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Maio KA, Moubayidin L. 'Organ'ising Floral Organ Development. PLANTS (BASEL, SWITZERLAND) 2024; 13:1595. [PMID: 38931027 PMCID: PMC11207604 DOI: 10.3390/plants13121595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 06/05/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024]
Abstract
Flowers are plant structures characteristic of the phylum Angiosperms composed of organs thought to have emerged from homologous structures to leaves in order to specialize in a distinctive function: reproduction. Symmetric shapes, colours, and scents all play important functional roles in flower biology. The evolution of flower symmetry and the morphology of individual flower parts (sepals, petals, stamens, and carpels) has significantly contributed to the diversity of reproductive strategies across flowering plant species. This diversity facilitates attractiveness for pollination, protection of gametes, efficient fertilization, and seed production. Symmetry, the establishment of body axes, and fate determination are tightly linked. The complex genetic networks underlying the establishment of organ, tissue, and cellular identity, as well as the growth regulators acting across the body axes, are steadily being elucidated in the field. In this review, we summarise the wealth of research already at our fingertips to begin weaving together how separate processes involved in specifying organ identity within the flower may interact, providing a functional perspective on how identity determination and axial regulation may be coordinated to inform symmetrical floral organ structures.
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Affiliation(s)
| | - Laila Moubayidin
- Department of Cell and Developmental Biology, John Innes Centre, Colney Lane, Norwich NR4 7UH, UK;
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2
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Jiang Y, Zhang A, He W, Li Q, Zhao B, Zhao H, Ke X, Guo Y, Sun P, Yang T, Wang Z, Jiang B, Shen J, Li Z. GRAS family member LATERAL SUPPRESSOR regulates the initiation and morphogenesis of watermelon lateral organs. PLANT PHYSIOLOGY 2023; 193:2592-2604. [PMID: 37584314 DOI: 10.1093/plphys/kiad445] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 06/21/2023] [Accepted: 07/05/2023] [Indexed: 08/17/2023]
Abstract
The lateral organs of watermelon (Citrullus lanatus), including lobed leaves, branches, flowers, and tendrils, together determine plant architecture and yield. However, the genetic controls underlying lateral organ initiation and morphogenesis remain unclear. Here, we found that knocking out the homologous gene of shoot branching regulator LATERAL SUPPRESSOR in watermelon (ClLs) repressed the initiation of branches, flowers, and tendrils and led to developing round leaves, indicating that ClLs undergoes functional expansion compared with its homologs in Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa), and tomato (Solanum lycopersicum). Using ClLs as the bait to screen against the cDNA library of watermelon, we identified several ClLs-interacting candidate proteins, including TENDRIL (ClTEN), PINOID (ClPID), and APETALA1 (ClAP1). Protein-protein interaction assays further demonstrated that ClLs could directly interact with ClTEN, ClPID, and ClAP1. The mRNA in situ hybridization assay revealed that the transcriptional patterns of ClLs overlapped with those of ClTEN, ClPID, and ClAP1 in the axillary meristems and leaf primordia. Mutants of ClTEN, ClPID, and ClAP1 generated by the CRISPR/Cas9 gene editing system lacked tendrils, developed round leaves, and displayed floral diapause, respectively, and all these phenotypes could be observed in ClLs knockout lines. Our findings indicate that ClLs acts as lateral organ identity protein by forming complexes with ClTEN, ClPID, and ClAP1, providing several gene targets for transforming the architecture of watermelon.
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Affiliation(s)
- Yanxin Jiang
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Anran Zhang
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Wenjing He
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Qingqing Li
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Bosi Zhao
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Hongjiao Zhao
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Xubo Ke
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Yalu Guo
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Piaoyun Sun
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Tongwen Yang
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Zheng Wang
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Biao Jiang
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Junjun Shen
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Zheng Li
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
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3
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Wang C, Niu J, Wei L, Li C, Li G, Tian Q, Ju M, Ma Q, Cao H, Duan Y, Guo H, Zhang H, Miao H. A 4.43-Kb deletion of chromosomal segment containing an ovate family protein confers long capsule in sesame (Sesamum indicum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:221. [PMID: 37819543 DOI: 10.1007/s00122-023-04465-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 09/14/2023] [Indexed: 10/13/2023]
Abstract
KEY MESSAGE A 4.43-Kb structural variation in the sesame genome results in the deletion of the Siofp1 gene and induces the long capsule length trait. Capsule length (CL) has a positive effect on seed weight and yield in various agronomically important species; however, the molecular mechanism underlying long capsule trait regulation in sesame remains unknown. The inheritance analysis showed that long capsule traits (CL > 4.0 cm) were dominant over normal length (average CL = 3.0 cm) and were controlled by a single gene pair. Association mapping with a RIL population and 259 natural sesame germplasm accessions indicated that the target interval was 52,830-730,961 bp of SiChr.10 in sesame. Meanwhile, the structural variation (SV) of the association mapping revealed that only SV_414325 on chromosome 10 was significantly associated with the CL trait, with a P value of 1.1135E-19. SV_414325 represents a 4430-bp deletion from 414,325 to 418,756 bp on SiChr.10, covering Sindi_2155000 (named SiOFP1). In the normal length type, Siofp1 encodes 411 amino acids of the ovate family proteins and is highly expressed in the leaf, stem, bud, and capsule tissues of sesame. In accordance with the transcriptional repressor character, Siofp1 overexpression in transgenic Arabidopsis (T0 and T1 generations) induced a 25-39% greater shortening of silique length than the wild type (P < 0.05), as well as round cauline leaves and short carpels. These results confirm that SiOFP1 plays a key role in regulating CL trait in sesame and other flowering plants. These findings provide a theoretical and material basis for sesame capsule development and high-yield breeding research.
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Affiliation(s)
- Cuiying Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People's Republic of China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China
| | - Jiaojiao Niu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Libin Wei
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People's Republic of China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China
| | - Chun Li
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People's Republic of China
- The Shennong Laboratory, Zhengzhou, 450002, Henan, China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China
| | - Guiting Li
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People's Republic of China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China
| | - Qiuzhen Tian
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People's Republic of China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China
| | - Ming Ju
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People's Republic of China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China
| | - Qin Ma
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People's Republic of China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China
| | - Hengchun Cao
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People's Republic of China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China
| | - Yinghui Duan
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People's Republic of China
- The Shennong Laboratory, Zhengzhou, 450002, Henan, China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China
| | - Hui Guo
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People's Republic of China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China
| | - Haiyang Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People's Republic of China.
- The Shennong Laboratory, Zhengzhou, 450002, Henan, China.
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China.
| | - Hongmei Miao
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People's Republic of China.
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China.
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Brazel AJ, Fattorini R, McCarthy J, Franzen R, Rümpler F, Coupland G, Ó’Maoiléidigh DS. AGAMOUS mediates timing of guard cell formation during gynoecium development. PLoS Genet 2023; 19:e1011000. [PMID: 37819989 PMCID: PMC10593234 DOI: 10.1371/journal.pgen.1011000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 10/23/2023] [Accepted: 09/27/2023] [Indexed: 10/13/2023] Open
Abstract
In Arabidopsis thaliana, stomata are composed of two guard cells that control the aperture of a central pore to facilitate gas exchange between the plant and its environment, which is particularly important during photosynthesis. Although leaves are the primary photosynthetic organs of flowering plants, floral organs are also photosynthetically active. In the Brassicaceae, evidence suggests that silique photosynthesis is important for optimal seed oil content. A group of transcription factors containing MADS DNA binding domains is necessary and sufficient to confer floral organ identity. Elegant models, such as the ABCE model of flower development and the floral quartet model, have been instrumental in describing the molecular mechanisms by which these floral organ identity proteins govern flower development. However, we lack a complete understanding of how the floral organ identity genes interact with the underlying leaf development program. Here, we show that the MADS domain transcription factor AGAMOUS (AG) represses stomatal development on the gynoecial valves, so that maturation of stomatal complexes coincides with fertilization. We present evidence that this regulation by AG is mediated by direct transcriptional repression of a master regulator of the stomatal lineage, MUTE, and show data that suggests this interaction is conserved among several members of the Brassicaceae. This work extends our understanding of the mechanisms underlying floral organ formation and provides a framework to decipher the mechanisms that control floral organ photosynthesis.
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Affiliation(s)
- Ailbhe J. Brazel
- Department of Biology, Maynooth University, Ireland
- The Max Plank Institute for Plant Breeding Research, Cologne, Germany
| | - Róisín Fattorini
- Department of Biochemistry and Systems Biology, The University of Liverpool, United Kingdom
| | - Jesse McCarthy
- Department of Biochemistry and Systems Biology, The University of Liverpool, United Kingdom
| | - Rainer Franzen
- The Max Plank Institute for Plant Breeding Research, Cologne, Germany
| | - Florian Rümpler
- Department of Genetics, Friedrich Schiller University Jena, Jena, Germany
| | - George Coupland
- The Max Plank Institute for Plant Breeding Research, Cologne, Germany
| | - Diarmuid S. Ó’Maoiléidigh
- Department of Biology, Maynooth University, Ireland
- The Max Plank Institute for Plant Breeding Research, Cologne, Germany
- Department of Biochemistry and Systems Biology, The University of Liverpool, United Kingdom
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5
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Su S, Lei Y, Zhou X, Suzuki T, Xiao W, Higashiyama T. A BLADE-ON-PETIOLE orthologue regulates corolla differentiation in the proximal region in Torenia fournieri. Nat Commun 2023; 14:4763. [PMID: 37553331 PMCID: PMC10409793 DOI: 10.1038/s41467-023-40399-3] [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: 07/20/2022] [Accepted: 07/26/2023] [Indexed: 08/10/2023] Open
Abstract
The three-dimensional shape of a flower is integrated by morphogenesis along different axes. Differentiation along the petal proximodistal axis is tightly linked to the specification of pollinators; however, it is still unclear how a petal patterns this axis. The corolla of Torenia fournieri exhibits strong differentiation along the proximodistal axis, and we previously found a proximal regulator, TfALOG3, controlling corolla neck differentiation. Here, we report another gene, TfBOP2, which is predominantly expressed in the proximal region of the corolla. TfBOP2 mutants have shorter proximal corolla tubes and longer distal lobe, demonstrating its function as a proximal regulator. Arabidopsis BOPs mutant shows similar defects, favouring a shared role of BOPs homologues. Genetic analysis demonstrates the interaction between TfBOP2 and TfALOG3, and we further found that TfALOG3 physically interacts with TfBOP2 and can recruit TfBOP2 to the nuclear region. Our study favours a hypothetical shared BOP-ALOG complex that is recruited to regulate corolla differentiation in the proximal region axis of T. fournieri.
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Affiliation(s)
- Shihao Su
- School of Agriculture, Sun Yat-sen University, 518107, Shenzhen, China.
| | - Yawen Lei
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, 510316, Guangzhou, Guangdong, China
| | - Xuan Zhou
- School of Agriculture, Sun Yat-sen University, 518107, Shenzhen, China
| | - Takamasa Suzuki
- College of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi, 487-8501, Japan
| | - Wei Xiao
- MBP-Center for Plant Molecular Biology, University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
| | - Tetsuya Higashiyama
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan
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6
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Somashekar H, Nonomura KI. Genetic Regulation of Mitosis-Meiosis Fate Decision in Plants: Is Callose an Oversighted Polysaccharide in These Processes? PLANTS (BASEL, SWITZERLAND) 2023; 12:1936. [PMID: 37653853 PMCID: PMC10223186 DOI: 10.3390/plants12101936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/28/2023] [Accepted: 05/04/2023] [Indexed: 09/02/2023]
Abstract
Timely progression of the meiotic cell cycle and synchronized establishment of male meiosis in anthers are key to ascertaining plant fertility. With the discovery of novel regulators of the plant cell cycle, the mechanisms underlying meiosis initiation and progression appear to be more complex than previously thought, requiring the conjunctive action of cyclins, cyclin-dependent kinases, transcription factors, protein-protein interactions, and several signaling components. Broadly, cell cycle regulators can be classified into two categories in plants based on the nature of their mutational effects: (1) those that completely arrest cell cycle progression; and (2) those that affect the timing (delay or accelerate) or synchrony of cell cycle progression but somehow complete the division process. Especially the latter effects reflect evasion or obstruction of major steps in the meiosis but have sometimes been overlooked due to their subtle phenotypes. In addition to meiotic regulators, very few signaling compounds have been discovered in plants to date. In this review, we discuss the current state of knowledge about genetic mechanisms to enter the meiotic processes, referred to as the mitosis-meiosis fate decision, as well as the importance of callose (β-1,3 glucan), which has been unsung for a long time in male meiosis in plants.
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Affiliation(s)
- Harsha Somashekar
- Plant Cytogenetics Laboratory, Department of Gene Function and Phenomics, National Institute of Genetics, Mishima 411-8540, Japan;
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima 411-8540, Japan
| | - Ken-Ichi Nonomura
- Plant Cytogenetics Laboratory, Department of Gene Function and Phenomics, National Institute of Genetics, Mishima 411-8540, Japan;
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima 411-8540, Japan
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7
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Zhao Y, Wang Y, Yan M, Liu C, Yuan Z. BELL1 interacts with CRABS CLAW and INNER NO OUTER to regulate ovule and seed development in pomegranate. PLANT PHYSIOLOGY 2023; 191:1066-1083. [PMID: 36477345 PMCID: PMC9922403 DOI: 10.1093/plphys/kiac554] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 11/03/2022] [Indexed: 06/17/2023]
Abstract
Pomegranate (Punica granatum) flowers are classified as bisexual flowers and functional male flowers. Functional male flowers have sterile pistils that show abnormal ovule development. In previous studies, we identified INNER NO OUTER (INO), CRABS CLAW (CRC), and BELL1 (BEL1), which were specifically expressed in bisexual and functional male flowers. However, the functions of ovule identity genes and the mechanism underlying ovule sterility in pomegranate remain unknown. Here, we found that the integument primordia formed and then ceased developing in the ovules of functional male flowers with a vertical diameter of 8.1-13.0 mm. Megaspore mother cells were observed in bisexual flowers when the vertical diameters of flowers were 10.1-13.0 mm, but not in functional male flowers. We analyzed the expression patterns of ovule-related genes in pomegranate ovule sterility and found that PgCRC mRNA was highly expressed at a critical stage of ovule development in bisexual flowers. Ectopic expression of PgCRC and PgINO was sufficient to increase seed number in transgenic lines. PgCRC partially complemented the Arabidopsis (Arabidopsis thaliana) crc mutant, and PgINO successfully rescued the seeds set in the Arabidopsis ino mutant. The results of yeast two-hybrid assays, bimolecular fluorescence complementation assays, and genetic data analyses showed that PgCRC and PgINO directly interact with PgBEL1. Our results also showed that PgCRC and PgINO could not interact directly with MADS-box proteins and that PgBEL1 interacted with SEPALLATA proteins. We report the function of PgCRC and PgINO in ovule and seed development and show that PgCRC and PgINO interact with PgBEL1. Thus, our results provide understanding of the genetic regulatory networks underlying ovule development in pomegranate.
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Affiliation(s)
- Yujie Zhao
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Yuying Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Ming Yan
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Cuiyu Liu
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China
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8
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Chang J, Duong TA, Schoeman C, Ma X, Roodt D, Barker N, Li Z, Van de Peer Y, Mizrachi E. The genome of the king protea, Protea cynaroides. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:262-276. [PMID: 36424853 PMCID: PMC10107735 DOI: 10.1111/tpj.16044] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 11/02/2022] [Accepted: 11/21/2022] [Indexed: 05/07/2023]
Abstract
The king protea (Protea cynaroides), an early-diverging eudicot, is the most iconic species from the Megadiverse Cape Floristic Region, and the national flower of South Africa. Perhaps best known for its iconic flower head, Protea is a key genus for the South African horticulture industry and cut-flower market. Ecologically, the genus and the family Proteaceae are important models for radiation and adaptation, particularly to soils with limited phosphorus bio-availability. Here, we present a high-quality chromosome-scale assembly of the P. cynaroides genome as the first representative of the fynbos biome. We reveal an ancestral whole-genome duplication event that occurred in the Proteaceae around the late Cretaceous that preceded the divergence of all crown groups within the family and its extant diversity in all Southern continents. The relatively stable genome structure of P. cynaroides is invaluable for comparative studies and for unveiling paleopolyploidy in other groups, such as the distantly related sister group Ranunculales. Comparative genomics in sequenced genomes of the Proteales shows loss of key arbuscular mycorrhizal symbiosis genes likely ancestral to the family, and possibly the order. The P. cynaroides genome empowers new research in plant diversification, horticulture and adaptation, particularly to nutrient-poor soils.
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Affiliation(s)
- Jiyang Chang
- Department of Plant Biotechnology and BioinformaticsGhent University and VIB Center for Plant Systems BiologyGhentBelgium
| | - Tuan A. Duong
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology InstituteUniversity of PretoriaPretoriaSouth Africa
| | - Cassandra Schoeman
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology InstituteUniversity of PretoriaPretoriaSouth Africa
| | - Xiao Ma
- Department of Plant Biotechnology and BioinformaticsGhent University and VIB Center for Plant Systems BiologyGhentBelgium
| | - Danielle Roodt
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology InstituteUniversity of PretoriaPretoriaSouth Africa
| | - Nigel Barker
- Department of Plant and Soil SciencesUniversity of PretoriaPretoriaSouth Africa
| | - Zhen Li
- Department of Plant Biotechnology and BioinformaticsGhent University and VIB Center for Plant Systems BiologyGhentBelgium
| | - Yves Van de Peer
- Department of Plant Biotechnology and BioinformaticsGhent University and VIB Center for Plant Systems BiologyGhentBelgium
- Department of Biochemistry, Genetics and MicrobiologyCentre for Microbial Ecology and Genomics, University of PretoriaPretoriaSouth Africa
- College of Horticulture, Academy for Advanced Interdisciplinary StudiesNanjing Agricultural UniversityNanjingChina
| | - Eshchar Mizrachi
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology InstituteUniversity of PretoriaPretoriaSouth Africa
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9
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Okada M, Yang Z, Mas P. Circadian autonomy and rhythmic precision of the Arabidopsis female reproductive organ. Dev Cell 2022; 57:2168-2180.e4. [PMID: 36115345 DOI: 10.1016/j.devcel.2022.08.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 07/12/2022] [Accepted: 08/26/2022] [Indexed: 11/03/2022]
Abstract
The plant circadian clock regulates essential biological processes including flowering time or petal movement. However, little is known about how the clock functions in flowers. Here, we identified the circadian components and transcriptional networks contributing to the generation of rhythms in pistils, the female reproductive organ. When detached from the rest of the flower, pistils sustain highly precise rhythms, indicating organ-specific circadian autonomy. Analyses of clock mutants and chromatin immunoprecipitation assays showed distinct expression patterns and specific regulatory functions for clock activators and repressors in pistils. Genetic interaction studies also suggested a hierarchy of the repressing activities that provide robustness and precision to the pistil clock. Globally, the circadian function in pistils primarily governs responses to environmental stimuli and photosynthesis and controls pistil growth and seed weight and production. Understanding the circadian intricacies in reproductive organs may prove useful for optimizing plant reproduction and productivity.
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Affiliation(s)
- Masaaki Okada
- Centre for Research in Agricultural Genomics (CRAG), CSIC, IRTA-UAB-UB, Campus UAB, Bellaterra, 08193 Barcelona, Spain
| | - Zhiyuan Yang
- Centre for Research in Agricultural Genomics (CRAG), CSIC, IRTA-UAB-UB, Campus UAB, Bellaterra, 08193 Barcelona, Spain
| | - Paloma Mas
- Centre for Research in Agricultural Genomics (CRAG), CSIC, IRTA-UAB-UB, Campus UAB, Bellaterra, 08193 Barcelona, Spain; Consejo Superior de Investigaciones Científicas (CSIC), 08028 Barcelona, Spain.
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10
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Zhang W, Zhou X, Chen F, Zhu H, Shi R, Sun C, Chen S, Hu M, Zhang J, Wang X. Fine Mapping and Candidate Gene Analysis of BnC08.cds, a Recessive Gene Responsible for Sepal-Specific Chlorophyll-Deficiency in Brassica napus L. FRONTIERS IN PLANT SCIENCE 2022; 13:850330. [PMID: 35360306 PMCID: PMC8960310 DOI: 10.3389/fpls.2022.850330] [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: 01/07/2022] [Accepted: 02/21/2022] [Indexed: 06/14/2023]
Abstract
Chloroplast development is crucial for photosynthesis and plant growth and many factors are involved in its regulation. The regulatory mechanism differs in different green tissues, and previous studies have focused on chloroplasts in leaves. In this study, a mutant with sepal-specific chlorophyll-deficiency was observed in Brassica napus and named as df74. Genetic analysis indicated that the phenotype was controlled by a single recessive nuclear gene. The gene was located on chromosome C08 by bulked-segregant analysis with whole-genome sequencing, which was designated as BnC08.cds. To fine-map the BnC08.cds, a F2 population was created from the cross of df74 and Zhongshuang11 (ZS11). Finally, the BnC08.cds was fine-mapped in the region between the single-nucleotide polymorphism (SNP) markers M5 and M6, corresponding to a 228.72 kb interval of the B. napus "ZS11" genome. Eighteen genes were predicted in the target region, and it was speculated that BnaC08G0442100ZS was the most likely candidate gene based on the results of transcriptome analyses and sequence variation analyses. These results provide a foundation to explore the regulation of chloroplast development in sepals.
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Affiliation(s)
- Wei Zhang
- Key Laboratory of Jiangsu Province for Agrobiology, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xiaoying Zhou
- Key Laboratory of Jiangsu Province for Agrobiology, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Feng Chen
- Key Laboratory of Jiangsu Province for Agrobiology, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Hongli Zhu
- Key Laboratory of Jiangsu Province for Agrobiology, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Rui Shi
- Key Laboratory of Jiangsu Province for Agrobiology, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Chengming Sun
- Key Laboratory of Jiangsu Province for Agrobiology, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Song Chen
- Key Laboratory of Jiangsu Province for Agrobiology, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Maolong Hu
- Key Laboratory of Jiangsu Province for Agrobiology, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Jiefu Zhang
- Key Laboratory of Jiangsu Province for Agrobiology, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Xiaodong Wang
- Key Laboratory of Jiangsu Province for Agrobiology, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
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11
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Silveira SR, Le Gloanec C, Gómez-Felipe A, Routier-Kierzkowska AL, Kierzkowski D. Live-imaging provides an atlas of cellular growth dynamics in the stamen. PLANT PHYSIOLOGY 2022; 188:769-781. [PMID: 34618064 PMCID: PMC8825458 DOI: 10.1093/plphys/kiab363] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 07/03/2021] [Indexed: 06/13/2023]
Abstract
Development of multicellular organisms is a complex process involving precise coordination of growth among individual cells. Understanding organogenesis requires measurements of cellular behaviors over space and time. In plants, such a quantitative approach has been successfully used to dissect organ development in both leaves and external floral organs, such as sepals. However, the observation of floral reproductive organs is hampered as they develop inside tightly closed floral buds, and are therefore difficult to access for imaging. We developed a confocal time-lapse imaging method, applied here to Arabidopsis (Arabidopsis thaliana), which allows full quantitative characterization of the development of stamens, the male reproductive organs. Our lineage tracing reveals the early specification of the filament and the anther. Formation of the anther lobes is associated with a temporal increase of growth at the lobe surface that correlates with intensive growth of the developing locule. Filament development is very dynamic and passes through three distinct phases: (1) initial intense, anisotropic growth, and high cell proliferation; (2) restriction of growth and proliferation to the filament proximal region; and (3) resumption of intense and anisotropic growth, displaced to the distal portion of the filament, without cell proliferation. This quantitative atlas of cellular growth dynamics provides a solid framework for future studies into stamen development.
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Affiliation(s)
- Sylvia R Silveira
- Department of Biological Sciences, IRBV, University of Montréal, Montréal, Quebec, Canada H1X 2B2
| | - Constance Le Gloanec
- Department of Biological Sciences, IRBV, University of Montréal, Montréal, Quebec, Canada H1X 2B2
| | - Andrea Gómez-Felipe
- Department of Biological Sciences, IRBV, University of Montréal, Montréal, Quebec, Canada H1X 2B2
| | | | - Daniel Kierzkowski
- Department of Biological Sciences, IRBV, University of Montréal, Montréal, Quebec, Canada H1X 2B2
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12
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Lin Z, Cao D, Damaris RN, Yang P. Comparative transcriptomic analysis provides insight into carpel petaloidy in lotus ( Nelumbo nucifera). PeerJ 2021; 9:e12322. [PMID: 34754621 PMCID: PMC8552788 DOI: 10.7717/peerj.12322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 09/25/2021] [Indexed: 11/20/2022] Open
Abstract
Lotus (Nelumbo nucifera) is a highly recognized flower with high ornamental value. Flower color and flower morphology are two main factors for flower lotus breeding. Petaloidy is a universal phenomenon in lotus flowers. However, the genetic regulation of floral organ petaloidy in lotus remains elusive. In this study, the transcriptomic analysis was performed among three organs, including petal, carpel petaloidy, and carpel in lotus. A total of 1,568 DEGs related to carpel petaloidy were identified. Our study identified one floral homeotic gene encoded by the MADS-box transcription factor, AGAMOUS (AG) as the candidate gene for petaloid in lotus. Meanwhile, a predicted labile boundary in floral organs of N. nucifera was hypothesized. In summary, our results explored the candidate genes related to carpel petaloidy, setting a theoretical basis for the molecular regulation of petaloid phenotype.
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Affiliation(s)
- Zhongyuan Lin
- Institute of Oceanography, Minjiang University, Fuzhou, China
| | - Dingding Cao
- Institute of Oceanography, Minjiang University, Fuzhou, China
| | - Rebecca Njeri Damaris
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
| | - Pingfang Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
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13
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Miller CN, Dumenil J, Lu FH, Smith C, McKenzie N, Chapman V, Ball J, Box M, Bevan M. Variation in the expression of a transmembrane protein influences cell growth in Arabidopsis thaliana petals by altering auxin responses. BMC PLANT BIOLOGY 2020; 20:482. [PMID: 33092536 PMCID: PMC7584087 DOI: 10.1186/s12870-020-02698-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 10/13/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND The same species of plant can exhibit very diverse sizes and shapes of organs that are genetically determined. Characterising genetic variation underlying this morphological diversity is an important objective in evolutionary studies and it also helps identify the functions of genes influencing plant growth and development. Extensive screens of mutagenised Arabidopsis populations have identified multiple genes and mechanisms affecting organ size and shape, but relatively few studies have exploited the rich diversity of natural populations to identify genes involved in growth control. RESULTS We screened a relatively well characterised collection of Arabidopsis thaliana accessions for variation in petal size. Association analyses identified sequence and gene expression variation on chromosome 4 that made a substantial contribution to differences in petal area. Variation in the expression of a previously uncharacterised gene At4g16850 (named as KSK) had a substantial role on variation in organ size by influencing cell size. Over-expression of KSK led to larger petals with larger cells and promoted the formation of stamenoid features. The expression of auxin-responsive genes known to limit cell growth was reduced in response to KSK over-expression. ANT expression was also reduced in KSK over-expression lines, consistent with altered floral identities. Auxin responses were reduced in KSK over-expressing cells, consistent with changes in auxin-responsive gene expression. KSK may therefore influence auxin responses during petal development. CONCLUSIONS Understanding how genetic variation influences plant growth is important for both evolutionary and mechanistic studies. We used natural populations of Arabidopsis thaliana to identify sequence variation in a promoter region of Arabidopsis accessions that mediated differences in the expression of a previously uncharacterised membrane protein. This variation contributed to altered auxin responses and cell size during petal growth.
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Affiliation(s)
- Charlotte N Miller
- Cell and Developmental Biology Department John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Jack Dumenil
- Cell and Developmental Biology Department John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Fu Hao Lu
- Cell and Developmental Biology Department John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Caroline Smith
- Cell and Developmental Biology Department John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Neil McKenzie
- Cell and Developmental Biology Department John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Volodymyr Chapman
- Cell and Developmental Biology Department John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Joshua Ball
- Cell and Developmental Biology Department John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Mathew Box
- Cell and Developmental Biology Department John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Michael Bevan
- Cell and Developmental Biology Department John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
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14
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Jiang Y, Wang M, Zhang R, Xie J, Duan X, Shan H, Xu G, Kong H. Identification of the target genes of AqAPETALA3-3 (AqAP3-3) in Aquilegia coerulea (Ranunculaceae) helps understand the molecular bases of the conserved and nonconserved features of petals. THE NEW PHYTOLOGIST 2020; 227:1235-1248. [PMID: 32285943 DOI: 10.1111/nph.16601] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 03/30/2020] [Indexed: 06/11/2023]
Abstract
Identification and comparison of the conserved and variable downstream genes of floral organ identity regulators are critical to understanding the mechanisms underlying the commonalities and peculiarities of floral organs. Yet, because of the lack of studies in nonmodel species, a general picture of the regulatory evolution between floral organ identity genes and their targets is still lacking. Here, by conducting extensive chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq), electrophoretic mobility shift assay and bioinformatic analyses, we identify and predict the target genes of a petal identity gene, AqAPETALA3-3 (AqAP3-3), in Aquilegia coerulea (Ranunculaceae) and compare them with those of its counterpart in Arabidopsis thaliana, AP3. In total, 7049 direct target genes are identified for AqAP3-3, of which 2394 are highly confident and 1085 are shared with AP3. Gene Ontology enrichment analyses further indicate that conserved targets are largely involved in the formation of identity-related features, whereas nonconserved targets are mostly required for the formation of species-specific features. These results not only help understand the molecular bases of the conserved and nonconserved features of petals, but also pave the way to studying the regulatory evolution between floral organ identity genes and their targets.
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Affiliation(s)
- Yongchao Jiang
- State Key Laboratory of Systematic and Evolutionary Botany, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Meimei Wang
- State Key Laboratory of Systematic and Evolutionary Botany, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Rui Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Jinghe Xie
- State Key Laboratory of Systematic and Evolutionary Botany, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoshan Duan
- State Key Laboratory of Systematic and Evolutionary Botany, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Hongyan Shan
- State Key Laboratory of Systematic and Evolutionary Botany, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Guixia Xu
- State Key Laboratory of Systematic and Evolutionary Botany, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Hongzhi Kong
- State Key Laboratory of Systematic and Evolutionary Botany, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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15
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Rodríguez-Cazorla E, Ripoll JJ, Ortuño-Miquel S, Martínez-Laborda A, Vera A. Dissection of the Arabidopsis HUA-PEP gene activity reveals that ovule fate specification requires restriction of the floral A-function. THE NEW PHYTOLOGIST 2020; 227:1222-1234. [PMID: 32259283 DOI: 10.1111/nph.16589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Accepted: 03/25/2020] [Indexed: 06/11/2023]
Abstract
Ovules are essential for sexual plant reproduction and seed formation, and are fundamental for agriculture. However, our understanding of the molecular mechanisms governing ovule development is far from complete. In Arabidopsis, ovule identity is determined by homeotic MADS-domain proteins that define the floral C- (AG) and D- (SHP1/SHP2, STK) functions. Pre-mRNA processing of these genes is critical and mediated by HUA-PEP activity, composed of genes encoding RNA-binding proteins. In strong hua-pep mutants, functional transcripts for C- and D-function genes are reduced, resulting in homeotic transformation of ovules. Thus, hua-pep mutants provide an unique sensitized background to study ovule morphogenesis when C- and D-functions are simultaneously compromised. We found that hua-pep ovules are morphologically sepaloid and show ectopic expression of the homeotic class-A gene AP1. Inactivation of AP1 or AP2 (A-function genes) in hua-pep mutants reduced homeotic conversions, rescuing ovule identity while promoting carpelloid traits in transformed ovules. Interestingly, increased AG dosage led to similar results. Our findings strongly suggest that HUA-PEP activity is required for correct C and D floral functions, which in turn prevents ectopic expression of class-A genes in ovules for their proper morphogenesis, evoking the classic A-C antagonism of the ABC model for floral organ development.
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Affiliation(s)
| | - Juan-José Ripoll
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093, USA
- TATA Institute for Genetics and Society (TIGS), University of California San Diego, La Jolla, CA, 92093, USA
| | - Samanta Ortuño-Miquel
- Area de Genética, Universidad Miguel Hernández, Campus de Sant Joan, Alicante, 03550, Spain
| | | | - Antonio Vera
- Area de Genética, Universidad Miguel Hernández, Campus de Sant Joan, Alicante, 03550, Spain
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16
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Nelissen H, Gonzalez N. Understanding plant organ growth: a multidisciplinary field. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:7-10. [PMID: 31725876 DOI: 10.1093/jxb/erz448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 09/27/2019] [Indexed: 06/10/2023]
Affiliation(s)
- Hilde Nelissen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark, Gent, Belgium
- Center for Plant Systems Biology, VIB, Technologiepark, Gent, Belgium
| | - Nathalie Gonzalez
- INRA, UMR1332 Biologie du fruit et Pathologie, INRA Bordeaux Aquitaine, CS20032, F-33882, Villenave d'Ornon cedex, France
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17
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Ding L, Zhao K, Zhang X, Song A, Su J, Hu Y, Zhao W, Jiang J, Chen F. Comprehensive characterization of a floral mutant reveals the mechanism of hooked petal morphogenesis in Chrysanthemum morifolium. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:2325-2340. [PMID: 31050173 PMCID: PMC6835125 DOI: 10.1111/pbi.13143] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 04/25/2019] [Accepted: 04/26/2019] [Indexed: 05/17/2023]
Abstract
The diversity of form of the chrysanthemum flower makes this species an ideal model for studying petal morphogenesis, but as yet, the molecular mechanisms underlying petal shape development remain largely unexplored. Here, a floral mutant, which arose as a bud sport in a plant of the variety 'Anastasia Dark Green', and formed straight, rather than hooked petals, was subjected to both comparative morphological analysis and transcriptome profiling. The hooked petals only became discernible during a late stage of flower development. At the late stage of 'Anastasia Dark Green', genes related to chloroplast, hormone metabolism, cell wall and microtubules were active, as were cell division-promoting factors. Auxin concentration was significantly reduced, and a positive regulator of cell expansion was down-regulated. Two types of critical candidates, boundary genes and adaxial-abaxial regulators, were identified from 7937 differentially expressed genes in pairwise comparisons, which were up-regulated at the late stage in 'Anastasia Dark Green' and another two hooked varieties. Ectopic expression of a candidate abaxial gene, CmYAB1, in chrysanthemum led to changes in petal curvature and inflorescence morphology. Our findings provide new insights into the regulatory networks underlying chrysanthemum petal morphogenesis.
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Affiliation(s)
- Lian Ding
- State Key Laboratory of Crop Genetics and Germplasm EnhancementKey Laboratory of LandscapingMinistry of Agriculture and Rural AffairsCollege of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Kunkun Zhao
- State Key Laboratory of Crop Genetics and Germplasm EnhancementKey Laboratory of LandscapingMinistry of Agriculture and Rural AffairsCollege of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Xue Zhang
- State Key Laboratory of Crop Genetics and Germplasm EnhancementKey Laboratory of LandscapingMinistry of Agriculture and Rural AffairsCollege of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Aiping Song
- State Key Laboratory of Crop Genetics and Germplasm EnhancementKey Laboratory of LandscapingMinistry of Agriculture and Rural AffairsCollege of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Jiangshuo Su
- State Key Laboratory of Crop Genetics and Germplasm EnhancementKey Laboratory of LandscapingMinistry of Agriculture and Rural AffairsCollege of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Yueheng Hu
- State Key Laboratory of Crop Genetics and Germplasm EnhancementKey Laboratory of LandscapingMinistry of Agriculture and Rural AffairsCollege of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Wenqian Zhao
- State Key Laboratory of Crop Genetics and Germplasm EnhancementKey Laboratory of LandscapingMinistry of Agriculture and Rural AffairsCollege of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Jiafu Jiang
- State Key Laboratory of Crop Genetics and Germplasm EnhancementKey Laboratory of LandscapingMinistry of Agriculture and Rural AffairsCollege of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Fadi Chen
- State Key Laboratory of Crop Genetics and Germplasm EnhancementKey Laboratory of LandscapingMinistry of Agriculture and Rural AffairsCollege of HorticultureNanjing Agricultural UniversityNanjingChina
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18
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Lee ZH, Tatsumi Y, Ichihashi Y, Suzuki T, Shibata A, Shirasu K, Yamaguchi N, Ito T. CRABS CLAW and SUPERMAN Coordinate Hormone-, Stress-, and Metabolic-Related Gene Expression During Arabidopsis Stamen Development. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00437] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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19
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Liu X, Hao N, Li H, Ge D, Du Y, Liu R, Wen C, Li Y, Zhang X, Wu T. PINOID is required for lateral organ morphogenesis and ovule development in cucumber. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:5715-5730. [PMID: 31407012 DOI: 10.1093/jxb/erz354] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Accepted: 08/01/2019] [Indexed: 05/10/2023]
Abstract
Lateral organ development is essential for cucumber production. The protein kinase PINOID (PID) participates in distinct aspects of plant development by mediating polar auxin transport in different species. Here, we obtained a round leaf (rl) mutant that displayed extensive phenotypes including round leaf shape, inhibited tendril outgrowth, abnormal floral organs, and disrupted ovule genesis. MutMap+ analysis revealed that rl encodes a cucumber ortholog of PID (CsPID). A non-synonymous single nucleotide polymorphism in the second exon of CsPID resulted in an amino acid substitution from arginine to lysine in the rl mutant. Allelic testing using the mutant allele C356 with similar phenotypes verified that CsPID was the causal gene. CsPID was preferentially expressed in young leaf and flower buds and down-regulated in the rl mutant. Subcellular localization showed that the mutant form, Cspid, showed a dotted pattern of localization, in contrast to the continuous pattern of CsPID in the periphery of the cell and nucleus. Complementation analysis in Arabidopsis showed that CsPID, but not Cspid, can partially rescue the pid-14 mutant phenotype. Moreover, indole-3-acetic acid content was greatly reduced in the rl mutant. Transcriptome profiling revealed that transcription factors, ovule morphogenesis, and auxin transport-related genes were significantly down-regulated in the rl mutant. Biochemical analysis showed that CsPID physically interacted with a key polarity protein, CsREV (REVOLUTA). We developed a model in which CsPID regulates lateral organ morphogenesis and ovule development by stimulating genes related to auxin transport and ovule development.
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Affiliation(s)
- Xiaofeng Liu
- College of Horticulture and Landscape Architecture, Hunan Agricultural University, Changsha, China
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, MOE Joint International Research Laboratory of Crop Molecular Breeding, China Agricultural University, Beijing, China
| | - Ning Hao
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture, Northeast Agricultural University, Harbin, China
| | - Huiyuan Li
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture, Northeast Agricultural University, Harbin, China
| | - Danfeng Ge
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai, China
| | - Yalin Du
- College of Horticulture and Landscape Architecture, Hunan Agricultural University, Changsha, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture, Northeast Agricultural University, Harbin, China
| | - Renyi Liu
- College of Horticulture, and FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Changlong Wen
- Beijing Vegetable Research Center, Beijing Academy of Agricultural and Forestry Sciences, Beijing Key Laboratory of Vegetable Germplasms Improvement, National Engineering Research Center for Vegetables, Beijing, China
| | - Yuhong Li
- College of Horticulture, Northwest A&F University, Yangling, Shanxi, China
| | - Xiaolan Zhang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, MOE Joint International Research Laboratory of Crop Molecular Breeding, China Agricultural University, Beijing, China
| | - Tao Wu
- College of Horticulture and Landscape Architecture, Hunan Agricultural University, Changsha, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture, Northeast Agricultural University, Harbin, China
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20
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Alvarez-Buylla ER, García-Ponce B, Sánchez MDLP, Espinosa-Soto C, García-Gómez ML, Piñeyro-Nelson A, Garay-Arroyo A. MADS-box genes underground becoming mainstream: plant root developmental mechanisms. THE NEW PHYTOLOGIST 2019; 223:1143-1158. [PMID: 30883818 DOI: 10.1111/nph.15793] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 02/26/2019] [Indexed: 05/19/2023]
Abstract
Plant growth is largely post-embryonic and depends on meristems that are active throughout the lifespan of an individual. Developmental patterns rely on the coordinated spatio-temporal expression of different genes, and the activity of transcription factors is particularly important during most morphogenetic processes. MADS-box genes constitute a transcription factor family in eukaryotes. In Arabidopsis, their proteins participate in all major aspects of shoot development, but their role in root development is still not well characterized. In this review we synthetize current knowledge pertaining to the function of MADS-box genes highly expressed in roots: XAL1, XAL2, ANR1 and AGL21, as well as available data for other MADS-box genes expressed in this organ. The role of Trithorax group and Polycomb group complexes on MADS-box genes' epigenetic regulation is also discussed. We argue that understanding the role of MADS-box genes in root development of species with contrasting architectures is still a challenge. Finally, we propose that MADS-box genes are key components of the gene regulatory networks that underlie various gene expression patterns, each one associated with the distinct developmental fates observed in the root. In the case of XAL1 and XAL2, their role within these networks could be mediated by regulatory feedbacks with auxin.
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Affiliation(s)
- Elena R Alvarez-Buylla
- Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Exterior, Ciudad Universitaria, Coyoacán, D.F. 04510, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, 3er Circuito Exterior, Ciudad Universitaria, Coyoacán, D.F. 04510, Mexico
| | - Berenice García-Ponce
- Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Exterior, Ciudad Universitaria, Coyoacán, D.F. 04510, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, 3er Circuito Exterior, Ciudad Universitaria, Coyoacán, D.F. 04510, Mexico
| | - María de la Paz Sánchez
- Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Exterior, Ciudad Universitaria, Coyoacán, D.F. 04510, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, 3er Circuito Exterior, Ciudad Universitaria, Coyoacán, D.F. 04510, Mexico
| | - Carlos Espinosa-Soto
- Instituto de Física, Universidad Autónoma de San Luis Potosí, Manuel Nava 6, Zona Universitaria, San Luis Potosí, CP 78290, Mexico
| | - Mónica L García-Gómez
- Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Exterior, Ciudad Universitaria, Coyoacán, D.F. 04510, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, 3er Circuito Exterior, Ciudad Universitaria, Coyoacán, D.F. 04510, Mexico
| | - Alma Piñeyro-Nelson
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, 3er Circuito Exterior, Ciudad Universitaria, Coyoacán, D.F. 04510, Mexico
- Departamento de Producción Agrícola y Animal, Universidad Autónoma Metropolitana Xochimilco, Ciudad de México, 04960, Mexico
| | - Adriana Garay-Arroyo
- Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Exterior, Ciudad Universitaria, Coyoacán, D.F. 04510, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, 3er Circuito Exterior, Ciudad Universitaria, Coyoacán, D.F. 04510, Mexico
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Echevin E, Le Gloanec C, Skowrońska N, Routier-Kierzkowska AL, Burian A, Kierzkowski D. Growth and biomechanics of shoot organs. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:3573-3585. [PMID: 31037307 DOI: 10.1093/jxb/erz205] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Accepted: 04/17/2019] [Indexed: 06/09/2023]
Abstract
Plant organs arise through complex interactions between biological and physical factors that control morphogenesis. While there has been tremendous progress in the understanding of the genetics behind development, we know much less about how mechanical forces control growth in plants. In recent years, new multidisciplinary research combining genetics, live-imaging, physics, and computational modeling has begun to fill this gap by revealing the crucial role of biomechanics in the establishment of plant organs. In this review, we provide an overview of our current understanding of growth during initiation, patterning, and expansion of shoot lateral organs. We discuss how growth is controlled by physical forces, and how mechanical stresses generated during growth can control morphogenesis at the level of both cells and tissues. Understanding the mechanical basis of growth and morphogenesis in plants is in its early days, and many puzzling facts are yet to be deciphered.
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Affiliation(s)
- Emilie Echevin
- Institut de Recherche en Biologie Végétale, Department of Biological Sciences, University of Montreal, Montréal, QC, Canada
| | - Constance Le Gloanec
- Institut de Recherche en Biologie Végétale, Department of Biological Sciences, University of Montreal, Montréal, QC, Canada
| | - Nikolina Skowrońska
- Department of Biophysics and Morphogenesis of Plants, University of Silesia, Jagiellońska, Katowice, Poland
| | - Anne-Lise Routier-Kierzkowska
- Institut de Recherche en Biologie Végétale, Department of Biological Sciences, University of Montreal, Montréal, QC, Canada
| | - Agata Burian
- Department of Biophysics and Morphogenesis of Plants, University of Silesia, Jagiellońska, Katowice, Poland
| | - Daniel Kierzkowski
- Institut de Recherche en Biologie Végétale, Department of Biological Sciences, University of Montreal, Montréal, QC, Canada
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22
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Ooi SE, Sarpan N, Abdul Aziz N, Nuraziyan A, Ong-Abdullah M. Differential expression of heat shock and floral regulatory genes in pseudocarpel initials of mantled female inflorescences from Elaeis guineensis Jacq. PLANT REPRODUCTION 2019; 32:167-179. [PMID: 30467592 DOI: 10.1007/s00497-018-0350-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 11/19/2018] [Indexed: 06/09/2023]
Abstract
Transcriptomes generated by laser capture microdissected abnormal staminodes revealed adoption of carpel programming during organ initiation with decreased expression of numerousHSPs,EgDEF1, EgGLO1but increasedLEAFYexpression. The abnormal mantled phenotype in oil palm involves a feminization of the male staminodes into pseudocarpels in pistillate inflorescences. Previous studies on oil palm flowering utilized entire inflorescences or spikelets, which comprised not only the male and female floral organs, but the surrounding tissues as well. Laser capture microdissection coupled with RNA sequencing was conducted to investigate the specific transcriptomes of male and female floral organs from normal and mantled female inflorescences. A higher number of differentially expressed genes (DEGs) were identified in abnormal versus normal male organs compared with abnormal versus normal female organs. In addition, the abnormal male organ transcriptome closely mimics the transcriptome of abnormal female organ. While the transcriptome of abnormal female organ was relatively similar to the normal female organ, a substantial amount of female DEGs encode HEAT SHOCK PROTEIN genes (HSPs). A similar high amount (20%) of male DEGs encode HSPs as well. As these genes exhibited decreased expression in abnormal floral organs, mantled floral organ development may be associated with lower stress indicators. Stamen identity genes EgDEF1 and EgGLO1 were the main floral regulatory genes with decreased expression in abnormal male organs or pseudocarpel initials. Expression of several floral transcription factors was elevated in pseudocarpel initials, notably LEAFY, FIL and DL orthologs, substantiating the carpel specification programming of abnormal staminodes. Specific transcriptomes thus obtained through this approach revealed a host of differentially regulated genes in pseudocarpel initials compared to normal male staminodes.
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Affiliation(s)
- Siew-Eng Ooi
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6 Persiaran Institusi, 43000, Kajang, Selangor, Malaysia.
| | - Norashikin Sarpan
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6 Persiaran Institusi, 43000, Kajang, Selangor, Malaysia
| | - Norazlin Abdul Aziz
- Molecular Pathology Unit, Cancer Research Centre (CaRC), Institute for Medical Research, Jalan Pahang, 50588, Kuala Lumpur, Malaysia
| | - Azimi Nuraziyan
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6 Persiaran Institusi, 43000, Kajang, Selangor, Malaysia
| | - Meilina Ong-Abdullah
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6 Persiaran Institusi, 43000, Kajang, Selangor, Malaysia.
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23
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Damerval C, Citerne H, Conde e Silva N, Deveaux Y, Delannoy E, Joets J, Simonnet F, Staedler Y, Schönenberger J, Yansouni J, Le Guilloux M, Sauquet H, Nadot S. Unraveling the Developmental and Genetic Mechanisms Underpinning Floral Architecture in Proteaceae. FRONTIERS IN PLANT SCIENCE 2019; 10:18. [PMID: 30740117 PMCID: PMC6357683 DOI: 10.3389/fpls.2019.00018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 01/08/2019] [Indexed: 05/30/2023]
Abstract
Proteaceae are a basal eudicot family with a highly conserved floral groundplan but which displays considerable variation in other aspects of floral and inflorescence morphology. Their morphological diversity and phylogenetic position make them good candidates for understanding the evolution of floral architecture, in particular the question of the homology of the undifferentiated perianth with the differentiated perianth of core eudicots, and the mechanisms underlying the repeated evolution of zygomorphy. In this paper, we combine a morphological approach to explore floral ontogenesis and a transcriptomic approach to access the genes involved in floral organ identity and development, focusing on Grevillea juniperina, a species from subfamily Grevilleoideae. We present developmental data for Grevillea juniperina and three additional species that differ in their floral symmetry using stereomicroscopy, SEM and High Resolution X-Ray Computed Tomography. We find that the adnation of stamens to tepals takes place at early developmental stages, and that the establishment of bilateral symmetry coincides with the asymmetrical growth of the single carpel. To set a framework for understanding the genetic basis of floral development in Proteaceae, we generated and annotated de novo a reference leaf/flower transcriptome from Grevillea juniperina. We found Grevillea homologs of all lineages of MADS-box genes involved in floral organ identity. Using Arabidopsis thaliana gene expression data as a reference, we found homologs of other genes involved in floral development in the transcriptome of G. juniperina. We also found at least 21 class I and class II TCP genes, a gene family involved in the regulation of growth processes, including floral symmetry. The expression patterns of a set of floral genes obtained from the transcriptome were characterized during floral development to assess their organ specificity and asymmetry of expression.
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Affiliation(s)
- Catherine Damerval
- GQE-Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Hélène Citerne
- GQE-Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Natalia Conde e Silva
- GQE-Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Yves Deveaux
- GQE-Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Etienne Delannoy
- Institute of Plant Sciences Paris-Saclay, CNRS, INRA, Universités Paris Diderot, Paris-Sud, Evry, Paris-Saclay, Gif-sur-Yvette, France
| | - Johann Joets
- GQE-Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Franck Simonnet
- GQE-Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
- Ecologie Systématique Evolution, AgroParisTech, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Orsay, France
| | - Yannick Staedler
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Jürg Schönenberger
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Jennifer Yansouni
- Institute of Plant Sciences Paris-Saclay, CNRS, INRA, Universités Paris Diderot, Paris-Sud, Evry, Paris-Saclay, Gif-sur-Yvette, France
| | - Martine Le Guilloux
- GQE-Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Hervé Sauquet
- Ecologie Systématique Evolution, AgroParisTech, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Orsay, France
- National Herbarium of New South Wales (NSW), Royal Botanic Gardens and Domain Trust, Sydney, NSW, Australia
| | - Sophie Nadot
- Ecologie Systématique Evolution, AgroParisTech, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Orsay, France
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25
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Shim S, Ha J, Kim MY, Choi MS, Kang ST, Jeong SC, Moon JK, Lee SH. GmBRC1 is a Candidate Gene for Branching in Soybean ( Glycine max (L.) Merrill). Int J Mol Sci 2019. [PMID: 30609682 DOI: 10.1007/s10681-017-2016-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023] Open
Abstract
Branch number is one of the main factors affecting the yield of soybean (Glycine max (L.)). In this study, we conducted a genome-wide association study combined with linkage analysis for the identification of a candidate gene controlling soybean branching. Five quantitative trait nucleotides (QTNs) were associated with branch numbers in a soybean core collection. Among these QTNs, a linkage disequilibrium (LD) block qtnBR6-1 spanning 20 genes was found to overlap a previously identified major quantitative trait locus qBR6-1. To validate and narrow down qtnBR6-1, we developed a set of near-isogenic lines (NILs) harboring high-branching (HB) and low-branching (LB) alleles of qBR6-1, with 99.96% isogenicity and different branch numbers. A cluster of single nucleotide polymorphisms (SNPs) segregating between NIL-HB and NIL-LB was located within the qtnBR6-1 LD block. Among the five genes showing differential expression between NIL-HB and NIL-LB, BRANCHED1 (BRC1; Glyma.06G210600) was down-regulated in the shoot apex of NIL-HB, and one missense mutation and two SNPs upstream of BRC1 were associated with branch numbers in 59 additional soybean accessions. BRC1 encodes TEOSINTE-BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTORS 1 and 2 transcription factor and functions as a regulatory repressor of branching. On the basis of these results, we propose BRC1 as a candidate gene for branching in soybean.
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Affiliation(s)
- Sangrea Shim
- Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea.
- Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea.
| | - Jungmin Ha
- Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea.
- Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea.
| | - Moon Young Kim
- Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea.
- Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea.
| | - Man Soo Choi
- National Institute of Crop Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Korea.
| | - Sung-Taeg Kang
- Department of Crop Science & Biotechnology, Dankook University, Cheonan-si, Chungcheongnam-do 31116, Korea.
| | - Soon-Chun Jeong
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju-si, Chungcheongbuk-do 28116, Korea.
| | - Jung-Kyung Moon
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju-si, Jeollabuk-do 54874, Korea.
| | - Suk-Ha Lee
- Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea.
- Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea.
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26
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Lin Z, Damaris RN, Shi T, Li J, Yang P. Transcriptomic analysis identifies the key genes involved in stamen petaloid in lotus (Nelumbo nucifera). BMC Genomics 2018; 19:554. [PMID: 30053802 PMCID: PMC6062958 DOI: 10.1186/s12864-018-4950-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 07/19/2018] [Indexed: 12/26/2022] Open
Abstract
Background Flower morphology, a phenomenon regulated by a complex network, is one of the vital ornamental features in Nelumbo nucifera. Stamen petaloid is very prevalent in lotus flowers. However, the mechanism underlying this phenomenon is still obscure. Results Here, the comparative transcriptomic analysis was performed among petal, stamen petaloid and stamen through RNA-seq. Using pairwise comparison analysis, a large number of genes involved in hormonal signal transduction pathways and transcription factors, especially the MADS-box genes, were identified as candidate genes for stamen petaloid in lotus. Conclusions Taken together, these results provide an insight into the molecular networks underlying lotus floral organ development and stamen petaloid. Electronic supplementary material The online version of this article (10.1186/s12864-018-4950-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhongyuan Lin
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.,University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Rebecca Njeri Damaris
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.,University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Tao Shi
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Juanjuan Li
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.,University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Pingfang Yang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China. .,Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China.
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27
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Abstract
The angiosperm flower develops through a modular programme which, although ancient and conserved, provides the flexibility that has allowed an almost infinite variety of floral forms to emerge. In this review, we explore the evolution of floral diversity, focusing on our recent understanding of the mechanistic basis of evolutionary change. We discuss the various ways in which flower size and floral organ size can be modified, the means by which flower shape and symmetry can change, and the ways in which floral organ position can be varied. We conclude that many challenges remain before we fully understand the ecological and molecular processes that facilitate the diversification of flower structure.
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28
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Abstract
Flowers are organized into concentric whorls of sepals, petals, stamens and carpels, with each of these floral organ types having a unique role in reproduction (Figure 1). Sepals enclose and protect the flower bud, while petals can be large and showy so as to attract pollinators (or people!). Stamens produce pollen grains that contain male gametes, while the carpels contain the ovules that when fertilized will produce the seeds. While the size, shape, number and elaboration of each of these organ types can be quite different, the same general organization of four floral organ types arranged in concentric whorls exists across all flowering plant (angiosperm) species. As I shall explain in this Primer, the 'ABC model' is a simple and satisfying explanation for how this conserved floral architecture is genetically specified.
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Affiliation(s)
- Vivian Irish
- Department of Molecular, Cellular and Developmental Biology, Department of Ecology and Evolutionary Biology, Yale University, 266 Whitney Ave, New Haven, CT 06520-8104, USA.
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29
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Gross T, Broholm S, Becker A. CRABS CLAW Acts as a Bifunctional Transcription Factor in Flower Development. FRONTIERS IN PLANT SCIENCE 2018; 9:835. [PMID: 29973943 PMCID: PMC6019494 DOI: 10.3389/fpls.2018.00835] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 05/29/2018] [Indexed: 05/06/2023]
Abstract
One of the crucial steps in the life cycle of angiosperms is the development of carpels. They are the most complex plant organs, harbor the seeds, and, after fertilization, develop into fruits and are thus an important ecological and economic trait. CRABS CLAW (CRC), a YABBY protein and putative transcription factor, is one of the major carpel developmental regulators in A. thaliana that includes a C2C2 zinc finger and a domain with similarities to an HMG box. CRC is involved in the regulation of processes such as carpel fusion and growth, floral meristem termination, and nectary formation. While its genetic interactions with other carpel development regulators are well described, its biochemical properties and molecular way of action remain unclear. We combined Bimolecular Fluorescence Complementation, Yeast Two-Hybrid, and Yeast One-Hybrid analyzes to shed light on the molecular biology of CRC. Our results showed that CRC dimerizes, also with other YABBY proteins, via the YABBY domain, and that its DNA binding is mainly cooperative and is mediated by the YABBY domain. Further, we identified that CRC is involved in floral meristem termination via transcriptional repression while it acts as a transcriptional activator in nectary development and carpel fusion and growth control. This work increases our understanding on how YABBY transcription factors interact with other proteins and how they regulate their targets.
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Affiliation(s)
- Thomas Gross
- Department of Biology, Institute of Botany, Justus Liebig University Giessen, Giessen, Germany
- *Correspondence: Thomas Gross,
| | - Suvi Broholm
- Biosciences and Environment Research Unit, Academy of Finland, Helsinki, Finland
| | - Annette Becker
- Department of Biology, Institute of Botany, Justus Liebig University Giessen, Giessen, Germany
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30
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Selection During Maize Domestication Targeted a Gene Network Controlling Plant and Inflorescence Architecture. Genetics 2017; 207:755-765. [PMID: 28754660 DOI: 10.1534/genetics.117.300071] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 07/24/2017] [Indexed: 01/11/2023] Open
Abstract
Selection during evolution, whether natural or artificial, acts through the phenotype. For multifaceted phenotypes such as plant and inflorescence architecture, the underlying genetic architecture is comprised of a complex network of interacting genes rather than single genes that act independently to determine the trait. As such, selection acts on entire gene networks. Here, we begin to define the genetic regulatory network to which the maize domestication gene, teosinte branched1 (tb1), belongs. Using a combination of molecular methods to uncover either direct or indirect regulatory interactions, we identified a set of genes that lie downstream of tb1 in a gene network regulating both plant and inflorescence architecture. Additional genes, known from the literature, also act in this network. We observed that tb1 regulates both core cell cycle genes and another maize domestication gene, teosinte glume architecture1 (tga1). We show that several members of the MADS-box gene family are either directly or indirectly regulated by tb1 and/or tga1, and that tb1 sits atop a cascade of transcriptional regulators controlling both plant and inflorescence architecture. Multiple members of the tb1 network appear to have been the targets of selection during maize domestication. Knowledge of the regulatory hierarchies controlling traits is central to understanding how new morphologies evolve.
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31
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Gene-regulatory networks controlling inflorescence and flower development in Arabidopsis thaliana. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:95-105. [PMID: 27487457 DOI: 10.1016/j.bbagrm.2016.07.014] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 07/21/2016] [Accepted: 07/22/2016] [Indexed: 11/23/2022]
Abstract
Reproductive development in plants is controlled by complex and intricate gene-regulatory networks of transcription factors. These networks integrate the information from endogenous, hormonal and environmental regulatory pathways. Many of the key players have been identified in Arabidopsis and other flowering plant species, and their interactions and molecular modes of action are being elucidated. An emerging theme is that there is extensive crosstalk between different pathways, which can be accomplished at the molecular level by modulation of transcription factor activity or of their downstream targets. In this review, we aim to summarize current knowledge on transcription factors and epigenetic regulators that control basic developmental programs during inflorescence and flower morphogenesis in the model plant Arabidopsis thaliana. This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer.
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32
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Clark NM, Hinde E, Winter CM, Fisher AP, Crosti G, Blilou I, Gratton E, Benfey PN, Sozzani R. Tracking transcription factor mobility and interaction in Arabidopsis roots with fluorescence correlation spectroscopy. eLife 2016; 5. [PMID: 27288545 PMCID: PMC4946880 DOI: 10.7554/elife.14770] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 06/10/2016] [Indexed: 01/17/2023] Open
Abstract
To understand complex regulatory processes in multicellular organisms, it is critical to be able to quantitatively analyze protein movement and protein-protein interactions in time and space. During Arabidopsis development, the intercellular movement of SHORTROOT (SHR) and subsequent interaction with its downstream target SCARECROW (SCR) control root patterning and cell fate specification. However, quantitative information about the spatio-temporal dynamics of SHR movement and SHR-SCR interaction is currently unavailable. Here, we quantify parameters including SHR mobility, oligomeric state, and association with SCR using a combination of Fluorescent Correlation Spectroscopy (FCS) techniques. We then incorporate these parameters into a mathematical model of SHR and SCR, which shows that SHR reaches a steady state in minutes, while SCR and the SHR-SCR complex reach a steady-state between 18 and 24 hr. Our model reveals the timing of SHR and SCR dynamics and allows us to understand how protein movement and protein-protein stoichiometry contribute to development.
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Affiliation(s)
- Natalie M Clark
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, United States.,Biomathematics Graduate Program, North Carolina State University, Raleigh, United States
| | - Elizabeth Hinde
- Laboratory for Fluorescence Dynamics, University of California, Irvine, Irvine, United States
| | - Cara M Winter
- Department of Biology, Howard Hughes Medical Institute, Duke University, Durham, United States
| | - Adam P Fisher
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, United States
| | - Giuseppe Crosti
- Department of Biology, Howard Hughes Medical Institute, Duke University, Durham, United States
| | - Ikram Blilou
- Plant Developmental Biology, Wageningen University, Wageningen, Netherlands
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, University of California, Irvine, Irvine, United States
| | - Philip N Benfey
- Department of Biology, Howard Hughes Medical Institute, Duke University, Durham, United States
| | - Rosangela Sozzani
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, United States
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Gardner AG, Fitz Gerald JN, Menz J, Shepherd KA, Howarth DG, Jabaily RS. Characterizing Floral Symmetry in the Core Goodeniaceae with Geometric Morphometrics. PLoS One 2016; 11:e0154736. [PMID: 27148960 PMCID: PMC4858217 DOI: 10.1371/journal.pone.0154736] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 04/18/2016] [Indexed: 11/19/2022] Open
Abstract
Core Goodeniaceae is a clade of ~330 species primarily distributed in Australia. Considerable variation in flower morphology exists within this group and we aim to use geometric morphometrics to characterize this variation across the two major subclades: Scaevola sensu lato (s.l.) and Goodenia s.l., the latter of which was hypothesized to exhibit greater variability in floral symmetry form. We test the hypothesis that floral morphological variation can be adequately characterized by our morphometric approach, and that discrete groups of floral symmetry morphologies exist, which broadly correlate with subjectively determined groups. From 335 images of 44 species in the Core Goodeniaceae, two principal components were computed that describe >98% of variation in all datasets. Increasing values of PC1 ventralize the dorsal petals (increasing the angle between them), whereas increasing values of PC2 primarily ventralize the lateral petals (decreasing the angle between them). Manipulation of these two morphological “axes” alone was sufficient to recreate any of the general floral symmetry patterns in the Core Goodeniaceae. Goodenia s.l. exhibits greater variance than Scaevola s.l. in PC1 and PC2, and has a significantly lower mean value for PC1. Clustering clearly separates fan-flowers (with dorsal petals at least 120° separated) from the others, whereas the distinction between pseudo-radial and bilabiate clusters is less clear and may form a continuum rather than two distinct groups. Transitioning from the average fan-flower to the average non-fan-flower is described almost exclusively by PC1, whereas PC2 partially describes the transition between bilabiate and pseudo-radial morphologies. Our geometric morphometric method accurately models Core Goodeniaceae floral symmetry diversity.
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Affiliation(s)
- Andrew G. Gardner
- Department of Biology, Rhodes College, 2000 N. Parkway, Memphis, Tennessee, United States of America
- * E-mail:
| | - Jonathan N. Fitz Gerald
- Department of Biology, Rhodes College, 2000 N. Parkway, Memphis, Tennessee, United States of America
| | - John Menz
- Department of Biology, Rhodes College, 2000 N. Parkway, Memphis, Tennessee, United States of America
| | - Kelly A. Shepherd
- Science and Conservation Division, Department of Parks and Wildlife, Kensington, Western Australia, Australia
| | - Dianella G. Howarth
- Department of Biological Sciences, St. John’s University, Queens, New York, United States of America
| | - Rachel S. Jabaily
- Department of Biology, Rhodes College, 2000 N. Parkway, Memphis, Tennessee, United States of America
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Yu H, Huang T. Molecular Mechanisms of Floral Boundary Formation in Arabidopsis. Int J Mol Sci 2016; 17:317. [PMID: 26950117 PMCID: PMC4813180 DOI: 10.3390/ijms17030317] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Revised: 02/21/2016] [Accepted: 02/23/2016] [Indexed: 01/03/2023] Open
Abstract
Boundary formation is a crucial developmental process in plant organogenesis. Boundaries separate cells with distinct identities and act as organizing centers to control the development of adjacent organs. In flower development, initiation of floral primordia requires the formation of the meristem-to-organ (M-O) boundaries and floral organ development depends on the establishment of organ-to-organ (O-O) boundaries. Studies in this field have revealed a suite of genes and regulatory pathways controlling floral boundary formation. Many of these genes are transcription factors that interact with phytohormone pathways. This review will focus on the functions and interactions of the genes that play important roles in the floral boundaries and discuss the molecular mechanisms that integrate these regulatory pathways to control the floral boundary formation.
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Affiliation(s)
- Hongyang Yu
- College of Life Sciences and Oceanography, Shenzhen University, 3688 Nanhai Ave., Shenzhen 518060, China.
- College of Optoelectronic Engineering, Shenzhen University, 3688 Nanhai Ave., Shenzhen 518060, China.
| | - Tengbo Huang
- College of Life Sciences and Oceanography, Shenzhen University, 3688 Nanhai Ave., Shenzhen 518060, China.
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Hecht V. Duplicate MADS genes with split roles. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:1609-1611. [PMID: 26956503 PMCID: PMC4783379 DOI: 10.1093/jxb/erw086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Affiliation(s)
- Valérie Hecht
- School of Biological Sciences, University of Tasmania, Hobart, Australia
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Stewart D, Graciet E, Wellmer F. Molecular and regulatory mechanisms controlling floral organ development. FEBS J 2016; 283:1823-30. [DOI: 10.1111/febs.13640] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 11/25/2015] [Accepted: 12/30/2015] [Indexed: 01/15/2023]
Affiliation(s)
- Darragh Stewart
- Smurfit Institute of Genetics; Trinity College; Dublin Ireland
| | | | - Frank Wellmer
- Smurfit Institute of Genetics; Trinity College; Dublin Ireland
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Huang T, Irish VF. Gene networks controlling petal organogenesis. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:61-8. [PMID: 26428062 DOI: 10.1093/jxb/erv444] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
One of the biggest unanswered questions in developmental biology is how growth is controlled. Petals are an excellent organ system for investigating growth control in plants: petals are dispensable, have a simple structure, and are largely refractory to environmental perturbations that can alter their size and shape. In recent studies, a number of genes controlling petal growth have been identified. The overall picture of how such genes function in petal organogenesis is beginning to be elucidated. This review will focus on studies using petals as a model system to explore the underlying gene networks that control organ initiation, growth, and final organ morphology.
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Affiliation(s)
- Tengbo Huang
- College of Life Sciences, Shenzhen University, 3688 Nanhai Ave., Shenzhen 518060, PR China Department of Molecular, Cellular and Developmental Biology, Yale University, 266 Whitney Ave., New Haven, CT 06520-8104. USA
| | - Vivian F Irish
- Department of Molecular, Cellular and Developmental Biology, Yale University, 266 Whitney Ave., New Haven, CT 06520-8104. USA Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT 06520-8106. USA
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Voogd C, Wang T, Varkonyi-Gasic E. Functional and expression analyses of kiwifruit SOC1-like genes suggest that they may not have a role in the transition to flowering but may affect the duration of dormancy. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:4699-710. [PMID: 25979999 PMCID: PMC4507769 DOI: 10.1093/jxb/erv234] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The MADS-domain transcription factor SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1) is one of the key integrators of endogenous and environmental signals that promote flowering in the annual species Arabidopsis thaliana. In the deciduous woody perennial vine kiwifruit (Actinidia spp.), environmental signals are integrated to regulate annual cycles of growth and dormancy. Accumulation of chilling during winter is required for dormancy break and flowering in spring. In order to understand the regulation of dormancy and flowering in kiwifruit, nine kiwifruit SOC1-like genes were identified and characterized. All genes affected flowering time of A. thaliana Col-0 and were able to rescue the late flowering phenotype of the soc1-2 mutant when ectopically expressed. A differential capacity for homodimerization was observed, but all proteins were capable of strong interactions with SHORT VEGETATIVE PHASE (SVP) MADS-domain proteins. Largely overlapping spatial domains but distinct expression profiles in buds were identified between the SOC1-like gene family members. Ectopic expression of AcSOC1e, AcSOC1i, and AcSOC1f in Actinidia chinensis had no impact on establishment of winter dormancy and failed to induce precocious flowering, but AcSOC1i reduced the duration of dormancy in the absence of winter chilling. These findings add to our understanding of the SOC1-like gene family and the potential diversification of SOC1 function in woody perennials.
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Affiliation(s)
- Charlotte Voogd
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Mt Albert, Private Bag 92169, Auckland 1142, New Zealand
| | - Tianchi Wang
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Mt Albert, Private Bag 92169, Auckland 1142, New Zealand
| | - Erika Varkonyi-Gasic
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Mt Albert, Private Bag 92169, Auckland 1142, New Zealand
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Ryan PT, Ó'Maoiléidigh DS, Drost HG, Kwaśniewska K, Gabel A, Grosse I, Graciet E, Quint M, Wellmer F. Patterns of gene expression during Arabidopsis flower development from the time of initiation to maturation. BMC Genomics 2015; 16:488. [PMID: 26126740 PMCID: PMC4488132 DOI: 10.1186/s12864-015-1699-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2015] [Accepted: 06/15/2015] [Indexed: 11/10/2022] Open
Abstract
Background The formation of flowers is one of the main model systems to elucidate the molecular mechanisms that control developmental processes in plants. Although several studies have explored gene expression during flower development in the model plant Arabidopsis thaliana on a genome-wide scale, a continuous series of expression data from the earliest floral stages until maturation has been lacking. Here, we used a floral induction system to close this information gap and to generate a reference dataset for stage-specific gene expression during flower formation. Results Using a floral induction system, we collected floral buds at 14 different stages from the time of initiation until maturation. Using whole-genome microarray analysis, we identified 7,405 genes that exhibit rapid expression changes during flower development. These genes comprise many known floral regulators and we found that the expression profiles for these regulators match their known expression patterns, thus validating the dataset. We analyzed groups of co-expressed genes for over-represented cellular and developmental functions through Gene Ontology analysis and found that they could be assigned specific patterns of activities, which are in agreement with the progression of flower development. Furthermore, by mapping binding sites of floral organ identity factors onto our dataset, we were able to identify gene groups that are likely predominantly under control of these transcriptional regulators. We further found that the distribution of paralogs among groups of co-expressed genes varies considerably, with genes expressed predominantly at early and intermediate stages of flower development showing the highest proportion of such genes. Conclusions Our results highlight and describe the dynamic expression changes undergone by a large number of genes during flower development. They further provide a comprehensive reference dataset for temporal gene expression during flower formation and we demonstrate that it can be used to integrate data from other genomics approaches such as genome-wide localization studies of transcription factor binding sites. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1699-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Patrick T Ryan
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Diarmuid S Ó'Maoiléidigh
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland.,Present address: Max Planck Institute for Plant Breeding Research, D-50829, Cologne, Germany
| | - Hajk-Georg Drost
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | | | - Alexander Gabel
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Ivo Grosse
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Emmanuelle Graciet
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland.,Department of Biology, National University of Ireland Maynooth, Maynooth, Ireland
| | - Marcel Quint
- Leibniz Institute of Plant Biochemistry, Department of Molecular Signal Processing, Halle (Saale), Germany.
| | - Frank Wellmer
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland.
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