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

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.

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Seascape Genomics of the Sugar Kelp Saccharina latissima along the North Eastern Atlantic Latitudinal Gradient

Genes ◽

10.3390/genes11121503 ◽

2020 ◽

Vol 11 (12) ◽

pp. 1503

Author(s):

Jaromir Guzinski ◽

Paolo Ruggeri ◽

Marion Ballenghien ◽

Stephane Mauger ◽

Bertrand Jacquemin ◽

...

Keyword(s):

Genetic Diversity ◽

Climatic Changes ◽

Statistical Correlation ◽

Limiting Factors ◽

Saccharina Latissima ◽

Nucleotide Polymorphisms ◽

Marker Allele ◽

The North ◽

Distribution Ranges ◽

Genetic Diversity And Structure

Temperature is one of the most important range-limiting factors for many seaweeds. Driven by the recent climatic changes, rapid northward shifts of species’ distribution ranges can potentially modify the phylogeographic signature of Last Glacial Maximum. We explored this question in detail in the cold-tolerant kelp species Saccharina latissima, using microsatellites and double digest restriction site-associated DNA sequencing ( ddRAD-seq) derived single nucleotide polymorphisms (SNPs) to analyze the genetic diversity and structure in 11 sites spanning the entire European Atlantic latitudinal range of this species. In addition, we checked for statistical correlation between genetic marker allele frequencies and three environmental proxies (sea surface temperature, salinity, and water turbidity). Our findings revealed that genetic diversity was significantly higher for the northernmost locality (Spitsbergen) compared to the southern ones (Northern Iberia), which we discuss in light of the current state of knowledge on phylogeography of S. latissima and the potential influence of the recent climatic changes on the population structure of this species. Seven SNPs and 12 microsatellite alleles were found to be significantly associated with at least one of the three environmental variables. We speculate on the putative adaptive functions of the genes associated with the outlier markers and the importance of these markers for successful conservation and aquaculture strategies for S. latissima in this age of rapid global change.

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A Genome-Wide Genetic Diversity Scan Reveals Multiple Signatures of Selection in a European Soybean Collection Compared to Chinese Collections of Wild and Cultivated Soybean Accessions

Frontiers in Plant Science ◽

10.3389/fpls.2021.631767 ◽

2021 ◽

Vol 12 ◽

Author(s):

Aamir Saleem ◽

Hilde Muylle ◽

Jonas Aper ◽

Tom Ruttink ◽

Jiao Wang ◽

...

Keyword(s):

Genetic Diversity ◽

Oil Content ◽

Selective Sweep ◽

Germplasm Collection ◽

Snp Markers ◽

Selective Sweeps ◽

Genome Wide ◽

Population Structure Analysis ◽

A Genome ◽

Signatures Of Selection

Targeted and untargeted selections including domestication and breeding efforts can reduce genetic diversity in breeding germplasm and create selective sweeps in crop genomes. The genomic regions at which selective sweeps are detected can reveal important information about signatures of selection. We have analyzed the genetic diversity within a soybean germplasm collection relevant for breeding in Europe (the EUCLEG collection), and have identified selective sweeps through a genome-wide scan comparing that collection to Chinese soybean collections. This work involved genotyping of 480 EUCLEG soybean accessions, including 210 improved varieties, 216 breeding lines and 54 landraces using the 355K SoySNP microarray. SNP calling of 477 EUCLEG accessions together with 328 Chinese soybean accessions identified 224,993 high-quality SNP markers. Population structure analysis revealed a clear differentiation between the EUCLEG collection and the Chinese materials. Further, the EUCLEG collection was sub-structured into five subgroups that were differentiated by geographical origin. No clear association between subgroups and maturity group was detected. The genetic diversity was lower in the EUCLEG collection compared to the Chinese collections. Selective sweep analysis revealed 23 selective sweep regions distributed over 12 chromosomes. Co-localization of these selective sweep regions with previously reported QTLs and genes revealed that various signatures of selection in the EUCLEG collection may be related to domestication and improvement traits including seed protein and oil content, phenology, nitrogen fixation, yield components, diseases resistance and quality. No signatures of selection related to stem determinacy were detected. In addition, absence of signatures of selection for a substantial number of QTLs related to yield, protein content, oil content and phenological traits suggests the presence of substantial genetic diversity in the EUCLEG collection. Taken together, the results obtained demonstrate that the available genetic diversity in the EUCLEG collection can be further exploited for research and breeding purposes. However, incorporation of exotic material can be considered to broaden its genetic base.

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Genetic diversity and structure of Musa balbisiana populations in Vietnam and its implications for the conservation of banana crop wild relatives

PLoS ONE ◽

10.1371/journal.pone.0253255 ◽

2021 ◽

Vol 16 (6) ◽

pp. e0253255

Author(s):

Arne Mertens ◽

Yves Bawin ◽

Samuel Vanden Abeele ◽

Simon Kallow ◽

Dang Toan Vu ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Crop Wild Relatives ◽

Wild Relatives ◽

Distribution Area ◽

Mountain Range ◽

Musa Balbisiana ◽

Northern Vietnam ◽

Central Vietnam ◽

Genetic Diversity And Structure

Crop wild relatives (CWR) are an indispensable source of alleles to improve desired traits in related crops. While knowledge on the genetic diversity of CWR can facilitate breeding and conservation strategies, it has poorly been assessed. Cultivated bananas are a major part of the diet and income of hundreds of millions of people and can be considered as one of the most important fruits worldwide. Here, we assessed the genetic diversity and structure of Musa balbisiana, an important CWR of plantains, dessert and cooking bananas. Musa balbisiana has its origin in subtropical and tropical broadleaf forests of northern Indo-Burma. This includes a large part of northern Vietnam where until now, no populations have been sampled. We screened the genetic variation and structure present within and between 17 Vietnamese populations and six from China using 18 polymorphic SSR markers. Relatively high variation was found in populations from China and central Vietnam. Populations from northern Vietnam showed varying levels of genetic variation, with low variation in populations near the Red River. Low genetic variation was found in populations of southern Vietnam. Analyses of population structure revealed that populations of northern Vietnam formed a distinct genetic cluster from populations sampled in China. Together with populations of central Vietnam, populations from northern Vietnam could be subdivided into five clusters, likely caused by mountain ranges and connected river systems. We propose that populations sampled in central Vietnam and on the western side of the Hoang Lien Son mountain range in northern Vietnam belong to the native distribution area and should be prioritised for conservation. Southern range edge populations in central Vietnam had especially high genetic diversity, with a high number of unique alleles and might be connected with core populations in northern Laos and southwest China. Southern Vietnamese populations are considered imported and not native.

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

Forests ◽

10.3390/f12020227 ◽

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.

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Genetic diversity and structure of walnut (Juglans regia L.) genotypes from Middle and High Atlas mountains of Morocco as investigated by Inter-Simple Sequence Repeat (ISSR) markers

Australian Journal of Crop Science ◽

10.21475/ajcs.19.13.12.p1932 ◽

2019 ◽

pp. 1983-1991

Author(s):

Ghizlane KABIRI ◽

Said BOUDA ◽

Mohammed ELHANSALI ◽

Abdelmajid HADDIOUI

Keyword(s):

Genetic Diversity ◽

Juglans Regia ◽

Issr Markers ◽

Conservation Strategies ◽

Gene Pools ◽

Mountain Range ◽

High Atlas ◽

Range Type ◽

Genetic Diversity And Structure ◽

Improvement Programs

The genetic diversity and genotypes structure of walnut (Juglans regia L.) are essential to understand and manage genetic resources of this species, as well as for further progress in breeding programs. ISSR markers were used to assess the genetic diversity of 66 individuals’ trees from 11 accessions, representing the main cropping area of walnut belonging to two ranges types of Mountain in Morocco: middle and high Atlas. Eleven ISSR primers rendered a total of 135 bands (91%) with 0.88 polymorphic information content. The utilization of 123 polymorphic bands revealed a high level of genetic variation within and among the examined accessions. The multi-locus values of Ht and Hs were 0.25 and 0.20, respectively. The AMOVA analysis showed that 71.30% of total genetic variability is accounted within accessions and 28.70% between accessions. This was congruent with the coefficient of genetic differentiation (GST=0.16). Bayesian model-based clustering approach identified three gene pools that were not correlated with mountain range type. This is the first application of ISSR markers for the assessment of genetic diversity in Moroccan germplasm of walnut. This information will be useful to define conservation strategies and improvement programs of this species.

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Hitchhiking in space: ancestry in adapting, spatially-extended populations

10.1101/084426 ◽

2016 ◽

Author(s):

Brent Allman ◽

Daniel B. Weissman

Keyword(s):

Genetic Diversity ◽

Small Region ◽

Genomic Region ◽

Spatial Distance ◽

Selective Sweeps ◽

Spatial Region ◽

Neutral Genetic Diversity ◽

Spatially Extended ◽

Neutral Mutations ◽

Spatial Locations

AbstractSelective sweeps reduce neutral genetic diversity. In sexual populations, this “hitchhiking” effect is thought to be limited to the local genomic region of the sweeping allele. While this is true in panmictic populations, we find that in spatially-extended populations the combined effects of many unlinked sweeps can affect patterns of ancestry (and therefore neutral genetic diversity) across the whole genome. Even low rates of sweeps can be enough to skew the spatial locations of ancestors such that neutral mutations that occur in an individual living outside a small region in the center of the range have virtually no chance of fixing in the population. The fact that nearly all ancestry rapidly traces back to a small spatial region also means that relatedness between individuals falls off very slowly as a function of the spatial distance between them.

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Genetic Diversity and Range Dynamics of Helleborus odorus subsp. cyclophyllus under Different Climate Change Scenarios

Forests ◽

10.3390/f11060620 ◽

2020 ◽

Vol 11 (6) ◽

pp. 620 ◽

Cited By ~ 2

Author(s):

Georgia Fassou ◽

Konstantinos Kougioumoutzis ◽

Gregoris Iatrou ◽

Panayiotis Trigas ◽

Vasileios Papasotiropoulos

Keyword(s):

Climate Change ◽

Genetic Diversity ◽

Range Shift ◽

Mountain Forest ◽

Mountain Range ◽

Peripheral Populations ◽

Climate Change Scenarios ◽

Genetic Composition ◽

The Balkans ◽

Genetic Diversity And Structure

Research Highlights: The effects of climate change on habitat loss, range shift and/or genetic impoverishment of mid-elevation plants has received less attention compared to alpine species. Moreover, genetic diversity patterns of mountain forest herbaceous species have scarcely been explored in the Balkans. In this context, our study is the first that aims to examine Helleborus odorus subsp. cyclophyllus, a medicinal plant endemic to the southern part of the Balkan Peninsula. Background and Objectives: We compare its genetic diversity and structure along the continuous mountain range of western Greece with the topographically less structured mountains of eastern Greece, and predict its present and future habitat suitability, using several environmental variables. Materials and Methods: Inter Simple Sequence Repeat (ISSR) markers were used to genotype 80 individuals from 8 populations, covering almost the species’ entire distribution range in Greece. We investigated the factors shaping its genetic composition and driving its current and future distribution. Results: High gene diversity (0.2239–0.3319), moderate population differentiation (0.0317–0.3316) and increased gene flow (Nm = 1.3098) was detected. According to any GCM/RCP/climate database combination, Helleborus odorus subsp. cyclophyllus is projected to lose a significant portion of its current distribution by 2070 and follow a trend towards genetic homogenization. Conclusions: Populations exhibit in terms of genetic structure a west–east genetic split, which becomes more evident southwards. This is mainly due to geographic/topographic factors and their interplay with Quaternary climatic oscillations, and to environmental constraints, which may have a negative impact on the species’ future distribution and genetic composition. Pindos mountain range seems to buffer climate change effects and will probably continue to host several populations. On the other hand, peripheral populations have lower genetic diversity compared to central populations, but still hold significant evolutionary potential due to the private alleles they maintain.

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GENETIC DIVERSITY OF ECHINOCOCCUS MULTILOCULARIS CESTODES IN EUROPE AS DETERMINED BY MITOCHONDRIAL AND NUCLEAR SEQUENCES

10.31016/978-5-9902340-8-6.2019.20.754-758 ◽

2019 ◽

pp. 754-758

Author(s):

Viliam Šnábel ◽

Tamás Sréter ◽

Bruno Gottstein ◽

Jakub Gawor ◽

Thomas Romig ◽

...

Keyword(s):

Genetic Diversity ◽

Central Europe ◽

Echinococcus Multilocularis ◽

Nuclear Dna ◽

Mountain Range ◽

Nucleotide Polymorphisms ◽

Arctic Regions ◽

European Distribution ◽

And Migration ◽

S Model

Alveolar echinococcosis caused by metacestode stage of the tapeworm Echinococcus multilocularis is considered as one of the most pathogenic zoonoses in temperate and arctic regions. To more thoroughly ascertain genetic diversity in E. multilocularis tapeworms from Europe and to indicate transmission patterns of parasite, 25 isolates from a contiguous territory of eight European countries were subjected to sequencing of mitochondrial and nuclear DNA. A total of 2 715 nucleotide sequences in nad1, cox1, rrnS, atp6 and actII genes were screened in the current study. Whereas in 24 isolates profiles belonging to a previously described European clade were identified, the interesting feature was related to the detection of the form being close to North American strain N1 (that appeared to have lower zoonotic potential) in Austrian patient. The known occurrence of this variant has thus extended from the St. Lawrence Island in the Bering Sea and Russian isolates in Yakutia to central Europe. The finding indicates that N1 genotype has not only circumpolar trans-Beringian distribution, but during glacial events in Pleistocene a more southerly fox dispersal has likely transmitted N1 into central Europe. Further distinguished genotype was confined to four isolates from southern Germany (mountain range of Swabian Jura) and had five substitutions compared to the main European form. One Latvian isolate had two mutations in cox1, one of which was identical to German isolates from Feldstetten. Single nucleotide polymorphisms were detected in single isolates from Slovakia, Hungary and France in cox1 and actIIgenes. Lower genetic diversity detected in the examined isolates in more peripheral zones of its European distribution has supported Knapp ́s model (2009) suggesting that parasite focus in Europe is governed by “mainland-island” transmission where ancestral foci supply hitherto non-endemic areas by dispersal generated by fox mobility and migration.

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Recombination and Gene Conversion in a 170-kb Genomic Region of Arabidopsis thaliana

Genetics ◽

10.1093/genetics/161.3.1269 ◽

2002 ◽

Vol 161 (3) ◽

pp. 1269-1278 ◽

Cited By ~ 7

Author(s):

Bernhard Haubold ◽

Jürgen Kroymann ◽

Andreas Ratzka ◽

Thomas Mitchell-Olds ◽

Thomas Wiehe

Keyword(s):

Genetic Diversity ◽

Arabidopsis Thaliana ◽

Linkage Disequilibrium ◽

Gene Conversion ◽

Genomic Sequence ◽

Genomic Region ◽

Resistance To Herbivory ◽

Linkage Disequilibria ◽

Coalescent Simulations ◽

The Mean

Abstract Arabidopsis thaliana is a highly selfing plant that nevertheless appears to undergo substantial recombination. To reconcile its selfing habit with the observations of recombination, we have sampled the genetic diversity of A. thaliana at 14 loci of ~500 bp each, spread across 170 kb of genomic sequence centered on a QTL for resistance to herbivory. A total of 170 of the 6321 nucleotides surveyed were polymorphic, with 169 being biallelic. The mean silent genetic diversity (πs) varied between 0.001 and 0.03. Pairwise linkage disequilibria between the polymorphisms were negatively correlated with distance, although this effect vanished when only pairs of polymorphisms with four haplotypes were included in the analysis. The absence of a consistent negative correlation between distance and linkage disequilibrium indicated that gene conversion might have played an important role in distributing genetic diversity throughout the region. We tested this by coalescent simulations and estimate that up to 90% of recombination is due to gene conversion.

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Genetic diversity and population structure of Plasmodium falciparum in Nigeria: insights from microsatellite loci analysis

Malaria Journal ◽

10.1186/s12936-021-03734-x ◽

2021 ◽

Vol 20 (1) ◽

Author(s):

Fehintola V. Ajogbasile ◽

Adeyemi T. Kayode ◽

Paul E. Oluniyi ◽

Kazeem O. Akano ◽

Jessica N. Uwanibe ◽

...

Keyword(s):

Genetic Diversity ◽

Plasmodium Falciparum ◽

Population Structure ◽

Microsatellite Loci ◽

Control Strategies ◽

Population Diversity ◽

Parasite Population ◽

Nested Polymerase Chain Reaction ◽

Public Health Burden ◽

Genetic Diversity And Structure

Abstract Background Malaria remains a public health burden especially in Nigeria. To develop new malaria control and elimination strategies or refine existing ones, understanding parasite population diversity and transmission patterns is crucial. Methods In this study, characterization of the parasite diversity and structure of Plasmodium falciparum isolates from 633 dried blood spot samples in Nigeria was carried out using 12 microsatellite loci of P. falciparum. These microsatellite loci were amplified via semi-nested polymerase chain reaction (PCR) and fragments were analysed using population genetic tools. Results Estimates of parasite genetic diversity, such as mean number of different alleles (13.52), effective alleles (7.13), allelic richness (11.15) and expected heterozygosity (0.804), were high. Overall linkage disequilibrium was weak (0.006, P < 0.001). Parasite population structure was low (Fst: 0.008–0.105, AMOVA: 0.039). Conclusion The high level of parasite genetic diversity and low population structuring in this study suggests that parasite populations circulating in Nigeria are homogenous. However, higher resolution methods, such as the 24 SNP barcode and whole genome sequencing, may capture more specific parasite genetic signatures circulating in the country. The results obtained can be used as a baseline for parasite genetic diversity and structure, aiding in the formulation of appropriate therapeutic and control strategies in Nigeria.

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