scholarly journals Genetic Diversity and Structure of Apomictic and Sexually Reproducing Lindera Species (Lauraceae) in Japan

Forests ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 227
Author(s):  
Mizuho Nakamura ◽  
Satoshi Nanami ◽  
Seiya Okuno ◽  
Shun K. Hirota ◽  
Ayumi Matsuo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Difference ◽  
Natural Populations ◽  
Genotyping By Sequencing ◽  
Geographic Area ◽  
Single Individual ◽  
Nucleotide Polymorphisms ◽  
Inbreeding Coefficients ◽  
Low Genetic Diversity ◽  
Genetic Diversity And Structure

Research Highlights: genetic diversity in populations were compared among related shrub species with different reproductive systems. Background and Objectives: Lindera species are dioecious trees or shrubs that produce seeds by mating of males and females. To evaluate the importance of genetic diversity for the persistence of natural populations, we compared genetic information among four Lindera species in Japan. Three are dioecious shrubs (Lindera praecox, Lindera umbellata, and Lindera obtusiloba) that produce seeds by sexual reproduction. The remaining species, Lindera glauca, reproduces by apomixis; only female plants are found in Japan. Materials and Methods: all four species were sampled across a wide geographic area, from Tohoku to Kyushu, Japan. Single nucleotide polymorphisms (SNPs) were detected by multiplexed ISSR genotyping by sequencing (MIG-seq) and the resulting genetic diversity parameters were compared among populations. Results: in all sexually reproducing species, the values of observed heterozygosity were close to the expected ones and the inbreeding coefficients were nearly 0. These results were supposed to be caused by their obligate outcrossing. The genetic difference increased, in ascending order, between a mother plant and its seeds, within populations, and across geographic space. We observed a substantial geographic component in the genetic structure of these species. For L. glauca, the genetic difference between a mother and its seeds, within populations, and across space were not significantly different from what would be expected from PCR errors. Genetic diversity within and among populations of L. glauca was extremely low. Conclusions: apomixis has the advantage of being able to found populations from a single individual, without mating, which may outweigh the disadvantages associated with the extremely low genetic diversity of L. glauca. This may explain why this species is so widely distributed in Japan. Provided that the current genotypes remain suited to environmental conditions, L. glauca may not be constrained by its limited genetic diversity.

scholarly journals Genetic diversity and structure in the Endangered Allen Cays Rock Iguana,Cyclura cychlura inornata

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1793 ◽  
Author(s):  
Andrea C. Aplasca ◽  
John B. Iverson ◽  
Mark E. Welch ◽  
Giuliano Colosimo ◽  
Evon R. Hekkala
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Gene ◽  
Population Decline ◽  
Natural Populations ◽  
Unknown Origin ◽  
Source Population ◽  
Effective Population ◽  
The Bahamas ◽  
Low Genetic Diversity ◽  
Genetic Diversity And Structure

The Endangered Allen Cays Rock Iguana (Cyclura cychlura inornata) is endemic to the Allen Cays, a tiny cluster of islands in the Bahamas. Naturally occurring populations exist on only two cays (<4 ha each). However, populations of unknown origin were recently discovered on four additional cays. To investigate patterns of genetic variation among these populations, we analyzed nuclear and mitochondrial markers for 268 individuals. Analysis of three mitochondrial gene regions (2,328 bp) and data for eight nuclear microsatellite loci indicated low genetic diversity overall. Estimates of effective population sizes based on multilocus genotypes were also extremely low. Despite low diversity, significant population structuring and variation in genetic diversity measures were detected among cays. Genetic data confirm the source population for an experimentally translocated population while raising concerns regarding other, unauthorized, translocations. Reduced heterozygosity is consistent with a documented historical population decline due to overharvest. This study provides the first range-wide genetic analysis of this subspecies. We suggest strategies to maximize genetic diversity during ongoing recovery including additional translocations to establish assurance populations and additional protective measures for the two remaining natural populations.

scholarly journals Evolutionary Toxicogenomics of the Striped Killifish (Fundulus majalis) in the New Bedford Harbor (Massachusetts, USA)

2019 ◽  
Vol 20 (5) ◽  
pp. 1129 ◽  
Author(s):  
Paolo Ruggeri ◽  
Xiao Du ◽  
Douglas Crawford ◽  
Marjorie Oleksiak
Keyword(s):  
Genetic Diversity ◽  
Enrichment Analysis ◽  
Genotyping By Sequencing ◽  
Pollution Level ◽  
Nucleotide Polymorphisms ◽  
Pollution Levels ◽  
Low Genetic Diversity ◽  
Aquatic Pollutants ◽  
New Bedford Harbor ◽  
Geographical Scale

In this paper, we used a Genotyping-by-Sequencing (GBS) approach to find and genotype more than 4000 genome-wide SNPs (Single Nucleotide Polymorphisms) from striped killifish exposed to a variety of polychlorinated biphenyls (PCBs) and other aromatic pollutants in New Bedford Harbor (NBH, Massachusetts, USA). The aims of this study were to identify the genetic consequences of exposure to aquatic pollutants and detect genes that may be under selection. Low genetic diversity (HE and π) was found in the site exposed to the highest pollution level, but the pattern of genetic diversity did not match the pollution levels. Extensive connectivity was detected among sampling sites, which suggests that balanced gene flow may explain the lack of genetic variation in response to pollution levels. Tests for selection identified 539 candidate outliers, but many of the candidate outliers were not shared among tests. Differences among test results likely reflect different test assumptions and the complex pollutant mixture. Potentially, selectively important loci are associated with 151 SNPs, and enrichment analysis suggests a likely involvement of these genes with pollutants that occur in NBH. This result suggests that selective processes at genes targeted by pollutants may be occurring, even at a small geographical scale, and may allow the local striped killifish to resist the high pollution levels.

scholarly journals Genetic Diversity, Structure, and Selective Sweeps in Spinacia turkestanica Associated With the Domestication of Cultivated Spinach

2021 ◽  
Vol 12 ◽  
Author(s):  
Sanjaya Gyawali ◽  
Gehendra Bhattarai ◽  
Ainong Shi ◽  
Chris Kik ◽  
Lindsey J. du Toit
Keyword(s):  
Genetic Diversity ◽  
Central Asia ◽  
Selective Sweep ◽  
Spinacia Oleracea ◽  
Genomic Region ◽  
Day Length ◽  
Mountain Range ◽  
Nucleotide Polymorphisms ◽  
Selective Sweeps ◽  
Genetic Diversity And Structure

Genotype-by-sequencing (GBS) was used to explore the genetic diversity and structure of Spinacia turkestanica, and the selective sweeps involved in domestication of cultivated spinach, S. oleracea, from S. turkestanica. A total 7,065 single nucleotide polymorphisms (SNPs) generated for 16 Spinacia oleracea and 76 S. turkestanica accessions placed the S. oleracea accessions in one group, Q1, and the 76 S. turkestanica accessions, which originated from Central Asia, in two distinct groups, Q2 and Q3. The Q2 group shared greater genetic identity with the S. oleracea accessions, Q1, than the Q3 S. turkestanica group. Likewise, the S. oleracea Q1 group had a smaller Fst (0.008) with the Q2 group than with the Q3 group (Fst = 0.012), and a greater gene flow (Nm = 30.13) with the Q2 group than with the Q3 group (Nm = 21.83). The Q2 accessions originated primarily from Uzbekistan while the Q3 accessions originated mostly from Tajikistan. The Zarafshan Mountain Range appears to have served as a physical barrier that largely separated members of the Q2 and Q3 groups of S. turkestanica. Accessions with admixtures of Q2 and Q3 were collected primarily from lower elevations at the southern end of the Zarafshan Mountain Range in Uzbekistan. Selective sweep regions identified at 32, 49, and 52 Mb on chromosomes 1, 2, and 3, respectively, appear to have played a vital role in the domestication of S. oleracea as they are correlated with important domestication traits, including day length sensitivity for bolting (flowering). High XP-CLR scores at the 52 Mb genomic region of chromosome three suggest that a selective sweep at this region was responsible for early differentiation of S. turkestanica into two groups in Central Asia.

scholarly journals Population Genetics and Evolution Analysis Reveal Diversity and Origin of Ammopiptanthus in China.

2021 ◽  
Author(s):  
Guai-qiang Chai ◽  
Yizhong Duan ◽  
Peipei Jiao ◽  
Zhongyu Du ◽  
Furen Kang
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Association Studies ◽  
Natural Populations ◽  
Principal Component ◽  
Nucleotide Polymorphisms ◽  
Future Design ◽  
Ammopiptanthus Nanus ◽  
Genome Wide

Abstract Background：Elucidating and revealing the population genetic structure, genetic diversity and recombination is essential for understanding the evolution and adaptation of species. Ammopiptanthus, which is an endangered survivor from the Tethys in the Tertiary Period, is the only evergreen broadleaf shrub grown in Northwest of China. However, little is known about its genetic diversity and underlying adaptation mechanisms. Results：Here, 111 Ammopiptanthus individuals collected from fifteen natural populations in estern China were analyzed by means of the specific locus amplified fragment sequencing (SLAF-seq). Based on the single nucleotide polymorphisms (SNPs) and insertions and deletions (InDels) detected by SLAF-seq, genetic diversity and markers associated with climate and geographical distribution variables were identified. The results of genetic diversity and genetic differentiation revealed that all fifteen populations showed medium genetic diversity, with PIC values ranging from 0.1648 to 0.3081. AMOVA and Fst indicated that a low genetic differentiation existed among populations. Phylogenetic analysis showed that NX-BG and NMG-DQH of fifteen populations have the highest homology，while the genetic structure analysis revealed that these Ammopiptanthus germplasm accessions were structured primarily along the basis of their geographic collection, and that an extensive admixture occurred in each group. In addition, the genome-wide linkage disequilibrium (LD) and principal component analysis showed that Ammopiptanthus nanus had a more diverse genomic background, and all genetic populations were clearly distinguished, although different degrees of introgression were detected in these groups. Conclusion：Our study could provide guidance to the future design of association studies and the systematic utilization and protection of the genetic variation characterizing the Ammopiptanthus.

scholarly journals Global range expansion history of pepper (Capsicum spp.) revealed by over 10,000 genebank accessions

2021 ◽  
Vol 118 (34) ◽  
pp. e2104315118
Author(s):  
Pasquale Tripodi ◽  
Mark Timothy Rabanus-Wallace ◽  
Lorenzo Barchi ◽  
Sandip Kale ◽  
Salvatore Esposito ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genotyping By Sequencing ◽  
Focal Region ◽  
Nucleotide Polymorphisms ◽  
Trade Routes ◽  
Genebank Management ◽  
Capsicum Spp ◽  
History Of ◽  
Cultural Commodity

Genebanks collect and preserve vast collections of plants and detailed passport information, with the aim of preserving genetic diversity for conservation and breeding. Genetic characterization of such collections has the potential to elucidate the genetic histories of important crops, use marker–trait associations to identify loci controlling traits of interest, search for loci undergoing selection, and contribute to genebank management by identifying taxonomic misassignments and duplicates. We conducted a genomic scan with genotyping by sequencing (GBS) derived single nucleotide polymorphisms (SNPs) of 10,038 pepper (Capsicum spp.) accessions from worldwide genebanks and investigated the recent history of this iconic staple. Genomic data detected up to 1,618 duplicate accessions within and between genebanks and showed that taxonomic ambiguity and misclassification often involve interspecific hybrids that are difficult to classify morphologically. We deeply interrogated the genetic diversity of the commonly consumed Capsicum annuum to investigate its history, finding that the kinds of peppers collected in broad regions across the globe overlap considerably. The method ReMIXTURE—using genetic data to quantify the similarity between the complement of peppers from a focal region and those from other regions—was developed to supplement traditional population genetic analyses. The results reflect a vision of pepper as a highly desirable and tradable cultural commodity, spreading rapidly throughout the globe along major maritime and terrestrial trade routes. Marker associations and possible selective sweeps affecting traits such as pungency were observed, and these traits were shown to be distributed nonuniformly across the globe, suggesting that human preferences exerted a primary influence over domesticated pepper genetic structure.

scholarly journals Genotyping-by-Sequencing Reveals Molecular Genetic Diversity in Italian Common Bean Landraces

Diversity ◽  
2019 ◽  
Vol 11 (9) ◽  
pp. 154 ◽  
Author(s):  
Lucia Lioi ◽  
Diana L. Zuluaga ◽  
Stefano Pavan ◽  
Gabriella Sonnante
Keyword(s):  
Genetic Diversity ◽  
Common Bean ◽  
Genotyping By Sequencing ◽  
Fixation Index ◽  
Most Probable Number ◽  
Probable Number ◽  
Individual Snps ◽  
Starting Point ◽  
Genetic Diversity And Structure ◽  
The Common

The common bean (Phaseolus vulgaris L.) is one of the main legumes worldwide and represents a valuable source of nutrients. Independent domestication events in the Americas led to the formation of two cultivated genepools, namely Mesoamerican and Andean, to which European material has been brought back. In this study, Italian common bean landraces were analyzed for their genetic diversity and structure, using single nucleotide polymorphism (SNP) markers derived from genotyping-by-sequencing (GBS) technology. After filtering, 11,866 SNPs were obtained and 798 markers, pruned for linkage disequilibrium, were used for structure analysis. The most probable number of subpopulations (K) was two, consistent with the presence of the two genepools, identified through the phaseolin diagnostic marker. Some landraces were admixed, suggesting probable hybridization events between Mesoamerican and Andean material. When increasing the number of possible Ks, the Andean germplasm appeared to be structured in two or three subgroups. The subdivision within the Andean material was also observed in a principal coordinate analysis (PCoA) plot and a dendrogram based on genetic distances. The Mesoamerican landraces showed a higher level of genetic diversity compared to the Andean landraces. Calculation of the fixation index (FST) at individual SNPs between the Mesoamerican and Andean genepools and within the Andean genepool evidenced clusters of highly divergent loci in specific chromosomal regions. This work may help to preserve landraces of the common bean from genetic erosion, and could represent a starting point for the identification of interesting traits that determine plant adaptation.

scholarly journals Using Random Amplified Polymorphic DNA to Assess Genetic Diversity and Structure of NaturalCalophyllum brasiliense(Clusiaceae) Populations in Riparian Forests

2014 ◽  
Vol 2014 ◽  
pp. 1-8
Author(s):  
Evânia Galvão Mendonça ◽  
Anderson Marcos de Souza ◽  
Fábio de Almeida Vieira ◽  
Regiane Abjaud Estopa ◽  
Cristiane Aparecida Fioravante Reis ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Random Amplified Polymorphic Dna ◽  
Natural Populations ◽  
Rio Grande ◽  
Shannon Index ◽  
High Genetic Diversity ◽  
Family Structures ◽  
Genetic Diversity And Structure ◽  
Kinship Coefficients

The objective of this study was to assess the genetic variability in two natural populations ofCalophyllum brasilienselocated along two different rivers in the state of Minas Gerais, Brazil, using RAPD molecular markers. Eighty-two polymorphic fragments were amplified using 27 primers. The values obtained for Shannon index (I) were 0.513 and 0.530 for the populations located on the margins of the Rio Grande and Rio das Mortes, respectively, demonstrating the high genetic diversity in the studied populations. Nei’s genetic diversity (He) was 0.341 for the Rio Grande population and 0.357 for the Rio das Mortes population. These results were not significantly different between populations and suggest a large proportion of heterozygote individuals within both populations. AMOVA showed that 70.42% of the genetic variability is found within populations and 29.58% is found among populations (ФST=0.2958). The analysis of kinship coefficients detected the existence of family structures in both populations. Average kinship coefficients between neighboring individuals were 0.053 (P<0.001) in Rio das Mortes and 0.040 (P<0.001) in Rio Grande. This could be due to restricted pollen and seed dispersal and the history of anthropogenic disturbance in the area. These factors are likely to contribute to the relatedness observed among these genotypes.

Low genetic diversity at allozyme loci in Juglans cinerea

2000 ◽  
Vol 78 (9) ◽  
pp. 1238-1243 ◽  
Author(s):  
Ricardo Morin ◽  
Jean Beaulieu ◽  
Marie Deslauriers ◽  
Gaëtan Daoust ◽  
Jean Bousquet
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Deciduous Forest ◽  
Polymorphic Locus ◽  
Natural Populations ◽  
Minor Component ◽  
Temperate Deciduous Forest ◽  
Juglans Cinerea ◽  
Low Genetic Diversity ◽  
Allozyme Loci

Butternut (Juglans cinerea L.) is a minor component of the temperate deciduous forest region of northeastern North America, but it is severely affected by the butternut canker (Sirococcus clavigignenti-juglandacearum Nair, Kostichka, and Kuntz) in the southern part of its natural range. Genetic diversity and population structure in as-yet unaffected or only slightly affected natural populations were evaluated at 12 isozyme loci. The genetic diversity estimates were low with values much below those estimated in other species of the same genus or in boreal tree species, with 25 and 13.9% polymorphic loci at the species and population levels, respectively; 1.3 and 2.3 alleles per locus and per polymorphic locus, respectively, at the species level; and an average observed heterozygosity of 0.028. Population differentiation was low, with the exception of one unique population. The implications for advanced conservation are discussed.Key words: butternut, isozymes, Sirococcus, canker, population structure.

Recent distribution changes affect geographic clines in genetic diversity and structure of Pinus densiflora natural populations in Japan

2013 ◽  
Vol 304 ◽  
pp. 407-416 ◽  
Author(s):  
Masakazu G. Iwaizumi ◽  
Yoshiaki Tsuda ◽  
Masato Ohtani ◽  
Yoshihiko Tsumura ◽  
Makoto Takahashi
Keyword(s):  
Genetic Diversity ◽  
Pinus Densiflora ◽  
Natural Populations ◽  
Genetic Diversity And Structure
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