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Jones DM, Hepworth J, Wells R, Pullen N, Trick M, Morris RJ. A transcriptomic time-series reveals differing trajectories during pre-floral development in the apex and leaf in winter and spring varieties of Brassica napus. Sci Rep 2024; 14:3538. [PMID: 38347020 PMCID: PMC10861513 DOI: 10.1038/s41598-024-53526-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 01/31/2024] [Indexed: 02/15/2024] Open
Abstract
Oilseed rape (Brassica napus) is an important global oil crop, with spring and winter varieties grown commercially. To understand the transcriptomic differences between these varieties, we collected transcriptomes from apex and leaf tissue from a spring variety, Westar, and a winter variety, Tapidor, before, during, and after vernalisation treatment, until the plants flowered. Large transcriptomic differences were noted in both varieties during the vernalisation treatment because of temperature and day length changes. Transcriptomic alignment revealed that the apex transcriptome reflects developmental state, whereas the leaf transcriptome is more closely aligned to the age of the plant. Similar numbers of copies of genes were expressed in both varieties during the time series, although key flowering time genes exhibited expression pattern differences. BnaFLC copies on A2 and A10 are the best candidates for the increased vernalisation requirement of Tapidor. Other BnaFLC copies show tissue-dependent reactivation of expression post-cold, with these dynamics suggesting some copies have retained or acquired a perennial nature. BnaSOC1 genes, also related to the vernalisation pathway, have expression profiles which suggest tissue subfunctionalisation. This understanding may help to breed varieties with more consistent or robust vernalisation responses, of special importance due to the milder winters resulting from climate change.
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Affiliation(s)
- D Marc Jones
- Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
- Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
- Synthace, The WestWorks, 195 Wood Lane, 4th Floor, London, W12 7FQ, UK.
| | - Jo Hepworth
- Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
- Department of Biosciences, Durham University, Stockton Road, Durham, DH1 3LE, UK
| | - Rachel Wells
- Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Nick Pullen
- Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
- Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Martin Trick
- Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Richard J Morris
- Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
- Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
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2
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Hao P, Lin B, Ren Y, Hu H, Xue B, Huang L, Hua S. Auxin-regulated timing of transition from vegetative to reproductive growth in rapeseed ( Brassica napus L.) under different nitrogen application rates. FRONTIERS IN PLANT SCIENCE 2022; 13:927662. [PMID: 36161032 PMCID: PMC9501695 DOI: 10.3389/fpls.2022.927662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 08/17/2022] [Indexed: 06/16/2023]
Abstract
Accelerating the differentiation of floral meristem (FM) from shoot apical meristems (SAM) which determines the conversion from vegetative to reproductive growth is of great significance for the production of rapeseed (Brassica napus L.). In this research, the mechanisms of different nitrogen (N) application rates (low N, N1; normal N, N2; and high N, N3) on different FM development stages triggering the regulation of FM differentiation genes through the auxin biosynthetic and signal transduction were investigated. We found that the stage of FM differentiation, which was identified through a stereomicroscope and scanning electron microscope, came 4 and 7 days earlier under high N rate than under normal and low N levels, with the seed yield increased by 11.1 and 22.6%, respectively. Analysis of the auxin and its derivatives contents showed that the main biosynthesis way of auxin was the indole acetaldehyde oxime (IAOx) pathway, with 3-Indole acetonitrile dramatically accumulated during FM differentiation. At the same time, an obvious decrease of IAA contents at each FM differentiation stage was detected, and then gradually rose. Results of the expression of genes involved in auxin biosynthesis, auxin signaling transduction, and FM identification under five FM differentiation stages and three nitrogen application rates showed that genes involved in auxin biosynthesis were regulated before the FM differentiation stage, while the regulation of FM identity genes appeared mainly at the middle and later periods of the five stages, and the regulation level of genes varied under different N rates. Taken together, a high nitrogen rate could accelerate the initiation of FM differentiation, and auxin involved a lot in this regulation.
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Affiliation(s)
- Pengfei Hao
- Institute of Crops and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Baogang Lin
- Institute of Crops and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yun Ren
- Huzhou Agricultural Science and Technology Development Center, Huzhou, China
| | - Hao Hu
- Institute of Digital Agriculture, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Bowen Xue
- Institute of Crops and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Lan Huang
- Institute of Crops and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Shuijin Hua
- Institute of Crops and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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3
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Vos RA, van der Veen-van Wijk CAM, Schranz ME, Vrieling K, Klinkhamer PGL, Lens F. Refining bulk segregant analyses: ontology-mediated discovery of flowering time genes in Brassica oleracea. PLANT METHODS 2022; 18:92. [PMID: 35780674 PMCID: PMC9252076 DOI: 10.1186/s13007-022-00921-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 06/16/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Bulk segregant analysis (BSA) can help identify quantitative trait loci (QTLs), but this may result in substantial bycatch of functionally irrelevant genes. RESULTS Here we develop a Gene Ontology-mediated approach to zoom in on specific genes located inside QTLs identified by BSA as implicated in a continuous trait. We apply this to a novel experimental system: flowering time in the giant woody Jersey kale, which we phenotyped in four bulks of flowering onset. Our inferred QTLs yielded tens of thousands of candidate genes. We reduced this by two orders of magnitude by focusing on genes annotated with terms contained within relevant subgraphs of the Gene Ontology. A pathway enrichment test then led to the circadian rhythm pathway. The genes that enriched this pathway are attested from previous research as regulating flowering time. Within that pathway, the genes CCA1, FT, and TSF were identified as having functionally significant variation compared to Arabidopsis. We validated and confirmed our ontology-mediated results through genome sequencing and homology-based SNP analysis. However, our ontology-mediated approach produced additional genes of putative importance, showing that the approach aids in exploration and discovery. CONCLUSIONS Our method is potentially applicable to the study of other complex traits and we therefore make our workflows available as open-source code and a reusable Docker container.
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Affiliation(s)
- Rutger A Vos
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA, Leiden, The Netherlands.
- Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands.
| | | | - M Eric Schranz
- Biosystematics Group, Wageningen University and Research, P.O. Box 16, 6700AP, Wageningen, The Netherlands
| | - Klaas Vrieling
- Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Peter G L Klinkhamer
- Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Frederic Lens
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA, Leiden, The Netherlands
- Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
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4
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Poza-Viejo L, Payá-Milans M, San Martín-Uriz P, Castro-Labrador L, Lara-Astiaso D, Wilkinson MD, Piñeiro M, Jarillo JA, Crevillén P. Conserved and distinct roles of H3K27me3 demethylases regulating flowering time in Brassica rapa. PLANT, CELL & ENVIRONMENT 2022; 45:1428-1441. [PMID: 35037269 DOI: 10.1111/pce.14258] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 12/08/2021] [Indexed: 05/28/2023]
Abstract
Epigenetic regulation is necessary for optimal organism development and preservation of gene expression profiles in the cell. In plants, the trimethylation of histone H3 lysine 27 (H3K27me3) is a silencing epigenetic mark relevant for developmental transitions like flowering. The floral transition is a key agronomic trait; however, the epigenetic mechanisms of flowering time regulation in crops remain poorly understood. Here we study the Jumonji H3K27me3 demethylases BraA.REF6 and BraA.ELF6 in Brassica rapa. Phenotypic characterization of novel mutant lines and genome-wide H3K27me3 chromatin immunoprecipitation and transcriptomic analyses indicated that BraA.REF6 plays a greater role than BraA.ELF6 in fine-tuning H3K27me3 levels. In addition, we found that braA.elf6 mutants were early flowering due to high H3K27me3 levels at B. rapa homologs of the floral repressor FLC. Unlike mutations in Arabidopsis thaliana, braA.ref6 mutants were late flowering without altering the expression of B. rapa FLC genes. Remarkably, we found that BraA.REF6 regulated a number of gibberellic acid (GA) biosynthetic genes, including a homolog of GA1, and that GA-treatment complemented the late flowering mutant phenotype. This study increases our understanding of the epigenetic regulation of flowering time in B. rapa, highlighting conserved and distinct regulatory mechanisms between model and crop species.
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Affiliation(s)
- Laura Poza-Viejo
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Pozuelo de Alarcón, Madrid, Spain
| | - Miriam Payá-Milans
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Pozuelo de Alarcón, Madrid, Spain
| | - Patxi San Martín-Uriz
- Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, Pamplona, Navarra, Spain
| | - Laura Castro-Labrador
- Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, Pamplona, Navarra, Spain
| | - David Lara-Astiaso
- Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, Pamplona, Navarra, Spain
| | - Mark D Wilkinson
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Pozuelo de Alarcón, Madrid, Spain
| | - Manuel Piñeiro
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Pozuelo de Alarcón, Madrid, Spain
| | - José A Jarillo
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Pozuelo de Alarcón, Madrid, Spain
| | - Pedro Crevillén
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Pozuelo de Alarcón, Madrid, Spain
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5
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Kim S, Kim JA, Kang H, Kim DH. A premature stop codon in BrFLC2 transcript results in early flowering in oilseed-type Brassica rapa plants. PLANT MOLECULAR BIOLOGY 2022; 108:241-255. [PMID: 35064421 DOI: 10.1007/s11103-021-01231-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 12/05/2021] [Indexed: 06/14/2023]
Abstract
Nonsense-mediated mRNA decay (NMD)-mediated degradation of BrFLC2 transcripts is the main cause of rapid flowering of oilseed-type B. rapa 'LP08' plants. Many Brassica species require vernalization (long-term winter-like cooling) for transition to the reproductive stage. In the past several decades, scientific efforts have been made to discern the molecular mechanisms underlying vernalization in many species. Thus, to identify the key regulators required for vernalization in Brassica rapa L., we constructed a linkage map composed of 7833 single nucleotide polymorphism markers using the late-flowering Chinese cabbage (B. rapa L. ssp. pekinensis) inbred line 'Chiifu' and the early-flowering yellow sarson (B. rapa L. ssp. trilocularis) line 'LP08' and identified a single major QTL on the upper-arm of the chromosome A02. In addition, we compared the transcriptomes of the lines 'Chiifu' and 'LP08' at five vernalization time points, including both non-vernalized and post-vernalization conditions. We observed that BrFLC2 was significantly downregulated in the early flowering 'LP08' and had two deletion sites (one at 4th exon and the other at 3' downstream region) around the BrFLC2 genomic region compared with the BrFLC2 genomic region in 'Chiifu'. Large deletion at 3' downstream region did not significantly affect transcription of both sense BrFLC2 transcript and antisense transcript, BrFLC2as along vernalization time course. However, the other deletion at 4th exon of BrFLC2 resulted in the generation of premature stop codon in BrFLC2 transcript in LP08 line. Cycloheximide treatment of LP08 line showed the de-repressed level of BrFLC2 in LP08, suggesting that low transcript level of BrFLC2 in LP08 might be caused by nonsense-mediated mRNA decay removing the nonsense transcript of BrFLC2. Collectively, this study provides a better understanding of the molecular mechanisms underlying floral transition in B. rapa.
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Affiliation(s)
- Sujeong Kim
- Department of Plant Science and Technology, Chung-Ang University, Anseong, South Korea
| | - Jin A Kim
- Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, Jeonju, South Korea
| | - Hajeong Kang
- Department of Plant Science and Technology, Chung-Ang University, Anseong, South Korea
| | - Dong-Hwan Kim
- Department of Plant Science and Technology, Chung-Ang University, Anseong, South Korea.
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6
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Patiranage DSR, Asare E, Maldonado-Taipe N, Rey E, Emrani N, Tester M, Jung C. Haplotype variations of major flowering time genes in quinoa unveil their role in the adaptation to different environmental conditions. PLANT, CELL & ENVIRONMENT 2021; 44:2565-2579. [PMID: 33878205 DOI: 10.1111/pce.14071] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 04/09/2021] [Accepted: 04/11/2021] [Indexed: 06/12/2023]
Abstract
Response to photoperiod is of major importance in crop production. It defines the adaptation of plants to local environments. Quinoa is a short-day plant which had been domesticated in the Andeans regions. We wanted to understand the adaptation to long-day conditions by studying orthologues of two major flowering time regulators of Arabidopsis, FLOWERING LOCUS T (FT) and CONSTANS (CO) in quinoa accessions with contrasting photoperiod response. By searching the quinoa reference genome sequence, we identified 24 FT and six CO homologs. CqFT genes displayed remarkably different expression patterns between long- and short-day conditions, whereas the influence of the photoperiod on CqCOL expressions was moderate. Cultivation of 276 quinoa accessions under short- and long-day conditions revealed great differences in photoperiod sensitivity. After sequencing their genomes, we identified large sequence variations in 12 flowering time genes. We found non-random distribution of haplotypes across accessions from different geographical origins, highlighting the role of CqFT and CqCOL genes in the adaptation to different day-length conditions. We identified five haplotypes causing early flowering under long days. This study provides assets for quinoa breeding because superior haplotypes can be assembled in a predictive breeding approach to produce well-adapted early flowering lines under long-day photoperiods.
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Affiliation(s)
| | - Edward Asare
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, Kiel, Germany
| | | | - Elodie Rey
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Nazgol Emrani
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Mark Tester
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Christian Jung
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, Kiel, Germany
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7
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Song C, Li G, Dai J, Deng H. Genome-Wide Analysis of PEBP Genes in Dendrobium huoshanense: Unveiling the Antagonistic Functions of FT/TFL1 in Flowering Time. Front Genet 2021; 12:687689. [PMID: 34306028 PMCID: PMC8299281 DOI: 10.3389/fgene.2021.687689] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 05/18/2021] [Indexed: 01/17/2023] Open
Abstract
Dendrobium is a semi-shade epiphytic Orchidaceae herb with important ornamental and medicinal value. Parts of the cultivation of Dendrobium germplasm resources, as well as the identification of medicinal components, are more studied, but the functional characterization of the flowering regulation in Dendrobium plants is less reported. Here, six PEBP family genes (DhFT3, DhFT1, DhMFT, DhTFL1b, DhFT2, and DhTFL1a) were identified from the Dendrobium huoshanense genome. The chromosome-level mapping showed that these genes were sequentially distributed on chromosomes 6, 9, 15, and 17. The paralogous gene DhTFL1b corresponded to DhTFL1a, which was determined through tandem duplication. The gene structure and conserved motif of DhPEBP indicated five PEBP genes apart from DhMFT contained four exons and three introns entirely. The phylogeny analysis showed that the PEBP gene family in A. thaliana, O. sativa, Z. mays, S. lycopersicum, and P. equestris were classified into three subclades, FT, TFL, and MFT, which maintained a high homology with D. huoshanense. The conserved domain of the amino acid demonstrated that two highly conserved short motifs (DPDXP and GXHR) embed in DhPEBPs, which may contribute to the conformation of the ligand binding bag. The 86th position of DhFTs was tyrosine (Y), while the 83th and 87th of DhTFL1s belonged to histidine (H), suggesting they should have distinct functions in flowering regulation. The promoter of six DhPEBPs contained several cis-elements related to hormone induction, light response, and abiotic stress, which indicated they could be regulated by the environmental stress and endogenous signaling pathways. The qRT-PCR analysis of DhPEBPs in short-term days induced by GA indicated the gene expressions of all DhFTs were gradually increased, whereas the expression of DhTFL1 was decreased. The results implied that DhPEBPs have various regulatory functions in modulating flowering, which will provide a scientific reference for the flowering regulation of Dendrobium plants.
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Affiliation(s)
- Cheng Song
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, China.,Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu'an, China
| | - Guohui Li
- College of Life Science, Anhui Agricultural University, Hefei, China
| | - Jun Dai
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, China.,Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu'an, China
| | - Hui Deng
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, China.,Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu'an, China
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8
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Jung H, Lee A, Jo SH, Park HJ, Jung WY, Kim HS, Lee HJ, Jeong SG, Kim YS, Cho HS. Nitrogen Signaling Genes and SOC1 Determine the Flowering Time in a Reciprocal Negative Feedback Loop in Chinese Cabbage ( Brassica rapa L.) Based on CRISPR/Cas9-Mediated Mutagenesis of Multiple BrSOC1 Homologs. Int J Mol Sci 2021; 22:ijms22094631. [PMID: 33924895 PMCID: PMC8124421 DOI: 10.3390/ijms22094631] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 04/23/2021] [Accepted: 04/26/2021] [Indexed: 11/29/2022] Open
Abstract
Precise flowering timing is critical for the plant life cycle. Here, we examined the molecular mechanisms and regulatory network associated with flowering in Chinese cabbage (Brassica rapa L.) by comparative transcriptome profiling of two Chinese cabbage inbred lines, “4004” (early bolting) and “50” (late bolting). RNA-Seq and quantitative reverse transcription PCR (qPCR) analyses showed that two positive nitric oxide (NO) signaling regulator genes, nitrite reductase (BrNIR) and nitrate reductase (BrNIA), were up-regulated in line “50” with or without vernalization. In agreement with the transcription analysis, the shoots in line “50” had substantially higher nitrogen levels than those in “4004”. Upon vernalization, the flowering repressor gene Circadian 1 (BrCIR1) was significantly up-regulated in line “50”, whereas the flowering enhancer genes named SUPPRESSOR OF OVEREXPRESSION OF CONSTANCE 1 homologs (BrSOC1s) were substantially up-regulated in line “4004”. CRISPR/Cas9-mediated mutagenesis in Chinese cabbage demonstrated that the BrSOC1-1/1-2/1-3 genes were involved in late flowering, and their expression was mutually exclusive with that of the nitrogen signaling genes. Thus, we identified two flowering mechanisms in Chinese cabbage: a reciprocal negative feedback loop between nitrogen signaling genes (BrNIA1 and BrNIR1) and BrSOC1s to control flowering time and positive feedback control of the expression of BrSOC1s.
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Affiliation(s)
- Haemyeong Jung
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea; (H.J.); (A.L.); (S.H.J.); (H.J.P.); (W.Y.J.); (H.-S.K.); (H.-J.L.)
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), Daejeon 34113, Korea
| | - Areum Lee
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea; (H.J.); (A.L.); (S.H.J.); (H.J.P.); (W.Y.J.); (H.-S.K.); (H.-J.L.)
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), Daejeon 34113, Korea
| | - Seung Hee Jo
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea; (H.J.); (A.L.); (S.H.J.); (H.J.P.); (W.Y.J.); (H.-S.K.); (H.-J.L.)
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), Daejeon 34113, Korea
| | - Hyun Ji Park
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea; (H.J.); (A.L.); (S.H.J.); (H.J.P.); (W.Y.J.); (H.-S.K.); (H.-J.L.)
| | - Won Yong Jung
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea; (H.J.); (A.L.); (S.H.J.); (H.J.P.); (W.Y.J.); (H.-S.K.); (H.-J.L.)
| | - Hyun-Soon Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea; (H.J.); (A.L.); (S.H.J.); (H.J.P.); (W.Y.J.); (H.-S.K.); (H.-J.L.)
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), Daejeon 34113, Korea
| | - Hyo-Jun Lee
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea; (H.J.); (A.L.); (S.H.J.); (H.J.P.); (W.Y.J.); (H.-S.K.); (H.-J.L.)
- Department of Functional Genomics, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), Daejeon 34113, Korea
| | - Seon-Geum Jeong
- Department of Biotechnology, NongWoo Bio, Anseong 17558, Korea;
| | - Youn-Sung Kim
- Department of Biotechnology, NongWoo Bio, Anseong 17558, Korea;
- Correspondence: (Y.-S.K.); (H.S.C.); Tel.: +82-31-652-5526 (Y.-S.K.); +82-42-860-4469 (H.S.C.)
| | - Hye Sun Cho
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea; (H.J.); (A.L.); (S.H.J.); (H.J.P.); (W.Y.J.); (H.-S.K.); (H.-J.L.)
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), Daejeon 34113, Korea
- Correspondence: (Y.-S.K.); (H.S.C.); Tel.: +82-31-652-5526 (Y.-S.K.); +82-42-860-4469 (H.S.C.)
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9
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Calderwood A, Hepworth J, Woodhouse S, Bilham L, Jones DM, Tudor E, Ali M, Dean C, Wells R, Irwin JA, Morris RJ. Comparative transcriptomics reveals desynchronisation of gene expression during the floral transition between Arabidopsis and Brassica rapa cultivars. QUANTITATIVE PLANT BIOLOGY 2021; 2:e4. [PMID: 37077206 PMCID: PMC10095958 DOI: 10.1017/qpb.2021.6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 03/07/2021] [Accepted: 03/09/2021] [Indexed: 05/03/2023]
Abstract
Comparative transcriptomics can be used to translate an understanding of gene regulatory networks from model systems to less studied species. Here, we use RNA-Seq to determine and compare gene expression dynamics through the floral transition in the model species Arabidopsis thaliana and the closely related crop Brassica rapa. We find that different curve registration functions are required for different genes, indicating that there is no single common 'developmental time' between Arabidopsis and B. rapa. A detailed comparison between Arabidopsis and B. rapa and between two B. rapa accessions reveals different modes of regulation of the key floral integrator SOC1, and that the floral transition in the B. rapa accessions is triggered by different pathways. Our study adds to the mechanistic understanding of the regulatory network of flowering time in rapid cycling B. rapa and highlights the importance of registration methods for the comparison of developmental gene expression data.
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Affiliation(s)
- Alexander Calderwood
- Department of Computational and Systems Biology, John Innes Centre, Norwich, United Kingdom
| | - Jo Hepworth
- Department of Crop Genetics, John Innes Centre, Norwich, United Kingdom
| | - Shannon Woodhouse
- Department of Computational and Systems Biology, John Innes Centre, Norwich, United Kingdom
| | - Lorelei Bilham
- Department of Crop Genetics, John Innes Centre, Norwich, United Kingdom
| | - D. Marc Jones
- Department of Computational and Systems Biology, John Innes Centre, Norwich, United Kingdom
- VIB-UGent Centre for Plant Systems Biology, Gent, Belgium
| | - Eleri Tudor
- Department of Crop Genetics, John Innes Centre, Norwich, United Kingdom
| | - Mubarak Ali
- Bangladesh Agricultural Research Institute, Gazipur, Bangladesh
| | - Caroline Dean
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
| | - Rachel Wells
- Department of Crop Genetics, John Innes Centre, Norwich, United Kingdom
| | - Judith A. Irwin
- Department of Crop Genetics, John Innes Centre, Norwich, United Kingdom
| | - Richard J. Morris
- Department of Computational and Systems Biology, John Innes Centre, Norwich, United Kingdom
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10
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Vollrath P, Chawla HS, Schiessl SV, Gabur I, Lee H, Snowdon RJ, Obermeier C. A novel deletion in FLOWERING LOCUS T modulates flowering time in winter oilseed rape. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1217-1231. [PMID: 33471161 PMCID: PMC7973412 DOI: 10.1007/s00122-021-03768-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 01/06/2021] [Indexed: 05/05/2023]
Abstract
A novel structural variant was discovered in the FLOWERING LOCUS T orthologue BnaFT.A02 by long-read sequencing. Nested association mapping in an elite winter oilseed rape population revealed that this 288 bp deletion associates with early flowering, putatively by modification of binding-sites for important flowering regulation genes. Perfect timing of flowering is crucial for optimal pollination and high seed yield. Extensive previous studies of flowering behavior in Brassica napus (canola, rapeseed) identified mutations in key flowering regulators which differentiate winter, semi-winter and spring ecotypes. However, because these are generally fixed in locally adapted genotypes, they have only limited relevance for fine adjustment of flowering time in elite cultivar gene pools. In crosses between ecotypes, the ecotype-specific major-effect mutations mask minor-effect loci of interest for breeding. Here, we investigated flowering time in a multiparental mapping population derived from seven elite winter oilseed rape cultivars which are fixed for major-effect mutations separating winter-type rapeseed from other ecotypes. Association mapping revealed eight genomic regions on chromosomes A02, C02 and C03 associating with fine modulation of flowering time. Long-read genomic resequencing of the seven parental lines identified seven structural variants coinciding with candidate genes for flowering time within chromosome regions associated with flowering time. Segregation patterns for these variants in the elite multiparental population and a diversity set of winter types using locus-specific assays revealed significant associations with flowering time for three deletions on chromosome A02. One of these was a previously undescribed 288 bp deletion within the second intron of FLOWERING LOCUS T on chromosome A02, emphasizing the advantage of long-read sequencing for detection of structural variants in this size range. Detailed analysis revealed the impact of this specific deletion on flowering-time modulation under extreme environments and varying day lengths in elite, winter-type oilseed rape.
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Affiliation(s)
- Paul Vollrath
- Department of Plant Breeding, Justus Liebig University, Giessen, Germany
| | - Harmeet S Chawla
- Department of Plant Breeding, Justus Liebig University, Giessen, Germany
| | - Sarah V Schiessl
- Department of Plant Breeding, Justus Liebig University, Giessen, Germany
| | - Iulian Gabur
- Department of Plant Breeding, Justus Liebig University, Giessen, Germany
| | - HueyTyng Lee
- Department of Plant Breeding, Justus Liebig University, Giessen, Germany
| | - Rod J Snowdon
- Department of Plant Breeding, Justus Liebig University, Giessen, Germany
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11
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Wei X, Rahim MA, Zhao Y, Yang S, Wang Z, Su H, Li L, Niu L, Harun-Ur-Rashid M, Yuan Y, Zhang X. Comparative Transcriptome Analysis of Early- and Late-Bolting Traits in Chinese Cabbage ( Brassica rapa). Front Genet 2021; 12:590830. [PMID: 33747036 PMCID: PMC7969806 DOI: 10.3389/fgene.2021.590830] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 01/18/2021] [Indexed: 12/27/2022] Open
Abstract
Chinese cabbage is one of the most important and widely consumed vegetables in China. The developmental transition from the vegetative to reproductive phase is a crucial process in the life cycle of flowering plants. In spring-sown Chinese cabbage, late bolting is desirable over early bolting. In this study, we analyzed double haploid (DH) lines of late bolting (“Y410-1” and “SY2004”) heading Chinese cabbage (Brassica rapa var. pekinensis) and early-bolting Chinese cabbage (“CX14-1”) (B. rapa ssp. chinensis var. parachinensis) by comparative transcriptome profiling using the Illumina RNA-seq platform. We assembled 721.49 million clean high-quality paired-end reads into 47,363 transcripts and 47,363 genes, including 3,144 novel unigenes. There were 12,932, 4,732, and 4,732 differentially expressed genes (DEGs) in pairwise comparisons of Y410-1 vs. CX14-1, SY2004 vs. CX14-1, and Y410-1 vs. SY2004, respectively. The RNA-seq results were confirmed by reverse transcription quantitative real-time PCR (RT-qPCR). A Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of DEGs revealed significant enrichment for plant hormone and signal transduction as well as starch and sucrose metabolism pathways. Among DEGs related to plant hormone and signal transduction, six unigenes encoding the indole-3-acetic acid-induced protein ARG7 (BraA02g009130), auxin-responsive protein SAUR41 (BraA09g058230), serine/threonine-protein kinase BSK11 (BraA07g032960), auxin-induced protein 15A (BraA10g019860), and abscisic acid receptor PYR1 (BraA08g012630 and BraA01g009450), were upregulated in both late bolting Chinese cabbage lines (Y410-1 and SY2004) and were identified as putative candidates for the trait. These results improve our understanding of the molecular mechanisms underlying flowering in Chinese cabbage and provide a foundation for studies of this key trait in related species.
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Affiliation(s)
- Xiaochun Wei
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Md Abdur Rahim
- Department of Genetics and Plant Breeding, Sher-e-Bangla Agricultural University, Dhaka, Bangladesh
| | - Yanyan Zhao
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Shuangjuan Yang
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Zhiyong Wang
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Henan Su
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Lin Li
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Liujing Niu
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Md Harun-Ur-Rashid
- Department of Genetics and Plant Breeding, Sher-e-Bangla Agricultural University, Dhaka, Bangladesh
| | - Yuxiang Yuan
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Xiaowei Zhang
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Zhengzhou, China
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12
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Kaur S, Atri C, Akhatar J, Mittal M, Kaur R, Banga SS. Genetics of days to flowering, maturity and plant height in natural and derived forms of Brassica rapa L. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:473-487. [PMID: 33084931 DOI: 10.1007/s00122-020-03707-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 10/10/2020] [Indexed: 06/11/2023]
Abstract
Genome wide association studies enabled prediction of many candidate genes for flowering, maturity and plant height under differing day-length conditions. Some genes were envisaged only from derived B. rapa. Flowering and plant height are the key life history traits. These are crucial for adaptation and productivity. Current investigations aimed to examine genotypic differences governing days to flowering, maturity and plant height under contrasting day-length conditions; and identify genomic regions governing the observed phenotypic variations. An association panel comprising 195 inbred lines, representing natural (NR) and derived (DR) forms of Brassica rapa (AA; 2n = 20), was evaluated at two sowing dates and two locations, representing different day-length regimes. Derived B. rapa is a unique pre-breeding material extracted from B. juncea (AABB; 2n = 36). Population structure analysis, using DArT genotypes established derived B. rapa as a genetic resource distinct from natural B. rapa. Genome wide association studies facilitated detection of many trait associated SNPs. Chromosomes A03, A05 and A09 harboured majority of these. Functional annotation of the associated SNPs and surrounding genome space(s) helped to predict 43 candidate genes. Many of these were predicted under specific day-length conditions. Important among these were the genes encoding floral meristem identity (SPL3, SPL15, AP3, BAM2), photoperiodic responses (COL2, AGL18, SPT, NF-YC4), gibberellic acid biosynthesis (GA1) and regulation of flowering (EBS). Some of the predicted genes were detected for DR subpanel alone. Genes controlling hormones, auxins and gibberellins appeared important for the regulation of plant height. Many of the significant SNPs were located on chromosomes harbouring previously reported QTLs and candidate genes. The identified loci may be used for marker-assisted selection after due validation.
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Affiliation(s)
- Snehdeep Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Chhaya Atri
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Javed Akhatar
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Meenakshi Mittal
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Rimaljeet Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Surinder S Banga
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India.
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13
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Tudor EH, Jones DM, He Z, Bancroft I, Trick M, Wells R, Irwin JA, Dean C. QTL-seq identifies BnaFT.A02 and BnaFLC.A02 as candidates for variation in vernalization requirement and response in winter oilseed rape (Brassica napus). PLANT BIOTECHNOLOGY JOURNAL 2020; 18:2466-2481. [PMID: 32452611 PMCID: PMC7680531 DOI: 10.1111/pbi.13421] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 03/10/2020] [Accepted: 05/11/2020] [Indexed: 05/05/2023]
Abstract
Winter, spring and biennial varieties of Brassica napus that vary in vernalization requirement are grown for vegetable and oil production. Here, we show that the obligate or facultative nature of the vernalization requirement in European winter oilseed rape is determined by allelic variation at a 10 Mbp region on chromosome A02. This region includes orthologues of the key floral regulators FLOWERING LOCUS C (BnaFLC.A02) and FLOWERING LOCUS T (BnaFT.A02). Polymorphism at BnaFLC.A02 and BnaFT.A02, mostly in cis-regulatory regions, results in distinct gene expression dynamics in response to vernalization treatment. Our data suggest allelic variation at BnaFT.A02 is associated with flowering time in the absence of vernalization, while variation at BnaFLC.A02 is associated with flowering time under vernalizing conditions. We hypothesize selection for BnaFLC.A02 and BnaFT.A02 gene expression variation has facilitated the generation of European winter oilseed rape varieties that are adapted to different winter climates. This knowledge will allow for the selection of alleles of flowering time regulators that alter the vernalization requirement of oilseed rape, informing the generation of new varieties with adapted flowering times and improved yields.
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Affiliation(s)
| | | | - Zhesi He
- Department of BiologyUniversity of YorkYorkUK
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14
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Alternative splicing of flowering time gene FT is associated with halving of time to flowering in coconut. Sci Rep 2020; 10:11640. [PMID: 32669611 PMCID: PMC7363896 DOI: 10.1038/s41598-020-68431-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 06/24/2020] [Indexed: 11/08/2022] Open
Abstract
Coconut palm has two distinct types-"tall" and "dwarf"-which differ morphologically. Tall coconut varieties need 8-10 years to start flowering, while dwarf coconut varieties only require 3-5 years. We compared seedling and reproductive stage transcriptomes for both coconut types to determine potential molecular mechanisms underlying control of flowering time in coconut. Several key genes in the photoperiod pathway were differentially expressed between seedling and reproductive leaf samples in both tall and dwarf coconut. These genes included suppressor of overexpression of constans (SOC1), flowering locus T (FT), and Apetala 1 (AP1). Alternative splicing analysis of genes in the photoperiod pathway further revealed that the FT gene produces different transcripts in tall compared to dwarf coconut. The shorter alternative splice variant of FT [which included a 6 bp deletion, alternative 3' splicing sites (A3SS)] was found to be exclusively present in dwarf coconut varieties but absent in most tall coconut varieties. Our results provide a valuable information resource as well as suggesting a probable mechanism for differentiation of flowering time onset in coconut, providing a target for future breeding work in accelerating time to flowering in this crop species.
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15
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The role of FRIGIDA and FLOWERING LOCUS C genes in flowering time of Brassica rapa leafy vegetables. Sci Rep 2019; 9:13843. [PMID: 31554847 PMCID: PMC6761103 DOI: 10.1038/s41598-019-50122-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 09/03/2019] [Indexed: 02/01/2023] Open
Abstract
There is a wide variation of flowering time among lines of Brassica rapa L. Most B. rapa leafy (Chinese cabbage etc.) or root (turnip) vegetables require prolonged cold exposure for flowering, known as vernalization. Premature bolting caused by low temperature leads to a reduction in the yield/quality of these B. rapa vegetables. Therefore, high bolting resistance is an important breeding trait, and understanding the molecular mechanism of vernalization is necessary to achieve this goal. In this study, we demonstrated that BrFRIb functions as an activator of BrFLC in B. rapa. We showed a positive correlation between the steady state expression levels of the sum of the BrFLC paralogs and the days to flowering after four weeks of cold treatment, suggesting that this is an indicator of the vernalization requirement. We indicate that BrFLCs are repressed by the accumulation of H3K27me3 and that the spreading of H3K27me3 promotes stable FLC repression. However, there was no clear relationship between the level of H3K27me3 in the BrFLC and the vernalization requirement. We also showed that if there was a high vernalization requirement, the rate of repression of BrFLC1 expression following prolonged cold treatments was lower.
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16
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Jian H, Zhang A, Ma J, Wang T, Yang B, Shuang LS, Liu M, Li J, Xu X, Paterson AH, Liu L. Joint QTL mapping and transcriptome sequencing analysis reveal candidate flowering time genes in Brassica napus L. BMC Genomics 2019; 20:21. [PMID: 30626329 PMCID: PMC6325782 DOI: 10.1186/s12864-018-5356-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 12/09/2018] [Indexed: 01/10/2023] Open
Abstract
Background Optimum flowering time is a key agronomic trait in Brassica napus. To investigate the genetic architecture and genetic regulation of flowering time in this important crop, we conducted quantitative trait loci (QTL) analysis of flowering time in a recombinant inbred line (RIL) population, including lines with extreme differences in flowering time, in six environments, along with RNA-Seq analysis. Results We detected 27 QTLs distributed on eight chromosomes among six environments, including one major QTL on chromosome C02 that explained 11–25% of the phenotypic variation and was stably detected in all six environments. RNA-Seq analysis revealed 105 flowering time-related differentially expressed genes (DEGs) that play roles in the circadian clock/photoperiod, autonomous pathway, and hormone and vernalization pathways. We focused on DEGs related to the regulation of flowering time, especially DEGs in QTL regions. Conclusions We identified 45 flowering time-related genes in these QTL regions, eight of which are DEGs, including key flowering time genes PSEUDO RESPONSE REGULATOR 7 (PRR7) and FY (located in a major QTL region on C02). These findings provide insights into the genetic architecture of flowering time in B. napus. Electronic supplementary material The online version of this article (10.1186/s12864-018-5356-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hongju Jian
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Academy of Agricultural Sciences, Chongqing, 400715, China.,Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30605, USA
| | - Aoxiang Zhang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Academy of Agricultural Sciences, Chongqing, 400715, China
| | - Jinqi Ma
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Academy of Agricultural Sciences, Chongqing, 400715, China
| | - Tengyue Wang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Academy of Agricultural Sciences, Chongqing, 400715, China
| | - Bo Yang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Academy of Agricultural Sciences, Chongqing, 400715, China
| | - Lan Shuan Shuang
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30605, USA
| | - Min Liu
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30605, USA
| | - Jiana Li
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Academy of Agricultural Sciences, Chongqing, 400715, China
| | - Xinfu Xu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Academy of Agricultural Sciences, Chongqing, 400715, China
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30605, USA.
| | - Liezhao Liu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Academy of Agricultural Sciences, Chongqing, 400715, China.
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17
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Wu D, Liang Z, Yan T, Xu Y, Xuan L, Tang J, Zhou G, Lohwasser U, Hua S, Wang H, Chen X, Wang Q, Zhu L, Maodzeka A, Hussain N, Li Z, Li X, Shamsi IH, Jilani G, Wu L, Zheng H, Zhang G, Chalhoub B, Shen L, Yu H, Jiang L. Whole-Genome Resequencing of a Worldwide Collection of Rapeseed Accessions Reveals the Genetic Basis of Ecotype Divergence. MOLECULAR PLANT 2019; 12:30-43. [PMID: 30472326 DOI: 10.1016/j.molp.2018.11.007] [Citation(s) in RCA: 117] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Revised: 11/17/2018] [Accepted: 11/18/2018] [Indexed: 05/18/2023]
Abstract
Rapeseed (Brassica napus), an important oilseed crop, has adapted to diverse climate zones and latitudes by forming three main ecotype groups, namely winter, semi-winter, and spring types. However, genetic variations underlying the divergence of these ecotypes are largely unknown. Here, we report the global pattern of genetic polymorphisms in rapeseed determined by resequencing a worldwide collection of 991 germplasm accessions. A total of 5.56 and 5.53 million single-nucleotide polymorphisms (SNPs) as well as 1.86 and 1.92 million InDels were identified by mapping reads to the reference genomes of "Darmor-bzh" and "Tapidor," respectively. We generated a map of allelic drift paths that shows splits and mixtures of the main populations, and revealed an asymmetric evolution of the two subgenomes of B. napus by calculating the genetic diversity and linkage disequilibrium parameters. Selective-sweep analysis revealed genetic changes in genes orthologous to those regulating various aspects of plant development and response to stresses. A genome-wide association study identified SNPs in the promoter regions of FLOWERING LOCUS T and FLOWERING LOCUS C orthologs that corresponded to the different rapeseed ecotype groups. Our study provides important insights into the genomic footprints of rapeseed evolution and flowering-time divergence among three ecotype groups, and will facilitate screening of molecular markers for accelerating rapeseed breeding.
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Affiliation(s)
- Dezhi Wu
- Institute of Crop Science, Zhejiang University, Hangzhou 310058, China
| | - Zhe Liang
- Temasek Life Sciences Laboratory and Department of Biological Science, National University of Singapore, Singapore 117543, Singapore
| | - Tao Yan
- Institute of Crop Science, Zhejiang University, Hangzhou 310058, China
| | - Ying Xu
- Institute of Crop Science, Zhejiang University, Hangzhou 310058, China
| | - Lijie Xuan
- Institute of Crop Science, Zhejiang University, Hangzhou 310058, China
| | - Juan Tang
- Biomarker Technologies Corporation, Beijing 101300, China
| | - Gang Zhou
- Biomarker Technologies Corporation, Beijing 101300, China
| | - Ulrike Lohwasser
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Stadt Seeland, Germany
| | - Shuijin Hua
- Institute of Crop and Nuclear Agricultural Sciences, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Haoyi Wang
- Institute of Crop Science, Zhejiang University, Hangzhou 310058, China
| | - Xiaoyang Chen
- Institute of Crop Science, Jinhua Academy of Agricultural Sciences, Jinhua 321017, China
| | - Qian Wang
- Institute of Crop Science, Zhejiang University, Hangzhou 310058, China
| | - Le Zhu
- Institute of Crop Science, Zhejiang University, Hangzhou 310058, China
| | - Antony Maodzeka
- Institute of Crop Science, Zhejiang University, Hangzhou 310058, China
| | - Nazim Hussain
- Institute of Crop Science, Zhejiang University, Hangzhou 310058, China
| | - Zhilan Li
- Institute of Crop Science, Zhejiang University, Hangzhou 310058, China
| | - Xuming Li
- Biomarker Technologies Corporation, Beijing 101300, China
| | | | - Ghulam Jilani
- Office of Research, Innovation & Commercialization, PMAS-Arid Agricultural University Rawalpindi, 46300 Rawalpindi, Pakistan
| | - Linde Wu
- Biomarker Technologies Corporation, Beijing 101300, China
| | - Hongkun Zheng
- Biomarker Technologies Corporation, Beijing 101300, China
| | - Guoping Zhang
- Institute of Crop Science, Zhejiang University, Hangzhou 310058, China
| | - Boulos Chalhoub
- Institute of Crop Science, Zhejiang University, Hangzhou 310058, China
| | - Lisha Shen
- Temasek Life Sciences Laboratory and Department of Biological Science, National University of Singapore, Singapore 117543, Singapore.
| | - Hao Yu
- Temasek Life Sciences Laboratory and Department of Biological Science, National University of Singapore, Singapore 117543, Singapore.
| | - Lixi Jiang
- Institute of Crop Science, Zhejiang University, Hangzhou 310058, China.
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18
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Leijten W, Koes R, Roobeek I, Frugis G. Translating Flowering Time From Arabidopsis thaliana to Brassicaceae and Asteraceae Crop Species. PLANTS 2018; 7:plants7040111. [PMID: 30558374 PMCID: PMC6313873 DOI: 10.3390/plants7040111] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 12/07/2018] [Accepted: 12/13/2018] [Indexed: 12/31/2022]
Abstract
Flowering and seed set are essential for plant species to survive, hence plants need to adapt to highly variable environments to flower in the most favorable conditions. Endogenous cues such as plant age and hormones coordinate with the environmental cues like temperature and day length to determine optimal time for the transition from vegetative to reproductive growth. In a breeding context, controlling flowering time would help to speed up the production of new hybrids and produce high yield throughout the year. The flowering time genetic network is extensively studied in the plant model species Arabidopsis thaliana, however this knowledge is still limited in most crops. This article reviews evidence of conservation and divergence of flowering time regulation in A. thaliana with its related crop species in the Brassicaceae and with more distant vegetable crops within the Asteraceae family. Despite the overall conservation of most flowering time pathways in these families, many genes controlling this trait remain elusive, and the function of most Arabidopsis homologs in these crops are yet to be determined. However, the knowledge gathered so far in both model and crop species can be already exploited in vegetable crop breeding for flowering time control.
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Affiliation(s)
- Willeke Leijten
- ENZA Zaden Research & Development B.V., Haling 1E, 1602 DB Enkhuizen, The Netherlands.
| | - Ronald Koes
- Swammerdam Institute for Life Sciences (SILS), University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands.
| | - Ilja Roobeek
- ENZA Zaden Research & Development B.V., Haling 1E, 1602 DB Enkhuizen, The Netherlands.
| | - Giovanna Frugis
- Istituto di Biologia e Biotecnologia Agraria (IBBA), Operative Unit of Rome, Consiglio Nazionale delle Ricerche (CNR), Via Salaria Km. 29,300 ⁻ 00015, Monterotondo Scalo, Roma, Italy.
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19
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Li H, Fan Y, Yu J, Chai L, Zhang J, Jiang J, Cui C, Zheng B, Jiang L, Lu K. Genome-Wide Identification of Flowering-Time Genes in Brassica Species and Reveals a Correlation between Selective Pressure and Expression Patterns of Vernalization-Pathway Genes in Brassica napus. Int J Mol Sci 2018; 19:E3632. [PMID: 30453667 PMCID: PMC6274771 DOI: 10.3390/ijms19113632] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 11/11/2018] [Accepted: 11/14/2018] [Indexed: 12/28/2022] Open
Abstract
Flowering time is a key agronomic trait, directly influencing crop yield and quality. Many flowering-time genes have been identified and characterized in the model plant Arabidopsis thaliana; however, these genes remain uncharacterized in many agronomically important Brassica crops. In this study, we identified 1064, 510, and 524 putative orthologs of A. thaliana flowering-time genes from Brassica napus, Brassica rapa, and Brassica oleracea, respectively, and found that genes involved in the aging and ambient temperature pathways were fewer than those in other flowering pathways. Flowering-time genes were distributed mostly on chromosome C03 in B. napus and B. oleracea, and on chromosome A09 in B. rapa. Calculation of non-synonymous (Ka)/synonymous substitution (Ks) ratios suggested that flowering-time genes in vernalization pathways experienced higher selection pressure than those in other pathways. Expression analysis showed that most vernalization-pathway genes were expressed in flowering organs. Approximately 40% of these genes were highly expressed in the anther, whereas flowering-time integrator genes were expressed in a highly organ-specific manner. Evolutionary selection pressures were negatively correlated with the breadth and expression levels of vernalization-pathway genes. These findings provide an integrated framework of flowering-time genes in these three Brassica crops and provide a foundation for deciphering the relationship between gene expression patterns and their evolutionary selection pressures in Brassica napus.
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Affiliation(s)
- Haojie Li
- Crop Research Institute, Sichuan Academy of Agricultural Science, Chengdu 610066, China.
| | - Yonghai Fan
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China.
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China.
| | - Jingyin Yu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture; Oil Crops Research Institute, the Chinese Academy of Agricultural Sciences, Wuhan 430062, China.
| | - Liang Chai
- Crop Research Institute, Sichuan Academy of Agricultural Science, Chengdu 610066, China.
| | - Jingfang Zhang
- Crop Research Institute, Sichuan Academy of Agricultural Science, Chengdu 610066, China.
| | - Jun Jiang
- Crop Research Institute, Sichuan Academy of Agricultural Science, Chengdu 610066, China.
| | - Cheng Cui
- Crop Research Institute, Sichuan Academy of Agricultural Science, Chengdu 610066, China.
| | - Benchuan Zheng
- Crop Research Institute, Sichuan Academy of Agricultural Science, Chengdu 610066, China.
| | - Liangcai Jiang
- Crop Research Institute, Sichuan Academy of Agricultural Science, Chengdu 610066, China.
| | - Kun Lu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China.
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China.
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Su T, Wang W, Li P, Zhang B, Li P, Xin X, Sun H, Yu Y, Zhang D, Zhao X, Wen C, Zhou G, Wang Y, Zheng H, Yu S, Zhang F. A Genomic Variation Map Provides Insights into the Genetic Basis of Spring Chinese Cabbage (Brassica rapa ssp. pekinensis) Selection. MOLECULAR PLANT 2018; 11:1360-1376. [PMID: 30217779 DOI: 10.1016/j.molp.2018.08.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Revised: 08/22/2018] [Accepted: 08/31/2018] [Indexed: 05/08/2023]
Abstract
Chinese cabbage is the most consumed leafy crop in East Asian countries. However, premature bolting induced by continuous low temperatures severely decreases the yield and quality of the Chinese cabbage, and therefore restricts its planting season and geographic distribution. In the past 40 years, spring Chinese cabbage with strong winterness has been selected to meet the market demand. Here, we report a genome variation map of Chinese cabbage generated from the resequencing data of 194 geographically diverse accessions of three ecotypes. In-depth analyses of the selection sweeps and genome-wide patterns revealed that spring Chinese cabbage was selected from a specific population of autumn Chinese cabbage around the area of Shandong peninsula in northern China. We identified 23 genomic loci that underwent intensive selection, and further demonstrated by gene expression and haplotype analyses that the incorporation of elite alleles of VERNALISATION INSENTIVE 3.1 (BrVIN3.1) and FLOWER LOCUS C 1 (BrFLC1) is a determinant genetic source of variation during selection. Moreover, we showed that the quantitative response of BrVIN3.1 to cold due to the sequence variations in the cis elements of the BrVIN3.1 promoter significantly contributes to bolting-time variation in Chinese cabbage. Collectively, our study provides valuable insights into the genetic basis of spring Chinese cabbage selection and will facilitate the breeding of bolting-resistant varieties by molecular-marker-assisted selection, transgenic or gene editing approaches.
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Affiliation(s)
- Tongbing Su
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing 100097, China; Department of Crop Genetics, John Innes Centre, Norwich NR4 7UH, UK; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China; Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Weihong Wang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing 100097, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China; Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Peirong Li
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing 100097, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China; Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Bin Zhang
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Pan Li
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China
| | - Xiaoyun Xin
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing 100097, China
| | - Honghe Sun
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing 100097, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China; Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Yangjun Yu
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing 100097, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China; Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Deshuang Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing 100097, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China; Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Xiuyun Zhao
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing 100097, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China; Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Changlong Wen
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing 100097, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China; Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Gang Zhou
- Biomarker Technologies Corporation, Beijing, China
| | - Yuntong Wang
- Biomarker Technologies Corporation, Beijing, China
| | | | - Shuancang Yu
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing 100097, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China; Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China.
| | - Fenglan Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing 100097, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China; Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China.
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Subtropical adaptation of a temperate plant (Brassica oleracea var. italica) utilizes non-vernalization-responsive QTLs. Sci Rep 2018; 8:13609. [PMID: 30206285 PMCID: PMC6134136 DOI: 10.1038/s41598-018-31987-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 08/28/2018] [Indexed: 11/08/2022] Open
Abstract
While many tropical plants have been adapted to temperate cultivation, few temperate plants have been adapted to the tropics. Originating in Western Europe, Brassica oleracea vernalization requires a period of low temperature and BoFLC2 regulates the transition to floral development. In B. oleracea germplasm selected in Taiwan, a non-vernalization pathway involving BoFLC3 rather than BoFLC2 regulates curd induction. In 112 subtropical breeding lines, specific haplotype combinations of BoFLC3 and PAN (involved in floral organ identity and a positional candidate for additional curd induction variation) adapt B. oleracea to high ambient temperature and short daylength. Duplicated genes permitted evolution of alternative pathways for control of flowering in temperate and tropical environments, a principle that might be utilized via natural or engineered approaches in other plants. New insight into regulation of Brassica flowering exemplifies translational agriculture, tapping knowledge of botanical models to improve food security under projected climate change scenarios.
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