Gene function beyond the single trait: natural variation, gene effects, and evolutionary ecology in Arabidopsis thaliana (original) (raw)
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Mapping the genetic basis of ecologically and evolutionarily relevant traits in Arabidopsis thaliana
Current Opinion in Plant Biology, 2012
There has been a long standing interest in the relationship between genetic and phenotypic variation in natural populations, in order to understand the genetic basis of adaptation and to discover natural alleles to improve crops. Here we review recent developments in mapping approaches that have significantly improved our ability to identify causal polymorphism explaining natural variation in ecological and evolutionarily relevant traits. However, challenges in interpreting these discoveries remain. In particular, we need more detailed transcriptomic, epigenomic, and gene network data to help understand the mechanisms behind identified associations. Also, more studies need to be performed under field conditions or using experimental evolution to determine whether polymorphisms identified in the lab are relevant for adaptation and improvement under natural conditions.
Towards identifying genes underlying ecologically relevant traits in Arabidopsis thaliana
Nature Reviews Genetics, 2010
A major challenge in evolutionary biology and plant breeding is to identify the genetic basis of complex quantitative traits, including those that contribute to adaptive variation. Here we review the development of new methods and resources to fine-map intraspecific genetic variation that underlies natural phenotypic variation in plants. In particular, the analysis of 107 quantitative traits reported in the first genome-wide association mapping study in Arabidopsis thaliana sets the stage for an exciting time in our understanding of plant adaptation. We also argue for the need to place phenotype-genotype association studies in an ecological context if one is to predict the evolutionary trajectories of plant species.
Despite the wealth of molecular information about inflorescence development in the model plant Arabidopsis thaliana, we know much less about how traits involved in reproduction vary and covary at a phenotypic level, even though phenotypic variation and covariation are the substrates of natural selection and subsequent evolution. If we are to understand A. thaliana’s microevolutionary dynamics to the same extent that we understand its molecular genetics, then we must first flesh out and describe this (co)-variation. We characterized the covariation of reproductive traits in A. thaliana, utilizing multiple natural genotypes to assess whether such covariation is genetically variable. We subjected plants to naturally relevant variation in apical meristem damage and nutrient levels to explore the degree to which the relationships among traits are plastic. We found that inflorescence ontogeny (as inferred from the relationships among reproductive traits) is altered in apically damaged plants, and that variation in nutrient levels affects ontogeny as well. We also found that genetically clustered groups of plants qualitatively differ in the relationships among traits. These findings are discussed in terms of constraints on selection and of possible selection pressures for different inflorescence ontogenies in this species.
Genetic analysis of variation in gene expression in Arabidopsis thaliana
Genetics, 2005
In Arabidopsis thaliana, significant efforts to determine the extent of genomic variation between phenotypically divergent accessions are under way, but virtually nothing is known about variation at the transcription level. We used microarrays to examine variation in transcript abundance among three inbred lines and two pairs of reciprocal F 1 hybrids of the highly self-fertilizing species Arabidopsis. Composite additive genetic effects for gene expression were estimated from pairwise comparisons of the three accessions Columbia (Col), Landsberg erecta (Ler), and Cape Verde Islands (Cvi). For the pair Col and Ler, 27.0% of the 4876 genes exhibited additive genetic effects in their expression (a ¼ 0.001) vs. 32.2 and 37.5% for Cvi with Ler and Col, respectively. Significant differential expression ranged from 32.45 down to 1.10 in fold change and typically differed by a factor of 1.56. Maternal or paternal transmission affected only a few genes, suggesting that the reciprocal effects observed in the two crosses analyzed were minimal. Dominance effects were estimated from the comparisons of hybrids with the corresponding midparent value. The percentage of genes showing dominance at the expression level in the F 1 hybrids ranged from 6.4 to 21.1% (a ¼ 0.001). Breakdown of these numbers of genes according to the magnitude of the dominance ratio revealed heterosis for expression for on average 9% of the genes. Further advances in the genetic analysis of gene expression variation may contribute to a better understanding of its role in affecting quantitative trait variation at the phenotypic level.
Current Genomics, 2011
Since the sequencing of the nuclear genome of Arabidopsis thaliana ten years ago, various large-scale analyses of gene function have been performed in this model species. In particular, the availability of collections of lines harbouring random T-DNA or transposon insertions, which include mutants for almost all of the ~27,000 A. thaliana genes, has been crucial for the success of forward and reverse genetic approaches. In the foreseeable future, genome-wide phenotypic data from mutant analyses will become available for Arabidopsis, and will stimulate a flood of novel in-depth genefunction analyses. In this review, we consider the present status of resources and concepts for systematic studies of gene function in A. thaliana. Current perspectives on the utility of loss-of-function and gain-of-function mutants will be discussed in light of the genetic and functional redundancy of many A. thaliana genes.
AraQTL - Workbench and Archive for systems genetics in Arabidopsis thaliana
The Plant journal : for cell and molecular biology, 2016
Genetical genomics studies uncover genome-wide genetic interactions between genes and their transcriptional regulators. High-throughput measurement of gene expression in recombinant inbred line populations enabled the investigation of the genetic architecture of gene expression variation. This has the potential to enrich the understanding of the molecular mechanisms affected by and underlying natural variation. Moreover, it contributes to the systems biology of natural variation, as a substantial number of experiments have resulted in a valuable amount of interconnectable phenotypic, molecular and genotypic data. For Arabidopsis thaliana a number of genetical genomics studies have been published, uncovering many expression quantitative trait loci (eQTLs). Yet, this complex data is not easily accessible to the plant research community, leaving most of the valuable genetic interactions unexplored as cross-analysis of these studies is a major effort. We address this with AraQTL www.bio...
Genetic approaches in plant physiology
New Phytologist, 1997
The use of genetics in plant biology aims at the physiological and molecular genetical characterization of the phenotypic variation for the trait under study. Efficient mutant and gene isolation procedures have been developed for a number of plant models such as Arabidopsis thaliana. For this, the map position of the genes and insertion mutagenesis are used. The latter also allows the characterization of genes that are not easily recognized in mutant approaches, by using enhancer or gene-trapping procedures and reverse genetics. In addition to mutants, natural variation present among wild and cultivated varieties of a species provides an important source of genetic variation. The use of molecular markers, advanced mapping populations and specific cytogenetic stocks in case of polyploids, enables a detailed characterization of such natural variation even when it is of a quantitative and polygenic nature. Examples of the various genetic approaches are given.