scholarly journals Schinus Terebinthifolia Raddi: A Comparative Framework On Population Genetic Structure In A Restored Area After 12 Years*

2021 ◽  
Author(s):  
Erica Moraes Santos de Souza ◽  
Sheila Valéria Álvares-Carvalho ◽  
Robério Anastácio Ferreira ◽  
Renata Silva Mann
Keyword(s):  
Genetic Diversity ◽  
Continuous Monitoring ◽  
Diversity Index ◽  
Limiting Factor ◽  
Effective Population ◽  
Natural Area ◽  
High Genetic Diversity ◽  
Seed Sources ◽  
Adult Trees ◽  
Ssr Primers

Abstract The success of restoration projects depends upon the genetic diversity of the implanted species. It is a limiting factor, often because the seed sources are immersed in highly fragmented landscapes. This work was carried out to compare the genetic diversities of the juveniles and the adult trees of Schinus terebinthifolia Raddi in a mixed reforestation area, both in the restoration process and in the remaining natural area in the Atlantic Forest. Through five SSR primers, it was observed that the implanted population showed a greater genetic diversity index (He) (0.553 adults and 0.505 juveniles) when compared to the wild population (0.487 adults and 0.483 juveniles). It indicated that the forested area was established with individuals of high genetic diversity. There was a reduction of genetic diversity, with the loss of exclusive alleles and maintenance of inbreeding and coancestry in the juveniles of the reforested population. It can be inferred that there was a low gene flow among the fragments. The effective population size in both populations (adults and juveniles) was lower than that recommended for conserving populations in the short and long terms. These results have shown that continuous monitoring of this particular area is of absolute necessity and for applying techniques that can promote the connectivity of the fragments. It would allow for a more significant reduction of genetic drift and the persistence of the planted populations.

scholarly journals Development of Microsatellite Markers Derived from Expressed Sequence Tags of Polyporales for Genetic Diversity Analysis of EndangeredPolyporus umbellatus

2015 ◽  
Vol 2015 ◽  
pp. 1-11 ◽  
Author(s):  
Yuejin Zhang ◽  
Yuanyuan Chen ◽  
Ruihong Wang ◽  
Ailin Zeng ◽  
Michael K. Deyholos ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Expressed Sequence Tags ◽  
Large Scale ◽  
Gene Diversity ◽  
High Genetic Diversity ◽  
Information Index ◽  
Polyporus Umbellatus ◽  
Ssr Primers ◽  
Expressed Sequence

A large scale of EST sequences of Polyporales was screened in this investigation in order to identify EST-SSR markers for various applications. The distribution of EST sequences and SSRs in five families of Polyporales was analyzed, respectively. Mononucleotide was the most abundant type, followed by trinucleotide. Among five families, Ganodermataceae occupied the most SSR markers, followed by Coriolaceae. Functional prediction of SSR marker-containing EST sequences inGanoderma lucidumobtained three main groups, namely, cellular component, biological process, and molecular function. Thirty EST-SSR primers were designed to evaluate the genetic diversity of 13 naturalPolyporus umbellatusaccessions. Twenty one EST-SSRs were polymorphic with average PIC value of 0.33 and transferability rate of 71%. These 13P.umbellatusaccessions showed relatively high genetic diversity. The expected heterozygosity, Nei’s gene diversity, and Shannon information index were 0.41, 0.39, and 0.57, respectively. Both UPGMA dendrogram and principal coordinate analysis (PCA) showed the same cluster result that divided the 13 accessions into three or four groups.

scholarly journals The Sri Lankan paradox: high genetic diversity in Plasmodium vivax populations despite decreasing levels of malaria transmission

Parasitology ◽  
2014 ◽  
Vol 141 (7) ◽  
pp. 880-890 ◽  
Author(s):  
SHARMINI GUNAWARDENA ◽  
MARCELO U. FERREIRA ◽  
G. M. G. KAPILANANDA ◽  
DYANN F. WIRTH ◽  
NADIRA D. KARUNAWEERA
Keyword(s):  
Genetic Diversity ◽  
Sri Lanka ◽  
Plasmodium Vivax ◽  
Malaria Transmission ◽  
Population Size ◽  
Effective Population Size ◽  
Allele Frequency Distribution ◽  
Effective Population ◽  
High Genetic Diversity ◽  
Mode Shift

SUMMARYHere we examined whether the recent dramatic decline in malaria transmission in Sri Lanka led to a major bottleneck in the local Plasmodium vivax population, with a substantial decrease in the effective population size. To this end, we typed 14 highly polymorphic microsatellite markers in 185 P. vivax patient isolates collected from 13 districts in Sri Lanka over a period of 5 years (2003–2007). Overall, we found a high degree of polymorphism, with 184 unique haplotypes (12–46 alleles per locus) and average genetic diversity (expected heterozygosity) of 0·8744. Almost 69% (n = 127) isolates had multiple-clone infections (MCI). Significant spatial and temporal differentiation (FST = 0·04–0·25; P⩽0·0009) between populations was observed. The effective population size was relatively high but showed a decline from 2003–4 to 2006–7 periods (estimated as 45 661 to 22 896 or 10 513 to 7057, depending on the underlying model used). We used three approaches – namely, mode-shift in allele frequency distribution, detection of heterozygote excess and the M-ratio statistics – to test for evidence of a recent population bottleneck but only the low values of M-ratio statistics (ranging between 0·15–0·33, mean 0·26) were suggestive of such a bottleneck. The persistence of high genetic diversity and high proportion of MCI, with little change in effective population size, despite the collapse in demographic population size of P. vivax in Sri Lanka indicates the importance of maintaining stringent control and surveillance measures to prevent resurgence.

scholarly journals Linkage disequilibrium and within-breed genetic diversity in Iranian Zandi sheep

2019 ◽  
Vol 62 (1) ◽  
pp. 143-151 ◽  
Author(s):  
Seyed Mohammad Ghoreishifar ◽  
Hossein Moradi-Shahrbabak ◽  
Nahid Parna ◽  
Pourya Davoudi ◽  
Majid Khansefid
Keyword(s):  
Genetic Diversity ◽  
Linkage Disequilibrium ◽  
Association Studies ◽  
Genome Wide Association Studies ◽  
Effective Population ◽  
High Genetic Diversity ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Snp Panel ◽  
Zandi Sheep

Abstract. This research aimed to measure the extent of linkage disequilibrium (LD), effective population size (Ne), and runs of homozygosity (ROHs) in one of the major Iranian sheep breeds (Zandi) using 96 samples genotyped with Illumina Ovine SNP50 BeadChip. The amount of LD (r2) for single-nucleotide polymorphism (SNP) pairs in short distances (10–20 kb) was 0.21±0.25 but rapidly decreased to 0.10±0.16 by increasing the distance between SNP pairs (40–60 kb). The Ne of Zandi sheep in past (approximately 3500 generations ago) and recent (five generations ago) populations was estimated to be 6475 and 122, respectively. The ROH-based inbreeding was 0.023. We found 558 ROH regions, of which 37 % were relatively long (> 10 Mb). Compared with the rate of LD reduction in other species (e.g., cattle and pigs), in Zandi, it was reduced more rapidly by increasing the distance between SNP pairs. According to the LD pattern and high genetic diversity of Zandi sheep, we need to use an SNP panel with a higher density than Illumina Ovine SNP50 BeadChip for genomic selection and genome-wide association studies in this breed.

Genetic Diversity and Genetic Differentiation of Rheum palmatum by Chloroplast matK Sequences

2020 ◽  
Vol 10 (2) ◽  
pp. 96-103
Author(s):  
Xiaoqin Zhang ◽  
Na Lin ◽  
Liping Chen ◽  
Zunjing Zhang ◽  
Houxing Lei ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Diversity Index ◽  
Geographic Distance ◽  
High Genetic Diversity ◽  
Rheum Palmatum ◽  
Wild Resources ◽  
Nj Tree ◽  
Matk Sequence ◽  
Over Exploitation

Background: Rheum palmatum is a medically important plant in the Polygonaceae family. Its wild resources have been declining due to over-exploitation. It is important and urgent to investigate the genetic diversity for the conservation of R. palmatum. Methods: The Chloroplast DNA matK sequences were used to assess genetic diversity among and within populations in this species. The genetic diversity index was calculated by Dnasp, PERMUT and Arlequin 3.0 software, and a Neighbor-Joining (NJ)-tree was constructed by MEGA 5.0 software. Results: Nine haplotypes were obtained based on the matK sequence analysis in fifteen populations. We found a relatively high genetic diversity in species level (Hd = 0.7414), and the genetic diversity among populations (FST = 0.81582) was higher than that within populations (FSC = 0.69526) according to the AMOVA analysis. The genetic distance between populations ranged from 0 to 0.0044, which within populations ranged from 0 to 0.001761. There was a significant correlation between genetic distance and geographic distance (r = 0.601, P < 0.001) according to the SPSS analysis. Conclusion: The genetic diversity among populations was higher than that within populations due to geographic isolation and decline in gene flow among populations. This study is significant for further studies concerned with efficient collection and preservation of wild resource of R. palmatum.

Genetic diversity among geographically separated populations of Nepenthes mirabilis

Biologia ◽  
2006 ◽  
Vol 61 (3) ◽  
Author(s):  
Arunrat Chaveerach ◽  
Alongkod Tanomtong ◽  
Runglawan Sudmoon ◽  
Tawatchai Tanee
Keyword(s):  
Genetic Diversity ◽  
Diversity Index ◽  
Geographical Area ◽  
Inter Simple Sequence Repeat ◽  
Genetic Distances ◽  
High Genetic Diversity ◽  
Total Genetic Diversity ◽  
Environmental Variations ◽  
Diversity Profile ◽  
Great Genetic Diversity

AbstractThe distribution of Nepenthes mirabilis ranges from Northeast (NE) to South (S) Thailand. Eleven individuals from NE, S and Suen Jatujak market in Bangkok, Central (C) Thailand, were collected and divided into four populations according to their geographical areas. These four populations were analyzed to determine a genetic diversity profile using thirteen inter-simple sequence repeat markers. The individuals produced 75.18% polymorphic banding profiles. The Shannon’s index was used to estimate genetic diversity. Total genetic diversity (H T) and inter-population genetic diversity (H S) were 0.854 and 0.678, respectively. The degree of genetic differentiation (G ST) of the species populations is 0.206, whereas the gene flow (Nm) among all the various geographical area populations is 1.016. Both the dendrogram and the results of the Shannon’s diversity index suggest great genetic diversity. These results support the broad range of distribution sites of Nepenthes mirabilis, which would require high genetic diversity to adapt to the environmental variations that can be found between NE, C, and S Thailand. ANOVA shows that the genetic diversity in each population is not significantly different (P > 0.05). Mantel tests reveal that geographical distance is an important factor for affecting the genetic distances among populations.

scholarly journals Genetic Distinctiveness but Low Diversity Characterizes Rear-Edge Thuja standishii (Gordon) Carr. (Cupressaceae) Populations in Southwest Japan

Diversity ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 185
Author(s):  
James R. P. Worth ◽  
Ichiro Tamaki ◽  
Ikutaro Tsuyama ◽  
Peter A. Harrison ◽  
Kyoko Sugai ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Human Impacts ◽  
Allelic Variation ◽  
Southwest Japan ◽  
Effective Population ◽  
High Genetic Diversity ◽  
Rear Edge ◽  
The Core ◽  
Edge Populations

Rear-edge populations are of significant scientific interest because they can contain allelic variation not found in core-range populations. However, such populations can differ in their level of genetic diversity and divergence reflecting variation in life-history traits, demographic histories and human impacts. Using 13 EST-microsatellites, we investigated the genetic diversity and differentiation of rear-edge populations of the Japanese endemic conifer Thuja standishii (Gordon) Carr. in southwest Japan from the core-range in northeast Japan. Range-wide genetic differentiation was moderate (Fst = 0.087), with northeast populations weakly differentiated (Fst = 0.047), but harboring high genetic diversity (average population-level Ar = 4.76 and Ho = 0.59). In contrast, rear-edge populations were genetically diverged (Fst = 0.168), but contained few unique alleles with lower genetic diversity (Ar = 3.73, Ho = 0.49). The divergence between rear-edge populations exceeding levels observed in the core-range and results from ABC analysis and species distribution modelling suggest that these populations are most likely relicts of the Last Glacial Maximum. However, despite long term persistence, low effective population size, low migration between populations and genetic drift have worked to promote the genetic differentiation of southwest Japan populations of T. standishii without the accumulation of unique alleles.

scholarly journals Genomic Uniqueness of Local Sheep Breeds From Morocco

2021 ◽  
Vol 12 ◽  
Author(s):  
Abdessamad Ouhrouch ◽  
Simon Boitard ◽  
Frédéric Boyer ◽  
Bertrand Servin ◽  
Anne Da Silva ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Demographic History ◽  
Large Set ◽  
Whole Genome ◽  
Selection Signatures ◽  
Effective Population ◽  
High Genetic Diversity ◽  
Sheep Breeds ◽  
Genome Data ◽  
Genomic Regions

Sheep farming is a major source of meat in Morocco and plays a key role in the country’s agriculture. This study aims at characterizing the whole-genome diversity and demographic history of the main Moroccan sheep breeds, as well as to identify selection signatures within and between breeds. Whole genome data from 87 individuals representing the five predominant local breeds were used to estimate their level of neutral genetic diversity and to infer the variation of their effective population size over time. In addition, we used two methods to detect selection signatures: either for detecting selective sweeps within each breed separately or by detecting differentially selected regions by contrasting different breeds. We identified hundreds of genomic regions putatively under selection, which related to several biological terms involved in local adaptation or the expression of zootechnical performances such as Growth, UV protection, Cell maturation or Feeding behavior. The results of this study revealed selection signatures in genes that have an important role in traits of interest and increased our understanding of how genetic diversity is distributed in these local breeds. Thus, Moroccan local sheep breeds exhibit both a high genetic diversity and a large set of adaptive variations, and therefore, represent a valuable genetic resource for the conservation of sheep in the context of climate change.

Genetic Relationship in Sainfoin (Onobrychis viciifolia) Landraces Cultivated East Anatolia by using RAPD and ISSR Markers

2021 ◽  
Author(s):  
Mehmet Macit Ertuş
Keyword(s):  
Genetic Diversity ◽  
Diversity Index ◽  
Calcareous Soils ◽  
Similarity Index ◽  
Issr Markers ◽  
High Genetic Diversity ◽  
Onobrychis Viciifolia ◽  
Young Leaves ◽  
Rapd And Issr ◽  
Issr Primers

Background: Sainfoin (Onobrychis viciifolia) is a forage crop that yields high in arid and calcareous soils and is cultivated in large areas. There aren’t many genetic diversity studies on the varieties of cultured sainfoin. This study was conducted to determine the genetic diversity and the degree of relationship between 23 cultivated landraces and one registered variety. Methods: To take samples from the populations, seeds were sown in the field in 2014. Samples were taken from the young leaves of the plants and preserved at -80oC in same year. RAPD and ISSR primers were used in the study. The bands obtained as a result of PCR were recorded and the data of both methods were also evaluated by combining them. Result: In the study, 5 RAPD and 4 ISSR primers were used and a total of 49 bands were obtained. Of 29 bands obtained using RAPD primers, 20 were found to be polymorphic and of 20 bands obtained using ISSR primers, 15 were found to be polymorphic. It was found that there was a very low correlation between the two methods. Using RAPD and ISSR markers and RAPD + ISSR combination, the similarity index among populations was found to be between 0.25-0.95, 0.5-1.00 and 0.45-0.91, respectively. The Nei’s genetic diversity index was found to be between 0.3365, 0.2656 and 0.3018 with RAPD, ISSR primers and RAPD + ISSR combination, respectively. Based on the dendrograms obtained using RAPD, ISSR primers and RAPD + ISSR combination, the populations under analysis were classified into 3, 3 and 5 groups, respectively. With this study, the closest populations were identified and a significantly high genetic diversity was detected.

scholarly journals Genetic Diversity of Phyllanthus emblica From Two Different Climate Type Areas

2020 ◽  
Vol 11 ◽  
Author(s):  
Xiongfang Liu ◽  
Yongpeng Ma ◽  
Youming Wan ◽  
Zhenghong Li ◽  
Hong Ma
Keyword(s):  
Genetic Diversity ◽  
Large Scale ◽  
Land Reclamation ◽  
Southern China ◽  
Natural Habitat ◽  
Phyllanthus Emblica ◽  
Effective Population ◽  
Edible Plant ◽  
High Genetic Diversity ◽  
Wet Climate

Phyllanthus emblica L. is a well-known medicinal and edible plant species. Various medicinal compounds in the fruit make it an important medicinal and promising economic material. The plant is widely distributed in Southwestern and Southern China. However, due to massive deforestation and land reclamation as well as deterioration of its natural habitat in recent years, the wild resources of this species have been sharply reduced, and it is rare to see large-scale wild P. emblica forests so far. In order to effectively protect and rationally utilize this species, we investigated the genetic diversity, genetic structure, and population dynamics of 260 individuals from 10 populations of P. emblica sampled from the dry climate area in Yunnan and wet climate area in Guangxi using 20 polymorphic EST-SSR markers. We found high genetic diversity at the species level (He = 0.796) and within populations (He = 0.792), but low genetic differentiation among populations (FST = 0.084). In addition, most genetic variation existed within populations (92.44%) compared with variation among the populations (7.56%). Meanwhile, the NJ tree, STRUCTURE, and hierarchical analysis suggested that the sampled individuals were clustered into two distinct genetic groups. In contrast, the genetic diversity of the dry climate group (He = 0.786, Na = 11.790, I = 1.962) was higher than that of the wet climate group (He = 0.673, Na = 9.060, I = 1.555), which might be attributed to the combined effects of altitude, precipitation, and geographic distance. Interestingly, only altitude and precipitation had significant pure effects on the genetic diversity, and the former was slightly stronger. In addition, DIYABC analysis suggested the effective population size of P. emblica might have contracted in the beginning of the Last Glacial Maximum. These genetic features provided vital information for the conservation and sustainable development of genetic resources of P. emblica, and they also provided new insights and guidelines for ecological restoration and economic development in dry-hot valleys of Yunnan and karst areas in Guangxi.

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