1
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Maple R, Zhu P, Hepworth J, Wang JW, Dean C. Flowering time: From physiology, through genetics to mechanism. PLANT PHYSIOLOGY 2024; 195:190-212. [PMID: 38417841 PMCID: PMC11060688 DOI: 10.1093/plphys/kiae109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 01/12/2024] [Accepted: 02/12/2024] [Indexed: 03/01/2024]
Abstract
Plant species have evolved different requirements for environmental/endogenous cues to induce flowering. Originally, these varying requirements were thought to reflect the action of different molecular mechanisms. Thinking changed when genetic and molecular analysis in Arabidopsis thaliana revealed that a network of environmental and endogenous signaling input pathways converge to regulate a common set of "floral pathway integrators." Variation in the predominance of the different input pathways within a network can generate the diversity of requirements observed in different species. Many genes identified by flowering time mutants were found to encode general developmental and gene regulators, with their targets having a specific flowering function. Studies of natural variation in flowering were more successful at identifying genes acting as nodes in the network central to adaptation and domestication. Attention has now turned to mechanistic dissection of flowering time gene function and how that has changed during adaptation. This will inform breeding strategies for climate-proof crops and help define which genes act as critical flowering nodes in many other species.
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Affiliation(s)
- Robert Maple
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Pan Zhu
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Jo Hepworth
- Department of Biosciences, Durham University, Stockton Road, Durham, DH1 3LE, UK
| | - Jia-Wei Wang
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai 200032, China
- School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China
- New Cornerstone Science Laboratory, Shanghai 200032, China
| | - Caroline Dean
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
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2
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Zhang B, Feng M, Zhang J, Song Z. Involvement of CONSTANS-like Proteins in Plant Flowering and Abiotic Stress Response. Int J Mol Sci 2023; 24:16585. [PMID: 38068908 PMCID: PMC10706179 DOI: 10.3390/ijms242316585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 12/18/2023] Open
Abstract
The process of flowering in plants is a pivotal stage in their life cycle, and the CONSTANS-like (COL) protein family, known for its photoperiod sensing ability, plays a crucial role in regulating plant flowering. Over the past two decades, homologous genes of COL have been identified in various plant species, leading to significant advancements in comprehending their involvement in the flowering pathway and response to abiotic stress. This article presents novel research progress on the structural aspects of COL proteins and their regulatory patterns within transcription complexes. Additionally, we reviewed recent information about their participation in flowering and abiotic stress response, aiming to provide a more comprehensive understanding of the functions of COL proteins.
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Affiliation(s)
- Bingqian Zhang
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain of Ministry of Agriculture and Rural Affairs, Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (B.Z.); (M.F.); (J.Z.)
- College of Life Science, Shandong Normal University, Jinan 250358, China
| | - Minghui Feng
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain of Ministry of Agriculture and Rural Affairs, Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (B.Z.); (M.F.); (J.Z.)
- College of Life Science, Shandong Normal University, Jinan 250358, China
| | - Jun Zhang
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain of Ministry of Agriculture and Rural Affairs, Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (B.Z.); (M.F.); (J.Z.)
- College of Life Science, Shandong Normal University, Jinan 250358, China
| | - Zhangqiang Song
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain of Ministry of Agriculture and Rural Affairs, Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (B.Z.); (M.F.); (J.Z.)
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3
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Tavares H, Readshaw A, Kania U, de Jong M, Pasam RK, McCulloch H, Ward S, Shenhav L, Forsyth E, Leyser O. Artificial selection reveals complex genetic architecture of shoot branching and its response to nitrate supply in Arabidopsis. PLoS Genet 2023; 19:e1010863. [PMID: 37616321 PMCID: PMC10482290 DOI: 10.1371/journal.pgen.1010863] [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: 06/18/2022] [Revised: 09/06/2023] [Accepted: 07/08/2023] [Indexed: 08/26/2023] Open
Abstract
Quantitative traits may be controlled by many loci, many alleles at each locus, and subject to genotype-by-environment interactions, making them difficult to map. One example of such a complex trait is shoot branching in the model plant Arabidopsis, and its plasticity in response to nitrate. Here, we use artificial selection under contrasting nitrate supplies to dissect the genetic architecture of this complex trait, where loci identified by association mapping failed to explain heritability estimates. We found a consistent response to selection for high branching, with correlated responses in other traits such as plasticity and flowering time. Genome-wide scans for selection and simulations suggest that at least tens of loci control this trait, with a distinct genetic architecture between low and high nitrate treatments. While signals of selection could be detected in the populations selected for high branching on low nitrate, there was very little overlap in the regions selected in three independent populations. Thus the regulatory network controlling shoot branching can be tuned in different ways to give similar phenotypes.
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Affiliation(s)
- Hugo Tavares
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Anne Readshaw
- Department of Biology, University of York, York, United Kingdom
| | - Urszula Kania
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Maaike de Jong
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Raj K. Pasam
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Hayley McCulloch
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Sally Ward
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
- Department of Biology, University of York, York, United Kingdom
| | - Liron Shenhav
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Elizabeth Forsyth
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Ottoline Leyser
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
- Department of Biology, University of York, York, United Kingdom
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4
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Wijnen CL, Becker FFM, Okkersen AA, de Snoo CB, Boer MP, van Eeuwijk FA, Wijnker E, Keurentjes JJB. Genetic Mapping of Genotype-by-Ploidy Effects in Arabidopsis thaliana. Genes (Basel) 2023; 14:1161. [PMID: 37372341 DOI: 10.3390/genes14061161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 05/22/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
Plants can express different phenotypic responses following polyploidization, but ploidy-dependent phenotypic variation has so far not been assigned to specific genetic factors. To map such effects, segregating populations at different ploidy levels are required. The availability of an efficient haploid inducer line in Arabidopsis thaliana allows for the rapid development of large populations of segregating haploid offspring. Because Arabidopsis haploids can be self-fertilised to give rise to homozygous doubled haploids, the same genotypes can be phenotyped at both the haploid and diploid ploidy level. Here, we compared the phenotypes of recombinant haploid and diploid offspring derived from a cross between two late flowering accessions to map genotype × ploidy (G × P) interactions. Ploidy-specific quantitative trait loci (QTLs) were detected at both ploidy levels. This implies that mapping power will increase when phenotypic measurements of monoploids are included in QTL analyses. A multi-trait analysis further revealed pleiotropic effects for a number of the ploidy-specific QTLs as well as opposite effects at different ploidy levels for general QTLs. Taken together, we provide evidence of genetic variation between different Arabidopsis accessions being causal for dissimilarities in phenotypic responses to altered ploidy levels, revealing a G × P effect. Additionally, by investigating a population derived from late flowering accessions, we revealed a major vernalisation-specific QTL for variation in flowering time, countering the historical bias of research in early flowering accessions.
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Affiliation(s)
- Cris L Wijnen
- Laboratory of Genetics, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Biometris, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Frank F M Becker
- Laboratory of Genetics, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Andries A Okkersen
- Laboratory of Genetics, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - C Bastiaan de Snoo
- Rijk Zwaan R&D Fijnaart, Eerste Kruisweg 9, 4793 RS Fijnaart, The Netherlands
| | - Martin P Boer
- Biometris, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Fred A van Eeuwijk
- Biometris, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Erik Wijnker
- Laboratory of Genetics, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Joost J B Keurentjes
- Laboratory of Genetics, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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5
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Liang Q, Chen L, Yang X, Yang H, Liu S, Kou K, Fan L, Zhang Z, Duan Z, Yuan Y, Liang S, Liu Y, Lu X, Zhou G, Zhang M, Kong F, Tian Z. Natural variation of Dt2 determines branching in soybean. Nat Commun 2022; 13:6429. [PMID: 36307423 PMCID: PMC9616897 DOI: 10.1038/s41467-022-34153-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 10/16/2022] [Indexed: 12/25/2022] Open
Abstract
Shoot branching is fundamentally important in determining soybean yield. Here, through genome-wide association study, we identify one predominant association locus on chromosome 18 that confers soybean branch number in the natural population. Further analyses determine that Dt2 is the corresponding gene and the natural variations in Dt2 result in significant differential transcriptional levels between the two major haplotypes. Functional characterization reveals that Dt2 interacts with GmAgl22 and GmSoc1a to physically bind to the promoters of GmAp1a and GmAp1d and to activate their transcription. Population genetic investigation show that the genetic differentiation of Dt2 display significant geographic structure. Our study provides a predominant gene for soybean branch number and may facilitate the breeding of high-yield soybean varieties.
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Affiliation(s)
- Qianjin Liang
- grid.418558.50000 0004 0596 2989State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Liyu Chen
- grid.411863.90000 0001 0067 3588Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Xia Yang
- grid.418558.50000 0004 0596 2989State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Hui Yang
- grid.411863.90000 0001 0067 3588Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Shulin Liu
- grid.418558.50000 0004 0596 2989State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Kun Kou
- grid.411863.90000 0001 0067 3588Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Lei Fan
- grid.418558.50000 0004 0596 2989State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Zhifang Zhang
- grid.418558.50000 0004 0596 2989State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Zongbiao Duan
- grid.418558.50000 0004 0596 2989State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yaqin Yuan
- grid.418558.50000 0004 0596 2989State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Shan Liang
- grid.418558.50000 0004 0596 2989State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Yucheng Liu
- grid.418558.50000 0004 0596 2989State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Xingtong Lu
- grid.418558.50000 0004 0596 2989State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Guoan Zhou
- grid.418558.50000 0004 0596 2989State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Min Zhang
- grid.418558.50000 0004 0596 2989State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Fanjiang Kong
- grid.411863.90000 0001 0067 3588Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Zhixi Tian
- grid.418558.50000 0004 0596 2989State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
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6
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Voogd C, Brian LA, Wu R, Wang T, Allan AC, Varkonyi-Gasic E. A MADS-box gene with similarity to FLC is induced by cold and correlated with epigenetic changes to control budbreak in kiwifruit. THE NEW PHYTOLOGIST 2022; 233:2111-2126. [PMID: 34907541 DOI: 10.1111/nph.17916] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 12/01/2021] [Indexed: 06/14/2023]
Abstract
Temperate perennials require exposure to chilling temperatures to resume growth in the following spring. Growth and dormancy cycles are controlled by complex genetic regulatory networks and are governed by epigenetic mechanisms, but the specific genes and mechanisms remain poorly understood. To understand how seasonal changes and chilling regulate dormancy and growth in the woody perennial vine kiwifruit (Ac, Actinidia chinensis), a transcriptome study of kiwifruit buds in the field and controlled conditions was performed. A MADS-box gene with homology to Arabidopsis FLOWERING LOCUS C (FLC) was identified and characterized. Elevated expression of AcFLC-like (AcFLCL) was detected during bud dormancy and chilling. A long noncoding (lnc) antisense transcript with an expression pattern opposite to AcFLCL and shorter sense noncoding RNAs were identified. Chilling induced an increase in trimethylation of lysine-4 of histone H3 (H3K4me3) in the 5' end of the gene, indicating multiple layers of epigenetic regulation in response to cold. Overexpression of AcFLCL in kiwifruit gave rise to plants with earlier budbreak, whilst gene editing using CRISPR-Cas9 resulted in transgenic lines with substantially delayed budbreak, suggesting a role in activation of growth. These results have implications for the future management and breeding of perennials for resilience to changing climate.
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Affiliation(s)
- Charlotte Voogd
- The New Zealand Institute for Plant and Food Research Limited (Plant & Food Research) Mt Albert, Private Bag 92169, Auckland Mail Centre, Auckland, 1142, New Zealand
| | - Lara A Brian
- The New Zealand Institute for Plant and Food Research Limited (Plant & Food Research) Mt Albert, Private Bag 92169, Auckland Mail Centre, Auckland, 1142, New Zealand
| | - Rongmei Wu
- The New Zealand Institute for Plant and Food Research Limited (Plant & Food Research) Mt Albert, Private Bag 92169, Auckland Mail Centre, Auckland, 1142, New Zealand
| | - Tianchi Wang
- The New Zealand Institute for Plant and Food Research Limited (Plant & Food Research) Mt Albert, Private Bag 92169, Auckland Mail Centre, Auckland, 1142, New Zealand
| | - Andrew C Allan
- The New Zealand Institute for Plant and Food Research Limited (Plant & Food Research) Mt Albert, Private Bag 92169, Auckland Mail Centre, Auckland, 1142, New Zealand
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Erika Varkonyi-Gasic
- The New Zealand Institute for Plant and Food Research Limited (Plant & Food Research) Mt Albert, Private Bag 92169, Auckland Mail Centre, Auckland, 1142, New Zealand
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7
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Hepworth J, Antoniou-Kourounioti RL, Berggren K, Selga C, Tudor EH, Yates B, Cox D, Collier Harris BR, Irwin JA, Howard M, Säll T, Holm S, Dean C. Natural variation in autumn expression is the major adaptive determinant distinguishing Arabidopsis FLC haplotypes. eLife 2020; 9:57671. [PMID: 32902380 PMCID: PMC7518893 DOI: 10.7554/elife.57671] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 09/08/2020] [Indexed: 12/27/2022] Open
Abstract
In Arabidopsis thaliana, winter is registered during vernalization through the temperature-dependent repression and epigenetic silencing of floral repressor FLOWERING LOCUS C (FLC). Natural Arabidopsis accessions show considerable variation in vernalization. However, which aspect of the FLC repression mechanism is most important for adaptation to different environments is unclear. By analysing FLC dynamics in natural variants and mutants throughout winter in three field sites, we find that autumnal FLC expression, rather than epigenetic silencing, is the major variable conferred by the distinct Arabidopsis FLChaplotypes. This variation influences flowering responses of Arabidopsis accessions resulting in an interplay between promotion and delay of flowering in different climates to balance survival and, through a post-vernalization effect, reproductive output. These data reveal how expression variation through non-coding cis variation at FLC has enabled Arabidopsis accessions to adapt to different climatic conditions and year-on-year fluctuations.
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Affiliation(s)
- Jo Hepworth
- Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
| | | | - Kristina Berggren
- Department of Natural Sciences, Mid Sweden University, Sundsvall, Sweden
| | - Catja Selga
- Department of Biology, Lund University, Lund, Sweden
| | - Eleri H Tudor
- Crop Genetics, John Innes Centre, Norwich, United Kingdom
| | - Bryony Yates
- Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
| | - Deborah Cox
- Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
| | | | - Judith A Irwin
- Crop Genetics, John Innes Centre, Norwich, United Kingdom
| | - Martin Howard
- Computational and Systems Biology, John Innes Centre, Norwich, United Kingdom
| | - Torbjörn Säll
- Department of Biology, Lund University, Lund, Sweden
| | - Svante Holm
- Department of Natural Sciences, Mid Sweden University, Sundsvall, Sweden
| | - Caroline Dean
- Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
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8
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Genotype networks of 80 quantitative Arabidopsis thaliana phenotypes reveal phenotypic evolvability despite pervasive epistasis. PLoS Comput Biol 2020; 16:e1008082. [PMID: 32790763 PMCID: PMC7447023 DOI: 10.1371/journal.pcbi.1008082] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 08/25/2020] [Accepted: 06/22/2020] [Indexed: 12/23/2022] Open
Abstract
We study the genotype-phenotype maps of 80 quantitative phenotypes in the model plant Arabidopsis thaliana, by representing the genotypes affecting each phenotype as a genotype network. In such a network, each vertex or node corresponds to an individual's genotype at all those genomic loci that affect a given phenotype. Two vertices are connected by an edge if the associated genotypes differ in exactly one nucleotide. The 80 genotype networks we analyze are based on data from genome-wide association studies of 199 A. thaliana accessions. They form connected graphs whose topography differs substantially among phenotypes. We focus our analysis on the incidence of epistasis (non-additive interactions among mutations) because a high incidence of epistasis can reduce the accessibility of evolutionary paths towards high or low phenotypic values. We find epistatic interactions in 67 phenotypes, and in 51 phenotypes every pairwise mutant interaction is epistatic. Moreover, we find phenotype-specific differences in the fraction of accessible mutational paths to maximum phenotypic values. However, even though epistasis affects the accessibility of maximum phenotypic values, the relationships between genotypic and phenotypic change of our analyzed phenotypes are sufficiently smooth that some evolutionary paths remain accessible for most phenotypes, even where epistasis is pervasive. The genotype network representation we use can complement existing approaches to understand the genetic architecture of polygenic traits in many different organisms.
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9
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Olatoye MO, Hu Z, Aikpokpodion PO. Epistasis Detection and Modeling for Genomic Selection in Cowpea ( Vigna unguiculata L. Walp.). Front Genet 2019; 10:677. [PMID: 31417604 PMCID: PMC6682672 DOI: 10.3389/fgene.2019.00677] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 06/27/2019] [Indexed: 12/24/2022] Open
Abstract
Genetic architecture reflects the pattern of effects and interaction of genes underlying phenotypic variation. Most mapping and breeding approaches generally consider the additive part of variation but offer limited knowledge on the benefits of epistasis which explains in part the variation observed in traits. In this study, the cowpea multiparent advanced generation inter-cross (MAGIC) population was used to characterize the epistatic genetic architecture of flowering time, maturity, and seed size. In addition, consideration for epistatic genetic architecture in genomic-enabled breeding (GEB) was investigated using parametric, semi-parametric, and non-parametric genomic selection (GS) models. Our results showed that large and moderate effect-sized two-way epistatic interactions underlie the traits examined. Flowering time QTL colocalized with cowpea putative orthologs of Arabidopsis thaliana and Glycine max genes like PHYTOCLOCK1 (PCL1 [Vigun11g157600]) and PHYTOCHROME A (PHY A [Vigun01g205500]). Flowering time adaptation to long and short photoperiod was found to be controlled by distinct and common main and epistatic loci. Parametric and semi-parametric GS models outperformed non-parametric GS model, while using known quantitative trait nucleotide(s) (QTNs) as fixed effects improved prediction accuracy when traits were controlled by large effect loci. In general, our study demonstrated that prior understanding of the genetic architecture of a trait can help make informed decisions in GEB.
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Affiliation(s)
- Marcus O. Olatoye
- Department of Crop Sciences, University of Illinois, Urbana-Champaign, IL, United States
| | - Zhenbin Hu
- Department of Agronomy, Kansas State University, Manhattan, KS, United States
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10
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Ortega R, Hecht VFG, Freeman JS, Rubio J, Carrasquilla-Garcia N, Mir RR, Penmetsa RV, Cook DR, Millan T, Weller JL. Altered Expression of an FT Cluster Underlies a Major Locus Controlling Domestication-Related Changes to Chickpea Phenology and Growth Habit. FRONTIERS IN PLANT SCIENCE 2019; 10:824. [PMID: 31333691 PMCID: PMC6616154 DOI: 10.3389/fpls.2019.00824] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 06/07/2019] [Indexed: 05/20/2023]
Abstract
Flowering time is a key trait in breeding and crop evolution, due to its importance for adaptation to different environments and for yield. In the particular case of chickpea, selection for early phenology was essential for the successful transition of this species from a winter to a summer crop. Here, we used genetic and expression analyses in two different inbred populations to examine the genetic control of domestication-related differences in flowering time and growth habit between domesticated chickpea and its wild progenitor Cicer reticulatum. A single major quantitative trait locus for flowering time under short-day conditions [Days To Flower (DTF)3A] was mapped to a 59-gene interval on chromosome three containing a cluster of three FT genes, which collectively showed upregulated expression in domesticated relative to wild parent lines. An equally strong association with growth habit suggests a pleiotropic effect of the region on both traits. These results indicate the likely molecular explanation for the characteristic early flowering of domesticated chickpea, and the previously described growth habit locus Hg. More generally, they point to de-repression of this specific gene cluster as a conserved mechanism for achieving adaptive early phenology in temperate legumes.
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Affiliation(s)
- Raul Ortega
- School of Natural Sciences, University of Tasmania, Hobart, TAS, Australia
| | | | - Jules S. Freeman
- School of Natural Sciences, University of Tasmania, Hobart, TAS, Australia
- Scion, Rotorua, New Zealand
| | - Josefa Rubio
- E. Genomica y Biotecnologia, Instituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA), Córdoba, Spain
| | | | - Reyazul Rouf Mir
- Department of Plant Pathology, University of California, Davis, Davis, CA, United States
- Division of Genetics and Plant Breeding, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - R. Varma Penmetsa
- Department of Plant Pathology, University of California, Davis, Davis, CA, United States
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Douglas R. Cook
- Department of Plant Pathology, University of California, Davis, Davis, CA, United States
| | - Teresa Millan
- Department of Genetics ETSIAM, University of Córdoba, Córdoba, Spain
| | - James L. Weller
- School of Natural Sciences, University of Tasmania, Hobart, TAS, Australia
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11
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Hughes PW, Soppe WJJ, Albani MC. Seed traits are pleiotropically regulated by the flowering time gene PERPETUAL FLOWERING 1 (PEP1) in the perennial Arabis alpina. Mol Ecol 2019; 28:1183-1201. [PMID: 30712274 PMCID: PMC6850658 DOI: 10.1111/mec.15034] [Citation(s) in RCA: 20] [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: 04/03/2018] [Revised: 10/22/2018] [Accepted: 11/19/2018] [Indexed: 01/20/2023]
Abstract
The life cycles of plants are characterized by two major life history transitions-germination and the initiation of flowering-the timing of which are important determinants of fitness. Unlike annuals, which make the transition from the vegetative to reproductive phase only once, perennials iterate reproduction in successive years. The floral repressor PERPETUAL FLOWERING 1 (PEP1), an ortholog of FLOWERING LOCUS C, in the alpine perennial Arabis alpina ensures the continuation of vegetative growth after flowering and thereby restricts the duration of the flowering episode. We performed greenhouse and garden experiments to compare flowering phenology, fecundity and seed traits between A. alpina accessions that have a functional PEP1 allele and flower seasonally and pep1 mutants and accessions that carry lesions in PEP1 and flower perpetually. In the garden, perpetual genotypes flower asynchronously and show higher winter mortality than seasonal ones. PEP1 also pleiotropically regulates seed dormancy and longevity in a way that is functionally divergent from FLC. Seeds from perpetual genotypes have shallow dormancy and reduced longevity regardless of whether they after-ripened in plants grown in the greenhouse or in the experimental garden. These results suggest that perpetual genotypes have higher mortality during winter but compensate by showing higher seedling establishment. Differences in seed traits between seasonal and perpetual genotypes are also coupled with differences in hormone sensitivity and expression of genes involved in hormonal pathways. Our study highlights the existence of pleiotropic regulation of seed traits by hub developmental regulators such as PEP1, suggesting that seed and flowering traits in perennial plants might be optimized in a coordinated fashion.
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Affiliation(s)
- Patrick William Hughes
- Max Planck Institute for Plant Breeding ResearchCologneGermany
- Botanical InstituteUniversity of CologneCologneGermany
| | - Wim J. J. Soppe
- Max Planck Institute for Plant Breeding ResearchCologneGermany
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO)University of BonnBonnGermany
- Present address:
Rijk ZwaanDe LierThe Netherlands
| | - Maria C. Albani
- Max Planck Institute for Plant Breeding ResearchCologneGermany
- Botanical InstituteUniversity of CologneCologneGermany
- Center of Excellence in Plant Sciences (CEPLAS)DüsseldorfGermany
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12
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van Hulten MHA, Paulo MJ, Kruijer W, Blankestijn-De Vries H, Kemperman B, Becker FFM, Yang J, Lauss K, Stam ME, van Eeuwijk FA, Keurentjes JJB. Assessment of heterosis in two Arabidopsis thaliana common-reference mapping populations. PLoS One 2018; 13:e0205564. [PMID: 30312352 PMCID: PMC6185836 DOI: 10.1371/journal.pone.0205564] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 09/27/2018] [Indexed: 12/01/2022] Open
Abstract
Hybrid vigour, or heterosis, has been of tremendous importance in agriculture for the improvement of both crops and livestock. Notwithstanding large efforts to study the phenomenon of heterosis in the last decades, the identification of common molecular mechanisms underlying hybrid vigour remain rare. Here, we conducted a systematic survey of the degree of heterosis in Arabidopsis thaliana hybrids. For this purpose, two overlapping Arabidopsis hybrid populations were generated by crossing a large collection of naturally occurring accessions to two common reference lines. In these Arabidopsis hybrid populations the range of heterosis for several developmental and yield related traits was examined, and the relationship between them was studied. The traits under study were projected leaf area at 17 days after sowing, flowering time, height of the main inflorescence, number of side branches from the main stem or from the rosette base, total seed yield, seed weight, seed size and the estimated number of seeds per plant. Predominantly positive heterosis was observed for leaf area and height of the main inflorescence, whereas mainly negative heterosis was observed for rosette branching. For the other traits both positive and negative heterosis was observed in roughly equal amounts. For flowering time and seed size only low levels of heterosis were detected. In general the observed heterosis levels were highly trait specific. Furthermore, no correlation was observed between heterosis levels and the genetic distance between the parental lines. Since all selected lines were a part of the Arabidopsis genome wide association (GWA) mapping panel, a genetic mapping approach was applied to identify possible regions harbouring genetic factors causal for heterosis, with separate calculations for additive and dominance effects. Our study showed that the genetic mechanisms underlying heterosis were highly trait specific in our hybrid populations and greatly depended on the genetic background, confirming the elusive character of heterosis.
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Affiliation(s)
| | - Maria-Joāo Paulo
- Biometris, Wageningen University and Research, Wageningen, The Netherlands
| | - Willem Kruijer
- Biometris, Wageningen University and Research, Wageningen, The Netherlands
| | | | - Brend Kemperman
- Laboratory of Genetics, Wageningen University and Research, Wageningen, the Netherlands
| | - Frank F. M. Becker
- Laboratory of Genetics, Wageningen University and Research, Wageningen, the Netherlands
| | - Jiaming Yang
- Laboratory of Genetics, Wageningen University and Research, Wageningen, the Netherlands
| | - Kathrin Lauss
- Plant Development & (Epi)Genetics, Faculty of Science, Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, Amsterdam, The Netherlands
| | - Maike E. Stam
- Plant Development & (Epi)Genetics, Faculty of Science, Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, Amsterdam, The Netherlands
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13
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Liu N, Liu J, Li W, Pan Q, Liu J, Yang X, Yan J, Xiao Y. Intraspecific variation of residual heterozygosity and its utility for quantitative genetic studies in maize. BMC PLANT BIOLOGY 2018; 18:66. [PMID: 29673320 PMCID: PMC5909218 DOI: 10.1186/s12870-018-1287-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 04/11/2018] [Indexed: 05/22/2023]
Abstract
BACKGROUND Residual heterozygosity (RH) in advanced inbred lines of plants benefits quantitative trait locus (QTL) mapping studies. However, knowledge of factors affecting the genome-wide distribution of RH remains limited. RESULTS A set of 2196 heterogeneous inbred family (HIF) maize lines derived from 12 recombinant inbred line (RIL) populations was genotyped using the Maize50K SNP chip. A total of 18,615 unique RH intervals were identified, ranging from 505 to 2095 intervals per population, with average maize genome coverage of 94.8%. Across all populations, there were 8.6 RH intervals per HIF line on average, ranging from 1.8 to 14 intervals; the average size of an RH interval was approximately 58.7 Mb, ranging from 7.2 to 74.1 Mb. A given RH region was present in an average of 5 different individuals within a population. Seven RH hotspots, where RH segments were enriched in the genome, were found to be subject to selection during population development. The RH patterns varied significantly across populations, presumably reflecting differences in the genetic background of each population, and 8 QTLs were found to affect heterozygosity levels in the RH hotspots. The potential use of this HIF library for the fine mapping of QTLs was assessed based on publicly available QTL information, achieving a ≤ 1 Mb resolution on average. CONCLUSION The examined library of HIF lines offers insight into the RH landscape and its intraspecific variation and provides a useful resource for the QTL cloning of important agronomic traits in maize.
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Affiliation(s)
- Nannan Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Jianxiao Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
- College of Informatics, Huazhong Agricultural University, Wuhan, 430070 China
| | - Wenqiang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Qingchun Pan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Jie Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Xiaohong Yang
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Yingjie Xiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
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Subrahmaniam HJ, Libourel C, Journet EP, Morel JB, Muños S, Niebel A, Raffaele S, Roux F. The genetics underlying natural variation of plant-plant interactions, a beloved but forgotten member of the family of biotic interactions. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:747-770. [PMID: 29232012 DOI: 10.1111/tpj.13799] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 12/02/2017] [Accepted: 12/06/2017] [Indexed: 05/22/2023]
Abstract
Despite the importance of plant-plant interactions on crop yield and plant community dynamics, our understanding of the genetic and molecular bases underlying natural variation of plant-plant interactions is largely limited in comparison with other types of biotic interactions. By listing 63 quantitative trait loci (QTL) mapping and global gene expression studies based on plants directly challenged by other plants, we explored whether the genetic architecture and the function of the candidate genes underlying natural plant-plant interactions depend on the type of interactions between two plants (competition versus commensalism versus reciprocal helping versus asymmetry). The 16 transcriptomic studies are unevenly distributed between competitive interactions (n = 12) and asymmetric interactions (n = 4, all focusing on response to parasitic plants). By contrast, 17 and 30 QTL studies were identified for competitive interactions and asymmetric interactions (either weed suppressive ability or response to parasitic plants), respectively. Surprisingly, no studies have been carried out on the identification of genetic and molecular bases underlying natural variation in positive interactions. The candidate genes underlying natural plant-plant interactions can be classified into seven categories of plant function that have been identified in artificial environments simulating plant-plant interactions either frequently (photosynthesis, hormones), only recently (cell wall modification and degradation, defense pathways against pathogens) or rarely (ABC transporters, histone modification and meristem identity/life history traits). Finally, we introduce several avenues that need to be explored in the future to obtain a thorough understanding of the genetic and molecular bases underlying plant-plant interactions within the context of realistic community complexity.
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Affiliation(s)
| | - Cyril Libourel
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Etienne-Pascal Journet
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
- AGIR, Université de Toulouse, INRA, INPT, INP-EI PURPAN, Castanet-Tolosan, France
| | - Jean-Benoît Morel
- BGPI, INRA, CIRAD, SupAgro, Université de Montpellier, Montpellier, France
| | - Stéphane Muños
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Andreas Niebel
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Sylvain Raffaele
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Fabrice Roux
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
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15
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Liu Y, Lin Y, Gao S, Li Z, Ma J, Deng M, Chen G, Wei Y, Zheng Y. A genome-wide association study of 23 agronomic traits in Chinese wheat landraces. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 91:861-873. [PMID: 28628238 DOI: 10.1111/tpj.13614] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 05/19/2017] [Indexed: 05/18/2023]
Abstract
Uncovering the genetic basis of agronomic traits in wheat landraces is important for ensuring global food security via the development of improved varieties. Here, 723 wheat landraces from 10 Chinese agro-ecological zones were evaluated for 23 agronomic traits in six environments. All accessions could be clustered into five subgroups based on phenotypic data via discriminant function analysis, which was highly consistent with genotypic classification. A genome-wide association study was conducted for these traits using 52 303 DArT-seq markers to identify marker-trait associations and candidate genes. Using both the general linear model and the mixed linear model, 149 significant markers were identified for 21 agronomic traits based on best linear unbiased prediction values. Considering the linkage disequilibrium decay distance in this study, significant markers within 10 cM were combined as a quantitative trait locus (QTL), with a total of 29 QTL identified for 15 traits. Of these, five QTL for heading date, flag leaf width, peduncle length, and thousand kernel weight had been reported previously. Twenty-five candidate genes associated with significant markers were identified. These included the known vernalization genes VRN-B1 and vrn-B3 and the photoperiod response genes Ppd and PRR. Overall, this study should be helpful in elucidating the underlying genetic mechanisms of complex agronomic traits and performing marker-assisted selection in wheat.
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Affiliation(s)
- Yaxi Liu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Yu Lin
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Shang Gao
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Zhanyi Li
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Jian Ma
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Mei Deng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Guoyue Chen
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Yuming Wei
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Youliang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
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16
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Liu J, Yu G, Jiang Y, Wang J. HiSeeker: Detecting High-Order SNP Interactions Based on Pairwise SNP Combinations. Genes (Basel) 2017; 8:genes8060153. [PMID: 28561745 PMCID: PMC5485517 DOI: 10.3390/genes8060153] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 05/06/2017] [Accepted: 05/25/2017] [Indexed: 01/27/2023] Open
Abstract
Detecting single nucleotide polymorphisms’ (SNPs) interaction is one of the most popular approaches for explaining the missing heritability of common complex diseases in genome-wide association studies. Many methods have been proposed for SNP interaction detection, but most of them only focus on pairwise interactions and ignore high-order ones, which may also contribute to complex traits. Existing methods for high-order interaction detection can hardly handle genome-wide data and suffer from low detection power, due to the exponential growth of search space. In this paper, we proposed a flexible two-stage approach (called HiSeeker) to detect high-order interactions. In the screening stage, HiSeeker employs the chi-squared test and logistic regression model to efficiently obtain candidate pairwise combinations, which have intermediate or significant associations with the phenotype for interaction detection. In the search stage, two different strategies (exhaustive search and ant colony optimization-based search) are utilized to detect high-order interactions from candidate combinations. The experimental results on simulated datasets demonstrate that HiSeeker can more efficiently and effectively detect high-order interactions than related representative algorithms. On two real case-control datasets, HiSeeker also detects several significant high-order interactions, whose individual SNPs and pairwise interactions have no strong main effects or pairwise interaction effects, and these high-order interactions can hardly be identified by related algorithms.
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Affiliation(s)
- Jie Liu
- College of Computer and Information Science, Southwest University, Chongqing 400715, China.
| | - Guoxian Yu
- College of Computer and Information Science, Southwest University, Chongqing 400715, China.
| | - Yuan Jiang
- College of Computer and Information Science, Southwest University, Chongqing 400715, China.
| | - Jun Wang
- College of Computer and Information Science, Southwest University, Chongqing 400715, China.
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17
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Weng L, Bai X, Zhao F, Li R, Xiao H. Manipulation of flowering time and branching by overexpression of the tomato transcription factor SlZFP2. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:2310-2321. [PMID: 27214796 PMCID: PMC5103233 DOI: 10.1111/pbi.12584] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 05/12/2016] [Accepted: 05/19/2016] [Indexed: 05/02/2023]
Abstract
Flowering of higher plants is orchestrated by complex regulatory networks through integration of various environmental signals such as photoperiod, temperature, light quality and developmental cues. In Arabidopsis, transcription of the flowering integrator gene FLOWERING LOCUS T (FT) that several flowering pathways converge to is directly regulated by more than ten transcription factors. However, very little is known about the transcriptional regulation of the FT homolog SINGLE FLOWER TRUESS (SFT) in the day-neutral plant tomato (Solanum lycopersicum). Previously, we showed that the zinc finger transcription factor SlZFP2 plays important roles in regulation of seed germination and fruit ripening in tomato and also found that overexpression of SlZFP2 impacted flowering and branching. Here, we characterized in detail the early flowering and high branching phenotypes by overexpression of this transcription factor. Our data showed that overexpression of SlZFP2 accelerated flowering in an SFT-dependent manner as demonstrated by elevated SFT expression in the leaves and the transcription factor's binding ability to SFT promoter in vitro and in vivo. Furthermore, overexpression of the SlZFP2 gene in the sft plants failed to rescue the mutant's late flowering. Through analysis of grafting phenotype, growth response of branches to auxin application and transcriptome profiling by RNA sequencing, we also showed that overexpression of SlZFP2 affected shoot apical dominance through multiple regulatory pathways. Our results suggest that the transcription factor SlZFP2 has potential applications in genetic modification of plant architecture and flowering time for tomato production and other crops as well.
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Affiliation(s)
- Lin Weng
- National Key Laboratory of Plant Molecular GeneticsCAS Center for Excellence in Molecular Plant SciencesInstitute of Plant Physiology and EcologyShanghai Institutes for Biological SciencesChinese Academy of SciencesShanghaiChina
| | - Xiaodong Bai
- Center for RNA Molecular BiologyCase Western Reserve UniversitySchool of MedicineClevelandOHUSA
| | - Fangfang Zhao
- National Key Laboratory of Plant Molecular GeneticsCAS Center for Excellence in Molecular Plant SciencesInstitute of Plant Physiology and EcologyShanghai Institutes for Biological SciencesChinese Academy of SciencesShanghaiChina
| | - Rong Li
- National Key Laboratory of Plant Molecular GeneticsCAS Center for Excellence in Molecular Plant SciencesInstitute of Plant Physiology and EcologyShanghai Institutes for Biological SciencesChinese Academy of SciencesShanghaiChina
| | - Han Xiao
- National Key Laboratory of Plant Molecular GeneticsCAS Center for Excellence in Molecular Plant SciencesInstitute of Plant Physiology and EcologyShanghai Institutes for Biological SciencesChinese Academy of SciencesShanghaiChina
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18
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Alonso-Blanco C, Andrade J, Becker C, Bemm F, Bergelson J, Borgwardt KM, Cao J, Chae E, Dezwaan TM, Ding W, Ecker JR, Exposito-Alonso M, Farlow A, Fitz J, Gan X, Grimm DG, Hancock AM, Henz SR, Holm S, Horton M, Jarsulic M, Kerstetter RA, Korte A, Korte P, Lanz C, Lee CR, Meng D, Michael TP, Mott R, Muliyati NW, Nägele T, Nagler M, Nizhynska V, Nordborg M, Novikova PY, Picó FX, Platzer A, Rabanal FA, Rodriguez A, Rowan BA, Salomé PA, Schmid KJ, Schmitz RJ, Seren Ü, Sperone FG, Sudkamp M, Svardal H, Tanzer MM, Todd D, Volchenboum SL, Wang C, Wang G, Wang X, Weckwerth W, Weigel D, Zhou X. 1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana. Cell 2016; 166:481-491. [PMID: 27293186 PMCID: PMC4949382 DOI: 10.1016/j.cell.2016.05.063] [Citation(s) in RCA: 723] [Impact Index Per Article: 90.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 04/20/2016] [Accepted: 05/17/2016] [Indexed: 12/30/2022]
Abstract
Arabidopsis thaliana serves as a model organism for the study of fundamental physiological, cellular, and molecular processes. It has also greatly advanced our understanding of intraspecific genome variation. We present a detailed map of variation in 1,135 high-quality re-sequenced natural inbred lines representing the native Eurasian and North African range and recently colonized North America. We identify relict populations that continue to inhabit ancestral habitats, primarily in the Iberian Peninsula. They have mixed with a lineage that has spread to northern latitudes from an unknown glacial refugium and is now found in a much broader spectrum of habitats. Insights into the history of the species and the fine-scale distribution of genetic diversity provide the basis for full exploitation of A. thaliana natural variation through integration of genomes and epigenomes with molecular and non-molecular phenotypes.
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19
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Méndez-Vigo B, Savic M, Ausín I, Ramiro M, Martín B, Picó FX, Alonso-Blanco C. Environmental and genetic interactions reveal FLOWERING LOCUS C as a modulator of the natural variation for the plasticity of flowering in Arabidopsis. PLANT, CELL & ENVIRONMENT 2016; 39:282-94. [PMID: 26173848 DOI: 10.1111/pce.12608] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 06/30/2015] [Accepted: 07/02/2015] [Indexed: 05/12/2023]
Abstract
The timing of flowering initiation depends strongly on the environment, a property termed as the plasticity of flowering. Such plasticity determines the adaptive potential of plants because it provides phenotypic buffer against environmental changes, and its natural variation contributes to evolutionary adaptation. We addressed the genetic mechanisms of the natural variation for this plasticity in Arabidopsis thaliana by analysing a population of recombinant inbred lines derived from Don-0 and Ler accessions collected from distinct climates. Quantitative trait locus (QTL) mapping in four environmental conditions differing in photoperiod, vernalization treatment and ambient temperature detected the folllowing: (i) FLOWERING LOCUS C (FLC) as a large effect QTL affecting flowering time differentially in all environments; (ii) numerous QTL displaying smaller effects specifically in some conditions; and (iii) significant genetic interactions between FLC and other loci. Hence, the variation for the plasticity of flowering is determined by a combination of environmentally sensitive and specific QTL, and epistasis. Analysis of FLC from Don identified a new and more active allele likely caused by a cis-regulatory deletion covering the non-coding RNA COLDAIR. Further characterization of four FLC natural alleles showed different environmental and genetic interactions. Thus, FLC appears as a major modulator of the natural variation for the plasticity of flowering to multiple environmental factors.
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Affiliation(s)
- Belén Méndez-Vigo
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, 28049, Spain
| | - Marija Savic
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, 28049, Spain
| | - Israel Ausín
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, 28049, Spain
| | - Mercedes Ramiro
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, 28049, Spain
| | - Beatriz Martín
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, 28049, Spain
| | - F Xavier Picó
- Departamento de Ecología Integrativa, Estación Biológica de Doñana (EBD), Sevilla, 41092, Spain
| | - Carlos Alonso-Blanco
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, 28049, Spain
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20
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Yu X, Duan X, Zhang R, Fu X, Ye L, Kong H, Xu G, Shan H. Prevalent Exon-Intron Structural Changes in the APETALA1/FRUITFULL, SEPALLATA, AGAMOUS-LIKE6, and FLOWERING LOCUS C MADS-Box Gene Subfamilies Provide New Insights into Their Evolution. FRONTIERS IN PLANT SCIENCE 2016; 7:598. [PMID: 27200066 PMCID: PMC4852290 DOI: 10.3389/fpls.2016.00598] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 04/18/2016] [Indexed: 05/19/2023]
Abstract
AP1/FUL, SEP, AGL6, and FLC subfamily genes play important roles in flower development. The phylogenetic relationships among them, however, have been controversial, which impedes our understanding of the origin and functional divergence of these genes. One possible reason for the controversy may be the problems caused by changes in the exon-intron structure of genes, which, according to recent studies, may generate non-homologous sites and hamper the homology-based sequence alignment. In this study, we first performed exon-by-exon alignments of these and three outgroup subfamilies (SOC1, AG, and STK). Phylogenetic trees reconstructed based on these matrices show improved resolution and better congruence with species phylogeny. In the context of these phylogenies, we traced evolutionary changes of exon-intron structures in each subfamily. We found that structural changes have occurred frequently following gene duplication and speciation events. Notably, exons 7 and 8 (if present) suffered more structural changes than others. With the knowledge of exon-intron structural changes, we generated more reasonable alignments containing all the focal subfamilies. The resulting trees showed that the SEP subfamily is sister to the monophyletic group formed by AP1/FUL and FLC subfamily genes and that the AGL6 subfamily forms a sister group to the three abovementioned subfamilies. Based on this topology, we inferred the evolutionary history of exon-intron structural changes among different subfamilies. Particularly, we found that the eighth exon originated before the divergence of AP1/FUL, FLC, SEP, and AGL6 subfamilies and degenerated in the ancestral FLC-like gene. These results provide new insights into the origin and evolution of the AP1/FUL, FLC, SEP, and AGL6 subfamilies.
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Affiliation(s)
- Xianxian Yu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of SciencesBeijing, China
- University of Chinese Academy of SciencesBeijing, China
| | - Xiaoshan Duan
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of SciencesBeijing, China
- University of Chinese Academy of SciencesBeijing, China
| | - Rui Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of SciencesBeijing, China
| | - Xuehao Fu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of SciencesBeijing, China
- University of Chinese Academy of SciencesBeijing, China
| | - Lingling Ye
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of SciencesBeijing, China
- University of Chinese Academy of SciencesBeijing, China
| | - Hongzhi Kong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of SciencesBeijing, China
| | - Guixia Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of SciencesBeijing, China
- *Correspondence: Guixia Xu
| | - Hongyan Shan
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of SciencesBeijing, China
- Hongyan Shan
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21
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Li F, Chen B, Xu K, Gao G, Yan G, Qiao J, Li J, Li H, Li L, Xiao X, Zhang T, Nishio T, Wu X. A genome-wide association study of plant height and primary branch number in rapeseed (Brassica napus). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 242:169-177. [PMID: 26566834 DOI: 10.1016/j.plantsci.2015.05.012] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 05/14/2015] [Accepted: 05/17/2015] [Indexed: 05/18/2023]
Abstract
Crop plant architecture plays a highly important role in its agronomic performance. Plant height (PH) and primary branch number (PB) are two major factors that affect the plant architecture of rapeseed (Brassica napus). Previous studies have shown that these two traits are controlled by multiple quantitative trait loci (QTL); however, QTLs have not been delimited to regions less than 10cM. Genome-wide association study (GWAS) is a highly efficient approach for identifying genetic loci controlling traits at relatively high resolution. In this study, variations in PH and PB of a panel of 472 rapeseed accessions that had previously been analyzed by a 60k SNP array were investigated for three consecutive years and studied by GWAS. Eight QTLs on chromosome A03, A05, A07 and C07 were identified for PH, and five QTLs on A01, A03, A07 and C07 were identified for PB. Although most QTLs have been detected in previous studies based on linkage analyses, the two QTLs of PH on A05 and the QTL of PB on C07 were novel. In the genomic regions close to the GWAS peaks, orthologs of the genes involved in flower development, phytohormone biosynthesis, metabolism and signaling in Arabidopsis were identified.
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Affiliation(s)
- Feng Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China; Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori Amamiyamachi, Aoba-ku, Sendai, Miyagi 981-8555, Japan
| | - Biyun Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Kun Xu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Guizhen Gao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Guixin Yan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Jiangwei Qiao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Jun Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Hao Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Lixia Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Xin Xiao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Tianyao Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Takeshi Nishio
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori Amamiyamachi, Aoba-ku, Sendai, Miyagi 981-8555, Japan
| | - Xiaoming Wu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China.
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22
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Wang J, Joshi T, Valliyodan B, Shi H, Liang Y, Nguyen HT, Zhang J, Xu D. A Bayesian model for detection of high-order interactions among genetic variants in genome-wide association studies. BMC Genomics 2015; 16:1011. [PMID: 26607428 PMCID: PMC4660815 DOI: 10.1186/s12864-015-2217-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 11/16/2015] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND A central question for disease studies and crop improvements is how genetics variants drive phenotypes. Genome Wide Association Study (GWAS) provides a powerful tool for characterizing the genotype-phenotype relationships in complex traits and diseases. Epistasis (gene-gene interaction), including high-order interaction among more than two genes, often plays important roles in complex traits and diseases, but current GWAS analysis usually just focuses on additive effects of single nucleotide polymorphisms (SNPs). The lack of effective computational modelling of high-order functional interactions often leads to significant under-utilization of GWAS data. RESULTS We have developed a novel Bayesian computational method with a Markov Chain Monte Carlo (MCMC) search, and implemented the method as a Bayesian High-order Interaction Toolkit (BHIT) for detecting epistatic interactions among SNPs. BHIT first builds a Bayesian model on both continuous data and discrete data, which is capable of detecting high-order interactions in SNPs related to case--control or quantitative phenotypes. We also developed a pipeline that enables users to apply BHIT on different species in different use cases. CONCLUSIONS Using both simulation data and soybean nutritional seed composition studies on oil content and protein content, BHIT effectively detected some high-order interactions associated with phenotypes, and it outperformed a number of other available tools. BHIT is freely available for academic users at http://digbio.missouri.edu/BHIT/.
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Affiliation(s)
- Juexin Wang
- College of Computer Science and Technology, Jilin University, Changchun, Jilin, China.
- Department of Computer Science, Informatics Institute, and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA.
| | - Trupti Joshi
- Department of Computer Science, Informatics Institute, and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA.
| | - Babu Valliyodan
- Division of Plant Sciences and National Center for Soybean Biotechnology (NCSB), University of Missouri, Columbia, MO, USA.
| | - Haiying Shi
- Division of Plant Sciences and National Center for Soybean Biotechnology (NCSB), University of Missouri, Columbia, MO, USA.
| | - Yanchun Liang
- College of Computer Science and Technology, Jilin University, Changchun, Jilin, China.
- Department of Computer Science, Informatics Institute, and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA.
| | - Henry T Nguyen
- Division of Plant Sciences and National Center for Soybean Biotechnology (NCSB), University of Missouri, Columbia, MO, USA.
| | - Jing Zhang
- Department of Statistics, Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA.
- Department of Mathematics and Statistics, Georgia State University, Atlanta, GA, USA.
| | - Dong Xu
- College of Computer Science and Technology, Jilin University, Changchun, Jilin, China.
- Department of Computer Science, Informatics Institute, and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA.
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23
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Baron E, Richirt J, Villoutreix R, Amsellem L, Roux F. The genetics of intra‐ and interspecific competitive response and effect in a local population of an annual plant species. Funct Ecol 2015. [DOI: 10.1111/1365-2435.12436] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Etienne Baron
- Laboratoire Génétique et Evolution des Populations Végétales UMR CNRS 8198 Université des Sciences et Technologies de Lille – Lille 1 F‐59655 Villeneuve d'Ascq Cedex France
- INRA Laboratoire des Interactions Plantes‐Microorganismes (LIPM) UMR441 F‐31326 Castanet‐Tolosan France
- CNRS Laboratoire des Interactions Plantes‐Microorganismes (LIPM) UMR2594 F‐31326 Castanet‐Tolosan France
| | - Julien Richirt
- Laboratoire Génétique et Evolution des Populations Végétales UMR CNRS 8198 Université des Sciences et Technologies de Lille – Lille 1 F‐59655 Villeneuve d'Ascq Cedex France
| | - Romain Villoutreix
- Laboratoire Génétique et Evolution des Populations Végétales UMR CNRS 8198 Université des Sciences et Technologies de Lille – Lille 1 F‐59655 Villeneuve d'Ascq Cedex France
| | - Laurent Amsellem
- Laboratoire Génétique et Evolution des Populations Végétales UMR CNRS 8198 Université des Sciences et Technologies de Lille – Lille 1 F‐59655 Villeneuve d'Ascq Cedex France
| | - Fabrice Roux
- Laboratoire Génétique et Evolution des Populations Végétales UMR CNRS 8198 Université des Sciences et Technologies de Lille – Lille 1 F‐59655 Villeneuve d'Ascq Cedex France
- INRA Laboratoire des Interactions Plantes‐Microorganismes (LIPM) UMR441 F‐31326 Castanet‐Tolosan France
- CNRS Laboratoire des Interactions Plantes‐Microorganismes (LIPM) UMR2594 F‐31326 Castanet‐Tolosan France
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24
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Rameau C, Bertheloot J, Leduc N, Andrieu B, Foucher F, Sakr S. Multiple pathways regulate shoot branching. FRONTIERS IN PLANT SCIENCE 2015; 5:741. [PMID: 25628627 PMCID: PMC4292231 DOI: 10.3389/fpls.2014.00741] [Citation(s) in RCA: 163] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 12/05/2014] [Indexed: 05/18/2023]
Abstract
Shoot branching patterns result from the spatio-temporal regulation of axillary bud outgrowth. Numerous endogenous, developmental and environmental factors are integrated at the bud and plant levels to determine numbers of growing shoots. Multiple pathways that converge to common integrators are most probably involved. We propose several pathways involving not only the classical hormones auxin, cytokinins and strigolactones, but also other signals with a strong influence on shoot branching such as gibberellins, sugars or molecular actors of plant phase transition. We also deal with recent findings about the molecular mechanisms and the pathway involved in the response to shade as an example of an environmental signal controlling branching. We propose the TEOSINTE BRANCHED1, CYCLOIDEA, PCF transcription factor TB1/BRC1 and the polar auxin transport stream in the stem as possible integrators of these pathways. We finally discuss how modeling can help to represent this highly dynamic system by articulating knowledges and hypothesis and calculating the phenotype properties they imply.
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Affiliation(s)
- Catherine Rameau
- Institut Jean-Pierre Bourgin, INRA, UMR 1318, ERL CNRS 3559, Saclay Plant Sciences, Versailles, France
- Institut Jean-Pierre Bourgin, AgroParisTech, UMR 1318, ERL CNRS 3559, Saclay Plant Sciences, Versailles, France
| | | | - Nathalie Leduc
- UMR1345 IRHS, Université d’Angers, SFR 4207 QUASAV, Angers, France
| | - Bruno Andrieu
- UMR1091 EGC, INRA, Thiverval-Grignon, France
- UMR1091 EGC, AgroParisTech, Thiverval-Grignon, France
| | | | - Soulaiman Sakr
- UMR1345 IRHS, Agrocampus-Ouest, SFR 4207 QUASAV, Angers, France
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25
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Fletcher RS, Mullen JL, Heiliger A, McKay JK. QTL analysis of root morphology, flowering time, and yield reveals trade-offs in response to drought in Brassica napus. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:245-56. [PMID: 25371500 PMCID: PMC4265167 DOI: 10.1093/jxb/eru423] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 08/16/2014] [Accepted: 09/15/2014] [Indexed: 05/18/2023]
Abstract
Drought escape and dehydration avoidance represent alternative strategies for drought adaptation in annual crops. The mechanisms underlying these two strategies are reported to have a negative correlation, suggesting a trade-off. We conducted a quantitative trait locus (QTL) analysis of flowering time and root mass, traits representing each strategy, in Brassica napus to understand if a trade-off exists and what the genetic basis might be. Our field experiment used a genotyped population of doubled haploid lines and included both irrigated and rainfed treatments, allowing analysis of plasticity in each trait. We found strong genetic correlations among all traits, suggesting a trade-off among traits may exist. Summing across traits and treatments we found 20 QTLs, but many of these co-localized to two major QTLs, providing evidence that the trade-off is genetically constrained. To understand the mechanistic relationship between root mass, flowering time, and QTLs, we analysed the data by conditioning upon correlated traits. Our results suggest a causal model where such QTLs affect root mass directly as well as through their impacts on flowering time. Additionally, we used draft Brassica genomes to identify orthologues of well characterized Arabidopsis thaliana flowering time genes as candidate genes. This research provides valuable clues to breeding for drought adaptation as it is the first to analyse the inheritance of the root system in B. napus in relation to drought.
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Affiliation(s)
- Richard S Fletcher
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523, USA Cargill Specialty Seeds and Oils, Fort Collins, CO 80525, USA
| | - Jack L Mullen
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523, USA
| | - Annie Heiliger
- Cargill Specialty Seeds and Oils, Fort Collins, CO 80525, USA Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - John K McKay
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523, USA Plant Genomics LLC, Fort Collins, CO 80524, USA
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26
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Liu L, Adrian J, Pankin A, Hu J, Dong X, von Korff M, Turck F. Induced and natural variation of promoter length modulates the photoperiodic response of FLOWERING LOCUS T. Nat Commun 2014; 5:4558. [PMID: 25087553 PMCID: PMC4143923 DOI: 10.1038/ncomms5558] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 06/30/2014] [Indexed: 12/15/2022] Open
Abstract
FLOWERING LOCUS T (FT) regulates the floral transition in many plant species by integrating environmental seasonal signals and internal cues. Here we show that two interdependent regulatory regions are necessary and sufficient to convey photoperiod responsiveness to FT. While a minimal distance between the regulatory regions is required to fully suppress FT expression under short days, increased distance reduces promoter response to long days. Natural variation at FT creating promoter length differences is widespread, correlates with longitudinal and latitudinal clines and affects a promoter region physically interacting with both photoperiod control regions. Three major FT promoter variants correlate with differences in FT allele usage in F1 hybrids. We propose that FT variation in cis could be adaptive by conferring differences in FT transcriptional control ultimately translating to increased fitness. Gene expression at FLOWERING LOCUS T controls floral transition in many plants and is regulated by both environmental signals and internal cues. Liu et al. show that the distance between two regulatory sequences in the FT promoter varies with geographical location and determines responsiveness to photoperiod.
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Affiliation(s)
- Liangyu Liu
- 1] Max Planck Institute for Plant Breeding Research, Department of Plant Developmental Biology, Carl von Linne Weg 10, 50829 Cologne, Germany [2] Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan 650223, China [3] University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jessika Adrian
- 1] Max Planck Institute for Plant Breeding Research, Department of Plant Developmental Biology, Carl von Linne Weg 10, 50829 Cologne, Germany [2]
| | - Artem Pankin
- Max Planck Institute for Plant Breeding Research, Department of Plant Developmental Biology, Carl von Linne Weg 10, 50829 Cologne, Germany
| | - Jinyong Hu
- Max Planck Institute for Plant Breeding Research, Department of Plant Breeding and Genetics, Carl von Linne Weg 10, 50829 Cologne, Germany
| | - Xue Dong
- Max Planck Institute for Plant Breeding Research, Department of Plant Developmental Biology, Carl von Linne Weg 10, 50829 Cologne, Germany
| | - Maria von Korff
- 1] Max Planck Institute for Plant Breeding Research, Department of Plant Developmental Biology, Carl von Linne Weg 10, 50829 Cologne, Germany [2] Institute of Plant Genetics, Heinrich-Heine-University, Cluster of Excellence on Plant Sciences "From Complex Traits towards Synthetic Modules", 40225 Düsseldorf, Germany
| | - Franziska Turck
- Max Planck Institute for Plant Breeding Research, Department of Plant Developmental Biology, Carl von Linne Weg 10, 50829 Cologne, Germany
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27
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Chardon F, Jasinski S, Durandet M, Lécureuil A, Soulay F, Bedu M, Guerche P, Masclaux-Daubresse C. QTL meta-analysis in Arabidopsis reveals an interaction between leaf senescence and resource allocation to seeds. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:3949-62. [PMID: 24692652 PMCID: PMC4106442 DOI: 10.1093/jxb/eru125] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Sequential and monocarpic senescence are observed at vegetative and reproductive stages, respectively. Both facilitate nitrogen (N) remobilization and control the duration of carbon (C) fixation. Genetic and environmental factors control N and C resource allocation to seeds. Studies of natural variation in Arabidopsis thaliana revealed differences between accessions for leaf senescence phenotypes, seed N and C contents, and N remobilization efficiency-related traits. Here, a quantitative genetics approach was used to gain a better understanding of seed filling regulation in relation to leaf senescence and resource allocation. For that purpose, three Arabidopsis recombinant inbred line populations (Ct-1×Col-0, Cvi-0×Col-0, Bur-0×Col-0) were used to map QTL (quantitative trait loci) for ten traits related to senescence, resource allocation, and seed filling. The use of common markers across the three different maps allowed direct comparisons of the positions of the detected QTL in a single consensus map. QTL meta-analysis was then used to identify interesting regions (metaQTL) where QTL for several traits co-localized. MetaQTL were compared with positions of candidate genes known to be involved in senescence processes and flowering time. Finally, investigation of the correlation between yield and seed N concentration in the three populations suggests that leaf senescence disrupts the negative correlation generally observed between these two traits.
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Affiliation(s)
- Fabien Chardon
- UMR1318 INRA AgroParisTech, Institut Jean-Pierre Bourgin, INRA Versailles, Route Saint Cyr, 78026 Versailles Cedex, France
| | - Sophie Jasinski
- UMR1318 INRA AgroParisTech, Institut Jean-Pierre Bourgin, INRA Versailles, Route Saint Cyr, 78026 Versailles Cedex, France
| | - Monique Durandet
- UMR1318 INRA AgroParisTech, Institut Jean-Pierre Bourgin, INRA Versailles, Route Saint Cyr, 78026 Versailles Cedex, France
| | - Alain Lécureuil
- UMR1318 INRA AgroParisTech, Institut Jean-Pierre Bourgin, INRA Versailles, Route Saint Cyr, 78026 Versailles Cedex, France
| | - Fabienne Soulay
- UMR1318 INRA AgroParisTech, Institut Jean-Pierre Bourgin, INRA Versailles, Route Saint Cyr, 78026 Versailles Cedex, France
| | - Magali Bedu
- UMR1318 INRA AgroParisTech, Institut Jean-Pierre Bourgin, INRA Versailles, Route Saint Cyr, 78026 Versailles Cedex, France
| | - Philippe Guerche
- UMR1318 INRA AgroParisTech, Institut Jean-Pierre Bourgin, INRA Versailles, Route Saint Cyr, 78026 Versailles Cedex, France
| | - Céline Masclaux-Daubresse
- UMR1318 INRA AgroParisTech, Institut Jean-Pierre Bourgin, INRA Versailles, Route Saint Cyr, 78026 Versailles Cedex, France
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28
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Alonso-Blanco C, Méndez-Vigo B. Genetic architecture of naturally occurring quantitative traits in plants: an updated synthesis. CURRENT OPINION IN PLANT BIOLOGY 2014; 18:37-43. [PMID: 24565952 DOI: 10.1016/j.pbi.2014.01.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 01/20/2014] [Accepted: 01/26/2014] [Indexed: 05/08/2023]
Abstract
Deciphering the genetic and molecular bases of quantitative variation is a long-standing challenge in plant biology because it is essential for understanding evolution and for accelerating plant breeding. Recent multi-trait analyses at different phenotypic levels are uncovering the pleiotropy and the genetic regulation underlying high-level complex traits. Thus, the number of known causal loci, genes and nucleotide polymorphisms is expanding. Current plant causal catalogs contain ∼400 genes and natural polymorphisms revealing several dysfunctional allelic series that involve multiple mutations. In addition, repeated evolution of quantitative traits mediated by large effect alleles is found across plant phylogeny. Finally, systematic analyses of genetic and environmental interactions are beginning to elucidate the molecular mechanisms of relevant interactions.
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Affiliation(s)
- Carlos Alonso-Blanco
- Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Darwin 3, Madrid 28049, Spain.
| | - Belén Méndez-Vigo
- Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Darwin 3, Madrid 28049, Spain
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29
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Liu L, Farrona S, Klemme S, Turck FK. Post-fertilization expression of FLOWERING LOCUS T suppresses reproductive reversion. FRONTIERS IN PLANT SCIENCE 2014; 5:164. [PMID: 24817870 PMCID: PMC4012189 DOI: 10.3389/fpls.2014.00164] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 04/07/2014] [Indexed: 05/08/2023]
Abstract
FLOWERING LOCUS T (FT) encodes a systemic signal communicating the perception of long day photoperiod from leaves to the shoot apex to induce the floral transition. Transient expression of FT in the phloem companion cells of rosette leaves for one to several days was previously shown to be sufficient to commit plants to flowering. Here we show that partial commitment results in pleiotropic inflorescence meristem reversion phenotypes. FT expression is much stronger in organs formed after the floral transition such as cauline leaves, sepals, and developing siliques. We show that expression of FT and its paralog TWIN SISTER OF FT (TSF) after the floral transition plays a role in inflorescence meristem stabilization even if plants flower very late in development. CONSTANS (CO), the major activator of FT, is not required to prevent late reproductive reversion. The requirement for FT is temporal since reproductive reversion to a vegetative state occurs only in recently formed inflorescence meristems. Unlike for the expression of FT in leaves, neither the distal putative FT enhancer nor long-day photoperiod is required for FT expression in developing siliques. Expression of FT in developing siliques and their supporting stems is sufficient to stabilize flowering during the sensitive developmental window indicating that fruit generated FT participates in inflorescence stabilization.
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Affiliation(s)
- Liangyu Liu
- Max Planck Institute for Plant Breeding Research, Carl von Linné Weg 10Cologne, Germany
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, KunmingYunnan, China
- University of Chinese Academy of SciencesBeijing, China
| | - Sara Farrona
- Max Planck Institute for Plant Breeding Research, Carl von Linné Weg 10Cologne, Germany
| | - Sonja Klemme
- Max Planck Institute for Plant Breeding Research, Carl von Linné Weg 10Cologne, Germany
| | - Franziska K. Turck
- Max Planck Institute for Plant Breeding Research, Carl von Linné Weg 10Cologne, Germany
- *Correspondence: Franziska K. Turck, Max Planck Institute for Plant Breeding Research, Carl von Linné Weg 10, Köln, NRW, Germany e-mail:
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