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5. Plant genetic effects on microbial hubs impact host fitness in repeated field trials

Author

Brachi, Benjamin, Filiault, Daniele, Whitehurst, Hannah, Darme, Paul, Le Gars, Pierre, Le Mentec, Marine, Morton, Timothy C., Kerdaffrec, Envel, Rabanal, Fernando, Anastasio, Alison, Box, Mathew S., Duncan, Susan, Huang, Feng, Leff, Riley, Novikova, Polina, Perisin, Matthew, Tsuchimatsu, Takashi, Woolley, Roderick, Dean, Caroline, Nordborg, Magnus, Holm, Svante, and Bergelson, Joy

Published
2022

9. 36‐year study reveals stability of a wild wheat population across microhabitats.

Author

Dahan‐Meir, Tal, Ellis, Thomas James, Mafessoni, Fabrizio, Sela, Hanan, Rudich, Ori, Manisterski, Jacob, Avivi‐Ragolsky, Naomi, Raz, Amir, Feldman, Moshe, Anikster, Yehoshua, Nordborg, Magnus, and Levy, Avraham A.

Subjects
ECOLOGICAL genetics, POPULATION ecology, CONSERVATION genetics, POPULATION dynamics, SPATIAL resolution
Abstract

Long‐term genetic studies of wild populations are very scarce, but are essential for connecting ecological and population genetics models, and for understanding the dynamics of biodiversity. We present a study of a wild wheat population sampled over a 36‐year period at high spatial resolution. We genotyped 832 individuals from regular sampling along transects during the course of the experiment. Genotypes were clustered into ecological microhabitats over scales of tens of metres, and this clustering was remarkably stable over the 36 generations of the study. Simulations show that it is difficult to determine whether this spatial and temporal stability reflects extremely limited dispersal or fine‐scale local adaptation to ecological parameters. Using a common‐garden experiment, we showed that the genotypes found in distinct microhabitats differ phenotypically. Our results provide a rare insight into the population genetics of a natural population over a long monitoring period. [ABSTRACT FROM AUTHOR]

Published
2024
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17. Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions

Author

Alonso-Blanco, Carlos, Andrade, Jorge, Becker, Claude, Bemm, Felix, Bergelson, Joy, Borgwardt, Karsten, Chae, Eunyoung, Dezwaan, Todd, Ding, Wei, Ecker, Joseph R., Expósito-Alonso, Moisés, Farlow, Ashley, Fitz, Joffrey, Gan, Xiangchao, Grimm, Dominik G., Hancock, Angela, Henz, Stefan R., Holm, Svante, Horton, Matthew, Jarsulic, Mike, Kerstetter, Randall A., Korte, Arthur, Korte, Pamela, Lanz, Christa, Lee, Chen-Ruei, Meng, Dazhe, Michael, Todd P., Mott, Richard, Muliyati, Ni Wayan, Nägele, Thomas, Nagler, Matthias, Nizhynska, Viktoria, Nordborg, Magnus, Novikova, Polina, Picó, F. Xavier, Platzer, Alexander, Rabanal, Fernando A., Rodriguez, Alex, Rowan, Beth A., Salomé, Patrice A., Schmid, Karl, Schmitz, Robert J., Seren, Ümit, Sperone, Felice Gianluca, Sudkamp, Mitchell, Svardal, Hannes, Tanzer, Matt M., Todd, Donald, Volchenboum, Samuel L., Wang, Congmao, Wang, George, Wang, Xi, Weckwerth, Wolfram, Weigel, Detlef, Zhou, Xuefeng, Kawakatsu, Taiji, Huang, Shao-shan Carol, Jupe, Florian, Sasaki, Eriko, Urich, Mark A., Castanon, Rosa, Nery, Joseph R., Barragan, Cesar, He, Yupeng, Chen, Huaming, Dubin, Manu, Lee, Cheng-Ruei, O’Neil, Ryan, O’Malley, Ronan C., Quarless, Danjuma X., and Schork, Nicholas J.

Published
2016
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18. 1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana

Author

Alonso-Blanco, Carlos, Andrade, Jorge, Becker, Claude, Bemm, Felix, Bergelson, Joy, Borgwardt, Karsten M., Cao, Jun, Chae, Eunyoung, Dezwaan, Todd M., Ding, Wei, Ecker, Joseph R., Exposito-Alonso, Moises, Farlow, Ashley, Fitz, Joffrey, Gan, Xiangchao, Grimm, Dominik G., Hancock, Angela M., Henz, Stefan R., Holm, Svante, Horton, Matthew, Jarsulic, Mike, Kerstetter, Randall A., Korte, Arthur, Korte, Pamela, Lanz, Christa, Lee, Cheng-Ruei, Meng, Dazhe, Michael, Todd P., Mott, Richard, Muliyati, Ni Wayan, Nägele, Thomas, Nagler, Matthias, Nizhynska, Viktoria, Nordborg, Magnus, Novikova, Polina Yu., Picó, F. Xavier, Platzer, Alexander, Rabanal, Fernando A., Rodriguez, Alex, Rowan, Beth A., Salomé, Patrice A., Schmid, Karl J., Schmitz, Robert J., Seren, Ümit, Sperone, Felice Gianluca, Sudkamp, Mitchell, Svardal, Hannes, Tanzer, Matt M., Todd, Donald, Volchenboum, Samuel L., Wang, Congmao, Wang, George, Wang, Xi, Weckwerth, Wolfram, Weigel, Detlef, and Zhou, Xuefeng

Published
2016
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26. Cycles of satellite and transposon evolution in Arabidopsis centromeres.

Author

Wlodzimierz, Piotr, Rabanal, Fernando A., Burns, Robin, Naish, Matthew, Primetis, Elias, Scott, Alison, Mandáková, Terezie, Gorringe, Nicola, Tock, Andrew J., Holland, Daniel, Fritschi, Katrin, Habring, Anette, Lanz, Christa, Patel, Christie, Schlegel, Theresa, Collenberg, Maximilian, Mielke, Miriam, Nordborg, Magnus, Roux, Fabrice, and Shirsekar, Gautam

Abstract

Centromeres are critical for cell division, loading CENH3 or CENPA histone variant nucleosomes, directing kinetochore formation and allowing chromosome segregation1,2. Despite their conserved function, centromere size and structure are diverse across species. To understand this centromere paradox3,4, it is necessary to know how centromeric diversity is generated and whether it reflects ancient trans-species variation or, instead, rapid post-speciation divergence. To address these questions, we assembled 346 centromeres from 66 Arabidopsis thaliana and 2 Arabidopsis lyrata accessions, which exhibited a remarkable degree of intra- and inter-species diversity. A. thaliana centromere repeat arrays are embedded in linkage blocks, despite ongoing internal satellite turnover, consistent with roles for unidirectional gene conversion or unequal crossover between sister chromatids in sequence diversification. Additionally, centrophilic ATHILA transposons have recently invaded the satellite arrays. To counter ATHILA invasion, chromosome-specific bursts of satellite homogenization generate higher-order repeats and purge transposons, in line with cycles of repeat evolution. Centromeric sequence changes are even more extreme in comparison between A. thaliana and A. lyrata. Together, our findings identify rapid cycles of transposon invasion and purging through satellite homogenization, which drive centromere evolution and ultimately contribute to speciation.Inter- and intra-species comparison of Arabidopsis centromere variation identifies rapid cycles of transposon invasion and purging through satellite homogenization that drive centromere evolution. [ABSTRACT FROM AUTHOR]

Published
2023
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27. On the causes of gene-body methylation variation in Arabidopsis thaliana.

Author

Pisupati, Rahul, Nizhynska, Viktoria, Mollá Morales, Almudena, and Nordborg, Magnus

Subjects
METHYLATION, GENETIC polymorphisms, GENETIC variation, ARABIDOPSIS thaliana, LARGE deviations (Mathematics), ZYGOTES
Abstract

Gene-body methylation (gbM) refers to sparse CG methylation of coding regions, which is especially prominent in evolutionarily conserved house-keeping genes. It is found in both plants and animals, but is directly and stably (epigenetically) inherited over multiple generations in the former. Studies in Arabidopsis thaliana have demonstrated that plants originating from different parts of the world exhibit genome-wide differences in gbM, which could reflect direct selection on gbM, but which could also reflect an epigenetic memory of ancestral genetic and/or environmental factors. Here we look for evidence of such factors in F2 plants resulting from a cross between a southern Swedish line with low gbM and a northern Swedish line with high gbM, grown at two different temperatures. Using bisulfite-sequencing data with nucleotide-level resolution on hundreds of individuals, we confirm that CG sites are either methylated (nearly 100% methylation across sampled cells) or unmethylated (approximately 0% methylation across sampled cells), and show that the higher level of gbM in the northern line is due to more sites being methylated. Furthermore, methylation variants almost always show Mendelian segregation, consistent with their being directly and stably inherited through meiosis. To explore how the differences between the parental lines could have arisen, we focused on somatic deviations from the inherited state, distinguishing between gains (relative to the inherited 0% methylation) and losses (relative to the inherited 100% methylation) at each site in the F2 generation. We demonstrate that deviations predominantly affect sites that differ between the parental lines, consistent with these sites being more mutable. Gains and losses behave very differently in terms of the genomic distribution, and are influenced by the local chromatin state. We find clear evidence for different trans-acting genetic polymorphism affecting gains and losses, with those affecting gains showing strong environmental interactions (G×E). Direct effects of the environment were minimal. In conclusion, we show that genetic and environmental factors can change gbM at a cellular level, and hypothesize that these factors can also lead to transgenerational differences between individuals via the inclusion of such changes in the zygote. If true, this could explain genographic pattern of gbM with selection, and would cast doubt on estimates of epimutation rates from inbred lines in constant environments. Author summary: Gene-body methylation, the sparse CG methylation that is associated with house-keeping genes, is found in both plants and animals, but can be directly inherited in the former. Recently, we discovered that Arabidopsis thaliana originating from different geographic regions exhibit different patterns of gbM, which could be due to direct selection on gbM, but could also reflect a transgenerational memory of genetic or environmental factors. Here we look for evidence of such factors using a genetic cross between two natural inbred lines: one with high, and one with low gbM. We confirm that methylation states are stably inherited, but also see large somatic deviations from the inherited state, in particular at sites that differ between the parental lines. We demonstrate that these deviations are affected by genetic variants in interaction with the environment, and hypothesize that geographic differences in gbM arise through the inclusion of such deviations in the zygote. [ABSTRACT FROM AUTHOR]

Published
2023
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34. A Single IGF1 Allele Is a Major Determinant of Small Size in Dogs

Author

Sutter, Nathan B., Bustamante, Carlos D., Chase, Kevin, Gray, Melissa M., Zhao, Keyan, Zhu, Lan, Padhukasahasram, Badri, Karlins, Eric, Davis, Sean, Jones, Paul G., Quignon, Pascale, Johnson, Gary S., Parker, Heidi G., Fretwell, Neale, Mosher, Dana S., Lawler, Dennis F., Satyaraj, Ebenezer, Nordborg, Magnus, Lark, K. Gordon, Wayne, Robert K., and Ostrander, Elaine A.

Published
2007
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39. Conditional GWAS of non-CG transposon methylation in Arabidopsis thaliana reveals major polymorphisms in five genes.

Author

Sasaki, Eriko, Gunis, Joanna, Reichardt-Gomez, Ilka, Nizhynska, Viktoria, and Nordborg, Magnus

Subjects
HEREDITY, METHYLATION, GENOME-wide association studies, DNA methylation, TRANSPOSONS, GENETIC polymorphisms
Abstract

Genome-wide association studies (GWAS) have revealed that the striking natural variation for DNA CHH-methylation (mCHH; H is A, T, or C) of transposons has oligogenic architecture involving major alleles at a handful of known methylation regulators. Here we use a conditional GWAS approach to show that CHG-methylation (mCHG) has a similar genetic architecture—once mCHH is statistically controlled for. We identify five key trans-regulators that appear to modulate mCHG levels, and show that they interact with a previously identified modifier of mCHH in regulating natural transposon mobilization. Author summary: DNA methylation is an epigenetic mark common across eukaryotes. It is associated with transcriptional silencing, in particular of transposable elements. Multiple elements, including epigenetic inheritance, shape DNA methylation patterns, and the complexity makes it challenging to dissect the regulation. Our work on the 1001 Arabidopsis Epigenomes project led to the unexpected discovery that much of the natural variation for CHH methylation (mCHH; H is A, T, or C) on transposable elements could be attributed to allelic variation in three genes known to be involved in epigenetic regulation. However, our analysis of methylation in other sequence contexts (mCHG and mCG) revealed no genetic regulator. Here we show that if mCHG variation is analyzed while taking mCHH into account, mCHG is also strongly influenced by allelic variation in a small number of genes with known or highly plausible direct roles in epigenetic regulation. The presence of common allelic variation of large effect is suggestive of some form of local adaptation. The nature of this adaptation remains obscure, but we present further evidence that allelic variation regulating DNA methylation influences transposon mobilization. [ABSTRACT FROM AUTHOR]

Published
2022
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40. GWAS with Heterogeneous Data: Estimating the Fraction of Phenotypic Variation Mediated by Gene Expression Data

Author

Sasaki, Eriko, Frommlet, Florian, and Nordborg, Magnus

Subjects
0106 biological sciences, 0301 basic medicine, Arabidopsis, Regulator, MADS Domain Proteins, Genome-wide association study, Locus (genetics), Flowers, Investigations, Biology, QH426-470, 01 natural sciences, 03 medical and health sciences, Gene Expression Regulation, Plant, mediation analysis, flowering time, Genetic variation, Genetics, Gene Regulatory Networks, natural variation, Molecular Biology, Gene, Genetics (clinical), correlation network, Genetic diversity, Polymorphism, Genetic, Arabidopsis Proteins, fungi, food and beverages, Phenotype, genetic architecture, Genetic architecture, FLC, 030104 developmental biology, Evolutionary biology, Genome-Wide Association Study, 010606 plant biology & botany
Abstract

Intermediate phenotypes such as gene expression values can be used to elucidate the mechanisms by which genetic variation causes phenotypic variation, but jointly analyzing such heterogeneous data are far from trivial. Here we extend a so-called mediation model to handle the confounding effects of genetic background, and use it to analyze flowering time variation in Arabidopsis thaliana, focusing in particular on the central role played by the key regulator FLOWERING TIME LOCUS C (FLC). FLC polymorphism and FLC expression are both strongly correlated with flowering time variation, but the effect of the former is only partly mediated through the latter. Furthermore, the latter also reflects genetic background effects. We demonstrate that it is possible to partition these effects, shedding light on the complex regulatory network that underlies flowering time variation.

Published
2018
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44. Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines

Author

Atwell, Susanna, Huang, Yu S., Vilhjálmsson, Bjarni J., Willems, Glenda, Horton, Matthew, Li, Yan, Meng, Dazhe, Platt, Alexander, Tarone, Aaron M., Hu, Tina T., Jiang, Rong, Muliyati, Wayan N., Zhang, Xu, Amer, Muhammad Ali, Baxter, Ivan, Brachi, Benjamin, Chory, Joanne, Dean, Caroline, Debieu, Marilyne, de Meaux, Juliette, Ecker, Joseph R., Faure, Nathalie, Kniskern, Joel M., Jones, Jonathan D. G., Michael, Todd, Nemri, Adnane, Roux, Fabrice, Salt, David E., Tang, Chunlao, Todesco, Marco, Traw, Brian M., Weigel, Detlef, Marjoram, Paul, Borevitz, Justin O., Bergelson, Joy, and Nordborg, Magnus

Published
2010
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50. Global Genetic Heterogeneity in Adaptive Traits.

Author

Lopez-Arboleda, William Andres, Reinert, Stephan, Nordborg, Magnus, and Korte, Arthur

Subjects
GENETIC engineering, GENOME-wide association studies, GENE expression, PLANT development, PLANT genes
Abstract

Understanding the genetic architecture of complex traits is a major objective in biology. The standard approach for doing so is genome-wide association studies (GWAS), which aim to identify genetic polymorphisms responsible for variation in traits of interest. In human genetics, consistency across studies is commonly used as an indicator of reliability. However, if traits are involved in adaptation to the local environment, we do not necessarily expect reproducibility. On the contrary, results may depend on where you sample, and sampling across a wide range of environments may decrease the power of GWAS because of increased genetic heterogeneity. In this study, we examine how sampling affects GWAS in the model plant species Arabidopsis thaliana. We show that traits like flowering time are indeed influenced by distinct genetic effects in local populations. Furthermore, using gene expression as a molecular phenotype, we show that some genes are globally affected by shared variants, whereas others are affected by variants specific to subpopulations. Remarkably, the former are essentially all cis -regulated, whereas the latter are predominately affected by trans -acting variants. Our result illustrate that conclusions about genetic architecture can be extremely sensitive to sampling and population structure. [ABSTRACT FROM AUTHOR]

Published
2021
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