1
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Lyu JI, Kim JH, Chuong NN, Doan PPT, Chu H, Baek SH, Lim PO, Kim J. ACCELERATED CELL DEATH 6 is a crucial genetic factor shaping the natural diversity of age- and salicylic acid-induced leaf senescence in Arabidopsis. PHYSIOLOGIA PLANTARUM 2024; 176:e14507. [PMID: 39221491 DOI: 10.1111/ppl.14507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 08/10/2024] [Accepted: 08/18/2024] [Indexed: 09/04/2024]
Abstract
Leaf senescence is a crucial process throughout evolution, vital for plant fitness as it facilitates the gradual shift of energy allocation between photosynthesis and catabolism overtime. This onset is influenced by a complex interplay of genetic and environmental factors, making senescence a key adaptation mechanism for plants in their natural habitats. Our study investigated the genetic mechanism underlying age-induced leaf senescence in Arabidopsis natural populations. Using a phenome high-throughput investigator, we comprehensively analyzed senescence responses across 234 Arabidopsis accessions and identified that environmental factors (e.g., ambient temperature) and physiological factors (e.g., defense responses) are substantially linked to senescence phenotypes. Through genome-wide association mapping, we identified the ACCELERATED CELL DEATH 6 (ACD6) locus as a potential regulator of senescence variation among natural accessions. Knocking out ACD6 in accessions with early and delayed senescence phenotypes resulted in varying degrees of delay in age-induced senescence, highlighting the accession-dependent regulatory role of ACD6 in leaf senescence. Furthermore, our findings suggest ACD6's involvement in senescence regulation via the salicylic acid signaling pathway. In summary, our study sheds light on the genetic regulation of leaf senescence in Arabidopsis natural populations, with the discovery of ACD6 as a potential candidate for genetic modification to enhance plant adaptation and survival.
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Affiliation(s)
- Jae Il Lyu
- Gene Engineering Division, National Institute of Agricultural Sciences, Republic of Korea
- Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, Republic of Korea
| | - Jin Hee Kim
- Subtropical Horticulture Research Institute, Jeju National University, Republic of Korea
| | - Nguyen Nguyen Chuong
- Interdisciplinary Graduate Program in Advanced Convergence Technology & Science, Jeju National University, Republic of Korea
| | - Phan Phuong Thao Doan
- Interdisciplinary Graduate Program in Advanced Convergence Technology & Science, Jeju National University, Republic of Korea
| | - Hyosub Chu
- Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, Republic of Korea
| | - Seung Hee Baek
- Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, Republic of Korea
| | - Pyung Ok Lim
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Republic of Korea
| | - Jeongsik Kim
- Subtropical Horticulture Research Institute, Jeju National University, Republic of Korea
- Interdisciplinary Graduate Program in Advanced Convergence Technology & Science, Jeju National University, Republic of Korea
- Faculty of Science Education, Jeju National University, Republic of Korea
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2
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Wang P, Lehti-Shiu MD, Lotreck S, Segura Abá K, Krysan PJ, Shiu SH. Prediction of plant complex traits via integration of multi-omics data. Nat Commun 2024; 15:6856. [PMID: 39127735 PMCID: PMC11316822 DOI: 10.1038/s41467-024-50701-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 07/18/2024] [Indexed: 08/12/2024] Open
Abstract
The formation of complex traits is the consequence of genotype and activities at multiple molecular levels. However, connecting genotypes and these activities to complex traits remains challenging. Here, we investigate whether integrating genomic, transcriptomic, and methylomic data can improve prediction for six Arabidopsis traits. We find that transcriptome- and methylome-based models have performances comparable to those of genome-based models. However, models built for flowering time using different omics data identify different benchmark genes. Nine additional genes identified as important for flowering time from our models are experimentally validated as regulating flowering. Gene contributions to flowering time prediction are accession-dependent and distinct genes contribute to trait prediction in different genotypes. Models integrating multi-omics data perform best and reveal known and additional gene interactions, extending knowledge about existing regulatory networks underlying flowering time determination. These results demonstrate the feasibility of revealing molecular mechanisms underlying complex traits through multi-omics data integration.
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Affiliation(s)
- Peipei Wang
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, USA.
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China.
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA.
| | | | - Serena Lotreck
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
- Department of Computational Mathematics, Science, and Engineering, Michigan State University, East Lansing, MI, USA
| | - Kenia Segura Abá
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, USA
- Genetics and Genome Sciences Program, Michigan State University, East Lansing, MI, USA
| | - Patrick J Krysan
- Department of Plant and Agroecosystem Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Shin-Han Shiu
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, USA.
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA.
- Department of Computational Mathematics, Science, and Engineering, Michigan State University, East Lansing, MI, USA.
- Genetics and Genome Sciences Program, Michigan State University, East Lansing, MI, USA.
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3
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Gravot A, Liégard B, Quadrana L, Veillet F, Aigu Y, Bargain T, Bénéjam J, Lariagon C, Lemoine J, Colot V, Manzanares-Dauleux MJ, Jubault M. Two adjacent NLR genes conferring quantitative resistance to clubroot disease in Arabidopsis are regulated by a stably inherited epiallelic variation. PLANT COMMUNICATIONS 2024; 5:100824. [PMID: 38268192 PMCID: PMC11121752 DOI: 10.1016/j.xplc.2024.100824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 12/21/2023] [Accepted: 01/19/2024] [Indexed: 01/26/2024]
Abstract
Clubroot caused by the protist Plasmodiophora brassicae is a major disease affecting cultivated Brassicaceae. Using a combination of quantitative trait locus (QTL) fine mapping, CRISPR-Cas9 validation, and extensive analyses of DNA sequence and methylation patterns, we revealed that the two adjacent neighboring NLR (nucleotide-binding and leucine-rich repeat) genes AT5G47260 and AT5G47280 cooperate in controlling broad-spectrum quantitative partial resistance to the root pathogen P. brassicae in Arabidopsis and that they are epigenetically regulated. The variation in DNA methylation is not associated with any nucleotide variation or any transposable element presence/absence variants and is stably inherited. Variations in DNA methylation at the Pb-At5.2 QTL are widespread across Arabidopsis accessions and correlate negatively with variations in expression of the two genes. Our study demonstrates that natural, stable, and transgenerationally inherited epigenetic variations can play an important role in shaping resistance to plant pathogens by modulating the expression of immune receptors.
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Affiliation(s)
- Antoine Gravot
- IGEPP Institut Agro, INRAE, Université de Rennes, 35650 Le Rheu, France
| | - Benjamin Liégard
- IGEPP Institut Agro, INRAE, Université de Rennes, 35650 Le Rheu, France
| | - Leandro Quadrana
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), 75005 Paris, France
| | - Florian Veillet
- IGEPP INRAE, Institut Agro, Université de Rennes, 29260 Ploudaniel, France
| | - Yoann Aigu
- IGEPP Institut Agro, INRAE, Université de Rennes, 35650 Le Rheu, France
| | - Tristan Bargain
- IGEPP Institut Agro, INRAE, Université de Rennes, 35650 Le Rheu, France
| | - Juliette Bénéjam
- IGEPP Institut Agro, INRAE, Université de Rennes, 35650 Le Rheu, France
| | | | - Jocelyne Lemoine
- IGEPP Institut Agro, INRAE, Université de Rennes, 35650 Le Rheu, France
| | - Vincent Colot
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), 75005 Paris, France
| | | | - Mélanie Jubault
- IGEPP Institut Agro, INRAE, Université de Rennes, 35650 Le Rheu, France.
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4
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Held JB, Rowles T, Schulz W, McNellis TW. Arabidopsis Wall-Associated Kinase 3 is required for harpin-activated immune responses. THE NEW PHYTOLOGIST 2024; 242:853-857. [PMID: 38379500 DOI: 10.1111/nph.19594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 01/25/2024] [Indexed: 02/22/2024]
Affiliation(s)
- Jeremy B Held
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, 16802, USA
- Intercollege Graduate Degree Program in Plant Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Taran Rowles
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - William Schulz
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Timothy W McNellis
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, 16802, USA
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5
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Laitinen RAE, Nikoloski Z. Strategies to identify and dissect trade-offs in plants. Mol Ecol 2024; 33:e16780. [PMID: 36380694 DOI: 10.1111/mec.16780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/13/2022] [Accepted: 10/31/2022] [Indexed: 11/17/2022]
Abstract
Trade-offs between traits arise and reflect constraints imposed by the environment and physicochemical laws. Trade-off situations are expected to be highly relevant for sessile plants, which have to respond to changes in the environment to ensure survival. Despite increasing interest in determining the genetic and molecular basis of plant trade-offs, there are still gaps and differences with respect to how trade-offs are defined, how they are measured, and how their genetic architecture is dissected. The first step to fill these gaps is to establish what is meant by trade-offs. In this review we provide a classification of the existing definitions of trade-offs according to: (1) the measures used for their quantification, (2) the dependence of trade-offs on environment, and (3) experimental designed used (i.e. a single individual across different environments or a population of individuals in single or multiple environments). We then compare the approaches for quantification of trade-offs based on phenotypic, between-individual, and genetic correlations, and stress the need for developing further quantification indices particularly for trade-offs between multiple traits. Lastly, we highlight the genetic mechanisms underpinning trade-offs and experimental designs that facilitate their discovery in plants, with focus on usage of natural variability. This review also offers a perspective for future research aimed at identification of plant trade-offs, dissection of their genetic architecture, and development of strategies to overcome trade-offs, with applications in crop breeding.
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Affiliation(s)
- Roosa A E Laitinen
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Zoran Nikoloski
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Systems Biology and Mathematical Modelling, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
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6
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Zhou H, McPeek MS. Overcoming the "feast or famine" effect: improved interaction testing in genome-wide association studies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.13.580168. [PMID: 38405994 PMCID: PMC10888770 DOI: 10.1101/2024.02.13.580168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
In genetic association analysis of complex traits, detection of interaction (either GxG or GxE) can help to elucidate the genetic architecture and biological mechanisms underlying the trait. Detection of interaction in a genome-wide association study (GWAS) can be methodologically challenging for various reasons, including a high burden of multiple comparisons when testing for epistasis between all possible pairs of a set of genomewide variants, as well as heteroscedasticity effects occurring in the presence of GxG or GxE interaction. In this paper, we address the problem of an even more striking phenomenon that we call the "feast or famine" effect that occurs when testing interaction in a genomewide context. As we verify, even in a simplified setting in which there is no interaction at all (and so no heteroscedasticity), in a GWAS to detect GxG or GxE interaction with a fixed genetic variant or environmental factor, the distribution of the genome-wide p-values under the null hypothesis is not the i.i.d. uniform one that is commonly assumed. Using standard methods, even if all SNPs are independent, some GWASs will have systematically underinflated p-values ("feast"), and others will have systematically overinflated p-values ("famine"), which can lead to false detection of interaction, reduced power, inconsistent results across studies, and failure to replicate true signal. This startling phenomenon is specific to detection of interaction in a GWAS, and it may partly explain why such detection has so far proved challenging and difficult to replicate. We show theoretically that the key cause of this phenomenon is which variables are conditioned on in the analysis, and this suggests an approach to correct the problem by changing the way the conditioning is done. Using this insight, we have developed the TINGA method to adjust the interaction test statistics to make their p-values closer to uniform under the null hypothesis. In simulations we show that TINGA both controls type 1 error and improves power. TINGA allows for covariates and population structure through use of a linear mixed model and accounts for heteroscedasticity. We apply TINGA to detection of epistasis in a study of flowering time in Arabidopsis thaliana.
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Affiliation(s)
- Huanlin Zhou
- Department of Statistics, The University of Chicago, Chicago, Illinois, U.S.A
| | - Mary Sara McPeek
- Department of Statistics, The University of Chicago, Chicago, Illinois, U.S.A
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, U.S.A
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7
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Chen J, Tan C, Zhu M, Zhang C, Wang Z, Ni X, Liu Y, Wei T, Wei X, Fang X, Xu Y, Huang X, Qiu J, Liu H. CropGS-Hub: a comprehensive database of genotype and phenotype resources for genomic prediction in major crops. Nucleic Acids Res 2024; 52:D1519-D1529. [PMID: 38000385 PMCID: PMC10767954 DOI: 10.1093/nar/gkad1062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/15/2023] [Accepted: 10/25/2023] [Indexed: 11/26/2023] Open
Abstract
The explosive amount of multi-omics data has brought a paradigm shift both in academic research and further application in life science. However, managing and reusing the growing resources of genomic and phenotype data points presents considerable challenges for the research community. There is an urgent need for an integrated database that combines genome-wide association studies (GWAS) with genomic selection (GS). Here, we present CropGS-Hub, a comprehensive database comprising genotype, phenotype, and GWAS signals, as well as a one-stop platform with built-in algorithms for genomic prediction and crossing design. This database encompasses a comprehensive collection of over 224 billion genotype data and 434 thousand phenotype data generated from >30 000 individuals in 14 representative populations belonging to 7 major crop species. Moreover, the platform implemented three complete functional genomic selection related modules including phenotype prediction, user model training and crossing design, as well as a fast SNP genotyper plugin-in called SNPGT specifically built for CropGS-Hub, aiming to assist crop scientists and breeders without necessitating coding skills. CropGS-Hub can be accessed at https://iagr.genomics.cn/CropGS/.
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Affiliation(s)
- Jiaxin Chen
- Shanghai Key Laboratory of Plant Molecular Sciences, Shanghai Collaborative Innovation Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Cong Tan
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
- BGI Research, Wuhan 430074, China
| | - Min Zhu
- Shanghai Key Laboratory of Plant Molecular Sciences, Shanghai Collaborative Innovation Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Chenyang Zhang
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
- BGI Bioverse, Shenzhen 518083, China
| | - Zhihan Wang
- Shanghai Key Laboratory of Plant Molecular Sciences, Shanghai Collaborative Innovation Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Xuemei Ni
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
- BGI Bioverse, Shenzhen 518083, China
| | - Yanlin Liu
- Shanghai Key Laboratory of Plant Molecular Sciences, Shanghai Collaborative Innovation Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Tong Wei
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
- BGI Research, Wuhan 430074, China
| | - XiaoFeng Wei
- China National GeneBank, BGI, Shenzhen 518120, China
| | - Xiaodong Fang
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
- BGI Research, Sanya 572025, China
| | - Yang Xu
- Agricultural College, Yangzhou University, Yangzhou 225009, China
| | - Xuehui Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, Shanghai Collaborative Innovation Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Jie Qiu
- Shanghai Key Laboratory of Plant Molecular Sciences, Shanghai Collaborative Innovation Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
- BGI Bioverse, Shenzhen 518083, China
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8
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Soudi S, Jahani M, Todesco M, Owens GL, Bercovich N, Rieseberg LH, Yeaman S. Repeatability of adaptation in sunflowers reveals that genomic regions harbouring inversions also drive adaptation in species lacking an inversion. eLife 2023; 12:RP88604. [PMID: 38095362 PMCID: PMC10721221 DOI: 10.7554/elife.88604] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023] Open
Abstract
Local adaptation commonly involves alleles of large effect, which experience fitness advantages when in positive linkage disequilibrium (LD). Because segregating inversions suppress recombination and facilitate the maintenance of LD between locally adapted loci, they are also commonly found to be associated with adaptive divergence. However, it is unclear what fraction of an adaptive response can be attributed to inversions and alleles of large effect, and whether the loci within an inversion could still drive adaptation in the absence of its recombination-suppressing effect. Here, we use genome-wide association studies to explore patterns of local adaptation in three species of sunflower: Helianthus annuus, Helianthus argophyllus, and Helianthus petiolaris, which each harbour a large number of species-specific inversions. We find evidence of significant genome-wide repeatability in signatures of association to phenotypes and environments, which are particularly enriched within regions of the genome harbouring an inversion in one species. This shows that while inversions may facilitate local adaptation, at least some of the loci can still harbour mutations that make substantial contributions without the benefit of recombination suppression in species lacking a segregating inversion. While a large number of genomic regions show evidence of repeated adaptation, most of the strongest signatures of association still tend to be species-specific, indicating substantial genotypic redundancy for local adaptation in these species.
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Affiliation(s)
- Shaghayegh Soudi
- Department of Biological Sciences, University of CalgaryCalgaryCanada
| | - Mojtaba Jahani
- Department of Biological Sciences, University of CalgaryCalgaryCanada
- Department of Botany, University of British ColumbiaVancouverCanada
| | - Marco Todesco
- Department of Botany, University of British ColumbiaVancouverCanada
- Michael Smith Laboratories, University of British ColumbiaVancouverCanada
- Irving K. Barber Faculty of Science, University of British Columbia OkanaganKelownaCanada
| | | | | | | | - Sam Yeaman
- Department of Biological Sciences, University of CalgaryCalgaryCanada
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9
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Chen J, Li L, Kim JH, Neuhäuser B, Wang M, Thelen M, Hilleary R, Chi Y, Wei L, Venkataramani K, Exposito-Alonso M, Liu C, Keck J, Barragan AC, Schwab R, Lutz U, Pei ZM, He SY, Ludewig U, Weigel D, Zhu W. Small proteins modulate ion-channel-like ACD6 to regulate immunity in Arabidopsis thaliana. Mol Cell 2023; 83:4386-4397.e9. [PMID: 37995686 DOI: 10.1016/j.molcel.2023.10.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 08/17/2023] [Accepted: 10/20/2023] [Indexed: 11/25/2023]
Abstract
The multi-pass transmembrane protein ACCELERATED CELL DEATH 6 (ACD6) is an immune regulator in Arabidopsis thaliana with an unclear biochemical mode of action. We have identified two loci, MODULATOR OF HYPERACTIVE ACD6 1 (MHA1) and its paralog MHA1-LIKE (MHA1L), that code for ∼7 kDa proteins, which differentially interact with specific ACD6 variants. MHA1L enhances the accumulation of an ACD6 complex, thereby increasing the activity of the ACD6 standard allele for regulating plant growth and defenses. The intracellular ankyrin repeats of ACD6 are structurally similar to those found in mammalian ion channels. Several lines of evidence link increased ACD6 activity to enhanced calcium influx, with MHA1L as a direct regulator of ACD6, indicating that peptide-regulated ion channels are not restricted to animals.
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Affiliation(s)
- Junbin Chen
- China Key Laboratory of Pest Monitoring and Green Management, MOA, State Key Laboratory of Maize Bio-breeding, and College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Lei Li
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, 72076 Tübingen, Germany
| | - Jong Hum Kim
- Department of Biology, Duke University, Durham, NC 27708, USA; Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA
| | - Benjamin Neuhäuser
- Nutritional Crop Physiology, University of Hohenheim, 70599 Stuttgart, Germany
| | - Mingyu Wang
- China Key Laboratory of Pest Monitoring and Green Management, MOA, State Key Laboratory of Maize Bio-breeding, and College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Michael Thelen
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, 72076 Tübingen, Germany
| | | | - Yuan Chi
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Luyang Wei
- China Key Laboratory of Pest Monitoring and Green Management, MOA, State Key Laboratory of Maize Bio-breeding, and College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Kavita Venkataramani
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, 72076 Tübingen, Germany
| | - Moises Exposito-Alonso
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, 72076 Tübingen, Germany
| | - Chang Liu
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, 72076 Tübingen, Germany; Institute of Biology, University of Hohenheim, 70599 Stuttgart, Germany
| | - Jakob Keck
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, 72076 Tübingen, Germany
| | - A Cristina Barragan
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, 72076 Tübingen, Germany
| | - Rebecca Schwab
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, 72076 Tübingen, Germany
| | - Ulrich Lutz
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, 72076 Tübingen, Germany
| | - Zhen-Ming Pei
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Sheng-Yang He
- Department of Biology, Duke University, Durham, NC 27708, USA; Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA
| | - Uwe Ludewig
- Nutritional Crop Physiology, University of Hohenheim, 70599 Stuttgart, Germany
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, 72076 Tübingen, Germany; Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany.
| | - Wangsheng Zhu
- China Key Laboratory of Pest Monitoring and Green Management, MOA, State Key Laboratory of Maize Bio-breeding, and College of Plant Protection, China Agricultural University, Beijing 100193, China; Department of Molecular Biology, Max Planck Institute for Biology Tübingen, 72076 Tübingen, Germany.
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10
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Ochoa JC, Mukhopadhyay S, Bieluszewski T, Jędryczka M, Malinowski R, Truman W. Natural variation in Arabidopsis responses to Plasmodiophora brassicae reveals an essential role for Resistance to Plasmodiophora brasssicae 1 (RPB1). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1421-1440. [PMID: 37646674 DOI: 10.1111/tpj.16438] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 08/09/2023] [Accepted: 08/16/2023] [Indexed: 09/01/2023]
Abstract
Despite the identification of clubroot resistance genes in various Brassica crops our understanding of the genetic basis of immunity to Plasmodiophora brassicae infection in the model plant Arabidopsis thaliana remains limited. To address this issue, we performed a screen of 142 natural accessions and identified 11 clubroot-resistant Arabidopsis lines. Genome-wide association analysis identified several genetic loci significantly linked with resistance. Three genes from two of these loci were targeted for deletion by CRISPR/Cas9 mutation in resistant accessions Est-1 and Uod-1. Deletion of Resistance to Plasmodiophora brassicae 1 (RPB1) rendered both lines susceptible to the P. brassicae pathotype P1+. Further analysis of rpb1 knock-out Est-1 and Uod-1 lines showed that the RPB1 protein is required for activation of downstream defence responses, such as the expression of phytoalexin biosynthesis gene CYP71A13. RPB1 has recently been shown to encode a cation channel localised in the endoplasmic reticulum. The clubroot susceptible Arabidopsis accession Col-0 lacks a functional RPB1 gene; when Col-0 is transformed with RPB1 expression driven by its native promoter it is capable of activating RPB1 transcription in response to infection, but this is not sufficient to confer resistance. Transient expression of RPB1 in Nicotiana tabacum induced programmed cell death in leaves. We conclude that RPB1 is a critical component of the defence response to P. brassicae infection in Arabidopsis, acting downstream of pathogen recognition but required for the elaboration of effective resistance.
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Affiliation(s)
- Juan Camilo Ochoa
- Institute of Plant Genetics, Polish Academy of Sciences, ul. Strzeszyńska 34, 60-479, Poznań, Poland
| | - Soham Mukhopadhyay
- Institute of Plant Genetics, Polish Academy of Sciences, ul. Strzeszyńska 34, 60-479, Poznań, Poland
| | - Tomasz Bieluszewski
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
| | - Małgorzata Jędryczka
- Institute of Plant Genetics, Polish Academy of Sciences, ul. Strzeszyńska 34, 60-479, Poznań, Poland
| | - Robert Malinowski
- Institute of Plant Genetics, Polish Academy of Sciences, ul. Strzeszyńska 34, 60-479, Poznań, Poland
| | - William Truman
- Institute of Plant Genetics, Polish Academy of Sciences, ul. Strzeszyńska 34, 60-479, Poznań, Poland
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11
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Chien PS, Chen PH, Lee CR, Chiou TJ. Transcriptome-wide association study coupled with eQTL analysis reveals the genetic connection between gene expression and flowering time in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:5653-5666. [PMID: 37419660 DOI: 10.1093/jxb/erad262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 07/06/2023] [Indexed: 07/09/2023]
Abstract
Genome-wide association study (GWAS) has improved our understanding of complex traits, but challenges exist in distinguishing causation versus association caused by linkage disequilibrium. Instead, transcriptome-wide association studies (TWAS) detect direct associations between expression levels and phenotypic variations, providing an opportunity to better prioritize candidate genes. To assess the feasibility of TWAS, we investigated the association between transcriptomes, genomes, and various traits in Arabidopsis, including flowering time. The associated genes formerly known to regulate growth allometry or metabolite production were first identified by TWAS. Next, for flowering time, six TWAS-newly identified genes were functionally validated. Analysis of the expression quantitative trait locus (eQTL) further revealed a trans-regulatory hotspot affecting the expression of several TWAS-identified genes. The hotspot covers the FRIGIDA (FRI) gene body, which possesses multiple haplotypes differentially affecting the expression of downstream genes, such as FLOWERING LOCUS C (FLC) and SUPPRESSOR OF OVEREXPRESSION OF CO 1 (SOC1). We also revealed multiple independent paths towards the loss of function of FRI in natural accessions. Altogether, this study demonstrates the potential of combining TWAS with eQTL analysis to identify important regulatory modules of FRI-FLC-SOC1 for quantitative traits in natural populations.
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Affiliation(s)
- Pei-Shan Chien
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Pin-Hua Chen
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Cheng-Ruei Lee
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
- Institute of Plant Biology, National Taiwan University, Taipei, Taiwan
| | - Tzyy-Jen Chiou
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
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12
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Rajaby R, Liu DX, Au CH, Cheung YT, Lau AYT, Yang QY, Sung WK. INSurVeyor: improving insertion calling from short read sequencing data. Nat Commun 2023; 14:3243. [PMID: 37277343 DOI: 10.1038/s41467-023-38870-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 05/18/2023] [Indexed: 06/07/2023] Open
Abstract
Insertions are one of the major types of structural variations and are defined as the addition of 50 nucleotides or more into a DNA sequence. Several methods exist to detect insertions from next-generation sequencing short read data, but they generally have low sensitivity. Our contribution is two-fold. First, we introduce INSurVeyor, a fast, sensitive and precise method that detects insertions from next-generation sequencing paired-end data. Using publicly available benchmark datasets (both human and non-human), we show that INSurVeyor is not only more sensitive than any individual caller we tested, but also more sensitive than all of them combined. Furthermore, for most types of insertions, INSurVeyor is almost as sensitive as long reads callers. Second, we provide state-of-the-art catalogues of insertions for 1047 Arabidopsis Thaliana genomes from the 1001 Genomes Project and 3202 human genomes from the 1000 Genomes Project, both generated with INSurVeyor. We show that they are more complete and precise than existing resources, and important insertions are missed by existing methods.
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Affiliation(s)
- Ramesh Rajaby
- Hong Kong Genome Institute, Hong Kong Science Park, Shatin, Hong Kong, China
- A*STAR Genome Institute of Singapore, 60 Biopolis Street, Singapore, 138672, Singapore
| | - Dong-Xu Liu
- National Key Laboratory of Crop Genetic Improvement, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chun Hang Au
- Hong Kong Genome Institute, Hong Kong Science Park, Shatin, Hong Kong, China
| | - Yuen-Ting Cheung
- Hong Kong Genome Institute, Hong Kong Science Park, Shatin, Hong Kong, China
| | - Amy Yuet Ting Lau
- Hong Kong Genome Institute, Hong Kong Science Park, Shatin, Hong Kong, China
| | - Qing-Yong Yang
- National Key Laboratory of Crop Genetic Improvement, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wing-Kin Sung
- Hong Kong Genome Institute, Hong Kong Science Park, Shatin, Hong Kong, China.
- A*STAR Genome Institute of Singapore, 60 Biopolis Street, Singapore, 138672, Singapore.
- National Key Laboratory of Crop Genetic Improvement, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China.
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China.
- Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong, China.
- Laboratory of Computational Genomics, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.
- School of Computing, National University of Singapore, 13 Computing Drive, Singapore, 117417, Singapore.
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13
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Estarague A, Violle C, Vile D, Hany A, Martino T, Moulin P, Vasseur F. Plant–herbivore interactions: Experimental demonstration of genetic variability in plant–plant signalling. Evol Appl 2023; 16:772-780. [PMID: 37124083 PMCID: PMC10130558 DOI: 10.1111/eva.13531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 01/12/2023] [Accepted: 01/15/2023] [Indexed: 03/31/2023] Open
Abstract
Plant-herbivore interactions mediated by plant-plant signalling have been documented in different species but its within-species variability has hardly been quantified. Here, we tested if herbivore foraging activity on plants was influenced by a prior contact with a damaged plant and if the effect of such plant-plant signalling was variable across 113 natural genotypes of Arabidopsis thaliana. We filmed the activity of the generalist herbivore Cornu aspersum during 1 h on two plants differing only in a prior contact with a damaged plant or not. We recorded each snails' first choice, and measured its first duration on a plant, the proportion of time spent on both plants and leaf consumption. Overall, plant-plant signalling modified the foraging activity of herbivores in A. thaliana. On average, snails spent more time and consumed more of plants that experienced a prior contact with a damaged plant. However, the effects of plant-plant signalling on snail behaviour was variable: depending on genotype identity, plant-plant signalling made undamaged plants more repellant or attractive to snails. Genome-wide associations revealed that genes related to stress coping ability and jasmonate pathway were associated to this variation. Together, our findings highlight the adaptive significance of plant-plant signalling for plant-herbivore interactions.
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Affiliation(s)
- Aurélien Estarague
- CEFE, Univ Montpellier, CNRS, EPHE, IRDMontpellierFrance
- LEPSE, Univ Montpellier, INRAE, Institut AgroMontpellierFrance
| | - Cyrille Violle
- CEFE, Univ Montpellier, CNRS, EPHE, IRDMontpellierFrance
| | - Denis Vile
- LEPSE, Univ Montpellier, INRAE, Institut AgroMontpellierFrance
| | - Anaïs Hany
- CEFE, Univ Montpellier, CNRS, EPHE, IRDMontpellierFrance
| | | | - Pierre Moulin
- CEFE, Univ Montpellier, CNRS, EPHE, IRDMontpellierFrance
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14
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Liang M, Cao S, Deng T, Du L, Li K, An B, Du Y, Xu L, Zhang L, Gao X, Li J, Guo P, Gao H. MAK: a machine learning framework improved genomic prediction via multi-target ensemble regressor chains and automatic selection of assistant traits. Brief Bioinform 2023; 24:7031157. [PMID: 36752363 DOI: 10.1093/bib/bbad043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 01/13/2023] [Accepted: 01/20/2023] [Indexed: 02/09/2023] Open
Abstract
Incorporating the genotypic and phenotypic of the correlated traits into the multi-trait model can significantly improve the prediction accuracy of the target trait in animal and plant breeding, as well as human genetics. However, in most cases, the phenotypic information of the correlated and target trait of the individual to be evaluated was null simultaneously, particularly for the newborn. Therefore, we propose a machine learning framework, MAK, to improve the prediction accuracy of the target trait by constructing the multi-target ensemble regression chains and selecting the assistant trait automatically, which predicted the genomic estimated breeding values of the target trait using genotypic information only. The prediction ability of MAK was significantly more robust than the genomic best linear unbiased prediction, BayesB, BayesRR and the multi trait Bayesian method in the four real animal and plant datasets, and the computational efficiency of MAK was roughly 100 times faster than BayesB and BayesRR.
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Affiliation(s)
- Mang Liang
- Chinese Academy of Agricultural Sciences Institute of Animal Science
| | - Sheng Cao
- Chinese Academy of Agricultural Sciences Institute of Animal Science
| | - Tianyu Deng
- Chinese Academy of Agricultural Sciences Institute of Animal Science
| | - Lili Du
- Chinese Academy of Agricultural Sciences Institute of Animal Science
| | - Keanning Li
- Chinese Academy of Agricultural Sciences Institute of Animal Science
| | - Bingxing An
- Chinese Academy of Agricultural Sciences Institute of Animal Science
| | - Yueying Du
- Chinese Academy of Agricultural Sciences Institute of Animal Science
| | - Lingyang Xu
- Chinese Academy of Agricultural Sciences Institute of Animal Science
| | - Lupei Zhang
- Chinese Academy of Agricultural Sciences Institute of Animal Science
| | - Xue Gao
- Chinese Academy of Agricultural Sciences Institute of Animal Science
| | - Junya Li
- Chinese Academy of Agricultural Sciences Institute of Animal Science
| | | | - Huijiang Gao
- Chinese Academy of Agricultural Sciences Institute of Animal Science
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15
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Sahoo DK, Hegde C, Bhattacharyya MK. Identification of multiple novel genetic mechanisms that regulate chilling tolerance in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2023; 13:1094462. [PMID: 36714785 PMCID: PMC9878698 DOI: 10.3389/fpls.2022.1094462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 12/28/2022] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Cold stress adversely affects the growth and development of plants and limits the geographical distribution of many plant species. Accumulation of spontaneous mutations shapes the adaptation of plant species to diverse climatic conditions. METHODS The genome-wide association study of the phenotypic variation gathered by a newly designed phenomic platform with the over six millions single nucleotide polymorphic (SNP) loci distributed across the genomes of 417 Arabidopsis natural variants collected from various geographical regions revealed 33 candidate cold responsive genes. RESULTS Investigation of at least two independent insertion mutants for 29 genes identified 16 chilling tolerance genes governing diverse genetic mechanisms. Five of these genes encode novel leucine-rich repeat domain-containing proteins including three nucleotide-binding site-leucine-rich repeat (NBS-LRR) proteins. Among the 16 identified chilling tolerance genes, ADS2 and ACD6 are the only two chilling tolerance genes identified earlier. DISCUSSION The 12.5% overlap between the genes identified in this genome-wide association study (GWAS) of natural variants with those discovered previously through forward and reverse genetic approaches suggests that chilling tolerance is a complex physiological process governed by a large number of genetic mechanisms.
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Affiliation(s)
- Dipak Kumar Sahoo
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | - Chinmay Hegde
- Department of Electrical and Computer Engineering, Iowa State University, Ames, IA, United States
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16
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John M, Grimm D, Korte A. Predicting Gene Regulatory Interactions Using Natural Genetic Variation. Methods Mol Biol 2023; 2698:301-322. [PMID: 37682482 DOI: 10.1007/978-1-0716-3354-0_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
Genome-wide association studies (GWAS) are a powerful tool to elucidate the genotype-phenotype map. Although GWAS are usually used to assess simple univariate associations between genetic markers and traits of interest, it is also possible to infer the underlying genetic architecture and to predict gene regulatory interactions. In this chapter, we describe the latest methods and tools to perform GWAS by calculating permutation-based significance thresholds. For this purpose, we first provide guidelines on univariate GWAS analyses that are extended in the second part of this chapter to more complex models that enable the inference of gene regulatory networks and how these networks vary.
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Affiliation(s)
- Maura John
- Technical University of Munich & Weihenstephan-Triesdorf University of Applied Sciences, Campus Straubing for Biotechnology and Sustainability, Bioinformatics, Straubing, Germany
| | - Dominik Grimm
- Technical University of Munich & Weihenstephan-Triesdorf University of Applied Sciences, Campus Straubing for Biotechnology and Sustainability, Bioinformatics, Straubing, Germany
| | - Arthur Korte
- Center for Computational and Theoretical Biology, University of Würzburg, Würzburg, Germany.
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17
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Bercovich N, Genze N, Todesco M, Owens GL, Légaré JS, Huang K, Rieseberg LH, Grimm DG. HeliantHOME, a public and centralized database of phenotypic sunflower data. Sci Data 2022; 9:735. [PMID: 36450875 PMCID: PMC9712528 DOI: 10.1038/s41597-022-01842-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 11/11/2022] [Indexed: 12/02/2022] Open
Abstract
Genomic studies often attempt to link natural genetic variation with important phenotypic variation. To succeed, robust and reliable phenotypic data, as well as curated genomic assemblies, are required. Wild sunflowers, originally from North America, are adapted to diverse and often extreme environments and have historically been a widely used model plant system for the study of population genomics, adaptation, and speciation. Moreover, cultivated sunflower, domesticated from a wild relative (Helianthus annuus) is a global oil crop, ranking fourth in production of vegetable oils worldwide. Public availability of data resources both for the plant research community and for the associated agricultural sector, are extremely valuable. We have created HeliantHOME ( http://www.helianthome.org ), a curated, public, and interactive database of phenotypes including developmental, structural and environmental ones, obtained from a large collection of both wild and cultivated sunflower individuals. Additionally, the database is enriched with external genomic data and results of genome-wide association studies. Finally, being a community open-source platform, HeliantHOME is expected to expand as new knowledge and resources become available.
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Affiliation(s)
- Natalia Bercovich
- grid.17091.3e0000 0001 2288 9830Department of Botany, University of British Columbia, Vancouver, British Columbia Canada ,grid.17091.3e0000 0001 2288 9830Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
| | - Nikita Genze
- grid.6936.a0000000123222966Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Bioinformatics, Straubing, Germany ,grid.4819.40000 0001 0704 7467Weihenstephan-Triesdorf University of Applied Sciences, Straubing, Germany
| | - Marco Todesco
- grid.17091.3e0000 0001 2288 9830Department of Botany, University of British Columbia, Vancouver, British Columbia Canada ,grid.17091.3e0000 0001 2288 9830Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
| | - Gregory L. Owens
- grid.17091.3e0000 0001 2288 9830Department of Botany, University of British Columbia, Vancouver, British Columbia Canada ,grid.17091.3e0000 0001 2288 9830Biodiversity Research Centre, University of British Columbia, Vancouver, Canada ,grid.143640.40000 0004 1936 9465Department of Biology, University of Victoria, Victoria, BC Canada
| | - Jean-Sébastien Légaré
- grid.17091.3e0000 0001 2288 9830Department of Botany, University of British Columbia, Vancouver, British Columbia Canada ,grid.17091.3e0000 0001 2288 9830Biodiversity Research Centre, University of British Columbia, Vancouver, Canada ,grid.17091.3e0000 0001 2288 9830Department of Computer Science, University of British Columbia, Vancouver, British Columbia Canada ,grid.17091.3e0000 0001 2288 9830Data Science Institute, University of British Columbia, Vancouver, British Columbia Canada
| | - Kaichi Huang
- grid.17091.3e0000 0001 2288 9830Department of Botany, University of British Columbia, Vancouver, British Columbia Canada ,grid.17091.3e0000 0001 2288 9830Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
| | - Loren H. Rieseberg
- grid.17091.3e0000 0001 2288 9830Department of Botany, University of British Columbia, Vancouver, British Columbia Canada ,grid.17091.3e0000 0001 2288 9830Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
| | - Dominik G. Grimm
- grid.6936.a0000000123222966Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Bioinformatics, Straubing, Germany ,grid.4819.40000 0001 0704 7467Weihenstephan-Triesdorf University of Applied Sciences, Straubing, Germany ,grid.6936.a0000000123222966Technical University of Munich, Department of Informatics, Garching, Germany
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18
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Wuest SE, Pires ND, Luo S, Vasseur F, Messier J, Grossniklaus U, Niklaus PA. Increasing plant group productivity through latent genetic variation for cooperation. PLoS Biol 2022; 20:e3001842. [PMID: 36445870 PMCID: PMC9707777 DOI: 10.1371/journal.pbio.3001842] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 09/20/2022] [Indexed: 12/02/2022] Open
Abstract
Historic yield advances in the major crops have, to a large extent, been achieved by selection for improved productivity of groups of plant individuals such as high-density stands. Research suggests that such improved group productivity depends on "cooperative" traits (e.g., erect leaves, short stems) that-while beneficial to the group-decrease individual fitness under competition. This poses a problem for some traditional breeding approaches, especially when selection occurs at the level of individuals, because "selfish" traits will be selected for and reduce yield in high-density monocultures. One approach, therefore, has been to select individuals based on ideotypes with traits expected to promote group productivity. However, this approach is limited to architectural and physiological traits whose effects on growth and competition are relatively easy to anticipate. Here, we developed a general and simple method for the discovery of alleles promoting cooperation in plant stands. Our method is based on the game-theoretical premise that alleles increasing cooperation benefit the monoculture group but are disadvantageous to the individual when facing noncooperative neighbors. Testing the approach using the model plant Arabidopsis thaliana, we found a major effect locus where the rarer allele was associated with increased cooperation and productivity in high-density stands. The allele likely affects a pleiotropic gene, since we find that it is also associated with reduced root competition but higher resistance against disease. Thus, even though cooperation is considered evolutionarily unstable except under special circumstances, conflicting selective forces acting on a pleiotropic gene might maintain latent genetic variation for cooperation in nature. Such variation, once identified in a crop, could rapidly be leveraged in modern breeding programs and provide efficient routes to increase yields.
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Affiliation(s)
- Samuel E. Wuest
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland,Department of Evolutionary Biology and Environmental Studies & Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland,Group Breeding Research, Division Plant Breeding, Agroscope, Wädenswil, Switzerland,* E-mail:
| | - Nuno D. Pires
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Shan Luo
- Lancaster Environment Centre, Lancaster University, Lancaster, United Kingdom
| | | | - Julie Messier
- Department of Biology, University of Waterloo, Waterloo, Canada
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Pascal A. Niklaus
- Department of Evolutionary Biology and Environmental Studies & Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
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19
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Katz E, Knapp A, Lensink M, Keller CK, Stefani J, Li JJ, Shane E, Tuermer-Lee K, Bloom AJ, Kliebenstein DJ. Genetic variation underlying differential ammonium and nitrate responses in Arabidopsis thaliana. THE PLANT CELL 2022; 34:4696-4713. [PMID: 36130068 PMCID: PMC9709984 DOI: 10.1093/plcell/koac279] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 09/05/2022] [Indexed: 06/15/2023]
Abstract
Nitrogen is an essential element required for plant growth and productivity. Understanding the mechanisms and natural genetic variation underlying nitrogen use in plants will facilitate the engineering of plant nitrogen use to maximize crop productivity while minimizing environmental costs. To understand the scope of natural variation that may influence nitrogen use, we grew 1,135 Arabidopsis thaliana natural genotypes on two nitrogen sources, nitrate and ammonium, and measured both developmental and defense metabolite traits. By using different environments and focusing on multiple traits, we identified a wide array of different nitrogen responses. These responses are associated with numerous genes, most of which were not previously associated with nitrogen responses. Only a small portion of these genes appear to be shared between environments or traits, while most are predominantly specific to a developmental or defense trait under a specific nitrogen source. Finally, by using a large population, we were able to identify unique nitrogen responses, such as preferring ammonium or nitrate, which appear to be generated by combinations of loci rather than a few large-effect loci. This suggests that it may be possible to obtain novel phenotypes in complex nitrogen responses by manipulating sets of genes with small effects rather than solely focusing on large-effect single gene manipulations.
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Affiliation(s)
- Ella Katz
- Department of Plant Sciences, University of California Davis, Davis, California 95616, USA
| | - Anna Knapp
- Department of Plant Sciences, University of California Davis, Davis, California 95616, USA
| | - Mariele Lensink
- Department of Plant Sciences, University of California Davis, Davis, California 95616, USA
- Integrative Genetics and Genomics Graduate Group, University of California Davis, Davis, California 95616, USA
| | - Caroline Kaley Keller
- Department of Plant Sciences, University of California Davis, Davis, California 95616, USA
- Plant Biology Graduate Group, University of California Davis, Davis, California 95616, USA
| | - Jordan Stefani
- Department of Plant Sciences, University of California Davis, Davis, California 95616, USA
| | - Jia-Jie Li
- Department of Plant Sciences, University of California Davis, Davis, California 95616, USA
| | - Emily Shane
- Department of Plant Sciences, University of California Davis, Davis, California 95616, USA
| | - Kaelyn Tuermer-Lee
- Department of Plant Sciences, University of California Davis, Davis, California 95616, USA
| | - Arnold J Bloom
- Department of Plant Sciences, University of California Davis, Davis, California 95616, USA
| | - Daniel J Kliebenstein
- Department of Plant Sciences, University of California Davis, Davis, California 95616, USA
- DynaMo Center of Excellence, University of Copenhagen, 1165 Copenhagen, Denmark
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20
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Temperature-mediated flower size plasticity in Arabidopsis. iScience 2022; 25:105411. [PMID: 36388994 PMCID: PMC9646949 DOI: 10.1016/j.isci.2022.105411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 08/10/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022] Open
Abstract
Organisms can rapidly mitigate the effects of environmental changes by changing their phenotypes, known as phenotypic plasticity. Yet, little is known about the temperature-mediated plasticity of traits that are directly linked to plant fitness such as flower size. We discovered substantial genetic variation in flower size plasticity to temperature both among selfing Arabidopsis thaliana and outcrossing A. arenosa individuals collected from a natural growth habitat. Genetic analysis using a panel of 290 A. thaliana accession and mutant lines revealed that MADS AFFECTING FLOWERING (MAF) 2-5 gene cluster, previously shown to regulate temperature-mediated flowering time, was associated to the flower size plasticity to temperature. Furthermore, our findings pointed that the control of plasticity differs from control of the trait itself. Altogether, our study advances the understanding of genetic and molecular factors underlying plasticity on fundamental fitness traits, such as flower size, in response to future climate scenarios.
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21
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John M, Ankenbrand MJ, Artmann C, Freudenthal JA, Korte A, Grimm DG. Efficient permutation-based genome-wide association studies for normal and skewed phenotypic distributions. Bioinformatics 2022; 38:ii5-ii12. [PMID: 36124808 PMCID: PMC9486594 DOI: 10.1093/bioinformatics/btac455] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
MOTIVATION Genome-wide association studies (GWAS) are an integral tool for studying the architecture of complex genotype and phenotype relationships. Linear mixed models (LMMs) are commonly used to detect associations between genetic markers and a trait of interest, while at the same time allowing to account for population structure and cryptic relatedness. Assumptions of LMMs include a normal distribution of the residuals and that the genetic markers are independent and identically distributed-both assumptions are often violated in real data. Permutation-based methods can help to overcome some of these limitations and provide more realistic thresholds for the discovery of true associations. Still, in practice, they are rarely implemented due to the high computational complexity. RESULTS We propose permGWAS, an efficient LMM reformulation based on 4D tensors that can provide permutation-based significance thresholds. We show that our method outperforms current state-of-the-art LMMs with respect to runtime and that permutation-based thresholds have lower false discovery rates for skewed phenotypes compared to the commonly used Bonferroni threshold. Furthermore, using permGWAS we re-analyzed more than 500 Arabidopsis thaliana phenotypes with 100 permutations each in less than 8 days on a single GPU. Our re-analyses suggest that applying a permutation-based threshold can improve and refine the interpretation of GWAS results. AVAILABILITY AND IMPLEMENTATION permGWAS is open-source and publicly available on GitHub for download: https://github.com/grimmlab/permGWAS. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Maura John
- To whom correspondence should be addressed. or
| | - Markus J Ankenbrand
- Center for Computational and Theoretical Biology, University of Würzburg, 97078 Würzburg, Germany
| | - Carolin Artmann
- Center for Computational and Theoretical Biology, University of Würzburg, 97078 Würzburg, Germany
| | - Jan A Freudenthal
- Center for Computational and Theoretical Biology, University of Würzburg, 97078 Würzburg, Germany
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22
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Liu S, Chen M, Li R, Li WX, Gal-On A, Jia Z, Ding SW. Identification of positive and negative regulators of antiviral RNA interference in Arabidopsis thaliana. Nat Commun 2022; 13:2994. [PMID: 35637208 PMCID: PMC9151786 DOI: 10.1038/s41467-022-30771-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 05/18/2022] [Indexed: 02/06/2023] Open
Abstract
Virus-host coevolution often drives virus immune escape. However, it remains unknown whether natural variations of plant virus resistance are enriched in genes of RNA interference (RNAi) pathway known to confer essential antiviral defense in plants. Here, we report two genome-wide association study screens to interrogate natural variation among wild-collected Arabidopsis thaliana accessions in quantitative resistance to the endemic cucumber mosaic virus (CMV). We demonstrate that the highest-ranked gene significantly associated with resistance from both screens acts to regulate antiviral RNAi in ecotype Columbia-0. One gene, corresponding to Reduced Dormancy 5 (RDO5), enhances resistance by promoting amplification of the virus-derived small interfering RNAs (vsiRNAs). Interestingly, the second gene, designated Antiviral RNAi Regulator 1 (VIR1), dampens antiviral RNAi so its genetic inactivation by CRISPR/Cas9 editing enhances both vsiRNA production and CMV resistance. Our findings identify positive and negative regulators of the antiviral RNAi defense that may play important roles in virus-host coevolution.
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Affiliation(s)
- Si Liu
- Department of Microbiology & Plant Pathology, University of California, Riverside, CA, USA
| | - Meijuan Chen
- Department of Microbiology & Plant Pathology, University of California, Riverside, CA, USA
| | - Ruidong Li
- Department of Botany & Plant Sciences, University of California, Riverside, CA, USA
| | - Wan-Xiang Li
- Department of Microbiology & Plant Pathology, University of California, Riverside, CA, USA
| | - Amit Gal-On
- Department of Plant Pathology and Weed Science, Volcani Center, Rishon LeZion, 7528809, Israel
| | - Zhenyu Jia
- Department of Botany & Plant Sciences, University of California, Riverside, CA, USA.
| | - Shou-Wei Ding
- Department of Microbiology & Plant Pathology, University of California, Riverside, CA, USA.
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23
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Zeng Q, Zhao B, Wang H, Wang M, Teng M, Hu J, Bao Z, Wang Y. Aquaculture Molecular Breeding Platform (AMBP): a comprehensive web server for genotype imputation and genetic analysis in aquaculture. Nucleic Acids Res 2022; 50:W66-W74. [PMID: 35639514 PMCID: PMC9252723 DOI: 10.1093/nar/gkac424] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/19/2022] [Accepted: 05/09/2022] [Indexed: 12/26/2022] Open
Abstract
It is of vital importance to understand the population structure, dissect the genetic bases of performance traits, and make proper strategies for selection in breeding programs. However, there is no single webserver covering the specific needs in aquaculture. We present Aquaculture Molecular Breeding Platform (AMBP), the first web server for genetic data analysis in aquatic species of farming interest. AMBP integrates the haplotype reference panels of 18 aquaculture species, which greatly improves the accuracy of genotype imputation. It also supports multiple tools to infer genetic structures, dissect the genetic architecture of performance traits, estimate breeding values, and predict optimum contribution. All the tools are coherently linked in a web-interface for users to generate interpretable results and evaluate statistical appropriateness. The webserver supports standard VCF and PLINK (PED, MAP) files, and implements automated pipelines for format transformation and visualization to simplify the process of analysis. As a demonstration, we applied the webserver to Pacific white shrimp and Atlantic salmon datasets. In summary, AMBP constitutes comprehensive resources and analytical tools for exploring genetic data and guiding practical breeding programs. AMBP is available at http://mgb.qnlm.ac.
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Affiliation(s)
- Qifan Zeng
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.,Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanog Inst, Ocean Univ China, Sanya 572000, Peoples R China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Baojun Zhao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Hao Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Mengqiu Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Mingxuan Teng
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Jingjie Hu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.,Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanog Inst, Ocean Univ China, Sanya 572000, Peoples R China
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.,Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanog Inst, Ocean Univ China, Sanya 572000, Peoples R China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Yangfan Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
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24
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Meng X, Li L, Pascual J, Rahikainen M, Yi C, Jost R, He C, Fournier-Level A, Borevitz J, Kangasjärvi S, Whelan J, Berkowitz O. GWAS on multiple traits identifies mitochondrial ACONITASE3 as important for acclimation to submergence stress. PLANT PHYSIOLOGY 2022; 188:2039-2058. [PMID: 35043967 PMCID: PMC8968326 DOI: 10.1093/plphys/kiac011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 12/03/2021] [Indexed: 05/26/2023]
Abstract
Flooding causes severe crop losses in many parts of the world. Genetic variation in flooding tolerance exists in many species; however, there are few examples for the identification of tolerance genes and their underlying function. We conducted a genome-wide association study (GWAS) in 387 Arabidopsis (Arabidopsis thaliana) accessions. Plants were subjected to prolonged submergence followed by desubmergence, and seven traits (score, water content, Fv/Fm, and concentrations of nitrate, chlorophyll, protein, and starch) were quantified to characterize their acclimation responses. These traits showed substantial variation across the range of accessions. A total of 35 highly significant single-nucleotide polymorphisms (SNPs) were identified across the 20 GWA datasets, pointing to 22 candidate genes, with functions in TCA cycle, DNA modification, and cell division. Detailed functional characterization of one candidate gene, ACONITASE3 (ACO3), was performed. Chromatin immunoprecipitation followed by sequencing showed that a single nucleotide polymorphism in the ACO3 promoter co-located with the binding site of the master regulator of retrograde signaling ANAC017, while subcellular localization of an ACO3-YFP fusion protein confirmed a mitochondrial localization during submergence. Analysis of mutant and overexpression lines determined changes in trait parameters that correlated with altered submergence tolerance and were consistent with the GWAS results. Subsequent RNA-seq experiments suggested that impairing ACO3 function increases the sensitivity to submergence by altering ethylene signaling, whereas ACO3 overexpression leads to tolerance by metabolic priming. These results indicate that ACO3 impacts submergence tolerance through integration of carbon and nitrogen metabolism via the mitochondrial TCA cycle and impacts stress signaling during acclimation to stress.
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Affiliation(s)
- Xiangxiang Meng
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Department of Animal, Plant and Soil Science, ARC Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Victoria 3086, Australia
| | | | | | - Moona Rahikainen
- Molecular Plant Biology, Department of Biochemistry, University of Turku, Turku, FI-20014, Finland
| | - Changyu Yi
- Department of Animal, Plant and Soil Science, ARC Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Ricarda Jost
- Department of Animal, Plant and Soil Science, ARC Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Cunman He
- Department of Animal, Plant and Soil Science, ARC Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Victoria 3086, Australia
| | | | - Justin Borevitz
- Research School of Biology and Centre for Biodiversity Analysis, ARC Centre of Excellence in Plant Energy Biology, Australian National University, Canberra, ACT 0200, Australia
| | - Saijaliisa Kangasjärvi
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, Helsinki University, FI-00014, Finland
- Department of Agricultural Sciences, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, FI-00014, Finland
- Viikki Plant Science Center, University of Helsinki, Helsinki, FI-00014, Finland
| | - James Whelan
- Department of Animal, Plant and Soil Science, ARC Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Victoria 3086, Australia
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25
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Todesco M, Bercovich N, Kim A, Imerovski I, Owens GL, Dorado Ruiz Ó, Holalu SV, Madilao LL, Jahani M, Légaré JS, Blackman BK, Rieseberg LH. Genetic basis and dual adaptive role of floral pigmentation in sunflowers. eLife 2022; 11:72072. [PMID: 35040432 PMCID: PMC8765750 DOI: 10.7554/elife.72072] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 11/28/2021] [Indexed: 12/25/2022] Open
Abstract
Variation in floral displays, both between and within species, has been long known to be shaped by the mutualistic interactions that plants establish with their pollinators. However, increasing evidence suggests that abiotic selection pressures influence floral diversity as well. Here, we analyse the genetic and environmental factors that underlie patterns of floral pigmentation in wild sunflowers. While sunflower inflorescences appear invariably yellow to the human eye, they display extreme diversity for patterns of ultraviolet pigmentation, which are visible to most pollinators. We show that this diversity is largely controlled by cis-regulatory variation affecting a single MYB transcription factor, HaMYB111, through accumulation of ultraviolet (UV)-absorbing flavonol glycosides in ligules (the ‘petals’ of sunflower inflorescences). Different patterns of ultraviolet pigments in flowers are strongly correlated with pollinator preferences. Furthermore, variation for floral ultraviolet patterns is associated with environmental variables, especially relative humidity, across populations of wild sunflowers. Ligules with larger ultraviolet patterns, which are found in drier environments, show increased resistance to desiccation, suggesting a role in reducing water loss. The dual role of floral UV patterns in pollinator attraction and abiotic response reveals the complex adaptive balance underlying the evolution of floral traits. Flowers are an important part of how many plants reproduce. Their distinctive colours, shapes and patterns attract specific pollinators, but they can also help to protect the plant from predators and environmental stresses. Many flowers contain pigments that absorb ultraviolet (UV) light to display distinct UV patterns – although invisible to the human eye, most pollinators are able to see them. For example, when seen in UV, sunflowers feature a ‘bullseye’ with a dark centre surrounded by a reflective outer ring. The sizes and thicknesses of these rings vary a lot within and between flower species, and so far, it has been unclear what causes this variation and how it affects the plants. To find out more, Todesco et al. studied the UV patterns in various wild sunflowers across North America by considering the ecology and molecular biology of different plants. This revealed great variation between the UV patterns of the different sunflower populations. Moreover, Todesco et al. found that a gene called HaMYB111 is responsible for the diverse UV patterns in the sunflowers. This gene controls how plants make chemicals called flavonols that absorb UV light. Flavonols also help to protect plants from damage caused by droughts and extreme temperatures. Todesco et al. showed that plants with larger bullseyes had more flavonols, attracted more pollinators, and were better at conserving water. Accordingly, these plants were found in drier locations. This study suggests that, at least in sunflowers, UV patterns help both to attract pollinators and to control water loss. These insights could help to improve pollination – and consequently yield – in cultivated plants, and to develop plants with better resistance to extreme weather. This work also highlights the importance of combining biology on small and large scales to understand complex processes, such as adaptation and evolution.
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Affiliation(s)
- Marco Todesco
- Department of Botany and Biodiversity Research Centre, University of British Columbia
| | - Natalia Bercovich
- Department of Botany and Biodiversity Research Centre, University of British Columbia
| | - Amy Kim
- Department of Botany and Biodiversity Research Centre, University of British Columbia
| | - Ivana Imerovski
- Department of Botany and Biodiversity Research Centre, University of British Columbia
| | - Gregory L Owens
- Department of Botany and Biodiversity Research Centre, University of British Columbia
- Department of Biology, University of Victoria
| | - Óscar Dorado Ruiz
- Department of Botany and Biodiversity Research Centre, University of British Columbia
| | | | - Lufiani L Madilao
- Michael Smith Laboratory and Wine Research Centre, University of British Columbia
| | - Mojtaba Jahani
- Department of Botany and Biodiversity Research Centre, University of British Columbia
| | - Jean-Sébastien Légaré
- Department of Botany and Biodiversity Research Centre, University of British Columbia
| | | | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia
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26
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Albert E, Sauvage C. Identification and Validation of Candidate Genes from Genome-Wide Association Studies. Methods Mol Biol 2022; 2481:249-272. [PMID: 35641769 DOI: 10.1007/978-1-0716-2237-7_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Exploiting the statistical associations coming out from a GWAS experiment to identify and validate candidate genes may be potentially difficult and time consuming. To fill the gap between the identification of candidate genes toward their functional validation onto the trait performance, the prioritization of variants underlying the GWAS-associated regions is necessary. In parallel, recent developments in genomics and statistical methods have been achieved notably in human genetic and they are accordingly being adopted in plant breeding toward the study of the genetic architecture of traits to sustain genetic gains. In this chapter, we aim at providing both theoretical and practical aspects underlying three main options including (1) the MetaGWAS analysis, (2) the statistical fine mapping and (3) the integration of functional data toward the identification and validation of candidate genes from a GWAS experiment.
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27
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Yi C, Wang X, Chen Q, Callahan DL, Fournier-Level A, Whelan J, Jost R. Diverse phosphate and auxin transport loci distinguish phosphate tolerant from sensitive Arabidopsis accessions. PLANT PHYSIOLOGY 2021; 187:2656-2673. [PMID: 34636851 PMCID: PMC8644285 DOI: 10.1093/plphys/kiab441] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 08/18/2021] [Indexed: 05/11/2023]
Abstract
Phosphorus (P) is an essential element for plant growth often limiting agroecosystems. To identify genetic determinants of performance under variable phosphate (Pi) supply, we conducted genome-wide association studies on five highly predictive Pi starvation response traits in 200 Arabidopsis (Arabidopsis thaliana) accessions. Pi concentration in Pi-limited organs had the strongest, and primary root length had the weakest genetic component. Of 70 trait-associated candidate genes, 17 responded to Pi withdrawal. The PHOSPHATE TRANSPORTER1 gene cluster on chromosome 5 comprises PHT1;1, PHT1;2, and PHT1;3 with known impact on P status. A second locus featured uncharacterized endomembrane-associated auxin efflux carrier encoding PIN-LIKES7 (PILS7) which was more strongly suppressed in Pi-limited roots of Pi-starvation sensitive accessions. In the Col-0 background, Pi uptake and organ growth were impaired in both Pi-limited pht1;1 and two pils7 T-DNA insertion mutants, while Pi -limited pht1;2 had higher biomass and pht1;3 was indistinguishable from wild-type. Copy number variation at the PHT1 locus with loss of the PHT1;3 gene and smaller scale deletions in PHT1;1 and PHT1;2 predicted to alter both protein structure and function suggest diversification of PHT1 is a key driver for adaptation to P limitation. Haplogroup analysis revealed a phosphorylation site in the protein encoded by the PILS7 allele from stress-sensitive accessions as well as additional auxin-responsive elements in the promoter of the "stress tolerant" allele. The former allele's inability to complement the pils7-1 mutant in the Col-0 background implies the presence of a kinase signaling loop controlling PILS7 activity in accessions from P-rich environments, while survival in P-poor environments requires fine-tuning of stress-responsive root auxin signaling.
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Affiliation(s)
- Changyu Yi
- Department of Animal, Plant and Soil Sciences and La Trobe Institute for Agriculture and Food (LIAF), ARC Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora VIC 3086, Australia
| | - Xinchao Wang
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, Tea Research Institute, Chinese Academy of Agricultural Sciences, Zhejiang 31008, China
| | - Qian Chen
- Department of Animal, Plant and Soil Sciences and La Trobe Institute for Agriculture and Food (LIAF), ARC Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora VIC 3086, Australia
| | - Damien L Callahan
- Centre for Chemistry and Biotechnology, School of Life and Environmental Sciences, Deakin University (Burwood Campus), Burwood VIC 3125, Australia
| | | | - James Whelan
- Department of Animal, Plant and Soil Sciences and La Trobe Institute for Agriculture and Food (LIAF), ARC Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora VIC 3086, Australia
| | - Ricarda Jost
- Department of Animal, Plant and Soil Sciences and La Trobe Institute for Agriculture and Food (LIAF), ARC Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora VIC 3086, Australia
- Author for communication:
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28
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Raimondi D, Corso M, Fariselli P, Moreau Y. From genotype to phenotype in Arabidopsis thaliana: in-silico genome interpretation predicts 288 phenotypes from sequencing data. Nucleic Acids Res 2021; 50:e16. [PMID: 34792168 PMCID: PMC8860592 DOI: 10.1093/nar/gkab1099] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 10/06/2021] [Accepted: 10/22/2021] [Indexed: 01/09/2023] Open
Abstract
In many cases, the unprecedented availability of data provided by high-throughput sequencing has shifted the bottleneck from a data availability issue to a data interpretation issue, thus delaying the promised breakthroughs in genetics and precision medicine, for what concerns Human genetics, and phenotype prediction to improve plant adaptation to climate change and resistance to bioagressors, for what concerns plant sciences. In this paper, we propose a novel Genome Interpretation paradigm, which aims at directly modeling the genotype-to-phenotype relationship, and we focus on A. thaliana since it is the best studied model organism in plant genetics. Our model, called Galiana, is the first end-to-end Neural Network (NN) approach following the genomes in/phenotypes out paradigm and it is trained to predict 288 real-valued Arabidopsis thaliana phenotypes from Whole Genome sequencing data. We show that 75 of these phenotypes are predicted with a Pearson correlation ≥0.4, and are mostly related to flowering traits. We show that our end-to-end NN approach achieves better performances and larger phenotype coverage than models predicting single phenotypes from the GWAS-derived known associated genes. Galiana is also fully interpretable, thanks to the Saliency Maps gradient-based approaches. We followed this interpretation approach to identify 36 novel genes that are likely to be associated with flowering traits, finding evidence for 6 of them in the existing literature.
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Affiliation(s)
| | - Massimiliano Corso
- Institut Jean-Pierre Bourgin, Université Paris-Saclay, INRAE, AgroParisTech, 78000 Versailles, France
| | - Piero Fariselli
- Department of Medical Sciences, University of Torino, 10123 Torino, Italy
| | - Yves Moreau
- ESAT-STADIUS, KU Leuven, 3001 Leuven, Belgium
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29
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Duarte GT, Pandey PK, Vaid N, Alseekh S, Fernie AR, Nikoloski Z, Laitinen RAE. Plasticity of rosette size in response to nitrogen availability is controlled by an RCC1-family protein. PLANT, CELL & ENVIRONMENT 2021; 44:3398-3411. [PMID: 34228823 DOI: 10.1111/pce.14146] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 07/01/2021] [Accepted: 07/02/2021] [Indexed: 05/12/2023]
Abstract
Nitrogen (N) is fundamental to plant growth, development and yield. Genes underlying N utilization and assimilation are well-characterized, but mechanisms underpinning plasticity of different phenotypes in response to N remain elusive. Here, using Arabidopsis thaliana accessions, we dissected the genetic architecture of plasticity in early and late rosette diameter, flowering time and yield, in response to three levels of N in the soil. Furthermore, we found that the plasticity in levels of primary metabolites were related with the plasticities of the studied traits. Genome-wide association analysis identified three significant associations for phenotypic plasticity, one for early rosette diameter and two for flowering time. We confirmed that the gene At1g19880, hereafter named as PLASTICITY OF ROSETTE TO NITROGEN 1 (PROTON1), encoding for a regulator of chromatin condensation 1 (RCC1) family protein, conferred plasticity of rosette diameter in response to N. Treatment of PROTON1 T-DNA line with salt implied that the reduced plasticity of early rosette diameter was not a general growth response to stress. We further showed that plasticities of growth and flowering-related traits differed between environmental cues, indicating decoupled genetic programs regulating these traits. Our findings provide a prospective to identify genes that stabilize performance under fluctuating environments.
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Affiliation(s)
- Gustavo Turqueto Duarte
- Molecular Mechanisms of Plant Adaptation - group, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Prashant K Pandey
- Molecular Mechanisms of Plant Adaptation - group, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
- National Research Council Canada (NRC-CNRC), Aquatic and Crop Resource Development (ACRD), Saskatoon, Saskatchewan, Canada
| | - Neha Vaid
- Molecular Mechanisms of Plant Adaptation - group, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
- Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Saleh Alseekh
- Central Metabolism - group, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
- Department of Plant Metabolomics, Center of Plant Systems Biology, Plovdiv, Bulgaria
| | - Alisdair R Fernie
- Central Metabolism - group, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
- Department of Plant Metabolomics, Center of Plant Systems Biology, Plovdiv, Bulgaria
| | - Zoran Nikoloski
- Systems Biology and Mathematical Modeling - group, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
- Department of Bioinformatics and Mathematical Modeling, Center of Plant Systems Biology, Plovdiv, Bulgaria
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Roosa A E Laitinen
- Molecular Mechanisms of Plant Adaptation - group, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
- Organismal and Evolutionary Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
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30
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Li D, Liu Q, Schnable PS. TWAS results are complementary to and less affected by linkage disequilibrium than GWAS. PLANT PHYSIOLOGY 2021; 186:1800-1811. [PMID: 33823025 PMCID: PMC8331151 DOI: 10.1093/plphys/kiab161] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 03/12/2021] [Indexed: 06/12/2023]
Abstract
A genome-wide association study (GWAS) is used to identify genetic markers associated with phenotypic variation. In contrast, a transcriptome-wide association study (TWAS) detects associations between gene expression levels and phenotypic variation. It has previously been shown that in the cross-pollinated species, maize (Zea mays), GWAS, and TWAS identify complementary sets of trait-associated genes, many of which exhibit characteristics of true positives. Here, we extend this conclusion to the self-pollinated species, Arabidopsis thaliana and soybean (Glycine max). Linkage disequilibrium (LD) can result in the identification, via GWAS, of false-positive associations. In all three analyzed plant species, most trait-associated genes identified via TWAS are well separated physically from other candidate genes. Hence, TWAS is less affected by LD than is GWAS, demonstrating that TWAS is particularly well suited for association studies in genomes with slow rates of LD decay, such as soybean. TWAS is reasonably robust to the plant organs/tissues used to determine expression levels. In summary, this study confirms that TWAS is a promising approach for accurate gene-level association mapping in plants that is complementary to GWAS, and established that TWAS can exhibit substantial advantages relative to GWAS in species with slow rates of LD decay.
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Affiliation(s)
- Delin Li
- Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
- Data Biotech (Beijing) Co. Ltd., Beijing, 100085, China
- National Key Facility for Gene Resources and Genetic Improvement, Key Lab of Crop Germplasm Utilization, Ministry of Agriculture, Institute of Crop Sciences, Chinese Academy of Agricultural Science, Beijing, 100081, China
| | - Qiang Liu
- Department of Agronomy, Iowa State University, Ames, Iowa 50011-3650, USA
| | - Patrick S Schnable
- Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
- Department of Agronomy, Iowa State University, Ames, Iowa 50011-3650, USA
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31
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Fernie AR, Alseekh S, Liu J, Yan J. Using precision phenotyping to inform de novo domestication. PLANT PHYSIOLOGY 2021; 186:1397-1411. [PMID: 33848336 PMCID: PMC8260140 DOI: 10.1093/plphys/kiab160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 03/22/2021] [Indexed: 05/09/2023]
Abstract
An update on the use of precision phenotyping to assess the potential of lesser cultivated species as candidates for de novo domestication or similar development for future agriculture.
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Affiliation(s)
- Alisdair R Fernie
- Max Planck Institute for Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
- Centre of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Saleh Alseekh
- Max Planck Institute for Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
- Centre of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Jie Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, Hubei, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, Hubei, China
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32
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Zhao L, Batta I, Matloff W, O'Driscoll C, Hobel S, Toga AW. Neuroimaging PheWAS (Phenome-Wide Association Study): A Free Cloud-Computing Platform for Big-Data, Brain-Wide Imaging Association Studies. Neuroinformatics 2021; 19:285-303. [PMID: 32822005 DOI: 10.1007/s12021-020-09486-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Large-scale, case-control genome-wide association studies (GWASs) have revealed genetic variations associated with diverse neurological and psychiatric disorders. Recent advances in neuroimaging and genomic databases of large healthy and diseased cohorts have empowered studies to characterize effects of the discovered genetic factors on brain structure and function, implicating neural pathways and genetic mechanisms in the underlying biology. However, the unprecedented scale and complexity of the imaging and genomic data requires new advanced biomedical data science tools to manage, process and analyze the data. In this work, we introduce Neuroimaging PheWAS (phenome-wide association study): a web-based system for searching over a wide variety of brain-wide imaging phenotypes to discover true system-level gene-brain relationships using a unified genotype-to-phenotype strategy. This design features a user-friendly graphical user interface (GUI) for anonymous data uploading, study definition and management, and interactive result visualizations as well as a cloud-based computational infrastructure and multiple state-of-art methods for statistical association analysis and multiple comparison correction. We demonstrated the potential of Neuroimaging PheWAS with a case study analyzing the influences of the apolipoprotein E (APOE) gene on various brain morphological properties across the brain in the Alzheimer's Disease Neuroimaging Initiative (ADNI) cohort. Benchmark tests were performed to evaluate the system's performance using data from UK Biobank. The Neuroimaging PheWAS system is freely available. It simplifies the execution of PheWAS on neuroimaging data and provides an opportunity for imaging genetics studies to elucidate routes at play for specific genetic variants on diseases in the context of detailed imaging phenotypic data.
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Affiliation(s)
- Lu Zhao
- Laboratory of Neuro Imaging, USC Mark and Mary Stevens Neuroimaging and Informatics Institute, University of Southern California, Los Angeles, CA, USA
| | - Ishaan Batta
- Laboratory of Neuro Imaging, USC Mark and Mary Stevens Neuroimaging and Informatics Institute, University of Southern California, Los Angeles, CA, USA
| | - William Matloff
- Laboratory of Neuro Imaging, USC Mark and Mary Stevens Neuroimaging and Informatics Institute, University of Southern California, Los Angeles, CA, USA
| | - Caroline O'Driscoll
- Laboratory of Neuro Imaging, USC Mark and Mary Stevens Neuroimaging and Informatics Institute, University of Southern California, Los Angeles, CA, USA
| | - Samuel Hobel
- Laboratory of Neuro Imaging, USC Mark and Mary Stevens Neuroimaging and Informatics Institute, University of Southern California, Los Angeles, CA, USA
| | - Arthur W Toga
- Laboratory of Neuro Imaging, USC Mark and Mary Stevens Neuroimaging and Informatics Institute, University of Southern California, Los Angeles, CA, USA.
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33
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Marsh JI, Hu H, Gill M, Batley J, Edwards D. Crop breeding for a changing climate: integrating phenomics and genomics with bioinformatics. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1677-1690. [PMID: 33852055 DOI: 10.1007/s00122-021-03820-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 03/18/2021] [Indexed: 05/05/2023]
Abstract
Safeguarding crop yields in a changing climate requires bioinformatics advances in harnessing data from vast phenomics and genomics datasets to translate research findings into climate smart crops in the field. Climate change and an additional 3 billion mouths to feed by 2050 raise serious concerns over global food security. Crop breeding and land management strategies will need to evolve to maximize the utilization of finite resources in coming years. High-throughput phenotyping and genomics technologies are providing researchers with the information required to guide and inform the breeding of climate smart crops adapted to the environment. Bioinformatics has a fundamental role to play in integrating and exploiting this fast accumulating wealth of data, through association studies to detect genomic targets underlying key adaptive climate-resilient traits. These data provide tools for breeders to tailor crops to their environment and can be introduced using advanced selection or genome editing methods. To effectively translate research into the field, genomic and phenomic information will need to be integrated into comprehensive clade-specific databases and platforms alongside accessible tools that can be used by breeders to inform the selection of climate adaptive traits. Here we discuss the role of bioinformatics in extracting, analysing, integrating and managing genomic and phenomic data to improve climate resilience in crops, including current, emerging and potential approaches, applications and bottlenecks in the research and breeding pipeline.
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Affiliation(s)
- Jacob I Marsh
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, 6009, Australia
| | - Haifei Hu
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, 6009, Australia
| | - Mitchell Gill
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, 6009, Australia
| | - Jacqueline Batley
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, 6009, Australia
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, 6009, Australia.
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Garreta L, Cerón‐Souza I, Palacio MR, Reyes‐Herrera PH. MultiGWAS: An integrative tool for Genome Wide Association Studies in tetraploid organisms. Ecol Evol 2021; 11:7411-7426. [PMID: 34188823 PMCID: PMC8216910 DOI: 10.1002/ece3.7572] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 03/22/2021] [Accepted: 03/23/2021] [Indexed: 12/27/2022] Open
Abstract
The genome-wide association studies (GWASs) are essential to determine the genetic bases of either ecological or economic phenotypic variation across individuals within populations of the model and nonmodel organisms. For this research question, the GWAS replication testing different parameters and models to validate the results' reproducibility is common. However, straightforward methodologies that manage both replication and tetraploid data are still missing. To solve this problem, we designed the MultiGWAS, a tool that does GWAS for diploid and tetraploid organisms by executing in parallel four software packages, two designed for polyploid data (GWASpoly and SHEsis) and two designed for diploid data (GAPIT and TASSEL). MultiGWAS has several advantages. It runs either in the command line or in a graphical interface; it manages different genotype formats, including VCF. Moreover, it allows control for population structure, relatedness, and several quality control checks on genotype data. Besides, MultiGWAS can test for additive and dominant gene action models, and, through a proprietary scoring function, select the best model to report its associations. Finally, it generates several reports that facilitate identifying false associations from both the significant and the best-ranked association Single Nucleotide Polymorphisms (SNPs) among the four software packages. We tested MultiGWAS with public tetraploid potato data for tuber shape and several simulated data under both additive and dominant models. These tests demonstrated that MultiGWAS is better at detecting reliable associations than using each of the four software packages individually. Moreover, the parallel analysis of polyploid and diploid software that only offers MultiGWAS demonstrates its utility in understanding the best genetic model behind the SNP association in tetraploid organisms. Therefore, MultiGWAS probed to be an excellent alternative for wrapping GWAS replication in diploid and tetraploid organisms in a single analysis environment.
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Affiliation(s)
- Luis Garreta
- Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA)CI TibaitatáBogotaColombia
| | - Ivania Cerón‐Souza
- Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA)CI TibaitatáBogotaColombia
| | | | - Paula H. Reyes‐Herrera
- Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA)CI TibaitatáBogotaColombia
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Dent CI, Singh S, Mukherjee S, Mishra S, Sarwade RD, Shamaya N, Loo KP, Harrison P, Sureshkumar S, Powell D, Balasubramanian S. Quantifying splice-site usage: a simple yet powerful approach to analyze splicing. NAR Genom Bioinform 2021; 3:lqab041. [PMID: 34017946 PMCID: PMC8121094 DOI: 10.1093/nargab/lqab041] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/24/2021] [Accepted: 04/28/2021] [Indexed: 02/07/2023] Open
Abstract
RNA splicing, and variations in this process referred to as alternative splicing, are critical aspects of gene regulation in eukaryotes. From environmental responses in plants to being a primary link between genetic variation and disease in humans, splicing differences confer extensive phenotypic changes across diverse organisms (1–3). Regulation of splicing occurs through differential selection of splice sites in a splicing reaction, which results in variation in the abundance of isoforms and/or splicing events. However, genomic determinants that influence splice-site selection remain largely unknown. While traditional approaches for analyzing splicing rely on quantifying variant transcripts (i.e. isoforms) or splicing events (i.e. intron retention, exon skipping etc.) (4), recent approaches focus on analyzing complex/mutually exclusive splicing patterns (5–8). However, none of these approaches explicitly measure individual splice-site usage, which can provide valuable information about splice-site choice and its regulation. Here, we present a simple approach to quantify the empirical usage of individual splice sites reflecting their strength, which determines their selection in a splicing reaction. Splice-site strength/usage, as a quantitative phenotype, allows us to directly link genetic variation with usage of individual splice-sites. We demonstrate the power of this approach in defining the genomic determinants of splice-site choice through GWAS. Our pilot analysis with more than a thousand splice sites hints that sequence divergence in cis rather than trans is associated with variations in splicing among accessions of Arabidopsis thaliana. This approach allows deciphering principles of splicing and has broad implications from agriculture to medicine.
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Affiliation(s)
- Craig I Dent
- School of Biological Sciences, Monash University, VIC 3800, Australia
| | - Shilpi Singh
- School of Biological Sciences, Monash University, VIC 3800, Australia
| | | | - Shikhar Mishra
- School of Biological Sciences, Monash University, VIC 3800, Australia
| | - Rucha D Sarwade
- School of Biological Sciences, Monash University, VIC 3800, Australia
| | - Nawar Shamaya
- School of Biological Sciences, Monash University, VIC 3800, Australia
| | - Kok Ping Loo
- School of Biological Sciences, Monash University, VIC 3800, Australia
| | - Paul Harrison
- Monash Bioinformatics Platform, Monash University, VIC 3800, Australia
| | | | - David Powell
- Monash Bioinformatics Platform, Monash University, VIC 3800, Australia
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Katz E, Li JJ, Jaegle B, Ashkenazy H, Abrahams SR, Bagaza C, Holden S, Pires CJ, Angelovici R, Kliebenstein DJ. Genetic variation, environment and demography intersect to shape Arabidopsis defense metabolite variation across Europe. eLife 2021; 10:67784. [PMID: 33949309 PMCID: PMC8205490 DOI: 10.7554/elife.67784] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 05/02/2021] [Indexed: 12/03/2022] Open
Abstract
Plants produce diverse metabolites to cope with the challenges presented by complex and ever-changing environments. These challenges drive the diversification of specialized metabolites within and between plant species. However, we are just beginning to understand how frequently new alleles arise controlling specialized metabolite diversity and how the geographic distribution of these alleles may be structured by ecological and demographic pressures. Here, we measure the variation in specialized metabolites across a population of 797 natural Arabidopsis thaliana accessions. We show that a combination of geography, environmental parameters, demography and different genetic processes all combine to influence the specific chemotypes and their distribution. This showed that causal loci in specialized metabolism contain frequent independently generated alleles with patterns suggesting potential within-species convergence. This provides a new perspective about the complexity of the selective forces and mechanisms that shape the generation and distribution of allelic variation that may influence local adaptation. Since plants cannot move, they have evolved chemical defenses to help them respond to changes in their surroundings. For example, where animals run from predators, plants may produce toxins to put predators off. This approach is why plants are such a rich source of drugs, poisons, dyes and other useful substances. The chemicals plants produce are known as specialized metabolites, and they can change a lot between, and even within, plant species. The variety of specialized metabolites is a result of genetic changes and evolution over millions of years. Evolution is a slow process, yet plants are able to rapidly develop new specialized metabolites to protect them from new threats. Even different populations of the same species produce many distinct metabolites that help them survive in their surroundings. However, the factors that lead plants to produce new metabolites are not well understood, and it is not known how this affects genetic variation. To gain a better understanding of this process, Katz et al. studied 797 European variants of a common weed species called Arabidopsis thaliana, which is widely studied. The investigation found that many factors affect the range of specialized metabolites in each variant. These included local geography and environment, as well as genetics and population history (demography). Katz et al. revealed a pattern of relationships between the variants that could mirror their evolutionary history as the species spread and adapted to new locations. These results highlight the complex network of factors that affect plant evolution. Rapid diversification is key to plant survival in new and changing environments and has resulted in a wide range of specialized metabolites. As such they are of interest both for studying plant evolution and for understanding their ecology. Expanding similar work to more populations and other species will broaden the scope of our ability to understand how plants adapt to their surroundings.
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Affiliation(s)
- Ella Katz
- Department of Plant Sciences, University of California, Davis, Davis, United States
| | - Jia-Jie Li
- Department of Plant Sciences, University of California, Davis, Davis, United States
| | - Benjamin Jaegle
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Haim Ashkenazy
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Shawn R Abrahams
- Division of Biological Sciences, Bond Life Sciences Center, University of Missouri, Columbia, United States
| | - Clement Bagaza
- Division of Biological Sciences, Interdisciplinary Plant Group, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, United States
| | - Samuel Holden
- Division of Biological Sciences, Interdisciplinary Plant Group, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, United States
| | - Chris J Pires
- Division of Biological Sciences, Bond Life Sciences Center, University of Missouri, Columbia, United States
| | - Ruthie Angelovici
- Division of Biological Sciences, Interdisciplinary Plant Group, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, United States
| | - Daniel J Kliebenstein
- Department of Plant Sciences, University of California, Davis, Davis, United States.,DynaMo Center of Excellence, University of Copenhagen, Frederiksberg, Denmark
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Yan W, Wang B, Chan E, Mitchell-Olds T. Genetic architecture and adaptation of flowering time among environments. THE NEW PHYTOLOGIST 2021; 230:1214-1227. [PMID: 33484593 PMCID: PMC8193995 DOI: 10.1111/nph.17229] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 01/07/2021] [Indexed: 05/17/2023]
Abstract
The genetic basis of flowering time changes across environments, and pleiotropy may limit adaptive evolution of populations in response to local conditions. However, little information is known about how genetic architecture changes among environments. We used genome-wide association studies (GWAS) in Boechera stricta (Graham) Al-Shehbaz, a relative of Arabidopsis, to examine flowering variation among environments and associations with climate conditions in home environments. Also, we used molecular population genetics to search for evidence of historical natural selection. GWAS found 47 significant quantitative trait loci (QTLs) that influence flowering time in one or more environments, control plastic changes in phenology between experiments, or show associations with climate in sites of origin. Genetic architecture of flowering varied substantially among environments. We found that some pairs of QTLs showed similar patterns of pleiotropy across environments. A large-effect QTL showed molecular signatures of adaptive evolution and is associated with climate in home environments. The derived allele at this locus causes later flowering and predominates in sites with greater water availability. This work shows that GWAS of climate associations and ecologically important traits across diverse environments can be combined with molecular signatures of natural selection to elucidate ecological genetics of adaptive evolution.
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Affiliation(s)
- Wenjie Yan
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA
| | - Baosheng Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650 China
| | - Emily Chan
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA
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Gumpinger AC, Rieck B, Grimm DG, Borgwardt K. Network-guided search for genetic heterogeneity between gene pairs. Bioinformatics 2021; 37:57-65. [PMID: 32573681 PMCID: PMC8034561 DOI: 10.1093/bioinformatics/btaa581] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 05/19/2020] [Accepted: 06/15/2020] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Correlating genetic loci with a disease phenotype is a common approach to improve our understanding of the genetics underlying complex diseases. Standard analyses mostly ignore two aspects, namely genetic heterogeneity and interactions between loci. Genetic heterogeneity, the phenomenon that genetic variants at different loci lead to the same phenotype, promises to increase statistical power by aggregating low-signal variants. Incorporating interactions between loci results in a computational and statistical bottleneck due to the vast amount of candidate interactions. RESULTS We propose a novel method SiNIMin that addresses these two aspects by finding pairs of interacting genes that are, upon combination, associated with a phenotype of interest under a model of genetic heterogeneity. We guide the interaction search using biological prior knowledge in the form of protein-protein interaction networks. Our method controls type I error and outperforms state-of-the-art methods with respect to statistical power. Additionally, we find novel associations for multiple Arabidopsis thaliana phenotypes, and, with an adapted variant of SiNIMin, for a study of rare variants in migraine patients. AVAILABILITY AND IMPLEMENTATION Code available at https://github.com/BorgwardtLab/SiNIMin. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Anja C Gumpinger
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4058, Switzerland.,SIB Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Bastian Rieck
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4058, Switzerland.,SIB Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Dominik G Grimm
- Technical University of Munich, TUM Campus Straubing for Biotechnology and Sustainability, Bioinformatics, Straubing 94315, Germany.,Weihenstephan-Triesdorf University of Applied Sciences, Bioinformatics, Straubing 94315, Germany
| | | | - Karsten Borgwardt
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4058, Switzerland.,SIB Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
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39
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McKinney RM, Valdez R, Ben-Shahar Y. The genetic architecture of larval aggregation behavior in Drosophila. J Neurogenet 2021; 35:274-284. [PMID: 33629904 DOI: 10.1080/01677063.2021.1887174] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Many insect species exhibit basal social behaviors such as aggregation, which play important roles in their feeding and mating ecologies. However, the evolutionary, genetic, and physiological mechanisms that regulate insect aggregation remain unknown for most species. Here, we used natural populations of Drosophila melanogaster to identify the genetic architecture that drives larval aggregation feeding behavior. By using quantitative and reverse genetic approaches, we have identified a complex neurogenetic network that plays a role in regulating the decision of larvae to feed in either solitude or as a group. Results from single gene, RNAi-knockdown experiments show that several of the identified genes represent key nodes in the genetic network that determines the level of aggregation while feeding. Furthermore, we show that a single non-coding variant in the gene CG14205, a putative acyltransferase, is associated with both decreased mRNA expression and increased aggregate formation, which suggests that it has a specific role in inhibiting aggregation behavior. Our results identify, for the first time, the genetic components which interact to regulate naturally occurring levels of aggregation in D. melanogaster larvae.
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Affiliation(s)
- Ross M McKinney
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
| | - Ryan Valdez
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
| | - Yehuda Ben-Shahar
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
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40
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Slaten ML, Chan YO, Shrestha V, Lipka AE, Angelovici R. HAPPI GWAS: Holistic Analysis with Pre- and Post-Integration GWAS. Bioinformatics 2021; 36:4655-4657. [PMID: 32579187 DOI: 10.1093/bioinformatics/btaa589] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 05/29/2020] [Accepted: 06/16/2020] [Indexed: 12/20/2022] Open
Abstract
MOTIVATION Advanced publicly available sequencing data from large populations have enabled informative genome-wide association studies (GWAS) that associate SNPs with phenotypic traits of interest. Many publicly available tools able to perform GWAS have been developed in response to increased demand. However, these tools lack a comprehensive pipeline that includes both pre-GWAS analysis, such as outlier removal, data transformation and calculation of Best Linear Unbiased Predictions or Best Linear Unbiased Estimates. In addition, post-GWAS analysis, such as haploblock analysis and candidate gene identification, is lacking. RESULTS Here, we present Holistic Analysis with Pre- and Post-Integration (HAPPI) GWAS, an open-source GWAS tool able to perform pre-GWAS, GWAS and post-GWAS analysis in an automated pipeline using the command-line interface. AVAILABILITY AND IMPLEMENTATION HAPPI GWAS is written in R for any Unix-like operating systems and is available on GitHub (https://github.com/Angelovici-Lab/HAPPI.GWAS.git). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Marianne L Slaten
- Division of Biological Sciences, MU Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
| | - Yen On Chan
- Division of Biological Sciences, MU Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
| | - Vivek Shrestha
- Division of Biological Sciences, MU Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
| | - Alexander E Lipka
- Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA
| | - Ruthie Angelovici
- Division of Biological Sciences, MU Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
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41
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Barragan AC, Collenberg M, Wang J, Lee RRQ, Cher WY, Rabanal FA, Ashkenazy H, Weigel D, Chae E. A Truncated Singleton NLR Causes Hybrid Necrosis in Arabidopsis thaliana. Mol Biol Evol 2021; 38:557-574. [PMID: 32966577 PMCID: PMC7826191 DOI: 10.1093/molbev/msaa245] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Hybrid necrosis in plants arises from conflict between divergent alleles of immunity genes contributed by different parents, resulting in autoimmunity. We investigate a severe hybrid necrosis case in Arabidopsis thaliana, where the hybrid does not develop past the cotyledon stage and dies 3 weeks after sowing. Massive transcriptional changes take place in the hybrid, including the upregulation of most NLR (nucleotide-binding site leucine-rich repeat) disease-resistance genes. This is due to an incompatible interaction between the singleton TIR-NLR gene DANGEROUS MIX 10 (DM10), which was recently relocated from a larger NLR cluster, and an unlinked locus, DANGEROUS MIX 11 (DM11). There are multiple DM10 allelic variants in the global A. thaliana population, several of which have premature stop codons. One of these, which has a truncated LRR-PL (leucine-rich repeat [LRR]-post-LRR) region, corresponds to the DM10 risk allele. The DM10 locus and the adjacent genomic region in the risk allele carriers are highly differentiated from those in the nonrisk carriers in the global A. thaliana population, suggesting that this allele became geographically widespread only relatively recently. The DM11 risk allele is much rarer and found only in two accessions from southwestern Spain-a region from which the DM10 risk haplotype is absent-indicating that the ranges of DM10 and DM11 risk alleles may be nonoverlapping.
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Affiliation(s)
- Ana Cristina Barragan
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Maximilian Collenberg
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Jinge Wang
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Rachelle R Q Lee
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Wei Yuan Cher
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Fernando A Rabanal
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Haim Ashkenazy
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Eunyoung Chae
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
- Department of Biological Sciences, National University of Singapore, Singapore
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42
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Genome-Wide Association Study of Natural Variation in Arabidopsis Exposed to Acid Mine Drainage Toxicity and Validation of Associated Genes with Reverse Genetics. PLANTS 2021; 10:plants10020191. [PMID: 33498421 PMCID: PMC7909446 DOI: 10.3390/plants10020191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 11/16/2022]
Abstract
Acid mine drainage (AMD) is a huge environmental problem in mountain-top mining regions worldwide, including the Appalachian Mountains in the United States. This study applied a genome-wide association study (GWAS) to uncover genomic loci in Arabidopsis associated with tolerance to AMD toxicity. We characterized five major root phenotypes—cumulative root length, average root diameter, root surface area, root volume, and primary root length—in 180 Arabidopsis accessions in response to AMD-supplemented growth medium. GWAS of natural variation in the panel revealed genes associated with tolerance to an acidic environment. Most of these genes were transcription factors, anion/cation transporters, metal transporters, and unknown proteins. Two T-DNA insertion mutants, At1g63005 (miR399b) and At2g05635 (DEAD helicase RAD3), showed enhanced acidity tolerance. Our GWAS and the reverse genetic approach revealed genes involved in conferring tolerance to coal AMD. Our results indicated that proton resistance in hydroponic conditions could be an important index to improve plant growth in acidic soil, at least in acid-sensitive plant species.
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43
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Lardon R, Wijnker E, Keurentjes J, Geelen D. The genetic framework of shoot regeneration in Arabidopsis comprises master regulators and conditional fine-tuning factors. Commun Biol 2020; 3:549. [PMID: 33009513 PMCID: PMC7532540 DOI: 10.1038/s42003-020-01274-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 09/04/2020] [Indexed: 12/21/2022] Open
Abstract
Clonal propagation and genetic engineering of plants requires regeneration, but many species are recalcitrant and there is large variability in explant responses. Here, we perform a genome-wide association study using 190 natural Arabidopsis accessions to dissect the genetics of shoot regeneration from root explants and several related in vitro traits. Strong variation is found in the recorded phenotypes and association mapping pinpoints a myriad of quantitative trait genes, including prior candidates and potential novel regeneration determinants. As most of these genes are trait- and protocol-specific, we propose a model wherein shoot regeneration is governed by many conditional fine-tuning factors and a few universal master regulators such as WUSCHEL, whose transcript levels correlate with natural variation in regenerated shoot numbers. Potentially novel genes in this last category are AT3G09925, SUP, EDA40 and DOF4.4. We urge future research in the field to consider multiple conditions and genetic backgrounds.
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Affiliation(s)
- Robin Lardon
- Department of Plants and Crops, Horticell Lab, Ghent University, 9000, Ghent, Belgium
| | - Erik Wijnker
- Department of Plant Sciences, Laboratory of Genetics, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
| | - Joost Keurentjes
- Department of Plant Sciences, Laboratory of Genetics, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
| | - Danny Geelen
- Department of Plants and Crops, Horticell Lab, Ghent University, 9000, Ghent, Belgium.
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44
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Renard J, Niñoles R, Martínez-Almonacid I, Gayubas B, Mateos-Fernández R, Bissoli G, Bueso E, Serrano R, Gadea J. Identification of novel seed longevity genes related to oxidative stress and seed coat by genome-wide association studies and reverse genetics. PLANT, CELL & ENVIRONMENT 2020; 43:2523-2539. [PMID: 32519347 DOI: 10.1111/pce.13822] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 06/01/2020] [Accepted: 06/06/2020] [Indexed: 05/26/2023]
Abstract
Seed longevity is a polygenic trait of relevance for agriculture and for understanding the effect of environment on the ageing of biological systems. In order to identify novel longevity genes, we have phenotyped the natural variation of 270 ecotypes of the model plant, Arabidopsis thaliana, for natural ageing and for three accelerated ageing methods. Genome-wide analysis, using publicly available single-nucleotide polymorphisms (SNPs) data sets, identified multiple genomic regions associated with variation in seed longevity. Reverse genetics of 20 candidate genes in Columbia ecotype resulted in seven genes positive for seed longevity (PSAD1, SSLEA, SSTPR, DHAR1, CYP86A8, MYB47 and SPCH) and five negative ones (RBOHD, RBOHE, RBOHF, KNAT7 and SEP3). In this uniform genetic background, natural and accelerated ageing methods provided similar results for seed-longevity in knock-out mutants. The NADPH oxidases (RBOHs), the dehydroascorbate reductase (DHAR1) and the photosystem I subunit (PSAD1) highlight the important role of oxidative stress on seed ageing. The cytochrome P-450 hydroxylase, CYP86A8, and the transcription factors, MYB47, KNAT7 and SEP3, support the protecting role of the seed coat during seed ageing.
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Affiliation(s)
- Joan Renard
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universitat Politècnica de València-C.S.I.C., Valencia, Spain
| | - Regina Niñoles
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universitat Politècnica de València-C.S.I.C., Valencia, Spain
| | - Irene Martínez-Almonacid
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universitat Politècnica de València-C.S.I.C., Valencia, Spain
| | - Beatriz Gayubas
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universitat Politècnica de València-C.S.I.C., Valencia, Spain
| | - Rubén Mateos-Fernández
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universitat Politècnica de València-C.S.I.C., Valencia, Spain
| | - Gaetano Bissoli
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universitat Politècnica de València-C.S.I.C., Valencia, Spain
| | - Eduardo Bueso
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universitat Politècnica de València-C.S.I.C., Valencia, Spain
| | - Ramón Serrano
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universitat Politècnica de València-C.S.I.C., Valencia, Spain
| | - José Gadea
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universitat Politècnica de València-C.S.I.C., Valencia, Spain
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45
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Massive haplotypes underlie ecotypic differentiation in sunflowers. Nature 2020; 584:602-607. [PMID: 32641831 DOI: 10.1038/s41586-020-2467-6] [Citation(s) in RCA: 186] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 04/16/2020] [Indexed: 12/22/2022]
Abstract
Species often include multiple ecotypes that are adapted to different environments1. However, it is unclear how ecotypes arise and how their distinctive combinations of adaptive alleles are maintained despite hybridization with non-adapted populations2-4. Here, by resequencing 1,506 wild sunflowers from 3 species (Helianthus annuus, Helianthus petiolaris and Helianthus argophyllus), we identify 37 large (1-100 Mbp in size), non-recombining haplotype blocks that are associated with numerous ecologically relevant traits, as well as soil and climate characteristics. Limited recombination in these haplotype blocks keeps adaptive alleles together, and these regions differentiate sunflower ecotypes. For example, haplotype blocks control a 77-day difference in flowering between ecotypes of the silverleaf sunflower H. argophyllus (probably through deletion of a homologue of FLOWERING LOCUS T (FT)), and are associated with seed size, flowering time and soil fertility in dune-adapted sunflowers. These haplotypes are highly divergent, frequently associated with structural variants and often appear to represent introgressions from other-possibly now-extinct-congeners. These results highlight a pervasive role of structural variation in ecotypic adaptation.
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46
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Model-based integration of genomics and metabolomics reveals SNP functionality in Mycobacterium tuberculosis. Proc Natl Acad Sci U S A 2020; 117:8494-8502. [PMID: 32229570 DOI: 10.1073/pnas.1915551117] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Human tuberculosis is caused by members of the Mycobacterium tuberculosis complex (MTBC) that vary in virulence and transmissibility. While genome-wide association studies have uncovered several mutations conferring drug resistance, much less is known about the factors underlying other bacterial phenotypes. Variation in the outcome of tuberculosis infection and diseases has been attributed primarily to patient and environmental factors, but recent evidence indicates an additional role for the genetic diversity among MTBC clinical strains. Here, we used metabolomics to unravel the effect of genetic variation on the strain-specific metabolic adaptive capacity and vulnerability. To define the functionality of single-nucleotide polymorphisms (SNPs) systematically, we developed a constraint-based approach that integrates metabolomic and genomic data. Our model-based predictions correctly classify SNP effects in pyruvate kinase and suggest a genetic basis for strain-specific inherent baseline susceptibility to the antibiotic para-aminosalicylic acid. Our method is broadly applicable across microbial life, opening possibilities for the development of more selective treatment strategies.
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47
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Togninalli M, Seren Ü, Freudenthal JA, Monroe JG, Meng D, Nordborg M, Weigel D, Borgwardt K, Korte A, Grimm DG. AraPheno and the AraGWAS Catalog 2020: a major database update including RNA-Seq and knockout mutation data for Arabidopsis thaliana. Nucleic Acids Res 2020; 48:D1063-D1068. [PMID: 31642487 PMCID: PMC7145550 DOI: 10.1093/nar/gkz925] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 09/26/2019] [Accepted: 10/08/2019] [Indexed: 12/23/2022] Open
Abstract
Genome-wide association studies (GWAS) are integral for studying genotype-phenotype relationships and gaining a deeper understanding of the genetic architecture underlying trait variation. A plethora of genetic associations between distinct loci and various traits have been successfully discovered and published for the model plant Arabidopsis thaliana. This success and the free availability of full genomes and phenotypic data for more than 1,000 different natural inbred lines led to the development of several data repositories. AraPheno (https://arapheno.1001genomes.org) serves as a central repository of population-scale phenotypes in A. thaliana, while the AraGWAS Catalog (https://aragwas.1001genomes.org) provides a publicly available, manually curated and standardized collection of marker-trait associations for all available phenotypes from AraPheno. In this major update, we introduce the next generation of both platforms, including new data, features and tools. We included novel results on associations between knockout-mutations and all AraPheno traits. Furthermore, AraPheno has been extended to display RNA-Seq data for hundreds of accessions, providing expression information for over 28 000 genes for these accessions. All data, including the imputed genotype matrix used for GWAS, are easily downloadable via the respective databases.
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Affiliation(s)
- Matteo Togninalli
- Machine Learning and Computational Biology Lab, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Ümit Seren
- Gregor Mendel Institute of Molecular Plant Biology, Vienna, Austria
| | - Jan A Freudenthal
- Center for Computational and Theoretical Biology, University Würzburg, Würzburg, Germany
| | - J Grey Monroe
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Dazhe Meng
- Gregor Mendel Institute of Molecular Plant Biology, Vienna, Austria
- Google, Mountain View, USA
| | - Magnus Nordborg
- Gregor Mendel Institute of Molecular Plant Biology, Vienna, Austria
| | - Detlef Weigel
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Karsten Borgwardt
- Machine Learning and Computational Biology Lab, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Arthur Korte
- Center for Computational and Theoretical Biology, University Würzburg, Würzburg, Germany
| | - Dominik G Grimm
- Technical University of Munich, TUM Campus Straubing for Biotechnology and Sustainability, Bioinformatics, Straubing, Germany
- Weihenstephan-Triesdorf University of Applied Sciences, Bioinformatics, Straubing, Germany
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48
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Kumagai M, Nishikawa D, Kawahara Y, Wakimoto H, Itoh R, Tabei N, Tanaka T, Itoh T. TASUKE+: a web-based platform for exploring genome-wide association studies results and large-scale resequencing data. DNA Res 2019; 26:445-452. [PMID: 31539030 PMCID: PMC7207078 DOI: 10.1093/dnares/dsz022] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 09/18/2019] [Indexed: 01/17/2023] Open
Abstract
Recent revolutionary advancements in sequencing technologies have made it possible to obtain mass quantities of genome-scale sequence data in a cost-effective manner and have drastically altered molecular biological studies. To utilize these sequence data, genome-wide association studies (GWASs) have become increasingly important. Hence, there is an urgent need to develop a visualization tool that enables efficient data retrieval, integration of GWAS results with diverse information and rapid public release of such large-scale genotypic and phenotypic data. We developed a web-based genome browser TASUKE+ (https://tasuke.dna.affrc.go.jp/), which is equipped with the following functions: (i) interactive GWAS results visualization with genome resequencing data and annotation information, (ii) PCR primer design, (iii) phylogenetic tree reconstruction and (iv) data sharing via the web. GWAS results can be displayed in parallel with polymorphism data, read depths and annotation information in an interactive and scalable manner. Users can design PCR primers for polymorphic sites of interest. In addition, a molecular phylogenetic tree of any region can be reconstructed so that the overall relationship among the examined genomes can be understood intuitively at a glance. All functions are implemented through user-friendly web-based interfaces so that researchers can easily share data with collaborators in remote places without extensive bioinformatics knowledge.
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Affiliation(s)
- Masahiko Kumagai
- Advanced Analysis Center, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8602, Japan
| | | | - Yoshihiro Kawahara
- Advanced Analysis Center, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8602, Japan
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8518, Japan
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
| | | | | | | | - Tsuyoshi Tanaka
- Advanced Analysis Center, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8602, Japan
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8518, Japan
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
| | - Takeshi Itoh
- Advanced Analysis Center, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8602, Japan
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
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49
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Kazakou E, Vasseur F, Sartori K, Baron E, Rowe N, Vile D. Secondary metabolites have more influence than morphophysiological traits on litter decomposability across genotypes of Arabidopsis thaliana. THE NEW PHYTOLOGIST 2019; 224:1532-1543. [PMID: 31179544 DOI: 10.1111/nph.15983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 05/29/2019] [Indexed: 06/09/2023]
Abstract
Although interspecific variation in plant phenotype is recognised to impact afterlife processes such as litter decomposability, it is still unclear which traits and selection pressures explain these relationships. Examining intraspecific variation is crucial to identify and compare trait effects on decomposability, and investigate the potential role of natural selection. We studied the genetic variability and relationships between decomposability, plant traits typically related to decomposability at species level (morphophysiological traits), and leaf metabolites among a set of genotypes of Arabidopsis thaliana grown under controlled conditions. We also investigated correlations between decomposability and environmental variables at genotypes collection site. We investigated the genetic architecture of decomposability with genome-wide association studies (GWAS). There was large genetic variability in decomposability that was correlated with precipitation. Morphophysiological traits had a minor effect, while secondary metabolites, especially glucosinolates, were correlated with decomposability. Consistently, GWAS suggested that genes and metabolites related to the composition of cell membranes and envelopes control the variation of decomposability across genotypes. Our study suggests that decomposability varies within species as a result of metabolic adaptation to climate. Our findings highlight that subtle variations of defence-related metabolites like glucosinolates may strongly influence after-life processes such as decomposability.
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Affiliation(s)
- Elena Kazakou
- Montpellier Supagro, Centre d'Ecologie Fonctionnelle et Evolutive (UMR CEFE), CNRS, Université de Montpellier, Université Paul-Valéry Montpellier, EPHE, Montpellier, 34090, France
| | - François Vasseur
- CEFE, CNRS, Université de Montpellier, Université Paul-Valéry Montpellier, EPHE, Montpellier, 34090, France
- LEPSE, INRA, Montpellier SupAgro, Université de Montpellier, Montpellier, 34060, France
| | - Kevin Sartori
- CEFE, CNRS, Université de Montpellier, Université Paul-Valéry Montpellier, EPHE, Montpellier, 34090, France
| | - Etienne Baron
- CEFE, CNRS, Université de Montpellier, Université Paul-Valéry Montpellier, EPHE, Montpellier, 34090, France
| | - Nick Rowe
- AMAP, CNRS, INRA, IRD, Univ Montpellier, CIRAD, Montpellier, 34090, France
| | - Denis Vile
- LEPSE, INRA, Montpellier SupAgro, Université de Montpellier, Montpellier, 34060, France
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50
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Togninalli M, Seren Ü, Meng D, Fitz J, Nordborg M, Weigel D, Borgwardt K, Korte A, Grimm DG. The AraGWAS Catalog: a curated and standardized Arabidopsis thaliana GWAS catalog. Nucleic Acids Res 2019; 46:D1150-D1156. [PMID: 29059333 PMCID: PMC5753280 DOI: 10.1093/nar/gkx954] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 10/06/2017] [Indexed: 12/21/2022] Open
Abstract
The abundance of high-quality genotype and phenotype data for the model organism Arabidopsis thaliana enables scientists to study the genetic architecture of many complex traits at an unprecedented level of detail using genome-wide association studies (GWAS). GWAS have been a great success in A. thaliana and many SNP-trait associations have been published. With the AraGWAS Catalog (https://aragwas.1001genomes.org) we provide a publicly available, manually curated and standardized GWAS catalog for all publicly available phenotypes from the central A. thaliana phenotype repository, AraPheno. All GWAS have been recomputed on the latest imputed genotype release of the 1001 Genomes Consortium using a standardized GWAS pipeline to ensure comparability between results. The catalog includes currently 167 phenotypes and more than 222 000 SNP-trait associations with P < 10−4, of which 3887 are significantly associated using permutation-based thresholds. The AraGWAS Catalog can be accessed via a modern web-interface and provides various features to easily access, download and visualize the results and summary statistics across GWAS.
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Affiliation(s)
- Matteo Togninalli
- Machine Learning and Computational Biology Lab, Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland.,Swiss Institute of Bioinformatics, 4056 Basel, Switzerland
| | - Ümit Seren
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Dazhe Meng
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030 Vienna, Austria.,Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90007, USA
| | - Joffrey Fitz
- Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Magnus Nordborg
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Detlef Weigel
- Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Karsten Borgwardt
- Machine Learning and Computational Biology Lab, Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland.,Swiss Institute of Bioinformatics, 4056 Basel, Switzerland
| | - Arthur Korte
- Center for Computational and Theoretical Biology, University Würzburg, 97074 Würzburg, Germany
| | - Dominik G Grimm
- Machine Learning and Computational Biology Lab, Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland.,Swiss Institute of Bioinformatics, 4056 Basel, Switzerland
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