scholarly journals The genomic architecture of flowering time varies across space and time in Mimulus guttatus

2017 ◽  
Author(s):  
Patrick J. Monnahan ◽  
John K. Kelly
Keyword(s):  
Flowering Time ◽  
Estimation Error ◽  
Natural Populations ◽  
Mimulus Guttatus ◽  
Genotype By Environment ◽  
Space And Time ◽  
Genomic Architecture ◽  
Pooled Sequencing ◽  
Evolution Of Genomes ◽  
Appreciable Variation

AbstractThe degree to which genomic architecture varies across space and time is central to the evolution of genomes in response to natural selection. Bulked-segregant mapping combined with pooled sequencing provides an efficient method to estimate the effect of genetic variants on quantitative traits. We develop a novel likelihood framework to identify segregating variation within multiple populations and generations while accommodating estimation error on a sample- and SNP-specific basis. We use this method to map loci for flowering time within natural populations of Mimulus guttatus, collecting the early and late flowering plants from each of three neighboring populations and two consecutive generations. We find appreciable variation in genetic effects on flowering time across both time and space; the greatest differences evident between populations. Structural variants, such as inversions, and genes from multiple flowering time pathways exhibit the strongest associations with flowering time. It is also clear that genotype-by-environment interactions are an important influence on flowering time variation.

scholarly journals The Genomic Architecture of Flowering Time Varies Across Space and Time inMimulus guttatus

Genetics ◽  
2017 ◽  
Vol 206 (3) ◽  
pp. 1621-1635 ◽  
Author(s):  
Patrick J. Monnahan ◽  
John K. Kelly
Keyword(s):  
Flowering Time ◽  
Space And Time ◽  
Genomic Architecture

scholarly journals Genome scan identifies flowering-independent effects of barley HsDry2.2 locus on yield traits under water deficit

2017 ◽  
Author(s):  
Lianne Merchuk-Ovnat ◽  
Roi Silberman ◽  
Efrat Laiba ◽  
Andreas Maurer ◽  
Klaus Pillen ◽  
...  
Keyword(s):  
Flowering Time ◽  
Water Deficit ◽  
Genome Wide Association Study ◽  
Grain Filling ◽  
Genotype By Environment Interactions ◽  
Shoot Morphology ◽  
Genotype By Environment ◽  
A Genome ◽  
Wild Allele ◽  
Novel Alleles

AbstractIncreasing crop productivity under climate change requires the identification, selection and utilization of novel alleles for breeding. We analyzed the genotype and field phenotype of the barley HEB-25 multi-parent mapping population under well-watered and water-limited (WW and WL) environments for two years. A genome-wide association study (GWAS) for genotype by-environment interactions was performed for ten traits including flowering time (HEA), plant grain yield (PGY). Comparison of the GWAS for traits per-se to that for QTL-by-environment interactions (QxE), indicates the prevalence of QxE mostly for reproductive traits. One QxE locus on chromosome 2, Hordeum spontaneum Dry2.2 (HsDry2.2), showed a positive and conditional effect on PGY and grain number (GN). The wild allele significantly reduced HEA, however this earliness was not conditioned by water deficit. Furthermore, BC2F1 lines segregating for the HsDry2.2 showed the wild allele confers an advantage over the cultivated in PGY, GN and harvest index as well as modified shoot morphology, longer grain filling period and reduced senescence (only under drought), therefore suggesting adaptation mechanism against water deficit other than escape. This study highlights the value of evaluating wild relatives in search of novel alleles and clues to resilience mechanism underlying crop adaptation to abiotic stress.HighlightA flowering-time independent reproductive advantage of wild over cultivated allele under drought identified in a barley GWAS for genotype-by-environment interactions, with modified shoot morphology, reduced senescence and longer grain filling

scholarly journals Effects of ambient temperature and photoperiod on flowering time in faba bean (Vicia faba L.)

2017 ◽  
Vol 68 (11) ◽  
pp. 893 ◽  
Author(s):  
Samuel C. Catt ◽  
Jeffrey G. Paull
Keyword(s):  
Ambient Temperature ◽  
Flowering Time ◽  
Vicia Faba ◽  
Faba Bean ◽  
Significant Variation ◽  
Controlled Environment ◽  
Significant Determinant ◽  
Genotype By Environment ◽  
Vicia Faba L ◽  
Main Factor

Flowering time is a vulnerable stage of plant development and is therefore a significant determinant of adaptation and grain yield in faba bean (Vicia faba L.). It is largely controlled by genotype, environmental factors of temperature and photoperiod, and genotype-by-environment interactions. The aim of this study was to evaluate variation in flowering time and the responses of flowering time to ambient temperature and photoperiod in Australian faba bean. Time of sowing experiments were carried out to assess variation among lines for flowering time (measured in days to flowering, thermal time to flowering and node of first flower) and to determine plant sensitivities to ambient temperature and photoperiod by regression analysis in the field, while four controlled environment experiments of differing temperature and photoperiod were undertaken to further analyse the variation in responses. Results showed significant variation in responses to both ambient temperature and photoperiod. Photoperiod was the main factor influencing variation in flowering time, with lines grouped as sensitive, intermediate or insensitive. The responses to ambient temperature were more complex. Most lines fit the traditional linear model, but with possible variation in optimal temperature and/or vernalisation response, while some lines showed temperature insensitivity.

Flowering time QTL in natural populations ofArabidopsis thalianaand implications for their adaptive value

2014 ◽  
Vol 23 (17) ◽  
pp. 4291-4303 ◽  
Author(s):  
Emily L. Dittmar ◽  
Christopher G. Oakley ◽  
Jon Ågren ◽  
Douglas W. Schemske
Keyword(s):  
Flowering Time ◽  
Natural Populations ◽  
Adaptive Value

scholarly journals Drosophila Evolution over Space and Time (DEST) - A New Population Genomics Resource

2021 ◽  
Author(s):  
Martin Kapun ◽  
Joaquin C B Nunez ◽  
María Bogaerts-Márquez ◽  
Jesús Murga-Moreno ◽  
Margot Paris ◽  
...  
Keyword(s):  
Evolutionary Dynamics ◽  
Population Genomics ◽  
Natural Populations ◽  
Easy Access ◽  
Data Repository ◽  
Bioinformatics Pipeline ◽  
Space And Time ◽  
Sequencing Technologies ◽  
Spatio Temporal ◽  
Demographic Inference

Abstract Drosophila melanogaster is a leading model in population genetics and genomics, and a growing number of whole-genome datasets from natural populations of this species have been published over the last years. A major challenge is the integration of disparate datasets, often generated using different sequencing technologies and bioinformatic pipelines, which hampers our ability to address questions about the evolution of this species. Here we address these issues by developing a bioinformatics pipeline that maps pooled sequencing (Pool-Seq) reads from D. melanogaster to a hologenome consisting of fly and symbiont genomes and estimates allele frequencies using either a heuristic (PoolSNP) or a probabilistic variant caller (SNAPE-pooled). We use this pipeline to generate the largest data repository of genomic data available for D. melanogaster to date, encompassing 271 previously published and unpublished population samples from over 100 locations in > 20 countries on four continents. Several of these locations have been sampled at different seasons across multiple years. This dataset, which we call Drosophila Evolution over Space and Time (DEST), is coupled with sampling and environmental meta-data. A web-based genome browser and web portal provide easy access to the SNP dataset. We further provide guidelines on how to use Pool-Seq data for model-based demographic inference. Our aim is to provide this scalable platform as a community resource which can be easily extended via future efforts for an even more extensive cosmopolitan dataset. Our resource will enable population geneticists to analyze spatio-temporal genetic patterns and evolutionary dynamics of D. melanogaster populations in unprecedented detail.

scholarly journals Quantifying multivariate genotype-by-environment interactions, evolutionary potential and its context-dependence in natural populations of the water flea, Daphnia magna

2020 ◽  
Author(s):  
Franziska S. Brunner ◽  
Alan Reynolds ◽  
Ian W. Wilson ◽  
Stephen Price ◽  
Steve Paterson ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Daphnia Magna ◽  
Natural Populations ◽  
Thermal Adaptation ◽  
Plastic Response ◽  
Evolutionary Potential ◽  
Genotype By Environment Interactions ◽  
Additive Genetic Variation ◽  
Genotype By Environment ◽  
Plastic Responses

ABSTRACTGenotype-by-environment interactions (G x E) underpin the evolution of plastic responses in natural populations. Theory assumes that G x E interactions exist but empirical evidence from natural populations is equivocal and difficult to interpret because G x E interactions are normally univariate plastic responses to a single environmental gradient. We compared multivariate plastic responses of 43 Daphnia magna clones from the same population in a factorial experiment that crossed temperature and food environments. Multivariate plastic responses explained more than 30% of the total phenotypic variation in each environment. G x E interactions were detected in most environment combinations irrespective of the methodology used. However, the nature of G x E interactions was context-dependent and led to environment-specific differences in additive genetic variation (G-matrices). Clones that deviated from the population average plastic response were not the same in each environmental context and there was no difference in whether clones varied in the nature (phenotypic integration) or magnitude of their plastic response in different environments. Plastic responses to food were aligned with additive genetic variation (gmax) at both temperatures, whereas plastic responses to temperature were not aligned with additive genetic variation (gmax) in either food environment. These results suggest that fundamental differences may exist in the potential for our population to evolve novel responses to food versus temperature changes, and challenges past interpretations of thermal adaptation based on univariate studies.

scholarly journals Genomic architecture of biomass heterosis inArabidopsis

2017 ◽  
Vol 114 (30) ◽  
pp. 8101-8106 ◽  
Author(s):  
Mei Yang ◽  
Xuncheng Wang ◽  
Diqiu Ren ◽  
Hao Huang ◽  
Miqi Xu ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Molecular Mechanisms ◽  
Association Studies ◽  
Expression Patterns ◽  
Natural Populations ◽  
Genome Wide Association Studies ◽  
Genomic Architecture ◽  
Genome Wide ◽  
Stimulus Responsive ◽  
Abiotic Stimuli

Heterosis is most frequently manifested by the substantially increased vigorous growth of hybrids compared with their parents. Investigating genomic variations in natural populations is essential to understand the initial molecular mechanisms underlying heterosis in plants. Here, we characterized the genomic architecture associated with biomass heterosis in 200Arabidopsishybrids. The genome-wide heterozygosity of hybrids makes a limited contribution to biomass heterosis, and no locus shows an obvious overdominance effect in hybrids. However, the accumulation of significant genetic loci identified in genome-wide association studies (GWAS) in hybrids strongly correlates with better-parent heterosis (BPH). Candidate genes for biomass BPH fall into diverse biological functions, including cellular, metabolic, and developmental processes and stimulus-responsive pathways. Important heterosis candidates includeWUSCHEL,ARGOS, and some genes that encode key factors involved in cell cycle regulation. Interestingly, transcriptomic analyses in representativeArabidopsishybrid combinations reveal that heterosis candidate genes are functionally enriched in stimulus-responsive pathways, including responses to biotic and abiotic stimuli and immune responses. In addition, stimulus-responsive genes are repressed to low-parent levels in hybrids with high BPH, whereas middle-parent expression patterns are exhibited in hybrids with no BPH. Our study reveals a genomic architecture for understanding the molecular mechanisms of biomass heterosis inArabidopsis, in which the accumulation of the superior alleles of genes involved in metabolic and cellular processes improve the development and growth of hybrids, whereas the overall repressed expression of stimulus-responsive genes prioritizes growth over responding to environmental stimuli in hybrids under normal conditions.

scholarly journals Large-effect flowering time mutations reveal conditionally adaptive paths through fitness landscapes in Arabidopsis thaliana

2019 ◽  
Vol 116 (36) ◽  
pp. 17890-17899 ◽  
Author(s):  
Mark A. Taylor ◽  
Amity M. Wilczek ◽  
Judith L. Roe ◽  
Stephen M. Welch ◽  
Daniel E. Runcie ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Flowering Time ◽  
Environmental Conditions ◽  
Regulatory Networks ◽  
Evolutionary Dynamics ◽  
Natural Populations ◽  
Fitness Landscapes ◽  
Natural Environments ◽  
Multiple Phenotypes ◽  
Mutant Phenotypes

Contrary to previous assumptions that most mutations are deleterious, there is increasing evidence for persistence of large-effect mutations in natural populations. A possible explanation for these observations is that mutant phenotypes and fitness may depend upon the specific environmental conditions to which a mutant is exposed. Here, we tested this hypothesis by growing large-effect flowering time mutants of Arabidopsis thaliana in multiple field sites and seasons to quantify their fitness effects in realistic natural conditions. By constructing environment-specific fitness landscapes based on flowering time and branching architecture, we observed that a subset of mutations increased fitness, but only in specific environments. These mutations increased fitness via different paths: through shifting flowering time, branching, or both. Branching was under stronger selection, but flowering time was more genetically variable, pointing to the importance of indirect selection on mutations through their pleiotropic effects on multiple phenotypes. Finally, mutations in hub genes with greater connectedness in their regulatory networks had greater effects on both phenotypes and fitness. Together, these findings indicate that large-effect mutations may persist in populations because they influence traits that are adaptive only under specific environmental conditions. Understanding their evolutionary dynamics therefore requires measuring their effects in multiple natural environments.

scholarly journals Marker-Based Inferences about the Genetic basis of Flowering time in Mimulus Guttatus

Hereditas ◽  
2004 ◽  
Vol 121 (3) ◽  
pp. 267-272 ◽  
Author(s):  
Yong-Bi Fu ◽  
Kermit Ritland
Keyword(s):  
Flowering Time ◽  
Genetic Basis ◽  
Mimulus Guttatus

An association mapping approach to identify flowering time genes in natural populations of Lolium perenne (L.)

2005 ◽  
Vol 15 (3) ◽  
pp. 233-245 ◽  
Author(s):  
Leif Skøt ◽  
Mervyn O. Humphreys ◽  
Ian Armstead ◽  
Sue Heywood ◽  
Kirsten P. Skøt ◽  
...  
Keyword(s):  
Association Mapping ◽  
Flowering Time ◽  
Lolium Perenne ◽  
Natural Populations ◽  
Lolium Perenne L ◽  
Mapping Approach ◽  
Association Mapping Approach
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