scholarly journals Using Brachypodium distachyon natural populations to uncover genomic regions under selection

2018 ◽  
Vol 96 (3) ◽  
pp. 485-486
Author(s):  
Sheila McCormick
Keyword(s):  
Brachypodium Distachyon ◽  
Natural Populations ◽  
Genomic Regions

scholarly journals Genetic Variability of Natural Populations of Grapevine leafroll-associated virus 2 in Pacific Northwest Vineyards

2010 ◽  
Vol 100 (7) ◽  
pp. 698-707 ◽  
Author(s):  
Sridhar Jarugula ◽  
Olufemi J. Alabi ◽  
Robert R. Martin ◽  
Rayapati A. Naidu
Keyword(s):  
Genetic Variability ◽  
Pacific Northwest ◽  
Current Knowledge ◽  
Natural Populations ◽  
Taxonomic Status ◽  
Amino Acid Sequences ◽  
Enzyme Linked Immunosorbent Assay ◽  
Polymorphism Analysis ◽  
Nonsynonymous Site ◽  
Genomic Regions

Genetic variability of field populations of Grapevine leafroll-associated virus 2 (GLRaV-2) in Pacific Northwest (PNW) vineyards was characterized by sequencing the entire coat protein (CP) and a portion of the heat-shock protein-70 homolog (HSP70h) genes. Phylogenetic analysis of CP and HSP70h nucleotide sequences obtained in this study and corresponding sequences from GenBank revealed segregation of GLRaV-2 isolates into six lineages with virus isolates from PNW distributed in ‘PN’, ‘H4’, and ‘RG’ lineages. An estimation of the ratio of nonsynonymous substitutions per nonsynonymous site to synonymous substitutions per synonymous site indicated that different selection pressures may be acting on the two genomic regions encoding proteins with distinct functions. Multiple alignments of CP amino acid sequences showed lineage-specific differences. Enzyme-linked immunosorbent assay results indicated that GLRaV-2-specific antibodies from a commercial source are unable to reliably detect GLRaV-2 isolates in the RG lineage, thereby limiting antibody-based diagnosis of all GLRaV-2 isolates currently found in PNW vineyards. A protocol based on reverse-transcription polymerase chain reaction and restriction fragment length polymorphism analysis was developed for differentiating GLRaV-2 isolates belonging to the three lineages present in the region. The taxonomic status of GLRaV-2 is discussed in light of the current knowledge of global genetic diversity of the virus.

QTLs for resistance to the false brome rust Puccinia brachypodii in the model grass Brachypodium distachyon L.

Genome ◽  
2012 ◽  
Vol 55 (2) ◽  
pp. 152-163 ◽  
Author(s):  
Mirko Barbieri ◽  
Thierry C. Marcel ◽  
Rients E. Niks ◽  
Enrico Francia ◽  
Marianna Pasquariello ◽  
...  
Keyword(s):  
Quantitative Resistance ◽  
Rust Fungus ◽  
Brachypodium Distachyon ◽  
Transgressive Segregation ◽  
Snp Markers ◽  
Growth Stages ◽  
Resistance Qtls ◽  
Ssr And Snp Markers ◽  
Model Grass ◽  
Genomic Regions

The potential of the model grass Brachypodium distachyon L. (Brachypodium) for studying grass–pathogen interactions is still underexploited. We aimed to identify genomic regions in Brachypodium associated with quantitative resistance to the false brome rust fungus Puccinia brachypodii . The inbred lines Bd3-1 and Bd1-1, differing in their level of resistance to P. brachypodii, were crossed to develop an F2 population. This was evaluated for reaction to a virulent isolate of P. brachypodii at both the seedling and advanced growth stages. To validate the results obtained on the F2, resistance was quantified in F2-derived F3 families in two experiments. Disease evaluations showed quantitative and transgressive segregation for resistance. A new AFLP-based Brachypodium linkage map consisting of 203 loci and spanning 812 cM was developed and anchored to the genome sequence with SSR and SNP markers. Three false brome rust resistance QTLs were identified on chromosomes 2, 3, and 4, and they were detected across experiments. This study is the first quantitative trait analysis in Brachypodium. Resistance to P. brachypodii was governed by a few QTLs: two acting at the seedling stage and one acting at both seedling and advanced growth stages. The results obtained offer perspectives to elucidate the molecular basis of quantitative resistance to rust fungi.

scholarly journals Explaining the heritability of an ecologically significant trait in terms of individual quantitative trait loci

2011 ◽  
Vol 7 (6) ◽  
pp. 896-898 ◽  
Author(s):  
Alison G. Scoville ◽  
Young Wha Lee ◽  
John H. Willis ◽  
John K. Kelly
Keyword(s):  
Qtl Mapping ◽  
Quantitative Trait ◽  
Complex Traits ◽  
Genetic Variance ◽  
Balancing Selection ◽  
Natural Populations ◽  
Population Based ◽  
Population Variation ◽  
Trait Locus ◽  
Genomic Regions

Most natural populations display substantial genetic variation in behaviour, morphology, physiology, life history and the susceptibility to disease. A major challenge is to determine the contributions of individual loci to variation in complex traits. Quantitative trait locus (QTL) mapping has identified genomic regions affecting ecologically significant traits of many species. In nearly all cases, however, the importance of these QTLs to population variation remains unclear. In this paper, we apply a novel experimental method to parse the genetic variance of floral traits of the annual plant Mimulus guttatus into contributions of individual QTLs. We first use QTL-mapping to identify nine loci and then conduct a population-based breeding experiment to estimate V Q , the genetic variance attributable to each QTL. We find that three QTLs with moderate effects explain up to one-third of the genetic variance in the natural population. Variation at these loci is probably maintained by some form of balancing selection. Notably, the largest effect QTLs were relatively minor in their contribution to heritability.

scholarly journals Large-Scale Integration of Meta-QTL and Genome-Wide Association Study Discovers the Genomic Regions and Candidate Genes for Yield and Yield-related Traits in Bread Wheat

2021 ◽  
Author(s):  
Yang Yang ◽  
Amo Aduragbemi ◽  
Di Wei ◽  
Yongmao Chai ◽  
Jie Zheng ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Large Scale ◽  
Genome Wide Association Study ◽  
Expression Patterns ◽  
Wheat Yield ◽  
Natural Populations ◽  
Wheat Breeding ◽  
High Yield ◽  
Photoperiod Response ◽  
Genomic Regions

Abstract Improving yield and yield-related traits are key goals in wheat breeding program. The integration of accumulated wheat genetic resources provides an opportunity to uncover important genomic regions and candidate genes that affect wheat yield. Here, a comprehensive Meta-QTL analysis was conducted on 2230 QTLs of yield-related traits obtained from 119 QTL studies. These QTLs were refined into 145 Meta-QTLs (MQTLs), and 89 MQTLs were verified by GWAS with different natural populations. The average confidence interval (CI) of these MQTLs was 2.92 times less than that of the initial QTLs. Furthermore, 76 core MQTL regions with a physical distance less than 25 Mb were detected. Based on the homology analysis and expression patterns, 237 candidate genes in the MQTLs involved in photoperiod response, grain development, multiple plant growth regulator pathways, carbon and nitrogen metabolism, and spike and flower organ development were determined. A novel candidate gene TaKAO-4A was confirmed to be significantly associated with grain size, and a CAPS marker was developed based on its dominant haplotype. In summary, this study clarified a method based on the integration of Meta-QTL, GWAS and homology comparison to reveal the genomic regions and candidate genes that affect important yield-related traits in wheat. This work will help to lay a foundation for the identification, transfer and aggregation of these important QTLs or candidate genes in wheat high-yield breeding.

scholarly journals Patterns of gene co-expression under water-deficit treatments and pan-genome occupancy in Brachypodium distachyon.

2021 ◽  
Author(s):  
Ruben Sancho ◽  
Pilar Catalan ◽  
Bruno Contreras-Moreira ◽  
Tom Juenger ◽  
David L Des Marais
Keyword(s):  
Brachypodium Distachyon ◽  
Natural Populations ◽  
Genomic Analysis ◽  
Drought Response ◽  
Primary Metabolism ◽  
Environmental Response ◽  
Hub Genes ◽  
Pan Genome ◽  
Expression Of Genes ◽  
Leaf Transcriptome

Natural populations are characterized by abundant genetic diversity driven by a range of different types of mutation. The tractability of sequence complete genomes has allowed new insights into the variable composition of genomes, summarized as a species pan-genome, which demonstrate that many genes are absent from the reference genomes whose analysis has dominated the initial years of the genomic era. Our field now turns towards understanding the functional consequence of these highly variable genomes. Here, we analyzed weighted gene co-expression networks from leaf transcriptome data for drought response in the purple false brome Brachypodium distachyon and investigated network topology and differential expression of genes putatively involved in adaptation to this stressor. We specifically asked whether genes with variable occupancy in the pan-genome (genes which are either present in all studied genotypes or missing in some genotypes) show different distributions among co-expression modules. Co-expression analysis united drought genes expressed in drought-stressed plants into 9 modules covering 343 hub genes (440 hub isoforms), and genes expressed under controlled water conditions into 13 modules, covering 724 hub genes (911 hub isoforms). We find that low occupancy pan-genes are under-represented among several modules, while other modules are over-enriched for low-occupancy pan-genes. We also provide new insight into the regulation of drought response in B. distachyon, specifically identifying one module with an apparent role in primary metabolism that is strongly responsive to drought. Our work shows the power of integrating pan-genomic analysis with transcriptomic data using factorial experiments to understand the functional genomics of environmental response.

Genome-wide marker-trait association analysis in a core set of Dolichos bean germplasm

2018 ◽  
Vol 17 (1) ◽  
pp. 1-11 ◽  
Author(s):  
P. V. Vaijayanthi ◽  
S. Ramesh ◽  
M. B. Gowda ◽  
A. M. Rao ◽  
C. M. Keerthi
Keyword(s):  
Linear Model ◽  
Ssr Markers ◽  
Natural Populations ◽  
Mixed Linear Model ◽  
Multiple Traits ◽  
False Discovery Rates ◽  
Genome Wide ◽  
Core Set ◽  
Fixation Indices ◽  
Genomic Regions

AbstractAssociation mapping (AM), an alternative method of quantitative trait loci (QTL) discovery, exploits historic linkage disequilibrium (LD) present in natural populations. AM is effective in self-pollinated crops such as Dolichos bean as LD extends over longer genomic distance driven-by low rate of recombination and thereby requiring fewer markers for exploring marker-traits associations. A core set of Dolichos bean germplasm consisting of 64 accessions was evaluated for nine quantitative traits (QTs) during 2014 and 2015 rainy seasons and genotyped using 234 simple sequence repeats (SSR) markers. Substantial diversity was observed among the core set accessions at loci controlling QTs and 95 of the 234 SSR markers were found polymorphic. The structure analysis and low magnitude of fixation indices suggested weak population structure, which in-turn indicated the low possibility of false discovery rates in the marker-QTs association. The marker allele's scores were regressed onto phenotypes at nine QTs following general linear model and mixed linear model for exploring marker-QTs associations. Significantly higher number of SSR markers was found associated with genomic regions controlling nine QTs. A few of the markers such as KT Dolichos (KTD) 200 for days to 50% flowering, KTD 273 for fresh pod yield per plant and KTD 130 for fresh pods per plant explained ≥10% of the trait variations. The study could also identify a few SSR markers such as KTD 273, KTD 271 and KTD 130 linked to multiple traits. These linked SSR markers are suggested for validation for their use in marker-assisted Dolichos bean improvement programmes.

scholarly journals Stress response, behavior, and development are shaped by transposable element-induced mutations in Drosophila

2018 ◽  
Author(s):  
Gabriel E. Rech ◽  
Maria Bogaerts-Marquez ◽  
Maite G. Barrón ◽  
Miriam Merenciano ◽  
José Luis Villanueva-Cañas ◽  
...  
Keyword(s):  
Transposable Element ◽  
Adaptive Evolution ◽  
Current Knowledge ◽  
Natural Populations ◽  
Nucleotide Polymorphisms ◽  
Induced Mutations ◽  
Phenotypic Effect ◽  
Single Nucleotide ◽  
Adaptive Mutations ◽  
Genomic Regions

AbstractMapping genotype to phenotype is challenging because of the difficulties in identifying both the traits under selection and the specific genetic variants underlying these traits. Most of the current knowledge of the genetic basis of adaptive evolution is based on the analysis of single nucleotide polymorphisms (SNPs). Despite increasing evidence for their causal role, the contribution of structural variants to adaptive evolution remains largely unexplored. In this work, we analyzed the population frequencies of 1,615 Transposable Element (TE) insertions in 91 samples from 60 worldwide natural populations of Drosophila melanogaster. We identified a set of 300 TEs that are present at high population frequencies, and located in genomic regions with high recombination rate, where the efficiency of natural selection is high. The age and the length of these 300 TEs are consistent with relatively young and long insertions reaching high frequencies due to the action of positive selection. Indeed, we, and others, found evidence of selective sweeps and/or population differentiation for 65 of them. The analysis of the genes located nearby these 65 candidate adaptive insertions suggested that the functional response to selection is related with the GO categories of response to stimulus, behavior, and development. We further showed that a subset of the candidate adaptive TEs affect expression of nearby genes, and five of them have already been linked to an ecologically relevant phenotypic effect. Our results provide a more complete understanding of the genetic variation and the fitness-related traits relevant for adaptive evolution. Similar studies should help uncover the importance of TE-induced adaptive mutations in other species as well.

scholarly journals Region-level Epimutation Rates in Arabidopsis thaliana

2020 ◽  
Author(s):  
Johanna Denkena ◽  
Frank Johannes ◽  
Maria Colomé-Tatché
Keyword(s):  
Association Studies ◽  
Natural Populations ◽  
Genetic Mutation ◽  
Genome Wide ◽  
Wide Scale ◽  
Functional Relevance ◽  
Genomic Regions ◽  
Methylation Patterns ◽  
Cg Dinucleotides ◽  
Gains And Losses

AbstractFailure to maintain DNA methylation patterns during plant development can occasionally give rise to so-called ‘spontaneous epimutations’. These stochastic methylation changes are sometimes heritable across generations and thus accumulate in plant genomes over time. Recent evidence indicates that spontaneous epimutations have a major role in shaping patterns of methylation diversity in plant populations. Using single CG dinucleotides as units of analysis, previous work has shown that the epimutation rate is several orders of magnitude higher than the genetic mutation rate. While these large rate differences have obvious implications for understanding genome-methylome co-evolution, the functional relevance of single CG methylation changes remains questionable. In contrast to single CG, solid experimental evidence has linked methylation gains and losses in larger genomic regions with transcriptional variation and heritable phentoypic effects. Here we show that such region-level changes arise stochastically at about the same rate as those at individual CG sites, are only marginal dependent on region size and cytosine density, but strongly dependent on chromosomal location. We also find consistent evidence that region-level epimutations are not restricted to CG contexts but also frequently occur in non-CG regions at the genome-wide scale. Taken together, our results support the view that many differentially methylated regions (DMRs) in natural populations originate from epimutational events and may not be effectively tagged by proximal SNPs. This possibility reinforces the need for epigenome-wide association studies (EWAS) in plants as away to identify the epigenetic basis of adaptive traits.

scholarly journals Selective Sweeps and Polygenic Adaptation Drive Local Adaptation along Moisture and Temperature Gradients in Natural Populations of Coast Redwood and Giant Sequoia

Genes ◽  
2021 ◽  
Vol 12 (11) ◽  
pp. 1826
Author(s):  
Amanda R. De La Torre ◽  
Manoj K. Sekhwal ◽  
David B. Neale
Keyword(s):  
Local Adaptation ◽  
Climate Adaptation ◽  
Natural Populations ◽  
Temperature Gradients ◽  
Selective Sweeps ◽  
Coast Redwood ◽  
Giant Sequoia ◽  
Polygenic Adaptation ◽  
Genomic Regions ◽  
Genomic Basis

Dissecting the genomic basis of local adaptation is a major goal in evolutionary biology and conservation science. Rapid changes in the climate pose significant challenges to the survival of natural populations, and the genomic basis of long-generation plant species is still poorly understood. Here, we investigated genome-wide climate adaptation in giant sequoia and coast redwood, two iconic and ecologically important tree species. We used a combination of univariate and multivariate genotype–environment association methods and a selective sweep analysis using non-overlapping sliding windows. We identified genomic regions of potential adaptive importance, showing strong associations to moisture variables and mean annual temperature. Our results found a complex architecture of climate adaptation in the species, with genomic regions showing signatures of selective sweeps, polygenic adaptation, or a combination of both, suggesting recent or ongoing climate adaptation along moisture and temperature gradients in giant sequoia and coast redwood. The results of this study provide a first step toward identifying genomic regions of adaptive significance in the species and will provide information to guide management and conservation strategies that seek to maximize adaptive potential in the face of climate change.

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