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.

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 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 Genome-Wide Association Study of H/L Traits in Chicken

Animals ◽  
2019 ◽  
Vol 9 (5) ◽  
pp. 260 ◽  
Author(s):  
Bo Zhu ◽  
Qinghe Li ◽  
Ranran Liu ◽  
Maiqing Zheng ◽  
Jie Wen ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Association Study ◽  
Genetic Basis ◽  
Molecular Mechanisms ◽  
Genome Wide Association Study ◽  
Gene Annotation ◽  
Immune Defense ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome

Presently, the heterophil-to-lymphocyte (H/L) ratio is being studied extensively as a disease resistance trait. Through intricate mechanisms to identify and destroy pathogenic microorganisms, heterophils play a pivotal role in the immune defense systems of avian species. To reveal the genetic basis and molecular mechanisms affecting the H/L ratio, phenotypic and H/L data from 1650 white feather chicken broilers were used in performing a genome-wide association study. A self-developed, chicken-specific 55K chip was used for heterophils, lymphocytes, and H/L classification, according to individual genomic DNA profiles. We identified five significant single nucleotide polymorphisms (SNPs) when the genome-wide significance threshold was set to 5% (p < 2.42 × 10−6). A total of 15 SNPs obtained seemingly significant levels (p < 4.84 × 10−5). Gene annotation indicated that CARD11 (Caspase recruitment domain family member 11), BRIX1 (Biogenesis of ribosomes BRX1), and BANP (BTG3 associated nuclear protein) play a role in H/L-associated cell regulation and potentially constitute candidate gene regions for cellular functions dependent on H/L ratios. These results lay the foundation for revealing the genetic basis of disease resistance and future marker-assisted selection for disease resistance.

scholarly journals Genome wide association study of plant height and tiller number in hulless barley

PLoS ONE ◽  
2021 ◽  
Vol 16 (12) ◽  
pp. e0260723
Author(s):  
Yixiong Bai ◽  
Xiaohong Zhao ◽  
Xiaohua Yao ◽  
Youhua Yao ◽  
Likun An ◽  
...  
Keyword(s):  
Association Study ◽  
Plant Height ◽  
Molecular Mechanisms ◽  
Genome Wide Association Study ◽  
Tiller Number ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Hulless Barley ◽  
Genome Wide ◽  
A Genome

Hulless barley (Hordeum vulgare L. var. nudum), also called naked barley, is a unique variety of cultivated barley. The genome-wide specific length amplified fragment sequencing (SLAF-seq) method is a rapid deep sequencing technology that is used for the selection and identification of genetic loci or markers. In this study, we collected 300 hulless barley accessions and used the SLAF-seq method to identify candidate genes involved in plant height (PH) and tiller number (TN). We obtained a total of 1407 M paired-end reads, and 228,227 SLAF tags were developed. After filtering using an integrity threshold of >0.8 and a minor allele frequency of >0.05, 14,504,892 single-nucleotide polymorphisms (SNP) loci were screened out. The remaining SNPs were used for the construction of a neighbour-joining phylogenetic tree, and the three subcluster members showed no obvious differentiation among regional varieties. We used a genome wide association study approach to identify 1006 and 113 SNPs associated with TN and PH, respectively. Based on best linear unbiased predictors (BLUP), 41 and 29 SNPs associated with TN and PH, respectively. Thus, several of genes, including Hd3a and CKX5, may be useful candidates for the future genetic breeding of hulless barley. Taken together, our results provide insight into the molecular mechanisms controlling barley architecture, which is important for breeding and yield.

scholarly journals Arabidopsis thaliana genes contributing to differences in the outcome of infection with generalist and specialist strains of Turnip mosaic virus identified by genome-wide association studies

2020 ◽  
Author(s):  
Anamarija Butković ◽  
Rubén González ◽  
Mark Paul Selda Rivarez ◽  
Santiago F. Elena
Keyword(s):  
Arabidopsis Thaliana ◽  
Association Study ◽  
Host Range ◽  
Host Species ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Null Mutant ◽  
Genome Wide ◽  
A Genome

AbstractPathogens can be classified as generalists or specialists depending on their host breadth. While generalists are able to successfully infect a wide variety of host species, the host range of specialists is limited to a few related species. Even though generalists seem to gain an advantage due to their wide host range, they usually pay a cost in terms of fitness within each host species (i.e., the jack-of-all trades, master of none). On the contrary, specialists have high fitness within their own host. A highly relevant yet poorly explored question is whether generalist and specialist viruses differ in the way they interact with their host’s gene expression networks. To identify host genetic factors relevant for the infection of specialist or generalist viruses, we undertook a genome-wide association study (GWAS) approach. Four hundred fifty natural accessions of Arabidopsis thaliana were inoculated with turnip mosaic potyvirus strains that were either generalist (TuMV-G) or specialist (TuMV-S). Several disease-related traits have been associated with different sets of host genes for each TuMV strain. While most of the mapped loci were traitor strain-specific, one shared locus was mapped for both strains, a disease resistance TIR-NBS-LRR class protein. Likewise, only one locus was found involved in more than one of the disease-related traits evaluated, a putative cysteine-rich receptor-like protein kinase 20. To validate these results, the corresponding null mutant plants were inoculated with TuMV-G or -S and the outcome of infection was characterized.Author summaryGeneralist and specialist viruses are commonly found in nature, where they have potential for epidemics, and are classified depending on their host breath. In this study we used a genome-wide association study to characterize differences in the genetic basis of both infection strategies from a host perspective. Our experimental setup consisted of 450 accessions of A. thaliana and two strains of TuMV. We found differences in the number of associated genes and their functions in disease-related traits. Results were validated by characterization of viral infections in null mutant plants deficient for a set of the identified genes.

Sign in / Sign up

Export Citation Format

Share Document