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Aykanat T, McLennan D, Metcalfe NB, Prokkola JM. Early survival in Atlantic salmon is associated with parental genotypes at loci linked to timing of maturation. Evolution 2024; 78:1441-1452. [PMID: 38736399 DOI: 10.1093/evolut/qpae072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 04/25/2024] [Accepted: 05/09/2024] [Indexed: 05/14/2024]
Abstract
Large effect loci often contain genes with critical developmental functions and potentially broad effects across life stages. However, their life stage-specific fitness consequences are rarely explored. In Atlantic salmon, variation in two large-effect loci, six6 and vgll3, is linked to age at maturity and several physiological and behavioral traits in early life. By genotyping the progeny of wild Atlantic salmon that were planted into natural streams with nutrient manipulations, we tested if genetic variation in these loci is associated with survival in early life. We found that higher early-life survival was linked to the genotype associated with late maturation in the vgll3, but with early maturation in the six6 locus. These effects were significant in high nutrients but not in low-nutrient streams. The differences in early survival were not explained by additive genetic effects in the offspring generation but by maternal genotypes in the six6 locus and by both parents' genotypes in the vgll3 locus. Our results suggest that indirect genetic effects of large-effect loci can be significant determinants of offspring fitness. This study demonstrates an intriguing case of how large-effect loci can exhibit complex fitness associations across life stages in the wild and indicates that predicting evolutionary dynamics is difficult.
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Affiliation(s)
- Tutku Aykanat
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Darryl McLennan
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Neil B Metcalfe
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Jenni M Prokkola
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Natural Resources Institute Finland (LUKE), Oulu, Finland
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2
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Han R, Ma L, Terzaghi W, Guo Y, Li J. Molecular mechanisms underlying coordinated responses of plants to shade and environmental stresses. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:1893-1913. [PMID: 38289877 DOI: 10.1111/tpj.16653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 01/09/2024] [Accepted: 01/17/2024] [Indexed: 02/01/2024]
Abstract
Shade avoidance syndrome (SAS) is triggered by a low ratio of red (R) to far-red (FR) light (R/FR ratio), which is caused by neighbor detection and/or canopy shade. In order to compete for the limited light, plants elongate hypocotyls and petioles by deactivating phytochrome B (phyB), a major R light photoreceptor, thus releasing its inhibition of the growth-promoting transcription factors PHYTOCHROME-INTERACTING FACTORs. Under natural conditions, plants must cope with abiotic stresses such as drought, soil salinity, and extreme temperatures, and biotic stresses such as pathogens and pests. Plants have evolved sophisticated mechanisms to simultaneously deal with multiple environmental stresses. In this review, we will summarize recent major advances in our understanding of how plants coordinately respond to shade and environmental stresses, and will also discuss the important questions for future research. A deep understanding of how plants synergistically respond to shade together with abiotic and biotic stresses will facilitate the design and breeding of new crop varieties with enhanced tolerance to high-density planting and environmental stresses.
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Affiliation(s)
- Run Han
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing, 100193, China
| | - Liang Ma
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing, 100193, China
| | - William Terzaghi
- Department of Biology, Wilkes University, Wilkes-Barre, Pennsylvania, 18766, USA
| | - Yan Guo
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing, 100193, China
| | - Jigang Li
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing, 100193, China
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3
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Xie Y, Zhao Y, Chen L, Wang Y, Xue W, Kong D, Li C, Zhou L, Li H, Zhao Y, Wang B, Xu M, Zhao B, Bilska-Kos A, Wang H. ZmELF3.1 integrates the RA2-TSH4 module to repress maize tassel branching. THE NEW PHYTOLOGIST 2024; 241:490-503. [PMID: 37858961 DOI: 10.1111/nph.19329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 09/08/2023] [Indexed: 10/21/2023]
Abstract
Tassel branch number (TBN) is a key agronomic trait for adapting to high-density planting and grain yield in maize. However, the molecular regulatory mechanisms underlying tassel branching are still largely unknown. Here, we used molecular and genetic studies together to show that ZmELF3.1 plays a critical role in regulating TBN in maize. Previous studies showed that ZmELF3.1 forms the evening complex through interacting with ZmELF4 and ZmLUX to regulate flowering in maize and that RA2 and TSH4 (ZmSBP2) suppresses and promotes TBN in maize, respectively. In this study, we show that loss-of-function mutants of ZmELF3.1 exhibit a significant increase of TBN. We also show that RA2 directly binds to the promoter of TSH4 and represses its expression, thus leading to reduced TBN. We further demonstrate that ZmELF3.1 directly interacts with both RA2 and ZmELF4.2 to form tri-protein complexes that further enhance the binding of RA2 to the promoter of TSH4, leading to suppressed TSH4 expression and consequently decreased TBN. Our combined results establish a novel functional link between the ELF3-ELF4-RA2 complex and miR156-SPL regulatory module in regulating tassel branching and provide a valuable target for genetic improvement of tassel branching in maize.
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Affiliation(s)
- Yurong Xie
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Hainan Yazhou Bay Seed Lab, Sanya, 572025, China
| | - Yongping Zhao
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lihong Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yanli Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Weicong Xue
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Dexin Kong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Changyu Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Linyu Zhou
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Huiru Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yanfeng Zhao
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Baobao Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Hainan Yazhou Bay Seed Lab, Sanya, 572025, China
| | - Miaoyun Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Hainan Yazhou Bay Seed Lab, Sanya, 572025, China
| | - Binbin Zhao
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Anna Bilska-Kos
- Plant Breeding and Acclimatization Institute-National Research Institute, Department of Biochemistry and Biotechnology, Radzików, 05-870, Błonie, Poland
| | - Haiyang Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
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4
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Sterken MG, Nijveen H, van Zanten M, Jiménez-Gómez JM, Geshnizjani N, Willems LAJ, Rienstra J, Hilhorst HWM, Ligterink W, Snoek BL. Plasticity of maternal environment-dependent expression-QTLs of tomato seeds. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:28. [PMID: 36810666 PMCID: PMC9944408 DOI: 10.1007/s00122-023-04322-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 10/27/2022] [Indexed: 06/18/2023]
Abstract
Seeds are essential for plant reproduction, survival, and dispersal. Germination ability and successful establishment of young seedlings strongly depend on seed quality and on environmental factors such as nutrient availability. In tomato (Solanum lycopersicum) and many other species, seed quality and seedling establishment characteristics are determined by genetic variation, as well as the maternal environment in which the seeds develop and mature. The genetic contribution to variation in seed and seedling quality traits and environmental responsiveness can be estimated at transcriptome level in the dry seed by mapping genomic loci that affect gene expression (expression QTLs) in contrasting maternal environments. In this study, we applied RNA-sequencing to construct a linkage map and measure gene expression of seeds of a tomato recombinant inbred line (RIL) population derived from a cross between S. lycopersicum (cv. Moneymaker) and S. pimpinellifolium (G1.1554). The seeds matured on plants cultivated under different nutritional environments, i.e., on high phosphorus or low nitrogen. The obtained single-nucleotide polymorphisms (SNPs) were subsequently used to construct a genetic map. We show how the genetic landscape of plasticity in gene regulation in dry seeds is affected by the maternal nutrient environment. The combined information on natural genetic variation mediating (variation in) responsiveness to the environment may contribute to knowledge-based breeding programs aiming to develop crop cultivars that are resilient to stressful environments.
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Affiliation(s)
- Mark G. Sterken
- Laboratory of Nematology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Harm Nijveen
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, 6708 PB Wageningen, The Netherlands
- Laboratory of Bioinformatics, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Martijn van Zanten
- Plant Stress Resilience, Institute of Environmental Biology, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Jose M. Jiménez-Gómez
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France
| | - Nafiseh Geshnizjani
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Leo A. J. Willems
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Juriaan Rienstra
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Henk W. M. Hilhorst
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Wilco Ligterink
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Basten L. Snoek
- Laboratory of Nematology, Wageningen University, 6708 PB Wageningen, The Netherlands
- Theoretical Biology and Bioinformatics, Institute of Biodynamics and Biocomplexity, Utrecht University, 3584 CH Utrecht, The Netherlands
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5
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Zhang H, Cao Y, Wang Z, Ye M, Wu R. Functional Mapping of Genes Modulating Plant Shade Avoidance Using Leaf Traits. PLANTS (BASEL, SWITZERLAND) 2023; 12:608. [PMID: 36771692 PMCID: PMC9920004 DOI: 10.3390/plants12030608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 01/19/2023] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
Shade avoidance syndrome (SAS) refers to a set of plant responses that increases light capture in dense stands. This process is crucial for plants in natural and agricultural environments as they compete for resources and avoid suboptimal conditions. Although the molecular, biochemical, and physiological mechanisms underlying the SAS response have been extensively studied, the genetic basis of developmental variation in leaves in regard to leaf area, petiole length, and leaf length (i.e., their allometric relationships) remains unresolved. In this study, with the recombinant inbred line (RIL) population, the developmental traits of leaves of Arabidopsis were investigated under two growth density conditions (high- and low-density plantings). The observed changes were then reconstructed digitally, and their allometric relationships were modelled. Taking the genome-wide association analysis, the SNP genotype and the dynamic phenotype of the leaf from both densities were combined to explore the allometry QTLs. Under different densities, leaf change phenotype was analyzed from two core ecological scenarios: (i) the allometric change of the leaf area with leaf length, and (ii) the change of the leaf length with petiole length. QTLs modulating these two scenarios were characterized as 'leaf shape QTLs' and 'leaf position QTLs'. With functional mapping, results showed a total of 30 and 24 significant SNPs for shapeQTLs and positionQTLs, respectively. By annotation, immune pathway genes, photosensory receptor genes, and phytohormone genes were identified to be involved in the SAS response. Interestingly, genes modulating the immune pathway and salt tolerance, i.e., systemic acquired resistance (SAR) regulatory proteins (MININ-1-related) and salt tolerance homologs (STH), were reported to mediate the SAS response. By dissecting and comparing QTL effects from low- and high-density conditions, our results elucidate the genetic control of leaf formation in the context of the SAS response. The mechanism with leaf development × density interaction can further aid the development of density-tolerant crop varieties for agricultural practices.
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Affiliation(s)
- Han Zhang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing 100083, China
| | - Yige Cao
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing 100083, China
| | - Zijian Wang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing 100083, China
| | - Meixia Ye
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing 100083, China
| | - Rongling Wu
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing 100083, China
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6
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Ruiz-Diaz MJ, Matsusaka D, Cascales J, Sánchez DH, Sánchez-Lamas M, Cerdán PD, Botto JF. Functional analysis of PHYB polymorphisms in Arabidopsis thaliana collected in Patagonia. FRONTIERS IN PLANT SCIENCE 2022; 13:952214. [PMID: 36161012 PMCID: PMC9490419 DOI: 10.3389/fpls.2022.952214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 08/11/2022] [Indexed: 06/16/2023]
Abstract
Arabidopsis thaliana shows a wide range of natural genetic variation in light responses. Shade avoidance syndrome is a strategy of major adaptive significance that includes seed germination, elongation of vegetative structures, leaf hyponasty, and acceleration of flowering. Previously, we found that the southernmost Arabidopsis accession, collected in the south of Patagonia (Pat), is hyposensitive to light and displays a reduced response to shade light. This work aimed to explore the genetic basis of the shade avoidance response (SAR) for hypocotyl growth by QTL mapping in a recently developed 162 RIL population between Col-0 and Pat. We mapped four QTL for seedling hypocotyl growth: WL1 and WL2 QTL in white light, SHADE1 QTL in shade light, and SAR1 QTL for the SAR. PHYB is the strongest candidate gene for SAR1 QTL. Here we studied the function of two polymorphic indels in the promoter region, a GGGR deletion, and three non-synonymous polymorphisms on the PHYB coding region compared with the Col-0 reference genome. To decipher the contribution and relevance of each PHYB-Pat polymorphism, we constructed transgenic lines with single or double polymorphisms by using Col-0 as a reference genome. We found that single polymorphisms in the coding region of PHYB have discrete functions in seed germination, seedling development, and shade avoidance response. These results suggest distinct functions for each PHYB polymorphism to the adjustment of plant development to variable light conditions.
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Affiliation(s)
- María Jimena Ruiz-Diaz
- IFEVA (CONICET-UBA), Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Daniel Matsusaka
- IFEVA (CONICET-UBA), Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Jimena Cascales
- IFEVA (CONICET-UBA), Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Diego H. Sánchez
- IFEVA (CONICET-UBA), Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina
| | | | - Pablo D. Cerdán
- Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires, Argentina
| | - Javier F. Botto
- IFEVA (CONICET-UBA), Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina
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7
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Zhao J, Shi X, Chen L, Chen Q, Tian X, Ai L, Zhao H, Yang C, Yan L, Zhang M. Genetic and transcriptome analyses reveal the candidate genes and pathways involved in the inactive shade-avoidance response enabling high-density planting of soybean. FRONTIERS IN PLANT SCIENCE 2022; 13:973643. [PMID: 35991396 PMCID: PMC9382032 DOI: 10.3389/fpls.2022.973643] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 07/11/2022] [Indexed: 06/15/2023]
Abstract
High-density planting is a major way to improve crop yields. However, shade-avoidance syndrome (SAS) is a major factor limiting increased planting density. First Green Revolution addressed grass lodging problem by using dwarf/semi-dwarf genes. However, it is not suitable for soybean, which bear seeds on stalk and whose seed yield depends on plant height. Hence, mining shade-tolerant germplasms and elucidating the underlying mechanism could provide meaningful resources and information for high-yield breeding. Here, we report a high-plant density-tolerant soybean cultivar, JiDou 17, which exhibited an inactive SAS (iSAS) phenotype under high-plant density or low-light conditions at the seedling stage. A quantitative trait locus (QTL) mapping analysis using a recombinant inbred line (RIL) population showed that this iSAS phenotype is related to a major QTL, named shade-avoidance response 1 (qSAR1), which was detected. The mapping region was narrowed by a haplotype analysis into a 554 kb interval harboring 44 genes, including 4 known to be key regulators of the SAS network and 4 with a variance response to low-light conditions between near isogenic line (NIL) stems. Via RNA-seq, we identified iSAS-specific genes based on one pair of near isogenic lines (NILs) and their parents. The iSAS-specific genes expressed in the stems were significantly enriched in the "proteasomal protein catabolic" process and the proteasome pathway, which were recently suggested to promote the shade-avoidance response by enhancing PIF7 stability. Most iSAS-specific proteasome-related genes were downregulated under low-light conditions. The expression of genes related to ABA, CK, and GA significantly varied between the low- and normal-light conditions. This finding is meaningful for the cloning of genes that harbor beneficial variation(s) conferring the iSAS phenotype fixed in domestication and breeding practice.
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Affiliation(s)
- Jing Zhao
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
- School of Life Sciences, Yantai University, Yantai, China
| | - Xiaolei Shi
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
| | - Lei Chen
- School of Life Sciences, Yantai University, Yantai, China
| | - Qiang Chen
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
- Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Collaboration Innovation Center for Cell Signaling, College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Xuan Tian
- Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Collaboration Innovation Center for Cell Signaling, College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Lijuan Ai
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
- Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Collaboration Innovation Center for Cell Signaling, College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Hongtao Zhao
- Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Collaboration Innovation Center for Cell Signaling, College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Chunyan Yang
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
| | - Long Yan
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
| | - Mengchen Zhang
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
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8
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Doody E, Zha Y, He J, Poethig RS. The genetic basis of natural variation in the timing of vegetative phase change in Arabidopsis thaliana. Development 2022; 149:275256. [PMID: 35502761 DOI: 10.1242/dev.200321] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 04/19/2022] [Indexed: 11/20/2022]
Abstract
The juvenile-to-adult transition in plants is known as vegetative phase change and is marked by changes in the expression of leaf traits in response to a decrease in the level of miR156 and miR157. To determine whether this is the only mechanism of vegetative phase change, we measured the appearance of phase-specific leaf traits in 70 natural accessions of Arabidopsis thaliana. We found that leaf shape was poorly correlated with abaxial trichome production (two adult traits), that variation in these traits was not necessarily correlated with the level of miR156, and that there was little to no correlation between the appearance of adult-specific vegetative traits and flowering time. We identified eight quantitative trait loci controlling phase-specific vegetative traits from a cross between the Columbia (Col-0) and Shakdara (Sha) accessions. Only one of these quantitative trait loci includes genes known to regulate vegetative phase change (MIR156A and TOE1), which were expressed at levels consistent with the precocious phenotype of Sha. Our results suggest that vegetative phase change is regulated both by the miR156/SPL module and by genes specific to different vegetative traits, and that natural variation in vegetative phase change can arise from either source.
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Affiliation(s)
- Erin Doody
- Biology Department, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yuqi Zha
- Biology Department, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jia He
- Biology Department, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - R Scott Poethig
- Biology Department, University of Pennsylvania, Philadelphia, PA 19104, USA
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9
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Du N, Ye F, Sun J, Liu K. Stimuli-Responsive Natural Proteins and Their Applications. Chembiochem 2021; 23:e202100416. [PMID: 34773331 DOI: 10.1002/cbic.202100416] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 11/12/2021] [Indexed: 01/02/2023]
Abstract
Natural proteins are essential biomacromolecules that fulfill versatile functions in the living organism, such as their usage as cytoskeleton, nutriment transporter, homeostasis controller, catalyzer, or immune guarder. Due to the excellent mechanical properties and good biocompatibility/biodegradability, natural protein-based biomaterials are well equipped for prospective applications in various fields. Among these natural proteins, stimuli-responsive proteins can be reversibly and precisely manipulated on demand, rendering the protein-based biomaterials promising candidates for numerous applications, including disease detection, drug delivery, bio-sensing, and regenerative medicine. Therefore, we present some typical natural proteins with diverse physical stimuli-responsive properties, including temperature, light, force, electrical, and magnetic sensing in this review. The structure-function mechanism of these proteins is discussed in detail. Finally, we give a summary and perspective for the development of stimuli-responsive proteins.
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Affiliation(s)
- Na Du
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, 325001, P. R. China.,State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China
| | - Fangfu Ye
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, 325001, P. R. China
| | - Jing Sun
- Institute of Organic Chemistry, University of Ulm, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Kai Liu
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China.,Department of Chemistry, Tsinghua University, Beijing, 100084, P. R. China
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10
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Xu X, Zheng C, Lu D, Song CP, Zhang L. Phase separation in plants: New insights into cellular compartmentalization. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:1835-1855. [PMID: 34314106 DOI: 10.1111/jipb.13152] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 07/16/2021] [Indexed: 05/16/2023]
Abstract
A fundamental challenge for cells is how to coordinate various biochemical reactions in space and time. To achieve spatiotemporal control, cells have developed organelles that are surrounded by lipid bilayer membranes. Further, membraneless compartmentalization, a process induced by dynamic physical association of biomolecules through phase transition offers another efficient mechanism for intracellular organization. While our understanding of phase separation was predominantly dependent on yeast and animal models, recent findings have provided compelling evidence for emerging roles of phase separation in plants. In this review, we first provide an overview of the current knowledge of phase separation, including its definition, biophysical principles, molecular features and regulatory mechanisms. Then we summarize plant-specific phase separation phenomena and describe their functions in plant biological processes in great detail. Moreover, we propose that phase separation is an evolutionarily conserved and efficient mechanism for cellular compartmentalization which allows for distinct metabolic processes and signaling pathways, and is especially beneficial for the sessile lifestyle of plants to quickly and efficiently respond to the changing environment.
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Affiliation(s)
- Xiumei Xu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Canhui Zheng
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Dandan Lu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Chun-Peng Song
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Lixin Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
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11
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Snoek BL, Sterken MG, Nijveen H, Volkers RJM, Riksen J, Rosenstiel PC, Schulenburg H, Kammenga JE. The genetics of gene expression in a Caenorhabditis elegans multiparental recombinant inbred line population. G3 (BETHESDA, MD.) 2021; 11:jkab258. [PMID: 34568931 PMCID: PMC8496280 DOI: 10.1093/g3journal/jkab258] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 07/17/2021] [Indexed: 11/29/2022]
Abstract
Studying genetic variation of gene expression provides a powerful way to unravel the molecular components underlying complex traits. Expression quantitative trait locus (eQTL) studies have been performed in several different model species, yet most of these linkage studies have been based on the genetic segregation of two parental alleles. Recently, we developed a multiparental segregating population of 200 recombinant inbred lines (mpRILs) derived from four wild isolates (JU1511, JU1926, JU1931, and JU1941) in the nematode Caenorhabditis elegans. We used RNA-seq to investigate how multiple alleles affect gene expression in these mpRILs. We found 1789 genes differentially expressed between the parental lines. Transgression, expression beyond any of the parental lines in the mpRILs, was found for 7896 genes. For expression QTL mapping almost 9000 SNPs were available. By combining these SNPs and the RNA-seq profiles of the mpRILs, we detected almost 6800 eQTLs. Most trans-eQTLs (63%) co-locate in six newly identified trans-bands. The trans-eQTLs found in previous two-parental allele eQTL experiments and this study showed some overlap (17.5-46.8%), highlighting on the one hand that a large group of genes is affected by polymorphic regulators across populations and conditions, on the other hand, it shows that the mpRIL population allows identification of novel gene expression regulatory loci. Taken together, the analysis of our mpRIL population provides a more refined insight into C. elegans complex trait genetics and eQTLs in general, as well as a starting point to further test and develop advanced statistical models for detection of multiallelic eQTLs and systems genetics studying the genotype-phenotype relationship.
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Affiliation(s)
- Basten L Snoek
- Laboratory of Nematology, Wageningen University, NL-6708 PB Wageningen, The Netherlands
- Theoretical Biology and Bioinformatics, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Mark G Sterken
- Laboratory of Nematology, Wageningen University, NL-6708 PB Wageningen, The Netherlands
| | - Harm Nijveen
- Bioinformatics Group, Wageningen University, NL-6708 PB Wageningen, The Netherlands
| | - Rita J M Volkers
- Laboratory of Nematology, Wageningen University, NL-6708 PB Wageningen, The Netherlands
| | - Joost Riksen
- Laboratory of Nematology, Wageningen University, NL-6708 PB Wageningen, The Netherlands
| | - Philip C Rosenstiel
- Institute for Clinical Molecular Biology, University of Kiel, 24098 Kiel, Germany
- Competence Centre for Genomic Analysis (CCGA) Kiel, University of Kiel, 24098 Kiel, Germany
| | - Hinrich Schulenburg
- Zoological Institute, University of Kiel, 24098 Kiel, Germany
- Max Planck Institute for Evolutionary Biology, 24306 Ploen, Germany
| | - Jan E Kammenga
- Laboratory of Nematology, Wageningen University, NL-6708 PB Wageningen, The Netherlands
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12
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Yuan HY, Caron CT, Ramsay L, Fratini R, de la Vega MP, Vandenberg A, Weller JL, Bett KE. Genetic and gene expression analysis of flowering time regulation by light quality in lentil. ANNALS OF BOTANY 2021; 128:481-496. [PMID: 34185828 PMCID: PMC8414921 DOI: 10.1093/aob/mcab083] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 06/28/2021] [Indexed: 05/24/2023]
Abstract
BACKGROUND AND AIMS Flowering time is important due to its roles in plant adaptation to different environments and subsequent formation of crop yield. Changes in light quality affect a range of developmental processes including flowering time, but little is known about light quality-induced flowering time control in lentil. This study aims to investigate the genetic basis for differences in flowering response to light quality in lentil. METHODS We explored variation in flowering time caused by changes in red/far-red-related light quality environments of a lentil interspecific recombinant inbred line (RIL) population developed from a cross between Lens culinaris cv. Lupa and L. orientalis accession BGE 016880. A genetic linkage map was constructed and then used for identifying quantitative trait loci (QTLs) associated with flowering time regulation under different light quality environments. Differential gene expression analysis through transcriptomic study and RT-qPCR were used to identify potential candidate genes. KEY RESULTS QTL mapping located 13 QTLs controlling flower time under different light quality environments, with phenotypic variance explained ranging from 1.7 to 62.9 %. Transcriptomic profiling and gene expression analysis for both parents of this interspecific RIL population identified flowering-related genes showing environment-specific differential expression (flowering DEGs). One of these, a member of the florigen gene family FTa1 (LcFTa1), was located close to three major QTLs. Furthermore, gene expression results suggested that two other florigen genes (LcFTb1 and LcFTb2), MADS-box transcription factors such as LcAGL6/13d, LcSVPb, LcSOC1b and LcFULb, as well as bHLH transcription factor LcPIF6 and Gibberellin 20 oxidase LcGA20oxC,G may also be involved in the light quality response. CONCLUSIONS Our results show that a major component of flowering time sensitivity to light quality is tightly linked to LcFTa1 and associated with changes in its expression. This work provides a foundation for crop improvement of lentil with better adaptation to variable light environments.
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Affiliation(s)
- Hai Ying Yuan
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Carolyn T Caron
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Larissa Ramsay
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Richard Fratini
- Area de Genética, Departamento de Biología Molecular, Universidad de León, León, Spain
| | | | - Albert Vandenberg
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - James L Weller
- School of Biological Sciences, University of Tasmania, Hobart, Tasmania, Australia
| | - Kirstin E Bett
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
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13
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Phytochrome A elevates plant circadian-clock components to suppress shade avoidance in deep-canopy shade. Proc Natl Acad Sci U S A 2021; 118:2108176118. [PMID: 34187900 DOI: 10.1073/pnas.2108176118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Shade-avoiding plants can detect the presence of neighboring vegetation and evoke escape responses before canopy cover limits photosynthesis. Rapid stem elongation facilitates light foraging and enables plants to overtop competitors. A major regulator of this response is the phytochrome B photoreceptor, which becomes inactivated in light environments with a low ratio of red to far-red light (low R:FR), characteristic of vegetational shade. Although shade avoidance can provide plants with a competitive advantage in fast-growing stands, excessive stem elongation can be detrimental to plant survival. As such, plants have evolved multiple feedback mechanisms to attenuate shade-avoidance signaling. The very low R:FR and reduced levels of photosynthetically active radiation (PAR) present in deep canopy shade can, together, trigger phytochrome A (phyA) signaling, inhibiting shade avoidance and promoting plant survival when resources are severely limited. The molecular mechanisms underlying this response have not been fully elucidated. Here, we show that Arabidopsis thaliana phyA elevates early-evening expression of the central circadian-clock components TIMING OF CAB EXPRESSION 1 (TOC1), PSEUDO RESPONSE REGULATOR 7 (PRR7), EARLY FLOWERING 3 (ELF3), and ELF4 in photocycles of low R:FR and low PAR. These collectively suppress stem elongation, antagonizing shade avoidance in deep canopy shade.
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14
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Francisco M, Kliebenstein DJ, Rodríguez VM, Soengas P, Abilleira R, Cartea ME. Fine mapping identifies NAD-ME1 as a candidate underlying a major locus controlling temporal variation in primary and specialized metabolism in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:454-467. [PMID: 33523525 DOI: 10.1111/tpj.15178] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 01/19/2021] [Indexed: 05/23/2023]
Abstract
Plant metabolism is modulated by a complex interplay between internal signals and external cues. A major goal of all quantitative metabolomic studies is to clone the underlying genes to understand the mechanistic basis of this variation. Using fine-scale genetic mapping, in this work we report the identification and initial characterization of NAD-DEPENDENT MALIC ENZYME 1 (NAD-ME1) as the candidate gene underlying the pleiotropic network Met.II.15 quantitative trait locus controlling variation in plant metabolism and circadian clock outputs in the Bay × Sha Arabidopsis population. Transcript abundance and promoter analysis in NAD-ME1Bay-0 and NAD-ME1Sha alleles confirmed allele-specific expression that appears to be due a polymorphism disrupting a putative circadian cis-element binding site. Analysis of transfer DNA insertion lines and heterogeneous inbred families showed that transcript variation of the NAD-ME1 gene led to temporal shifts of tricarboxylic acid cycle intermediates, glucosinolate (GSL) accumulation, and altered regulation of several GSL biosynthesis pathway genes. Untargeted metabolomic analyses revealed complex regulatory networks of NAD-ME1 dependent upon the daytime. The mutant led to shifts in plant primary metabolites, cell wall components, isoprenoids, fatty acids, and plant immunity phytochemicals, among others. Our findings suggest that NAD-ME1 may act as a key gene to coordinate plant primary and secondary metabolism in a time-dependent manner.
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Affiliation(s)
- Marta Francisco
- Misión Biológica de Galicia (MBG-CSIC), P.O. Box 28, Pontevedra, 36080, Spain
| | - Daniel J Kliebenstein
- Department of Plant Sciences, University of California at Davis, Davis, CA, 95616, USA
- DynaMo Center of Excellence, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, DK-1871, Denmark
| | - Víctor M Rodríguez
- Misión Biológica de Galicia (MBG-CSIC), P.O. Box 28, Pontevedra, 36080, Spain
| | - Pilar Soengas
- Misión Biológica de Galicia (MBG-CSIC), P.O. Box 28, Pontevedra, 36080, Spain
| | - Rosaura Abilleira
- Misión Biológica de Galicia (MBG-CSIC), P.O. Box 28, Pontevedra, 36080, Spain
| | - María E Cartea
- Misión Biológica de Galicia (MBG-CSIC), P.O. Box 28, Pontevedra, 36080, Spain
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15
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Zhao H, Xu D, Tian T, Kong F, Lin K, Gan S, Zhang H, Li G. Molecular and functional dissection of EARLY-FLOWERING 3 (ELF3) and ELF4 in Arabidopsis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 303:110786. [PMID: 33487361 DOI: 10.1016/j.plantsci.2020.110786] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 10/31/2020] [Accepted: 11/28/2020] [Indexed: 05/18/2023]
Abstract
The circadian clock is an endogenous timekeeper system that generates biological rhythms of approximately 24 h in most organisms. EARLY FLOWERING 3 (ELF3) and ELF4 were initially identified as negative regulators of flowering time in Arabidopsis thaliana. They were then found to play crucial roles in the circadian clock by integrating environmental light and ambient temperature signals and transmitting them to the central oscillator, thereby regulating various downstream cellular and physiological processes. At dusk, ELF3 acts as a scaffold, interacting with ELF4 and the transcription factor LUX ARRHYTHMO (PHYTOCLOCK1) to form an EVENING COMPLEX (EC). This complex represses the transcription of multiple circadian clock-related genes, thus inhibiting hypocotyl elongation and flowering. Subsequent studies have expanded knowledge about the regulatory roles of the EC in thermomorphogenesis and shade responses. In addition, ELF3 and ELF4 also form multiple complexes with other proteins including chromatin remodeling factors, histone deacetylase, and transcription factors, thus enabling the transcriptional repression of diverse targets. In this review, we summarize the recent advances in elucidating the regulatory mechanisms of ELF3 and ELF4 in plants and discuss directions for future research on ELF3 and ELF4.
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Affiliation(s)
- Hang Zhao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271000, China; College of Life Sciences, Qufu Normal University, Qufu, 273165, China
| | - Di Xu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271000, China
| | - Tian Tian
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271000, China
| | - Fanying Kong
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271000, China
| | - Ke Lin
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271000, China; Department of Biology Science and Technology, Taishan University, Tai'an, 271000, China
| | - Shuo Gan
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271000, China
| | - Haisen Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271000, China
| | - Gang Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271000, China.
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16
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Mapping quantitative trait loci and predicting candidate genes for leaf angle in maize. PLoS One 2021; 16:e0245129. [PMID: 33406127 PMCID: PMC7787474 DOI: 10.1371/journal.pone.0245129] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 12/22/2020] [Indexed: 11/29/2022] Open
Abstract
Leaf angle of maize is a fundamental determinant of plant architecture and an important trait influencing photosynthetic efficiency and crop yields. To broaden our understanding of the genetic mechanisms of leaf angle formation, we constructed a F3:4 recombinant inbred lines (RIL) population to map QTL for leaf angle. The RIL was derived from a cross between a model inbred line (B73) with expanded leaf architecture and an elite inbred line (Zheng58) with compact leaf architecture. A sum of eight QTL were detected on chromosome 1, 2, 3, 4 and 8. Single QTL explained 4.3 to 14.2% of the leaf angle variance. Additionally, some important QTL were confirmed through a heterogeneous inbred family (HIF) approach. Furthermore, twenty-four candidate genes for leaf angle were predicted through whole-genome re-sequencing and expression analysis in qLA02-01and qLA08-01 regions. These results will be helpful to elucidate the genetic mechanism of leaf angle formation in maize and benefit to clone the favorable allele for leaf angle. Besides, this will be helpful to develop the novel maize varieties with ideal plant architecture through marker-assisted selection.
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17
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Genome-Wide Association Studies in Arabidopsis thaliana: Statistical Analysis and Network-Based Augmentation of Signals. Methods Mol Biol 2020; 2200:187-210. [PMID: 33175379 DOI: 10.1007/978-1-0716-0880-7_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
Genome-wide association studies (GWAS) have proven effective at identifying genetic variants and genes that are associated with phenotypes in humans, animals, and plants. Since most phenotypes of plant species are complex traits regulated by many genes and their functional interactions, GWAS are increasing in popularity for genetic dissections of plant phenotypes. For the reference plant, Arabidopsis thaliana, detailed information on genetic variations became available with the completion of the 1001 Genomes Project, enabling highly resolved association mapping between chromosomal loci and complex traits. Improvements have been made in the statistical analysis methods for testing the significance of genotype-to-phenotype associations, thereby substantially reducing the confounding effects of population structures. Furthermore, there have been large efforts toward post-GWAS augmentation of signals via integration with other types of information to overcome the limited statistical power of GWAS. This chapter describes the stepwise procedure of GWAS in Arabidopsis, focusing on data analysis processes including preprocessing of genotype and phenotype data, statistical analysis to identify phenotype-associated chromosomal loci, identification of phenotype-associated genes based on the phenotype-associated loci, and finally network-based augmentation of GWAS signals to identify additional candidate genes for the phenotype.
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18
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Network Analysis Prioritizes DEWAX and ICE1 as the Candidate Genes for Major eQTL Hotspots in Seed Germination of Arabidopsis thaliana. G3-GENES GENOMES GENETICS 2020; 10:4215-4226. [PMID: 32963085 PMCID: PMC7642920 DOI: 10.1534/g3.120.401477] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Seed germination is characterized by a constant change of gene expression across different time points. These changes are related to specific processes, which eventually determine the onset of seed germination. To get a better understanding on the regulation of gene expression during seed germination, we performed a quantitative trait locus mapping of gene expression (eQTL) at four important seed germination stages (primary dormant, after-ripened, six-hour after imbibition, and radicle protrusion stage) using Arabidopsis thaliana Bay x Sha recombinant inbred lines (RILs). The mapping displayed the distinctness of the eQTL landscape for each stage. We found several eQTL hotspots across stages associated with the regulation of expression of a large number of genes. Interestingly, an eQTL hotspot on chromosome five collocates with hotspots for phenotypic and metabolic QTL in the same population. Finally, we constructed a gene co-expression network to prioritize the regulatory genes for two major eQTL hotspots. The network analysis prioritizes transcription factors DEWAX and ICE1 as the most likely regulatory genes for the hotspot. Together, we have revealed that the genetic regulation of gene expression is dynamic along the course of seed germination.
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19
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Multiple Loci Control Variation in Plasticity to Foliar Shade Throughout Development in Arabidopsis thaliana. G3-GENES GENOMES GENETICS 2020; 10:4103-4114. [PMID: 32988993 PMCID: PMC7642929 DOI: 10.1534/g3.120.401259] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The shade avoidance response is a set of developmental changes exhibited by plants to avoid shading by competitors, and is an important model of adaptive plant plasticity. While the mechanisms of sensing shading by other plants are well-known and appear conserved across plants, less is known about the developmental mechanisms that result in the diverse array of morphological and phenological responses to shading. This is particularly true for traits that appear later in plant development. Here we use a nested association mapping (NAM) population of Arabidopsis thaliana to decipher the genetic architecture of the shade avoidance response in late-vegetative and reproductive plants. We focused on four traits: bolting time, rosette size, inflorescence growth rate, and inflorescence size, found plasticity in each trait in response to shade, and detected 17 total QTL; at least one of which is a novel locus not previously identified for shade responses in Arabidopsis. Using path analysis, we dissected each colocalizing QTL into direct effects on each trait and indirect effects transmitted through direct effects on earlier developmental traits. Doing this separately for each of the seven NAM populations in each environment, we discovered considerable heterogeneity among the QTL effects across populations, suggesting allelic series at multiple QTL or interactions between QTL and the genetic background or the environment. Our results provide insight into the development and variation in shade avoidance responses in Arabidopsis, and emphasize the value of directly modeling the relationships among traits when studying the genetics of complex developmental syndromes.
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20
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Sterken MG, Bevers RPJ, Volkers RJM, Riksen JAG, Kammenga JE, Snoek BL. Dissecting the eQTL Micro-Architecture in Caenorhabditis elegans. Front Genet 2020; 11:501376. [PMID: 33240309 PMCID: PMC7670075 DOI: 10.3389/fgene.2020.501376] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 10/13/2020] [Indexed: 01/11/2023] Open
Abstract
The study of expression quantitative trait loci (eQTL) using natural variation in inbred populations has yielded detailed information about the transcriptional regulation of complex traits. Studies on eQTL using recombinant inbred lines (RILs) led to insights on cis and trans regulatory loci of transcript abundance. However, determining the underlying causal polymorphic genes or variants is difficult, but ultimately essential for the understanding of regulatory networks of complex traits. This requires insight into whether associated loci are single eQTL or a combination of closely linked eQTL, and how this QTL micro-architecture depends on the environment. We addressed these questions by testing for independent replication of previously mapped eQTL in Caenorhabditis elegans using new data from introgression lines (ILs). Both populations indicate that the overall heritability of gene expression, number, and position of eQTL differed among environments. Across environments we were able to replicate 70% of the cis- and 40% of the trans-eQTL using the ILs. Testing eight different simulation models, we suggest that additive effects explain up to 60-93% of RIL/IL heritability for all three environments. Closely linked eQTL explained up to 40% of RIL/IL heritability in the control environment whereas only 7% in the heat-stress and recovery environments. In conclusion, we show that reproducibility of eQTL was higher for cis vs. trans eQTL and that the environment affects the eQTL micro-architecture.
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Affiliation(s)
- Mark G. Sterken
- Laboratory of Nematology, Wageningen University & Research, Wageningen, Netherlands
| | - Roel P. J. Bevers
- Laboratory of Nematology, Wageningen University & Research, Wageningen, Netherlands
| | - Rita J. M. Volkers
- Laboratory of Nematology, Wageningen University & Research, Wageningen, Netherlands
| | - Joost A. G. Riksen
- Laboratory of Nematology, Wageningen University & Research, Wageningen, Netherlands
| | - Jan E. Kammenga
- Laboratory of Nematology, Wageningen University & Research, Wageningen, Netherlands
| | - Basten L. Snoek
- Laboratory of Nematology, Wageningen University & Research, Wageningen, Netherlands
- Theoretical Biology & Bioinformatics, Utrecht University, Utrecht, Netherlands
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21
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Hew B, Tan QW, Goh W, Ng JWX, Mutwil M. LSTrAP-Crowd: prediction of novel components of bacterial ribosomes with crowd-sourced analysis of RNA sequencing data. BMC Biol 2020; 18:114. [PMID: 32883264 PMCID: PMC7470450 DOI: 10.1186/s12915-020-00846-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 08/12/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Bacterial resistance to antibiotics is a growing health problem that is projected to cause more deaths than cancer by 2050. Consequently, novel antibiotics are urgently needed. Since more than half of the available antibiotics target the structurally conserved bacterial ribosomes, factors involved in protein synthesis are thus prime targets for the development of novel antibiotics. However, experimental identification of these potential antibiotic target proteins can be labor-intensive and challenging, as these proteins are likely to be poorly characterized and specific to few bacteria. Here, we use a bioinformatics approach to identify novel components of protein synthesis. RESULTS In order to identify these novel proteins, we established a Large-Scale Transcriptomic Analysis Pipeline in Crowd (LSTrAP-Crowd), where 285 individuals processed 26 terabytes of RNA-sequencing data of the 17 most notorious bacterial pathogens. In total, the crowd processed 26,269 RNA-seq experiments and used the data to construct gene co-expression networks, which were used to identify more than a hundred uncharacterized genes that were transcriptionally associated with protein synthesis. We provide the identity of these genes together with the processed gene expression data. CONCLUSIONS We identified genes related to protein synthesis in common bacterial pathogens and thus provide a resource of potential antibiotic development targets for experimental validation. The data can be used to explore additional vulnerabilities of bacteria, while our approach demonstrates how the processing of gene expression data can be easily crowd-sourced.
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Affiliation(s)
- Benedict Hew
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Qiao Wen Tan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - William Goh
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Jonathan Wei Xiong Ng
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Marek Mutwil
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
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Jung JH, Barbosa AD, Hutin S, Kumita JR, Gao M, Derwort D, Silva CS, Lai X, Pierre E, Geng F, Kim SB, Baek S, Zubieta C, Jaeger KE, Wigge PA. A prion-like domain in ELF3 functions as a thermosensor in Arabidopsis. Nature 2020. [PMID: 32848244 DOI: 10.1038/s41586-020-2644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Temperature controls plant growth and development, and climate change has already altered the phenology of wild plants and crops1. However, the mechanisms by which plants sense temperature are not well understood. The evening complex is a major signalling hub and a core component of the plant circadian clock2,3. The evening complex acts as a temperature-responsive transcriptional repressor, providing rhythmicity and temperature responsiveness to growth through unknown mechanisms2,4-6. The evening complex consists of EARLY FLOWERING 3 (ELF3)4,7, a large scaffold protein and key component of temperature sensing; ELF4, a small α-helical protein; and LUX ARRYTHMO (LUX), a DNA-binding protein required to recruit the evening complex to transcriptional targets. ELF3 contains a polyglutamine (polyQ) repeat8-10, embedded within a predicted prion domain (PrD). Here we find that the length of the polyQ repeat correlates with thermal responsiveness. We show that ELF3 proteins in plants from hotter climates, with no detectable PrD, are active at high temperatures, and lack thermal responsiveness. The temperature sensitivity of ELF3 is also modulated by the levels of ELF4, indicating that ELF4 can stabilize the function of ELF3. In both Arabidopsis and a heterologous system, ELF3 fused with green fluorescent protein forms speckles within minutes in response to higher temperatures, in a PrD-dependent manner. A purified fragment encompassing the ELF3 PrD reversibly forms liquid droplets in response to increasing temperatures in vitro, indicating that these properties reflect a direct biophysical response conferred by the PrD. The ability of temperature to rapidly shift ELF3 between active and inactive states via phase transition represents a previously unknown thermosensory mechanism.
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Affiliation(s)
- Jae-Hoon Jung
- Sainsbury Laboratory, University of Cambridge, Cambridge, UK
- Department of Biological Sciences, Sungkyunkwan University, Suwon, South Korea
| | | | - Stephanie Hutin
- Laboratoire de Physiologie Cellulaire and Végétale, Université Grenoble Alpes/CNRS/CEA/INRAE, Grenoble, France
| | - Janet R Kumita
- Department of Chemistry, University of Cambridge, Cambridge, UK
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - Mingjun Gao
- Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | | | - Catarina S Silva
- Laboratoire de Physiologie Cellulaire and Végétale, Université Grenoble Alpes/CNRS/CEA/INRAE, Grenoble, France
| | - Xuelei Lai
- Sainsbury Laboratory, University of Cambridge, Cambridge, UK
- Laboratoire de Physiologie Cellulaire and Végétale, Université Grenoble Alpes/CNRS/CEA/INRAE, Grenoble, France
| | - Elodie Pierre
- Laboratoire de Physiologie Cellulaire and Végétale, Université Grenoble Alpes/CNRS/CEA/INRAE, Grenoble, France
| | - Feng Geng
- Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Sol-Bi Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, South Korea
| | - Sujeong Baek
- Department of Biological Sciences, Sungkyunkwan University, Suwon, South Korea
| | - Chloe Zubieta
- Laboratoire de Physiologie Cellulaire and Végétale, Université Grenoble Alpes/CNRS/CEA/INRAE, Grenoble, France
| | - Katja E Jaeger
- Sainsbury Laboratory, University of Cambridge, Cambridge, UK
- Leibniz-Institut für Gemüse- und Zierpflanzenbau, Großbeeren, Germany
| | - Philip A Wigge
- Sainsbury Laboratory, University of Cambridge, Cambridge, UK.
- Leibniz-Institut für Gemüse- und Zierpflanzenbau, Großbeeren, Germany.
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany.
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Jung JH, Barbosa AD, Hutin S, Kumita JR, Gao M, Derwort D, Silva CS, Lai X, Pierre E, Geng F, Kim SB, Baek S, Zubieta C, Jaeger KE, Wigge PA. A prion-like domain in ELF3 functions as a thermosensor in Arabidopsis. Nature 2020; 585:256-260. [DOI: 10.1038/s41586-020-2644-7] [Citation(s) in RCA: 176] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 07/15/2020] [Indexed: 12/11/2022]
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LSTrAP-Cloud: A User-Friendly Cloud Computing Pipeline to Infer Coexpression Networks. Genes (Basel) 2020; 11:genes11040428. [PMID: 32316247 PMCID: PMC7230309 DOI: 10.3390/genes11040428] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/08/2020] [Accepted: 04/13/2020] [Indexed: 12/15/2022] Open
Abstract
As genomes become more and more available, gene function prediction presents itself as one of the major hurdles in our quest to extract meaningful information on the biological processes genes participate in. In order to facilitate gene function prediction, we show how our user-friendly pipeline, the Large-Scale Transcriptomic Analysis Pipeline in Cloud (LSTrAP-Cloud), can be useful in helping biologists make a shortlist of genes involved in a biological process that they might be interested in, by using a single gene of interest as bait. The LSTrAP-Cloud is based on Google Colaboratory, and provides user-friendly tools that process quality-control RNA sequencing data streamed from the European Nucleotide Archive. The LSTRAP-Cloud outputs a gene coexpression network that can be used to identify functionally related genes for any organism with a sequenced genome and publicly available RNA sequencing data. Here, we used the biosynthesis pathway of Nicotiana tabacum as a case study to demonstrate how enzymes, transporters, and transcription factors involved in the synthesis, transport, and regulation of nicotine can be identified using our pipeline.
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Ferrari C, Shivhare D, Hansen BO, Pasha A, Esteban E, Provart NJ, Kragler F, Fernie A, Tohge T, Mutwil M. Expression Atlas of Selaginella moellendorffii Provides Insights into the Evolution of Vasculature, Secondary Metabolism, and Roots. THE PLANT CELL 2020; 32:853-870. [PMID: 31988262 PMCID: PMC7145505 DOI: 10.1105/tpc.19.00780] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 01/08/2020] [Accepted: 01/14/2020] [Indexed: 05/20/2023]
Abstract
Selaginella moellendorffii is a representative of the lycophyte lineage that is studied to understand the evolution of land plant traits such as the vasculature, leaves, stems, roots, and secondary metabolism. However, only a few studies have investigated the expression and transcriptional coordination of Selaginella genes, precluding us from understanding the evolution of the transcriptional programs behind these traits. We present a gene expression atlas comprising all major organs, tissue types, and the diurnal gene expression profiles for S. moellendorffii We show that the transcriptional gene module responsible for the biosynthesis of lignocellulose evolved in the ancestor of vascular plants and pinpoint the duplication and subfunctionalization events that generated multiple gene modules involved in the biosynthesis of various cell wall types. We demonstrate how secondary metabolism is transcriptionally coordinated and integrated with other cellular pathways. Finally, we identify root-specific genes and show that the evolution of roots did not coincide with an increased appearance of gene families, suggesting that the development of new organs does not coincide with increased fixation of new gene functions. Our updated database at conekt.plant.tools represents a valuable resource for studying the evolution of genes, gene families, transcriptomes, and functional gene modules in the Archaeplastida kingdom.
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Affiliation(s)
- Camilla Ferrari
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Devendra Shivhare
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Bjoern Oest Hansen
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Asher Pasha
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Eddi Esteban
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Nicholas J Provart
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Friedrich Kragler
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Alisdair Fernie
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Takayuki Tohge
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Marek Mutwil
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
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Ferrari C, Mutwil M. Gene expression analysis of Cyanophora paradoxa reveals conserved abiotic stress responses between basal algae and flowering plants. THE NEW PHYTOLOGIST 2020; 225:1562-1577. [PMID: 31602652 DOI: 10.1111/nph.16257] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 10/04/2019] [Indexed: 05/25/2023]
Abstract
The glaucophyte Cyanophora paradoxa represents the most basal member of the kingdom Archaeplastida, but the function and expression of most of its genes are unknown. This information is needed to uncover how functional gene modules, that is groups of genes performing a given function, evolved in the plant kingdom. We have generated a gene expression atlas capturing responses of Cyanophora to various abiotic stresses. The data were included in the CoNekT-Plants database, enabling comparative transcriptomic analyses across two algae and six land plants. We demonstrate how the database can be used to study gene expression, co-expression networks and gene function in Cyanophora, and how conserved transcriptional programs can be identified. We identified gene modules involved in phycobilisome biosynthesis, response to high light and cell division. While we observed no correlation between the number of differentially expressed genes and the impact on growth of Cyanophora, we found that the response to stress involves a conserved, kingdom-wide transcriptional reprogramming, which is activated upon most stresses in algae and land plants. The Cyanophora stress gene expression atlas and the tools found in the https://conekt.plant.tools/ database thus provide a useful resource to reveal functionally related genes and stress responses in the plant kingdom.
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Affiliation(s)
- Camilla Ferrari
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam, Germany
| | - Marek Mutwil
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam, Germany
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
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Jiang Y, Yang C, Huang S, Xie F, Xu Y, Liu C, Li L. The ELF3-PIF7 Interaction Mediates the Circadian Gating of the Shade Response in Arabidopsis. iScience 2019; 22:288-298. [PMID: 31805433 PMCID: PMC6909221 DOI: 10.1016/j.isci.2019.11.029] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 06/04/2019] [Accepted: 11/14/2019] [Indexed: 12/20/2022] Open
Abstract
Light filtered through dense planting initiates the shade avoidance syndrome (SAS) in plants, which helps them compete against their neighbors. Quantitative trait loci (QTL)-based analysis identified the nighttime-expressed clock component ELF3 as a new player in the SAS, but its detailed mechanism is unclear. Here, we show that the circadian clock gates shade-induced gene expression and hypocotyl elongation at night. ELF3 is involved in nighttime suppression via interaction with and inactivation of PHYTOCHROME-INTERACTING FACTOR 7 (PIF7). Loss of function of ELF3 restores the shade induction, which is largely reduced in the absence of PIF7, indicating that ELF3 acts upstream of PIF7. Finally, we found that the repressive activity of ELF3 on the shade response is stronger under short days than under long days. Our results reveal that the interaction between ELF3 and PIF7 mediates the circadian gating of the SAS, which coordinates the daily control of physiological outputs. ELF3 is involved in the inhibition of the shade response at night ELF3 interacts with PIF7 and prevents PIF7 from binding DNA ELF3 acts upstream of PIF7 in shade-induced growth Repressive activity of ELF3 is stronger under SDs than under LDs
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Affiliation(s)
- Yupei Jiang
- State Key Laboratory of Genetic Engineering and Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, People's Republic of China
| | - Chuanwei Yang
- State Key Laboratory of Genetic Engineering and Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, People's Republic of China
| | - Sha Huang
- State Key Laboratory of Genetic Engineering and Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, People's Republic of China
| | - Famin Xie
- State Key Laboratory of Genetic Engineering and Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, People's Republic of China
| | - Yitian Xu
- State Key Laboratory of Genetic Engineering and Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, People's Republic of China
| | - Chang Liu
- State Key Laboratory of Genetic Engineering and Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, People's Republic of China
| | - Lin Li
- State Key Laboratory of Genetic Engineering and Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, People's Republic of China.
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Tan QW, Mutwil M. Inferring biosynthetic and gene regulatory networks from Artemisia annua RNA sequencing data on a credit card-sized ARM computer. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1863:194429. [PMID: 31634636 DOI: 10.1016/j.bbagrm.2019.194429] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 09/06/2019] [Accepted: 09/06/2019] [Indexed: 02/05/2023]
Abstract
Prediction of gene function and gene regulatory networks is one of the most active topics in bioinformatics. The accumulation of publicly available gene expression data for hundreds of plant species, together with advances in bioinformatical methods and affordable computing, sets ingenuity as one of the major bottlenecks in understanding gene function and regulation. Here, we show how a credit card-sized computer retailing for <50 USD can be used to rapidly predict gene function and infer regulatory networks from RNA sequencing data. To achieve this, we constructed a bioinformatical pipeline that downloads and allows quality-control of RNA sequencing data; and generates a gene co-expression network that can reveal enzymes and transcription factors participating and controlling a given biosynthetic pathway. We exemplify this by first identifying genes and transcription factors involved in the biosynthesis of secondary cell wall in the plant Artemisia annua, the main natural source of the anti-malarial drug artemisinin. Networks were then used to dissect the artemisinin biosynthesis pathway, which suggest potential transcription factors regulating artemisinin biosynthesis. We provide the source code of our pipeline (https://github.com/mutwil/LSTrAP-Lite) and envision that the ubiquity of affordable computing, availability of biological data and increased bioinformatical training of biologists will transform the field of bioinformatics. This article is part of a Special Issue entitled: Transcriptional Profiles and Regulatory Gene Networks edited by Dr. Dr. Federico Manuel Giorgi and Dr. Shaun Mahony.
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Affiliation(s)
- Qiao Wen Tan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Marek Mutwil
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
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30
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Galvāo VC, Fiorucci AS, Trevisan M, Franco-Zorilla JM, Goyal A, Schmid-Siegert E, Solano R, Fankhauser C. PIF transcription factors link a neighbor threat cue to accelerated reproduction in Arabidopsis. Nat Commun 2019; 10:4005. [PMID: 31488833 PMCID: PMC6728355 DOI: 10.1038/s41467-019-11882-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Accepted: 08/08/2019] [Indexed: 12/18/2022] Open
Abstract
Changes in light quality indicative of competition for this essential resource influence plant growth and developmental transitions; however, little is known about neighbor proximity-induced acceleration of reproduction. Phytochrome B (phyB) senses light cues from plant competitors, ultimately leading to the expression of the floral inducers FLOWERING LOCUS T (FT) and TWIN SISTER of FT (TSF). Here we show that PHYTOCHROME INTERACTING FACTORs 4, 5 and 7 (PIF4, PIF5 and PIF7) mediate neighbor proximity-induced flowering, with PIF7 playing a prominent role. These transcriptional regulators act directly downstream of phyB to promote expression of FT and TSF. Neighbor proximity enhances PIF accumulation towards the end of the day, coinciding with enhanced floral inducer expression. We present evidence supporting direct PIF-regulated TSF expression. The relevance of our findings is illustrated by the prior identification of FT, TSF and PIF4 as loci underlying flowering time regulation in natural conditions.
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Affiliation(s)
- Vinicius Costa Galvāo
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015, Lausanne, Switzerland
| | - Anne-Sophie Fiorucci
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015, Lausanne, Switzerland
| | - Martine Trevisan
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015, Lausanne, Switzerland
| | - José Manuel Franco-Zorilla
- Genomics Unit and Plant Molecular Biology Department, Centro Nacional de Biotecnologia (CSIC), Campus de Cantoblanco, Darwin 3, 28049, Madrid, Spain
| | - Anupama Goyal
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015, Lausanne, Switzerland
- Syngene International Ltd, Bangalore, 560 099, India
| | - Emanuel Schmid-Siegert
- SIB Swiss Institute for Bioinformatics, University of Lausanne, 1015, Lausanne, Switzerland
| | - Roberto Solano
- Genomics Unit and Plant Molecular Biology Department, Centro Nacional de Biotecnologia (CSIC), Campus de Cantoblanco, Darwin 3, 28049, Madrid, Spain
| | - Christian Fankhauser
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015, Lausanne, Switzerland.
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Li Y, Jiang H, Sun X, Muhammad AA, Liu J, Liu W, Shu K, Shang J, Yang F, Wu X, Yong T, Wang X, Yu L, Liu C, Yang W, Du J. Quantitative proteomic analyses identified multiple sugar metabolic proteins in soybean under shade stress. J Biochem 2019; 165:277-288. [PMID: 30496541 DOI: 10.1093/jb/mvy103] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 11/28/2018] [Indexed: 12/20/2022] Open
Abstract
Soybean-based intercropping is important for sustainable agricultural practice on a regional and global scale. However, most soybean varieties use shade avoidance strategy to acquire more light absorption when suffered in canopy shade in intercropping systems, thus reduced the yield of the whole population on a farmland. The mechanisms underlying early response of soybean in shade avoidance is still largely unknown. Here we report our identification of differentially accumulated proteins in shade-sensitive soybean seedlings by global quantitative proteome analysis under white light (WL) and shade conditions. By using Tandem Mass Tag (TMT) labelling and HPLC fractionation followed by high-resolution LC-MS/MS analysis, 29 proteins were found up-regulated and 412 proteins were found down-regulated in soybean seedlings by 2-h shade stress than that by 2-h WL treatment. Multiple differentially expressed proteins are enriched in carbohydrate metabolic process especially in the biosynthetic pathways of cell wall polysaccharides in soybean seedlings by shade stress comparing to those in WL growth conditions. Physiological assays showed that saccharides were rapidly declined in shoot apex of soybean seedlings under a short-term shading. Our results would provide new insights into the mechanisms of shade avoidance responses in soybean seedlings.
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Affiliation(s)
- Yan Li
- Key Laboratory of Crop Eco-physiology and Farming System in Southwest China (Ministry of Agriculture), College of Agronomy, Sichuan Agricultural University, 211 Huimin Road, Wenjiang district, Chengdu, China
| | - Hengke Jiang
- Key Laboratory of Crop Eco-physiology and Farming System in Southwest China (Ministry of Agriculture), College of Agronomy, Sichuan Agricultural University, 211 Huimin Road, Wenjiang district, Chengdu, China
| | - Xin Sun
- Key Laboratory of Crop Eco-physiology and Farming System in Southwest China (Ministry of Agriculture), College of Agronomy, Sichuan Agricultural University, 211 Huimin Road, Wenjiang district, Chengdu, China
| | - Ahsan Asghar Muhammad
- Key Laboratory of Crop Eco-physiology and Farming System in Southwest China (Ministry of Agriculture), College of Agronomy, Sichuan Agricultural University, 211 Huimin Road, Wenjiang district, Chengdu, China
| | - Jiang Liu
- Key Laboratory of Crop Eco-physiology and Farming System in Southwest China (Ministry of Agriculture), College of Agronomy, Sichuan Agricultural University, 211 Huimin Road, Wenjiang district, Chengdu, China
| | - Weiguo Liu
- Key Laboratory of Crop Eco-physiology and Farming System in Southwest China (Ministry of Agriculture), College of Agronomy, Sichuan Agricultural University, 211 Huimin Road, Wenjiang district, Chengdu, China
| | - Kai Shu
- Key Laboratory of Crop Eco-physiology and Farming System in Southwest China (Ministry of Agriculture), College of Agronomy, Sichuan Agricultural University, 211 Huimin Road, Wenjiang district, Chengdu, China
| | - Jing Shang
- Key Laboratory of Crop Eco-physiology and Farming System in Southwest China (Ministry of Agriculture), College of Agronomy, Sichuan Agricultural University, 211 Huimin Road, Wenjiang district, Chengdu, China
| | - Feng Yang
- Key Laboratory of Crop Eco-physiology and Farming System in Southwest China (Ministry of Agriculture), College of Agronomy, Sichuan Agricultural University, 211 Huimin Road, Wenjiang district, Chengdu, China
| | - Xiaoling Wu
- Key Laboratory of Crop Eco-physiology and Farming System in Southwest China (Ministry of Agriculture), College of Agronomy, Sichuan Agricultural University, 211 Huimin Road, Wenjiang district, Chengdu, China
| | - Taiwen Yong
- Key Laboratory of Crop Eco-physiology and Farming System in Southwest China (Ministry of Agriculture), College of Agronomy, Sichuan Agricultural University, 211 Huimin Road, Wenjiang district, Chengdu, China
| | - Xiaochun Wang
- Key Laboratory of Crop Eco-physiology and Farming System in Southwest China (Ministry of Agriculture), College of Agronomy, Sichuan Agricultural University, 211 Huimin Road, Wenjiang district, Chengdu, China
| | - Liang Yu
- Key Laboratory of Crop Eco-physiology and Farming System in Southwest China (Ministry of Agriculture), College of Agronomy, Sichuan Agricultural University, 211 Huimin Road, Wenjiang district, Chengdu, China
| | - Chunyan Liu
- Key Laboratory of Crop Eco-physiology and Farming System in Southwest China (Ministry of Agriculture), College of Agronomy, Sichuan Agricultural University, 211 Huimin Road, Wenjiang district, Chengdu, China
| | - Wenyu Yang
- Key Laboratory of Crop Eco-physiology and Farming System in Southwest China (Ministry of Agriculture), College of Agronomy, Sichuan Agricultural University, 211 Huimin Road, Wenjiang district, Chengdu, China
| | - Junbo Du
- Key Laboratory of Crop Eco-physiology and Farming System in Southwest China (Ministry of Agriculture), College of Agronomy, Sichuan Agricultural University, 211 Huimin Road, Wenjiang district, Chengdu, China
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Cheng CH, Shen BN, Shang QW, Liu LYD, Peng KC, Chen YH, Chen FF, Hu SF, Wang YT, Wang HC, Wu HY, Lo CT, Lin SS. Gene-to-Gene Network Analysis of the Mediation of Plant Innate Immunity by the Eliciting Plant Response-Like 1 (Epl1) Elicitor of Trichoderma formosa. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:683-691. [PMID: 29436965 DOI: 10.1094/mpmi-01-18-0002-ta] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
A new clade, Trichoderma formosa, secretes eliciting plant response-like 1 (Epl1), a small peptide elicitor that stimulates plant immunity. Nicotiana benthamiana pretreated with Epl1 for 3 days developed immunity against Tomato mosaic virus (ToMV) infection. The transcriptome profiles of T. formosa and N. benthamiana were obtained by deep sequencing; the transcript of Epl1 is 736 nt in length and encodes a 12-kDa peptide. Identifying critical genes in Epl1-mediated immunity was challenging due to high similarity between the transcriptome expression profiles of Epl1-treated and ToMV-infected N. benthamiana samples. Therefore, an efficient bioinformatics data mining approach was used for high-throughput transcriptomic assays in this study. We integrated gene-to-gene network analysis into the ContigViews transcriptome database, and genes related to jasmonic acid and ethylene signaling, salicylic acid signaling, leucine-rich repeats, transcription factors, and histone variants were hubs in the gene-to-gene networks. In this study, the Epl1 of T. formosa triggers plant immunity against various pathogen infections. Moreover, we demonstrated that high-throughput data mining and gene-to-gene network analysis can be used to identify critical candidate genes for further studies on the mechanisms of plant immunity.
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Affiliation(s)
- Chi-Hua Cheng
- 1 Department of Biotechnology, National Formosa University, Yulin, Taiwan
| | - Bing-Nan Shen
- 2 Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Qian-Wen Shang
- 2 Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | | | - Kou-Cheng Peng
- 4 Institute of Biotechnology, National Dong-Hwa University, Hualien, Taiwan
| | - Yan-Huey Chen
- 2 Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Fang-Fang Chen
- 2 Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Sin-Fen Hu
- 2 Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Yu-Tai Wang
- 5 National Center for High-Performance Computing, National Applied Research Laboratories, Hsinchu, Taiwan
| | - Hao-Ching Wang
- 6 Graduate Institute of Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Hsin-Yi Wu
- 7 Instrumentation Center, National Taiwan University
| | - Chaur-Tsuen Lo
- 1 Department of Biotechnology, National Formosa University, Yulin, Taiwan
| | - Shih-Shun Lin
- 2 Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
- 5 National Center for High-Performance Computing, National Applied Research Laboratories, Hsinchu, Taiwan
- 8 Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan; and
- 9 Center of Biotechnology, National Taiwan University
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Hansen BO, Meyer EH, Ferrari C, Vaid N, Movahedi S, Vandepoele K, Nikoloski Z, Mutwil M. Ensemble gene function prediction database reveals genes important for complex I formation in Arabidopsis thaliana. THE NEW PHYTOLOGIST 2018; 217:1521-1534. [PMID: 29205376 DOI: 10.1111/nph.14921] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 10/24/2017] [Indexed: 05/25/2023]
Abstract
Recent advances in gene function prediction rely on ensemble approaches that integrate results from multiple inference methods to produce superior predictions. Yet, these developments remain largely unexplored in plants. We have explored and compared two methods to integrate 10 gene co-function networks for Arabidopsis thaliana and demonstrate how the integration of these networks produces more accurate gene function predictions for a larger fraction of genes with unknown function. These predictions were used to identify genes involved in mitochondrial complex I formation, and for five of them, we confirmed the predictions experimentally. The ensemble predictions are provided as a user-friendly online database, EnsembleNet. The methods presented here demonstrate that ensemble gene function prediction is a powerful method to boost prediction performance, whereas the EnsembleNet database provides a cutting-edge community tool to guide experimentalists.
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Affiliation(s)
- Bjoern Oest Hansen
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, Potsdam, 14476, Germany
- Institut für Medizinische Informatik, Universitätsmedizin Göttingen, Robert-Koch-Str. 40, Göttingen, 37075, Germany
| | - Etienne H Meyer
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, Potsdam, 14476, Germany
| | - Camilla Ferrari
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, Potsdam, 14476, Germany
| | - Neha Vaid
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, Potsdam, 14476, Germany
| | - Sara Movahedi
- Department of Plant Biotechnology and Bioinformatics, VIB Center for Plant Systems Biology, Ghent University, Technologiepark 927, Gent, B-9052, Belgium
- Rijk Zwaan Breeding BV, Burgemeester Crezéelaan 40, PO Box 40, De Lier, 2678 ZG, the Netherlands
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, VIB Center for Plant Systems Biology, Ghent University, Technologiepark 927, Gent, B-9052, Belgium
| | - Zoran Nikoloski
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, Potsdam, 14476, Germany
- Bioinformatics Group, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, Potsdam-Golm, 14476, Germany
| | - Marek Mutwil
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, Potsdam, 14476, Germany
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
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Serin EAR, Snoek LB, Nijveen H, Willems LAJ, Jiménez-Gómez JM, Hilhorst HWM, Ligterink W. Construction of a High-Density Genetic Map from RNA-Seq Data for an Arabidopsis Bay-0 × Shahdara RIL Population. Front Genet 2017; 8:201. [PMID: 29259624 PMCID: PMC5723289 DOI: 10.3389/fgene.2017.00201] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 11/21/2017] [Indexed: 12/17/2022] Open
Abstract
High-density genetic maps are essential for high resolution mapping of quantitative traits. Here, we present a new genetic map for an Arabidopsis Bayreuth × Shahdara recombinant inbred line (RIL) population, built on RNA-seq data. RNA-seq analysis on 160 RILs of this population identified 30,049 single-nucleotide polymorphisms (SNPs) covering the whole genome. Based on a 100-kbp window SNP binning method, 1059 bin-markers were identified, physically anchored on the genome. The total length of the RNA-seq genetic map spans 471.70 centimorgans (cM) with an average marker distance of 0.45 cM and a maximum marker distance of 4.81 cM. This high resolution genotyping revealed new recombination breakpoints in the population. To highlight the advantages of such high-density map, we compared it to two publicly available genetic maps for the same population, comprising 69 PCR-based markers and 497 gene expression markers derived from microarray data, respectively. In this study, we show that SNP markers can effectively be derived from RNA-seq data. The new RNA-seq map closes many existing gaps in marker coverage, saturating the previously available genetic maps. Quantitative trait locus (QTL) analysis for published phenotypes using the available genetic maps showed increased QTL mapping resolution and reduced QTL confidence interval using the RNA-seq map. The new high-density map is a valuable resource that facilitates the identification of candidate genes and map-based cloning approaches.
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Affiliation(s)
- Elise A R Serin
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Wageningen, Netherlands
| | - L B Snoek
- Laboratory of Nematology, Wageningen University, Wageningen, Netherlands.,Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, Netherlands
| | - Harm Nijveen
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Wageningen, Netherlands.,Laboratory of Bioinformatics, Wageningen University, Wageningen, Netherlands
| | - Leo A J Willems
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Wageningen, Netherlands
| | - Jose M Jiménez-Gómez
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany.,Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National de la Recherche Scientifique, Université Paris-Saclay, Versailles Cedex, France
| | - Henk W M Hilhorst
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Wageningen, Netherlands
| | - Wilco Ligterink
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Wageningen, Netherlands
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Oakenfull RJ, Davis SJ. Shining a light on the Arabidopsis circadian clock. PLANT, CELL & ENVIRONMENT 2017; 40:2571-2585. [PMID: 28732105 DOI: 10.1111/pce.13033] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 07/10/2017] [Accepted: 07/11/2017] [Indexed: 05/23/2023]
Abstract
The circadian clock provides essential timing information to ensure optimal growth to prevailing external environmental conditions. A major time-setting mechanism (zeitgeber) in clock synchronization is light. Differing light wavelengths, intensities, and photoperiodic duration are processed for the clock-setting mechanism. Many studies on light-input pathways to the clock have focused on Arabidopsis thaliana. Photoreceptors are specific chromic proteins that detect light signals and transmit this information to the central circadian oscillator through a number of different signalling mechanisms. The most well-characterized clock-mediating photoreceptors are cryptochromes and phytochromes, detecting blue, red, and far-red wavelengths of light. Ultraviolet and shaded light are also processed signals to the oscillator. Notably, the clock reciprocally generates rhythms of photoreceptor action leading to so-called gating of light responses. Intermediate proteins, such as Phytochrome interacting factors (PIFs), constitutive photomorphogenic 1 (COP1) and EARLY FLOWERING 3 (ELF3), have been established in signalling pathways downstream of photoreceptor activation. However, the precise details for these signalling mechanisms are not fully established. This review highlights both historical and recent efforts made to understand overall light input to the oscillator, first looking at how each wavelength of light is detected, this is then related to known input mechanisms and their interactions.
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Affiliation(s)
| | - Seth J Davis
- Department of Biology, University of York, York, YO10 5DD, UK
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Sibout R, Proost S, Hansen BO, Vaid N, Giorgi FM, Ho-Yue-Kuang S, Legée F, Cézart L, Bouchabké-Coussa O, Soulhat C, Provart N, Pasha A, Le Bris P, Roujol D, Hofte H, Jamet E, Lapierre C, Persson S, Mutwil M. Expression atlas and comparative coexpression network analyses reveal important genes involved in the formation of lignified cell wall in Brachypodium distachyon. THE NEW PHYTOLOGIST 2017; 215:1009-1025. [PMID: 28617955 DOI: 10.1111/nph.14635] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 04/26/2017] [Indexed: 05/08/2023]
Abstract
While Brachypodium distachyon (Brachypodium) is an emerging model for grasses, no expression atlas or gene coexpression network is available. Such tools are of high importance to provide insights into the function of Brachypodium genes. We present a detailed Brachypodium expression atlas, capturing gene expression in its major organs at different developmental stages. The data were integrated into a large-scale coexpression database ( www.gene2function.de), enabling identification of duplicated pathways and conserved processes across 10 plant species, thus allowing genome-wide inference of gene function. We highlight the importance of the atlas and the platform through the identification of duplicated cell wall modules, and show that a lignin biosynthesis module is conserved across angiosperms. We identified and functionally characterised a putative ferulate 5-hydroxylase gene through overexpression of it in Brachypodium, which resulted in an increase in lignin syringyl units and reduced lignin content of mature stems, and led to improved saccharification of the stem biomass. Our Brachypodium expression atlas thus provides a powerful resource to reveal functionally related genes, which may advance our understanding of important biological processes in grasses.
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Affiliation(s)
- Richard Sibout
- Institut Jean-Pierre Bourgin, UMR 1318, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, Versailles Cedex, 78026, France
| | - Sebastian Proost
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, Potsdam, 14476, Germany
| | - Bjoern Oest Hansen
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, Potsdam, 14476, Germany
| | - Neha Vaid
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, Potsdam, 14476, Germany
| | - Federico M Giorgi
- Cancer Research UK, Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
| | - Severine Ho-Yue-Kuang
- Institut Jean-Pierre Bourgin, UMR 1318, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, Versailles Cedex, 78026, France
| | - Frédéric Legée
- Institut Jean-Pierre Bourgin, UMR 1318, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, Versailles Cedex, 78026, France
| | - Laurent Cézart
- Institut Jean-Pierre Bourgin, UMR 1318, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, Versailles Cedex, 78026, France
| | - Oumaya Bouchabké-Coussa
- Institut Jean-Pierre Bourgin, UMR 1318, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, Versailles Cedex, 78026, France
| | - Camille Soulhat
- Institut Jean-Pierre Bourgin, UMR 1318, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, Versailles Cedex, 78026, France
| | - Nicholas Provart
- Department of Cell and Systems Biology, Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON, M5S 3B2, Canada
| | - Asher Pasha
- Department of Cell and Systems Biology, Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON, M5S 3B2, Canada
| | - Philippe Le Bris
- Institut Jean-Pierre Bourgin, UMR 1318, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, Versailles Cedex, 78026, France
| | - David Roujol
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Castanet-Tolosan, France
| | - Herman Hofte
- Institut Jean-Pierre Bourgin, UMR 1318, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, Versailles Cedex, 78026, France
| | - Elisabeth Jamet
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Castanet-Tolosan, France
| | - Catherine Lapierre
- Institut Jean-Pierre Bourgin, UMR 1318, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, Versailles Cedex, 78026, France
| | - Staffan Persson
- School of Biosciences, University of Melbourne, Parkville, Vic., 3010, Australia
| | - Marek Mutwil
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, Potsdam, 14476, Germany
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Davila Olivas NH, Frago E, Thoen MPM, Kloth KJ, Becker FFM, van Loon JJA, Gort G, Keurentjes JJB, van Heerwaarden J, Dicke M. Natural variation in life history strategy of Arabidopsis thaliana determines stress responses to drought and insects of different feeding guilds. Mol Ecol 2017; 26:2959-2977. [PMID: 28295823 PMCID: PMC5485070 DOI: 10.1111/mec.14100] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Revised: 02/21/2017] [Accepted: 02/27/2017] [Indexed: 12/31/2022]
Abstract
Plants are sessile organisms and, consequently, are exposed to a plethora of stresses in their local habitat. As a result, different populations of a species are subject to different selection pressures leading to adaptation to local conditions and intraspecific divergence. The annual brassicaceous plant Arabidopsis thaliana is an attractive model for ecologists and evolutionary biologists due to the availability of a large collection of resequenced natural accessions. Accessions of A. thaliana display one of two different life cycle strategies: summer and winter annuals. We exposed a collection of 308 European Arabidopsis accessions, that have been genotyped for 250K SNPs, to a range of stresses: one abiotic stress (drought), four biotic stresses (Pieris rapae caterpillars, Plutella xylostella caterpillars, Frankliniella occidentalis thrips and Myzus persicae aphids) and two combined stresses (drought plus P. rapae and Botrytis cinerea fungus plus P. rapae). We identified heritable genetic variation for responses to the different stresses, estimated by narrow-sense heritability. We found that accessions displaying different life cycle strategies differ in their response to stresses. Winter annuals are more resistant to drought, aphids and thrips and summer annuals are more resistant to P. rapae and P. xylostella caterpillars. Summer annuals are also more resistant to the combined stresses of drought plus P. rapae and infection by the fungus Botryris cinerea plus herbivory by P. rapae. Adaptation to drought displayed a longitudinal gradient. Finally, trade-offs were recorded between the response to drought and responses to herbivory by caterpillars of the specialist herbivore P. rapae.
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Affiliation(s)
| | - Enric Frago
- Laboratory of EntomologyWageningen UniversityWageningenThe Netherlands
| | - Manus P. M. Thoen
- Laboratory of EntomologyWageningen UniversityWageningenThe Netherlands
- Wageningen Plant ResearchWageningen University and ResearchWageningenThe Netherlands
- Laboratory of Plant PhysiologyWageningen UniversityWageningenThe Netherlands
| | - Karen J. Kloth
- Laboratory of EntomologyWageningen UniversityWageningenThe Netherlands
- Wageningen Plant ResearchWageningen University and ResearchWageningenThe Netherlands
- Laboratory of Plant PhysiologyWageningen UniversityWageningenThe Netherlands
| | | | | | - Gerrit Gort
- BiometrisWageningen University and ResearchWageningenThe Netherlands
| | | | | | - Marcel Dicke
- Laboratory of EntomologyWageningen UniversityWageningenThe Netherlands
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Legris M, Nieto C, Sellaro R, Prat S, Casal JJ. Perception and signalling of light and temperature cues in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:683-697. [PMID: 28008680 DOI: 10.1111/tpj.13467] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 12/17/2016] [Accepted: 12/20/2016] [Indexed: 05/18/2023]
Abstract
Light and temperature patterns are often correlated under natural plant growth conditions. In this review, we analyse the perception and signalling mechanisms shared by both these environmental cues and discuss the functional implications of their convergence to control plant growth. The first point of integration is the phytochrome B (phyB) receptor, which senses light and temperature. Downstream of phyB, the signalling core comprises two branches, one involving PHYTOCHROME INTERACTING FACTOR 4 (PIF4) and the other CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) and ELONGATED HYPOCOTYL 5 (HY5). The dynamics of accumulation and/or localization of each of these core signalling components depend on light and temperature conditions. These pathways are connected through COP1, which enhances the activity of PIF4. The circadian clock modulates this circuit, since EARLY FLOWERING 3 (ELF3), an essential component of the evening complex (EC), represses expression of the PIF4 gene and PIF4 transcriptional activity. Phytochromes are probably not the only entry point of temperature into this network, but other sensors remain to be established. The sharing of mechanisms of action for two distinct environmental cues is to some extent unexpected, as it renders these responses mutually dependent. There are nonetheless many ecological contexts in which such a mutual influence could be beneficial.
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Affiliation(s)
- Martina Legris
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires-CONICET, 1405, Buenos Aires, Argentina
| | - Cristina Nieto
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, Darwin 3, 28049, Madrid, Spain
| | - Romina Sellaro
- IFEVA, Facultad de Agronomía, Universidad de Buenos Aires and CONICET, Av. San Martín 4453, 1417, Buenos Aires, Argentina
| | - Salomé Prat
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, Darwin 3, 28049, Madrid, Spain
| | - Jorge J Casal
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires-CONICET, 1405, Buenos Aires, Argentina
- IFEVA, Facultad de Agronomía, Universidad de Buenos Aires and CONICET, Av. San Martín 4453, 1417, Buenos Aires, Argentina
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40
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Nijveen H, Ligterink W, Keurentjes JJB, Loudet O, Long J, Sterken MG, Prins P, Hilhorst HW, de Ridder D, Kammenga JE, Snoek BL. AraQTL - workbench and archive for systems genetics in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 89:1225-1235. [PMID: 27995664 DOI: 10.1111/tpj.13457] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 11/24/2016] [Accepted: 12/06/2016] [Indexed: 06/06/2023]
Abstract
Genetical genomics studies uncover genome-wide genetic interactions between genes and their transcriptional regulators. High-throughput measurement of gene expression in recombinant inbred line populations has enabled investigation of the genetic architecture of variation in gene expression. This has the potential to enrich our understanding of the molecular mechanisms affected by and underlying natural variation. Moreover, it contributes to the systems biology of natural variation, as a substantial number of experiments have resulted in a valuable amount of interconnectable phenotypic, molecular and genotypic data. A number of genetical genomics studies have been published for Arabidopsis thaliana, uncovering many expression quantitative trait loci (eQTLs). However, these complex data are not easily accessible to the plant research community, leaving most of the valuable genetic interactions unexplored as cross-analysis of these studies is a major effort. We address this problem with AraQTL (http://www.bioinformatics.nl/Ara QTL/), an easily accessible workbench and database for comparative analysis and meta-analysis of all published Arabidopsis eQTL datasets. AraQTL provides a workbench for comparing, re-using and extending upon the results of these experiments. For example, one can easily screen a physical region for specific local eQTLs that could harbour candidate genes for phenotypic QTLs, or detect gene-by-environment interactions by comparing eQTLs under different conditions.
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Affiliation(s)
- Harm Nijveen
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, Wageningen, NL-6708 PB, The Netherlands
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, Wageningen, NL-6708 PB, The Netherlands
| | - Wilco Ligterink
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, Wageningen, NL-6708 PB, The Netherlands
| | - Joost J B Keurentjes
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, Wageningen, NL-6708 PB, The Netherlands
| | - Olivier Loudet
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, 78000, France
| | - Jiao Long
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, Wageningen, NL-6708 PB, The Netherlands
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, Wageningen, NL-6708 PB, The Netherlands
| | - Mark G Sterken
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, Wageningen, NL-6708 PB, The Netherlands
| | - Pjotr Prins
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, 38163, USA
| | - Henk W Hilhorst
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, Wageningen, NL-6708 PB, The Netherlands
| | - Dick de Ridder
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, Wageningen, NL-6708 PB, The Netherlands
| | - Jan E Kammenga
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, Wageningen, NL-6708 PB, The Netherlands
| | - Basten L Snoek
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, Wageningen, NL-6708 PB, The Netherlands
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Gommers CMM, Keuskamp DH, Buti S, van Veen H, Koevoets IT, Reinen E, Voesenek LACJ, Pierik R. Molecular Profiles of Contrasting Shade Response Strategies in Wild Plants: Differential Control of Immunity and Shoot Elongation. THE PLANT CELL 2017; 29:331-344. [PMID: 28138015 PMCID: PMC5354195 DOI: 10.1105/tpc.16.00790] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 01/10/2017] [Accepted: 01/25/2017] [Indexed: 05/06/2023]
Abstract
Plants growing at high densities elongate their shoots to reach for light, a response known as the shade avoidance syndrome (SAS). Phytochrome-mediated detection of far-red light reflection from neighboring plants activates growth-promoting molecular pathways leading to SAS However, it is unknown how plants that complete their life cycle in the forest understory and are shade tolerant prevent SAS when exposed to shade. Here, we show how two wild Geranium species from different native light environments regulate contrasting responses to light quality cues. A comparative RNA sequencing approach unveiled the molecular underpinnings of their contrasting growth responses to far-red light enrichment. It also identified differential phytochrome control of plant immunity genes and confirmed that far-red enrichment indeed contrastingly affects resistance against Botrytis cinerea between the two species. Furthermore, we identify a number of candidate regulators of differential shade avoidance. Three of these, the receptor-like kinases FERONIA and THESEUS1 and the non-DNA binding bHLH protein KIDARI, are functionally validated in Arabidopsis thaliana through gene knockout and/or overexpression studies. We propose that these components may be associated with either showing or not showing shade avoidance responses.
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Affiliation(s)
- Charlotte M M Gommers
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Diederik H Keuskamp
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Sara Buti
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Hans van Veen
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Iko T Koevoets
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Emilie Reinen
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Laurentius A C J Voesenek
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Ronald Pierik
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, 3584 CH Utrecht, The Netherlands
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Christie N, Myburg AA, Joubert F, Murray SL, Carstens M, Lin YC, Meyer J, Crampton BG, Christensen SA, Ntuli JF, Wighard SS, Van de Peer Y, Berger DK. Systems genetics reveals a transcriptional network associated with susceptibility in the maize-grey leaf spot pathosystem. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 89:746-763. [PMID: 27862526 DOI: 10.1111/tpj.13419] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Revised: 10/20/2016] [Accepted: 11/04/2016] [Indexed: 05/20/2023]
Abstract
We used a systems genetics approach to elucidate the molecular mechanisms of the responses of maize to grey leaf spot (GLS) disease caused by Cercospora zeina, a threat to maize production globally. Expression analysis of earleaf samples in a subtropical maize recombinant inbred line population (CML444 × SC Malawi) subjected in the field to C. zeina infection allowed detection of 20 206 expression quantitative trait loci (eQTLs). Four trans-eQTL hotspots coincided with GLS disease QTLs mapped in the same field experiment. Co-expression network analysis identified three expression modules correlated with GLS disease scores. The module (GY-s) most highly correlated with susceptibility (r = 0.71; 179 genes) was enriched for the glyoxylate pathway, lipid metabolism, diterpenoid biosynthesis and responses to pathogen molecules such as chitin. The GY-s module was enriched for genes with trans-eQTLs in hotspots on chromosomes 9 and 10, which also coincided with phenotypic QTLs for susceptibility to GLS. This transcriptional network has significant overlap with the GLS susceptibility response of maize line B73, and may reflect pathogen manipulation for nutrient acquisition and/or unsuccessful defence responses, such as kauralexin production by the diterpenoid biosynthesis pathway. The co-expression module that correlated best with resistance (TQ-r; 1498 genes) was enriched for genes with trans-eQTLs in hotspots coinciding with GLS resistance QTLs on chromosome 9. Jasmonate responses were implicated in resistance to GLS through co-expression of COI1 and enrichment of genes with the Gene Ontology term 'cullin-RING ubiquitin ligase complex' in the TQ-r module. Consistent with this, JAZ repressor expression was highly correlated with the severity of GLS disease in the GY-s susceptibility network.
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Affiliation(s)
- Nanette Christie
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa
- Centre for Bioinformatics and Computational Biology, Genomics Research Institute, Department of Biochemistry, University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa
| | - Alexander A Myburg
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa
| | - Fourie Joubert
- Centre for Bioinformatics and Computational Biology, Genomics Research Institute, Department of Biochemistry, University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa
| | - Shane L Murray
- Centre for Proteomic and Genomic Research, 0A Anzio Rd, Observatory, Cape Town, 7925, South Africa
- Department of Molecular and Cell Biology, University of Cape Town, Private Bag, Rondebosch, 7701, South Africa
| | - Maryke Carstens
- Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa
| | - Yao-Cheng Lin
- Department of Plant Systems Biology, VIB, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | - Jacqueline Meyer
- Centre for Proteomic and Genomic Research, 0A Anzio Rd, Observatory, Cape Town, 7925, South Africa
- Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa
| | - Bridget G Crampton
- Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa
| | - Shawn A Christensen
- Center for Medical, Agricultural, and Veterinary Entomology, United States Department of Agriculture, Agricultural Research Service, Chemistry Research Unit, Gainesville, FL, 32608, USA
| | - Jean F Ntuli
- Department of Molecular and Cell Biology, University of Cape Town, Private Bag, Rondebosch, 7701, South Africa
| | - Sara S Wighard
- Department of Molecular and Cell Biology, University of Cape Town, Private Bag, Rondebosch, 7701, South Africa
| | - Yves Van de Peer
- Department of Plant Systems Biology, VIB, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
- Department of Genetics, Genomics Research Institute, University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa
| | - Dave K Berger
- Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa
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Kuroha T, Nagai K, Kurokawa Y, Nagamura Y, Kusano M, Yasui H, Ashikari M, Fukushima A. eQTLs Regulating Transcript Variations Associated with Rapid Internode Elongation in Deepwater Rice. FRONTIERS IN PLANT SCIENCE 2017; 8:1753. [PMID: 29081784 PMCID: PMC5645499 DOI: 10.3389/fpls.2017.01753] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 09/25/2017] [Indexed: 05/09/2023]
Abstract
To avoid low oxygen, oxygen deficiency or oxygen deprivation, deepwater rice cultivated in flood planes can develop elongated internodes in response to submergence. Knowledge of the gene regulatory networks underlying rapid internode elongation is important for an understanding of the evolution and adaptation of major crops in response to flooding. To elucidate the genetic and molecular basis controlling their deepwater response we used microarrays and performed expression quantitative trait loci (eQTL) and phenotypic QTL (phQTL) analyses of internode samples of 85 recombinant inbred line (RIL) populations of non-deepwater (Taichung 65)- and deepwater rice (Bhadua). After evaluating the phenotypic response of the RILs exposed to submergence, confirming the genotypes of the populations, and generating 188 genetic markers, we identified 10,047 significant eQTLs comprised of 2,902 cis-eQTLs and 7,145 trans-eQTLs and three significant eQTL hotspots on chromosomes 1, 4, and 12 that affect the expression of many genes. The hotspots on chromosomes 1 and 4 located at different position from phQTLs detected in this study and other previous studies. We then regarded the eQTL hotspots as key regulatory points to infer causal regulatory networks of deepwater response including rapid internode elongation. Our results suggest that the downstream regulation of the eQTL hotspots on chromosomes 1 and 4 is independent, and that the target genes are partially regulated by SNORKEL1 and SNORKEL2 genes (SK1/2), key ethylene response factors. Subsequent bioinformatic analyses, including gene ontology-based annotation and functional enrichment analysis and promoter enrichment analysis, contribute to enhance our understanding of SK1/2-dependent and independent pathways. One remarkable observation is that the functional categories related to photosynthesis and light signaling are significantly over-represented in the candidate target genes of SK1/2. The combined results of these investigations together with genetical genomics approaches using structured populations with a deepwater response are also discussed in the context of current molecular models concerning the rapid internode elongation in deepwater rice. This study provides new insights into the underlying genetic architecture of gene expression regulating the response to flooding in deepwater rice and will be an important community resource for analyses on the genetic basis of deepwater responses.
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Affiliation(s)
- Takeshi Kuroha
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Japan
- Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
- *Correspondence: Takeshi Kuroha, Atsushi Fukushima,
| | - Keisuke Nagai
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Japan
| | - Yusuke Kurokawa
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Japan
| | - Yoshiaki Nagamura
- Genome Resource Unit, National Institute of Agrobiological Sciences, Tsukuba, Japan
| | - Miyako Kusano
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Hideshi Yasui
- Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Motoyuki Ashikari
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Japan
| | - Atsushi Fukushima
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- *Correspondence: Takeshi Kuroha, Atsushi Fukushima,
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Davila Olivas NH, Kruijer W, Gort G, Wijnen CL, van Loon JJA, Dicke M. Genome-wide association analysis reveals distinct genetic architectures for single and combined stress responses in Arabidopsis thaliana. THE NEW PHYTOLOGIST 2017; 213:838-851. [PMID: 27604707 PMCID: PMC5217058 DOI: 10.1111/nph.14165] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 07/11/2016] [Indexed: 05/20/2023]
Abstract
Plants are commonly exposed to abiotic and biotic stresses. We used 350 Arabidopsis thaliana accessions grown under controlled conditions. We employed genome-wide association analysis to investigate the genetic architecture and underlying loci involved in genetic variation in resistance to: two specialist insect herbivores, Pieris rapae and Plutella xylostella; and combinations of stresses, i.e. drought followed by P. rapae and infection by the fungal pathogen Botrytis cinerea followed by infestation by P. rapae. We found that genetic variation in resistance to combined stresses by drought plus P. rapae was limited compared with B. cinerea plus P. rapae or P. rapae alone. Resistance to the two caterpillars is controlled by different genetic components. There is limited overlap in the quantitative trait loci (QTLs) underlying resistance to combined stresses by drought plus P. rapae or B. cinerea plus P. rapae and P. rapae alone. Finally, several candidate genes involved in the biosynthesis of aliphatic glucosinolates and proteinase inhibitors were identified to be involved in resistance to P. rapae and P. xylostella, respectively. This study underlines the importance of investigating plant responses to combinations of stresses. The value of this approach for breeding plants for resistance to combinatorial stresses is discussed.
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Affiliation(s)
| | - Willem Kruijer
- BiometrisWageningen UniversityPO Box 166700 AAWageningenthe Netherlands
| | - Gerrit Gort
- BiometrisWageningen UniversityPO Box 166700 AAWageningenthe Netherlands
| | - Cris L. Wijnen
- Laboratory of EntomologyWageningen UniversityPO Box 166700 AAWageningenthe Netherlands
| | - Joop J. A. van Loon
- Laboratory of EntomologyWageningen UniversityPO Box 166700 AAWageningenthe Netherlands
| | - Marcel Dicke
- Laboratory of EntomologyWageningen UniversityPO Box 166700 AAWageningenthe Netherlands
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Discovering Single Nucleotide Polymorphisms Regulating Human Gene Expression Using Allele Specific Expression from RNA-seq Data. Genetics 2016; 204:1057-1064. [PMID: 27765809 DOI: 10.1534/genetics.115.177246] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2015] [Accepted: 09/07/2016] [Indexed: 12/20/2022] Open
Abstract
The study of the genetics of gene expression is of considerable importance to understanding the nature of common, complex diseases. The most widely applied approach to identifying relationships between genetic variation and gene expression is the expression quantitative trait loci (eQTL) approach. Here, we increased the computational power of eQTL with an alternative and complementary approach based on analyzing allele specific expression (ASE). We designed a novel analytical method to identify cis-acting regulatory variants based on genome sequencing and measurements of ASE from RNA-sequencing (RNA-seq) data. We evaluated the power and resolution of our method using simulated data. We then applied the method to map regulatory variants affecting gene expression in lymphoblastoid cell lines (LCLs) from 77 unrelated northern and western European individuals (CEU), which were part of the HapMap project. A total of 2309 SNPs were identified as being associated with ASE patterns. The SNPs associated with ASE were enriched within promoter regions and were significantly more likely to signal strong evidence for a regulatory role. Finally, among the candidate regulatory SNPs, we identified 108 SNPs that were previously associated with human immune diseases. With further improvements in quantifying ASE from RNA-seq, the application of our method to other datasets is expected to accelerate our understanding of the biological basis of common diseases.
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Abstract
One of the central goals in biology is to understand how and how much of the phenotype of an organism is encoded in its genome. Although many genes that are crucial for organismal processes have been identified, much less is known about the genetic bases underlying quantitative phenotypic differences in natural populations. We discuss the fundamental gap between the large body of knowledge generated over the past decades by experimental genetics in the laboratory and what is needed to understand the genotype-to-phenotype problem on a broader scale. We argue that systems genetics, a combination of systems biology and the study of natural variation using quantitative genetics, will help to address this problem. We present major advances in these two mostly disconnected areas that have increased our understanding of the developmental processes of flowering time control and root growth. We conclude by illustrating and discussing the efforts that have been made toward systems genetics specifically in plants.
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Affiliation(s)
- Takehiko Ogura
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030 Vienna, Austria;
| | - Wolfgang Busch
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030 Vienna, Austria;
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Endo M, Araki T, Nagatani A. Tissue-specific regulation of flowering by photoreceptors. Cell Mol Life Sci 2016; 73:829-39. [PMID: 26621669 PMCID: PMC11108494 DOI: 10.1007/s00018-015-2095-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 11/09/2015] [Accepted: 11/12/2015] [Indexed: 01/09/2023]
Abstract
Plants use various kinds of environmental signals to adjust the timing of the transition from the vegetative to reproductive phase (flowering). Since flowering at the appropriate time is crucial for plant reproductive strategy, several kinds of photoreceptors are deployed to sense environmental light conditions. In this review, we will update our current understanding of light signaling pathways in flowering regulation, especially, in which tissue do photoreceptors regulate flowering in response to light quality and photoperiod. Since light signaling is also integrated into other flowering pathways, we also introduce recent progress on how photoreceptors are involved in tissue-specific thermosensation and the gibberellin pathway. Finally, we discuss the importance of cell-type-specific analyses for future plant studies.
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Affiliation(s)
- Motomu Endo
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501, Japan
| | - Takashi Araki
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501, Japan
| | - Akira Nagatani
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501, Japan.
- Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan.
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McClung CR, Lou P, Hermand V, Kim JA. The Importance of Ambient Temperature to Growth and the Induction of Flowering. FRONTIERS IN PLANT SCIENCE 2016; 7:1266. [PMID: 27602044 PMCID: PMC4993786 DOI: 10.3389/fpls.2016.01266] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 08/09/2016] [Indexed: 05/17/2023]
Abstract
Plant development is exquisitely sensitive to the environment. Light quantity, quality, and duration (photoperiod) have profound effects on vegetative morphology and flowering time. Recent studies have demonstrated that ambient temperature is a similarly potent stimulus influencing morphology and flowering. In Arabidopsis, ambient temperatures that are high, but not so high as to induce a heat stress response, confer morphological changes that resemble the shade avoidance syndrome. Similarly, these high but not stressful temperatures can accelerate flowering under short day conditions as effectively as exposure to long days. Photoperiodic flowering entails a series of external coincidences, in which environmental cycles of light and dark must coincide with an internal cycle in gene expression established by the endogenous circadian clock. It is evident that a similar model of external coincidence applies to the effects of elevated ambient temperature on both vegetative morphology and the vegetative to reproductive transition. Further study is imperative, because global warming is predicted to have major effects on the performance and distribution of wild species and strong adverse effects on crop yields. It is critical to understand temperature perception and response at a mechanistic level and to integrate this knowledge with our understanding of other environmental responses, including biotic and abiotic stresses, in order to improve crop production sufficiently to sustainably feed an expanding world population.
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Affiliation(s)
- C. R. McClung
- Department of Biological Sciences, Dartmouth College, Hanover, NHUSA
- *Correspondence: C. R. McClung, Jin A. Kim,
| | - Ping Lou
- Department of Biological Sciences, Dartmouth College, Hanover, NHUSA
| | - Victor Hermand
- Department of Biological Sciences, Dartmouth College, Hanover, NHUSA
| | - Jin A. Kim
- Department of Biological Sciences, Dartmouth College, Hanover, NHUSA
- Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, Jeonju-siSouth Korea
- *Correspondence: C. R. McClung, Jin A. Kim,
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Serin EAR, Nijveen H, Hilhorst HWM, Ligterink W. Learning from Co-expression Networks: Possibilities and Challenges. FRONTIERS IN PLANT SCIENCE 2016; 7:444. [PMID: 27092161 PMCID: PMC4825623 DOI: 10.3389/fpls.2016.00444] [Citation(s) in RCA: 186] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 03/21/2016] [Indexed: 05/18/2023]
Abstract
Plants are fascinating and complex organisms. A comprehensive understanding of the organization, function and evolution of plant genes is essential to disentangle important biological processes and to advance crop engineering and breeding strategies. The ultimate aim in deciphering complex biological processes is the discovery of causal genes and regulatory mechanisms controlling these processes. The recent surge of omics data has opened the door to a system-wide understanding of the flow of biological information underlying complex traits. However, dealing with the corresponding large data sets represents a challenging endeavor that calls for the development of powerful bioinformatics methods. A popular approach is the construction and analysis of gene networks. Such networks are often used for genome-wide representation of the complex functional organization of biological systems. Network based on similarity in gene expression are called (gene) co-expression networks. One of the major application of gene co-expression networks is the functional annotation of unknown genes. Constructing co-expression networks is generally straightforward. In contrast, the resulting network of connected genes can become very complex, which limits its biological interpretation. Several strategies can be employed to enhance the interpretation of the networks. A strategy in coherence with the biological question addressed needs to be established to infer reliable networks. Additional benefits can be gained from network-based strategies using prior knowledge and data integration to further enhance the elucidation of gene regulatory relationships. As a result, biological networks provide many more applications beyond the simple visualization of co-expressed genes. In this study we review the different approaches for co-expression network inference in plants. We analyse integrative genomics strategies used in recent studies that successfully identified candidate genes taking advantage of gene co-expression networks. Additionally, we discuss promising bioinformatics approaches that predict networks for specific purposes.
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Affiliation(s)
- Elise A. R. Serin
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen UniversityWageningen, Netherlands
| | - Harm Nijveen
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen UniversityWageningen, Netherlands
- Laboratory of Bioinformatics, Wageningen UniversityWageningen, Netherlands
| | - Henk W. M. Hilhorst
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen UniversityWageningen, Netherlands
| | - Wilco Ligterink
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen UniversityWageningen, Netherlands
- *Correspondence: Wilco Ligterink
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Gene expression changes triggered by end-of-day far-red light treatment on early developmental stages of Eustoma grandiflorum (Raf.) Shinn. Sci Rep 2015; 5:17864. [PMID: 26642764 PMCID: PMC4672308 DOI: 10.1038/srep17864] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 11/06/2015] [Indexed: 11/28/2022] Open
Abstract
To better understand the molecular mechanisms related to growth promotion in the early developmental stages of Eustoma grandiflorum (Raf.) Shinn. under end-of-day far-red light (EOD-FR) treatment, we analyzed the leaf transcriptome of treated (EOD) and untreated plants (Cont) by using RNA-seq technology. EOD-FR treatment for only about 2 weeks in regions with limited sunshine during winter resulted in significantly higher internode length between the 3rd and 4th nodes on the main stem in EOD than in Cont. Among the differentially expressed genes (DEGs) related to synthesis or transport of auxin, higher levels of YUCCA (CL6581) and PIN4 (CL6181) were noted after treatment in EOD than in Cont in the leaf. In addition, high expression levels of GA20ox (Unigene11862) related to gibberellin (GA) synthesis and transcription factor bHLH 135 (CL7761) were observed in the stem of EOD, 3 h after treatment. A vertical section of the stem showed that the pith length of cells at the 4th node was longer in EOD than in Cont. Collectively, these results suggested that EOD-FR treatment increased the expression of DEGs related to GA and auxin biosynthesis, bHLH transcription factor, and internodal cell elongation along the longitudinal axis of Eustoma plants.
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