scholarly journals Pleistocene climate changes explain large-scale genetic variation in a dominant grassland species, Lolium perenne L

2018 ◽  
Author(s):  
J.L. Blanco-Pastor ◽  
S. Manel ◽  
P. Barre ◽  
A.M. Roschanski ◽  
E. Willner ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Lolium Perenne ◽  
Large Scale ◽  
Agricultural Land ◽  
Natural Populations ◽  
Genomic Diversity ◽  
Cooling Period ◽  
Grassland Species ◽  
Continental Scale ◽  
Natural Grasslands

AbstractAimGrasslands have been pivotal in the development of herbivore breeding since the Neolithic and are still nowadays the most widespread agricultural land-use across Europe. However, it remains unclear whether the current large-scale genetic variation of plant species found in natural grasslands of Europe is the result of human activities or natural processes.LocationEurope.TaxonLolium perenne L (perennial ryegrass).MethodsWe reconstructed the phylogeographic history of L. perenne, a dominant grassland species, using 481 natural populations including 11 populations from closely related taxa. We combined the Genotyping-by-Sequencing (GBS) and Pool-sequencing (Pool-seq) methods to obtain high-quality allele frequency calls of ~ 500 k SNP loci. We performed genetic structure analyses and demographic reconstructions based on the site frequency spectrum (SFS). We additionally used the same genotyping protocol to assess the genomic diversity of a set of 32 cultivars representative of the L. perenne cultivars widely used for forage purposes.ResultsExpansion across Europe took place during the Würm glaciation (12-110 kya), a cooling period that decreased the dominance of trees in favour of grasses. Splits and admixtures in L. perenne fit historical sea level changes in the Mediterranean basin. The development of agriculture in Europe (7-3.5 kya), that caused an increase in the abundance of grasslands, did not have an effect on the demographic patterns of L. perenne. We found little differentiation between modern cultivars and certain natural variants. However, modern cultivars do not represent the wide genetic variation found in natural populations.Main conclusionsDemographic events in L. perenne can be explained by the changing climatic conditions during the Pleistocene. Natural populations maintain a wide genomic variability at continental scale that has been underused by recent breeding activities. This variability constitutes valuable standing genetic variation for future adaptation of grasslands to climate change, safeguarding the agricultural services they provide.

scholarly journals Genomics of clinal local adaptation in Pinus sylvestris under continuous environmental and spatial genetic setting

2019 ◽  
Author(s):  
Jaakko S. Tyrmi ◽  
Jaana Vuosku ◽  
Juan J. Acosta ◽  
Zhen Li ◽  
Lieven Sterck ◽  
...  
Keyword(s):  
Pinus Sylvestris ◽  
Local Adaptation ◽  
Large Scale ◽  
Molecular Genetic ◽  
Natural Populations ◽  
Keystone Species ◽  
Evolutionary Genetics ◽  
Genomic Diversity ◽  
Landscape Genomics ◽  
Polygenic Adaptation

AbstractUnderstanding the consequences of local adaptation at the genomic diversity is a central goal in evolutionary genetics of natural populations. In species with large continuous geographical distributions the phenotypic signal of local adaptation is frequently clear, but the genetic background often remains elusive. We examined the patterns of genetic diversity in Pinus sylvestris, a keystone species in many Eurasian ecosystems with a huge distribution range and decades of forestry research showing that it is locally adapted to the vast range of environmental conditions. Making P. sylvestris an even more attractive subject of local adaptation study, population structure has been shown to be weak previously and in this study. However, little is known about the molecular genetic basis of adaptation, as the massive size of gymnosperm genomes has prevented large scale genomic surveys. We generated a both geographically and genomically extensive dataset using a targeted sequencing approach. By applying divergence-based and landscape genomics methods we found that several coding loci contribute to local adaptation. We also discovered a very large (ca. 300 Mbp) putative inversion with a signal of local adaptation, which to our knowledge is the first such discovery in conifers. Our results call for more detailed analysis of structural variation in relation to genomic basis of local adaptation, emphasize the lack of large effect loci contributing to local adaptation in the coding regions and thus point out to the need for more attention towards multi-locus analysis of polygenic adaptation.

scholarly journals High-Throughput Genome-Wide Genotyping To Optimize the Use of Natural Genetic Resources in the Grassland Species Perennial Ryegrass (Lolium perenne L.)

2020 ◽  
Vol 10 (9) ◽  
pp. 3347-3364 ◽  
Author(s):  
Thomas Keep ◽  
Jean-Paul Sampoux ◽  
José Luis Blanco-Pastor ◽  
Klaus J Dehmer ◽  
Matthew J Hegarty ◽  
...  
Keyword(s):  
Genetic Resources ◽  
Lolium Perenne ◽  
Prediction Models ◽  
Natural Populations ◽  
Snp Markers ◽  
Lolium Perenne L ◽  
Grassland Species ◽  
Synthetic Populations ◽  
Natural Diversity ◽  
Almost All

Abstract The natural genetic diversity of agricultural species is an essential genetic resource for breeding programs aiming to improve their ecosystem and production services. A large natural ecotype diversity is usually available for most grassland species. This could be used to recombine natural climatic adaptations and agronomic value to create improved populations of grassland species adapted to future regional climates. However describing natural genetic resources can be long and costly. Molecular markers may provide useful information to help this task. This opportunity was investigated for Lolium perenne L., using a set of 385 accessions from the natural diversity of this species collected right across Europe and provided by genebanks of several countries. For each of these populations, genotyping provided the allele frequencies of 189,781 SNP markers. GWAS were implemented for over 30 agronomic and/or putatively adaptive traits recorded in three climatically contrasted locations (France, Belgium, Germany). Significant associations were detected for hundreds of markers despite a strong confounding effect of the genetic background; most of them pertained to phenology traits. It is likely that genetic variability in these traits has had an important contribution to environmental adaptation and ecotype differentiation. Genomic prediction models calibrated using natural diversity were found to be highly effective to describe natural populations for almost all traits as well as commercial synthetic populations for some important traits such as disease resistance, spring growth or phenological traits. These results will certainly be valuable information to help the use of natural genetic resources of other species.

Genetic Variation and Phenotypic Plasticity in Populations of Paterson's Curse (Echium plantagineum L.) In South-Eastern Australia

1985 ◽  
Vol 33 (6) ◽  
pp. 677 ◽  
Author(s):  
H Wood ◽  
R Degabriele
Keyword(s):  
Genetic Variation ◽  
Phenotypic Plasticity ◽  
Large Scale ◽  
Natural Populations ◽  
Moisture Stress ◽  
Climatic Indices ◽  
South Eastern ◽  
Moisture Regimes ◽  
Eastern Australia ◽  
South Eastern Australia

Natural populations of Echium plantagineum on an east-west line across south-eastern Australia were sampled on three occasions during the growing season, and seeds collected from individual plants in each population were grown in a common glasshouse. In another experiment seedlings of E. plantagineum were divided and clones from each plant were grown under two soil moisture regimes. Field populations differed significantly in all seven characters measured at all sampling dates but, with one exception, between-population differences were unrelated to five climatic indices. Glasshouse populations differed significantly in 15 of 27 characters; variations in some of these characters were related by regression analysis to one or more of the climatic indices. Clones grown under moisture stress flowered later, had proportionally wider leaves and were smaller than well watered clones. The data suggest that an ecocline has developed, or is developing, in E. plantagineum in south- eastern Australia in response to large-scale and long-term aspects of climate, although extensive genetic variation between individuals in each population was also observed. This species exhibits a great deal of phenotypic plasticity in response to localized environmental factors.

scholarly journals Comparative Population Genomics Analysis of the Mammalian Fungal PathogenPneumocystis

mBio ◽  
2018 ◽  
Vol 9 (3) ◽  
pp. e00381-18 ◽  
Author(s):  
Ousmane H. Cissé ◽  
Liang Ma ◽  
Da Wei Huang ◽  
Pavel P. Khil ◽  
John P. Dekker ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Large Scale ◽  
Population Genomics ◽  
Demographic History ◽  
Natural Populations ◽  
Severe Pneumonia ◽  
Population Declines ◽  
Host Shifts ◽  
Rats And Mice

ABSTRACTPneumocystisspecies are opportunistic mammalian pathogens that cause severe pneumonia in immunocompromised individuals. These fungi are highly host specific and uncultivablein vitro. HumanPneumocystisinfections present major challenges because of a limited therapeutic arsenal and the rise of drug resistance. To investigate the diversity and demographic history of natural populations ofPneumocystisinfecting humans, rats, and mice, we performed whole-genome and large-scale multilocus sequencing of infected tissues collected in various geographic locations. Here, we detected reduced levels of recombination and variations in historical demography, which shape the global population structures. We report estimates of evolutionary rates, levels of genetic diversity, and population sizes. Molecular clock estimates indicate thatPneumocystisspecies diverged before their hosts, while the asynchronous timing of population declines suggests host shifts. Our results have uncovered complex patterns of genetic variation influenced by multiple factors that shaped the adaptation ofPneumocystispopulations during their spread across mammals.IMPORTANCEUnderstanding how natural pathogen populations evolve and identifying the determinants of genetic variation are central issues in evolutionary biology.Pneumocystis, a fungal pathogen which infects mammals exclusively, provides opportunities to explore these issues. In humans,Pneumocystiscan cause a life-threatening pneumonia in immunosuppressed individuals. In analysis of differentPneumocystisspecies infecting humans, rats, and mice, we found that there are high infection rates and that natural populations maintain a high level of genetic variation despite low levels of recombination. We found no evidence of population structuring by geography. Our comparisons of the times of divergence of these species to their respective hosts suggest thatPneumocystismay have undergone recent host shifts. The results demonstrate thatPneumocystisstrains are widely disseminated geographically and provide a new understanding of the evolution of these pathogens.

scholarly journals Identifying tagging SNPs for African specific genetic variation from the African Diaspora Genome

2017 ◽  
Author(s):  
Henry Richard Johnston ◽  
Yi-Juan Hu ◽  
Jingjing Gao ◽  
Timoty D. O’Connor ◽  
Goncalo Abecasis ◽  
...  
Keyword(s):  
Genetic Variation ◽  
African Diaspora ◽  
Large Scale ◽  
Sequence Data ◽  
African Ancestry ◽  
Genomic Diversity ◽  
Whole Genome Sequence ◽  
Genotyping Array ◽  
Wide Range ◽  
Novel Variation

A primary goal of The Consortium on Asthma among African-ancestry Populations in the Americas (CAAPA) is to develop an ‘African Diaspora Power Chip’ (ADPC), a genotyping array consisting of tagging SNPs, useful in comprehensively identifying African specific genetic variation. This array is designed based on the novel variation identified in 642 CAAPA samples of African ancestry with high coverage whole genome sequence data (~30x depth). This novel variation extends the pattern of variation catalogued in the 1000 Genomes and Exome Sequencing Projects to a spectrum of populations representing the wide range of West African genomic diversity. These individuals from CAAPA also comprise a large swath of the African Diaspora population and incorporate historical genetic diversity covering nearly the entire Atlantic coast of the Americas. Here we show the results of designing and producing such a microchip array. This novel array covers African specific variation far better than other commercially available arrays, and will enable better GWAS analyses for researchers with individuals of African descent in their study populations. A recent study1 cataloging variation in continental African populations suggests this type of African-specific genotyping array is both necessary and valuable for facilitating large-scale GWAS in populations of African ancestry.

Partnerships Generate Co-Benefits in Agricultural Stream Restoration (Canterbury, New Zealand)

2020 ◽  
Vol 4 (1) ◽  
Author(s):  
Catherine M. Febria ◽  
Maggie Bayfield ◽  
Kathryn E. Collins ◽  
Hayley S. Devlin ◽  
Brandon C. Goeller ◽  
...  
Keyword(s):  
New Zealand ◽  
Large Scale ◽  
Agricultural Land ◽  
Indigenous Rights ◽  
Freshwater Ecosystem ◽  
Reduced Pressure ◽  
Ecosystem Integrity ◽  
Riparian Management ◽  
Scale Change ◽  
Large Scale Change

In Aotearoa New Zealand, agricultural land-use intensification and decline in freshwater ecosystem integrity pose complex challenges for science and society. Despite riparian management programmes across the country, there is frustration over a lack in widespread uptake, upfront financial costs, possible loss in income, obstructive legislation and delays in ecological recovery. Thus, social, economic and institutional barriers exist when implementing and assessing agricultural freshwater restoration. Partnerships are essential to overcome such barriers by identifying and promoting co-benefits that result in amplifying individual efforts among stakeholder groups into coordinated, large-scale change. Here, we describe how initial progress by a sole farming family at the Silverstream in the Canterbury region, South Island, New Zealand, was used as a catalyst for change by the Canterbury Waterway Rehabilitation Experiment, a university-led restoration research project. Partners included farmers, researchers, government, industry, treaty partners (Indigenous rights-holders) and practitioners. Local capacity and capability was strengthened with practitioner groups, schools and the wider community. With partnerships in place, co-benefits included lowered costs involved with large-scale actions (e.g., earth moving), reduced pressure on individual farmers to undertake large-scale change (e.g., increased participation and engagement), while also legitimising the social contracts for farmers, scientists, government and industry to engage in farming and freshwater management. We describe contributions and benefits generated from the project and describe iterative actions that together built trust, leveraged and aligned opportunities. These actions were scaled from a single farm to multiple catchments nationally.

Phosphorus Leaching Under Cut Grassland

1999 ◽  
Vol 39 (12) ◽  
pp. 63-67 ◽  
Author(s):  
B. L. Turner ◽  
P. M. Haygarth
Keyword(s):  
Surface Waters ◽  
Large Scale ◽  
Agricultural Land ◽  
Algal Growth ◽  
Soil Types ◽  
P Fractions ◽  
Inorganic P ◽  
Potential Source ◽  
Significant Mechanism ◽  
Total P

Phosphorus (P) transfer from agricultural land to surface waters can contribute to eutrophication, excess algal growth and associated water quality problems. Grasslands have a high potential for P transfer, as they receive P inputs as mineral fertiliser and concentrates cycled through livestock manures. The transfer of P can occur through surface and subsurface pathways, although the capacity of most soils to fix inorganic P has meant that subsurface P transfer by leaching mechanisms has often been perceived as negligible. We investigated this using large-scale monolith lysimeters (135 cm deep, 80 cm diameter) to monitor leachate P under four grassland soil types. Leachate was collected during the 1997–98 drainage year and analysed for a range of P fractions. Mean concentrations of total P routinely exceeded 100 μg l−1 from all soil types and, therefore, exceeded P concentrations above which eutrophication and algal growth can occur. The majority of the leachate P was in algal-available Mo-reactive (inorganic) forms, although a large proportion occurred in unreactive (organic) forms. We suggest that subsurface transfer by leaching can represent a significant mechanism for agricultural P transfer from some soils and must be given greater consideration as a potential source of diffuse P pollution to surface waters.

“Community Interests” and the Role of International Law in the Creation of a Global Market for Agricultural Land

2018 ◽  
Author(s):  
Jochen von Bernstorff
Keyword(s):  
International Law ◽  
Large Scale ◽  
Agricultural Land ◽  
Food Sovereignty ◽  
Global Market ◽  
Negative Consequences ◽  
Cultural Rights ◽  
Land Grab ◽  
Large Scale Land ◽  
The One

The chapter explores the notion of “community interests” with regard to the global “land-grab” phenomenon. Over the last decade, a dramatic increase of foreign investment in agricultural land could be observed. Bilateral investment treaties protect around 75 per cent of these large-scale land acquisitions, many of which came with associated social problems, such as displaced local populations and negative consequences for food security in Third World countries receiving these large-scale foreign investments. Hence, two potentially conflicting areas of international law are relevant in this context: Economic, social, and cultural rights and the principles of permanent sovereignty over natural resources and “food sovereignty” challenging large-scale investments on the one hand, and specific norms of international economic law stabilizing them on the other. The contribution discusses the usefulness of the concept of “community interests” in cases where the two colliding sets of norms are both considered to protect such interests.

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