scholarly journals The Genomic Architecture of Competitive Response of Arabidopsis thaliana Is Highly Flexible Among Plurispecific Neighborhoods

2021 ◽  
Vol 12 ◽  
Author(s):  
Cyril Libourel ◽  
Etienne Baron ◽  
Juliana Lenglet ◽  
Laurent Amsellem ◽  
Dominique Roby ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Plant Species ◽  
Stress Responses ◽  
Genome Wide Association Study ◽  
Species Assemblages ◽  
Phenotypic Traits ◽  
Limited Information ◽  
Competitive Response ◽  
Stellaria Media ◽  
A Genome

Plants are daily challenged by multiple abiotic and biotic stresses. A major biotic constraint corresponds to competition with other plant species. Although plants simultaneously interact with multiple neighboring species throughout their life cycle, there is still very limited information about the genetics of the competitive response in the context of plurispecific interactions. Using a local mapping population of Arabidopsis thaliana, we set up a genome wide association study (GWAS) to estimate the extent of genetic variation of competitive response in 12 plant species assemblages, based on three competitor species (Poa annua, Stellaria media, and Veronica arvensis). Based on five phenotypic traits, we detected strong crossing reaction norms not only between the three bispecific neighborhoods but also among the plurispecific neighborhoods. The genetic architecture of competitive response was highly dependent on the identity and the relative abundance of the neighboring species. In addition, most of the enriched biological processes underlying competitive responses largely differ among neighborhoods. While the RNA related processes might confer a broad range response toolkit for multiple traits in diverse neighborhoods, some processes, such as signaling and transport, might play a specific role in particular assemblages. Altogether, our results suggest that plants can integrate and respond to different species assemblages depending on the identity and number of each neighboring species, through a large range of candidate genes associated with diverse and unexpected processes leading to developmental and stress responses.

scholarly journals The genomic architecture of competitive response of Arabidopsis thaliana is highly flexible between monospecific and plurispecific neighborhoods

2019 ◽  
Author(s):  
Cyril Libourel ◽  
Etienne Baron ◽  
Juliana Lenglet ◽  
Laurent Amsellem ◽  
Dominique Roby ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Stress Responses ◽  
Genetic Architecture ◽  
Genome Wide Association Study ◽  
Species Assemblages ◽  
Phenotypic Traits ◽  
Limited Information ◽  
Competitive Response ◽  
A Genome ◽  
Set Up

AbstractAlthough plants simultaneously interact with multiple neighboring species throughout their life cycle, there is still very limited information about the genetics of the competitive response in the context of plurispecific interactions. Using a local mapping population of Arabidopsis thaliana, we set up a Genome Wide Association study to estimate the extent of genetic variation of the competitive response in presence of 12 plant species assemblages, and to compare the genetic architecture of the competitive response between monospecific and plurispecific neighborhoods. Based on four phenotypic traits, we detected strong crossing reaction norms not only among the three monospecific neighborhoods, but also among the different plant assemblages. Accordingly, the genetic architecture of the competitive response was highly dependent on the identity and the relative abundance of the neighboring species. In addition, enriched biological processes underlying the competitive response largely differ between monospecific and plurispecific neighborhoods. In particular, receptor-like kinases and transporters were significantly enriched in plurispecific neighborhoods. Our results suggest that plants can integrate and respond to different species assemblages depending on the identity and number of each neighboring species, through a large range of genes associated mainly with perception and signaling processes leading to developmental and stress responses.

scholarly journals Genome-wide association study on metabolite accumulation in a wild barley NAM population reveals natural variation in sugar metabolism

PLoS ONE ◽  
2021 ◽  
Vol 16 (2) ◽  
pp. e0246510
Author(s):  
Mathias Ruben Gemmer ◽  
Chris Richter ◽  
Thomas Schmutzer ◽  
Manish L. Raorane ◽  
Björn Junker ◽  
...  
Keyword(s):  
Association Study ◽  
Stress Responses ◽  
Genome Wide Association Study ◽  
Wild Barley ◽  
Genome Wide Association ◽  
Phenotypic Traits ◽  
Genetic Components ◽  
Genome Wide ◽  
A Genome ◽  
Metabolite Accumulation

Metabolites play a key role in plants as they are routing plant developmental processes and are involved in biotic and abiotic stress responses. Their analysis can offer important information on the underlying processes. Regarding plant breeding, metabolite concentrations can be used as biomarkers instead of or in addition to genetic markers to predict important phenotypic traits (metabolic prediction). In this study, we applied a genome-wide association study (GWAS) in a wild barley nested association mapping (NAM) population to identify metabolic quantitative trait loci (mQTL). A set of approximately 130 metabolites, measured at early and late sampling dates, was analysed. For four metabolites from the early and six metabolites from the late sampling date significant mQTL (grouped as 19 mQTL for the early and 25 mQTL for the late sampling date) were found. Interestingly, all of those metabolites could be classified as sugars. Sugars are known to be involved in signalling, plant growth and plant development. Sugar-related genes, encoding mainly sugar transporters, have been identified as candidate genes for most of the mQTL. Moreover, several of them co-localized with known flowering time genes like Ppd-H1, HvELF3, Vrn-H1, Vrn-H2 and Vrn-H3, hinting on the known role of sugars in flowering. Furthermore, numerous disease resistance-related genes were detected, pointing to the signalling function of sugars in plant resistance. An mQTL on chromosome 1H in the region of 13 Mbp to 20 Mbp stood out, that alone explained up to 65% of the phenotypic variation of a single metabolite. Analysis of family-specific effects within the diverse NAM population showed the available natural genetic variation regarding sugar metabolites due to different wild alleles. The study represents a step towards a better understanding of the genetic components of metabolite accumulation, especially sugars, thereby linking them to biological functions in barley.

scholarly journals Genome-Wide Analyses Identifies Known and New Markers Responsible of Chicken Plumage Color

Animals ◽  
2020 ◽  
Vol 10 (3) ◽  
pp. 493
Author(s):  
Salvatore Mastrangelo ◽  
Filippo Cendron ◽  
Gianluca Sottile ◽  
Giovanni Niero ◽  
Baldassare Portolano ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Snp Array ◽  
Fixation Index ◽  
Phenotypic Traits ◽  
Plumage Color ◽  
Phenotypic Marker ◽  
Genome Wide ◽  
A Genome ◽  
The Difference ◽  
Genomic Regions

Through the development of the high-throughput genotyping arrays, molecular markers and genes related to phenotypic traits have been identified in livestock species. In poultry, plumage color is an important qualitative trait that can be used as phenotypic marker for breed identification. In order to assess sources of genetic variation related to the Polverara chicken breed plumage colour (black vs. white), we carried out a genome-wide association study (GWAS) and a genome-wide fixation index (FST) scan to uncover the genomic regions involved. A total of 37 animals (17 white and 20 black) were genotyped with the Affymetrix 600 K Chicken single nucleotide polymorphism (SNP) Array. The combination of results from GWAS and FST revealed a total of 40 significant markers distributed on GGA 01, 03, 08, 12 and 21, and located within or near known genes. In addition to the well-known TYR, other candidate genes have been identified in this study, such as GRM5, RAB38 and NOTCH2. All these genes could explain the difference between the two Polverara breeds. Therefore, this study provides the basis for further investigation of the genetic mechanisms involved in plumage color in chicken.

scholarly journals Systems approaches provide new insights into Arabidopsis thaliana root growth under mineral nutrient limitation

2018 ◽  
Author(s):  
Nadia Bouain ◽  
Arthur Korte ◽  
Santosh B. Satbhai ◽  
Seung Y. Rhee ◽  
Wolfgang Busch ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Root Growth ◽  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Functional Module ◽  
Molecular Genetic ◽  
Chromatin Modification ◽  
Nutrient Deficiency ◽  
Mineral Nutrient ◽  
A Genome

AbstractThe molecular genetic mechanisms by which plants modulate their root growth rate (RGR) in response to nutrient deficiency are largely unknown. Using a panel of Arabidopsis thaliana natural accessions, we provide a comprehensive combinatorial analysis of RGR variation under macro- and micronutrient deficiency, namely phosphorus (P), iron (Fe), and zinc (Zn), which affect root growth in opposite directions. We found that while -P stimulates early RGR of most accessions, -Fe or -Zn reduces it. The combination of either -P-Fe or -P-Zn leads to suppression of the growth inhibition exerted by -Fe or -Zn alone. Surprisingly, Arabidopsis reference accession Columbia (Col-0) is not representative of the species under -P and -Zn. Using a genome wide association study, we identify candidate genes that control RGR under the assayed nutrient deficiency conditions. By using a network biology driven search using these candidate genes, we further identify a functional module enriched in regulation of cell cycle, DNA replication and chromatin modification that possibly underlies the suppression of root growth reduction in -P-Fe conditions. Collectively, our findings provide a framework for understanding the regulation of RGR under nutrient deficiency, and open new routes for the identification of both large effect genes and favorable allelic variations to improve root growth.

scholarly journals The maternal environment interacts with genetic variation in regulating seed dormancy in Arabidopsis thaliana

2017 ◽  
Author(s):  
Envel Kerdaffrec ◽  
Magnus Nordborg
Keyword(s):  
Arabidopsis Thaliana ◽  
Association Study ◽  
Seed Dormancy ◽  
Genome Wide Association Study ◽  
Seed Maturation ◽  
Genome Wide Association ◽  
Maternal Environment ◽  
Genome Wide ◽  
A Genome ◽  
Wide Range

AbstractSeed dormancy is a complex adaptive trait that controls the timing of seed germination, one of the major fitness components in many plant species. Despite being highly heritable, seed dormancy is extremely plastic and influenced by a wide range of environmental cues. Here, using a set of 92 Arabidopsis thaliana lines from Sweden, we investigate the effect of seed maturation temperature on dormancy variation at the population level. The response to temperature differs dramatically between lines, demonstrating that genotype and the maternal environment interact in controlling the trait. By performing a genome-wide association study (GWAS), we identified several candidate genes that could account for this plasticity, two of which are involved in the photoinduction of germination. Altogether, our results provide insight into both the molecular mechanisms and the evolution of dormancy plasticity, and can serve to improve our understanding of environmentally dependent life-history transitions.HighlightThe effect of low seed-maturation temperatures on seed dormancy is highly variable in Arabidopsis thaliana accessions from Sweden, denoting strong genotype-environment interactions, and a genome-wide association study identified compelling candidates that could account for this plasticity.

scholarly journals Temporal dynamics of QTL effects on vegetative growth in Arabidopsis thaliana

2020 ◽  
Author(s):  
Rhonda C Meyer ◽  
Kathleen Weigelt-Fischer ◽  
Dominic Knoch ◽  
Marc Heuermann ◽  
Yusheng Zhao ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Vegetative Growth ◽  
Molecular Mechanisms ◽  
Genome Wide Association Study ◽  
Temporal Dynamics ◽  
Expression Patterns ◽  
Snp Array ◽  
Relative Growth Rates ◽  
Continuous Formation ◽  
A Genome

Abstract We assessed early vegetative growth in a population of 382 accessions of Arabidopsis thaliana using automated non-invasive high-throughput phenotyping. All accessions were imaged daily from 7 d to 18 d after sowing in three independent experiments and genotyped using the Affymetrix 250k SNP array. Projected leaf area (PLA) was derived from image analysis and used to calculate relative growth rates (RGRs). In addition, initial seed size was determined. The generated datasets were used jointly for a genome-wide association study that identified 238 marker–trait associations (MTAs) individually explaining up to 8% of the total phenotypic variation. Co-localization of MTAs occurred at 33 genomic positions. At 21 of these positions, sequential co-localization of MTAs for 2–9 consecutive days was observed. The detected MTAs for PLA and RGR could be grouped according to their temporal expression patterns, emphasizing that temporal variation of MTA action can be observed even during the vegetative growth phase, a period of continuous formation and enlargement of seemingly similar rosette leaves. This indicates that causal genes may be differentially expressed in successive periods. Analyses of the temporal dynamics of biological processes are needed to gain important insight into the molecular mechanisms of growth-controlling processes in plants.

scholarly journals Major QTL with pleiotropic effects controlling time of leaf budburst and flowering-related traits in walnut (Juglans regia L.)

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Şakir Burak Bükücü ◽  
Mehmet Sütyemez ◽  
Sina Kefayati ◽  
Aibibula Paizila ◽  
Abdulqader Jighly ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Juglans Regia ◽  
Genotypic Variation ◽  
Phenotypic Traits ◽  
Juvenile Period ◽  
Phenotypic Data ◽  
Breeding Programs ◽  
Genome Wide ◽  
A Genome ◽  
Major Qtl

Abstract Breeding studies in walnut (Juglans regia L.) are usually time consuming due to the long juvenile period and therefore, this study aimed to determine markers associated with time of leaf budburst and flowering-related traits by performing a genome-wide association study (GWAS). We investigated genotypic variation and its association with time of leaf budburst and flowering-related traits in 188 walnut accessions. Phenotypic data was obtained from 13 different traits during 3 consecutive years. We used DArT-seq for genotyping with a total of 33,519 (14,761 SNP and 18,758 DArT) markers for genome-wide associations to identify marker underlying these traits. Significant correlations were determined among the 13 different traits. Linkage disequilibrium decayed very quickly in walnut in comparison with other plants. Sixteen quantitative trait loci (QTL) with major effects (R2 between 0.08 and 0.23) were found to be associated with a minimum of two phenotypic traits each. Of these QTL, QTL05 had the maximum number of associated traits (seven). Our study is GWAS for time of leaf budburst and flowering-related traits in Juglans regia L. and has a strong potential to efficiently implement the identified QTL in walnut breeding programs.

scholarly journals Temporal dynamics of QTL effects on vegetative growth in Arabidopsis thaliana

2020 ◽  
Author(s):  
Rhonda C. Meyer ◽  
Kathleen Weigelt-Fischer ◽  
Dominic Knoch ◽  
Marc Heuermann ◽  
Yusheng Zhao ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Association Study ◽  
Vegetative Growth ◽  
Molecular Mechanisms ◽  
Genome Wide Association Study ◽  
Temporal Dynamics ◽  
Expression Patterns ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome

ABSTRACTWe assessed early vegetative growth in a population of 382 accessions of Arabidopsis thaliana using automated non-invasive high-throughput phenotyping. All accessions were imaged daily from seven to 18 days after sowing in three independent experiments and genotyped using the Affymetrix 250k SNP array. Projected leaf area (PLA) was derived from image analysis and used to calculate relative growth rates (RGR). In addition, initial seed size was determined. The generated data sets were used jointly for a genome-wide association study that identified 238 marker-trait associations (MTAs) individually explaining up to 8 % of the total phenotypic variation. Co-localisation of MTAs occurred at 33 genomic positions. At 21 of these positions, sequential co-localisation of MTAs for two to nine consecutive days was observed. The detected MTAs for PLA and RGR could be grouped according to their temporal expression patterns, emphasising that temporal variation of MTA action can be observed even during the vegetative growth phase, a period of continuous formation and enlargement of seemingly similar rosette leaves. This indicates that causal genes may be differentially expressed in successive periods. Analyses of the temporal dynamics of biological processes are needed to gain important insight into the molecular mechanisms of growth-controlling processes in plants.HighlightA genome-wide association study including the factor time highlighted that early plant growth in Arabidopsis is governed by several medium and many small effect loci, most of which act only during short phases of two to nine days.

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