scholarly journals Genomic Variation Shaped by Environmental and Geographical Factors in Prairie Cordgrass Natural Populations Collected across Its Native Range in the USA

Genes ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 1240
Author(s):  
Jia Guo ◽  
Patrick J. Brown ◽  
Albert L. Rayburn ◽  
Carolyn J. Butts-Wilmsmeyer ◽  
Arvid Boe ◽  
...  
Keyword(s):  
Abiotic Stress Tolerance ◽  
Natural Populations ◽  
Genomic Variation ◽  
Biofuel Production ◽  
Breeding Value ◽  
Grass Species ◽  
Gene Pools ◽  
Ploidy Levels ◽  
Geographical Factors ◽  
Prairie Cordgrass

Prairie cordgrass (Spartina pectinata Link) is a native perennial warm-season (C4) grass common in North American prairies. With its high biomass yield and abiotic stress tolerance, there is a high potential of developing prairie cordgrass for conservation practices and as a dedicated bioenergy crop for sustainable cellulosic biofuel production. However, as with many other undomesticated grass species, little information is known about the genetic diversity or population structure of prairie cordgrass natural populations as compared to their ecotypic and geographic adaptation in North America. In this study, we sampled and characterized a total of 96 prairie cordgrass natural populations with 9315 high quality SNPs from a genotyping-by-sequencing (GBS) approach. The natural populations were collected from putative remnant prairie sites throughout the Midwest and Eastern USA, which are the major habitats for prairie cordgrass. Partitioning of genetic variance using SNP marker data revealed significant variance among and within populations. Two potential gene pools were identified as being associated with ploidy levels, geographical separation, and climatic separation. Geographical factors such as longitude and altitude, and environmental factors such as annual temperature, annual precipitation, temperature of the warmest month, precipitation of the wettest month, precipitation of Spring, and precipitation of the wettest month are important in affecting the intraspecific distribution of prairie cordgrass. The divergence of prairie cordgrass natural populations also provides opportunities to increase breeding value of prairie cordgrass as a bioenergy and conservation crop.

scholarly journals Ploidy frequencies in plants with ploidy heterogeneity: fitting a general gametic model to empirical population data

2013 ◽  
Vol 280 (1751) ◽  
pp. 20122387 ◽  
Author(s):  
Jan Suda ◽  
Tomáš Herben
Keyword(s):  
Natural Populations ◽  
Evolutionary Process ◽  
Optimization Procedure ◽  
Population Data ◽  
Unreduced Gametes ◽  
Unreduced Gamete ◽  
Model Parameters ◽  
Main Mode ◽  
Ploidy Levels ◽  
Polyploid Formation

Genome duplication (polyploidy) is a recurrent evolutionary process in plants, often conferring instant reproductive isolation and thus potentially leading to speciation. Outcome of the process is often seen in the field as different cytotypes co-occur in many plant populations. Failure of meiotic reduction during gametogenesis is widely acknowledged to be the main mode of polyploid formation. To get insight into its role in the dynamics of polyploidy generation under natural conditions, and coexistence of several ploidy levels, we developed a general gametic model for diploid–polyploid systems. This model predicts equilibrium ploidy frequencies as functions of several parameters, namely the unreduced gamete proportions and fertilities of higher ploidy plants. We used data on field ploidy frequencies for 39 presumably autopolyploid plant species/populations to infer numerical values of the model parameters (either analytically or using an optimization procedure). With the exception of a few species, the model fit was very high. The estimated proportions of unreduced gametes (median of 0.0089) matched published estimates well. Our results imply that conditions for cytotype coexistence in natural populations are likely to be less restrictive than previously assumed. In addition, rather simple models show sufficiently rich behaviour to explain the prevalence of polyploids among flowering plants.

Haploidy and plant breeding

1981 ◽  
Vol 292 (1062) ◽  
pp. 499-507 ◽  
Keyword(s):  
Plant Breeding ◽  
Doubled Haploids ◽  
Chromosome Complement ◽  
Basic Research ◽  
Breeding Value ◽  
Additive Variance ◽  
Ploidy Levels ◽  
Breeding Programmes ◽  
Dh Lines

A haploid is an organism that looks like a sporophyte, but has the chromosome complement of a reduced gamete. There are several ways in which haploids can occur or be induced in vivo : spontaneously, mostly associated with polyembryony, and through abnormal processes after crosses, like pseudogamy, semigamy, preferential elimination of the chromosomes of one parental species, and androgenesis. In the crops described, haploids are or are near to being used in basic research and plant breeding. The application of haploids in breeding self-pollinated crops is based on their potential for producing fully homozygous lines in one generation, which can be assessed directly in the field. Early generation testing of segregating populations is possible through haploids, because doubled haploids (DH) possess additive variance only. Haploids can also be applied in classical breeding programmes to make these more efficient through improved reliability of selection. The application of haploids in cross-pollinated crops is also based on a rapid production of DH-lines, which can be used as inbred lines for the production of hybrid varieties. By means of haploids all natural barriers to repeated selfing are bypassed. In autotetraploid crops there are two types of haploid. One cycle of haploidization leads to dihaploids; a second cycle produces monohaploids. The significance of dihaploids is in their greatly simplified genetics and breeding and in the possibility of estimation of the breeding value of tetraploid cultivars by assessing their dihaploids. The main drawback of dihaploids is their restriction to two alleles per locus. Also, after doubling, it is impossible to achieve tetra-allelism at many loci, the requirement for maximal performance of autotetraploid cultivars. Tetra-allelism can be obtained when improved dihaploids have a genetically controlled mechanism of forming highly heterozygous restitution gametes with the unreduced number of chromosomes. Monohaploids, after doubling or twice doubling, may lead to fully homozygous diploids and tetraploids. These are important for basic research, but not yet for practical application. Meiotic data of potato homozygotes at three ploidy levels are presented.

scholarly journals Structural genome analysis in cultivated potato taxa

2019 ◽  
Vol 133 (3) ◽  
pp. 951-966 ◽  
Author(s):  
Maria Kyriakidou ◽  
Sai Reddy Achakkagari ◽  
José Héctor Gálvez López ◽  
Xinyi Zhu ◽  
Chen Yu Tang ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Agronomic Traits ◽  
Genomic Variation ◽  
Sequencing Data ◽  
Structural Variations ◽  
Structural Genomic ◽  
Ploidy Levels ◽  
Cultivated Potato ◽  
Number Variation

Abstract Key message Twelve potato accessions were selected to represent two principal views on potato taxonomy. The genomes were sequenced and analyzed for structural variation (copy number variation) against three published potato genomes. Abstract The common potato (Solanum tuberosum L.) is an important staple crop with a highly heterozygous and complex tetraploid genome. The other taxa of cultivated potato contain varying ploidy levels (2X–5X), and structural variations are common in the genomes of these species, likely contributing to the diversification or agronomic traits during domestication. Increased understanding of the genomes and genomic variation will aid in the exploration of novel agronomic traits. Thus, sequencing data from twelve potato landraces, representing the four ploidy levels, were used to identify structural genomic variation compared to the two currently available reference genomes, a double monoploid potato genome and a diploid inbred clone of S. chacoense. The results of a copy number variation analysis showed that in the majority of the genomes, while the number of deletions is greater than the number of duplications, the number of duplicated genes is greater than the number of deleted ones. Specific regions in the twelve potato genomes have a high density of CNV events. Further, the auxin-induced SAUR genes (involved in abiotic stress), disease resistance genes and the 2-oxoglutarate/Fe(II)-dependent oxygenase superfamily proteins, among others, had increased copy numbers in these sequenced genomes relative to the references.

The Institute of Evolution Wild Cereal Gene Bank at the University of Haifa

2018 ◽  
Vol 65 (3-4) ◽  
pp. 129-146 ◽  
Author(s):  
Tamar Krugman ◽  
Eviatar Nevo ◽  
Alex Beharav ◽  
Hanan Sela ◽  
Tzion Fahima
Keyword(s):  
Agronomic Traits ◽  
Natural Populations ◽  
Ecological Factors ◽  
Triticum Dicoccoides ◽  
Grain Protein Content ◽  
Hordeum Spontaneum ◽  
Gene Bank ◽  
Gene Pools ◽  
Wide Range ◽  
The University

The Institute of Evolution Wild Cereal Gene Bank (ICGB) at the University of Haifa, Israel, harbors extensive collections of wild emmer wheat (WEW), Triticum dicoccoides, and wild barley (WB), Hordeum spontaneum, the primary progenitors of wheat and barley, respectively. The ICGB also includes minor collections of 10 species of Aegilops, wild oat (Avena barbata), and Brachypodium stacei and B. hybridum (previously distachyon). Here, we describe the WEW and WB collections, explain sampling strategies, and introduce related studies. Natural populations were sampled across Israel along aridity gradients, occurring from north to south and from west to east, and in local microsites with variable (or contrasting) ecological factors. The collection sites varied greatly in terms of climatic (rainfall, temperature and humidity), edaphic (soil types), and topography (altitude, slope) variables. Thus, the ICGB collections represent wild cereals adapted to a wide range of habitats and eco-geographical conditions. We have collected and preserved these unique gene pools since mid-70th, and further used them for theoretical and applied studies in population genetics, evolution, domestication, adaptation to local and regional habitats, and coping mechanisms for a plethora of biotic and abiotic stresses. Our studies revealed that WEW and WB populations from Israel harbor high adaptive genetic diversity that can serve as a reservoir of beneficial alleles to improve important agronomic traits such as disease resistance, drought tolerance and improved grain protein content. These mostly untapped genetic resources could contribute to increasing world food production for the constantly rising human population.

There Is No Evidence of Geographical Patterning among Invasive Kentucky Bluegrass (Poa pratensis) Populations in the Northern Great Plains

Weed Science ◽  
2016 ◽  
Vol 64 (3) ◽  
pp. 409-420 ◽  
Author(s):  
Lauren A. Dennhardt ◽  
Edward S. DeKeyser ◽  
Sarah A. Tennefos ◽  
Steven E. Travers
Keyword(s):  
Genetic Diversity ◽  
Great Plains ◽  
Propagule Pressure ◽  
Poa Pratensis ◽  
Natural Populations ◽  
Kentucky Bluegrass ◽  
Grass Species ◽  
Northern Great Plains ◽  
Wild Populations ◽  
High Genetic Diversity

The study of colonizing and of dominant grass species is essential for prairie conservation efforts. We sought to answer how naturalized Kentucky bluegrass in the northern Great Plains has become successful in the last 20 yr despite its long history in the northern Great Plains. We tested for evidence of geographical differentiation using flow cytometry and microsatellite markers to ascertain the population genetics of Kentucky bluegrass. Across all tested wild populations, high levels of genetic diversity were detected along with moderate levels of structure. Mantel tests of geographical patterns were not significant. Using clonal assignment, we found two major clones that made up the majority of the tested wild populations. When we compared the wild individuals to pedigree cultivars, we found virtually no genetic overlap across all tests, which did not support our hypothesis of developed cultivars contributing to high genetic diversity in natural populations. Furthermore, DNA content tests indicated a narrow range in ploidy in wild populations compared with lawn cultivars, further supporting a hypothesis of divergence between wild and pedigree cultivars. These results indicate the recent invasion of Kentucky bluegrass in the northern Great Plains is not because of adaptation or propagule pressure, but rather likely an environmental or land use shift.

scholarly journals Genomic Variation in Natural Populations ofDrosophila melanogaster

Genetics ◽  
2012 ◽  
Vol 192 (2) ◽  
pp. 533-598 ◽  
Author(s):  
Charles H. Langley ◽  
Kristian Stevens ◽  
Charis Cardeno ◽  
Yuh Chwen G. Lee ◽  
Daniel R. Schrider ◽  
...  
Keyword(s):  
Natural Populations ◽  
Genomic Variation

scholarly journals A New Catalog of Structural Variants in 1,301 A. thaliana Lines from Africa, Eurasia, and North America Reveals a Signature of Balancing Selection at Defense Response Genes

2020 ◽  
Author(s):  
Mehmet Göktay ◽  
Andrea Fulgione ◽  
Angela M Hancock
Keyword(s):  
North America ◽  
Defense Response ◽  
Balancing Selection ◽  
Natural Populations ◽  
Housekeeping Genes ◽  
Intermediate Frequency ◽  
Genomic Variation ◽  
Nucleotide Polymorphisms ◽  
Structural Variants ◽  
Defense Response Genes

Abstract Genomic variation in the model plant Arabidopsis thaliana has been extensively used to understand evolutionary processes in natural populations, mainly focusing on single-nucleotide polymorphisms. Conversely, structural variation has been largely ignored in spite of its potential to dramatically affect phenotype. Here, we identify 155,440 indels and structural variants ranging in size from 1 bp to 10 kb, including presence/absence variants (PAVs), inversions, and tandem duplications in 1,301 A. thaliana natural accessions from Morocco, Madeira, Europe, Asia, and North America. We show evidence for strong purifying selection on PAVs in genes, in particular for housekeeping genes and homeobox genes, and we find that PAVs are concentrated in defense-related genes (R-genes, secondary metabolites) and F-box genes. This implies the presence of a “core” genome underlying basic cellular processes and a “flexible” genome that includes genes that may be important in spatially or temporally varying selection. Further, we find an excess of intermediate frequency PAVs in defense response genes in nearly all populations studied, consistent with a history of balancing selection on this class of genes. Finally, we find that PAVs in genes involved in the cold requirement for flowering (vernalization) and drought response are strongly associated with temperature at the sites of origin.

Biotechnology for bioenergy dedicated trees: meeting future energy demands

2018 ◽  
Vol 73 (1-2) ◽  
pp. 15-32 ◽  
Author(s):  
Hani Al-Ahmad
Keyword(s):  
In Vitro Regeneration ◽  
Abiotic Stress Tolerance ◽  
Wood Properties ◽  
Biofuel Production ◽  
Growth And Yield ◽  
Biotic And Abiotic Stress ◽  
Lignocellulosic Feedstock ◽  
Geographical Regions ◽  
Site Adaptability

AbstractWith the increase in human demands for energy, purpose-grown woody crops could be part of the global renewable energy solution, especially in geographical regions where plantation forestry is feasible and economically important. In addition, efficient utilization of woody feedstocks would engage in mitigating greenhouse gas emissions, decreasing the challenge of food and energy security, and resolving the conflict between land use for food or biofuel production. This review compiles existing knowledge on biotechnological and genomics-aided improvements of biomass performance of purpose-grown poplar, willow, eucalyptus and pine species, and their relative hybrids, for efficient and sustainable bioenergy applications. This includes advancements in tree in vitro regeneration, and stable expression or modification of selected genes encoding desirable traits, which enhanced growth and yield, wood properties, site adaptability, and biotic and abiotic stress tolerance. Genetic modifications used to alter lignin/cellulose/hemicelluloses ratio and lignin composition, towards effective lignocellulosic feedstock conversion into cellulosic ethanol, are also examined. Biotech-trees still need to pass challengeable regulatory authorities’ processes, including biosafety and risk assessment analyses prior to their commercialization release. Hence, strategies developed to contain transgenes, or to mitigate potential transgene flow risks, are discussed.

Population cytogenetic studies on Simulium feuerborni Edwards (Diptera: Simuliidae) from northern Thailand

Genome ◽  
1999 ◽  
Vol 42 (1) ◽  
pp. 80-86 ◽  
Author(s):  
Chaliow Kuvangkadilok ◽  
Suwannee Phayuhasena ◽  
Visut Baimai
Keyword(s):  
Polytene Chromosomes ◽  
Natural Populations ◽  
Gene Pools ◽  
Northern Thailand ◽  
Y Chromosomes ◽  
Larval Salivary Gland ◽  
Hardy Weinberg Equilibrium ◽  
Chiang Mai Province ◽  
Chromosome I ◽  
Paracentric Inversions

A standard photographic map of Simulium feuerborni (Diptera: Simuliidae) was constructed from larval salivary gland polytene chromosomes and is described herein. Analysis of polytene chromosomes was made from wild larvae collected from the four populations at Doi Inthanon National Park, Chiang Mai Province, northern Thailand. Simulium feuerborni has three pairs of chromosomes (2n = 6) which are arranged from the longest to the shortest. Chromosome I is metacentric while chromosomes II and III are submetacentric. A total of six simple paracentric inversions have been detected in these natural populations of S. feuerborni. These inversions (IS-1, IL-1, IIL-1, IIL-2, IIIS-1, IIIL-1) occurred in all chromosome arms except for the arm IIS. Significant deviation from Hardy-Weinberg equilibrium has been observed in inversion IIIL-1 at Hui Sai Luaeng suggesting the existence of two gene pools in this population. There is no indication of sex linkage associated with an inversion sequence in these populations. Thus, the X and Y chromosomes of S. feuerborni could not be recognized in this study.Key words: Simulium, polytene chromosome map, inversion polymorphisms

scholarly journals Contrasted histories of organelle and nuclear genomes underlying physiological diversification in a grass species

2020 ◽  
Vol 287 (1938) ◽  
pp. 20201960
Author(s):  
Matheus E. Bianconi ◽  
Luke T. Dunning ◽  
Emma V. Curran ◽  
Oriane Hidalgo ◽  
Robyn F. Powell ◽  
...  
Keyword(s):  
Gene Flow ◽  
Population Genomics ◽  
Nuclear Genome ◽  
Its Region ◽  
Grass Species ◽  
Region Of Origin ◽  
Ploidy Levels ◽  
Lower Elevation ◽  
Limited Dispersal ◽  
Genome Analyses

C 4 photosynthesis evolved multiple times independently in angiosperms, but most origins are relatively old so that the early events linked to photosynthetic diversification are blurred. The grass Alloteropsis semialata is an exception, as this species encompasses C 4 and non-C 4 populations. Using phylogenomics and population genomics, we infer the history of dispersal and secondary gene flow before, during and after photosynthetic divergence in A. semialata . We further analyse the genome composition of individuals with varied ploidy levels to establish the origins of polyploids in this species. Detailed organelle phylogenies indicate limited seed dispersal within the mountainous region of origin and the emergence of a C 4 lineage after dispersal to warmer areas of lower elevation. Nuclear genome analyses highlight repeated secondary gene flow. In particular, the nuclear genome associated with the C 4 phenotype was swept into a distantly related maternal lineage probably via unidirectional pollen flow. Multiple intraspecific allopolyploidy events mediated additional secondary genetic exchanges between photosynthetic types. Overall, our results show that limited dispersal and isolation allowed lineage divergence, with photosynthetic innovation happening after migration to new environments, and pollen-mediated gene flow led to the rapid spread of the derived C 4 physiology away from its region of origin.

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