scholarly journals Population Transcriptomes Reveal the Interspecific Adaptive Genetic Differentiation of Liriodendron by Landscape Genetics

2020 ◽  
Author(s):  
Yufang Shen ◽  
Hui Xia ◽  
Zhonghua Tu ◽  
Yaxian Zong ◽  
Lichun Yang ◽  
...  
Keyword(s):  
Population Structure ◽  
Environmental Factors ◽  
Genetic Differentiation ◽  
Ecological Niche ◽  
Genetic Variations ◽  
Biological Pathways ◽  
Environmental Data ◽  
Genomic Resources ◽  
Population Structure Analysis ◽  
Precipitation Seasonality

Abstract Background: Adaptive genetic differentiation is a hotspot in the research of speciation mechanisms in evolutionary biology. Genomic resources are important for detecting ecological adaptive evolution of non-model plants. Using RNA-seq for non-model plants is a good approach to obtain their genomic resources. The combination of population transcriptome resources and environmental data can provide insights into the genetic mechanism of adaptive genetic differentiation.Results: Based on the population transcriptome data, we investigated the spatial distribution of genetic variations in Liriodendron to detect relationships between ecological factors and genetic differentiation. Environmental data and genetic variations from 17 populations were integrated to detect the population structure, adaptive genes and key environmental factors that shape the population genetic structure by landscape genetic approach. Here, we identified 16592 high-quality single nucleotide polymorphisms (SNPs). The population structure analysis results showed that 17 populations were divided into three groups: L. tulipifera, eastern group and western group of L. chinense. Redundancy analysis and latent factor mixed model analysis suggested that precipitation seasonality, precipitation in the driest quarter, diurnal temperature, and solar radiation in May were closely associated with the adaptive genetic differentiation of Liriodendron. Ecological niche differentiation analysis implied significant ecological niche divergence between L. chinense and L. tulipifera habitats. In total, 858 environment-related loci were identified, which were associated with 464 genes. Pathway enrichment analysis revealed that these genes were significantly enriched in multiple biological pathways. Related studies confirmed that these biological pathways play vital roles in plant growth, development, stress, immune response and photosynthesis.Conclusions: Our research provided empirical evidence that environmental factors may play a key role in driving adaptive genetic differentiation of species. Furthermore, the combination of population transcriptome resources and environmental datasets provides new insights into the study of adaptive genetic differentiation of species.

scholarly journals Microsatellite based molecular epidemiology of Leishmania infantum from re-emerging foci of visceral leishmaniasis in Armenia and pilot risk assessment by ecological niche modeling

2021 ◽  
Vol 15 (4) ◽  
pp. e0009288
Author(s):  
Katrin Kuhls ◽  
Olga Moskalenko ◽  
Anna Sukiasyan ◽  
Dezdemonia Manukyan ◽  
Gayane Melik-Andreasyan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Visceral Leishmaniasis ◽  
Central Asia ◽  
Causative Agent ◽  
Ecological Niche ◽  
Ecological Niche Modeling ◽  
Niche Modeling ◽  
Population Structure Analysis ◽  
First Time

Background Visceral leishmaniasis (VL) is re-emerging in Armenia since 1999 with 167 cases recorded until 2019. The objectives of this study were (i) to determine for the first time the genetic diversity and population structure of the causative agent of VL in Armenia; (ii) to compare these genotypes with those from most endemic regions worldwide; (iii) to monitor the diversity of vectors in Armenia; (iv) to predict the distribution of the vectors and VL in time and space by ecological niche modeling. Methodology/Principal findings Human samples from different parts of Armenia previously identified by ITS-1-RFLP as L. infantum were studied by Multilocus Microsatellite Typing (MLMT). These data were combined with previously typed L. infantum strains from the main global endemic regions for population structure analysis. Within the 23 Armenian L. infantum strains 22 different genotypes were identified. The combined analysis revealed that all strains belong to the worldwide predominating MON1-population, however most closely related to a subpopulation from Southeastern Europe, Maghreb, Middle East and Central Asia. The three observed Armenian clusters grouped within this subpopulation with strains from Greece/Turkey, and from Central Asia, respectively. Ecological niche modeling based on VL cases and collected proven vectors (P. balcanicus, P. kandelakii) identified Yerevan and districts Lori, Tavush, Syunik, Armavir, Ararat bordering Georgia, Turkey, Iran and Azerbaijan as most suitable for the vectors and with the highest risk for VL transmission. Due to climate change the suitable habitat for VL transmission will expand in future all over Armenia. Conclusions Genetic diversity and population structure of the causative agent of VL in Armenia were addressed for the first time. Further genotyping studies should be performed with samples from infected humans, animals and sand flies from all active foci including the neighboring countries to understand transmission cycles, re-emergence, spread, and epidemiology of VL in Armenia and the entire Transcaucasus enabling epidemiological monitoring.

scholarly journals Population structure and adaptive variation of Helichrysum italicum (Roth) G. Don along eastern Adriatic temperature and precipitation gradient

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Tonka Ninčević ◽  
Marija Jug-Dujaković ◽  
Martina Grdiša ◽  
Zlatko Liber ◽  
Filip Varga ◽  
...  
Keyword(s):  
Population Structure ◽  
Genetic Variation ◽  
Genetic Differentiation ◽  
Environmental Gradient ◽  
Conservation Strategies ◽  
Mediterranean Plants ◽  
Outlier Loci ◽  
Precipitation Seasonality ◽  
Genetic Diversity And Structure ◽  
Bioclimatic Variables

AbstractImmortelle (Helichrysum italicum (Roth) G. Don; Asteraceae) is a perennial plant species native to the Mediterranean region, known for many properties with wide application mainly in perfume and cosmetic industry. A total of 18 wild H. italicum populations systematically sampled along the eastern Adriatic environmental gradient were studied using AFLP markers to determine genetic diversity and structure and to identify loci potentially responsible for adaptive divergence. Results showed higher levels of intrapopulation diversity than interpopulation diversity. Genetic differentiation among populations was significant but low, indicating extensive gene flow between populations. Bayesian analysis of population structure revealed the existence of two genetic clusters. Combining the results of FST - outlier analysis (Mcheza and BayeScan) and genome-environment association analysis (Samβada, LFMM) four AFLP loci strongly associated with the bioclimatic variables Bio03 Isothermality, Bio08 Mean temperature of the wettest quarter, Bio15 Precipitation seasonality, and Bio17 Precipitation of driest quarter were found to be the main variables driving potential adaptive genetic variation in H. italicum along the eastern Adriatic environmental gradient. Redundancy analysis revealed that the partitioning of genetic variation was mainly associated with the adaptation to temperature oscillations. The results of the research may contribute to a clearer understanding of the importance of local adaptations for the genetic differentiation of Mediterranean plants and allow the planning of appropriate conservation strategies. However, considering that the identified outlier loci may be linked to genes under selection rather than being the target of natural selection, future studies must aim at their additional analysis.

scholarly journals EVALUACIÓN DE AMPLIFICACIÓN CRUZADA DE MICROSATÉLITES PARA ESTUDIOS DE GENÉTICA POBLACIONAL DEL CAZÓN ANTILLANO RHIZOPRIONODON POROSUS (CARCHARHINIDAE) EN EL CARIBE COLOMBIANO

2016 ◽  
Vol 45 (1) ◽  
Author(s):  
Mónica Almanza Bernal ◽  
Edna J. Márquez ◽  
Luis Chasqui
Keyword(s):  
Population Structure ◽  
Genetic Differentiation ◽  
Distribution Range ◽  
Small Scale ◽  
Formulation Development ◽  
Significant Genetic Differentiation ◽  
Fishery Resource ◽  
Genotype Frequencies ◽  
Population Structure Analysis ◽  
The Caribbean

The Caribbean sharpnose shark, Rhizoprionodon porosus is an important resource for artisanal small-scale fisheries. It is one of the most abundant coastal sharks within its distribution range, and plays an important role as a predator in coastal marine ecosystems. For its coastal habits, it is susceptible to intensive extraction, especially the juveniles. To accomplish proper management and conservation of exploited Rhizoprionodon populations, knowledge about its genetic diversity and its population structure within their distribution range is needed. The ability of heterologous primers developed for other requiem sharks to amplify microsatellite molecular markers in R. porosus was tested in this study (cross amplification). The change in allele frequency of four microsatellite loci served to assess the genetic structure of R. porosus in the Colombian Caribbean. Analysis of molecular variance Amova and population structure analysis using the Фst statistical of genotype frequencies indicate low but significant genetic differentiation among R. porosus from the departments analyzed (Фst (3,165) = 0.002; p = 0.000). Besides, the analysis of pairs of departments indicates that there is significant genetic differentiation among La Guajira and the other samples analyzed of the Antillean sharpnose shark (all p values = 0.000). The information obtained helps to understand the dynamics of natural populations of the Caribbean sharpnose shark, serving as a baseline for the formulation, development of conservation strategies and management of this fishery resource; however, due the low number of heterologous loci useful for population genetics studies, research efforts on the development of specific markers for the species should be done for further population genetic studies of this species.

scholarly journals cpDNA-Gene-Sequence-Based Genetic Diversity, Population Structure, and Gene Flow Analysis of Ethiopian Lowland Bamboo (Bambusinea: Oxytenanthera abyssinica (A. Rich.) Munro)

2021 ◽  
Vol 2021 ◽  
pp. 1-13
Author(s):  
Oumer Abdie Oumer ◽  
Kassahun Tesfaye ◽  
Tileye Feyissa ◽  
Dagnew Yibeyen ◽  
Jayaraman Durai ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Gene Flow ◽  
Genetic Differentiation ◽  
Gc Content ◽  
Wood Products ◽  
Population Structure Analysis ◽  
The World ◽  
Oxytenanthera Abyssinica ◽  
Metekel Zone

Background. As a member of Poaceae and subfamily Bambusoideae, Ethiopian lowland bamboo (Oxytenanthera abyssinica) is one of the most important nontimber forest resources or a potential alternative to wood and wood products. Ethiopia contributes 86% of the total area of bamboo on the continent, Africa, and 7% of the world. O. abyssinica in Ethiopia accounts for 85% of the total national coverage of bamboo. Several studies have been performed on the genetic diversity and population structure analysis of various bamboo species throughout the world but almost nothing in Ethiopia and O. abyssinica. Methods. Young fresh leaves of O. abyssinica from thirteen natural lowland bamboo growing areas across the country were collected. DNA was isolated using a modified CTAB DNA isolation method. Three cpDNA gene sequences (matK, ndhF3, and rps16) were used for the study. PCR products were analyzed, purified, and pair-end sequenced to calculate AC/GC content, average number of nucleotide differences (k), nucleotide diversity (π) and population mutation rates per 100 sites ( θ w ), InDel (Insertion-Deletion), DNA divergence, gene flow, and genetic differentiation. Results. Metekel Zone was found to have extremely higher k, π, and θ w . Higher frequency of genetic differentiation was found between Metekel Zone vs. the distant populations. Higher frequency of gene flow was found between Assosa Zone vs. Oromia populations. Kurmuk haplotype from gaps or missing data considered and Bambasi haplotype from not considered has descendants around them. Conclusion. Using sequences of cpDNA genes, populations of O. abyssinica collected in Ethiopia show clear diversity based on their geographic location. Metekel Zone was found to have the most diverse population, Assosa Zone has been found to be the source of evolution of O. abyssinica, and Gambella population shows a difference from other O. abyssinica populations.

scholarly journals Population Structure Analysis of Globally Diverse Bull Genomes

2016 ◽  
Author(s):  
Neo Christopher Chung ◽  
Joanna Szyda ◽  
Magdalena Fra̧szczak ◽  
Keyword(s):  
Population Structure ◽  
Genetic Differentiation ◽  
Latent Variable ◽  
Bos Taurus ◽  
Complex Structure ◽  
Management Strategies ◽  
Structural Complexity ◽  
Genetic Management ◽  
Population Structure Analysis ◽  
Wide Range

AbstractSince domestication, population bottlenecks, breed formation, and selective breeding have radically shaped the genealogy and genetics of Bos taurus. In turn, characterization of population structure among globally diverse bull genomes enables detailed assessment of genetic resources and origins. By analyzing 432 unrelated bull genomes from 13 breeds and 16 countries, we demonstrate genetic diversity and structural complexity among the global bull population. Importantly, we relaxed a strong assumption of discrete or admixed population, by adapting latent variable models for individual-specific allele frequencies that directly capture a wide range of complex structure from genome-wide genotypes. We identified a highly complex population structure that defies the conventional hypothesis based on discrete membership and contributes to pervasive genetic differentiation in bull genomes. As measured by magnitude of differentiation, selection pressure on SNPs within genes is substantially greater than that on intergenic regions. Additionally, broad regions of chromosome 6 harboring largest genetic differentiation suggest positive selection underlying population structure. We carried out gene set analysis using SNP annotations to identify enriched functional categories such as energy-related processes and multiple development stages. Our comprehensive analysis of bull population structure can support genetic management strategies that capture structural complexity and promote sustainable genetic breadth.

scholarly journals Genetic diversity of Ethiopian durum wheat landraces

PLoS ONE ◽  
2021 ◽  
Vol 16 (2) ◽  
pp. e0247016
Author(s):  
Kefyalew Negisho ◽  
Surafel Shibru ◽  
Klaus Pillen ◽  
Frank Ordon ◽  
Gwendolin Wehner
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Gene Flow ◽  
Genetic Differentiation ◽  
Durum Wheat ◽  
Total Variation ◽  
Population Structure Analysis ◽  
Wheat Landraces ◽  
Wheat Lines ◽  
Durum Wheat Landraces

Genetic diversity and population structure assessment in crops is essential for marker trait association, marker assisted breeding and crop germplasm conservation. We analyzed a set of 285 durum wheat accessions comprising 215 Ethiopian durum wheat landraces, 10 released durum wheat varieties, 10 advanced durum wheat lines from Ethiopia, and 50 durum wheat lines from CIMMYT. We investigated the genetic diversity and population structure for the complete panel as well as for the 215 landraces, separately based on 11,919 SNP markers with known physical positions. The whole panel was clustered into two populations representing on the one hand mainly the landraces, and on the other hand mainly released, advanced and CIMMYT lines. Further population structure analysis of the landraces uncovered 4 subgroups emphasizing the high degree of genetic diversity within Ethiopian durum landraces. Population structure based AMOVA for both sets unveiled significant (P < 0.001) variation between populations and within populations. Total variation within population accessions (81%, 76%) was higher than total variation between populations (19%, 24%) for both sets. Population structure analysis based genetic differentiation (FST) and gene flow (Nm) for the whole set and the Ethiopian landraces were 0.19 and 0.24, 1.04, and 0.81, respectively indicating high genetic differentiation and limited gene flow. Diversity indices verify that the landrace panel was more diverse with (I = 0.7, He = 0.46, uHe = 0.46) than the advanced lines (I = 0.6, He = 0.42, uHe = 0.42). Similarly, differences within the landrace clusters were observed. In summary a high genetic diversity within Ethiopian durum wheat landraces was detected, which may be a target for national and international wheat improvement programs to exploit valuable traits for biotic and abiotic stresses.

scholarly journals Exploring the genomic resources and analysing the genetic diversity and population structure of Chinese indigenous rabbit breeds by RAD-seq

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Chenmiao Liu ◽  
Shuhui Wang ◽  
Xianggui Dong ◽  
Jiping Zhao ◽  
Xiangyang Ye ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
New Zealand ◽  
Principal Component ◽  
Enrichment Analysis ◽  
Snp Markers ◽  
Selection Signature ◽  
Genomic Resources ◽  
Population Structure Analysis ◽  
New Zealand Rabbits

Abstract Background Chinese indigenous rabbits have distinct characteristics, such as roughage resistance, stress resistance and environmental adaptability, which are of great significance to the sustainable development of the rabbit industry in China. Therefore, it is necessary to study the genetic diversity and population structure of this species and develop genomic resources. Results In this study, we used restriction site-associated DNA sequencing (RAD-seq) to obtain 1,006,496 SNP markers from six Chinese indigenous rabbit breeds and two imported rabbit breeds. Jiuyishan and Fujian Yellow rabbits showed the highest nucleotide diversity (π) and decay of linkage disequilibrium (LD), as well as higher observed heterozygosity (Ho) and expected heterozygosity (He), indicating higher genetic diversity than other rabbits. The inbreeding coefficient (FIS) of New Zealand rabbits and Belgian rabbits was higher than that of other rabbits. The neighbour-joining (NJ) tree, principal component analysis (PCA), and population structure analysis of autosomes and Y chromosomes showed that Belgian, New Zealand, Wanzai, Sichuan White, and Minxinan Black rabbits clustered separately, and Fujian Yellow, Yunnan Colourful, and Jiuyishan rabbits clustered together. Wanzai rabbits were clearly separated from other populations (K = 3), which was consistent with the population differentiation index (FST) analysis. The selection signature analysis was performed in two populations with contrasting coat colours. With Sichuan White and New Zealand rabbits as the reference populations and Minxinan Black and Wanzai rabbits as the target populations, 408, 454, 418, and 518 genes with a selection signature, respectively, were obtained. Gene Ontology (GO) classification and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were performed on the genes with a selection signature. The results showed that the genes with a selection signature were enriched in the melanogenesis pathway in all four sets of selection signature analyses. Conclusions Our study provides the first insights into the genetics and genomics of Chinese indigenous rabbit breeds and serves as a valuable resource for the further effective utilization of the species.

scholarly journals Assessing genomic diversity and signatures of selection in Jiaxian Red cattle using whole-genome sequencing data

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Xiaoting Xia ◽  
Shunjin Zhang ◽  
Huaju Zhang ◽  
Zijing Zhang ◽  
Ningbo Chen ◽  
...  
Keyword(s):  
Population Structure ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genomic Variation ◽  
Genomic Diversity ◽  
System Response ◽  
Whole Genome ◽  
Population Structure Analysis ◽  
Native Cattle ◽  
Genomic Regions

Abstract Background Native cattle breeds are an important source of genetic variation because they might carry alleles that enable them to adapt to local environment and tough feeding conditions. Jiaxian Red, a Chinese native cattle breed, is reported to have originated from crossbreeding between taurine and indicine cattle; their history as a draft and meat animal dates back at least 30 years. Using whole-genome sequencing (WGS) data of 30 animals from the core breeding farm, we investigated the genetic diversity, population structure and genomic regions under selection of Jiaxian Red cattle. Furthermore, we used 131 published genomes of world-wide cattle to characterize the genomic variation of Jiaxian Red cattle. Results The population structure analysis revealed that Jiaxian Red cattle harboured the ancestry with East Asian taurine (0.493), Chinese indicine (0.379), European taurine (0.095) and Indian indicine (0.033). Three methods (nucleotide diversity, linkage disequilibrium decay and runs of homozygosity) implied the relatively high genomic diversity in Jiaxian Red cattle. We used θπ, CLR, FST and XP-EHH methods to look for the candidate signatures of positive selection in Jiaxian Red cattle. A total number of 171 (θπ and CLR) and 17 (FST and XP-EHH) shared genes were identified using different detection strategies. Functional annotation analysis revealed that these genes are potentially responsible for growth and feed efficiency (CCSER1), meat quality traits (ROCK2, PPP1R12A, CYB5R4, EYA3, PHACTR1), fertility (RFX4, SRD5A2) and immune system response (SLAMF1, CD84 and SLAMF6). Conclusion We provide a comprehensive overview of sequence variations in Jiaxian Red cattle genomes. Selection signatures were detected in genomic regions that are possibly related to economically important traits in Jiaxian Red cattle. We observed a high level of genomic diversity and low inbreeding in Jiaxian Red cattle. These results provide a basis for further resource protection and breeding improvement of this breed.

scholarly journals Comprehensive genotyping of a Brazilian cassava (Manihot esculenta Crantz) germplasm bank: insights into diversification and domestication

2021 ◽  
Vol 134 (5) ◽  
pp. 1343-1362
Author(s):  
Alex C. Ogbonna ◽  
Luciano Rogerio Braatz de Andrade ◽  
Lukas A. Mueller ◽  
Eder Jorge de Oliveira ◽  
Guillaume J. Bauchet
Keyword(s):  
Population Genetics ◽  
Population Structure ◽  
Manihot Esculenta ◽  
Ex Situ ◽  
Germplasm Bank ◽  
Effective Population ◽  
Manihot Esculenta Crantz ◽  
Genetic Groups ◽  
Population Structure Analysis ◽  
Modern Breeding

Abstract Key message Brazilian cassava diversity was characterized through population genetics and clustering approaches, highlighting contrasted genetic groups and spatial genetic differentiation. Abstract Cassava (Manihot esculenta Crantz) is a major staple root crop of the tropics, originating from the Amazonian region. In this study, 3354 cassava landraces and modern breeding lines from the Embrapa Cassava Germplasm Bank (CGB) were characterized. All individuals were subjected to genotyping-by-sequencing (GBS), identifying 27,045 single-nucleotide polymorphisms (SNPs). Identity-by-state and population structure analyses revealed a unique set of 1536 individuals and 10 distinct genetic groups with heterogeneous linkage disequilibrium (LD). On this basis, a density of 1300–4700 SNP markers were selected for large-effect quantitative trait loci (QTL) detection. Identified genetic groups were further characterized for population genetics parameters including minor allele frequency (MAF), observed heterozygosity $$({H}_{o})$$ ( H o ) , effective population size estimate $$\widehat{{(N}_{e}}$$ ( N e ^ ) and polymorphism information content (PIC). Selection footprints and introgressions of M. glaziovii were detected. Spatial population structure analysis revealed five ancestral populations related to distinct Brazilian ecoregions. Estimation of historical relationships among identified populations suggests an early population split from Amazonian to Atlantic forest and Caatinga ecoregions and active gene flows. This study provides a thorough genetic characterization of ex situ germplasm resources from cassava’s center of origin, South America, with results shedding light on Brazilian cassava characteristics and its biogeographical landscape. These findings support and facilitate the use of genetic resources in modern breeding programs including implementation of association mapping and genomic selection strategies.

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