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Wijnen CL, Botet R, van de Belt J, Deurhof L, de Jong H, de Snoo CB, Dirks R, Boer MP, van Eeuwijk FA, Wijnker E, Keurentjes JJB. A complete chromosome substitution mapping panel reveals genome-wide epistasis in Arabidopsis. Heredity (Edinb) 2024:10.1038/s41437-024-00705-1. [PMID: 38982296 DOI: 10.1038/s41437-024-00705-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 07/02/2024] [Accepted: 07/03/2024] [Indexed: 07/11/2024] Open
Abstract
Chromosome substitution lines (CSLs) are tentatively supreme resources to investigate non-allelic genetic interactions. However, the difficulty of generating such lines in most species largely yielded imperfect CSL panels, prohibiting a systematic dissection of epistasis. Here, we present the development and use of a unique and complete panel of CSLs in Arabidopsis thaliana, allowing the full factorial analysis of epistatic interactions. A first comparison of reciprocal single chromosome substitutions revealed a dependency of QTL detection on different genetic backgrounds. The subsequent analysis of the complete panel of CSLs enabled the mapping of the genetic interactors and identified multiple two- and three-way interactions for different traits. Some of the detected epistatic effects were as large as any observed main effect, illustrating the impact of epistasis on quantitative trait variation. We, therefore, have demonstrated the high power of detection and mapping of genome-wide epistasis, confirming the assumed supremacy of comprehensive CSL sets.
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Affiliation(s)
- Cris L Wijnen
- Wageningen University and Research, Laboratory of Genetics, Wageningen, The Netherlands
| | - Ramon Botet
- Wageningen University and Research, Laboratory of Genetics, Wageningen, The Netherlands
| | - José van de Belt
- Wageningen University and Research, Laboratory of Genetics, Wageningen, The Netherlands
| | - Laurens Deurhof
- Wageningen University and Research, Laboratory of Genetics, Wageningen, The Netherlands
| | - Hans de Jong
- Wageningen University and Research, Laboratory of Genetics, Wageningen, The Netherlands
| | | | - Rob Dirks
- Rijk Zwaan, Molecular Biology Research, Fijnaart, The Netherlands
- Managerial Genetics Consulting, Maaseik, Belgium
| | - Martin P Boer
- Wageningen University and Research, Biometris, Wageningen, The Netherlands
| | - Fred A van Eeuwijk
- Wageningen University and Research, Biometris, Wageningen, The Netherlands
| | - Erik Wijnker
- Wageningen University and Research, Laboratory of Genetics, Wageningen, The Netherlands
| | - Joost J B Keurentjes
- Wageningen University and Research, Laboratory of Genetics, Wageningen, The Netherlands.
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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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Lee E, Yang X, Ha J, Kim MY, Park KY, Lee SH. Identification of a Locus Controlling Compound Raceme Inflorescence in Mungbean [ Vigna radiata (L.) R. Wilczek]. Front Genet 2021; 12:642518. [PMID: 33763121 PMCID: PMC7982598 DOI: 10.3389/fgene.2021.642518] [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: 12/16/2020] [Accepted: 02/16/2021] [Indexed: 11/13/2022] Open
Abstract
Mungbean [Vigna radiata (L.) R. Wilczek] produces a compound raceme inflorescence that branches into secondary inflorescences, which produce flowers. This architecture results in the less-domesticated traits of asynchronous pod maturity and multiple harvest times. This study identified the genetic factors responsible for the compound raceme of mungbean, providing a unique biological opportunity to improve simultaneous flowering. Using a recombinant inbred line (RIL) population derived from VC1973A, an elite cultivar with a compound raceme type, and IT208075, a natural mutant with a simple raceme type, a single locus that determined the inflorescence type was identified based on 1:1 segregation ratio in the F8 generation, and designated Comraceme. Linkage map analysis showed Comraceme was located on chromosome 4 within a marker interval spanning 520 kb and containing 64 genes. RILs carrying heterozygous fragments around Comraceme produced compound racemes, indicating this form was dominant to the simple raceme type. Quantitative trait loci related to plant architecture and inflorescence have been identified in genomic regions of soybean syntenic to Comraceme. In IT208075, 15 genes were present as distinct variants not observed in other landrace varieties or wild mungbean. These genes included Vradi04g00002481, a development-related gene encoding a B3 transcriptional factor. The upstream region of Vradi04g00002481 differed between lines producing the simple and compound types of raceme. Expression of Vradi04g00002481 was significantly lower at the early vegetative stage and higher at the early reproductive stage, in IT208075 than in VC1973A. Vradi04g00002481 was therefore likely to determine inflorescence type in mungbean. Although further study is required to determine the functional mechanism, this finding provides valuable genetic information for understanding the architecture of the compound raceme in mungbean.
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Affiliation(s)
- Eunsoo Lee
- Department of Agriculture, Forestry and Bioresources and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Xuefei Yang
- Department of Agriculture, Forestry and Bioresources and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea.,Plant Genomics and Breeding Institute, Seoul National University, Seoul, South Korea
| | - Jungmin Ha
- Department of Plant Science, Gangneung-Wonju National University, Gangneung, South Korea
| | - Moon Young Kim
- Department of Agriculture, Forestry and Bioresources and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea.,Plant Genomics and Breeding Institute, Seoul National University, Seoul, South Korea
| | - Keum Yong Park
- Department of Agriculture, Forestry and Bioresources and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea.,Plant Genomics and Breeding Institute, Seoul National University, Seoul, South Korea
| | - Suk-Ha Lee
- Department of Agriculture, Forestry and Bioresources and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea.,Plant Genomics and Breeding Institute, Seoul National University, Seoul, South Korea
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Gupta A, Jaiswal V, Sawant SV, Yadav HK. Mapping QTLs for 15 morpho-metric traits in Arabidopsis thaliana using Col-0 × Don-0 population. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:1021-1034. [PMID: 32377050 PMCID: PMC7196571 DOI: 10.1007/s12298-020-00800-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 01/24/2020] [Accepted: 03/17/2020] [Indexed: 05/13/2023]
Abstract
Genome wide quantitative trait loci (QTL) mapping was conducted in Arabidopsis thaliana using F2 mapping population (Col-0 × Don-0) and SNPs markers. A total of five linkage groups were obtained with number of SNPs varying from 45 to 59 per linkage group. The composite interval mapping detected a total of 36 QTLs for 15 traits and the number of QTLs ranged from one (root length, root dry biomass, cauline leaf width, number of internodes and internode distance) to seven (for bolting days). The range of phenotypic variance explained (PVE) and logarithm of the odds ratio of these 36 QTLs was found be 0.19-38.17% and 3.0-6.26 respectively. Further, the epistatic interaction detected one main effect QTL and four epistatic QTLs. Five major QTLs viz. Qbd.nbri.4.3, Qfd.nbri.4.2, Qrdm.nbri.5.1, Qncl.nbri.2.2, Qtd.nbri.4.1 with PVE > 15.0% might be useful for fine mapping to identify genes associated with respective traits, and also for development of specialized population through marker assisted selection. The identification of additive and dominant effect QTLs and desirable alleles of each of above mentioned traits would also be important for future research.
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Affiliation(s)
- Astha Gupta
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, UP 226 001 India
- Academy of Scientific and Innovative Research (AcSIR), New Delhi, 110 025 India
- Department of Botany, University of Delhi, New Delhi, 110 007 India
| | - Vandana Jaiswal
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, UP 226 001 India
| | - Samir V. Sawant
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, UP 226 001 India
- Academy of Scientific and Innovative Research (AcSIR), New Delhi, 110 025 India
| | - Hemant Kumar Yadav
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, UP 226 001 India
- Academy of Scientific and Innovative Research (AcSIR), New Delhi, 110 025 India
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5
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Genetic Analysis of the Transition from Wild to Domesticated Cotton ( Gossypium hirsutum L.). G3-GENES GENOMES GENETICS 2020; 10:731-754. [PMID: 31843806 PMCID: PMC7003101 DOI: 10.1534/g3.119.400909] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The evolution and domestication of cotton is of great interest from both economic and evolutionary standpoints. Although many genetic and genomic resources have been generated for cotton, the genetic underpinnings of the transition from wild to domesticated cotton remain poorly known. Here we generated an intraspecific QTL mapping population specifically targeting domesticated cotton phenotypes. We used 466 F2 individuals derived from an intraspecific cross between the wild Gossypium hirsutum var. yucatanense (TX2094) and the elite cultivar G. hirsutum cv. Acala Maxxa, in two environments, to identify 120 QTL associated with phenotypic changes under domestication. While the number of QTL recovered in each subpopulation was similar, only 22 QTL were considered coincident (i.e., shared) between the two locations, eight of which shared peak markers. Although approximately half of QTL were located in the A-subgenome, many key fiber QTL were detected in the D-subgenome, which was derived from a species with unspinnable fiber. We found that many QTL are environment-specific, with few shared between the two environments, indicating that QTL associated with G. hirsutum domestication are genomically clustered but environmentally labile. Possible candidate genes were recovered and are discussed in the context of the phenotype. We conclude that the evolutionary forces that shape intraspecific divergence and domestication in cotton are complex, and that phenotypic transformations likely involved multiple interacting and environmentally responsive factors.
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Rubin MJ, Brock MT, Davis SJ, Weinig C. QTL Underlying Circadian Clock Parameters Under Seasonally Variable Field Settings in Arabidopsis thaliana. G3 (BETHESDA, MD.) 2019; 9:1131-1139. [PMID: 30755409 PMCID: PMC6469418 DOI: 10.1534/g3.118.200770] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 02/06/2019] [Indexed: 11/18/2022]
Abstract
The circadian clock facilitates coordination of the internal rhythms of an organism to daily environmental conditions, such as the light-dark cycle of one day. Circadian period length (the duration of one endogenous cycle) and phase (the timing of peak activity) exhibit quantitative variation in natural populations. Here, we measured circadian period and phase in June, July and September in three Arabidopsis thaliana recombinant inbred line populations. Circadian period and phase were estimated from bioluminescence of a genetic construct between a native circadian clock gene (COLD CIRCADIAN RHYTHM RNA BINDING 2) and the reporter gene (LUCIFERASE) after lines were entrained under field settings. Using a Bayesian mapping approach, we estimated the median number and effect size of genomic regions (Quantitative Trait Loci, QTL) underlying circadian parameters and the degree to which these regions overlap across months of the growing season. We also tested for QTL associations between the circadian clock and plant morphology. The genetic architecture of circadian phase was largely independent across months, as evidenced by the fact that QTL determining phase values in one month of the growing season were different from those determining phase in a second month. QTL for circadian parameters were shared with both cauline and rosette branching in at least one mapping population. The results provide insights into the QTL architecture of the clock under field settings, and suggest that the circadian clock is highly responsive to changing environments and that selection can act on clock phase in a nuanced manner.
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Affiliation(s)
- Matthew J Rubin
- Department of Botany, University of Wyoming, Laramie, WY 82071
- Program in Ecology, University of Wyoming, Laramie, WY 82071
| | - Marcus T Brock
- Department of Botany, University of Wyoming, Laramie, WY 82071
| | - Seth J Davis
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - Cynthia Weinig
- Department of Botany, University of Wyoming, Laramie, WY 82071
- Program in Ecology, University of Wyoming, Laramie, WY 82071
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071
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Ojangu EL, Ilau B, Tanner K, Talts K, Ihoma E, Dolja VV, Paves H, Truve E. Class XI Myosins Contribute to Auxin Response and Senescence-Induced Cell Death in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2018; 9:1570. [PMID: 30538710 PMCID: PMC6277483 DOI: 10.3389/fpls.2018.01570] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 10/08/2018] [Indexed: 05/24/2023]
Abstract
The integrity and dynamics of actin cytoskeleton is necessary not only for plant cell architecture but also for membrane trafficking-mediated processes such as polar auxin transport, senescence, and cell death. In Arabidopsis, the inactivation of actin-based molecular motors, class XI myosins, affects the membrane trafficking and integrity of actin cytoskeleton, and thus causes defective plant growth and morphology, altered lifespan and reduced fertility. To evaluate the potential contribution of class XI myosins to the auxin response, senescence and cell death, we followed the flower and leaf development in the triple gene knockout mutant xi1 xi2 xik (3KO) and in rescued line stably expressing myosin XI-K:YFP (3KOR). Assessing the development of primary inflorescence shoots we found that the 3KO plants produced more axillary branches. Exploiting the auxin-dependent reporters DR5::GUS and IAA2::GUS, a significant reduction in auxin responsiveness was found throughout the development of the 3KO plants. Examination of the flower development of the plants stably expressing the auxin transporter PIN1::PIN1-GFP revealed partial loss of PIN1 polarization in developing 3KO pistils. Surprisingly, the stable expression of PIN1::PIN1-GFP significantly enhanced the semi-sterile phenotype of the 3KO plants. Further we investigated the localization of myosin XI-K:YFP in the 3KOR floral organs and revealed its expression pattern in floral primordia, developing pistils, and anther filaments. Interestingly, the XI-K:YFP and PIN1::PIN1-GFP shared partially overlapping but distinct expression patterns throughout floral development. Assessing the foliar development of the 3KO plants revealed increased rosette leaf production with signs of premature yellowing. Symptoms of the premature senescence correlated with massive loss of chlorophyll, increased cell death, early plasmolysis of epidermal cells, and strong up-regulation of the stress-inducible senescence-associated gene SAG13 in 3KO plants. Simultaneously, the reduced auxin responsiveness and premature leaf senescence were accompanied by significant anthocyanin accumulation in 3KO tissues. Collectively, our results provide genetic evidences that Arabidopsis class XI myosins arrange the flower morphogenesis and leaf longevity via contributing to auxin responses, leaf senescence, and cell death.
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Affiliation(s)
- Eve-Ly Ojangu
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Birger Ilau
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Krista Tanner
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Kristiina Talts
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Eliis Ihoma
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Valerian V. Dolja
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Heiti Paves
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Erkki Truve
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
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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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Zhang YY, Latzel V, Fischer M, Bossdorf O. Understanding the evolutionary potential of epigenetic variation: a comparison of heritable phenotypic variation in epiRILs, RILs, and natural ecotypes of Arabidopsis thaliana. Heredity (Edinb) 2018; 121:257-265. [PMID: 29875373 PMCID: PMC6082859 DOI: 10.1038/s41437-018-0095-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 05/08/2018] [Accepted: 05/16/2018] [Indexed: 11/08/2022] Open
Abstract
Increasing evidence for epigenetic variation within and among natural plant populations has led to much speculation about its role in the evolution of plant phenotypes. However, we still have a very limited understanding of the evolutionary potential of epigenetic variation, in particular in comparison to DNA sequence-based variation. To address this question, we compared the magnitudes of heritable phenotypic variation in epigenetic recombinant inbred lines (epiRILs) of Arabidopsis thaliana-lines that mainly differ in DNA methylation but only very little in DNA sequence-with other types of A. thaliana lines that differ strongly also in DNA sequence. We grew subsets of two epiRIL populations with subsets of two genetic RIL populations, of natural ecotype collections, and of lines from a natural population in a common environment and assessed their heritable variation in growth, phenology, and fitness. Among-line phenotypic variation and broad-sense heritabilities tended to be largest in natural ecotypes, but for some traits the variation among epiRILs was comparable to that among RILs and natural ecotypes. Within-line phenotypic variation was generally similar in epiRILs, RILs, and ecotypes. Provided that phenotypic variation in epiRILs is mainly caused by epigenetic differences, whereas in RILs and natural lines it is largely driven by sequence variation, our results indicate that epigenetic variation has the potential to create phenotypic variation that is stable and substantial, and thus of evolutionary significance.
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Affiliation(s)
- Yuan-Ye Zhang
- Institute of Plant Sciences, University of Bern, CH-3013, Bern, Switzerland.
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China.
| | - Vit Latzel
- Institute of Plant Sciences, University of Bern, CH-3013, Bern, Switzerland
- Institute of Botany of the ASCR, CZ-252 43, Průhonice, Czech Republic
| | - Markus Fischer
- Institute of Plant Sciences, University of Bern, CH-3013, Bern, Switzerland
| | - Oliver Bossdorf
- Institute of Plant Sciences, University of Bern, CH-3013, Bern, Switzerland
- Plant Evolutionary Ecology, University of Tübingen, D-72076, Tübingen, Germany
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Theißen G, Rümpler F, Gramzow L. Array of MADS-Box Genes: Facilitator for Rapid Adaptation? TRENDS IN PLANT SCIENCE 2018; 23:563-576. [PMID: 29802068 DOI: 10.1016/j.tplants.2018.04.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 04/24/2018] [Accepted: 04/25/2018] [Indexed: 05/18/2023]
Abstract
In a world of global warming, the question emerges whether all plants have suitable mechanisms to keep pace with the rapidly changing environment. Most previous studies have focused on either the ability of plants to rapidly acclimatize via physiological and developmental plasticity, or long-term adaptation over thousands of years. However, we wonder whether plants can also adapt to changes in the environment within only a few generations. We hypothesize that rapidly evolving clusters of tandemly duplicated developmental control genes represent a source for fast adaptation. Specifically, we propose that a tandem cluster of FLC-like MADS-box genes involved in the transition to flowering in Arabidopsis functions as a facilitator for rapid adaptation to changes in ambient temperature.
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Affiliation(s)
- Günter Theißen
- Friedrich Schiller University Jena, Matthias Schleiden Institute for Genetics, Bioinformatics and Molecular Botany, Philosophenweg 12, D-07743 Jena, Germany.
| | - Florian Rümpler
- Friedrich Schiller University Jena, Matthias Schleiden Institute for Genetics, Bioinformatics and Molecular Botany, Philosophenweg 12, D-07743 Jena, Germany
| | - Lydia Gramzow
- Friedrich Schiller University Jena, Matthias Schleiden Institute for Genetics, Bioinformatics and Molecular Botany, Philosophenweg 12, D-07743 Jena, Germany
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11
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Su J, Yang X, Zhang F, Wu S, Xiong S, Shi L, Guan Z, Fang W, Chen F. Dynamic and epistatic QTL mapping reveals the complex genetic architecture of waterlogging tolerance in chrysanthemum. PLANTA 2018; 247:899-924. [PMID: 29273861 DOI: 10.1007/s00425-017-2833-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 12/14/2017] [Indexed: 05/21/2023]
Abstract
37 unconditional QTLs, 51 conditional QTLs and considerable epistatic QTLs were detected for waterlogging tolerance, and six favourable combinations were selected accelerating the possible application of MAS in chrysanthemum breeding. Chrysanthemum is seriously impacted by soil waterlogging. To determine the genetic characteristics of waterlogging tolerance (WAT) in chrysanthemum, a population of 162 F1 lines was used to construct a genetic map to identify the dynamic and epistatic quantitative trait loci (QTLs) for four WAT traits: wilting index (WI), dead leaf ratio (DLR), chlorosis score (Score) and membership function value of waterlogging (MFVW). The h B2 for the WAT traits ranged from 0.49 to 0.64, and transgressive segregation was observed in both directions. A total of 37 unconditional consensus QTLs with 5.81-18.21% phenotypic variation explanation (PVE) and 51 conditional consensus QTLs with 5.90-24.56% PVE were detected. Interestingly, three unconditional consensus QTLs were consistently identified across different stages, whereas no conditional consensus QTLs were consistently expressed. In addition, considerable epistatic QTLs, all with PVE values ranging from 0.01 to 8.87%, were detected by a joint analysis of WAT phenotypes. These results illustrated that the QTLs (genes) controlling WAT were environmentally dependent and selectively expressed at different times and indicated that both additive and epistatic effects underlie the inheritance of WAT in chrysanthemum. The findings of the current study provide insights into the complex genetic architecture of WAT, and the identification of favourable alleles represents an important step towards the application of molecular marker-assisted selection (MAS) and QTL pyramiding in chrysanthemum WAT breeding programmes.
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Affiliation(s)
- Jiangshuo Su
- Key Laboratory of Landscape Agriculture, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Xincheng Yang
- Key Laboratory of Landscape Agriculture, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Fei Zhang
- Key Laboratory of Landscape Agriculture, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Shaofang Wu
- Key Laboratory of Landscape Agriculture, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Siyi Xiong
- Key Laboratory of Landscape Agriculture, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Liming Shi
- Key Laboratory of Landscape Agriculture, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Zhiyong Guan
- Key Laboratory of Landscape Agriculture, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Weimin Fang
- Key Laboratory of Landscape Agriculture, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Fadi Chen
- Key Laboratory of Landscape Agriculture, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, People's Republic of China.
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12
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Distributions of Mutational Effects and the Estimation of Directional Selection in Divergent Lineages of Arabidopsis thaliana. Genetics 2017; 206:2105-2117. [PMID: 28550014 DOI: 10.1534/genetics.116.199190] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 05/22/2017] [Indexed: 12/22/2022] Open
Abstract
Mutations are crucial to evolution, providing the ultimate source of variation on which natural selection acts. Due to their key role, the distribution of mutational effects on quantitative traits is a key component to any inference regarding historical selection on phenotypic traits. In this paper, we expand on a previously developed test for selection that could be conducted assuming a Gaussian mutation effect distribution by developing approaches to also incorporate any of a family of heavy-tailed Laplace distributions of mutational effects. We apply the test to detect directional natural selection on five traits along the divergence of Columbia and Landsberg lineages of Arabidopsis thaliana, constituting the first test for natural selection in any organism using quantitative trait locus and mutation accumulation data to quantify the intensity of directional selection on a phenotypic trait. We demonstrate that the results of the test for selection can depend on the mutation effect distribution specified. Using the distributions exhibiting the best fit to mutation accumulation data, we infer that natural directional selection caused divergence in the rosette diameter and trichome density traits of the Columbia and Landsberg lineages.
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13
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Yuan W, Flowers JM, Sahraie DJ, Ehrenreich IM, Purugganan MD. Extreme QTL mapping of germination speed in Arabidopsis thaliana. Mol Ecol 2016; 25:4177-96. [DOI: 10.1111/mec.13768] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2015] [Revised: 07/01/2016] [Accepted: 07/06/2016] [Indexed: 12/21/2022]
Affiliation(s)
- Wei Yuan
- Department of Biology; Center for Genomics and Systems Biology; New York University; 12 Waverly Place New York NY 10003 USA
| | - Jonathan M. Flowers
- Department of Biology; Center for Genomics and Systems Biology; New York University; 12 Waverly Place New York NY 10003 USA
- Center for Genomics and Systems Biology; NYU Abu Dhabi Research Institute; New York University Abu Dhabi; Saadiyat Island Abu Dhabi United Arab Emirates
| | - Dustin J. Sahraie
- Department of Biology; Center for Genomics and Systems Biology; New York University; 12 Waverly Place New York NY 10003 USA
| | - Ian M. Ehrenreich
- Molecular and Computational Biology Section; University of Southern California; Ray R. Irani Hall 201 Los Angeles CA 90089-2910 USA
| | - Michael D. Purugganan
- Department of Biology; Center for Genomics and Systems Biology; New York University; 12 Waverly Place New York NY 10003 USA
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14
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Kooke R, Kruijer W, Bours R, Becker F, Kuhn A, van de Geest H, Buntjer J, Doeswijk T, Guerra J, Bouwmeester H, Vreugdenhil D, Keurentjes JJB. Genome-Wide Association Mapping and Genomic Prediction Elucidate the Genetic Architecture of Morphological Traits in Arabidopsis. PLANT PHYSIOLOGY 2016; 170:2187-203. [PMID: 26869705 PMCID: PMC4825126 DOI: 10.1104/pp.15.00997] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 02/11/2016] [Indexed: 05/05/2023]
Abstract
Quantitative traits in plants are controlled by a large number of genes and their interaction with the environment. To disentangle the genetic architecture of such traits, natural variation within species can be explored by studying genotype-phenotype relationships. Genome-wide association studies that link phenotypes to thousands of single nucleotide polymorphism markers are nowadays common practice for such analyses. In many cases, however, the identified individual loci cannot fully explain the heritability estimates, suggesting missing heritability. We analyzed 349 Arabidopsis accessions and found extensive variation and high heritabilities for different morphological traits. The number of significant genome-wide associations was, however, very low. The application of genomic prediction models that take into account the effects of all individual loci may greatly enhance the elucidation of the genetic architecture of quantitative traits in plants. Here, genomic prediction models revealed different genetic architectures for the morphological traits. Integrating genomic prediction and association mapping enabled the assignment of many plausible candidate genes explaining the observed variation. These genes were analyzed for functional and sequence diversity, and good indications that natural allelic variation in many of these genes contributes to phenotypic variation were obtained. For ACS11, an ethylene biosynthesis gene, haplotype differences explaining variation in the ratio of petiole and leaf length could be identified.
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Affiliation(s)
- Rik Kooke
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., R.B., A.K., H.B., D.V.); Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., F.B., J.J.B.K.); Centre for Biosystems Genomics, Wageningen Campus, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., H.v.d.G., D.V., J.J.B.K); Biometris, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (W.K.); PRI Bioinformatics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (H.v.d.G.); and Keygene, Agro Business Park 90, 6708 PW Wageningen, the Netherlands (J.B., T.D., J.G.)
| | - Willem Kruijer
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., R.B., A.K., H.B., D.V.); Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., F.B., J.J.B.K.); Centre for Biosystems Genomics, Wageningen Campus, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., H.v.d.G., D.V., J.J.B.K); Biometris, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (W.K.); PRI Bioinformatics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (H.v.d.G.); and Keygene, Agro Business Park 90, 6708 PW Wageningen, the Netherlands (J.B., T.D., J.G.)
| | - Ralph Bours
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., R.B., A.K., H.B., D.V.); Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., F.B., J.J.B.K.); Centre for Biosystems Genomics, Wageningen Campus, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., H.v.d.G., D.V., J.J.B.K); Biometris, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (W.K.); PRI Bioinformatics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (H.v.d.G.); and Keygene, Agro Business Park 90, 6708 PW Wageningen, the Netherlands (J.B., T.D., J.G.)
| | - Frank Becker
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., R.B., A.K., H.B., D.V.); Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., F.B., J.J.B.K.); Centre for Biosystems Genomics, Wageningen Campus, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., H.v.d.G., D.V., J.J.B.K); Biometris, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (W.K.); PRI Bioinformatics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (H.v.d.G.); and Keygene, Agro Business Park 90, 6708 PW Wageningen, the Netherlands (J.B., T.D., J.G.)
| | - André Kuhn
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., R.B., A.K., H.B., D.V.); Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., F.B., J.J.B.K.); Centre for Biosystems Genomics, Wageningen Campus, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., H.v.d.G., D.V., J.J.B.K); Biometris, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (W.K.); PRI Bioinformatics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (H.v.d.G.); and Keygene, Agro Business Park 90, 6708 PW Wageningen, the Netherlands (J.B., T.D., J.G.)
| | - Henri van de Geest
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., R.B., A.K., H.B., D.V.); Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., F.B., J.J.B.K.); Centre for Biosystems Genomics, Wageningen Campus, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., H.v.d.G., D.V., J.J.B.K); Biometris, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (W.K.); PRI Bioinformatics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (H.v.d.G.); and Keygene, Agro Business Park 90, 6708 PW Wageningen, the Netherlands (J.B., T.D., J.G.)
| | - Jaap Buntjer
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., R.B., A.K., H.B., D.V.); Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., F.B., J.J.B.K.); Centre for Biosystems Genomics, Wageningen Campus, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., H.v.d.G., D.V., J.J.B.K); Biometris, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (W.K.); PRI Bioinformatics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (H.v.d.G.); and Keygene, Agro Business Park 90, 6708 PW Wageningen, the Netherlands (J.B., T.D., J.G.)
| | - Timo Doeswijk
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., R.B., A.K., H.B., D.V.); Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., F.B., J.J.B.K.); Centre for Biosystems Genomics, Wageningen Campus, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., H.v.d.G., D.V., J.J.B.K); Biometris, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (W.K.); PRI Bioinformatics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (H.v.d.G.); and Keygene, Agro Business Park 90, 6708 PW Wageningen, the Netherlands (J.B., T.D., J.G.)
| | - José Guerra
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., R.B., A.K., H.B., D.V.); Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., F.B., J.J.B.K.); Centre for Biosystems Genomics, Wageningen Campus, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., H.v.d.G., D.V., J.J.B.K); Biometris, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (W.K.); PRI Bioinformatics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (H.v.d.G.); and Keygene, Agro Business Park 90, 6708 PW Wageningen, the Netherlands (J.B., T.D., J.G.)
| | - Harro Bouwmeester
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., R.B., A.K., H.B., D.V.); Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., F.B., J.J.B.K.); Centre for Biosystems Genomics, Wageningen Campus, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., H.v.d.G., D.V., J.J.B.K); Biometris, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (W.K.); PRI Bioinformatics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (H.v.d.G.); and Keygene, Agro Business Park 90, 6708 PW Wageningen, the Netherlands (J.B., T.D., J.G.)
| | - Dick Vreugdenhil
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., R.B., A.K., H.B., D.V.); Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., F.B., J.J.B.K.); Centre for Biosystems Genomics, Wageningen Campus, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., H.v.d.G., D.V., J.J.B.K); Biometris, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (W.K.); PRI Bioinformatics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (H.v.d.G.); and Keygene, Agro Business Park 90, 6708 PW Wageningen, the Netherlands (J.B., T.D., J.G.)
| | - Joost J B Keurentjes
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., R.B., A.K., H.B., D.V.); Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., F.B., J.J.B.K.); Centre for Biosystems Genomics, Wageningen Campus, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., H.v.d.G., D.V., J.J.B.K); Biometris, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (W.K.); PRI Bioinformatics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (H.v.d.G.); and Keygene, Agro Business Park 90, 6708 PW Wageningen, the Netherlands (J.B., T.D., J.G.)
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15
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Carvalho LC, Coito JL, Gonçalves EF, Chaves MM, Amâncio S. Differential physiological response of the grapevine varieties Touriga Nacional and Trincadeira to combined heat, drought and light stresses. PLANT BIOLOGY (STUTTGART, GERMANY) 2016; 18 Suppl 1:101-11. [PMID: 26518605 DOI: 10.1111/plb.12410] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 10/19/2015] [Indexed: 05/06/2023]
Abstract
Worldwide, extensive agricultural losses are attributed to drought, often in combination with heat in Mediterranean climate regions, where grapevine traditionally grows. The available scenarios for climate change suggest increases in aridity in these regions. Under natural conditions plants are affected by a combination of stresses, triggering synergistic or antagonistic physiological, metabolic or transcriptomic responses unique to the combination. However the study of such stresses in a controlled environment can elucidate important mechanisms by allowing the separation of the effects of individual stresses. To gather those effects, cuttings of two grapevine varieties, Touriga Nacional (TN) and Trincadeira (TR), were grown under controlled conditions and subjected to three abiotic stresses (drought - WS, heat - HS and high light - LS) individually and in combination two-by-two (WSHS, WSLS, HSLS) or all three (WSHSLS). Photosynthesis, water status, contents of H2 O2 , abscisic acid and metabolites of the ascorbate-glutathione cycle were measured in the leaves. Common and distinct response features were identified in the different stress combinations. Photosynthesis was not hindered in TN by LS, while even individual stresses severely affect photosynthesis in TR. Abscisic acid may be implicated in grapevine osmotic responses since it is correlated with tolerance parameters, especially in combined stresses involving drought. Overall, the responses to drought-including treatments were clearly distinct to those without drought. From the specific behaviours of the varieties, it can be concluded that TN shows a higher capacity for heat dissipation and for withstanding high light intensities, indicating better adjustment to warm conditions, provided that water supply is plentiful.
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Affiliation(s)
- L C Carvalho
- DRAT, LEAF, ISA, Universidade de Lisboa, Lisboa, Portugal
| | - J L Coito
- DRAT, LEAF, ISA, Universidade de Lisboa, Lisboa, Portugal
| | - E F Gonçalves
- DCEB, LEAF, ISA, Universidade de Lisboa, Lisboa, Portugal
| | - M M Chaves
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - S Amâncio
- DRAT, LEAF, ISA, Universidade de Lisboa, Lisboa, Portugal
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16
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Remington DL. Alleles versus mutations: Understanding the evolution of genetic architecture requires a molecular perspective on allelic origins. Evolution 2015; 69:3025-38. [DOI: 10.1111/evo.12775] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 07/06/2015] [Accepted: 09/08/2015] [Indexed: 01/02/2023]
Affiliation(s)
- David L. Remington
- Department of Biology; University of North Carolina at Greensboro; Greensboro North Carolina 27402
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17
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Kooke R, Johannes F, Wardenaar R, Becker F, Etcheverry M, Colot V, Vreugdenhil D, Keurentjes JJB. Epigenetic basis of morphological variation and phenotypic plasticity in Arabidopsis thaliana. THE PLANT CELL 2015; 27:337-48. [PMID: 25670769 PMCID: PMC4456930 DOI: 10.1105/tpc.114.133025] [Citation(s) in RCA: 129] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 01/14/2015] [Accepted: 01/30/2015] [Indexed: 05/18/2023]
Abstract
Epigenetics is receiving growing attention in the plant science community. Epigenetic modifications are thought to play a particularly important role in fluctuating environments. It is hypothesized that epigenetics contributes to plant phenotypic plasticity because epigenetic modifications, in contrast to DNA sequence variation, are more likely to be reversible. The population of decrease in DNA methylation 1-2 (ddm1-2)-derived epigenetic recombinant inbred lines (epiRILs) in Arabidopsis thaliana is well suited for studying this hypothesis, as DNA methylation differences are maximized and DNA sequence variation is minimized. Here, we report on the extensive heritable epigenetic variation in plant growth and morphology in neutral and saline conditions detected among the epiRILs. Plant performance, in terms of branching and leaf area, was both reduced and enhanced by different quantitative trait loci (QTLs) in the ddm1-2 inherited epigenotypes. The variation in plasticity associated significantly with certain genomic regions in which the ddm1-2 inherited epigenotypes caused an increased sensitivity to environmental changes, probably due to impaired genetic regulation in the epiRILs. Many of the QTLs for morphology and plasticity overlapped, suggesting major pleiotropic effects. These findings indicate that epigenetics contributes substantially to variation in plant growth, morphology, and plasticity, especially under stress conditions.
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Affiliation(s)
- Rik Kooke
- Laboratory of Genetics, Wageningen University, 6708 PB Wageningen, The Netherlands Laboratory of Plant Physiology, Wageningen University, 6708 PB Wageningen, The Netherlands Centre for Biosystem Genomics, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Frank Johannes
- Groningen Bioinformatics Centre, University of Groningen, 9747 AG Groningen, The Netherlands
| | - René Wardenaar
- Groningen Bioinformatics Centre, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Frank Becker
- Laboratory of Genetics, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Mathilde Etcheverry
- Ecole Normale Supérieure, Institut de Biologie, Centre National de la Recherche Scientifique UMR8197, Institut National de la Santé et de la Recherche Médicale U1024, Paris F-75005, France
| | - Vincent Colot
- Ecole Normale Supérieure, Institut de Biologie, Centre National de la Recherche Scientifique UMR8197, Institut National de la Santé et de la Recherche Médicale U1024, Paris F-75005, France
| | - Dick Vreugdenhil
- Laboratory of Plant Physiology, Wageningen University, 6708 PB Wageningen, The Netherlands Centre for Biosystem Genomics, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Joost J B Keurentjes
- Laboratory of Genetics, Wageningen University, 6708 PB Wageningen, The Netherlands Centre for Biosystem Genomics, Wageningen University, 6708 PB Wageningen, The Netherlands
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18
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Golembeski GS, Imaizumi T. Photoperiodic Regulation of Florigen Function in Arabidopsis thaliana. THE ARABIDOPSIS BOOK 2015; 13:e0178. [PMID: 26157354 PMCID: PMC4489636 DOI: 10.1199/tab.0178] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
One mechanism through which flowering in response to seasonal change is brought about is by sensing the fluctuation in day-length; the photoperiod. Flowering induction occurs through the production of the florigenic protein FLOWERING LOCUS T (FT) and its movement from the phloem companion cells in the leaf vasculature into the shoot apex, where meristematic reprogramming occurs. FT activation in response to photoperiod condition is accomplished largely through the activity of the transcription factor CONSTANS (CO). Regulation of CO expression and protein stability, as well as the timing of other components via the circadian clock, is a critical mechanism by which plants are able to respond to photoperiod to initiate the floral transition. Modulation of FT expression in response to external and internal stimuli via components of the flowering network is crucial to mediate a fluid flowering response to a variety of environmental parameters. In addition, the regulated movement of FT protein from the phloem to the shoot apex, and interactions that determine floral meristem cell fate, constitute novel mechanisms through which photoperiodic information is translated into flowering time.
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Affiliation(s)
- Greg S. Golembeski
- University of Washington, Department of Biology, Seattle, WA, 98195-1800
| | - Takato Imaizumi
- University of Washington, Department of Biology, Seattle, WA, 98195-1800
- Address correspondence to
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19
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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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20
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Correa J, Mamani M, Muñoz-Espinoza C, Laborie D, Muñoz C, Pinto M, Hinrichsen P. Heritability and identification of QTLs and underlying candidate genes associated with the architecture of the grapevine cluster (Vitis vinifera L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:1143-62. [PMID: 24556794 DOI: 10.1007/s00122-014-2286-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Accepted: 02/04/2014] [Indexed: 05/18/2023]
Abstract
We have identified 19 QTLs for rachis architecture, a key and complex trait for grapevine production. Fifty out of 1,173 genes underlying these QTLs are candidates to be further explored. In the table grape industry, the rachis architecture has economic and management implications. Therefore, understanding the genetics of this trait is key for its breeding. The aim of this work was to identify genetic determinants of traits associated with the cluster architecture. Characterisations of eight traits was performed on a 'Ruby Seedless' × 'Sultanina' crossing (F1: n = 137) during three seasons, with and without gibberellic acid (GA3) applications. The genotypic effects and the genotype × GA3 interactions were significant for several traits. Rachis length (rl), lateral shoulder length and node number along the central axis were the most prominent traits. On average, the heritability of these traits was ~71 %, with heritability of rl being 76 % as estimated under different seasons. Quantitative trait loci (QTLs) analyses showed that linkage group 5 (LG5) and LG18 harboured the largest number of QTLs for these traits. According to the variance explained, the main QTL (corresponding to rl) was found on LG9. These QTLs were supported mainly by a paternal additive effect and revealed possible pleiotropic effects. Based on the grapevine reference genome, we identified 1,173 genes located under these QTL confidence intervals. Fifty of the 891 annotated genes of this list were selected for their further characterisation because of their possible participation in the rachis architecture. In conclusion, the QTLs detected indicate that these traits and their GA3 responsiveness have a clear genetic basis. Due to the percentage of the total variance explained, they are good candidates to participate in the genetic determination of the cluster architecture.
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Affiliation(s)
- J Correa
- Facultad de Agronomía, Universidad de Chile, Santiago, Chile
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21
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Dechaine JM, Brock MT, Iniguez-Luy FL, Weinig C. Quantitative trait loci × environment interactions for plant morphology vary over ontogeny in Brassica rapa. THE NEW PHYTOLOGIST 2014; 201:657-669. [PMID: 26012723 DOI: 10.1111/nph.12520] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 08/15/2013] [Indexed: 05/16/2023]
Abstract
Growth in plants occurs via the addition of repeating modules, suggesting that the genetic architecture of similar subunits may vary between earlier- and later-developing modules. These complex environment × ontogeny interactions are not well elucidated, as studies examining quantitative trait loci (QTLs) expression over ontogeny have not included multiple environments. Here, we characterized the genetic architecture of vegetative traits and onset of reproduction over ontogeny in recombinant inbred lines of Brassica rapa in the field and glasshouse. The magnitude of genetic variation in plasticity of seedling internodes was greater than in those produced later in ontogeny. We correspondingly detected that QTLs for seedling internode length were environment-specific, whereas later in ontogeny the majority of QTLs affected internode lengths in all treatments. The relationship between internode traits and onset of reproduction varied with environment and ontogenetic stage. This relationship was observed only in the glasshouse environment and was largely attributable to one environment-specific QTL. Our results provide the first evidence of a QTL × environment × ontogeny interaction, and provide QTL resolution for differences between early- and later-stage plasticity for stem elongation. These results also suggest potential constraints on morphological evolution in early vs later modules as a result of associations with reproductive timing.
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Affiliation(s)
- Jennifer M Dechaine
- Department of Biological Sciences, Central Washington University, Ellensburg, WA, 98926, USA
| | - Marcus T Brock
- Department of Botany, University of Wyoming, Laramie, WY, 82071, USA
| | - Federico L Iniguez-Luy
- Agri-Aquaculture Nutritional Genomic Center, Genetic and Bioinformatics Unit, Instituto de Investigaciones Agropecuarias-Carillanca, Codigo Postal, 4780000, Temuco, Chile
| | - Cynthia Weinig
- Department of Botany, University of Wyoming, Laramie, WY, 82071, USA
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22
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Rajon E, Plotkin JB. The evolution of genetic architectures underlying quantitative traits. Proc Biol Sci 2013; 280:20131552. [PMID: 23986107 DOI: 10.1098/rspb.2013.1552] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
In the classic view introduced by R. A. Fisher, a quantitative trait is encoded by many loci with small, additive effects. Recent advances in quantitative trait loci mapping have begun to elucidate the genetic architectures underlying vast numbers of phenotypes across diverse taxa, producing observations that sometimes contrast with Fisher's blueprint. Despite these considerable empirical efforts to map the genetic determinants of traits, it remains poorly understood how the genetic architecture of a trait should evolve, or how it depends on the selection pressures on the trait. Here, we develop a simple, population-genetic model for the evolution of genetic architectures. Our model predicts that traits under moderate selection should be encoded by many loci with highly variable effects, whereas traits under either weak or strong selection should be encoded by relatively few loci. We compare these theoretical predictions with qualitative trends in the genetics of human traits, and with systematic data on the genetics of gene expression levels in yeast. Our analysis provides an evolutionary explanation for broad empirical patterns in the genetic basis for traits, and it introduces a single framework that unifies the diversity of observed genetic architectures, ranging from Mendelian to Fisherian.
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Affiliation(s)
- Etienne Rajon
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
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23
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Huang X, Ding J, Effgen S, Turck F, Koornneef M. Multiple loci and genetic interactions involving flowering time genes regulate stem branching among natural variants of Arabidopsis. THE NEW PHYTOLOGIST 2013; 199:843-57. [PMID: 23668187 DOI: 10.1111/nph.12306] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Accepted: 04/04/2013] [Indexed: 05/02/2023]
Abstract
Shoot branching is a major determinant of plant architecture. Genetic variants for reduced stem branching in the axils of cauline leaves of Arabidopsis were found in some natural accessions and also at low frequency in the progeny of multiparent crosses. Detailed genetic analysis using segregating populations derived from backcrosses with the parental lines and bulked segregant analysis was used to identify the allelic variation controlling reduced stem branching. Eight quantitative trait loci (QTLs) contributing to natural variation for reduced stem branching were identified (REDUCED STEM BRANCHING 1-8 (RSB1-8)). Genetic analysis showed that RSB6 and RSB7, corresponding to flowering time genes FLOWERING LOCUS C (FLC) and FRIGIDA (FRI), epistatically regulate stem branching. Furthermore, FLOWERING LOCUS T (FT), which corresponds to RSB8 as demonstrated by fine-mapping, transgenic complementation and expression analysis, caused pleiotropic effects not only on flowering time, but, in the specific background of active FRI and FLC alleles, also on the RSB trait. The consequence of allelic variation only expressed in late-flowering genotypes revealed novel and thus far unsuspected roles of several genes well characterized for their roles in flowering time control.
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Affiliation(s)
- Xueqing Huang
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
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24
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Fournier-Level A, Wilczek AM, Cooper MD, Roe JL, Anderson J, Eaton D, Moyers BT, Petipas RH, Schaeffer RN, Pieper B, Reymond M, Koornneef M, Welch SM, Remington DL, Schmitt J. Paths to selection on life history loci in different natural environments across the native range of Arabidopsis thaliana. Mol Ecol 2013; 22:3552-66. [PMID: 23506537 DOI: 10.1111/mec.12285] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Revised: 12/17/2012] [Accepted: 01/29/2013] [Indexed: 01/17/2023]
Abstract
Selection on quantitative trait loci (QTL) may vary among natural environments due to differences in the genetic architecture of traits, environment-specific allelic effects or changes in the direction and magnitude of selection on specific traits. To dissect the environmental differences in selection on life history QTL across climatic regions, we grew a panel of interconnected recombinant inbred lines (RILs) of Arabidopsis thaliana in four field sites across its native European range. For each environment, we mapped QTL for growth, reproductive timing and development. Several QTL were pleiotropic across environments, three colocalizing with known functional polymorphisms in flowering time genes (CRY2, FRI and MAF2-5), but major QTL differed across field sites, showing conditional neutrality. We used structural equation models to trace selection paths from QTL to lifetime fitness in each environment. Only three QTL directly affected fruit number, measuring fitness. Most QTL had an indirect effect on fitness through their effect on bolting time or leaf length. Influence of life history traits on fitness differed dramatically across sites, resulting in different patterns of selection on reproductive timing and underlying QTL. In two oceanic field sites with high prereproductive mortality, QTL alleles contributing to early reproduction resulted in greater fruit production, conferring selective advantage, whereas alleles contributing to later reproduction resulted in larger size and higher fitness in a continental site. This demonstrates how environmental variation leads to change in both QTL effect sizes and direction of selection on traits, justifying the persistence of allelic polymorphism at life history QTL across the species range.
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25
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Grillo MA, Li C, Hammond M, Wang L, Schemske DW. Genetic architecture of flowering time differentiation between locally adapted populations of Arabidopsis thaliana. THE NEW PHYTOLOGIST 2013; 197:1321-1331. [PMID: 23311994 DOI: 10.1111/nph.12109] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Accepted: 11/15/2012] [Indexed: 05/18/2023]
Abstract
To gain an understanding of the genetic basis of adaptation, we conducted quantitative trait locus (QTL) mapping for flowering time variation between two winter annual populations of Arabidopsis thaliana that are locally adapted and display distinct flowering times. QTL mapping was performed with large (n = 384) F(2) populations with and without vernalization, in order to reveal both the genetic basis of a vernalization requirement and that of variation in flowering time given vernalization. In the nonvernalization treatment, none of the Sweden parents flowered, whereas all of the Italy parents and 42% of the F(2)s flowered. We identified three QTLs for flowering without vernalization, with much of the variation being attributed to a QTL co-localizing with FLOWERING LOCUS C (FLC). In the vernalization treatment, all parents and F(2)s flowered, and six QTLs of small to moderate effect were revealed, with underlying candidate genes that are members of the vernalization pathway. We found no evidence for a role of FRIGIDA in the regulation of flowering times. These results contribute to a growing body of evidence aimed at the identification of ecologically relevant genetic variation for flowering time in Arabidopsis, and set the stage for functional studies to determine the link between flowering time loci and fitness.
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Affiliation(s)
- Michael A Grillo
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Changbao Li
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Mark Hammond
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Lijuan Wang
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Douglas W Schemske
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
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26
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Zhang YY, Fischer M, Colot V, Bossdorf O. Epigenetic variation creates potential for evolution of plant phenotypic plasticity. THE NEW PHYTOLOGIST 2013; 197:314-322. [PMID: 23121242 DOI: 10.1111/nph.12010] [Citation(s) in RCA: 196] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 09/15/2012] [Indexed: 05/18/2023]
Abstract
Heritable variation in plant phenotypes, and thus potential for evolutionary change, can in principle not only be caused by variation in DNA sequence, but also by underlying epigenetic variation. However, the potential scope of such phenotypic effects and their evolutionary significance are largely unexplored. Here, we conducted a glasshouse experiment in which we tested the response of a large number of epigenetic recombinant inbred lines (epiRILs) of Arabidopsis thaliana--lines that are nearly isogenic but highly variable at the level of DNA methylation--to drought and increased nutrient conditions. We found significant heritable variation among epiRILs both in the means of several ecologically important plant traits and in their plasticities to drought and nutrients. Significant selection gradients, that is, fitness correlations, of several mean traits and plasticities suggest that selection could act on this epigenetically based phenotypic variation. Our study provides evidence that variation in DNA methylation can cause substantial heritable variation of ecologically important plant traits, including root allocation, drought tolerance and nutrient plasticity, and that rapid evolution based on epigenetic variation alone should thus be possible.
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Affiliation(s)
- Yuan-Ye Zhang
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, CH-3013, Bern, Switzerland
| | - Markus Fischer
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, CH-3013, Bern, Switzerland
| | - Vincent Colot
- Institut de Biologie de l'Ecole Normale Supérieure, Centre National de la Recherche Scientifique Unité Mixte de Recherche 8197, Institut National de la Santé et de la Recherche Médicale Unité 1024, Paris F-75005, France
| | - Oliver Bossdorf
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, CH-3013, Bern, Switzerland
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27
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Huang X, Effgen S, Meyer RC, Theres K, Koornneef M. Epistatic natural allelic variation reveals a function of AGAMOUS-LIKE6 in axillary bud formation in Arabidopsis. THE PLANT CELL 2012; 24:2364-79. [PMID: 22730404 PMCID: PMC3406895 DOI: 10.1105/tpc.112.099168] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Revised: 05/22/2012] [Accepted: 06/06/2012] [Indexed: 05/18/2023]
Abstract
In the Arabidopsis multiparent recombinant inbred line mapping population, a limited number of plants were detected that lacked axillary buds in most of the axils of the cauline (stem) leaves, but formed such buds in almost all rosette axils. Genetic analysis showed that polymorphisms in at least three loci together constitute this phenotype, which only occurs in late-flowering plants. Early flowering is epistatic to two of these loci, called REDUCED SHOOT BRANCHING1 (RSB1) and RSB2, which themselves do not affect flowering time. Map-based cloning and confirmation by transformation with genes from the region where RSB1 was identified by fine-mapping showed that a specific allele of AGAMOUS-Like6 from accession C24 conferred reduced branching in the cauline leaves. Site-directed mutagenesis in the Columbia allele revealed the causal amino acid substitution, which behaved as dominant negative, as was concluded from a loss-of-function mutation that showed the same phenotype in the late-flowering genetic background. This causal allele occurs at a frequency of 15% in the resequenced Arabidopsis thaliana accessions and correlated with reduced stem branching only in late-flowering accessions. The data show the importance of natural variation and epistatic interactions in revealing gene function.
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Affiliation(s)
- Xueqing Huang
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Sigi Effgen
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | | | - Klaus Theres
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Maarten Koornneef
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
- Laboratory of Genetics, Wageningen University, NL-6708 PE Wageningen, The Netherlands
- Address correspondence to
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28
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Edwards CE, Ewers BE, McClung CR, Lou P, Weinig C. Quantitative variation in water-use efficiency across water regimes and its relationship with circadian, vegetative, reproductive, and leaf gas-exchange traits. MOLECULAR PLANT 2012; 5:653-68. [PMID: 22319207 DOI: 10.1093/mp/sss004] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Drought limits light harvesting, resulting in lower plant growth and reproduction. One trait important for plant drought response is water-use efficiency (WUE). We investigated (1) how the joint genetic architecture of WUE, reproductive characters, and vegetative traits changed across drought and well-watered conditions, (2) whether traits with distinct developmental bases (e.g. leaf gas exchange versus reproduction) differed in the environmental sensitivity of their genetic architecture, and (3) whether quantitative variation in circadian period was related to drought response in Brassica rapa. Overall, WUE increased in drought, primarily because stomatal conductance, and thus water loss, declined more than carbon fixation. Genotypes with the highest WUE in drought expressed the lowest WUE in well-watered conditions, and had the largest vegetative and floral organs in both treatments. Thus, large changes in WUE enabled some genotypes to approach vegetative and reproductive trait optima across environments. The genetic architecture differed for gas-exchange and vegetative traits across drought and well-watered conditions, but not for floral traits. Correlations between circadian and leaf gas-exchange traits were significant but did not vary across treatments, indicating that circadian period affects physiological function regardless of water availability. These results suggest that WUE is important for drought tolerance in Brassica rapa and that artificial selection for increased WUE in drought will not result in maladaptive expression of other traits that are correlated with WUE.
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29
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Davidowitz G, Nijhout HF, Roff DA. Predicting the response to simultaneous selection: genetic architecture and physiological constraints. Evolution 2012; 66:2916-28. [PMID: 22946812 DOI: 10.1111/j.1558-5646.2012.01644.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A great deal is known about the evolutionary significance of body size and development time. They are determined by the nonlinear interaction of three physiological traits: two hormonal events and growth rate (GR). In this study we investigate how the genetic architecture of the underlying three physiological traits affects the simultaneous response to selection on the two life-history traits in the hawkmoth Manduca sexta. The genetic architecture suggests that when the two life-history traits are both selected in the same direction (to increase or decrease) the response to selection is primarily determined by the hormonal mechanism. When the life-history traits are selected in opposite directions (one to increase and one to decrease) the response to selection is primarily determined by factors that affect the GR. To determine how the physiological traits affect the response to selection of the life-history traits, we simulated the predicted response to 10 generations of selection. A total of 83% of our predictions were supported by the simulation. The main components of this physiological framework also exist in unicellular organisms, vertebrates, and plants and can thus provide a robust framework for understanding how underlying physiology can determine the simultaneous evolution of life-history traits.
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Affiliation(s)
- Goggy Davidowitz
- Department of Entomology, University of Arizona, 1140 E South Campus Drive, Forbes 410, Tucson, Arizona 85721, USA.
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30
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Zerjal T, Rousselet A, Mhiri C, Combes V, Madur D, Grandbastien MA, Charcosset A, Tenaillon MI. Maize genetic diversity and association mapping using transposable element insertion polymorphisms. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 124:1521-1537. [PMID: 22350086 DOI: 10.1007/s00122-012-1807-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Accepted: 01/31/2012] [Indexed: 05/31/2023]
Abstract
Transposable elements are the major component of the maize genome and presumably highly polymorphic yet they have not been used in population genetics and association analyses. Using the Transposon Display method, we isolated and converted into PCR-based markers 33 Miniature Inverted Repeat Transposable Elements (MITE) polymorphic insertions. These polymorphisms were genotyped on a population-based sample of 26 American landraces for a total of 322 plants. Genetic diversity was high and partitioned within and among landraces. The genetic groups identified using Bayesian clustering were in agreement with published data based on SNPs and SSRs, indicating that MITE polymorphisms reflect maize genetic history. To explore the contribution of MITEs to phenotypic variation, we undertook an association mapping approach in a panel of 367 maize lines phenotyped for 26 traits. We found a highly significant association between the marker ZmV1-9, on chromosome 1, and male flowering time. The variance explained by this association is consistent with a flowering delay of +123 degree-days. This MITE insertion is located at only 289 nucleotides from the 3' end of a Cytochrome P450-like gene, a region that was never identified in previous association mapping or QTL surveys. Interestingly, we found (i) a non-synonymous mutation located in the exon 2 of the gene in strong linkage disequilibrium with the MITE polymorphism, and (ii) a perfect sequence homology between the MITE sequence and a maize siRNA that could therefore potentially interfere with the expression of the Cytochrome P450-like gene. Those two observations among others offer exciting perspectives to validate functionally the role of this region on phenotypic variation.
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Affiliation(s)
- Tatiana Zerjal
- CNRS, UMR 0320/UMR 8120 Génétique Végétale, Ferme Du Moulon, 91190 Gif sur Yvette, France.
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31
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Strange A, Li P, Lister C, Anderson J, Warthmann N, Shindo C, Irwin J, Nordborg M, Dean C. Major-effect alleles at relatively few loci underlie distinct vernalization and flowering variation in Arabidopsis accessions. PLoS One 2011; 6:e19949. [PMID: 21625501 PMCID: PMC3098857 DOI: 10.1371/journal.pone.0019949] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Accepted: 04/07/2011] [Indexed: 12/31/2022] Open
Abstract
We have explored the genetic basis of variation in vernalization requirement and
response in Arabidopsis accessions, selected on the basis of their phenotypic
distinctiveness. Phenotyping of F2 populations in different environments, plus
fine mapping, indicated possible causative genes. Our data support the
identification of FRI and FLC as candidates
for the major-effect QTL underlying variation in vernalization response, and
identify a weak FLC allele, caused by a Mutator-like
transposon, contributing to flowering time variation in two N. American
accessions. They also reveal a number of additional QTL that contribute to
flowering time variation after saturating vernalization. One of these was the
result of expression variation at the FT locus. Overall, our
data suggest that distinct phenotypic variation in the vernalization and
flowering response of Arabidopsis accessions is accounted for by variation that
has arisen independently at relatively few major-effect loci.
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Affiliation(s)
- Amy Strange
- Department of Cell and Developmental Biology, John Innes Centre, Norwich,
England, United Kingdom
| | - Peijin Li
- Department of Cell and Developmental Biology, John Innes Centre, Norwich,
England, United Kingdom
| | - Clare Lister
- Department of Cell and Developmental Biology, John Innes Centre, Norwich,
England, United Kingdom
| | - Jillian Anderson
- Department of Cell and Developmental Biology, John Innes Centre, Norwich,
England, United Kingdom
| | - Norman Warthmann
- Department of Molecular Biology, Max Planck Institute for Developmental
Biology, Tübingen, Germany
| | - Chikako Shindo
- Department of Cell and Developmental Biology, John Innes Centre, Norwich,
England, United Kingdom
| | - Judith Irwin
- Department of Cell and Developmental Biology, John Innes Centre, Norwich,
England, United Kingdom
| | - Magnus Nordborg
- Department of Molecular and Computational Biology, University of Southern
California, Los Angeles, California, United States of America
| | - Caroline Dean
- Department of Cell and Developmental Biology, John Innes Centre, Norwich,
England, United Kingdom
- * E-mail:
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Ravi K, Vadez V, Isobe S, Mir RR, Guo Y, Nigam SN, Gowda MVC, Radhakrishnan T, Bertioli DJ, Knapp SJ, Varshney RK. Identification of several small main-effect QTLs and a large number of epistatic QTLs for drought tolerance related traits in groundnut (Arachis hypogaea L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 122:1119-32. [PMID: 21191568 PMCID: PMC3057011 DOI: 10.1007/s00122-010-1517-0] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2010] [Accepted: 12/08/2010] [Indexed: 05/18/2023]
Abstract
Cultivated groundnut or peanut (Arachis hypogaea L.), an allotetraploid (2n = 4x = 40), is a self pollinated and widely grown crop in the semi-arid regions of the world. Improvement of drought tolerance is an important area of research for groundnut breeding programmes. Therefore, for the identification of candidate QTLs for drought tolerance, a comprehensive and refined genetic map containing 191 SSR loci based on a single mapping population (TAG 24 x ICGV 86031), segregating for drought and surrogate traits was developed. Genotyping data and phenotyping data collected for more than ten drought related traits in 2-3 seasons were analyzed in detail for identification of main effect QTLs (M-QTLs) and epistatic QTLs (E-QTLs) using QTL Cartographer, QTLNetwork and Genotype Matrix Mapping (GMM) programmes. A total of 105 M-QTLs with 3.48-33.36% phenotypic variation explained (PVE) were identified using QTL Cartographer, while only 65 M-QTLs with 1.3-15.01% PVE were identified using QTLNetwork. A total of 53 M-QTLs were such which were identified using both programmes. On the other hand, GMM identified 186 (8.54-44.72% PVE) and 63 (7.11-21.13% PVE), three and two loci interactions, whereas only 8 E-QTL interactions with 1.7-8.34% PVE were identified through QTLNetwork. Interestingly a number of co-localized QTLs controlling 2-9 traits were also identified. The identification of few major, many minor M-QTLs and QTL × QTL interactions during the present study confirmed the complex and quantitative nature of drought tolerance in groundnut. This study suggests deployment of modern approaches like marker-assisted recurrent selection or genomic selection instead of marker-assisted backcrossing approach for breeding for drought tolerance in groundnut.
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Affiliation(s)
- K. Ravi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324 India
| | - V. Vadez
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324 India
| | - S. Isobe
- Kazusa DNA Research Institute (KDRI), Chiba, 292-0818 Japan
| | - R. R. Mir
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324 India
| | - Y. Guo
- Institute of Plant Breeding, Genetics, and Genomics, The University of Georgia, Athens, GA 30602 USA
| | - S. N. Nigam
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324 India
| | - M. V. C. Gowda
- University of Agricultural Sciences, Dharwad, 580005 India
| | | | - D. J. Bertioli
- Universidade Católica de Brasília (UCB), Brasília, DF, CEP 70.790-160 Brazil
- Universidade de Brasília, Brasilia, DF, CEP 70.910-900 Brazil
| | - S. J. Knapp
- Institute of Plant Breeding, Genetics, and Genomics, The University of Georgia, Athens, GA 30602 USA
| | - R. K. Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324 India
- Generation Challenge Programme (GCP), c/o CIMMYT, 06600 Mexico DF, Mexico
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Anderson JT, Lee CR, Mitchell-Olds T. Life-history QTLS and natural selection on flowering time in Boechera stricta, a perennial relative of Arabidopsis. Evolution 2011; 65:771-87. [PMID: 21083662 PMCID: PMC3155413 DOI: 10.1111/j.1558-5646.2010.01175.x] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Plants must precisely time flowering to capitalize on favorable conditions. Although we know a great deal about the genetic basis of flowering phenology in model species under controlled conditions, the genetic architecture of this ecologically important trait is poorly understood in nonmodel organisms. Here, we evaluated the transition from vegetative growth to flowering in Boechera stricta, a perennial relative of Arabidopsis thaliana. We examined flowering time QTLs using 7920 recombinant inbred individuals, across seven laboratory and field environments differing in vernalization, temperature, and photoperiod. Genetic and environmental factors strongly influenced the transition to reproduction. We found directional selection for earlier flowering in the field. In the growth chamber experiment, longer winters accelerated flowering, whereas elevated ambient temperatures delayed flowering. Our analyses identified one large effect QTL (nFT), which influenced flowering time in the laboratory and the probability of flowering in the field. In Montana, homozygotes for the native allele at nFT showed a selective advantage of 6.6%. Nevertheless, we found relatively low correlations between flowering times in the field and the growth chambers. Additionally, we detected flowering-related QTLs in the field that were absent across the full range of laboratory conditions, thus emphasizing the need to conduct experiments in natural environments.
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Affiliation(s)
- Jill T. Anderson
- Institute for Genome Sciences and Policy Department of Biology Duke University P.O. Box 90338 Durham, North Carolina 27708 USA
| | - Cheng-Ruei Lee
- Institute for Genome Sciences and Policy Department of Biology Duke University P.O. Box 90338 Durham, North Carolina 27708 USA
| | - Thomas Mitchell-Olds
- Institute for Genome Sciences and Policy Department of Biology Duke University P.O. Box 90338 Durham, North Carolina 27708 USA
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Nicotra AB, Atkin OK, Bonser SP, Davidson AM, Finnegan EJ, Mathesius U, Poot P, Purugganan MD, Richards CL, Valladares F, van Kleunen M. Plant phenotypic plasticity in a changing climate. TRENDS IN PLANT SCIENCE 2010; 15:684-92. [PMID: 20970368 DOI: 10.1016/j.tplants.2010.09.008] [Citation(s) in RCA: 865] [Impact Index Per Article: 61.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2009] [Revised: 09/21/2010] [Accepted: 09/21/2010] [Indexed: 05/19/2023]
Abstract
Climate change is altering the availability of resources and the conditions that are crucial to plant performance. One way plants will respond to these changes is through environmentally induced shifts in phenotype (phenotypic plasticity). Understanding plastic responses is crucial for predicting and managing the effects of climate change on native species as well as crop plants. Here, we provide a toolbox with definitions of key theoretical elements and a synthesis of the current understanding of the molecular and genetic mechanisms underlying plasticity relevant to climate change. By bringing ecological, evolutionary, physiological and molecular perspectives together, we hope to provide clear directives for future research and stimulate cross-disciplinary dialogue on the relevance of phenotypic plasticity under climate change.
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Affiliation(s)
- A B Nicotra
- Research School of Biology, The Australian National University, Canberra, ACT, Australia.
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Fakheran S, Paul-Victor C, Heichinger C, Schmid B, Grossniklaus U, Turnbull LA. Adaptation and extinction in experimentally fragmented landscapes. Proc Natl Acad Sci U S A 2010; 107:19120-5. [PMID: 20956303 PMCID: PMC2973902 DOI: 10.1073/pnas.1010846107] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Competition and disturbance are potent ecological forces that shape evolutionary trajectories. These forces typically work in opposition: when disturbance is infrequent, densities are high and competition is intense. In contrast, frequent disturbance creates a low-density environment in which competition is weak and good dispersal essential. We exploited recent advances in genomic research to quantify the response to selection by these powerful ecological forces at the phenotypic and molecular genetic level in experimental landscapes. We grew the annual plant Arabidopsis thaliana in discrete patches embedded in a hostile matrix and varied the number and size of patches and the intensity of disturbance, by creating both static and dynamic landscapes. In static landscapes all patches were undisturbed, whereas in dynamic landscapes all patches were destroyed in each generation, forcing seeds to disperse to new locations. We measured the resulting changes in phenotypic, genetic, and genotypic diversity after five generations of selection. Simulations revealed that the observed loss of genetic diversity dwarfed that expected under drift, with dramatic diversity loss, particularly from dynamic landscapes. In line with ecological theory, static landscapes favored good competitors; however, competitive ability was linked to growth rate and not, as expected, to seed mass. In dynamic landscapes, there was strong selection for increased dispersal ability in the form of increased inflorescence height and reduced seed mass. The most competitive genotypes were almost eliminated from highly disturbed landscapes, raising concern over the impact of increased levels of human-induced disturbance in natural landscapes.
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Affiliation(s)
- Sima Fakheran
- Institute of Evolutionary Biology and Environmental Studies and Zürich-Basel Plant Science Center, University of Zürich, CH-8057 Zürich, Switzerland; and
| | - Cloé Paul-Victor
- Institute of Evolutionary Biology and Environmental Studies and Zürich-Basel Plant Science Center, University of Zürich, CH-8057 Zürich, Switzerland; and
| | - Christian Heichinger
- Institute of Plant Biology and Zürich-Basel Plant Science Center, University of Zürich, CH-8008 Zürich, Switzerland
| | - Bernhard Schmid
- Institute of Evolutionary Biology and Environmental Studies and Zürich-Basel Plant Science Center, University of Zürich, CH-8057 Zürich, Switzerland; and
| | - Ueli Grossniklaus
- Institute of Plant Biology and Zürich-Basel Plant Science Center, University of Zürich, CH-8008 Zürich, Switzerland
| | - Lindsay A. Turnbull
- Institute of Evolutionary Biology and Environmental Studies and Zürich-Basel Plant Science Center, University of Zürich, CH-8057 Zürich, Switzerland; and
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Prinzenberg AE, Barbier H, Salt DE, Stich B, Reymond M. Relationships between growth, growth response to nutrient supply, and ion content using a recombinant inbred line population in Arabidopsis. PLANT PHYSIOLOGY 2010; 154:1361-71. [PMID: 20826703 PMCID: PMC2971612 DOI: 10.1104/pp.110.161398] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2010] [Accepted: 09/05/2010] [Indexed: 05/18/2023]
Abstract
Growth is an integrative trait that responds to environmental factors and is crucial for plant fitness. A major environmental factor influencing plant growth is nutrient supply. In order to explore this relationship further, we quantified growth-related traits, ion content, and other biochemical traits (protein, hexose, and chlorophyll contents) of a recombinant inbred line population of Arabidopsis (Arabidopsis thaliana) grown on different levels of potassium and phosphate. Performing an all subsets multiple regression analyses revealed a link between growth-related traits and mineral nutrient content. Based on our results, up to 85% of growth variation can be explained by variation in ion content, highlighting the importance of ionomics for a broader understanding of plant growth. In addition, quantitative trait loci (QTLs) were detected for growth-related traits, ion content, further biochemical traits, and their responses to reduced supplies of potassium or phosphate. Colocalization of these QTLs is explored, and candidate genes are discussed. A QTL for rosette weight response to reduced potassium supply was identified on the bottom of chromosome 5, and its effects were validated using selected near isogenic lines. These lines retained over 20% more rosette weight in reduced potassium supply, accompanied by an increase in potassium content in their leaves.
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Affiliation(s)
| | | | | | | | - Matthieu Reymond
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany (A.E.P., B.S., M.R.); Institut de Biologie Moléculaire des Plantes du CNRS, Institut de Biologie Moléculaire des Plantes-CNRS-UPR2357, 67084 Strasbourg, France (H.B.); Center for Plant Environmental Stress Physiology, Horticulture and Landscape Architecture Department, Purdue University, West Lafayette, Indiana 47907 (D.E.S.); Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, INRA Centre de Versailles-Grignon, 78026 Versailles cedex, France (M.R.)
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Shiringani AL, Frisch M, Friedt W. Genetic mapping of QTLs for sugar-related traits in a RIL population of Sorghum bicolor L. Moench. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 121:323-36. [PMID: 20229249 DOI: 10.1007/s00122-010-1312-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2009] [Accepted: 02/22/2010] [Indexed: 05/05/2023]
Abstract
The productivity of sorghum is mainly determined by quantitative traits such as grain yield and stem sugar-related characteristics. Substantial crop improvement has been achieved by breeding in the last decades. Today, genetic mapping and characterization of quantitative trait loci (QTLs) is considered a valuable tool for trait enhancement. We have investigated QTL associated with the sugar components (Brix, glucose, sucrose, and total sugar content) and sugar-related agronomic traits (flowering date, plant height, stem diameter, tiller number per plant, fresh panicle weight, and estimated juice weight) in four different environments (two locations) using a population of 188 recombinant inbred lines (RILs) from a cross between grain (M71) and sweet sorghum (SS79). A genetic map with 157 AFLP, SSR, and EST-SSR markers was constructed, and several QTLs were detected using composite interval mapping (CIM). Further, additive x additive interaction and QTL x environmental interaction were estimated. CIM identified more than five additive QTLs in most traits explaining a range of 6.0-26.1% of the phenotypic variation. A total of 24 digenic epistatic locus pairs were identified in seven traits, supporting the hypothesis that QTL analysis without considering epistasis can result in biased estimates. QTLs showing multiple effects were identified, where the major QTL on SBI-06 was significantly associated with most of the traits, i.e., flowering date, plant height, Brix, sucrose, and sugar content. Four out of ten traits studied showed a significant QTL x environmental interaction. Our results are an important step toward marker-assisted selection for sugar-related traits and biofuel yield in sorghum.
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Affiliation(s)
- Amukelani Lacrecia Shiringani
- Department of Plant Breeding, Research Centre for Biosystems, Land Use and Nutrition (IFZ), Justus-Liebig University of Giessen, Heinrich-Buff-Ring 26-32, Giessen, Germany
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Conte M, de Simone S, Simmons SJ, Ballaré CL, Stapleton AE. Chromosomal loci important for cotyledon opening under UV-B in Arabidopsis thaliana. BMC PLANT BIOLOGY 2010; 10:112. [PMID: 20565708 PMCID: PMC3095277 DOI: 10.1186/1471-2229-10-112] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2010] [Accepted: 06/16/2010] [Indexed: 05/08/2023]
Abstract
BACKGROUND Understanding of the genetic architecture of plant UV-B responses allows extensive targeted testing of candidate genes or regions, along with combinations of those genes, for placement in metabolic or signal transduction pathways. RESULTS Composite interval mapping and single-marker analysis methods were used to identify significant loci for cotyledon opening under UV-B in four sets of recombinant inbred lines. In addition, loci important for canalization (stability) of cotyledon opening were detected in two mapping populations. One candidate locus contained the gene HY5. Mutant analysis demonstrated that HY5 was required for UV-B-specific cotyledon opening. CONCLUSIONS Structured mapping populations provide key information on the degree of complexity in the genetic control of UV-B-induced cotyledon opening in Arabidopsis. The loci identified using quantitative trait analysis methods are useful for follow-up testing of candidate genes.
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Affiliation(s)
- Mariana Conte
- Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura, Consejo Nacional de Investigaciones Científicas y Técnicas and Universidad de Buenos Aires, C1417 DSE Buenos Aires, Argentina
| | - Silvia de Simone
- Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura, Consejo Nacional de Investigaciones Científicas y Técnicas and Universidad de Buenos Aires, C1417 DSE Buenos Aires, Argentina
| | - Susan J Simmons
- Department of Mathematics and Statistics, University of North Carolina at Wilmington, Wilmington, NC 28403 USA
| | - Carlos L Ballaré
- Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura, Consejo Nacional de Investigaciones Científicas y Técnicas and Universidad de Buenos Aires, C1417 DSE Buenos Aires, Argentina
| | - Ann E Stapleton
- Department of Biology and Marine Biology, University of North Carolina at Wilmington, Wilmington, NC 28403 USA
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van Zanten M, Basten Snoek L, van Eck-Stouten E, Proveniers MCG, Torii KU, Voesenek LACJ, Peeters AJM, Millenaar FF. Ethylene-induced hyponastic growth in Arabidopsis thaliana is controlled by ERECTA. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 61:83-95. [PMID: 19796369 DOI: 10.1111/j.1365-313x.2009.04035.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Plants can respond quickly and profoundly to detrimental changes in their environment. For example, Arabidopsis thaliana can induce an upward leaf movement response through differential petiole growth (hyponastic growth) to outgrow complete submergence. This response is induced by accumulation of the phytohormone ethylene in the plant. Currently, only limited information is available on how this response is molecularly controlled. In this study, we utilized quantitative trait loci (QTL) analysis of natural genetic variation among Arabidopsis accessions to isolate novel factors controlling constitutive petiole angles and ethylene-induced hyponastic growth. Analysis of mutants in various backgrounds and complementation analysis of naturally occurring mutant accessions provided evidence that the leucin-rich repeat receptor-like Ser/Thr kinase gene, ERECTA, controls ethylene-induced hyponastic growth. Moreover, ERECTA controls leaf positioning in the absence of ethylene treatment. Our data demonstrate that this is not due to altered ethylene production or sensitivity.
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Affiliation(s)
- Martijn van Zanten
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
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40
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Sano CM, Bohn MO, Paige KN, Jacobs TW. Heritable variation in the inflorescence replacement program of Arabidopsis thaliana. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2009; 119:1461-1476. [PMID: 19787332 DOI: 10.1007/s00122-009-1148-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2008] [Accepted: 08/30/2009] [Indexed: 05/28/2023]
Abstract
Owing to their sessile habits and trophic position within global ecosystems, higher plants display a sundry assortment of adaptations to the threat of predation. Unlike animals, nearly all higher plants can replace reproductive structures lost to predators by activating reserved growing points called axillary meristems. As the first step in a program aimed at defining the genetic architecture of the inflorescence replacement program (IRP) of Arabidopsis thaliana, we describe the results of a quantitative germplasm survey of developmental responses to loss of the primary reproductive axis. Eighty-five diverse accessions were grown in a replicated common garden and assessed for six life history traits and four IRP traits, including the number and lengths of axillary inflorescences present on the day that the first among them re-flowered after basal clipping of the primary inflorescence. Significant natural variation and high heritabilities were observed for all measured characters. Pairwise correlations among the 10 focal traits revealed a multi-dimensional phenotypic space sculpted by ontogenic and plastic allometries as well as apparent constraints and outliers of genetic interest. Cluster analysis of the IRP traits sorted the 85 accessions into 5 associations, a topology that establishes the boundaries within which the evolving Arabidopsis genome extends and restricts the species' IRP repertoire to that observable worldwide.
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Affiliation(s)
- Cecile M Sano
- Department of Plant Biology, University of Illinois, 191 Edward R. Madigan Laboratory, 1201 West Gregory Drive, Urbana, IL, 61801, USA
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41
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Flowers JM, Hanzawa Y, Hall MC, Moore RC, Purugganan MD. Population Genomics of the Arabidopsis thaliana Flowering Time Gene Network. Mol Biol Evol 2009; 26:2475-86. [DOI: 10.1093/molbev/msp161] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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42
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A Multiparent Advanced Generation Inter-Cross to fine-map quantitative traits in Arabidopsis thaliana. PLoS Genet 2009; 5:e1000551. [PMID: 19593375 PMCID: PMC2700969 DOI: 10.1371/journal.pgen.1000551] [Citation(s) in RCA: 366] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2009] [Accepted: 06/08/2009] [Indexed: 12/29/2022] Open
Abstract
Identifying natural allelic variation that underlies quantitative trait variation remains a fundamental problem in genetics. Most studies have employed either simple synthetic populations with restricted allelic variation or performed association mapping on a sample of naturally occurring haplotypes. Both of these approaches have some limitations, therefore alternative resources for the genetic dissection of complex traits continue to be sought. Here we describe one such alternative, the Multiparent Advanced Generation Inter-Cross (MAGIC). This approach is expected to improve the precision with which QTL can be mapped, improving the outlook for QTL cloning. Here, we present the first panel of MAGIC lines developed: a set of 527 recombinant inbred lines (RILs) descended from a heterogeneous stock of 19 intermated accessions of the plant Arabidopsis thaliana. These lines and the 19 founders were genotyped with 1,260 single nucleotide polymorphisms and phenotyped for development-related traits. Analytical methods were developed to fine-map quantitative trait loci (QTL) in the MAGIC lines by reconstructing the genome of each line as a mosaic of the founders. We show by simulation that QTL explaining 10% of the phenotypic variance will be detected in most situations with an average mapping error of about 300 kb, and that if the number of lines were doubled the mapping error would be under 200 kb. We also show how the power to detect a QTL and the mapping accuracy vary, depending on QTL location. We demonstrate the utility of this new mapping population by mapping several known QTL with high precision and by finding novel QTL for germination data and bolting time. Our results provide strong support for similar ongoing efforts to produce MAGIC lines in other organisms. Most traits of economic and evolutionary interest vary quantitatively and have multiple genes affecting their expression. Dissecting the genetic basis of such traits is crucial for the improvement of crops and management of diseases. Here, we develop a new resource to identify genes underlying such quantitative traits in Arabidopsis thaliana, a genetic model organism in plants. We show that using a large population of inbred lines derived from intercrossing 19 parents, we can localize the genes underlying quantitative traits better than with existing methods. Using these lines, we were able to replicate the identification of previously known genes that affect developmental traits in A. thaliana and identify some new ones. This paper also presents all the necessary biological and computational material necessary for the scientific community to use these lines in their own research. Our results suggest that the use of lines derived from a multiparent advanced generation inter-cross (MAGIC lines) should be very useful in other organisms.
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Abstract
The pathways responsible for flowering time in Arabidopsis thaliana comprise one of the best characterized genetic networks in plants. We harness this extensive molecular genetic knowledge to identify potential flowering time quantitative trait genes (QTGs) through candidate gene association mapping using 51 flowering time loci. We genotyped common single nucleotide polymorphisms (SNPs) at these genes in 275 A. thaliana accessions that were also phenotyped for flowering time and rosette leaf number in long and short days. Using structured association techniques, we find that haplotype-tagging SNPs in 27 flowering time genes show significant associations in various trait/environment combinations. After correction for multiple testing, between 2 and 10 genes remain significantly associated with flowering time, with CO arguably possessing the most promising associations. We also genotyped a subset of these flowering time gene SNPs in an independent recombinant inbred line population derived from the intercrossing of 19 accessions. Approximately one-third of significant polymorphisms that were associated with flowering time in the accessions and genotyped in the outbred population were replicated in both mapping populations, including SNPs at the CO, FLC, VIN3, PHYD, and GA1 loci, and coding region deletions at the FRI gene. We conservatively estimate that approximately 4-14% of known flowering time genes may harbor common alleles that contribute to natural variation in this life history trait.
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van Zanten M, Snoek LB, Proveniers MCG, Peeters AJM. The many functions of ERECTA. TRENDS IN PLANT SCIENCE 2009; 14:214-8. [PMID: 19303350 DOI: 10.1016/j.tplants.2009.01.010] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2008] [Revised: 01/12/2009] [Accepted: 01/22/2009] [Indexed: 05/19/2023]
Abstract
The Arabidopsis thaliana accession Landsberg erecta contains an induced mutation in the leucine-rich repeat receptor-like Ser/Thr kinase gene ERECTA. Landsberg erecta is commonly used as a genetic background in mutant screens and in natural variation studies. Therefore, the erecta mutation is present in many loss-of-function mutants and recombinant inbred lines. Information on how the absence of functional ERECTA affects the interpretation of obtained phenotypic results is scattered. In this report we inventoried ERECTA functions and highlight ERECTA as a pleiotropic regulator of developmental and physiological processes, as well as a modulator of responses to environmental stimuli.
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Affiliation(s)
- Martijn van Zanten
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands
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45
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Caicedo AL, Richards C, Ehrenreich IM, Purugganan MD. Complex rearrangements lead to novel chimeric gene fusion polymorphisms at the Arabidopsis thaliana MAF2-5 flowering time gene cluster. Mol Biol Evol 2009; 26:699-711. [PMID: 19139056 DOI: 10.1093/molbev/msn300] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Tandem gene clusters of multigene families are rearrangement hotspots and may be a major source of novel gene formation. Here, we report on a molecular population genetic analysis of the MAF2-5 gene cluster of the model plant species, Arabidopsis thaliana. The MAF2-5 genes are a MADS-box multigene family cluster spanning approximately 24 kbp on chromosome 5. We find heterogeneous evolutionary dynamics among these genes, all of which are closely related to the floral repressor, FLC, and are believed to play a role in the control of flowering time in A. thaliana. Low levels of nonsynonymous single nucleotide polymorphism (SNP) observed for MAF4 and MAF5 suggest purifying selection and conservation of function. In contrast, high levels of nonsynonymous SNPs, insertion-deletion, and rearrangements are observed for MAF2 and MAF3, including novel gene fusions that persist as a moderate-frequency polymorphism in A. thaliana. These fused genes, involving MAF2 and portions of MAF3, are expressed, resulting in the production of chimeric, alternatively spliced transcripts of MAF2. Association studies support a correlation between the described MAF2-MAF3 gene rearrangements and flowering time variation in the species. The finding that complex rearrangements within gene clusters, such as those observed for MAF2, might play a role in the generation of ecologically important phenotypic variation, emphasize the need for emerging high throughput genotyping and sequencing techniques to correctly reconstruct gene chimeras and other complex polymorphisms.
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Affiliation(s)
- Ana L Caicedo
- Biology Department, 221 Morrill Science Center, University of Massachusetts, USA
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46
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Ghandilyan A, Ilk N, Hanhart C, Mbengue M, Barboza L, Schat H, Koornneef M, El-Lithy M, Vreugdenhil D, Reymond M, Aarts MGM. A strong effect of growth medium and organ type on the identification of QTLs for phytate and mineral concentrations in three Arabidopsis thaliana RIL populations. JOURNAL OF EXPERIMENTAL BOTANY 2009; 60:1409-25. [PMID: 19346258 DOI: 10.1093/jxb/erp084] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The regulation of mineral accumulation in plants is genetically complex, with several genetic loci involved in the control of one mineral and loci affecting the accumulation of different minerals. To investigate the role of growth medium and organ type on the genetics of mineral accumulation, two existing (LerxKond, LerxAn-1) and one new (LerxEri-1) Arabidopsis thaliana Recombinant Inbred Line populations were raised on soil and hydroponics as substrates. Seeds, roots, and/or rosettes were sampled for the determination of their Ca, Fe, K, Mg, Mn, P or Zn concentrations. For seeds only, the concentration of phytate (IP6), a strong chelator of seed minerals, was determined. Correlations between minerals/IP6, populations, growth conditions, and organs were determined and mineral/IP6 concentration data were used to identify quantitative trait loci (QTLs) for these traits. A striking difference was found between QTLs identified for soil-grown versus hydroponics-grown populations and between QTLs identified for different plant organs. Three common QTLs were identified for several populations, growth conditions, and organs, one of which corresponded to the ERECTA locus, variation of which has a strong effect on plant morphology.
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Parh DK, Jordan DR, Aitken EAB, Mace ES, Jun-ai P, McIntyre CL, Godwin ID. QTL analysis of ergot resistance in sorghum. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2008; 117:369-82. [PMID: 18481043 DOI: 10.1007/s00122-008-0781-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2007] [Accepted: 04/23/2008] [Indexed: 05/05/2023]
Abstract
Sorghum ergot, caused predominantly by Claviceps africana Frederickson, Mantle, de Milliano, is a significant threat to the sorghum industry worldwide. The objectives of this study were firstly, to identify molecular markers linked to ergot resistance and to two pollen traits, pollen quantity (PQ) and pollen viability (PV), and secondly, to assess the relationship between the two pollen traits and ergot resistance in sorghum. A genetic linkage map of sorghum RIL population R931945-2-2 x IS 8525 (resistance source) was constructed using 303 markers including 36 SSR, 117 AFLP , 148 DArT and two morphological trait loci. Composite interval mapping identified nine, five, and four QTL linked to molecular markers for percentage ergot infection (PCERGOT), PQ and PV, respectively, at a LOD >2.0. Co-location/linkage of QTL were identified on four chromosomes while other QTL for the three traits mapped independently, indicating that both pollen and non pollen-based mechanisms of ergot resistance were operating in this sorghum population. Of the nine QTL identified for PCERGOT, five were identified using the overall data set while four were specific to the group data sets defined by temperature and humidity. QTL identified on SBI-02 and SBI-06 were further validated in additional populations. This is the first report of QTL associated with ergot resistance in sorghum. The markers reported herein could be used for marker-assisted selection for this important disease of sorghum.
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Affiliation(s)
- D K Parh
- School of Land and Food Sciences, University of Queensland, Brisbane, QLD 4072, Australia.
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48
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Ngwako S. Mapping quantitative trait loci using the marker regression and the interval mapping methods. Pak J Biol Sci 2008; 11:553-8. [PMID: 18817125 DOI: 10.3923/pjbs.2008.553.558] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The marker regression and the interval mapping methods were used for the detection of qualitative trait loci (QTL) in Arabidopsis thaliana in a cross between early flowering ecotypes Landsberg erecta and Columbia. The interval mapping method employs pairs of neighbouring markers to obtain maximum linkage information about the presence of a QTL within the enclosed segment of the chromosome, whereas the marker regression approach fits a model to all the marker means on a given chromosome simultaneously and obtains significance tests by simulation. The interval mapping method detected 22 QTL in seven traits and the marker regression method detected 22 QTL in six traits. The two methods detected sixteen QTL at similar positions of the Arabidopsis chromosomes and QTL for similar traits were localised to similar regions of the chromosomes and they showed similar mode of additive effect. This suggested that the two methods are similar in their QTL detection even though they employed different significant levels.
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Affiliation(s)
- S Ngwako
- Department of Crop Science and Production, Botswana College of Agriculture, P/Bag 0027, Gaborone, Botswana
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Pauwels M, Willems G, Roosens N, Frérot H, Saumitou-Laprade P. Merging methods in molecular and ecological genetics to study the adaptation of plants to anthropogenic metal-polluted sites: implications for phytoremediation. Mol Ecol 2008; 17:108-19. [PMID: 17784915 DOI: 10.1111/j.1365-294x.2007.03486.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Metallophyte species that occur naturally on metal-enriched soils represent major biological resources for the improvement of phytoremediation, a benign and cost-effective technology that uses plants to clean up anthropogenic metal-polluted soils. Within the last decade, molecular genetic studies carried out on several model organisms (including Arabidopsis halleri) have considerably enhanced our understanding of metal tolerance and hyperaccumulation in plants, but the identification of the genes of interest for phytoremediation purposes remains a challenge. To meet this challenge, we propose to combine '-omics' with molecular ecology methods. Using A. halleri, we confronted molecular genetic results with: (i) within-species polymorphism and large-scale population differentiation for zinc tolerance; (ii) the demographical context (e.g. migration pattern) of the species for zinc tolerance evolution; (iii) the Quantitative Trait Loci (QTL) analysis of the genetic architecture for zinc tolerance; and (iv) the fine-scale dissection of identified QTL regions, to discuss more precisely the nature of the genes potentially involved in the adaptation to zinc-polluted soils.
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Affiliation(s)
- Maxime Pauwels
- Laboratoire de Génétique et Evolution des Populations Végétales, UMR CNRS 8016, Université des Sciences et Technologies de Lille, Bâtiment SN2, F-59655 Villeneuve d'Ascq Cedex, France
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Hopkins R, Schmitt J, Stinchcombe JR. A latitudinal cline and response to vernalization in leaf angle and morphology in Arabidopsis thaliana (Brassicaceae). THE NEW PHYTOLOGIST 2008; 179:155-164. [PMID: 18422898 DOI: 10.1111/j.1469-8137.2008.02447.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Adaptation to latitudinal patterns of environmental variation is predicted to result in clinal variation in leaf traits. Therefore, this study tested for geographic differentiation and plastic responses to vernalization in leaf angle and leaf morphology in Arabidopsis thaliana. Twenty-one European ecotypes were grown in a common growth chamber environment. Replicates of each ecotype were exposed to one of four treatments: 0, 10, 20 or 30 d of vernalization. Ecotypes from lower latitudes had more erect leaves, as predicted from functional arguments about selection to maximize photosynthesis. Lower-latitude ecotypes also had more elongated petioles as predicted by a biomechanical constraint hypothesis. In addition, extended vernalization resulted in shorter and more erect leaves. As predicted by functional and adaptive hypotheses, our results show genetically based clinal variation as well as environmentally induced variation in leaf traits.
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Affiliation(s)
- Robin Hopkins
- Ecology and Evolutionary Biology, Brown University, Providence, RI, USA
- Present address: Biology, Duke University, Durham, NC, USA
| | - Johanna Schmitt
- Ecology and Evolutionary Biology, Brown University, Providence, RI, USA
| | - John R Stinchcombe
- Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada
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