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Ma YQ, Li Q, Cheng H, Hou XF, Tan XM, Meng Q, Huang X, Chang W, Yang L, Xu ZQ. Alternative splicing variants of IiSEP3 in Isatis indigotica are involved in floral transition and flower development. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 216:109153. [PMID: 39342659 DOI: 10.1016/j.plaphy.2024.109153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 09/23/2024] [Accepted: 09/24/2024] [Indexed: 10/01/2024]
Abstract
The SEPALLATA3 genes regulate several aspects of plant development. This study identified four distinct splicing isoforms of the SEPALLATA3 gene in Isatis indigotica (I. indigotica). IiSEP3-1 and IiSEP3-2 have eight exons and were named as IiSEP3-2/1. However, IiSEP3-3 and IiSEP3-4 with the missing sixth exon were labeled IiSEP3ΔK3. Furthermore, the IiSEP3-1 and IiSEP3-4 amino acids sequences lack the V90. IiSEP3 splicing variants were primarily expressed in floral organs, with petals showing the highest expression. Ectopic expression of IiSEP3-2 or IiSEP3-3 may cause early flowering and reduce the number of sepals, petals, and stamens. The ectopic expression of IiSEP3-2 resulted in cauline leaves and sepals converting to carpelloid structures. In contrast, the four floral whorls prematurely wilted, and the entire flower displayed an abortive state when IiSEP3-3 was expressed ectopically. Silencing the IiSEP3 gene of I. indigotica employing VIGS (tobacco rattle virus-mediated virus-induced gene silencing) technology using the TRV-IiSEP3-2/1 vector delayed flowering time and reduced the number of petals and stamens. Plants silenced with TRV-IiSEP3ΔK3 also exhibited similar phenotypes, including fewer sepals. The transcriptome analysis of silenced plants (TRV-IiSEP3-2/1 treatment group) indicated significant alterations in 1861 genes, with 1035 upregulated and 826 downregulated. TRV-IiSEP3ΔK3 treatment altered the expression of 2063 genes in plants, with 1289 genes upregulated and 774 genes transcription inhibited. Y2H and BIFC experiments revealed that IiSEP3-2 and IiSEP3-3 had distinct interacting proteins. Thus, we can conclude that IiSEP3-2 and IiSEP3-3 interact with different proteins, affecting floral transition and organ development in I. indigotica.
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Affiliation(s)
- Yan-Qin Ma
- Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Horticultural Crops Biology and Germplasm Enhancement in Southwest Regions Key Laboratory of Ministry of Agriculture Rural Affairs, Vegetable Germplasm Innovation and Variety Improvement Key Laboratory of Sichuan Province, Chengdu, 610066, People's Republic of China; Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education) Provincial Key Laboratory of Biotechnology College of Life Sciences Northwest University, Xi'an, People's Republic of China, 710069
| | - Qi Li
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education) Provincial Key Laboratory of Biotechnology College of Life Sciences Northwest University, Xi'an, People's Republic of China, 710069
| | - Hao Cheng
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education) Provincial Key Laboratory of Biotechnology College of Life Sciences Northwest University, Xi'an, People's Republic of China, 710069
| | - Xiao-Fang Hou
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education) Provincial Key Laboratory of Biotechnology College of Life Sciences Northwest University, Xi'an, People's Republic of China, 710069
| | - Xiao-Min Tan
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education) Provincial Key Laboratory of Biotechnology College of Life Sciences Northwest University, Xi'an, People's Republic of China, 710069
| | - Qi Meng
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education) Provincial Key Laboratory of Biotechnology College of Life Sciences Northwest University, Xi'an, People's Republic of China, 710069
| | - Xuan Huang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education) Provincial Key Laboratory of Biotechnology College of Life Sciences Northwest University, Xi'an, People's Republic of China, 710069
| | - Wei Chang
- Sichuan Institute of Edible Fungi, Chengdu, People's Republic of China, 610066
| | - Liang Yang
- Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Horticultural Crops Biology and Germplasm Enhancement in Southwest Regions Key Laboratory of Ministry of Agriculture Rural Affairs, Vegetable Germplasm Innovation and Variety Improvement Key Laboratory of Sichuan Province, Chengdu, 610066, People's Republic of China.
| | - Zi-Qin Xu
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education) Provincial Key Laboratory of Biotechnology College of Life Sciences Northwest University, Xi'an, People's Republic of China, 710069.
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Wang P, Lehti-Shiu MD, Lotreck S, Segura Abá K, Krysan PJ, Shiu SH. Prediction of plant complex traits via integration of multi-omics data. Nat Commun 2024; 15:6856. [PMID: 39127735 PMCID: PMC11316822 DOI: 10.1038/s41467-024-50701-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 07/18/2024] [Indexed: 08/12/2024] Open
Abstract
The formation of complex traits is the consequence of genotype and activities at multiple molecular levels. However, connecting genotypes and these activities to complex traits remains challenging. Here, we investigate whether integrating genomic, transcriptomic, and methylomic data can improve prediction for six Arabidopsis traits. We find that transcriptome- and methylome-based models have performances comparable to those of genome-based models. However, models built for flowering time using different omics data identify different benchmark genes. Nine additional genes identified as important for flowering time from our models are experimentally validated as regulating flowering. Gene contributions to flowering time prediction are accession-dependent and distinct genes contribute to trait prediction in different genotypes. Models integrating multi-omics data perform best and reveal known and additional gene interactions, extending knowledge about existing regulatory networks underlying flowering time determination. These results demonstrate the feasibility of revealing molecular mechanisms underlying complex traits through multi-omics data integration.
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Affiliation(s)
- Peipei Wang
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, USA.
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China.
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA.
| | | | - Serena Lotreck
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
- Department of Computational Mathematics, Science, and Engineering, Michigan State University, East Lansing, MI, USA
| | - Kenia Segura Abá
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, USA
- Genetics and Genome Sciences Program, Michigan State University, East Lansing, MI, USA
| | - Patrick J Krysan
- Department of Plant and Agroecosystem Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Shin-Han Shiu
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, USA.
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA.
- Department of Computational Mathematics, Science, and Engineering, Michigan State University, East Lansing, MI, USA.
- Genetics and Genome Sciences Program, Michigan State University, East Lansing, MI, USA.
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3
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Gramzow L, Sharma R, Theißen G. Evolutionary Dynamics of FLC-like MADS-Box Genes in Brassicaceae. PLANTS (BASEL, SWITZERLAND) 2023; 12:3281. [PMID: 37765445 PMCID: PMC10536770 DOI: 10.3390/plants12183281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 09/06/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023]
Abstract
MADS-box genes encode transcription factors that play important roles in the development and evolution of plants. There are more than a dozen clades of MADS-box genes in angiosperms, of which those with functions in the specification of floral organ identity are especially well-known. From what has been elucidated in the model plant Arabidopsis thaliana, the clade of FLC-like MADS-box genes, comprising FLC-like genes sensu strictu and MAF-like genes, are somewhat special among the MADS-box genes of plants since FLC-like genes, especially MAF-like genes, show unusual evolutionary dynamics, in that they generate clusters of tandemly duplicated genes. Here, we make use of the latest genomic data of Brassicaceae to study this remarkable feature of the FLC-like genes in a phylogenetic context. We have identified all FLC-like genes in the genomes of 29 species of Brassicaceae and reconstructed the phylogeny of these genes employing a Maximum Likelihood method. In addition, we conducted selection analyses using PAML. Our results reveal that there are three major clades of FLC-like genes in Brassicaceae that all evolve under purifying selection but with remarkably different strengths. We confirm that the tandem arrangement of MAF-like genes in the genomes of Brassicaceae resulted in a high rate of duplications and losses. Interestingly, MAF-like genes also seem to be prone to transposition. Considering the role of FLC-like genes sensu lato (s.l.) in the timing of floral transition, we hypothesize that this rapid evolution of the MAF-like genes was a main contributor to the successful adaptation of Brassicaceae to different environments.
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Affiliation(s)
- Lydia Gramzow
- Matthias Schleiden Institute/Genetics, Friedrich Schiller University Jena, 07743 Jena, Germany
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4
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Meng Y, Lyu X, Liu J, Gao W, Ma Y, Liao N, Li Z, Bo Y, Hu Z, Yang J, Zhang M. Structural variation of GL1 gene determines the trichome formation in Brassica juncea. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:75. [PMID: 36952042 DOI: 10.1007/s00122-023-04301-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 01/14/2023] [Indexed: 06/18/2023]
Abstract
A 448 kb region on chromosome B02 was delimited to be associated with trichome trait in Brassica juncea, in which the BjuVB02G54610 gene with a structural variation of 3 kb structure variation (SV) encoding a MYB transcription factor was predicted as the possible candidate gene. Mustards (Brassica juncea) are allopolyploid crops in the worldwide, and trichomes are essential quality attributes that significantly influence its taste and palpability in vegetable-use cultivars. As important accessory tissues from specialized epidermal cells, trichomes also play an important role in mitigating biotic and abiotic stresses. In this study, we constructed a F2 segregating population using YJ27 with intensive trichome leaves and 03B0307 with glabrous leaves as parents. By bulked segregant analysis (BSA-seq), we obtained a 2.1 Mb candidate region on B02 chromosome associated with the trichome or glabrous trait formation. Then, we used 13 Kompetitive Allele Specific PCR (KASP) markers for fine mapping and finally narrowed down the candidate region to about 448 kb in length. Interestingly, among the region, there was a 3 kb sequence deletion that located on the BjuVB02G54610 gene in the F2 individuals with trichome leaves. Genotyping results of F2 populations confirmed this deletion (R2 = 81.44%) as a major QTL. Natural population re-sequencing analysis and genotyping results further validated the key role of the 3 kb structure variation (SV) of insertion/deletion type in trichome development in B. juncea. Our findings provide important information on the formation of trichomes and potential target gene for breeding vegetable mustards.
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Affiliation(s)
- Yiqing Meng
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, People's Republic of China
| | - Xiagolong Lyu
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, People's Republic of China
| | - Jiaqi Liu
- Hainan Institute of Zhejiang University, Yazhou District, Sanya, People's Republic of China
| | - Wei Gao
- Hainan Institute of Zhejiang University, Yazhou District, Sanya, People's Republic of China
| | - Yuyuan Ma
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, People's Republic of China
| | - Nanqiao Liao
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, People's Republic of China
| | - Zhangping Li
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, People's Republic of China
| | - Yongming Bo
- Ningbo Weimeng Seed Industry Co.Ltd, Ningbo, People's Republic of China
| | - Zhongyuan Hu
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, People's Republic of China
- Hainan Institute of Zhejiang University, Yazhou District, Sanya, People's Republic of China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou, People's Republic of China
| | - Jinghua Yang
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, People's Republic of China
- Hainan Institute of Zhejiang University, Yazhou District, Sanya, People's Republic of China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou, People's Republic of China
| | - Mingfang Zhang
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, People's Republic of China.
- Hainan Institute of Zhejiang University, Yazhou District, Sanya, People's Republic of China.
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou, People's Republic of China.
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5
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Montes CM, Fox C, Sanz-Sáez Á, Serbin SP, Kumagai E, Krause MD, Xavier A, Specht JE, Beavis WD, Bernacchi CJ, Diers BW, Ainsworth EA. High-throughput characterization, correlation, and mapping of leaf photosynthetic and functional traits in the soybean (Glycine max) nested association mapping population. Genetics 2022; 221:iyac065. [PMID: 35451475 PMCID: PMC9157091 DOI: 10.1093/genetics/iyac065] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Accepted: 04/03/2022] [Indexed: 11/14/2022] Open
Abstract
Photosynthesis is a key target to improve crop production in many species including soybean [Glycine max (L.) Merr.]. A challenge is that phenotyping photosynthetic traits by traditional approaches is slow and destructive. There is proof-of-concept for leaf hyperspectral reflectance as a rapid method to model photosynthetic traits. However, the crucial step of demonstrating that hyperspectral approaches can be used to advance understanding of the genetic architecture of photosynthetic traits is untested. To address this challenge, we used full-range (500-2,400 nm) leaf reflectance spectroscopy to build partial least squares regression models to estimate leaf traits, including the rate-limiting processes of photosynthesis, maximum Rubisco carboxylation rate, and maximum electron transport. In total, 11 models were produced from a diverse population of soybean sampled over multiple field seasons to estimate photosynthetic parameters, chlorophyll content, leaf carbon and leaf nitrogen percentage, and specific leaf area (with R2 from 0.56 to 0.96 and root mean square error approximately <10% of the range of calibration data). We explore the utility of these models by applying them to the soybean nested association mapping population, which showed variability in photosynthetic and leaf traits. Genetic mapping provided insights into the underlying genetic architecture of photosynthetic traits and potential improvement in soybean. Notably, the maximum Rubisco carboxylation rate mapped to a region of chromosome 19 containing genes encoding multiple small subunits of Rubisco. We also mapped the maximum electron transport rate to a region of chromosome 10 containing a fructose 1,6-bisphosphatase gene, encoding an important enzyme in the regeneration of ribulose 1,5-bisphosphate and the sucrose biosynthetic pathway. The estimated rate-limiting steps of photosynthesis were low or negatively correlated with yield suggesting that these traits are not influenced by the same genetic mechanisms and are not limiting yield in the soybean NAM population. Leaf carbon percentage, leaf nitrogen percentage, and specific leaf area showed strong correlations with yield and may be of interest in breeding programs as a proxy for yield. This work is among the first to use hyperspectral reflectance to model and map the genetic architecture of the rate-limiting steps of photosynthesis.
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Affiliation(s)
| | - Carolyn Fox
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Álvaro Sanz-Sáez
- Department of Crop, Soil, and Environmental Sciences, Auburn, AL 36849, USA
| | - Shawn P Serbin
- Environmental and Climate Sciences Department, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Etsushi Kumagai
- Institute of Agro-environmental Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8604, Japan
| | - Matheus D Krause
- Department of Agronomy, Iowa State University, Agronomy Hall, Ames, IA 50011, USA
| | - Alencar Xavier
- Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA
- Department of Biostatistics, Corteva Agrisciences, Johnston, IA 50131, USA
| | - James E Specht
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68583, USA
| | - William D Beavis
- Department of Agronomy, Iowa State University, Agronomy Hall, Ames, IA 50011, USA
| | - Carl J Bernacchi
- Global Change and Photosynthesis Research Unit, USDA ARS, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, Urbana, IL 61801, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Brian W Diers
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Elizabeth A Ainsworth
- Global Change and Photosynthesis Research Unit, USDA ARS, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, Urbana, IL 61801, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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6
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Gao X, Wang L, Zhang H, Zhu B, Lv G, Xiao J. Transcriptome analysis and identification of genes associated with floral transition and fruit development in rabbiteye blueberry (Vaccinium ashei). PLoS One 2021; 16:e0259119. [PMID: 34710165 PMCID: PMC8553168 DOI: 10.1371/journal.pone.0259119] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 10/12/2021] [Indexed: 11/30/2022] Open
Abstract
Flowering and fruit set are important traits affecting fruit quality and yield in rabbiteye blueberry (Vaccinium ashei). Intense efforts have been made to elucidate the influence of vernalization and phytohormones on flowering, but the molecular mechanisms of flowering and fruit set remain unclear. To unravel these mechanisms, we performed transcriptome analysis to explore blueberry transcripts from flowering to early fruit stage. We divided flowering and fruit set into flower bud (S2), initial flower (S3), bloom flower (S4), pad fruit (S5), and cup fruit (S6) based on phenotype and identified 1,344, 69, 658, and 189 unique differentially expressed genes (DEGs) in comparisons of S3/S2, S4/S3, S5/S4, and S6/S5, respectively. There were obviously more DEGs in S3/S2 and S5/S4 than in S4/S3, and S6/S5, suggesting that S3/S2 and S5/S4 represent major transitions from buds to fruit in blueberry. GO and KEGG enrichment analysis indicated these DEGs were mostly enriched in phytohormone biosynthesis and signaling, transporter proteins, photosynthesis, anthocyanins biosynthesis, disease resistance protein and transcription factor categories, in addition, transcript levels of phytohormones and transporters changed greatly throughout the flowering and fruit set process. Gibberellic acid and jasmonic acid mainly acted on the early stage of flowering development like expression of the florigen gene FT, while the expression of auxin response factor genes increased almost throughout the process from bud to fruit development. Transporter proteins were mainly associated with minerals during the early flowering development stage and sugars during the early fruit stage. At the early fruit stage, anthocyanins started to accumulate, and the fruit was susceptible to diseases such as fungal infection. Expression of the transcription factor MYB86 was up-regulated during initial fruit development, which may promote anthocyanin accumulation. These results will aid future studies exploring the molecular mechanism underlying flowering and fruit set of rabbiteye blueberry.
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Affiliation(s)
- Xuan Gao
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases and Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, Anhui Normal University, Wuhu, Anhui, China
| | - Lida Wang
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases and Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, Anhui Normal University, Wuhu, Anhui, China
| | - Hong Zhang
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases and Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, Anhui Normal University, Wuhu, Anhui, China
- Anhui Microanaly Gene Limited Liability Company, Hefei, Anhui, China
| | - Bo Zhu
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases and Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, Anhui Normal University, Wuhu, Anhui, China
| | - Guosheng Lv
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases and Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, Anhui Normal University, Wuhu, Anhui, China
| | - Jiaxin Xiao
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases and Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, Anhui Normal University, Wuhu, Anhui, China
- * E-mail:
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7
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Transposition and duplication of MADS-domain transcription factor genes in annual and perennial Arabis species modulates flowering. Proc Natl Acad Sci U S A 2021; 118:2109204118. [PMID: 34548402 PMCID: PMC8488671 DOI: 10.1073/pnas.2109204118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/27/2021] [Indexed: 12/02/2022] Open
Abstract
Annual and perennial species differ in their timing and intensity of flowering, but the underlying mechanisms are poorly understood. We hybridized closely related annual and perennial plants and used genetics, transgenesis, and genomics to characterize differences in the activity and function of their flowering-time genes. We identify a gene encoding a transcription factor that moved between chromosomes and is retained in the annual but absent from the perennial. This gene strongly delays flowering, and we propose that it has been retained in the annual to compensate for reduced activity of closely related genes. This study highlights the value of using direct hybridization between closely related plant species to characterize functional differences in fast-evolving reproductive traits. The timing of reproduction is an adaptive trait in many organisms. In plants, the timing, duration, and intensity of flowering differ between annual and perennial species. To identify interspecies variation in these traits, we studied introgression lines derived from hybridization of annual and perennial species, Arabis montbretiana and Arabis alpina, respectively. Recombination mapping identified two tandem A. montbretiana genes encoding MADS-domain transcription factors that confer extreme late flowering on A. alpina. These genes are related to the MADS AFFECTING FLOWERING (MAF) cluster of floral repressors of other Brassicaceae species and were named A. montbretiana (Am) MAF-RELATED (MAR) genes. AmMAR1 but not AmMAR2 prevented floral induction at the shoot apex of A. alpina, strongly enhancing the effect of the MAF cluster, and MAR1 is absent from the genomes of all A. alpina accessions analyzed. Exposure of plants to cold (vernalization) represses AmMAR1 transcription and overcomes its inhibition of flowering. Assembly of the tandem arrays of MAR and MAF genes of six A. alpina accessions and three related species using PacBio long-sequence reads demonstrated that the MARs arose within the Arabis genus by interchromosomal transposition of a MAF1-like gene followed by tandem duplication. Time-resolved comparative RNA-sequencing (RNA-seq) suggested that AmMAR1 may be retained in A. montbretiana to enhance the effect of the AmMAF cluster and extend the duration of vernalization required for flowering. Our results demonstrate that MAF genes transposed independently in different Brassicaceae lineages and suggest that they were retained to modulate adaptive flowering responses that differ even among closely related species.
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Temperature-Dependent Alternative Splicing of Precursor mRNAs and Its Biological Significance: A Review Focused on Post-Transcriptional Regulation of a Cold Shock Protein Gene in Hibernating Mammals. Int J Mol Sci 2020; 21:ijms21207599. [PMID: 33066638 PMCID: PMC7590145 DOI: 10.3390/ijms21207599] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/12/2020] [Accepted: 10/13/2020] [Indexed: 01/18/2023] Open
Abstract
Multiple mRNA isoforms are often generated during processing such as alternative splicing of precursor mRNAs (pre-mRNA), resulting in a diversity of generated proteins. Alternative splicing is an essential mechanism for the functional complexity of eukaryotes. Temperature, which is involved in all life activities at various levels, is one of regulatory factors for controlling patterns of alternative splicing. Temperature-dependent alternative splicing is associated with various phenotypes such as flowering and circadian clock in plants and sex determination in poikilothermic animals. In some specific situations, temperature-dependent alternative splicing can be evoked even in homothermal animals. For example, the splicing pattern of mRNA for a cold shock protein, cold-inducible RNA-binding protein (CIRP or CIRBP), is changed in response to a marked drop in body temperature during hibernation of hamsters. In this review, we describe the current knowledge about mechanisms and functions of temperature-dependent alternative splicing in plants and animals. Then we discuss the physiological significance of hypothermia-induced alternative splicing of a cold shock protein gene in hibernating and non-hibernating animals.
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9
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Gaudinier A, Blackman BK. Evolutionary processes from the perspective of flowering time diversity. THE NEW PHYTOLOGIST 2020; 225:1883-1898. [PMID: 31536639 DOI: 10.1111/nph.16205] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 08/30/2019] [Indexed: 05/18/2023]
Abstract
Although it is well appreciated that genetic studies of flowering time regulation have led to fundamental advances in the fields of molecular and developmental biology, the ways in which genetic studies of flowering time diversity have enriched the field of evolutionary biology have received less attention despite often being equally profound. Because flowering time is a complex, environmentally responsive trait that has critical impacts on plant fitness, crop yield, and reproductive isolation, research into the genetic architecture and molecular basis of its evolution continues to yield novel insights into our understanding of domestication, adaptation, and speciation. For instance, recent studies of flowering time variation have reconstructed how, when, and where polygenic evolution of phenotypic plasticity proceeded from standing variation and de novo mutations; shown how antagonistic pleiotropy and temporally varying selection maintain polymorphisms in natural populations; and provided important case studies of how assortative mating can evolve and facilitate speciation with gene flow. In addition, functional studies have built detailed regulatory networks for this trait in diverse taxa, leading to new knowledge about how and why developmental pathways are rewired and elaborated through evolutionary time.
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Affiliation(s)
- Allison Gaudinier
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Benjamin K Blackman
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
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10
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Kulkarni SR, Jones DM, Vandepoele K. Enhanced Maps of Transcription Factor Binding Sites Improve Regulatory Networks Learned from Accessible Chromatin Data. PLANT PHYSIOLOGY 2019; 181:412-425. [PMID: 31345953 PMCID: PMC6776849 DOI: 10.1104/pp.19.00605] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 07/12/2019] [Indexed: 05/05/2023]
Abstract
Determining where transcription factors (TFs) bind in genomes provides insight into which transcriptional programs are active across organs, tissue types, and environmental conditions. Recent advances in high-throughput profiling of regulatory DNA have yielded large amounts of information about chromatin accessibility. Interpreting the functional significance of these data sets requires knowledge of which regulators are likely to bind these regions. This can be achieved by using information about TF-binding preferences, or motifs, to identify TF-binding events that are likely to be functional. Although different approaches exist to map motifs to DNA sequences, a systematic evaluation of these tools in plants is missing. Here, we compare four motif-mapping tools widely used in the Arabidopsis (Arabidopsis thaliana) research community and evaluate their performance using chromatin immunoprecipitation data sets for 40 TFs. Downstream gene regulatory network (GRN) reconstruction was found to be sensitive to the motif mapper used. We further show that the low recall of Find Individual Motif Occurrences, one of the most frequently used motif-mapping tools, can be overcome by using an Ensemble approach, which combines results from different mapping tools. Several examples are provided demonstrating how the Ensemble approach extends our view on transcriptional control for TFs active in different biological processes. Finally, a protocol is presented to effectively derive more complete cell type-specific GRNs through the integrative analysis of open chromatin regions, known binding site information, and expression data sets. This approach will pave the way to increase our understanding of GRNs in different cellular conditions.
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Affiliation(s)
- Shubhada R Kulkarni
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, 9052 Ghent, Belgium
| | - D Marc Jones
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, 9052 Ghent, Belgium
| | - Klaas Vandepoele
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, 9052 Ghent, Belgium
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11
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Taylor MA, Cooper MD, Schmitt J. Phenological and fitness responses to climate warming depend upon genotype and competitive neighbourhood in
Arabidopsis thaliana. Funct Ecol 2019. [DOI: 10.1111/1365-2435.13262] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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12
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Nelson TC, Monnahan PJ, McIntosh MK, Anderson K, MacArthur-Waltz E, Finseth FR, Kelly JK, Fishman L. Extreme copy number variation at a tRNA ligase gene affecting phenology and fitness in yellow monkeyflowers. Mol Ecol 2018; 28:1460-1475. [PMID: 30346101 DOI: 10.1111/mec.14904] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 10/03/2018] [Accepted: 10/08/2018] [Indexed: 12/15/2022]
Abstract
Copy number variation (CNV) is a major part of the genetic diversity segregating within populations, but remains poorly understood relative to single nucleotide variation. Here, we report on a tRNA ligase gene (Migut.N02091; RLG1a) exhibiting unprecedented, and fitness-relevant, CNV within an annual population of the yellow monkeyflower Mimulus guttatus. RLG1a variation was associated with multiple traits in pooled population sequencing (PoolSeq) scans of phenotypic and phenological cohorts. Resequencing of inbred lines revealed intermediate-frequency three-copy variants of RLG1a (trip+; 5/35 = 14%), and trip+ lines exhibited elevated RLG1a expression under multiple conditions. trip+ carriers, in addition to being over-represented in late-flowering and large-flowered PoolSeq populations, flowered later under stressful conditions in a greenhouse experiment (p < 0.05). In wild population samples, we discovered an additional rare RLG1a variant (high+) that carries 250-300 copies of RLG1a totalling ~5.7 Mb (20-40% of a chromosome). In the progeny of a high+ carrier, Mendelian segregation of diagnostic alleles and qPCR-based copy counts indicate that high+ is a single tandem array unlinked to the single-copy RLG1a locus. In the wild, high+ carriers had highest fitness in two particularly dry and/or hot years (2015 and 2017; both p < 0.01), while single-copy individuals were twice as fecund as either CNV type in a lush year (2016: p < 0.005). Our results demonstrate fluctuating selection on CNVs affecting phenological traits in a wild population, suggest that plant tRNA ligases mediate stress-responsive life-history traits, and introduce a novel system for investigating the molecular mechanisms of gene amplification.
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Affiliation(s)
- Thomas C Nelson
- Division of Biological Sciences, University of Montana, Missoula, Montana
| | - Patrick J Monnahan
- Department of Ecology and Evolution, University of Kansas, Lawrence, Kansas
| | - Mariah K McIntosh
- Division of Biological Sciences, University of Montana, Missoula, Montana
| | - Kayli Anderson
- Division of Biological Sciences, University of Montana, Missoula, Montana
| | | | - Findley R Finseth
- Division of Biological Sciences, University of Montana, Missoula, Montana
| | - John K Kelly
- Department of Ecology and Evolution, University of Kansas, Lawrence, Kansas
| | - Lila Fishman
- Division of Biological Sciences, University of Montana, Missoula, Montana
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13
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Theißen G, Rümpler F, Gramzow L. Array of MADS-Box Genes: Facilitator for Rapid Adaptation? TRENDS IN PLANT SCIENCE 2018; 23:563-576. [PMID: 29802068 DOI: 10.1016/j.tplants.2018.04.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 04/24/2018] [Accepted: 04/25/2018] [Indexed: 05/18/2023]
Abstract
In a world of global warming, the question emerges whether all plants have suitable mechanisms to keep pace with the rapidly changing environment. Most previous studies have focused on either the ability of plants to rapidly acclimatize via physiological and developmental plasticity, or long-term adaptation over thousands of years. However, we wonder whether plants can also adapt to changes in the environment within only a few generations. We hypothesize that rapidly evolving clusters of tandemly duplicated developmental control genes represent a source for fast adaptation. Specifically, we propose that a tandem cluster of FLC-like MADS-box genes involved in the transition to flowering in Arabidopsis functions as a facilitator for rapid adaptation to changes in ambient temperature.
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Affiliation(s)
- Günter Theißen
- Friedrich Schiller University Jena, Matthias Schleiden Institute for Genetics, Bioinformatics and Molecular Botany, Philosophenweg 12, D-07743 Jena, Germany.
| | - Florian Rümpler
- Friedrich Schiller University Jena, Matthias Schleiden Institute for Genetics, Bioinformatics and Molecular Botany, Philosophenweg 12, D-07743 Jena, Germany
| | - Lydia Gramzow
- Friedrich Schiller University Jena, Matthias Schleiden Institute for Genetics, Bioinformatics and Molecular Botany, Philosophenweg 12, D-07743 Jena, Germany
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14
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Taylor MA, Cooper MD, Sellamuthu R, Braun P, Migneault A, Browning A, Perry E, Schmitt J. Interacting effects of genetic variation for seed dormancy and flowering time on phenology, life history, and fitness of experimental Arabidopsis thaliana populations over multiple generations in the field. THE NEW PHYTOLOGIST 2017; 216:291-302. [PMID: 28752957 DOI: 10.1111/nph.14712] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 06/19/2017] [Indexed: 06/07/2023]
Abstract
Major alleles for seed dormancy and flowering time are well studied, and can interact to influence seasonal timing and fitness within generations. However, little is known about how this interaction controls phenology, life history, and population fitness across multiple generations in natural seasonal environments. To examine how seed dormancy and flowering time shape annual plant life cycles over multiple generations, we established naturally dispersing populations of recombinant inbred lines of Arabidopsis thaliana segregating early and late alleles for seed dormancy and flowering time in a field experiment. We recorded seasonal phenology and fitness of each genotype over 2 yr and several generations. Strong seed dormancy suppressed mid-summer germination in both early- and late-flowering genetic backgrounds. Strong dormancy and late-flowering genotypes were both necessary to confer a winter annual life history; other genotypes were rapid-cycling. Strong dormancy increased within-season fecundity in an early-flowering background, but decreased it in a late-flowering background. However, there were no detectable differences among genotypes in population growth rates. Seasonal phenology, life history, and cohort fitness over multiple generations depend strongly upon interacting genetic variation for dormancy and flowering. However, similar population growth rates across generations suggest that different life cycle genotypes can coexist in natural populations.
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Affiliation(s)
- Mark A Taylor
- University of California at Davis, Davis, CA, 95616, USA
| | | | | | - Peter Braun
- Brown University, Providence, RI, 02912, USA
- California State University at San Bernardino, San Bernardino, CA, 92407, USA
| | | | | | - Emily Perry
- Brown University, Providence, RI, 02912, USA
| | - Johanna Schmitt
- University of California at Davis, Davis, CA, 95616, USA
- Brown University, Providence, RI, 02912, USA
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15
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Gould BA, Stinchcombe JR. Population genomic scans suggest novel genes underlie convergent flowering time evolution in the introduced range of Arabidopsis thaliana. Mol Ecol 2016; 26:92-106. [PMID: 27064998 DOI: 10.1111/mec.13643] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 04/06/2016] [Accepted: 04/08/2016] [Indexed: 01/08/2023]
Abstract
A long-standing question in evolutionary biology is whether the evolution of convergent phenotypes results from selection on the same heritable genetic components. Using whole-genome sequencing and genome scans, we tested whether the evolution of parallel longitudinal flowering time clines in the native and introduced ranges of Arabidopsis thaliana has a similar genetic basis. We found that common variants of large effect on flowering time in the native range do not appear to have been under recent strong selection in the introduced range. We identified a set of 38 new candidate genes that are putatively linked to the evolution of flowering time. A high degree of conditional neutrality of flowering time variants between the native and introduced range may preclude parallel evolution at the level of genes. Overall, neither gene pleiotropy nor available standing genetic variation appears to have restricted the evolution of flowering time to high-frequency variants from the native range or to known flowering time pathway genes.
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Affiliation(s)
- Billie A Gould
- Department of Plant Biology, Michigan State University, 612 Wilson Rd, East Lansing, MI, 48823, USA
| | - John R Stinchcombe
- Department of Plant Biology, Michigan State University, 612 Wilson Rd, East Lansing, MI, 48823, USA
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16
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Kooke R, Kruijer W, Bours R, Becker F, Kuhn A, van de Geest H, Buntjer J, Doeswijk T, Guerra J, Bouwmeester H, Vreugdenhil D, Keurentjes JJB. Genome-Wide Association Mapping and Genomic Prediction Elucidate the Genetic Architecture of Morphological Traits in Arabidopsis. PLANT PHYSIOLOGY 2016; 170:2187-203. [PMID: 26869705 PMCID: PMC4825126 DOI: 10.1104/pp.15.00997] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 02/11/2016] [Indexed: 05/05/2023]
Abstract
Quantitative traits in plants are controlled by a large number of genes and their interaction with the environment. To disentangle the genetic architecture of such traits, natural variation within species can be explored by studying genotype-phenotype relationships. Genome-wide association studies that link phenotypes to thousands of single nucleotide polymorphism markers are nowadays common practice for such analyses. In many cases, however, the identified individual loci cannot fully explain the heritability estimates, suggesting missing heritability. We analyzed 349 Arabidopsis accessions and found extensive variation and high heritabilities for different morphological traits. The number of significant genome-wide associations was, however, very low. The application of genomic prediction models that take into account the effects of all individual loci may greatly enhance the elucidation of the genetic architecture of quantitative traits in plants. Here, genomic prediction models revealed different genetic architectures for the morphological traits. Integrating genomic prediction and association mapping enabled the assignment of many plausible candidate genes explaining the observed variation. These genes were analyzed for functional and sequence diversity, and good indications that natural allelic variation in many of these genes contributes to phenotypic variation were obtained. For ACS11, an ethylene biosynthesis gene, haplotype differences explaining variation in the ratio of petiole and leaf length could be identified.
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Affiliation(s)
- Rik Kooke
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., R.B., A.K., H.B., D.V.); Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., F.B., J.J.B.K.); Centre for Biosystems Genomics, Wageningen Campus, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., H.v.d.G., D.V., J.J.B.K); Biometris, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (W.K.); PRI Bioinformatics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (H.v.d.G.); and Keygene, Agro Business Park 90, 6708 PW Wageningen, the Netherlands (J.B., T.D., J.G.)
| | - Willem Kruijer
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., R.B., A.K., H.B., D.V.); Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., F.B., J.J.B.K.); Centre for Biosystems Genomics, Wageningen Campus, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., H.v.d.G., D.V., J.J.B.K); Biometris, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (W.K.); PRI Bioinformatics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (H.v.d.G.); and Keygene, Agro Business Park 90, 6708 PW Wageningen, the Netherlands (J.B., T.D., J.G.)
| | - Ralph Bours
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., R.B., A.K., H.B., D.V.); Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., F.B., J.J.B.K.); Centre for Biosystems Genomics, Wageningen Campus, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., H.v.d.G., D.V., J.J.B.K); Biometris, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (W.K.); PRI Bioinformatics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (H.v.d.G.); and Keygene, Agro Business Park 90, 6708 PW Wageningen, the Netherlands (J.B., T.D., J.G.)
| | - Frank Becker
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., R.B., A.K., H.B., D.V.); Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., F.B., J.J.B.K.); Centre for Biosystems Genomics, Wageningen Campus, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., H.v.d.G., D.V., J.J.B.K); Biometris, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (W.K.); PRI Bioinformatics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (H.v.d.G.); and Keygene, Agro Business Park 90, 6708 PW Wageningen, the Netherlands (J.B., T.D., J.G.)
| | - André Kuhn
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., R.B., A.K., H.B., D.V.); Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., F.B., J.J.B.K.); Centre for Biosystems Genomics, Wageningen Campus, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., H.v.d.G., D.V., J.J.B.K); Biometris, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (W.K.); PRI Bioinformatics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (H.v.d.G.); and Keygene, Agro Business Park 90, 6708 PW Wageningen, the Netherlands (J.B., T.D., J.G.)
| | - Henri van de Geest
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., R.B., A.K., H.B., D.V.); Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., F.B., J.J.B.K.); Centre for Biosystems Genomics, Wageningen Campus, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., H.v.d.G., D.V., J.J.B.K); Biometris, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (W.K.); PRI Bioinformatics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (H.v.d.G.); and Keygene, Agro Business Park 90, 6708 PW Wageningen, the Netherlands (J.B., T.D., J.G.)
| | - Jaap Buntjer
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., R.B., A.K., H.B., D.V.); Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., F.B., J.J.B.K.); Centre for Biosystems Genomics, Wageningen Campus, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., H.v.d.G., D.V., J.J.B.K); Biometris, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (W.K.); PRI Bioinformatics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (H.v.d.G.); and Keygene, Agro Business Park 90, 6708 PW Wageningen, the Netherlands (J.B., T.D., J.G.)
| | - Timo Doeswijk
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., R.B., A.K., H.B., D.V.); Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., F.B., J.J.B.K.); Centre for Biosystems Genomics, Wageningen Campus, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., H.v.d.G., D.V., J.J.B.K); Biometris, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (W.K.); PRI Bioinformatics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (H.v.d.G.); and Keygene, Agro Business Park 90, 6708 PW Wageningen, the Netherlands (J.B., T.D., J.G.)
| | - José Guerra
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., R.B., A.K., H.B., D.V.); Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., F.B., J.J.B.K.); Centre for Biosystems Genomics, Wageningen Campus, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., H.v.d.G., D.V., J.J.B.K); Biometris, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (W.K.); PRI Bioinformatics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (H.v.d.G.); and Keygene, Agro Business Park 90, 6708 PW Wageningen, the Netherlands (J.B., T.D., J.G.)
| | - Harro Bouwmeester
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., R.B., A.K., H.B., D.V.); Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., F.B., J.J.B.K.); Centre for Biosystems Genomics, Wageningen Campus, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., H.v.d.G., D.V., J.J.B.K); Biometris, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (W.K.); PRI Bioinformatics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (H.v.d.G.); and Keygene, Agro Business Park 90, 6708 PW Wageningen, the Netherlands (J.B., T.D., J.G.)
| | - Dick Vreugdenhil
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., R.B., A.K., H.B., D.V.); Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., F.B., J.J.B.K.); Centre for Biosystems Genomics, Wageningen Campus, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., H.v.d.G., D.V., J.J.B.K); Biometris, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (W.K.); PRI Bioinformatics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (H.v.d.G.); and Keygene, Agro Business Park 90, 6708 PW Wageningen, the Netherlands (J.B., T.D., J.G.)
| | - Joost J B Keurentjes
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., R.B., A.K., H.B., D.V.); Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., F.B., J.J.B.K.); Centre for Biosystems Genomics, Wageningen Campus, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., H.v.d.G., D.V., J.J.B.K); Biometris, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (W.K.); PRI Bioinformatics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (H.v.d.G.); and Keygene, Agro Business Park 90, 6708 PW Wageningen, the Netherlands (J.B., T.D., J.G.)
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17
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Méndez-Vigo B, Savic M, Ausín I, Ramiro M, Martín B, Picó FX, Alonso-Blanco C. Environmental and genetic interactions reveal FLOWERING LOCUS C as a modulator of the natural variation for the plasticity of flowering in Arabidopsis. PLANT, CELL & ENVIRONMENT 2016; 39:282-94. [PMID: 26173848 DOI: 10.1111/pce.12608] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 06/30/2015] [Accepted: 07/02/2015] [Indexed: 05/12/2023]
Abstract
The timing of flowering initiation depends strongly on the environment, a property termed as the plasticity of flowering. Such plasticity determines the adaptive potential of plants because it provides phenotypic buffer against environmental changes, and its natural variation contributes to evolutionary adaptation. We addressed the genetic mechanisms of the natural variation for this plasticity in Arabidopsis thaliana by analysing a population of recombinant inbred lines derived from Don-0 and Ler accessions collected from distinct climates. Quantitative trait locus (QTL) mapping in four environmental conditions differing in photoperiod, vernalization treatment and ambient temperature detected the folllowing: (i) FLOWERING LOCUS C (FLC) as a large effect QTL affecting flowering time differentially in all environments; (ii) numerous QTL displaying smaller effects specifically in some conditions; and (iii) significant genetic interactions between FLC and other loci. Hence, the variation for the plasticity of flowering is determined by a combination of environmentally sensitive and specific QTL, and epistasis. Analysis of FLC from Don identified a new and more active allele likely caused by a cis-regulatory deletion covering the non-coding RNA COLDAIR. Further characterization of four FLC natural alleles showed different environmental and genetic interactions. Thus, FLC appears as a major modulator of the natural variation for the plasticity of flowering to multiple environmental factors.
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Affiliation(s)
- Belén Méndez-Vigo
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, 28049, Spain
| | - Marija Savic
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, 28049, Spain
| | - Israel Ausín
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, 28049, Spain
| | - Mercedes Ramiro
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, 28049, Spain
| | - Beatriz Martín
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, 28049, Spain
| | - F Xavier Picó
- Departamento de Ecología Integrativa, Estación Biológica de Doñana (EBD), Sevilla, 41092, Spain
| | - Carlos Alonso-Blanco
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, 28049, Spain
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18
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Capovilla G, Pajoro A, Immink RGH, Schmid M. Role of alternative pre-mRNA splicing in temperature signaling. CURRENT OPINION IN PLANT BIOLOGY 2015; 27:97-103. [PMID: 26190743 DOI: 10.1016/j.pbi.2015.06.016] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 06/18/2015] [Accepted: 06/20/2015] [Indexed: 05/20/2023]
Abstract
Developmental plasticity enables plants to respond rapidly to changing environmental conditions, such as temperature fluctuations. Understanding how plants measure temperature and integrate this information into developmental programs at the molecular level will be essential to breed thermo-tolerant crop varieties. Recent studies identified alternative splicing (AS) as a possible 'molecular thermometer', allowing plants to quickly adjust the abundance of functional transcripts to environmental perturbations. In this review, recent advances regarding the effects of temperature-responsive AS on plant development will be discussed, with emphasis on the circadian clock and flowering time control. The challenge for the near future will be to understand the molecular mechanisms by which temperature can influence AS regulation.
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Affiliation(s)
- Giovanna Capovilla
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72074 Tübingen, Germany
| | - Alice Pajoro
- Plant Research International, Bioscience, 6708 PB Wageningen, The Netherlands; Laboratory of Molecular Biology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Richard G H Immink
- Plant Research International, Bioscience, 6708 PB Wageningen, The Netherlands; Laboratory of Molecular Biology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Markus Schmid
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72074 Tübingen, Germany; Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, S-901 87 Umea, Sweden.
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19
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MAF2 Is Regulated by Temperature-Dependent Splicing and Represses Flowering at Low Temperatures in Parallel with FLM. PLoS One 2015; 10:e0126516. [PMID: 25955034 PMCID: PMC4425511 DOI: 10.1371/journal.pone.0126516] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 04/03/2015] [Indexed: 11/19/2022] Open
Abstract
Plants enter their reproductive phase when the environmental conditions are favourable for the successful production of progeny. The transition from vegetative to reproductive phase is influenced by several environmental factors including ambient temperature. In the model plant Arabidopsis thaliana, SHORT VEGETATIVE PHASE (SVP) is critical for this pathway; svp mutants cannot modify their flowering time in response to ambient temperature. SVP encodes a MADS-box transcription factor that directly represses genes that promote flowering. SVP binds DNA in complexes with other MADS-box transcription factors, including FLOWERING LOCUS M (FLM), which acts with SVP to repress the floral transition at low temperatures. Small temperature changes post-transcriptionally regulate FLM through temperature-dependent alternative splicing (TD-AS). As ambient temperature increases, the predominant FLM splice isoform shifts to encode a protein incapable of exerting a repressive effect on flowering. Here we characterize a closely related MADS-box transcription factor, MADS AFFECTING FLOWERING2 (MAF2), which has independently evolved TD-AS. At low temperatures the most abundant MAF2 splice variant encodes a protein that interacts with SVP to repress flowering. At increased temperature the relative abundance of splice isoforms shifts in favour of an intron-retaining variant that introduces a premature termination codon. We show that this isoform encodes a protein that cannot interact with SVP or repress flowering. At lower temperatures MAF2 and SVP repress flowering in parallel with FLM and SVP, providing an additional input to sense ambient temperature for the control of flowering.
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Hori K, Nonoue Y, Ono N, Shibaya T, Ebana K, Matsubara K, Ogiso-Tanaka E, Tanabata T, Sugimoto K, Taguchi-Shiobara F, Yonemaru JI, Mizobuchi R, Uga Y, Fukuda A, Ueda T, Yamamoto SI, Yamanouchi U, Takai T, Ikka T, Kondo K, Hoshino T, Yamamoto E, Adachi S, Nagasaki H, Shomura A, Shimizu T, Kono I, Ito S, Mizubayashi T, Kitazawa N, Nagata K, Ando T, Fukuoka S, Yamamoto T, Yano M. Genetic architecture of variation in heading date among Asian rice accessions. BMC PLANT BIOLOGY 2015; 15:115. [PMID: 25953146 PMCID: PMC4424449 DOI: 10.1186/s12870-015-0501-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 04/22/2015] [Indexed: 05/08/2023]
Abstract
BACKGROUND Heading date, a crucial factor determining regional and seasonal adaptation in rice (Oryza sativa L.), has been a major selection target in breeding programs. Although considerable progress has been made in our understanding of the molecular regulation of heading date in rice during last two decades, the previously isolated genes and identified quantitative trait loci (QTLs) cannot fully explain the natural variation for heading date in diverse rice accessions. RESULTS To genetically dissect naturally occurring variation in rice heading date, we collected QTLs in advanced-backcross populations derived from multiple crosses of the japonica rice accession Koshihikari (as a common parental line) with 11 diverse rice accessions (5 indica, 3 aus, and 3 japonica) that originate from various regions of Asia. QTL analyses of over 14,000 backcrossed individuals revealed 255 QTLs distributed widely across the rice genome. Among the detected QTLs, 128 QTLs corresponded to genomic positions of heading date genes identified by previous studies, such as Hd1, Hd6, Hd3a, Ghd7, DTH8, and RFT1. The other 127 QTLs were detected in different chromosomal regions than heading date genes. CONCLUSIONS Our results indicate that advanced-backcross progeny allowed us to detect and confirm QTLs with relatively small additive effects, and the natural variation in rice heading date could result from combinations of large- and small-effect QTLs. We also found differences in the genetic architecture of heading date (flowering time) among maize, Arabidopsis, and rice.
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Affiliation(s)
- Kiyosumi Hori
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Yasunori Nonoue
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
- Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, 446-1 Ippaizuka, Kamiyokoba, 305-0854, Tsukuba, Ibaraki, Japan.
| | - Nozomi Ono
- Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, 446-1 Ippaizuka, Kamiyokoba, 305-0854, Tsukuba, Ibaraki, Japan.
| | - Taeko Shibaya
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Kaworu Ebana
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Kazuki Matsubara
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Eri Ogiso-Tanaka
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Takanari Tanabata
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Kazuhiko Sugimoto
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Fumio Taguchi-Shiobara
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Jun-ichi Yonemaru
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Ritsuko Mizobuchi
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Yusaku Uga
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Atsunori Fukuda
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Tadamasa Ueda
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Shin-ichi Yamamoto
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Utako Yamanouchi
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Toshiyuki Takai
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Takashi Ikka
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Katsuhiko Kondo
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Tomoki Hoshino
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Eiji Yamamoto
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Shunsuke Adachi
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Hideki Nagasaki
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Ayahiko Shomura
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
- Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, 446-1 Ippaizuka, Kamiyokoba, 305-0854, Tsukuba, Ibaraki, Japan.
| | - Takehiko Shimizu
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
- Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, 446-1 Ippaizuka, Kamiyokoba, 305-0854, Tsukuba, Ibaraki, Japan.
| | - Izumi Kono
- Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, 446-1 Ippaizuka, Kamiyokoba, 305-0854, Tsukuba, Ibaraki, Japan.
| | - Sachie Ito
- Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, 446-1 Ippaizuka, Kamiyokoba, 305-0854, Tsukuba, Ibaraki, Japan.
| | - Tatsumi Mizubayashi
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
- Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, 446-1 Ippaizuka, Kamiyokoba, 305-0854, Tsukuba, Ibaraki, Japan.
| | - Noriyuki Kitazawa
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Kazufumi Nagata
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Tsuyu Ando
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
- Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, 446-1 Ippaizuka, Kamiyokoba, 305-0854, Tsukuba, Ibaraki, Japan.
| | - Shuichi Fukuoka
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Toshio Yamamoto
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
| | - Masahiro Yano
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan.
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Ilk N, Ding J, Ihnatowicz A, Koornneef M, Reymond M. Natural variation for anthocyanin accumulation under high-light and low-temperature stress is attributable to the ENHANCER OF AG-4 2 (HUA2) locus in combination with PRODUCTION OF ANTHOCYANIN PIGMENT1 (PAP1) and PAP2. THE NEW PHYTOLOGIST 2015; 206:422-435. [PMID: 25425527 DOI: 10.1111/nph.13177] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 10/16/2014] [Indexed: 05/12/2023]
Abstract
Growing conditions combining high light intensities and low temperatures lead to anthocyanin accumulation in plants. This response was contrasted between two Arabidopsis thaliana accessions, which were used to decipher the genetic and molecular bases underlying the variation of this response. Quantitative trait loci (QTLs) for flowering time (FT) and anthocyanin accumulation under a high-light and low-temperature scenario versus a control environment were mapped. Major QTLs were confirmed using near-isogenic lines. Candidate genes were examined using mutants and gene expression studies as well as transgenic complementation. Several QTLs were found for FT and for anthocyanin content, of which one QTL co-located at the ENHANCER OF AG-4 2 (HUA2) locus. That HUA2 is a regulator of both pathways was confirmed by the analysis of loss-of-function mutants. For a strong expression of anthocyanin, additional allelic variation was detected for the PRODUCTION OF ANTHOCYANIN PIGMENT1 (PAP1) and PAP2 genes which control the anthocyanin pathway. The genetic control of variation for anthocyanin content was dissected in A. thaliana and shown to be affected by a common regulator of flowering and anthocyanin biosynthesis together with anthocyanin-specific regulators.
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Affiliation(s)
- Nadine Ilk
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Jia Ding
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Anna Ihnatowicz
- Laboratory of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology UG & MUG, Gdansk, Poland
| | - Maarten Koornneef
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Laboratory of Genetics, Wageningen University, Wageningen, NL-6708 PE, the Netherlands
| | - Matthieu Reymond
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, Versailles, France
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Suter L, Rüegg M, Zemp N, Hennig L, Widmer A. Gene regulatory variation mediates flowering responses to vernalization along an altitudinal gradient in Arabidopsis. PLANT PHYSIOLOGY 2014; 166:1928-42. [PMID: 25339407 PMCID: PMC4256870 DOI: 10.1104/pp.114.247346] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Steep environmental gradients provide ideal settings for studies of potentially adaptive phenotypic and genetic variation in plants. The accurate timing of flowering is crucial for reproductive success and is regulated by several pathways, including the vernalization pathway. Among the numerous genes known to enable flowering in response to vernalization, the most prominent is FLOWERING LOCUS C (FLC). FLC and other genes of the vernalization pathway vary extensively among natural populations and are thus candidates for the adaptation of flowering time to environmental gradients such as altitude. We used 15 natural Arabidopsis (Arabidopsis thaliana) genotypes originating from an altitudinal gradient (800-2,700 m above sea level) in the Swiss Alps to test whether flowering time correlated with altitude under different vernalization scenarios. Additionally, we measured the expression of 12 genes of the vernalization pathway and its downstream targets. Flowering time correlated with altitude in a nonlinear manner for vernalized plants. Flowering time could be explained by the expression and regulation of the vernalization pathway, most notably by AGAMOUS LIKE19 (AGL19), FLOWERING LOCUS T (FT), and FLC. The expression of AGL19, FT, and VERNALIZATION INSENSITIVE3 was associated with altitude, and the regulation of MADS AFFECTING FLOWERING2 (MAF2) and MAF3 differed between low- and high-altitude genotypes. In conclusion, we found clinal variation across an altitudinal gradient both in flowering time and the expression and regulation of genes in the flowering time control network, often independent of FLC, suggesting that the timing of flowering may contribute to altitudinal adaptation.
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Affiliation(s)
- Léonie Suter
- Eidgenössisch Technische Hochschule Zürich, Institute of Integrative Biology, 8092 Zurich, Switzerland (L.S., M.R., N.Z., A.W.); andDepartment of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-75007 Uppsala, Sweden (L.H.)
| | - Marlene Rüegg
- Eidgenössisch Technische Hochschule Zürich, Institute of Integrative Biology, 8092 Zurich, Switzerland (L.S., M.R., N.Z., A.W.); andDepartment of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-75007 Uppsala, Sweden (L.H.)
| | - Niklaus Zemp
- Eidgenössisch Technische Hochschule Zürich, Institute of Integrative Biology, 8092 Zurich, Switzerland (L.S., M.R., N.Z., A.W.); andDepartment of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-75007 Uppsala, Sweden (L.H.)
| | - Lars Hennig
- Eidgenössisch Technische Hochschule Zürich, Institute of Integrative Biology, 8092 Zurich, Switzerland (L.S., M.R., N.Z., A.W.); andDepartment of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-75007 Uppsala, Sweden (L.H.)
| | - Alex Widmer
- Eidgenössisch Technische Hochschule Zürich, Institute of Integrative Biology, 8092 Zurich, Switzerland (L.S., M.R., N.Z., A.W.); andDepartment of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-75007 Uppsala, Sweden (L.H.)
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23
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Chardon F, Jasinski S, Durandet M, Lécureuil A, Soulay F, Bedu M, Guerche P, Masclaux-Daubresse C. QTL meta-analysis in Arabidopsis reveals an interaction between leaf senescence and resource allocation to seeds. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:3949-62. [PMID: 24692652 PMCID: PMC4106442 DOI: 10.1093/jxb/eru125] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Sequential and monocarpic senescence are observed at vegetative and reproductive stages, respectively. Both facilitate nitrogen (N) remobilization and control the duration of carbon (C) fixation. Genetic and environmental factors control N and C resource allocation to seeds. Studies of natural variation in Arabidopsis thaliana revealed differences between accessions for leaf senescence phenotypes, seed N and C contents, and N remobilization efficiency-related traits. Here, a quantitative genetics approach was used to gain a better understanding of seed filling regulation in relation to leaf senescence and resource allocation. For that purpose, three Arabidopsis recombinant inbred line populations (Ct-1×Col-0, Cvi-0×Col-0, Bur-0×Col-0) were used to map QTL (quantitative trait loci) for ten traits related to senescence, resource allocation, and seed filling. The use of common markers across the three different maps allowed direct comparisons of the positions of the detected QTL in a single consensus map. QTL meta-analysis was then used to identify interesting regions (metaQTL) where QTL for several traits co-localized. MetaQTL were compared with positions of candidate genes known to be involved in senescence processes and flowering time. Finally, investigation of the correlation between yield and seed N concentration in the three populations suggests that leaf senescence disrupts the negative correlation generally observed between these two traits.
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Affiliation(s)
- Fabien Chardon
- UMR1318 INRA AgroParisTech, Institut Jean-Pierre Bourgin, INRA Versailles, Route Saint Cyr, 78026 Versailles Cedex, France
| | - Sophie Jasinski
- UMR1318 INRA AgroParisTech, Institut Jean-Pierre Bourgin, INRA Versailles, Route Saint Cyr, 78026 Versailles Cedex, France
| | - Monique Durandet
- UMR1318 INRA AgroParisTech, Institut Jean-Pierre Bourgin, INRA Versailles, Route Saint Cyr, 78026 Versailles Cedex, France
| | - Alain Lécureuil
- UMR1318 INRA AgroParisTech, Institut Jean-Pierre Bourgin, INRA Versailles, Route Saint Cyr, 78026 Versailles Cedex, France
| | - Fabienne Soulay
- UMR1318 INRA AgroParisTech, Institut Jean-Pierre Bourgin, INRA Versailles, Route Saint Cyr, 78026 Versailles Cedex, France
| | - Magali Bedu
- UMR1318 INRA AgroParisTech, Institut Jean-Pierre Bourgin, INRA Versailles, Route Saint Cyr, 78026 Versailles Cedex, France
| | - Philippe Guerche
- UMR1318 INRA AgroParisTech, Institut Jean-Pierre Bourgin, INRA Versailles, Route Saint Cyr, 78026 Versailles Cedex, France
| | - Céline Masclaux-Daubresse
- UMR1318 INRA AgroParisTech, Institut Jean-Pierre Bourgin, INRA Versailles, Route Saint Cyr, 78026 Versailles Cedex, France
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24
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Alonso-Blanco C, Méndez-Vigo B. Genetic architecture of naturally occurring quantitative traits in plants: an updated synthesis. CURRENT OPINION IN PLANT BIOLOGY 2014; 18:37-43. [PMID: 24565952 DOI: 10.1016/j.pbi.2014.01.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 01/20/2014] [Accepted: 01/26/2014] [Indexed: 05/08/2023]
Abstract
Deciphering the genetic and molecular bases of quantitative variation is a long-standing challenge in plant biology because it is essential for understanding evolution and for accelerating plant breeding. Recent multi-trait analyses at different phenotypic levels are uncovering the pleiotropy and the genetic regulation underlying high-level complex traits. Thus, the number of known causal loci, genes and nucleotide polymorphisms is expanding. Current plant causal catalogs contain ∼400 genes and natural polymorphisms revealing several dysfunctional allelic series that involve multiple mutations. In addition, repeated evolution of quantitative traits mediated by large effect alleles is found across plant phylogeny. Finally, systematic analyses of genetic and environmental interactions are beginning to elucidate the molecular mechanisms of relevant interactions.
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Affiliation(s)
- Carlos Alonso-Blanco
- Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Darwin 3, Madrid 28049, Spain.
| | - Belén Méndez-Vigo
- Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Darwin 3, Madrid 28049, Spain
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25
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Marroni F, Pinosio S, Morgante M. Structural variation and genome complexity: is dispensable really dispensable? CURRENT OPINION IN PLANT BIOLOGY 2014; 18:31-6. [PMID: 24548794 DOI: 10.1016/j.pbi.2014.01.003] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Revised: 01/08/2014] [Accepted: 01/26/2014] [Indexed: 05/18/2023]
Abstract
Structural variants (SVs) such as copy number variants (CNVs) and presence/absence variants (PAVs) substantially contribute to genetic variation and have an important effect on phenotypic diversity. Since unbalanced SVs are by definition sequences present only in some individuals, they have therefore been referred to as dispensable genome and are not necessary for survival, even though they may provide an important contribution to phenotypic diversity within the species. However, some multi-copy sequences of the dispensable genomes (e.g., multigene families) may be needed in a given proportion by each individual, thus belonging to a conditionally dispensable portion of the pan-genome. Another interesting aspect reported by recent studies is that the rate at which SVs are formed might be influenced by the mating system and by common environmental stresses. In conclusion the dispensable genome plays an important role in genome evolution and in the complex interplay between the genome and the environment.
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Affiliation(s)
- Fabio Marroni
- Dipartimento di Scienze Agrarie e Ambientali, Università di Udine, 33100 Udine, Italy; Istituto di Genomica Applicata (IGA), 33100 Udine, Italy
| | - Sara Pinosio
- Institute of Biosciences and Bioresources, National Research Council, Via Madonna del Piano 10, 50019 Sesto Fiorentino (Firenze), Italy; Istituto di Genomica Applicata (IGA), 33100 Udine, Italy
| | - Michele Morgante
- Dipartimento di Scienze Agrarie e Ambientali, Università di Udine, 33100 Udine, Italy; Istituto di Genomica Applicata (IGA), 33100 Udine, Italy.
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Genetic mapping of adaptation reveals fitness tradeoffs in Arabidopsis thaliana. Proc Natl Acad Sci U S A 2013; 110:21077-82. [PMID: 24324156 DOI: 10.1073/pnas.1316773110] [Citation(s) in RCA: 129] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Organisms inhabiting different environments are often locally adapted, and yet despite a considerable body of theory, the genetic basis of local adaptation is poorly understood. Unanswered questions include the number and effect sizes of adaptive loci, whether locally favored loci reduce fitness elsewhere (i.e., fitness tradeoffs), and whether a lack of genetic variation limits adaptation. To address these questions, we mapped quantitative trait loci (QTL) for total fitness in 398 recombinant inbred lines derived from a cross between locally adapted populations of the highly selfing plant Arabidopsis thaliana from Sweden and Italy and grown for 3 consecutive years at the parental sites (>40,000 plants monitored). We show that local adaptation is controlled by relatively few genomic regions of small to modest effect. A third of the 15 fitness QTL we detected showed evidence of tradeoffs, which contrasts with the minimal evidence for fitness tradeoffs found in previous studies. This difference may reflect the power of our multiyear study to distinguish conditionally neutral QTL from those that reflect fitness tradeoffs. In Sweden, but not in Italy, the local genotype underlying fitness QTL was often maladaptive, suggesting that adaptation there is constrained by a lack of adaptive genetic variation, attributable perhaps to genetic bottlenecks during postglacial colonization of Scandinavia or to recent changes in selection regime caused by climate change. Our results suggest that adaptation to markedly different environments can be achieved through changes in relatively few genomic regions, that fitness tradeoffs are common, and that lack of genetic variation can limit adaptation.
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27
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Seedat N, Dinsdale A, Ong EK, Gendall AR. Acceleration of flowering in Arabidopsis thaliana by Cape Verde Islands alleles of FLOWERING H is dependent on the floral promoter FD. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:2767-2778. [PMID: 23667042 PMCID: PMC3697943 DOI: 10.1093/jxb/ert120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Flowering time in the model plant Arabidopsis thaliana is regulated by both external environmental signals and internal developmental pathways. Natural variation at the FLOWERING H (FLH) locus has previously been described, with alleles present in the Cape Verde Islands accession causing early flowering, particularly after vernalization. The mechanism of FLH-induced early flowering is not understood. Here, the integration of FLH activity into the known flowering time pathways is described using molecular and genetic approaches. The identification of molecular markers that co-segregated with the FLH locus allowed the generation of multiple combinations of FLH alleles with mutations in flowering time genes in different flowering pathways. Combining an early flowering FLH allele with mutations in vernalization pathway genes that regulate FLC expression revealed that FLH appears to act in parallel to FLC. Surprisingly, the early flowering allele of FLH requires the floral integrator FD, but not FT, to accelerate flowering. This suggests a model in which some alleles of FLH are able to affect the FD-dependent activity of the floral activator complex.
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Affiliation(s)
- Noorina Seedat
- Department of Botany, La Trobe University, Bundoora, Victoria, 3086Australia
- AgriBio, Centre for AgriBiosciences, 5 Ring Road, Bundoora, Victoria, 3086, Australia
| | - Adrian Dinsdale
- Department of Botany, La Trobe University, Bundoora, Victoria, 3086Australia
| | - Eng Kok Ong
- Department of Botany, La Trobe University, Bundoora, Victoria, 3086Australia
| | - Anthony Richard Gendall
- Department of Botany, La Trobe University, Bundoora, Victoria, 3086Australia
- AgriBio, Centre for AgriBiosciences, 5 Ring Road, Bundoora, Victoria, 3086, Australia
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Fournier-Level A, Wilczek AM, Cooper MD, Roe JL, Anderson J, Eaton D, Moyers BT, Petipas RH, Schaeffer RN, Pieper B, Reymond M, Koornneef M, Welch SM, Remington DL, Schmitt J. Paths to selection on life history loci in different natural environments across the native range of Arabidopsis thaliana. Mol Ecol 2013; 22:3552-66. [PMID: 23506537 DOI: 10.1111/mec.12285] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Revised: 12/17/2012] [Accepted: 01/29/2013] [Indexed: 01/17/2023]
Abstract
Selection on quantitative trait loci (QTL) may vary among natural environments due to differences in the genetic architecture of traits, environment-specific allelic effects or changes in the direction and magnitude of selection on specific traits. To dissect the environmental differences in selection on life history QTL across climatic regions, we grew a panel of interconnected recombinant inbred lines (RILs) of Arabidopsis thaliana in four field sites across its native European range. For each environment, we mapped QTL for growth, reproductive timing and development. Several QTL were pleiotropic across environments, three colocalizing with known functional polymorphisms in flowering time genes (CRY2, FRI and MAF2-5), but major QTL differed across field sites, showing conditional neutrality. We used structural equation models to trace selection paths from QTL to lifetime fitness in each environment. Only three QTL directly affected fruit number, measuring fitness. Most QTL had an indirect effect on fitness through their effect on bolting time or leaf length. Influence of life history traits on fitness differed dramatically across sites, resulting in different patterns of selection on reproductive timing and underlying QTL. In two oceanic field sites with high prereproductive mortality, QTL alleles contributing to early reproduction resulted in greater fruit production, conferring selective advantage, whereas alleles contributing to later reproduction resulted in larger size and higher fitness in a continental site. This demonstrates how environmental variation leads to change in both QTL effect sizes and direction of selection on traits, justifying the persistence of allelic polymorphism at life history QTL across the species range.
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Méndez-Vigo B, Martínez-Zapater JM, Alonso-Blanco C. The flowering repressor SVP underlies a novel Arabidopsis thaliana QTL interacting with the genetic background. PLoS Genet 2013; 9:e1003289. [PMID: 23382706 PMCID: PMC3561112 DOI: 10.1371/journal.pgen.1003289] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Accepted: 12/15/2012] [Indexed: 01/17/2023] Open
Abstract
The timing of flowering initiation is a fundamental trait for the adaptation of annual plants to different environments. Large amounts of intraspecific quantitative variation have been described for it among natural accessions of many species, but the molecular and evolutionary mechanisms underlying this genetic variation are mainly being determined in the model plant Arabidopsis thaliana. To find novel A. thaliana flowering QTL, we developed introgression lines from the Japanese accession Fuk, which was selected based on the substantial transgression observed in an F2 population with the reference strain Ler. Analysis of an early flowering line carrying a single Fuk introgression identified Flowering Arabidopsis QTL1 (FAQ1). We fine-mapped FAQ1 in an 11 kb genomic region containing the MADS transcription factor gene SHORT VEGETATIVE PHASE (SVP). Complementation of the early flowering phenotype of FAQ1-Fuk with a SVP-Ler transgen demonstrated that FAQ1 is SVP. We further proved by directed mutagenesis and transgenesis that a single amino acid substitution in SVP causes the loss-of-function and early flowering of Fuk allele. Analysis of a worldwide collection of accessions detected FAQ1/SVP-Fuk allele only in Asia, with the highest frequency appearing in Japan, where we could also detect a potential ancestral genotype of FAQ1/SVP-Fuk. In addition, we evaluated allelic and epistatic interactions of SVP natural alleles by analysing more than one hundred transgenic lines carrying Ler or Fuk SVP alleles in five genetic backgrounds. Quantitative analyses of these lines showed that FAQ1/SVP effects vary from large to small depending on the genetic background. These results support that the flowering repressor SVP has been recently selected in A. thaliana as a target for early flowering, and evidence the relevance of genetic interactions for the intraspecific evolution of FAQ1/SVP and flowering time. In many plant species, the timing of flowering initiation shows abundant quantitative variation among natural varieties, which reflects the importance of this trait for adaptation to different environments. Currently, a major goal in plant biology is to determine the molecular and evolutionary bases of this natural genetic variation. In this study we demonstrate that the central flowering regulator SHORT VEGETATIVE PHASE (SVP), encoding a MADS transcription factor, is involved in the flowering natural variation of the model organism Arabidopsis thaliana. In particular, we prove that a structural change caused by a single amino acid substitution generates a SVP early flowering allele that is distributed only in Asia. Furthermore, genetic interactions have been shown to be a component of the natural variation for many important adaptive traits. However, very few studies, either in animals or plants, have systematically addressed the extent of genetic interactions among specific alleles responsible for the natural variation of complex traits. Our study shows that the flowering effects of SVP natural alleles depend significantly on the genetic background; and, subsequently, we demonstrate the relevance of epistasis for the evolution of this crucial transcription factor and flowering time.
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Affiliation(s)
- Belén Méndez-Vigo
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - José M. Martínez-Zapater
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- Instituto de Ciencias de la Vid y del Vino (ICVV), Consejo Superior de Investigaciones Científicas (CSIC), Universidad de La Rioja, Gobierno de La Rioja, Logroño, Spain
| | - Carlos Alonso-Blanco
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- * E-mail:
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Rosloski SM, Singh A, Jali SS, Balasubramanian S, Weigel D, Grbic V. Functional analysis of splice variant expression of MADS AFFECTING FLOWERING 2 of Arabidopsis thaliana. PLANT MOLECULAR BIOLOGY 2013; 81:57-69. [PMID: 23111501 PMCID: PMC3527738 DOI: 10.1007/s11103-012-9982-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Accepted: 10/19/2012] [Indexed: 05/19/2023]
Abstract
The MADS-AFFECTING FLOWERING 2 (MAF2) gene of Arabidopsis thaliana has been characterized as a repressor of flowering. The molecular basis of MAF2 gene function and role of alternative MAF2 transcripts in flowering time modulation is not understood. MAF2 splice variant expression was quantified in cold-acclimated plants by quantitative RT-PCR. Cold influenced the abundance of splice variants and prompted a functional study of splice forms. Individual variants were overexpressed in the Col background and were assayed for their ability to delay flowering. Overexpression of MAF2 variants 2 and 4 had limited effect on flowering time. Overexpression of MAF2 splice variant 1 resulted in early flowering and affected the expression of the endogenous MAF2 gene and its paralogues, confounding functional assessment. In the Ll-2 Arabidopsis accession, a MAF2, MAF3, MAF4 and FLC null line, MAF2 var1 was consistent in its effect on reproductive delay under ambient and reduced temperatures, indicating that it acts as a repressor of flowering.
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Affiliation(s)
| | - Anandita Singh
- Department of Molecular Biology, Max-Planck Institute for Developmental Biology, 72076 Tübingen, Germany
- Present Address: Department of Biotechnology, Faculty of Applied Science, TERI University, 10 Institutional Area, Vasant Kunj, New Delhi, 110070 India
| | | | - Sureshkumar Balasubramanian
- Department of Molecular Biology, Max-Planck Institute for Developmental Biology, 72076 Tübingen, Germany
- Present Address: School of Biological Sciences, Monash University, Clayton, VIC 3800 Australia
| | - Detlef Weigel
- Department of Molecular Biology, Max-Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Vojislava Grbic
- Department of Biology, Western University, London, ON N6A 5B8 Canada
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Abstract
Soybean genome sequences were blasted with Arabidopsis thaliana regulatory genes involved in photoperioddependent flowering. This approach enabled the identification of 118 genes involved in the flowering pathway. Two genome sequences of cultivated (Williams 82) and wild (IT182932) soybeans were employed to survey functional DNA variations in the flowering-related homologs. Forty genes exhibiting nonsynonymous substitutions between G. max and G. soja were catalogued. In addition, 22 genes were found to co-localize with QTLs for six traits including flowering time, first flower, pod maturity, beginning of pod, reproductive period, and seed filling period. Among the genes overlapping the QTL regions, two LHY/CCA1 genes, GI and SFR6 contained amino acid changes. The recently duplicated sequence regions of the soybean genome were used as additional criteria for the speculation of the putative function of the homologs. Two duplicated regions showed redundancy of both flowering-related genes and QTLs. ID 12398025, which contains the homeologous regions between chr 7 and chr 16, was redundant for the LHY/CCA1 and SPA1 homologs and the QTLs. Retaining of the CRY1 gene and the pod maturity QTLs were observed in the duplicated region of ID 23546507 on chr 4 and chr 6. Functional DNA variation of the LHY/CCA1 gene (Glyma07g05410) was present in a counterpart of the duplicated region on chr 7, while the gene (Glyma16g01980) present in the other portion of the duplicated region on chr 16 did not show a functional sequence change. The gene list catalogued in this study provides primary insight for understanding the regulation of flowering time and maturity in soybean.
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Affiliation(s)
- Moon Young Kim
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
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Weigel D. Natural variation in Arabidopsis: from molecular genetics to ecological genomics. PLANT PHYSIOLOGY 2012; 158:2-22. [PMID: 22147517 PMCID: PMC3252104 DOI: 10.1104/pp.111.189845] [Citation(s) in RCA: 242] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Accepted: 12/05/2011] [Indexed: 05/18/2023]
Affiliation(s)
- Detlef Weigel
- Max Planck Institute for Developmental Biology, 72076 Tuebingen, Germany.
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Abstract
The onset of flowering is an important adaptive trait in plants. The small ephemeral species Arabidopsis thaliana grows under a wide range of temperature and day-length conditions across much of the Northern hemisphere, and a number of flowering-time loci that vary between different accessions have been identified before. However, only few studies have addressed the species-wide genetic architecture of flowering-time control. We have taken advantage of a set of 18 distinct accessions that present much of the common genetic diversity of A. thaliana and mapped quantitative trait loci (QTL) for flowering time in 17 F₂ populations derived from these parents. We found that the majority of flowering-time QTL cluster in as few as five genomic regions, which include the locations of the entire FLC/MAF clade of transcription factor genes. By comparing effects across shared parents, we conclude that in several cases there might be an allelic series caused by rare alleles. While this finding parallels results obtained for maize, in contrast to maize much of the variation in flowering time in A. thaliana appears to be due to large-effect alleles.
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