1
|
Ahn JY, Subburaj S, Yan F, Yao J, Chandrasekaran A, Ahn KG, Lee GJ. Molecular Evaluation of the Effects of FLC Homologs and Coordinating Regulators on the Flowering Responses to Vernalization in Cabbage ( Brassica oleracea var. capitata) Genotypes. Genes (Basel) 2024; 15:154. [PMID: 38397144 PMCID: PMC10887945 DOI: 10.3390/genes15020154] [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: 11/15/2023] [Revised: 01/08/2024] [Accepted: 01/20/2024] [Indexed: 02/25/2024] Open
Abstract
The flowering loci of cabbage must be understood to boost their productivity. In this study, to clarify the flowering mechanisms of cabbage, we examined the three flowering repressors BoFLC1, 2 and 3, and the flowering regulators BoGI, BoCOOLAIR, and BoVIN3 of early (CAB1), middle (CAB3), and late (CAB5) flowering cabbage genotypes. Analysis of allele-specifically amplified genomic DNA and various sequence alignments demonstrated that maximal insertions and deletions influenced cabbage flowering behavior, notably in CAB3 and CAB5. Phylogenetic studies showed that BoFLC1, 2, and 3 in the CAB1, 3, and 5 genotypes had the highest homologies to other Brassica species, with CAB3 and 5 the most similar. Although CAB3 and CAB5 have comparable genetic patterns, flowering repressors and flowering regulators were investigated individually with and without vernalization to determine their minor flowering differences. The expression investigation revealed that vernalized CAB5 downregulated all BoFLC genes compared to CAB3 and, in contrast, CAB3 exhibited upregulated BoCOOLAIR. We hypothesized that the CAB3 BoFLC locus' additional insertions may have led to BoCOOLAIR overexpression and BoFLC downregulation. This study sheds light on cabbage genotypes-particularly those of CAB1 and CAB5-and suggests that structural variations in BoFLC2 and 3 bind flowering regulators, such as COOLAIR, which may affect cabbage flowering time.
Collapse
Affiliation(s)
- Ju-Young Ahn
- Department of Horticulture, Chungnam National University, Daejeon 34134, Republic of Korea; (J.-Y.A.); (S.S.); (A.C.)
| | - Saminathan Subburaj
- Department of Horticulture, Chungnam National University, Daejeon 34134, Republic of Korea; (J.-Y.A.); (S.S.); (A.C.)
| | - Fanzhuang Yan
- Department of Smart Agriculture Systems, Chungnam National University, Daejeon 34134, Republic of Korea; (F.Y.); (J.Y.)
| | - Jian Yao
- Department of Smart Agriculture Systems, Chungnam National University, Daejeon 34134, Republic of Korea; (F.Y.); (J.Y.)
| | - Ajithan Chandrasekaran
- Department of Horticulture, Chungnam National University, Daejeon 34134, Republic of Korea; (J.-Y.A.); (S.S.); (A.C.)
- Department of Smart Agriculture Systems, Chungnam National University, Daejeon 34134, Republic of Korea; (F.Y.); (J.Y.)
| | - Kyoung-Gu Ahn
- Joen Seed Co., Ltd., Goesan 28051, Republic of Korea;
| | - Geung-Joo Lee
- Department of Horticulture, Chungnam National University, Daejeon 34134, Republic of Korea; (J.-Y.A.); (S.S.); (A.C.)
- Department of Smart Agriculture Systems, Chungnam National University, Daejeon 34134, Republic of Korea; (F.Y.); (J.Y.)
| |
Collapse
|
2
|
Jiang X, Song Q, Ye W, Chen ZJ. Concerted genomic and epigenomic changes accompany stabilization of Arabidopsis allopolyploids. Nat Ecol Evol 2021; 5:1382-1393. [PMID: 34413505 PMCID: PMC8484014 DOI: 10.1038/s41559-021-01523-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 06/24/2021] [Indexed: 02/06/2023]
Abstract
During evolution successful allopolyploids must overcome 'genome shock' between hybridizing species but the underlying process remains elusive. Here, we report concerted genomic and epigenomic changes in resynthesized and natural Arabidopsis suecica (TTAA) allotetraploids derived from Arabidopsis thaliana (TT) and Arabidopsis arenosa (AA). A. suecica shows conserved gene synteny and content with more gene family gain and loss in the A and T subgenomes than respective progenitors, although A. arenosa-derived subgenome has more structural variation and transposon distributions than A. thaliana-derived subgenome. These balanced genomic variations are accompanied by pervasive convergent and concerted changes in DNA methylation and gene expression among allotetraploids. The A subgenome is hypomethylated rapidly from F1 to resynthesized allotetraploids and convergently to the T-subgenome level in natural A. suecica, despite many other methylated loci being inherited from F1 to all allotetraploids. These changes in DNA methylation, including small RNAs, in allotetraploids may affect gene expression and phenotypic variation, including flowering, silencing of self-incompatibility and upregulation of meiosis- and mitosis-related genes. In conclusion, concerted genomic and epigenomic changes may improve stability and adaptation during polyploid evolution.
Collapse
Affiliation(s)
- Xinyu Jiang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Qingxin Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Wenxue Ye
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Z Jeffrey Chen
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
| |
Collapse
|
3
|
Xu S, Ding Y, Sun J, Zhang Z, Wu Z, Yang T, Shen F, Xue G. A high-quality genome assembly of Jasminum sambac provides insight into floral trait formation and Oleaceae genome evolution. Mol Ecol Resour 2021; 22:724-739. [PMID: 34460989 DOI: 10.1111/1755-0998.13497] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 08/23/2021] [Accepted: 08/24/2021] [Indexed: 11/29/2022]
Abstract
As one of the most economically significant Oleaceae family members, Jasminum sambac is renowned for its distinct sweet, heady fragrance. Using Illumina reads, Nanopore long reads, and HiC-sequencing, we efficiently assembled and annotated the J. sambac genome. The high-quality genome assembly consisted of a total of 507 Mb sequence (contig N50 = 17.6 Mb) with 13 pseudomolecules. A total of 21,143 protein-coding genes and 303 Mb repeat sequences were predicted. An ancient whole-genome triplication event at the base of Oleaceae (~66 million years ago [Ma], Late Cretaceous) was identified and this may have contributed to the diversification of the Oleaceae ancestor and its divergence from the Lamiales. Stress-related (e.g., WRKY) and flowering-related (e.g., MADS-box) genes were located in the triplicated regions, suggesting that the polyploidy event might have contributed adaptive potential. Genes related to terpenoid biosynthesis, for example, FTA and TPS, were observed to be duplicated to a great extent in the J. sambac genome, perhaps explaining the strong fragrance of the flowers. Copy number changes in distinct phylogenetic clades of the MADS-box family were observed in J. sambac genome, for example, AGL6- and Mα- were lost and SOC- expanded, features that might underlie the long flowering period of J. sambac. The structural genes implicated in anthocyanin biosynthesis were depleted and this may explain the absence of vivid colours in jasmine. Collectively, assembling the J. sambac genome provides new insights into the genome evolution of the Oleaceae family and provides mechanistic insights into floral properties.
Collapse
Affiliation(s)
- Shixiao Xu
- Tobacco College, Henan Agricultural University, Zhengzhou City, Henan Province, China.,Scientific Observation and Experiment Station of Tobacco Biology & Processing, Ministry of Agriculture, Zhengzhou City, Henan Province, China.,National Tobacco Cultivation & Physiology & Biochemisty Research Centre, Zhengzhou City, Henan Province, China
| | - Yongle Ding
- Tobacco College, Henan Agricultural University, Zhengzhou City, Henan Province, China.,Scientific Observation and Experiment Station of Tobacco Biology & Processing, Ministry of Agriculture, Zhengzhou City, Henan Province, China.,National Tobacco Cultivation & Physiology & Biochemisty Research Centre, Zhengzhou City, Henan Province, China
| | - Juntao Sun
- Tobacco College, Henan Agricultural University, Zhengzhou City, Henan Province, China.,Scientific Observation and Experiment Station of Tobacco Biology & Processing, Ministry of Agriculture, Zhengzhou City, Henan Province, China.,National Tobacco Cultivation & Physiology & Biochemisty Research Centre, Zhengzhou City, Henan Province, China
| | - Zhiqiang Zhang
- Tobacco College, Henan Agricultural University, Zhengzhou City, Henan Province, China.,Scientific Observation and Experiment Station of Tobacco Biology & Processing, Ministry of Agriculture, Zhengzhou City, Henan Province, China.,National Tobacco Cultivation & Physiology & Biochemisty Research Centre, Zhengzhou City, Henan Province, China
| | - Zhaoyun Wu
- Tobacco College, Henan Agricultural University, Zhengzhou City, Henan Province, China.,Scientific Observation and Experiment Station of Tobacco Biology & Processing, Ministry of Agriculture, Zhengzhou City, Henan Province, China.,National Tobacco Cultivation & Physiology & Biochemisty Research Centre, Zhengzhou City, Henan Province, China
| | - Tiezhao Yang
- Tobacco College, Henan Agricultural University, Zhengzhou City, Henan Province, China
| | - Fei Shen
- Beijing Agro-biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Gang Xue
- Tobacco College, Henan Agricultural University, Zhengzhou City, Henan Province, China.,Scientific Observation and Experiment Station of Tobacco Biology & Processing, Ministry of Agriculture, Zhengzhou City, Henan Province, China.,National Tobacco Cultivation & Physiology & Biochemisty Research Centre, Zhengzhou City, Henan Province, China
| |
Collapse
|
4
|
Wei Y, Li G, Zhang S, Zhang S, Zhang H, Sun R, Zhang R, Li F. Analysis of Transcriptional Changes in Different Brassica napus Synthetic Allopolyploids. Genes (Basel) 2021; 12:82. [PMID: 33440604 PMCID: PMC7827416 DOI: 10.3390/genes12010082] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/28/2020] [Accepted: 01/04/2021] [Indexed: 11/23/2022] Open
Abstract
Allopolyploidy is an evolutionary and mechanistically intriguing process involving the reconciliation of two or more sets of diverged genomes and regulatory interactions, resulting in new phenotypes. In this study, we explored the gene expression patterns of eight F2 synthetic Brassica napus using RNA sequencing. We found that B. napus allopolyploid formation was accompanied by extensive changes in gene expression. A comparison between F2 and the parent shows a certain proportion of differentially expressed genes (DEG) and activation\silent gene, and the two genomes (female parent (AA)\male parent (CC) genomes) showed significant differences in response to whole-genome duplication (WGD); non-additively expressed genes represented a small portion, while Gene Ontology (GO) enrichment analysis showed that it played an important role in responding to WGD. Besides, genome-wide expression level dominance (ELD) was biased toward the AA genome, and the parental expression pattern of most genes showed a high degree of conservation. Moreover, gene expression showed differences among eight individuals and was consistent with the results of a cluster analysis of traits. Furthermore, the differential expression of waxy synthetic pathways and flowering pathway genes could explain the performance of traits. Collectively, gene expression of the newly formed allopolyploid changed dramatically, and this was different among the selfing offspring, which could be a prominent cause of the trait separation. Our data provide novel insights into the relationship between the expression of differentially expressed genes and trait segregation and provide clues into the evolution of allopolyploids.
Collapse
Affiliation(s)
- Yunxiao Wei
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Beijing 100081, China; (Y.W.); (G.L.); (S.Z.); (S.Z.); (H.Z.); (R.S.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Guoliang Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Beijing 100081, China; (Y.W.); (G.L.); (S.Z.); (S.Z.); (H.Z.); (R.S.)
| | - Shujiang Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Beijing 100081, China; (Y.W.); (G.L.); (S.Z.); (S.Z.); (H.Z.); (R.S.)
| | - Shifan Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Beijing 100081, China; (Y.W.); (G.L.); (S.Z.); (S.Z.); (H.Z.); (R.S.)
| | - Hui Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Beijing 100081, China; (Y.W.); (G.L.); (S.Z.); (S.Z.); (H.Z.); (R.S.)
| | - Rifei Sun
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Beijing 100081, China; (Y.W.); (G.L.); (S.Z.); (S.Z.); (H.Z.); (R.S.)
| | - Rui Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Fei Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Beijing 100081, China; (Y.W.); (G.L.); (S.Z.); (S.Z.); (H.Z.); (R.S.)
| |
Collapse
|
5
|
Soppe WJJ, Viñegra de la Torre N, Albani MC. The Diverse Roles of FLOWERING LOCUS C in Annual and Perennial Brassicaceae Species. FRONTIERS IN PLANT SCIENCE 2021; 12:627258. [PMID: 33679840 PMCID: PMC7927791 DOI: 10.3389/fpls.2021.627258] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 01/25/2021] [Indexed: 05/07/2023]
Abstract
Most temperate species require prolonged exposure to winter chilling temperatures to flower in the spring. In the Brassicaceae, the MADS box transcription factor FLOWERING LOCUS C (FLC) is a major regulator of flowering in response to prolonged cold exposure, a process called vernalization. Winter annual Arabidopsis thaliana accessions initiate flowering in the spring due to the stable silencing of FLC by vernalization. The role of FLC has also been explored in perennials within the Brassicaceae family, such as Arabis alpina. The flowering pattern in A. alpina differs from the one in A. thaliana. A. alpina plants initiate flower buds during vernalization but only flower after subsequent exposure to growth-promoting conditions. Here we discuss the role of FLC in annual and perennial Brassicaceae species. We show that, besides its conserved role in flowering, FLC has acquired additional functions that contribute to vegetative and seed traits. PERPETUAL FLOWERING 1 (PEP1), the A. alpina FLC ortholog, contributes to the perennial growth habit. We discuss that PEP1 directly and indirectly, regulates traits such as the duration of the flowering episode, polycarpic growth habit and shoot architecture. We suggest that these additional roles of PEP1 are facilitated by (1) the ability of A. alpina plants to form flower buds during long-term cold exposure, (2) age-related differences between meristems, which enable that not all meristems initiate flowering during cold exposure, and (3) differences between meristems in stable silencing of PEP1 after long-term cold, which ensure that PEP1 expression levels will remain low after vernalization only in meristems that commit to flowering during cold exposure. These features result in spatiotemporal seasonal changes of PEP1 expression during the A. alpina life cycle that contribute to the perennial growth habit. FLC and PEP1 have also been shown to influence the timing of another developmental transition in the plant, seed germination, by influencing seed dormancy and longevity. This suggests that during evolution, FLC and its orthologs adopted both similar and divergent roles to regulate life history traits. Spatiotemporal changes of FLC transcript accumulation drive developmental decisions and contribute to life history evolution.
Collapse
Affiliation(s)
| | - Natanael Viñegra de la Torre
- Institute for Plant Sciences, University of Cologne, Cologne, Germany
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Cluster of Excellence on Plant Sciences, “SMART Plants for Tomorrow’s Needs,” Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Maria C. Albani
- Institute for Plant Sciences, University of Cologne, Cologne, Germany
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Cluster of Excellence on Plant Sciences, “SMART Plants for Tomorrow’s Needs,” Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- *Correspondence: Maria C. Albani, ;
| |
Collapse
|
6
|
Relaxed purifying selection in autopolyploids drives transposable element over-accumulation which provides variants for local adaptation. Nat Commun 2019; 10:5818. [PMID: 31862875 PMCID: PMC6925279 DOI: 10.1038/s41467-019-13730-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 11/21/2019] [Indexed: 11/28/2022] Open
Abstract
Polyploidization is frequently associated with increased transposable element (TE) content. However, what drives TE dynamics following whole genome duplication (WGD) and the evolutionary implications remain unclear. Here, we leverage whole-genome resequencing data available for ~300 individuals of Arabidopsis arenosa, a well characterized natural diploid-autotetraploid plant species, to address these questions. Based on 43,176 TE insertions we detect in these genomes, we demonstrate that relaxed purifying selection rather than transposition bursts is the main driver of TE over-accumulation after WGD. Furthermore, the increased pool of TE insertions in tetraploids is especially enriched within or near environmentally responsive genes. Notably, we show that the major flowering-time repressor gene FLC is disrupted by a TE insertion specifically in the rapid-cycling tetraploid lineage that colonized mainland railways. Together, our findings indicate that tetrasomy leads to an enhanced accumulation of genic TE insertions, some of which likely contribute to local adaptation. Why transposable elements (TEs) accumulate in polyploids and the evolutionary implications remain unclear. Here, the authors show that following whole genome duplication, relaxed purifying selection is the main driver of TE over-accumulation, which provides variants for rapid local adaptation.
Collapse
|
7
|
Kemi U, Leinonen PH, Savolainen O, Kuittinen H. Inflorescence shoot elongation, but not flower primordia formation, is photoperiodically regulated in Arabidopsis lyrata. ANNALS OF BOTANY 2019; 124:91-102. [PMID: 31321402 PMCID: PMC6676387 DOI: 10.1093/aob/mcz035] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 02/22/2019] [Indexed: 05/23/2023]
Abstract
BACKGROUND AND AIMS Photoperiod contains information about the progress of seasons. Plants use the changing photoperiod as a cue for the correct timing of important life history events, including flowering. Here the effect of photoperiod on flowering in four Arabidopsis lyrata populations originating from different latitudes was studied, as well as expression levels of candidate genes for governing the between-population differences. METHODS Flowering of plants from four A. lyrata populations was studied in three different photoperiods after vernalization. Flowering development was separated into three steps: flower primordia formation, inflorescence shoot elongation and opening of the first flower. Circadian expression rhythms of the A. lyrata homologues of GIGANTEA (GI), FLAVIN-BINDING, KELCH REPEAT, F-BOX 1 (FKF1), CONSTANS (CO) and FLOWERING LOCUS T (FT) were studied in three of the populations in the intermediate (14 h) photoperiod treatment. KEY RESULTS Most plants in all populations formed visible flower primordia during vernalization. Further inflorescence development after vernalization was strongly inhibited by short days in the northern European population (latitude 61°N), only slightly in the central European population (49°N) and not at all in the North American populations (36°N and 42°N). In the 14 h daylength, where all plants from the three southernmost populations but only 60 % of the northernmost population flowered, the circadian expression rhythm of the A. lyrata FT was only detected in the southern populations, suggesting differentiation in the critical daylength for activation of the long-day pathway. However, circadian expression rhythms of A. lyrata GI, FKF1 and CO were similar between populations. CONCLUSIONS The results indicate that in A. lyrata, transition to flowering can occur through pathways independent of long days, but elongation of inflorescences is photoperiodically regulated.
Collapse
Affiliation(s)
- Ulla Kemi
- Department of Ecology and Genetics, University of Oulu, FIN-90014 Oulu, Finland
- Max Planck Institute for Plant Breeding Research, Carl von Linné Weg, Cologne, Germany
| | - Päivi H Leinonen
- Department of Ecology and Genetics, University of Oulu, FIN-90014 Oulu, Finland
- Biodiversity Unit, University of Turku, Turku, Finland
| | - Outi Savolainen
- Department of Ecology and Genetics, University of Oulu, FIN-90014 Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Helmi Kuittinen
- Department of Ecology and Genetics, University of Oulu, FIN-90014 Oulu, Finland
| |
Collapse
|
8
|
Genetic basis and evolution of rapid cycling in railway populations of tetraploid Arabidopsis arenosa. PLoS Genet 2018; 14:e1007510. [PMID: 29975688 PMCID: PMC6049958 DOI: 10.1371/journal.pgen.1007510] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 07/17/2018] [Accepted: 06/22/2018] [Indexed: 12/31/2022] Open
Abstract
Spatially structured plant populations with diverse adaptations provide powerful models to investigate evolution. Human-generated ruderal habitats are abundant and low-competition, but are challenging for plants not adapted to them. Ruderal habitats also sometimes form networked corridors (e.g. roadsides and railways) that allow rapid long-distance spread of successfully adapted variants. Here we use transcriptomic and genomic analyses, coupled with genetic mapping and transgenic follow-up, to understand the evolution of rapid cycling during adaptation to railway sites in autotetraploid Arabidopsis arenosa. We focus mostly on a hybrid population that is likely a secondary colonist of a railway site. These mountain railway plants are phenotypically similar to their cosmopolitan cousins. We thus hypothesized that colonization primarily involved the flow of adaptive alleles from the cosmopolitan railway variant. But our data shows that it is not that simple: while there is evidence of selection having acted on introgressed alleles, selection also acted on rare standing variation, and new mutations may also contribute. Among the genes we show have allelic divergence with functional relevance to flowering time are known regulators of flowering, including FLC and CONSTANS. Prior implications of these genes in weediness and rapid cycling supports the idea that these are “evolutionary hotspots” for these traits. We also find that one of two alleles of CONSTANS under selection in the secondary colonist was selected from rare standing variation in mountain populations, while the other was introgressed from the cosmopolitan railway populations. The latter allele likely arose in diploid populations over 700km away, highlighting how ruderal populations could act as allele conduits and thus influence local adaptation.
Collapse
|
9
|
Gustafsson C, Willforss J, Lopes-Pinto F, Ortiz R, Geleta M. Identification of genes regulating traits targeted for domestication of field cress (Lepidium campestre) as a biennial and perennial oilseed crop. BMC Genet 2018; 19:36. [PMID: 29843613 PMCID: PMC5975587 DOI: 10.1186/s12863-018-0624-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 05/18/2018] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND The changing climate and the desire to use renewable oil sources necessitate the development of new oilseed crops. Field cress (Lepidium campestre) is a species in the Brassicaceae family that has been targeted for domestication not only as an oilseed crop that produces seeds with a desirable industrial oil quality but also as a cover/catch crop that provides valuable ecosystem services. Lepidium is closely related to Arabidopsis and display significant proportions of syntenic regions in their genomes. Arabidopsis genes are among the most characterized genes in the plant kingdom and, hence, comparative genomics of Lepidium-Arabidopsis would facilitate the identification of Lepidium candidate genes regulating various desirable traits. RESULTS Homologues of 30 genes known to regulate vernalization, flowering time, pod shattering, oil content and quality in Arabidopsis were identified and partially characterized in Lepidium. Alignments of sequences representing field cress and two of its closely related perennial relatives: L. heterophyllum and L. hirtum revealed 243 polymorphic sites across the partial sequences of the 30 genes, of which 95 were within the predicted coding regions and 40 led to a change in amino acids of the target proteins. Within field cress, 34 polymorphic sites including nine non-synonymous substitutions were identified. The phylogenetic analysis of the data revealed that field cress is more closely related to L. heterophyllum than to L. hirtum. CONCLUSIONS There is significant variation within and among Lepidium species within partial sequences of the 30 genes known to regulate traits targeted in the present study. The variation within these genes are potentially useful to speed-up the process of domesticating field cress as future oil crop. The phylogenetic relationship between the Lepidium species revealed in this study does not only shed some light on Lepidium genome evolution but also provides important information to develop efficient schemes for interspecific hybridization between different Lepidium species as part of the domestication efforts.
Collapse
Affiliation(s)
- Cecilia Gustafsson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Box 101, SE-23053, Alnarp, Sweden
| | - Jakob Willforss
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Box 102, SE-23053, Alnarp, Sweden
| | - Fernando Lopes-Pinto
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, SE-750 07, Uppsala, Sweden
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Box 101, SE-23053, Alnarp, Sweden
| | - Mulatu Geleta
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Box 101, SE-23053, Alnarp, Sweden.
| |
Collapse
|
10
|
Ding M, Chen ZJ. Epigenetic perspectives on the evolution and domestication of polyploid plant and crops. CURRENT OPINION IN PLANT BIOLOGY 2018; 42:37-48. [PMID: 29502038 PMCID: PMC6058195 DOI: 10.1016/j.pbi.2018.02.003] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 02/07/2018] [Accepted: 02/13/2018] [Indexed: 05/19/2023]
Abstract
Polyploidy or whole genome duplication (WGD) is a prominent feature for genome evolution of some animals and all flowering plants, including many important crops such as wheat, cotton, and canola. In autopolyploids, genome duplication often perturbs dosage regulation on biological networks. In allopolyploids, interspecific hybridization could induce genetic and epigenetic changes, the effects of which could be amplified by genome doubling (ploidy changes). Albeit the importance of genetic changes, some epigenetic changes can be stabilized and transmitted as epialleles into the progeny, which are subject to natural selection, adaptation, and domestication. Here we review recent advances for general and specific roles of epigenetic changes in the evolution of flowering plants and domestication of agricultural crops.
Collapse
Affiliation(s)
- Mingquan Ding
- Departments of Molecular Biosciences and Integrative Biology, Institute for Cellular and Molecular Biology, and Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX 78712, USA
| | - Z Jeffrey Chen
- Departments of Molecular Biosciences and Integrative Biology, Institute for Cellular and Molecular Biology, and Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX 78712, USA; State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.
| |
Collapse
|
11
|
Kiefer C, Severing E, Karl R, Bergonzi S, Koch M, Tresch A, Coupland G. Divergence of annual and perennial species in the Brassicaceae and the contribution of cis-acting variation at FLC orthologues. Mol Ecol 2017; 26:3437-3457. [PMID: 28261921 PMCID: PMC5485006 DOI: 10.1111/mec.14084] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 02/15/2017] [Accepted: 02/21/2017] [Indexed: 12/31/2022]
Abstract
Variation in life history contributes to reproductive success in different environments. Divergence of annual and perennial angiosperm species is an extreme example that has occurred frequently. Perennials survive for several years and restrict the duration of reproduction by cycling between vegetative growth and flowering, whereas annuals live for 1 year and flower once. We used the tribe Arabideae (Brassicaceae) to study the divergence of seasonal flowering behaviour among annual and perennial species. In perennial Brassicaceae, orthologues of FLOWERING LOCUS C (FLC), a floral inhibitor in Arabidopsis thaliana, are repressed by winter cold and reactivated in spring conferring seasonal flowering patterns, whereas in annuals, they are stably repressed by cold. We isolated FLC orthologues from three annual and two perennial Arabis species and found that the duplicated structure of the A. alpina locus is not required for perenniality. The expression patterns of the genes differed between annuals and perennials, as observed among Arabidopsis species, suggesting a broad relevance of these patterns within the Brassicaceae. Also analysis of plants derived from an interspecies cross of A. alpina and annual A. montbretiana demonstrated that cis-regulatory changes in FLC orthologues contribute to their different transcriptional patterns. Sequence comparisons of FLC orthologues from annuals and perennials in the tribes Arabideae and Camelineae identified two regulatory regions in the first intron whose sequence variation correlates with divergence of the annual and perennial expression patterns. Thus, we propose that related cis-acting changes in FLC orthologues occur independently in different tribes of the Brassicaceae during life history evolution.
Collapse
Affiliation(s)
- C Kiefer
- Max Planck Institute for Plant Breeding Research, Plant Developmental Biology, Carl-von-Linné Weg 10, 50829, Cologne, Germany
| | - E Severing
- Max Planck Institute for Plant Breeding Research, Plant Developmental Biology, Carl-von-Linné Weg 10, 50829, Cologne, Germany
| | - R Karl
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies, INF 345, 69120, Heidelberg, Germany
| | - S Bergonzi
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - M Koch
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies, INF 345, 69120, Heidelberg, Germany
| | - A Tresch
- Max Planck Institute for Plant Breeding Research, Plant Developmental Biology, Carl-von-Linné Weg 10, 50829, Cologne, Germany
- Cologne Biocenter, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - G Coupland
- Max Planck Institute for Plant Breeding Research, Plant Developmental Biology, Carl-von-Linné Weg 10, 50829, Cologne, Germany
| |
Collapse
|
12
|
Chen F, Zhang X, Liu X, Zhang L. Evolutionary Analysis of MIKC c-Type MADS-Box Genes in Gymnosperms and Angiosperms. FRONTIERS IN PLANT SCIENCE 2017; 8:895. [PMID: 28611810 PMCID: PMC5447709 DOI: 10.3389/fpls.2017.00895] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 05/12/2017] [Indexed: 05/02/2023]
Abstract
MIKCc-type MADS-box genes encode transcription factors that control floral organ morphogenesis and flowering time in flowering plants. Here, in order to determine when the subfamilies of MIKCc originated and their early evolutionary trajectory, we sampled and analyzed the genomes and large-scale transcriptomes representing all the orders of gymnosperms and basal angiosperms. Through phylogenetic inference, the MIKCc-type MADS-box genes were subdivided into 14 monophyletic clades. Among them, the gymnosperm orthologs of AGL6, SEP, AP1, GMADS, SOC1, AGL32, AP3/PI, SVP, AGL15, ANR1, and AG were identified. We identified and characterized the origin of a novel subfamily GMADS within gymnosperms but lost orthologs in monocots and Brassicaceae. ABCE model prototype genes were relatively conserved in terms of gene number in gymnosperms, but expanded in angiosperms, whereas SVP, SOC1, and GMADS had dramatic expansions in gymnosperms but conserved in angiosperms. Our results provided the most detailed evolutionary history of all MIKCc gene clades in gymnosperms and angiosperms. We proposed that although the near complete set of MIKCc genes had evolved in gymnosperms, the duplication and expressional transition of ABCE model MIKCc genes in the ancestor of angiosperms triggered the first flower.
Collapse
|
13
|
Evolutionary conservation of cold-induced antisense RNAs of FLOWERING LOCUS C in Arabidopsis thaliana perennial relatives. Nat Commun 2014; 5:4457. [PMID: 25030056 PMCID: PMC4109010 DOI: 10.1038/ncomms5457] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 06/19/2014] [Indexed: 11/11/2022] Open
Abstract
Antisense RNA (asRNA) COOLAIR is expressed at A. thaliana FLOWERING LOCUS C (FLC) in response to winter temperatures. Its contribution to cold-induced silencing of FLC was proposed but its functional and evolutionary significance remain unclear. Here we identify a highly conserved block containing the COOLAIR first exon and core promoter at the 3′ end of several FLC orthologues. Furthermore, asRNAs related to COOLAIR are expressed at FLC loci in the perennials A. alpina and A. lyrata, although some splicing variants differ from A. thaliana. Study of the A. alpina orthologue, PERPETUAL FLOWERING 1 (PEP1), demonstrates that AaCOOLAIR is induced each winter of the perennial life cycle. Introduction of PEP1 into A. thaliana reveals that AaCOOLAIR cis-elements confer cold-inducibility in this heterologous species while the difference between PEP1 and FLC mRNA patterns depends on both cis-elements and species-specific trans-acting factors. Thus, expression of COOLAIR is highly conserved, supporting its importance in FLC regulation. FLOWERING LOCUS C (FLC) is thought to control the flowering time of A. thaliana in response to winter temperatures, in a process known as vernalization. Here, the authors suggest that the COOLAIR antisense RNA, which is conserved across plant species, acts to repress the expression of FLC during vernalization.
Collapse
|
14
|
Turck F, Coupland G. Natural variation in epigenetic gene regulation and its effects on plant developmental traits. Evolution 2013; 68:620-31. [PMID: 24117443 DOI: 10.1111/evo.12286] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 09/30/2013] [Indexed: 01/02/2023]
Abstract
In plants, epigenetic variation contributes to phenotypic differences in developmental traits. At the mechanistic level, this variation is conferred by DNA methylation and histone modifications. We describe several examples in which changes in gene expression caused by variation in DNA methylation lead to alterations in plant development. In these examples, the presence of repeated sequences or transposons within the promoters of the affected genes are associated with DNA methylation and gene inactivation. Small interfering RNAs expressed from these sequences recruit DNA methylation to the gene. Some of these methylated alleles are unstable giving rise to revertant sectors during mitosis and to progeny in which the methylated state is lost. However, others are stable for many generations and persist through speciation. These examples indicate that although DNA methylation influences gene expression, this is frequently dependent on classical changes to DNA sequence such as transposon insertions. By contrast, forms of histone methylation cause repression of gene expression that is stably inherited through mitosis but that can also be erased over time or during meiosis. A striking example involves the induction of flowering by exposure to low winter temperatures in Arabidopsis thaliana and its relatives. Histone methylation participates in repression of expression of an inhibitor of flowering during cold. In annual, semelparous species such as A. thaliana, this histone methylation is stably inherited through mitosis after return from cold to warm temperatures allowing the plant to flower continuously during spring and summer until it senesces. However, in perennial, iteroparous relatives the histone modification rapidly disappears when temperatures rise, allowing expression of the floral inhibitor to increase and limiting flowering to a short interval. In this case, epigenetic histone modifications control a key adaptive trait, and their pattern changes rapidly during evolution associated with life-history strategy. We discuss these examples of epigenetic developmental traits with emphasis on the underlying mechanisms, their stability, and adaptive value.
Collapse
Affiliation(s)
- Franziska Turck
- Max Planck Institute for Plant Breeding Research, Carl von Linne Weg 10, D-50829, Cologne, Germany.
| | | |
Collapse
|
15
|
Ruelens P, de Maagd RA, Proost S, Theißen G, Geuten K, Kaufmann K. FLOWERING LOCUS C in monocots and the tandem origin of angiosperm-specific MADS-box genes. Nat Commun 2013; 4:2280. [DOI: 10.1038/ncomms3280] [Citation(s) in RCA: 113] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Accepted: 07/10/2013] [Indexed: 12/11/2022] Open
|
16
|
Graeber K, Voegele A, Büttner-Mainik A, Sperber K, Mummenhoff K, Leubner-Metzger G. Spatiotemporal seed development analysis provides insight into primary dormancy induction and evolution of the Lepidium delay of germination1 genes. PLANT PHYSIOLOGY 2013; 161:1903-17. [PMID: 23426197 PMCID: PMC3613464 DOI: 10.1104/pp.112.213298] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Seed dormancy is a block to the completion of germination of an intact viable seed under favorable conditions and is an adaptive and agronomically important trait. Thus, elucidating conserved features of dormancy mechanisms is of great interest. The worldwide-distributed genus Lepidium (Brassicaceae) is well suited for cross-species comparisons investigating the origin of common or specific early-life-history traits. We show here that homologs of the seed dormancy-specific gene delay of germination1 (DOG1) from Arabidopsis (Arabidopsis thaliana) are widespread in the genus Lepidium. The highly dormant Lepidium papillosum is a polyploid species and possesses multiple structurally diversified DOG1 genes (LepaDOG1), some being expressed in seeds. We used the largely elongated and well-structured infructescence of L. papillosum for studying primary dormancy induction during seed development and maturation with high temporal resolution. Using simultaneous germination assays and marker protein expression detection, we show that LepaDOG1 proteins are expressed in seeds during maturation prior to dormancy induction. Accumulation of LepaDOG1 takes place in seeds that gain premature germinability before and during the seed-filling stage and declines during the late maturation and desiccation phase when dormancy is induced. These analyses of the Lepidium DOG1 genes and their protein expression patterns highlight similarities and species-specific differences of primary dormancy induction mechanism(s) in the Brassicaceae.
Collapse
|
17
|
Kemi U, Niittyvuopio A, Toivainen T, Pasanen A, Quilot-Turion B, Holm K, Lagercrantz U, Savolainen O, Kuittinen H. Role of vernalization and of duplicated FLOWERING LOCUS C in the perennial Arabidopsis lyrata. THE NEW PHYTOLOGIST 2013; 197:323-335. [PMID: 23106477 DOI: 10.1111/j.1469-8137.2012.04378.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Accepted: 09/07/2012] [Indexed: 05/08/2023]
Abstract
FLOWERING LOCUS C (FLC) is one of the main genes influencing the vernalization requirement and natural flowering time variation in the annual Arabidopsis thaliana. Here we studied the effects of vernalization on flowering and its genetic basis in the perennial Arabidopsis lyrata. Two tandemly duplicated FLC genes (FLC1 and FLC2) were compared with respect to expression and DNA sequence. The effect of vernalization on flowering and on the expression of FLC1 was studied in three European populations. The genetic basis of the FLC1 expression difference between two of the populations was further studied by expression quantitative trait locus (eQTL) mapping and sequence analysis. FLC1 was shown to have a likely role in the vernalization requirement for flowering in A. lyrata. Vernalization decreased its expression and the northern study populations showed higher FLC1 expression than the southern one. eQTL mapping between two of the populations revealed one eQTL affecting FLC1 expression in the genomic region containing the FLC genes. Most FLC1 sequence differences between the study populations were found in the promoter region and in the first intron. Variation in the FLC1 sequence may cause differences in FLC1 expression between late- and early-flowering A. lyrata populations.
Collapse
Affiliation(s)
- Ulla Kemi
- Department of Biology, University of Oulu, PO Box 3000, FIN-90401, Oulu, Finland
| | - Anne Niittyvuopio
- Department of Biology, University of Oulu, PO Box 3000, FIN-90401, Oulu, Finland
| | - Tuomas Toivainen
- Department of Biology, University of Oulu, PO Box 3000, FIN-90401, Oulu, Finland
- Biocenter Oulu, University of Oulu, 90014, Oulu, Finland
| | - Anu Pasanen
- Department of Biology, University of Oulu, PO Box 3000, FIN-90401, Oulu, Finland
| | - Bénédicte Quilot-Turion
- Department of Biology, University of Oulu, PO Box 3000, FIN-90401, Oulu, Finland
- INRA, UR1052 Génétique et Amélioration des Fruits et Légumes, F-84143, Montfavet, France
| | - Karl Holm
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752, 36 Uppsala, Sweden
| | - Ulf Lagercrantz
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752, 36 Uppsala, Sweden
| | - Outi Savolainen
- Department of Biology, University of Oulu, PO Box 3000, FIN-90401, Oulu, Finland
- Biocenter Oulu, University of Oulu, 90014, Oulu, Finland
| | - Helmi Kuittinen
- Department of Biology, University of Oulu, PO Box 3000, FIN-90401, Oulu, Finland
| |
Collapse
|
18
|
Albani MC, Castaings L, Wötzel S, Mateos JL, Wunder J, Wang R, Reymond M, Coupland G. PEP1 of Arabis alpina is encoded by two overlapping genes that contribute to natural genetic variation in perennial flowering. PLoS Genet 2012; 8:e1003130. [PMID: 23284298 PMCID: PMC3527215 DOI: 10.1371/journal.pgen.1003130] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2012] [Accepted: 10/15/2012] [Indexed: 11/18/2022] Open
Abstract
Higher plants exhibit a variety of different life histories. Annual plants live for less than a year and after flowering produce seeds and senesce. By contrast perennials live for many years, dividing their life cycle into episodes of vegetative growth and flowering. Environmental cues control key check points in both life histories. Genes controlling responses to these cues exhibit natural genetic variation that has been studied most in short-lived annuals. We characterize natural genetic variation conferring differences in the perennial life cycle of Arabis alpina. Previously the accession Pajares was shown to flower after prolonged exposure to cold (vernalization) and only for a limited period before returning to vegetative growth. We describe five accessions of A. alpina that do not require vernalization to flower and flower continuously. Genetic complementation showed that these accessions carry mutant alleles at PERPETUAL FLOWERING 1 (PEP1), which encodes a MADS box transcription factor orthologous to FLOWERING LOCUS C in the annual Arabidopsis thaliana. Each accession carries a different mutation at PEP1, suggesting that such variation has arisen independently many times. Characterization of these alleles demonstrated that in most accessions, including Pajares, the PEP1 locus contains a tandem arrangement of a full length and a partial PEP1 copy, which give rise to two full-length transcripts that are differentially expressed. This complexity contrasts with the single gene present in A. thaliana and might contribute to the more complex expression pattern of PEP1 that is associated with the perennial life-cycle. Our work demonstrates that natural accessions of A. alpina exhibit distinct life histories conferred by differences in PEP1 activity, and that continuous flowering forms have arisen multiple times by inactivation of the floral repressor PEP1. Similar phenotypic variation is found in other herbaceous perennial species, and our results provide a paradigm for how characteristic perennial phenotypes might arise. Perennial plants live for many years and cycle between flowering and vegetative growth. These stages of the life cycle are often initiated by environmental conditions and occur seasonally. However, many herbaceous perennial species such as strawberry, rose, or Arabis alpina contain varieties that flower continuously irrespective of the seasons. Here we characterize this genetic variation in A. alpina and show that five continuously flowering accessions carry independent mutations in the PERPETUAL FLOWERING 1 (PEP1) gene. These mutations impair the activity of the PEP1 floral repressor causing the plants to flower without requirement for winter cold and to flower continuously. This result has interesting parallels with strawberry and rose, where inactivation of a different floral repressor controlling response to day length gives rise to naturally occurring perpetual flowering forms. We also show that PEP1 in A. alpina has a complex duplicated structure that gives rise to two overlapping transcripts. This arrangement differs from the simple structure of PEP1 orthologues in related annual species, such as FLC of Arabidopsis thaliana, suggesting that duplication of PEP1 might contribute to the complex transcriptional patterns associated with PEP1 function in perennials. Our work provides insight into genetic variation contributing to the perennial life history of plants.
Collapse
Affiliation(s)
- Maria C. Albani
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Loren Castaings
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Stefan Wötzel
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | | | - Jörg Wunder
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Renhou Wang
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Mathieu Reymond
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - George Coupland
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
- * E-mail:
| |
Collapse
|
19
|
Smaczniak C, Immink RGH, Angenent GC, Kaufmann K. Developmental and evolutionary diversity of plant MADS-domain factors: insights from recent studies. Development 2012; 139:3081-98. [PMID: 22872082 DOI: 10.1242/dev.074674] [Citation(s) in RCA: 340] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Members of the MADS-box transcription factor family play essential roles in almost every developmental process in plants. Many MADS-box genes have conserved functions across the flowering plants, but some have acquired novel functions in specific species during evolution. The analyses of MADS-domain protein interactions and target genes have provided new insights into their molecular functions. Here, we review recent findings on MADS-box gene functions in Arabidopsis and discuss the evolutionary history and functional diversification of this gene family in plants. We also discuss possible mechanisms of action of MADS-domain proteins based on their interactions with chromatin-associated factors and other transcriptional regulators.
Collapse
Affiliation(s)
- Cezary Smaczniak
- Laboratory of Molecular Biology, Wageningen University, 6708PB Wageningen, The Netherlands
| | | | | | | |
Collapse
|
20
|
Huang HR, Yan PC, Lascoux M, Ge XJ. Flowering time and transcriptome variation in Capsella bursa-pastoris (Brassicaceae). THE NEW PHYTOLOGIST 2012; 194:676-689. [PMID: 22409515 DOI: 10.1111/j.1469-8137.2012.04101.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
• Flowering is a major developmental transition and its timing in relation to environmental conditions is of crucial importance to plant fitness. Understanding the genetic basis of flowering time variation is important to determining how plants adapt locally. • Here, we investigated flowering time variation of Capsella bursa-pastoris collected from different latitudes in China. We also used a digital gene expression (DGE) system to generate partial gene expression profiles for 12 selected samples. • We found that flowering time was highly variable and most strongly correlated with day length and winter temperature. Significant differences in gene expression between early- and late-flowering samples were detected for 72 candidate genes for flowering time. Genes related to circadian rhythms were significantly overrepresented among the differentially expressed genes. • Our data suggest that circadian rhythms and circadian clock genes play an important role in the evolution of flowering time, and C. bursa-pastoris plants exhibit expression differences for candidate genes likely to affect flowering time across the broad range of environments they face in China.
Collapse
Affiliation(s)
- Hui-Run Huang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, the Chinese Academy of Sciences, Guangzhou 510650, China
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China
| | - Peng-Cheng Yan
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Martin Lascoux
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden
- Laboratory of Evolutionary Genomics, CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, the Chinese Academy of Sciences, Shanghai, China
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, the Chinese Academy of Sciences, Guangzhou 510650, China
| |
Collapse
|
21
|
Matyasek R, Fulnecek J, Leitch AR, Kovarik A. Analysis of two abundant, highly related satellites in the allotetraploid Nicotiana arentsii using double-strand conformation polymorphism analysis and sequencing. THE NEW PHYTOLOGIST 2011; 192:747-59. [PMID: 21777247 DOI: 10.1111/j.1469-8137.2011.03827.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
• Allopolyploidy, a driving force in plant evolution, can induce rapid structural changes in parental subgenomes. Here, we examined the fate of homologous subtelomeric satellites in intrasection allotetraploid Nicotiana arentsii formed from N. undulata and N. wigandioides progenitors < 200,000 yr ago. • We cloned and sequenced a number of monomers from progenitors and the allotetraploid. Structural features of both cloned and genomic monomers were studied using double-strand conformation polymorphism analysis. • Two homologous satellites were isolated from N. undulata (called NUNSSP) and N. wigandioides (NWISSP). While the NUNSSP monomers were highly homogeneous in nucleotide sequences, the NWISSP monomers formed two separate clades. Likewise, the genomic NUNSSP monomers showed less DNA conformation heterogeneity than NWISSP monomers, with distinct conformations. While both satellites predominantly occupy subtelomeric positions, a fraction of the NWISSP repeats was found in an intercalary location, supporting the hypothesis that dispersion prevents the repeats becoming homogeneous. Sequence, structural and chromosomal features of the parental satellites were faithfully inherited by N. arentsii. • Our study revealed that intergenomic homogenization of subtelomeric satellite repeats does not occur in N. arentsii allotetraploid. We propose that the sequence and structural divergence of subtelomeric satellites may render allopolyploid chromosomes less vulnerable to intergenomic exchanges.
Collapse
Affiliation(s)
- Roman Matyasek
- Institute of Biophysics, Academy of Sciences of the Czech Republic, vvi, Brno, Czech Republic.
| | | | | | | |
Collapse
|
22
|
|