Abstract
Understanding the molecular mechanisms that have enabled phenotypic diversification in response to natural selection is one of the greatest challenges in modern biology. Complex traits with a polygenic basis such as growth rate are important for plant performance under natural conditions. However, determining the molecular basis of adaptation in these traits is challenging due to the small effect sizes expected and the population structure between genotypes. My work aimed to characterize the genetic basis of complex phenotypes with a polygenic basis in the model species Arabidopsis thaliana. First, I examined signatures of local growth adaptation in geographically distant populations. Therefore, I measured rosette growth in artificial mimicking latitudinal differences as well as in natural field conditions imposing different levels of competition, for a set of genotypes representative of four major regional populations, including the long separated population of China. Rosette size at the end of the growth phase proved to be the most strongly heritable component of growth rate. All genotypes significantly increased their rosette diameter when light levels were reduced, indicating that environmental plasticity is a predominant source of variation for adjusting plant size to prevailing light conditions. Phenotypic divergence between regional populations indicate that growth rate evolution is generally constrained by stabilizing selection. To understand the genetic basis underlying differences in growth rate, I conducted genomewide association studies (GWAS). Few loci associated with genetic variation for growth above the Bonferroni confidence level. However, marginally associated variants were significantly enriched among genes with annotated roles in growth and stress responses. Polygenic scores calculated from marginally associated variants confirmed the polygenic basis of growth variation. A meta-analysis of GWAS signals across environmental conditions confirmed the relevance of sub-significant associations. By associating loss-of-function alleles with growth dynamics, I identified and validated that genes related to chloroplast maturation modulate growth under limiting light conditions. To overcome limitations imposed by functional classification in Gene Ontology (GO), I sought to identify genes specifically associated with growth modifications in response to light or competition, by quantifying differences in gene expression between wild-type plants and mutants in key light signaling genes. The group of genes I identified using this approach showed overlapped significantly with genes whose variants associate with growth variation in the natural population. Since associations in GWAS can be confounded by population structure, I characterized the genetics of gene expression divergence between regions by quantifying allele-specific expression (ASE) differences within inter-regional F1 hybrids. To do this, I generated interpopulation hybrids between genotypes from 4 different regions (Morocco, Sweden, Spain, China). Comparison with differential parental gene expression (trans) showed a significant correlation between cis and trans, indicating that these genetic variants contribute significantly to expression divergence. We used quantitative models to determine the phylogeographic origin of these regulatory variants and document marked inter-regional differences in their functional distribution. Overall, this work illustrates that the genetic basis of growth adaptation is complex and polygenic. By combining information from a reductionist approach (using mutants), a quantitative genetic approach (using GWAS), and a transcriptomic approach (identifying patterns of ASE evolution), I reveal the molecular targets of natural selection. The overlap between signatures of polygenic selection on cis-regulatory variation, the study of phenotypic variation using GWAS, and the experimental identification of regulatory changes associated with growth alterations collectively support the notion that functions related to light perception, hormones, defense/stress, and growth regulation are involved in the local adaptation of plant growth. My work highlights the complex signatures of polygenic adaptation in A. thaliana, and pioneers novel innovative approach to overcome the experimental limitations caused by complex genetic architecture, confounding effects of population structure, and detection bias of genetic variants.
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Claims 12
Claim · model-written summary
Final rosette size was the most heritable growth rate component.
- Taxon
- Arabidopsis thaliana
Arabidopsis thalianat0 - Organ / stage
- end of the growth phasee0
- Outcome
- Rosette sizee0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Rosette size at the end of the growth phase proved to be the most strongly heritable component of growth rate.”
t0“Arabidopsis thaliana”
Claim · model-written summary
All genotypes significantly increased rosette diameter under reduced light.
- Taxon
- Arabidopsis thalianaArabidopsis thalianat0
- Treatment
- light levels were reducede0
- Outcome
- rosette diametere0
- Direction
- increasede0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“All genotypes significantly increased their rosette diameter when light levels were reduced”
t0“Arabidopsis thaliana”
Claim · model-written summary
Regional population divergence suggested stabilizing selection constrains growth rate evolution.
- Taxon
- Arabidopsis thalianaArabidopsis thalianat0
- Material
- regional populationse0
- Outcome
- growth rate evolutione0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Phenotypic divergence between regional populations indicate that growth rate evolution is generally constrained by stabilizing selection.”
t0“Arabidopsis thaliana”
Claim · model-written summary
Few loci associated with growth variation above the Bonferroni level.
- Taxon
- Arabidopsis thalianaArabidopsis thalianat0
- Gene
- locie0
- Outcome
- genetic variation for growthe0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Few loci associated with genetic variation for growth above the Bonferroni confidence level.”
t0“Arabidopsis thaliana”
Claim · model-written summary
Marginal growth associated variants were enriched in growth and stress genes.
- Taxon
- Arabidopsis thalianaArabidopsis thalianat0
- Gene
- genes with annotated roles in growth and stress responsese0
- Outcome
- marginally associated variantse0
- Direction
- enrichede0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“marginally associated variants were significantly enriched among genes with annotated roles in growth and stress responses.”
t0“Arabidopsis thaliana”
Claim · model-written summary
Polygenic scores confirmed polygenic growth variation.
- Taxon
- Arabidopsis thalianaArabidopsis thalianat0
- Outcome
- polygenic basis of growth variatione0
- Comparator
- marginally associated variantse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Polygenic scores calculated from marginally associated variants confirmed the polygenic basis of growth variation.”
t0“Arabidopsis thaliana”
Claim · model-written summary
Cross environment GWAS meta-analysis supported sub-significant associations.
- Taxon
- Arabidopsis thalianaArabidopsis thalianat0
- Outcome
- relevance of sub-significant associationse0
- Comparator
- environmental conditionse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“A meta-analysis of GWAS signals across environmental conditions confirmed the relevance of sub-significant associations.”
t0“Arabidopsis thaliana”
Claim · model-written summary
Chloroplast maturation genes modulated growth under limited light.
- Taxon
- Arabidopsis thalianaArabidopsis thalianat0
- Gene
- genes related to chloroplast maturatione0
- Outcome
- growthe0
- Qualifier
- limiting light conditionse0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“genes related to chloroplast maturation modulate growth under limiting light conditions.”
t0“Arabidopsis thaliana”
Claim · model-written summary
Expression identified growth modification genes significantly overlapped naturally associated variants.
- Taxon
- Arabidopsis thalianaArabidopsis thalianat0
- Gene
- group of genese0
- Outcome
- growth variatione0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“The group of genes I identified using this approach showed overlapped significantly with genes whose variants associate with growth variation in the natural population.”
t0“Arabidopsis thaliana”
Claim · model-written summary
Cis and trans expression differences were significantly correlated.
- Taxon
- Arabidopsis thalianaArabidopsis thalianat0
- Gene
- differential parental gene expressione0
- Outcome
- correlation between cis and transe0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Comparison with differential parental gene expression (trans) showed a significant correlation between cis and trans”
t0“Arabidopsis thaliana”
Claim · model-written summary
Regulatory variants differed markedly in functional distribution across regions.
- Taxon
- Arabidopsis thalianaArabidopsis thalianat0
- Gene
- regulatory variantse1
- Outcome
- functional distributione0
- Direction
- differencese0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“document marked inter-regional differences in their functional distribution.”
e1“regulatory variants”
t0“Arabidopsis thaliana”
Claim · model-written summary
Selection, GWAS and experimental results implicated light perception, hormones, stress and growth regulation in local growth adaptation.
- Taxon
- Arabidopsis thalianaArabidopsis thalianat0
- Gene
- growth regulatione0
- Outcome
- local adaptation of plant growthe0
- Qualifier
- functions related to light perception, hormones, defense/stress, and growth regulatione0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“functions related to light perception, hormones, defense/stress, and growth regulation are involved in the local adaptation of plant growth.”
t0“Arabidopsis thaliana”
The same questions in other papers
light · growth · Arabidopsis thaliana (thale cress)Results differ
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