalyptus in response to extreme climate and forest management.

scholarly journals Genetic diversity and natural selection on the thrombospondin-related adhesive protein (TRAP) gene of Plasmodium falciparum on Bioko Island, Equatorial Guinea and global comparative analysis

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Li-Yun Lin ◽  
Hui-Ying Huang ◽  
Xue-Yan Liang ◽  
Dong-De Xie ◽  
Jiang-Tao Chen ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Plasmodium Falciparum ◽  
Natural Selection ◽  
Protein Structure ◽  
Transmembrane Protein ◽  
Fixation Index ◽  
Bioko Island ◽  
Adhesive Protein ◽  
Trap Gene ◽  
Selection Of

Abstract Background Thrombospondin-related adhesive protein (TRAP) is a transmembrane protein that plays a crucial role during the invasion of Plasmodium falciparum into liver cells. As a potential malaria vaccine candidate, the genetic diversity and natural selection of PfTRAP was assessed and the global PfTRAP polymorphism pattern was described. Methods 153 blood spot samples from Bioko malaria patients were collected during 2016–2018 and the target TRAP gene was amplified. Together with the sequences from database, nucleotide diversity and natural selection analysis, and the structural prediction were preformed using bioinformatical tools. Results A total of 119 Bioko PfTRAP sequences were amplified successfully. On Bioko Island, PfTRAP shows its high degree of genetic diversity and heterogeneity, with π value for 0.01046 and Hd for 0.99. The value of dN–dS (6.2231, p < 0.05) hinted at natural selection of PfTRAP on Bioko Island. Globally, the African PfTRAPs showed more diverse than the Asian ones, and significant genetic differentiation was discovered by the fixation index between African and Asian countries (Fst > 0.15, p < 0.05). 667 Asian isolates clustered in 136 haplotypes and 739 African isolates clustered in 528 haplotypes by network analysis. The mutations I116T, L221I, Y128F, G228V and P299S were predicted as probably damaging by PolyPhen online service, while mutations L49V, R285G, R285S, P299S and K421N would lead to a significant increase of free energy difference (ΔΔG > 1) indicated a destabilization of protein structure. Conclusions Evidences in the present investigation supported that PfTRAP gene from Bioko Island and other malaria endemic countries is highly polymorphic (especially at T cell epitopes), which provided the genetic information background for developing an PfTRAP-based universal effective vaccine. Moreover, some mutations have been shown to be detrimental to the protein structure or function and deserve further study and continuous monitoring.

Assessment of diversity in tropical soybean (Glycine max (L.) Merr.) varieties and elite breeding lines using single nucleotide polymorphism markers

2021 ◽  
Vol 19 (1) ◽  
pp. 20-28
Author(s):  
Abush Tesfaye Abebe ◽  
Adesike Oladoyin Kolawole ◽  
Nnanna Unachukwu ◽  
Godfree Chigeza ◽  
Hailu Tefera ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Single Nucleotide Polymorphism ◽  
Glycine Max ◽  
Snp Markers ◽  
Fixation Index ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Breeding Lines ◽  
Soybean Germplasm ◽  
Elite Breeding Lines

AbstractSoybean (Glycine max (L.) Merr.) is an important legume crop with high commercial value widely cultivated globally. Thus, the genetic characterization of the existing soybean germplasm will provide useful information for enhanced conservation, improvement and future utilization. This study aimed to assess the extent of genetic diversity of soybean elite breeding lines and varieties developed by the soybean breeding programme of the International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria. The genetic diversity of 65 soybean genotypes was studied using single-nucleotide polymorphism (SNP) markers. The result revealed that 2446 alleles were detected, and the indicators for allelic richness and diversity had good differentiating power in assessing the diversity of the genotypes. The three complementary approaches used in the study grouped the germplasm into three major clusters based on genetic relatedness. The analysis of molecular variance revealed that 71% (P < 0.001) variation was due to among individual genotypes, while 11% (P < 0.001) was ascribed to differences among the three clusters, and the fixation index (FST) was 0.11 for the SNP loci, signifying moderate genetic differentiation among the genotypes. The identified private alleles indicate that the soybean germplasm contains diverse variability that is yet to be exploited. The SNP markers revealed high diversity in the studied germplasm and found to be efficient for assessing genetic diversity in the crop. These results provide valuable information that might be utilized for assessing the genetic variability of soybean and other legume crops germplasm by breeding programmes.

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