Antagonistic pleiotropic effects reduce the potential adaptive value of the FRIGIDA locus

Scarcelli, Nora; Cheverud, James M.; Schaal, Barbara A.; Kover, Paula X.

doi:10.1073/pnas.0708209104

Cited by 97 publications

(120 citation statements)

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“…This locus was previously identified by Loudet et al [34] in a study of flowering time and maps to a region of the genome that encompasses the FRI gene. FRI has previously been shown to have pleiotropic effects on fitness-related traits [42,43], and our analysis shows that it appears to also have relatively strong indirect effects on partners (the indirect effects alone are significant at the genome level). As expected, this QTL did have a direct effect on BOLT.…”

Section: Discussionmentioning

confidence: 77%

“…Support that this QTL is due to molecular variation in FRI comes from the fact that the Bay-0 parental accession has a non-functional copy of this gene (known to accelerate flowering time), while Shahdara has a functional copy. FRI is one of the best-characterized flowering genes in Arabidopsis [40] and has also been shown to affect fitness of A. thaliana plants in the field [41], as well as drought tolerance [42] and inflorescence architecture [43].…”

Section: Results (A) Quantitative Trait Loci Analysismentioning

confidence: 99%

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Functional genetics of intraspecific ecological interactions in Arabidopsis thaliana

Wolf

Mutic

Kover

2011

Phil. Trans. R. Soc. B

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Studying the genetic basis of traits involved in ecological interactions is a fundamental part of elucidating the connections between evolutionary and ecological processes. Such knowledge allows one to link genetic models of trait evolution with ecological models describing interactions within and between species. Previous work has shown that connections between genetic and ecological processes in Arabidopsis thaliana may be mediated by the fact that quantitative trait loci (QTL) with 'direct' effects on traits of individuals also have pleiotropic 'indirect' effects on traits expressed in neighbouring plants. Here, we further explore these connections by examining functional relationships between traits affected directly and indirectly by the same QTL. We develop a novel approach using structural equation models (SEMs) to determine whether observed pleiotropic effects result from traits directly affected by the QTL in focal individuals causing the changes in the neighbours' phenotypes. This hypothesis was assessed using SEMs to test whether focal plant phenotypes appear to mediate the connection between the focal plants' genotypes and the phenotypes of their neighbours, or alternatively, whether the connection between the focal plants' genotypes and the neighbours' phenotypes is mediated by unmeasured traits. We implement this analysis using a QTL of major effect that maps to the well-characterized flowering locus, FRIGIDA. The SEMs support the hypothesis that the pleiotropic indirect effects of this locus arise from size and developmental timing-related traits in focal plants affecting the expression of developmental traits in their neighbours. Our findings provide empirical insights into the genetics and nature of intraspecific ecological interactions. Our technique holds promise in directing future work into the genetic basis and functional relationship of traits mediating and responding to ecological interactions.

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Section: Discussionmentioning

confidence: 77%

Section: Results (A) Quantitative Trait Loci Analysismentioning

confidence: 99%

Functional genetics of intraspecific ecological interactions in Arabidopsis thaliana

Wolf

Mutic

Kover

2011

Phil. Trans. R. Soc. B

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“…Empirical studies provide evidence of past adaptation to climate change (36)(37)(38), but measuring multigenerational evolutionary response to experimental environmental change is only feasible for organisms with very short life cycles (39, 40, but also refer to 41,42). Theoretical quantitative genetic models provide important general predictions of phenotypic evolution in response to environmental change (3, 4, 43, 44) but lack biological specificity.…”

Section: Discussionmentioning

confidence: 99%

Predicting the evolutionary dynamics of seasonal adaptation to novel climates in Arabidopsis thaliana

Fournier‐Level

Perry

Wang

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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Predicting whether and how populations will adapt to rapid climate change is a critical goal for evolutionary biology. To examine the genetic basis of fitness and predict adaptive evolution in novel climates with seasonal variation, we grew a diverse panel of the annual plant Arabidopsis thaliana (multiparent advanced generation intercross lines) in controlled conditions simulating four climates: a present-day reference climate, an increased-temperature climate, a winter-warming only climate, and a poleward-migration climate with increased photoperiod amplitude. In each climate, four successive seasonal cohorts experienced dynamic daily temperature and photoperiod variation over a year. We measured 12 traits and developed a genomic prediction model for fitness evolution in each seasonal environment. This model was used to simulate evolutionary trajectories of the base population over 50 y in each climate, as well as 100-y scenarios of gradual climate change following adaptation to a reference climate. Patterns of plastic and evolutionary fitness response varied across seasons and climates. The increased-temperature climate promoted genetic divergence of subpopulations across seasons, whereas in the winter-warming and poleward-migration climates, seasonal genetic differentiation was reduced. In silico "resurrection experiments" showed limited evolutionary rescue compared with the plastic response of fitness to seasonal climate change. The genetic basis of adaptation and, consequently, the dynamics of evolutionary change differed qualitatively among scenarios. Populations with fewer founding genotypes and populations with genetic diversity reduced by prior selection adapted less well to novel conditions, demonstrating that adaptation to rapid climate change requires the maintenance of sufficient standing variation.climate change | annual plant | genomic prediction | season O ngoing climate change is causing rapid shifts in environmental selective pressures within local populations (1, 2). To persist, populations must track the shifting multivariate trait optimum by phenotypic plasticity or adaptive evolution (3, 4), or migrate to keep up with poleward shifts in their original climate niche (1). The outcome of these responses to climate change will depend upon the seasonal variation a population experiences, particularly in temperate climates, where seasonality is a major source of environmental heterogeneity (5, 6). Understanding adaptation to seasonal environments is critical for predicting the response to climate change in short-lived organisms with multiple generations per year, like many insects and annual plants. Such prediction requires theoretical projections based on solid empirical foundations, tracking phenotypic change in complex traits as well as in the molecular variation present within populations as they adapt to different seasons. Here, we use a genomic prediction model, based on experimental data from Arabidopsis thaliana, to simulate trajectories of adaptation to novel climate scenarios in season...

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“…We simulated the MAGIC lines as described in Scarcelli et al (2007) by intermating 19 founders lines for five generations producing 342 F5 outcrossed families. More precisely, in the first generation, a complete diallele cross (the 19 · 18 ¼ 342 possible F 1 crosses) was simulated.…”

Section: Estimation Of Ibd Probabilitiesmentioning

confidence: 99%

Modeling of Identity-by-Descent Processes Along a Chromosome Between Haplotypes and Their Genotyped Ancestors

Druet¹,

Farnir

2011

Genetics

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Identity-by-descent probabilities are important for many applications in genetics. Here we propose a method for modeling the transmission of the haplotypes from the closest genotyped relatives along an entire chromosome. The method relies on a hidden Markov model where hidden states correspond to the set of all possible origins of a haplotype within a given pedigree. Initial state probabilities are estimated from average genetic contribution of each origin to the modeled haplotype while transition probabilities are computed from recombination probabilities and pedigree relationships between the modeled haplotype and the various possible origins. The method was tested on three simulated scenarios based on real data sets from dairy cattle, Arabidopsis thaliana, and maize. The mean identity-by-descent probabilities estimated for the truly inherited parental chromosome ranged from 0.94 to 0.98 according to the design and the marker density. The lowest values were observed in regions close to crossing over or where the method was not able to discriminate between several origins due to their similarity. It is shown that the estimated probabilities were correctly calibrated. For marker imputation (or QTL allele prediction for fine mapping or genomic selection), the method was efficient, with 3.75% allelic imputation error rates on a dairy cattle data set with a low marker density map (1 SNP/Mb). The method should prove useful for situations we are facing now in experimental designs and in plant and animal breeding, where founders are genotyped with relatively high markers densities and last generation(s) genotyped with a lower-density panel.T WO alleles at a single locus are identical-by-descent (IBD) if they derive from a common ancestor without mutation. The probability for two alleles to be IBD (IBDp) is an information of high importance as it is used in several applications such as gene or Estimation of IBDp may rely on linkage or linkage disequilibrium information, or on both. With linkage, the estimation of IBDp is based on Mendelian segregation rules, recombination, pedigree, and genotypes. With such information, IBDp are most often estimated between parents and offspring with the sole informative flanking markers (e.g., Fernando and Grossman 1989;Wang et al. 1995;Pong-Wong et al. 2001). IBDp between more distant relatives are obtained by transmitting the parent-offspring information along the path between the relatives. If some individuals on this path are not genotyped, transmission of chromosomes can no longer be traced unambiguously. In addition, since the information relies only on flanking markers, it is rapidly eroded along the pedigree path.Other methods estimate IBDp probabilities using multipoint linkage and segregation analysis and by considering all the pedigree links. Lander and Green (1987) proposed such a method considering each alternative gene flow pattern in a pedigree separately. However, it results in high computational costs when the pedigree increases. Abecasis et al. (2002) descr...

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Antagonistic pleiotropic effects reduce the potential adaptive value of the FRIGIDA locus

Cited by 97 publications

References 57 publications

Functional genetics of intraspecific ecological interactions in Arabidopsis thaliana

Functional genetics of intraspecific ecological interactions in Arabidopsis thaliana

Predicting the evolutionary dynamics of seasonal adaptation to novel climates in Arabidopsis thaliana

Modeling of Identity-by-Descent Processes Along a Chromosome Between Haplotypes and Their Genotyped Ancestors

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