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Song J, Liu Y, Cai W, Zhou S, Fan X, Hu H, Ren L, Xue Y. Unregulated GmAGL82 due to Phosphorus Deficiency Positively Regulates Root Nodule Growth in Soybean. Int J Mol Sci 2024; 25:1802. [PMID: 38339080 PMCID: PMC10855635 DOI: 10.3390/ijms25031802] [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: 12/24/2023] [Revised: 01/28/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024] Open
Abstract
Nitrogen fixation, occurring through the symbiotic relationship between legumes and rhizobia in root nodules, is crucial in sustainable agriculture. Nodulation and soybean production are influenced by low levels of phosphorus stress. In this study, we discovered a MADS transcription factor, GmAGL82, which is preferentially expressed in nodules and displays significantly increased expression under conditions of phosphate (Pi) deficiency. The overexpression of GmAGL82 in composite transgenic plants resulted in an increased number of nodules, higher fresh weight, and enhanced soluble Pi concentration, which subsequently increased the nitrogen content, phosphorus content, and overall growth of soybean plants. Additionally, transcriptome analysis revealed that the overexpression of GmAGL82 significantly upregulated the expression of genes associated with nodule growth, such as GmENOD100, GmHSP17.1, GmHSP17.9, GmSPX5, and GmPIN9d. Based on these findings, we concluded that GmAGL82 likely participates in the phosphorus signaling pathway and positively regulates nodulation in soybeans. The findings of this research may lay the theoretical groundwork for further studies and candidate gene resources for the genetic improvement of nutrient-efficient soybean varieties in acidic soils.
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Affiliation(s)
- Jia Song
- College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang 524088, China; (J.S.); (Y.L.); (H.H.)
| | - Ying Liu
- College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang 524088, China; (J.S.); (Y.L.); (H.H.)
- South China Branch of National Saline-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang 524088, China
| | - Wangxiao Cai
- College of Chemistry and Environment, Guangdong Ocean University, Zhanjiang 524088, China; (W.C.); (S.Z.); (X.F.)
| | - Silin Zhou
- College of Chemistry and Environment, Guangdong Ocean University, Zhanjiang 524088, China; (W.C.); (S.Z.); (X.F.)
| | - Xi Fan
- College of Chemistry and Environment, Guangdong Ocean University, Zhanjiang 524088, China; (W.C.); (S.Z.); (X.F.)
| | - Hanqiao Hu
- College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang 524088, China; (J.S.); (Y.L.); (H.H.)
- South China Branch of National Saline-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang 524088, China
| | - Lei Ren
- College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang 524088, China; (J.S.); (Y.L.); (H.H.)
- South China Branch of National Saline-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang 524088, China
| | - Yingbin Xue
- College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang 524088, China; (J.S.); (Y.L.); (H.H.)
- South China Branch of National Saline-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang 524088, China
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Chopy M, Cavallini-Speisser Q, Chambrier P, Morel P, Just J, Hugouvieux V, Rodrigues Bento S, Zubieta C, Vandenbussche M, Monniaux M. Cell layer-specific expression of the homeotic MADS-box transcription factor PhDEF contributes to modular petal morphogenesis in petunia. THE PLANT CELL 2024; 36:324-345. [PMID: 37804091 PMCID: PMC10827313 DOI: 10.1093/plcell/koad258] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 08/31/2023] [Accepted: 09/18/2023] [Indexed: 10/08/2023]
Abstract
Floral homeotic MADS-box transcription factors ensure the correct morphogenesis of floral organs, which are organized in different cell layers deriving from distinct meristematic layers. How cells from these distinct layers acquire their respective identities and coordinate their growth to ensure normal floral organ morphogenesis is unresolved. Here, we studied petunia (Petunia × hybrida) petals that form a limb and tube through congenital fusion. We identified petunia mutants (periclinal chimeras) expressing the B-class MADS-box gene DEFICIENS in the petal epidermis or in the petal mesophyll, called wico and star, respectively. Strikingly, wico flowers form a strongly reduced tube while their limbs are almost normal, while star flowers form a normal tube but greatly reduced and unpigmented limbs, showing that petunia petal morphogenesis is highly modular. These mutants highlight the layer-specific roles of PhDEF during petal development. We explored the link between PhDEF and petal pigmentation, a well-characterized limb epidermal trait. The anthocyanin biosynthesis pathway was strongly downregulated in star petals, including its major regulator ANTHOCYANIN2 (AN2). We established that PhDEF directly binds to the AN2 terminator in vitro and in vivo, suggesting that PhDEF might regulate AN2 expression and therefore petal epidermis pigmentation. Altogether, we show that cell layer-specific homeotic activity in petunia petals differently impacts tube and limb development, revealing the relative importance of the different cell layers in the modular architecture of petunia petals.
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Affiliation(s)
- Mathilde Chopy
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Lyon 69007, France
| | - Quentin Cavallini-Speisser
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Lyon 69007, France
| | - Pierre Chambrier
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Lyon 69007, France
| | - Patrice Morel
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Lyon 69007, France
| | - Jérémy Just
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Lyon 69007, France
| | - Véronique Hugouvieux
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble-Alpes, CNRS, CEA, INRAE, IRIG-DBSCI, Grenoble 38000, France
| | - Suzanne Rodrigues Bento
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Lyon 69007, France
| | - Chloe Zubieta
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble-Alpes, CNRS, CEA, INRAE, IRIG-DBSCI, Grenoble 38000, France
| | - Michiel Vandenbussche
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Lyon 69007, France
| | - Marie Monniaux
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Lyon 69007, France
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Lu J, Qu L, Xing G, Liu Z, Lu X, Han X. Genome-Wide Identification and Expression Analysis of the MADS Gene Family in Tulips ( Tulipa gesneriana). Genes (Basel) 2023; 14:1974. [PMID: 37895323 PMCID: PMC10606154 DOI: 10.3390/genes14101974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/17/2023] [Accepted: 10/20/2023] [Indexed: 10/29/2023] Open
Abstract
To investigate the cold response mechanism and low temperature regulation of flowering in tulips, this study identified 32 MADS-box transcription factor family members in tulips based on full-length transcriptome sequencing, named TgMADS1-TgMADS32. Phylogenetic analysis revealed that these genes can be divided into two classes: type I and type II. Structural analysis showed that TgMADS genes from different subfamilies have a similar distribution of conserved motifs. Quantitative real-time PCR results demonstrated that some TgMADS genes (e.g., TgMADS3, TgMADS15, TgMADS16, and TgMADS19) were significantly upregulated in buds and stems under cold conditions, implying their potential involvement in the cold response of tulips. In summary, this study systematically identified MADS family members in tulips and elucidated their evolutionary relationships, gene structures, and cold-responsive expression patterns, laying the foundation for further elucidating the roles of these transcription factors in flowering and the cold adaptability of tulips.
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Affiliation(s)
- Jiaojiao Lu
- Liaoning Academy of Agriculture Sciences, Shenyang 110161, China; (J.L.); (L.Q.); (G.X.); (Z.L.)
- College of Land and Environment, Shenyang Agricultural University, Shenyang 110866, China
| | - Lianwei Qu
- Liaoning Academy of Agriculture Sciences, Shenyang 110161, China; (J.L.); (L.Q.); (G.X.); (Z.L.)
| | - Guimei Xing
- Liaoning Academy of Agriculture Sciences, Shenyang 110161, China; (J.L.); (L.Q.); (G.X.); (Z.L.)
| | - Zhenlei Liu
- Liaoning Academy of Agriculture Sciences, Shenyang 110161, China; (J.L.); (L.Q.); (G.X.); (Z.L.)
| | - Xiaochun Lu
- Liaoning Academy of Agriculture Sciences, Shenyang 110161, China; (J.L.); (L.Q.); (G.X.); (Z.L.)
| | - Xiaori Han
- College of Land and Environment, Shenyang Agricultural University, Shenyang 110866, China
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Dry Climate Filters Gymnosperms but Not Angiosperms through Seed Mass. DIVERSITY 2023. [DOI: 10.3390/d15030401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
In the context of climate change in recent years, the fate of woody plant seed has an important impact on forest regeneration. Seed mass is an important reproductive strategy of plants. There are huge differences between gymnosperms (mainly conifers) and angiosperms (flowering plants) in terms of reproduction and hydraulic strategies; however, little is known about changes in seed mass along climate aridity gradients between taxonomical groups such as gymnosperms and angiosperms, which limit our understanding on the fate of woody plants under warming-induced climate drying. We collected seed mass data from a total of 2575 woody plant individuals, including 145 species of gymnosperms and 1487 species of angiosperms, across different climatic zones in China. We mapped the distribution pattern of gymnosperm and angiosperm seed mass in China, with angiosperms being maximal near the 400 mm iso-precipitation line. Our phylogenetic analysis results show that seed mass exhibited significant phylogenic signals (p < 0.001) and was also strongly influenced by functional traits (growth type, fruit type, and dispersal mode). The results of linear regression and hierarchical partitioning analysis showed a stronger correlation between gymnosperm seed mass and environmental factors, and a higher independent aridity index effect on gymnosperm seed mass than angiosperm seed mass. The different patterns of seed mass along a climate aridity gradient between gymnosperms and angiosperms may point to different future fates for these two taxonomic groups, while the higher sensitivity of gymnosperm seed mass to environmental conditions may reduce their reproductive rate under the background of climate warming and drying.
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Song M, Zhang Y, Jia Q, Huang S, An R, Chen N, Zhu Y, Mu J, Hu S. Systematic analysis of MADS-box gene family in the U's triangle species and targeted mutagenesis of BnaAG homologs to explore its role in floral organ identity in Brassica napus. FRONTIERS IN PLANT SCIENCE 2023; 13:1115513. [PMID: 36714735 PMCID: PMC9878456 DOI: 10.3389/fpls.2022.1115513] [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: 12/04/2022] [Accepted: 12/23/2022] [Indexed: 06/18/2023]
Abstract
MADS-box transcription factors play an important role in regulating floral organ development and participate in environmental responses. To date, the MADS-box gene family has been widely identified in Brassica rapa (B. rapa), Brassica oleracea (B. oleracea), and Brassica napus (B. napus); however, there are no analogous reports in Brassica nigra (B. nigra), Brassica juncea (B. juncea), and Brassica carinata (B. carinata). In this study, a whole-genome survey of the MADS-box gene family was performed for the first time in the triangle of U species, and a total of 1430 MADS-box genes were identified. Based on the phylogenetic relationship and classification of MADS-box genes in Arabidopsis thaliana (A. thaliana), 1430 MADS-box genes were categorized as M-type subfamily (627 genes), further divided into Mα, Mβ, Mγ, and Mδ subclades, and MIKC-type subfamily (803 genes), further classified into 35 subclades. Gene structure and conserved protein motifs of MIKC-type MADS-box exhibit diversity and specificity among different subclades. Comparative analysis of gene duplication events and syngenic gene pairs among different species indicated that polyploidy is beneficial for MIKC-type gene expansion. Analysis of transcriptome data within diverse tissues and stresses in B. napus showed tissue-specific expression of MIKC-type genes and a broad response to various abiotic stresses, particularly dehydration stress. In addition, four representative floral organ mutants (wtl, feml, aglf-2, and aglf-1) in the T0 generation were generated by editing four AGAMOUS (BnaAG) homoeologs in B. napus that enriched the floral organ variant phenotype. In brief, this study provides useful information for investigating the function of MADS-box genes and contributes to revealing the regulatory mechanisms of floral organ development in the genetic improvement of new varieties.
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Affiliation(s)
- Min Song
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest Agriculture and Forestry University, Yangling, Shaanxi, China
| | - Yanfeng Zhang
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, Shaanxi, China
| | - Qingli Jia
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, Shaanxi, China
| | - Shuhua Huang
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, Shaanxi, China
| | - Ran An
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, Shaanxi, China
| | - Nana Chen
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, Shaanxi, China
| | - Yantao Zhu
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, Shaanxi, China
| | - Jianxin Mu
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, Shaanxi, China
| | - Shengwu Hu
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest Agriculture and Forestry University, Yangling, Shaanxi, China
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Wang Y, Yang T, Li Y, Hou J, He J, Ma N, Zhou X. Genome-wide identification and expression analysis of MIKC C genes in rose provide insight into their effects on flower development. FRONTIERS IN PLANT SCIENCE 2022; 13:1059925. [PMID: 36407632 PMCID: PMC9666904 DOI: 10.3389/fpls.2022.1059925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
The MIKCC-type gene family plays important roles in plant growth, development, and tolerance of biotic and abiotic stress, especially during floral organ differentiation. However, there have been no studies of MIKCC-type genes in rose, and functional differentiation of family members has not been explored. In this study, we identified 42 MIKCC-type genes in rose, classified the genes into 12 subfamilies, and constructed a phylogenetic tree. We performed expression analysis of these genes, and found that expression patterns correlated with the predicted subfamily, indicating that the features of MIKCC-type genes were broadly conserved during evolution. Collinear analysis of MIKCC genes among Rosaceae species confirmed the occurrence of whole genome duplications (WGD) and revealed some species-specific MIKCC genes. Transcriptome analysis showed that the expression of some MIKCC-type genes responded to low temperatures (4°C, 24 h) during flower organ differentiation. These conserved, duplicated, and novel expression patterns of MIKCC-type genes may have facilitated the adaptation of rose to various internal and external environmental changes. The results of this study provide a theoretical basis for future functional analysis of the MIKCC genes in rose and investigation of the evolutionary pattern of the MIKCC gene family in the Rosaceae genome.
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Li H, Li Y, Zhang X, Cai K, Li Y, Wang Q, Qu G, Han R, Zhao X. Genome-wide identification and expression analysis of the MADS-box gene family during female and male flower development in Juglans mandshurica. FRONTIERS IN PLANT SCIENCE 2022; 13:1020706. [PMID: 36388573 PMCID: PMC9664150 DOI: 10.3389/fpls.2022.1020706] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
The MADS-box gene family plays a crucial role in multiple developmental processes of plants, especially in floral organ specification and the regulation of fruit development and ripening. Juglans mandshurica is a precious fruit material whose quality and yield are determined by floral organ development. The molecular mechanism of J. mandshurica female and male flower development depending on MADS-box genes remains unclear. In our study, 67 JmMADS genes were identified and unevenly distributed on 15 of 16 J. mandshurica chromosomes. These genes were divided into two types [type I (Mα, Mγ, Mδ) and type II (MIKC)]. The gene structure and motif analyses showed that most genes belonging to the same type had similar gene structures and conserved motifs. The analysis of syntenic relationships showed that MADS-box genes in J. mandshurica, J. sigillata, and J. regia exhibited the highest homology and great collinearity. Analysis of cis-acting elements showed that JmMADS gene promoter regions contained light, stress and hormone response cis-acting elements. The gene expression patterns demonstrated that 30 and 26 JmMADS genes were specifically expressed in the female and male flowers, respectively. In addition, 12 selected genes common to J. mandshurica female and male flowers were significantly upregulated at the mature stage and were used to validate the reliability of the transcriptome data using quantitative real-time PCR. This comprehensive and systematic analysis of J. mandshurica MADS-box genes lays a foundation for future studies on MADS-box gene family functions.
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Affiliation(s)
- Hanxi Li
- State Key Laboratory of tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland Science, Jilin Agricultural University, Changchun, China
| | - Yuxi Li
- State Key Laboratory of tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Xinxin Zhang
- State Key Laboratory of tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Kewei Cai
- State Key Laboratory of tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Yan Li
- State Key Laboratory of tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland Science, Jilin Agricultural University, Changchun, China
| | - Qingcheng Wang
- State Key Laboratory of tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Guanzheng Qu
- State Key Laboratory of tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Rui Han
- State Key Laboratory of tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland Science, Jilin Agricultural University, Changchun, China
| | - Xiyang Zhao
- State Key Laboratory of tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland Science, Jilin Agricultural University, Changchun, China
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Mou Y, Yuan C, Sun Q, Yan C, Zhao X, Wang J, Wang Q, Shan S, Li C. MIKC-type MADS-box transcription factor gene family in peanut: Genome-wide characterization and expression analysis under abiotic stress. FRONTIERS IN PLANT SCIENCE 2022; 13:980933. [PMID: 36340369 PMCID: PMC9631947 DOI: 10.3389/fpls.2022.980933] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 09/09/2022] [Indexed: 06/16/2023]
Abstract
Peanut (Arachis hypogaea) is one of the most important economic crops around the world, especially since it provides vegetable oil and high-quality protein for humans. Proteins encoded by MADS-box transcription factors are widely involved in regulating plant growth and development as well as responses to abiotic stresses. However, the MIKC-type MADS-box TFs in peanut remains currently unclear. Hence, in this study, 166 MIKC-type MADS-box genes were identified in both cultivated and wild-type peanut genomes, which were divided into 12 subfamilies. We found a variety of development-, hormone-, and stress-related cis-acting elements in the promoter region of peanut MIKC-type MADS-box genes. The chromosomal distribution of peanut MADS-box genes was not random, and gene duplication contributed to the expansion of the MADS-box gene family. The interaction network of the peanut AhMADS proteins was established. Expression pattern analysis showed that AhMADS genes were specifically expressed in tissues and under abiotic stresses. It was further confirmed via the qRT-PCR technique that five selected AhMADS genes could be induced by abiotic and hormone treatments and presented different expressive profiles under various stresses. Taken together, these findings provide valuable information for the exploration of candidate genes in molecular breeding and further study of AhMADS gene functions.
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Jiang L, Fan T, Wang L, Zhang L, Xu J. Divergence of flowering-related genes to control flowering in five Euphorbiaceae genomes. FRONTIERS IN PLANT SCIENCE 2022; 13:1015114. [PMID: 36340397 PMCID: PMC9627276 DOI: 10.3389/fpls.2022.1015114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
Reproductive growth and vegetative growth are a pair of main contradictions in the process of plant growth. Flowering, as part of reproductive growth, is a key switch in the life cycle of higher plants, which affects the yield and economic benefits of plants to a certain extent. The Euphorbiaceae species, including castor bean (Ricinus communis), physic nut (Jatropha curcas), tung tree (Vernicia fordii), cassava (Manihot esculenta), and rubber tree (Hevea brasiliensis), have important economic values because they are raw materials for the production of biodiesel, rubber, etc. The flowering mechanisms are still excluded in the Euphorbiaceae species. The flowering-related genes of Arabidopsis thaliana (Arabidopsis) were used as a reference to determine the orthologs of these genes in Euphorbiaceae genomes. The result showed that 146, 144, 114, 114, and 149 of 207 A. thaliana genes were respectively matched to R. communis, V. fordii, J. curcas, H. brasiliensis, and M. esculenta. These identified genes were clustered into seven pathways including gibberellins, floral meristem identity (FMI), vernalization, photoperiod, floral pathway integrators (FPIs), and autonomous pathways. Then, some key numbers of flowering-related genes are widely conserved in the Euphorbiaceae genomes including but not limited to FPI genes LFY, SOC1, FT, and FMI genes AG, CAL, and FUL. However, some genes, including FRI, FLC, and GO, were missing in several or all five Euphorbiaceae species. In this study, we proposed the putative mechanisms of flowering-related genes to control flowering and provided new candidate flowering genes for using marker-assisted breeding to improve variety quality.
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Affiliation(s)
- Lan Jiang
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Yijishan Hospital of Wannan Medical College, Wuhu, China
- Anhui Provincial Clinical Research Center for Critical Respiratory Disease, Wuhu, China
| | - Tingting Fan
- Forestry College, Central South University of Forestry and Technology, Changsha, China
| | - Lihu Wang
- School of Landscape and Ecological Engineering, Hebei University of Engineering, Handan, China
| | - Lin Zhang
- College of Basic Medical Sciences, Hubei University of Chinese Medicine, Wuhan, China
| | - Jun Xu
- Hunan Institute of Microbiology, Changsha, China
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Fritsche S, Rippel Salgado L, Boron AK, Hanning KR, Donaldson LA, Thorlby G. Transcriptional Regulation of Pine Male and Female Cone Initiation and Development: Key Players Identified Through Comparative Transcriptomics. Front Genet 2022; 13:815093. [PMID: 35368695 PMCID: PMC8971679 DOI: 10.3389/fgene.2022.815093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 02/24/2022] [Indexed: 11/24/2022] Open
Abstract
With long reproductive timescales, large complex genomes, and a lack of reliable reference genomes, understanding gene function in conifers is extremely challenging. Consequently, our understanding of which genetic factors influence the development of reproductive structures (cones) in monoecious conifers remains limited. Genes with inferred roles in conifer reproduction have mostly been identified through homology and phylogenetic reconstruction with their angiosperm counterparts. We used RNA-sequencing to generate transcriptomes of the early morphological stages of cone development in the conifer species Pinus densiflora and used these to gain a deeper insight into the transcriptional changes during male and female cone development. Paired-end Illumina sequencing was used to generate transcriptomes from non-reproductive tissue and male and female cones at four time points with a total of 382.82 Gbp of data generated. After assembly and stringent filtering, a total of 37,164 transcripts were retrieved, of which a third were functionally annotated using the Mercator plant pipeline. Differentially expressed gene (DEG) analysis resulted in the identification of 172,092 DEGs in the nine tissue types. This, alongside GO gene enrichment analyses, pinpointed transcripts putatively involved in conifer reproductive structure development, including co-orthologs of several angiosperm flowering genes and several that have not been previously reported in conifers. This study provides a comprehensive transcriptome resource for male and early female cone development in the gymnosperm species Pinus densiflora. Characterisation of this resource has allowed the identification of potential key players and thus provides valuable insights into the molecular regulation of reproductive structure development in monoecious conifers.
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Affiliation(s)
- Steffi Fritsche
- Forest Genetics and Biotechnology, Scion, Rotorua, New Zealand
| | - Leonardo Rippel Salgado
- Forest Genetics and Biotechnology, Scion, Rotorua, New Zealand
- Molecular and Digital Breeding, The New Zealand Institute for Plant and Food Research, Te Puke, New Zealand
| | | | | | | | - Glenn Thorlby
- Forest Genetics and Biotechnology, Scion, Rotorua, New Zealand
- *Correspondence: Glenn Thorlby,
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Abstract
BACKGROUND The LEAFY (LFY) transcription factors are present in algae and across land plants. The available expression and functional data of these genes in embryophytes suggest that LFY genes control a plethora of processes including the first zygotic cell division in bryophytes, shoot cell divisions of the gametophyte and sporophyte in ferns, cone differentiation in gymnosperms and floral meristem identity in flowering plants. However, their putative plesiomorphic role in plant reproductive transition in vascular plants remains untested. RESULTS We perform Maximum Likelihood (ML) phylogenetic analyses for the LFY gene lineage in embryophytes with expanded sampling in lycophytes and ferns. We recover the previously identified seed plant duplication that results in LEAFY and NEEDLY paralogs. In addition, we recover multiple species-specific duplications in ferns and lycophytes and large-scale duplications possibly correlated with the occurrence of whole genome duplication (WGD) events in Equisetales and Salviniales. To test putative roles in diverse ferns and lycophytes we perform LFY expression analyses in Adiantum raddianum, Equisetum giganteum and Selaginella moellendorffii. Our results show that LFY genes are active in vegetative and reproductive tissues, with higher expression in early fertile developmental stages and during sporangia differentiation. CONCLUSIONS Our data point to previously unrecognized roles of LFY genes in sporangia differentiation in lycophytes and ferns and suggests that functions linked to reproductive structure development are not exclusive to seed plant LFY homologs.
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Åstrand J, Knight C, Robson J, Talle B, Wilson ZA. Evolution and diversity of the angiosperm anther: trends in function and development. PLANT REPRODUCTION 2021; 34:307-319. [PMID: 34173886 PMCID: PMC8566645 DOI: 10.1007/s00497-021-00416-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 05/28/2021] [Indexed: 05/21/2023]
Abstract
Anther development and dehiscence is considered from an evolutionary perspective to identify drivers for differentiation, functional conservation and to identify key questions for future male reproduction research. Development of viable pollen and its timely release from the anther are essential for fertilisation of angiosperm flowers. The formation and subsequent dehiscence of the anther are under tight regulatory control, and these processes are remarkably conserved throughout the diverse families of the angiosperm clade. Anther development is a complex process, which requires timely formation and communication between the multiple somatic anther cell layers (the epidermis, endothecium, middle layer and tapetum) and the developing pollen. These layers go through regulated development and selective degeneration to facilitate the formation and ultimate release of the pollen grains. Insight into the evolution and divergence of anther development and dehiscence, especially between monocots and dicots, is driving greater understanding of the male reproductive process and increased, resilient crop yields. This review focuses on anther structure from an evolutionary perspective by highlighting their diversity across plant species. We summarise new findings that illustrate the complexities of anther development and evaluate how they challenge established models of anther form and function, and how they may help to deliver future sustainable crop yields.
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Affiliation(s)
- Johanna Åstrand
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD UK
| | - Christopher Knight
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD UK
| | - Jordan Robson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD UK
| | - Behzad Talle
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD UK
| | - Zoe A. Wilson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD UK
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13
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Elorriaga E, Klocko AL, Ma C, du Plessis M, An X, Myburg AA, Strauss SH. Genetic containment in vegetatively propagated forest trees: CRISPR disruption of LEAFY function in Eucalyptus gives sterile indeterminate inflorescences and normal juvenile development. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1743-1755. [PMID: 33774917 PMCID: PMC8428835 DOI: 10.1111/pbi.13588] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 02/27/2021] [Accepted: 03/14/2021] [Indexed: 05/05/2023]
Abstract
Eucalyptus is among the most widely planted taxa of forest trees worldwide. However, its spread as an exotic or genetically engineered form can create ecological and social problems. To mitigate gene flow via pollen and seeds, we mutated the Eucalyptus orthologue of LEAFY (LFY) by transforming a Eucalyptus grandis × urophylla wild-type hybrid and two Flowering Locus T (FT) overexpressing (and flowering) lines with CRISPR Cas9 targeting its LFY orthologue, ELFY. We achieved high rates of elfy biallelic knockouts, often approaching 100% of transgene insertion events. Frameshift mutations and deletions removing conserved amino acids caused strong floral alterations, including indeterminacy in floral development and an absence of male and female gametes. These mutants were otherwise visibly normal and did not differ statistically from transgenic controls in juvenile vegetative growth rate or leaf morphology in greenhouse trials. Genes upstream or near to ELFY in the floral development pathway were overexpressed, whereas floral organ identity genes downstream of ELFY were severely depressed. We conclude that disruption of ELFY function appears to be a useful tool for sexual containment, without causing statistically significant or large adverse effects on juvenile vegetative growth or leaf morphology.
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Affiliation(s)
- Estefania Elorriaga
- Department of Forest Ecosystems and SocietyOregon State UniversityCorvallisORUSA
- Present address:
Department of Molecular and Structural BiochemistryNorth Carolina State UniversityRaleighNCUSA
| | - Amy L. Klocko
- Department of BiologyUniversity of Colorado Colorado SpringsColorado SpringsCOUSA
| | - Cathleen Ma
- Department of Forest Ecosystems and SocietyOregon State UniversityCorvallisORUSA
| | - Marc du Plessis
- Department of Zoology and EntomologyUniversity of PretoriaPretoriaSouth Africa
| | - Xinmin An
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignNational Engineering Laboratory for Tree BreedingCollege of Biological Sciences and BiotechnologyBeijing Forestry UniversityBeijingChina
| | - Alexander A. Myburg
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI)University of PretoriaPretoriaSouth Africa
| | - Steven H. Strauss
- Department of Forest Ecosystems and SocietyOregon State UniversityCorvallisORUSA
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14
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Sharma R, Upadhyay S, Bhattacharya S, Singh A. Abiotic Stress-Responsive miRNA and Transcription Factor-Mediated Gene Regulatory Network in Oryza sativa: Construction and Structural Measure Study. Front Genet 2021; 12:618089. [PMID: 33643383 PMCID: PMC7907651 DOI: 10.3389/fgene.2021.618089] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 01/19/2021] [Indexed: 11/13/2022] Open
Abstract
Climate changes and environmental stresses have a consequential association with crop plant growth and yield, meaning it is necessary to cultivate crops that have tolerance toward the changing climate and environmental disturbances such as water stress, temperature fluctuation, and salt toxicity. Recent studies have shown that trans-acting regulatory elements, including microRNAs (miRNAs) and transcription factors (TFs), are emerging as promising tools for engineering naive improved crop varieties with tolerance for multiple environmental stresses and enhanced quality as well as yield. However, the interwoven complex regulatory function of TFs and miRNAs at transcriptional and post-transcriptional levels is unexplored in Oryza sativa. To this end, we have constructed a multiple abiotic stress responsive TF-miRNA-gene regulatory network for O. sativa using a transcriptome and degradome sequencing data meta-analysis approach. The theoretical network approach has shown the networks to be dense, scale-free, and small-world, which makes the network stable. They are also invariant to scale change where an efficient, quick transmission of biological signals occurs within the network on extrinsic hindrance. The analysis also deciphered the existence of communities (cluster of TF, miRNA, and genes) working together to help plants in acclimatizing to multiple stresses. It highlighted that genes, TFs, and miRNAs shared by multiple stress conditions that work as hubs or bottlenecks for signal propagation, for example, during the interaction between stress-responsive genes (TFs/miRNAs/other genes) and genes involved in floral development pathways under multiple environmental stresses. This study further highlights how the fine-tuning feedback mechanism works for balancing stress tolerance and how timely flowering enable crops to survive in adverse conditions. This study developed the abiotic stress-responsive regulatory network, APRegNet database (http://lms.snu.edu.in/APRegNet), which may help researchers studying the roles of miRNAs and TFs. Furthermore, it advances current understanding of multiple abiotic stress tolerance mechanisms.
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Affiliation(s)
- Rinku Sharma
- Department of Life Sciences, Shiv Nadar University, Gautam Buddha Nagar, India
| | | | | | - Ashutosh Singh
- Department of Life Sciences, Shiv Nadar University, Gautam Buddha Nagar, India
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15
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Abraham-Juárez MJ, Schrager-Lavelle A, Man J, Whipple C, Handakumbura P, Babbitt C, Bartlett M. Evolutionary Variation in MADS Box Dimerization Affects Floral Development and Protein Abundance in Maize. THE PLANT CELL 2020; 32:3408-3424. [PMID: 32873631 PMCID: PMC7610293 DOI: 10.1105/tpc.20.00300] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 08/19/2020] [Accepted: 09/01/2020] [Indexed: 05/19/2023]
Abstract
Interactions between MADS box transcription factors are critical in the regulation of floral development, and shifting MADS box protein-protein interactions are predicted to have influenced floral evolution. However, precisely how evolutionary variation in protein-protein interactions affects MADS box protein function remains unknown. To assess the impact of changing MADS box protein-protein interactions on transcription factor function, we turned to the grasses, where interactions between B-class MADS box proteins vary. We tested the functional consequences of this evolutionary variability using maize (Zea mays) as an experimental system. We found that differential B-class dimerization was associated with subtle, quantitative differences in stamen shape. In contrast, differential dimerization resulted in large-scale changes to downstream gene expression. Differential dimerization also affected B-class complex composition and abundance, independent of transcript levels. This indicates that differential B-class dimerization affects protein degradation, revealing an important consequence for evolutionary variability in MADS box interactions. Our results highlight complexity in the evolution of developmental gene networks: changing protein-protein interactions could affect not only the composition of transcription factor complexes but also their degradation and persistence in developing flowers. Our results also show how coding change in a pleiotropic master regulator could have small, quantitative effects on development.
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Affiliation(s)
- María Jazmín Abraham-Juárez
- Biology Department, University of Massachusetts, Amherst, 01003 Massachusetts
- CONACYT-Instituto Potosino de Investigación Científica y Tecnológica A.C., 78216 San Luis Potosi, Mexico
| | - Amanda Schrager-Lavelle
- Biology Department, University of Massachusetts, Amherst, 01003 Massachusetts
- Biology Department, Colorado Mesa University, Grand Junction, 81501 Colorado
| | - Jarrett Man
- Biology Department, University of Massachusetts, Amherst, 01003 Massachusetts
| | - Clinton Whipple
- Biology Department, Brigham Young University, Provo, 84602 Utah
| | - Pubudu Handakumbura
- Biology Department, University of Massachusetts, Amherst, 01003 Massachusetts
- Pacific Northwest National Laboratory, Richland, 99354 Washington
| | - Courtney Babbitt
- Biology Department, University of Massachusetts, Amherst, 01003 Massachusetts
| | - Madelaine Bartlett
- Biology Department, University of Massachusetts, Amherst, 01003 Massachusetts
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16
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Singh G, Singh V, Singh V. Genome-wide interologous interactome map (TeaGPIN) of Camellia sinensis. Genomics 2020; 113:553-564. [PMID: 33002625 DOI: 10.1016/j.ygeno.2020.09.048] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 08/15/2020] [Accepted: 09/22/2020] [Indexed: 11/27/2022]
Abstract
Tea, prepared from the young leaves of Camellia sinensis, is a non-alcoholic beverage globally consumed due to its antioxidant properties, strong taste and aroma. Although, the genomic data of this medicinally and commercially important plant is available, studies related to its sub-cellular interactomic maps are less explored. In this work, we propose a genome-wide interologous protein-protein interaction (PPI) network of tea, termed as TeaGPIN, consisting of 12,033 nodes and 216,107 interactions, developed using draft genome of tea and known PPIs exhaustively collected from 49 template plants. TeaGPIN interactions are prioritized using domain-domain interactions along with the interolog information. A high-confidence TeaGPIN consisting of 5983 nodes and 58,867 edges is reported and its interactions are further evaluated using protein co-localization similarities. Based on three network centralities (degree, betweenness and eigenvector), 1302 key proteins are reported in tea to have p-value <0.01 by comparing the TeaGPIN with 10,000 realizations of Erdős-Rényi and Barabási-Albert based corresponding random network models. Functional content of TeaGPIN is assessed using KEGG and GO annotations and its modular architecture is explored. Network based characterization is carried-out on the transcription factors, and proteins involved flavonoid biosynthesis and photosynthesis pathways to find novel candidates involved in various regulatory processes. We believe the proposed TeaGPIN will impart useful insights in understanding various mechanisms related to growth and development as well as defence against biotic and abiotic perturbations.
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Affiliation(s)
- Gagandeep Singh
- Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, Dharamshala 176206, India
| | - Vikram Singh
- Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, Dharamshala 176206, India
| | - Vikram Singh
- Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, Dharamshala 176206, India.
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17
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Hu MJ, Sun WH, Tsai WC, Xiang S, Lai XK, Chen DQ, Liu XD, Wang YF, Le YX, Chen SM, Zhang DY, Yu X, Hu WQ, Zhou Z, Chen YQ, Zou SQ, Liu ZJ. Chromosome-scale assembly of the Kandelia obovata genome. HORTICULTURE RESEARCH 2020; 7:75. [PMID: 32377365 PMCID: PMC7195387 DOI: 10.1038/s41438-020-0300-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 03/11/2020] [Accepted: 03/16/2020] [Indexed: 05/19/2023]
Abstract
The mangrove Kandelia obovata (Rhizophoraceae) is an important coastal shelterbelt and landscape tree distributed in tropical and subtropical areas across East Asia and Southeast Asia. Herein, a chromosome-level reference genome of K. obovata based on PacBio, Illumina, and Hi-C data is reported. The high-quality assembled genome size is 177.99 Mb, with a contig N50 value of 5.74 Mb. A large number of contracted gene families and a small number of expanded gene families, as well as a small number of repeated sequences, may account for the small K. obovata genome. We found that K. obovata experienced two whole-genome polyploidization events: one whole-genome duplication shared with other Rhizophoreae and one shared with most eudicots (γ event). We confidently annotated 19,138 protein-coding genes in K. obovata and identified the MADS-box gene class and the RPW8 gene class, which might be related to flowering and resistance to powdery mildew in K. obovata and Rhizophora apiculata, respectively. The reference K. obovata genome described here will be very useful for further molecular elucidation of various traits, the breeding of this coastal shelterbelt species, and evolutionary studies with related taxa.
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Affiliation(s)
- Min-Jie Hu
- Key Laboratory of Humid Sub-tropical Eco-Geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou, 350007 China
| | - Wei-Hong Sun
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at the College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Wen-Chieh Tsai
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, 701 China
| | - Shuang Xiang
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at the College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Xing-Kai Lai
- Administration of the Quanzhou Bay Estuary Wetland Nature Reserve, Quanzhou, 362000 China
| | - De-Qiang Chen
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at the College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Xue-Die Liu
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Yi-Fan Wang
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Yi-Xun Le
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Si-Ming Chen
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Ocean College, Minjiang University, Fuzhou, 350002 China
| | - Di-Yang Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at the College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Xia Yu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at the College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Wen-Qi Hu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at the College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Zhuang Zhou
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at the College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Yan-Qiong Chen
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at the College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Shuang-Quan Zou
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at the College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at the College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Henry Fok College of Biology and Agriculture, Shaoguan University, Shaoguan, 512005 China
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18
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Induction of PrMADS10 on the lower side of bent pine tree stems: potential role in modifying plant cell wall properties and wood anatomy. Sci Rep 2019; 9:18981. [PMID: 31831838 PMCID: PMC6908731 DOI: 10.1038/s41598-019-55276-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 11/07/2019] [Indexed: 12/20/2022] Open
Abstract
The molecular mechanisms underlying inclination responses in trees are unclear. In this study, we identified a MADS-box transcription factor differentially expressed early after inclination in the stems of Pinus radiata D. Don. PrMADS10 has a CDS of 582 bp and encodes a group II MADS-box transcription factor. We measured highest accumulation of this transcript on the lower side of inclined pine stems. In an effort to identify putative targets, we stably transformed Arabidopsis thaliana with a 35S::PrMADS10 construct. Transcriptome analysis revealed 1,219 genes differentially-expressed, with 690 and 529 genes up- and down-regulated respectively, when comparing the transgenic and wild-type. Differentially-expressed genes belong to different biological processes, but were enriched in cell wall remodeling and phenylpropanoid metabolic functions. Interestingly, lignin content was 30% higher in transgenic as compared to wild-type plants consistent with observed changes in gene expression. Differentially expressed transcription factors and phenylpropanoid genes were analyzed using STRING. Several MYB and NAC transcription factors showed interactions with genes of the phenylpropanoid pathway. Together, these results implicate PrMADS10 as a regulatory factor, triggering the expression of other transcription factors and genes involved in the synthesis of lignin.
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19
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Hugouvieux V, Silva CS, Jourdain A, Stigliani A, Charras Q, Conn V, Conn SJ, Carles CC, Parcy F, Zubieta C. Tetramerization of MADS family transcription factors SEPALLATA3 and AGAMOUS is required for floral meristem determinacy in Arabidopsis. Nucleic Acids Res 2019; 46:4966-4977. [PMID: 29562355 PMCID: PMC6007258 DOI: 10.1093/nar/gky205] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 03/08/2018] [Indexed: 01/24/2023] Open
Abstract
The MADS transcription factors (TF) constitute an ancient family of TF found in all eukaryotes that bind DNA as obligate dimers. Plants have dramatically expanded the functional diversity of the MADS family during evolution by adding protein-protein interaction domains to the core DNA-binding domain, allowing the formation of heterotetrameric complexes. Tetramerization of plant MADS TFs is believed to play a central role in the evolution of higher plants by acting as one of the main determinants of flower formation and floral organ specification. The MADS TF, SEPALLATA3 (SEP3), functions as a central protein-protein interaction hub, driving tetramerization with other MADS TFs. Here, we use a SEP3 splice variant, SEP3Δtet, which has dramatically abrogated tetramerization capacity to decouple SEP3 tetramerization and DNA-binding activities. We unexpectedly demonstrate that SEP3 heterotetramer formation is required for correct termination of the floral meristem, but plays a lesser role in floral organogenesis. The heterotetramer formed by SEP3 and the MADS protein, AGAMOUS, is necessary to activate two target genes, KNUCKLES and CRABSCLAW, which are required for meristem determinacy. These studies reveal unique and highly specific roles of tetramerization in flower development and suggest tetramerization may be required to activate only a subset of target genes in closed chromatin regions.
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Affiliation(s)
- Véronique Hugouvieux
- Laboratoire de Physiologie Cellulaire & Végétale, CEA, Univ. Grenoble Alpes, CNRS, INRA, BIG, Grenoble
| | - Catarina S Silva
- Laboratoire de Physiologie Cellulaire & Végétale, CEA, Univ. Grenoble Alpes, CNRS, INRA, BIG, Grenoble.,European Synchrotron Radiation Facility, Structural Biology Group, 71, Avenue des Martyrs, F-38000 Grenoble, France
| | - Agnès Jourdain
- Laboratoire de Physiologie Cellulaire & Végétale, CEA, Univ. Grenoble Alpes, CNRS, INRA, BIG, Grenoble
| | - Arnaud Stigliani
- Laboratoire de Physiologie Cellulaire & Végétale, CEA, Univ. Grenoble Alpes, CNRS, INRA, BIG, Grenoble
| | - Quentin Charras
- Laboratoire de Physiologie Cellulaire & Végétale, CEA, Univ. Grenoble Alpes, CNRS, INRA, BIG, Grenoble
| | - Vanessa Conn
- Laboratoire de Physiologie Cellulaire & Végétale, CEA, Univ. Grenoble Alpes, CNRS, INRA, BIG, Grenoble.,Flinders Centre for Innovation in Cancer, School of Medicine, Flinders University, Sturt Road, Bedford Park 5042, South Australia, Australia
| | - Simon J Conn
- Laboratoire de Physiologie Cellulaire & Végétale, CEA, Univ. Grenoble Alpes, CNRS, INRA, BIG, Grenoble.,Flinders Centre for Innovation in Cancer, School of Medicine, Flinders University, Sturt Road, Bedford Park 5042, South Australia, Australia
| | - Cristel C Carles
- Laboratoire de Physiologie Cellulaire & Végétale, CEA, Univ. Grenoble Alpes, CNRS, INRA, BIG, Grenoble
| | - François Parcy
- Laboratoire de Physiologie Cellulaire & Végétale, CEA, Univ. Grenoble Alpes, CNRS, INRA, BIG, Grenoble
| | - Chloe Zubieta
- Laboratoire de Physiologie Cellulaire & Végétale, CEA, Univ. Grenoble Alpes, CNRS, INRA, BIG, Grenoble
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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: 38] [Impact Index Per Article: 7.6] [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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21
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Gao B, Chen M, Li X, Zhang J. Ancient duplications and grass-specific transposition influenced the evolution of LEAFY transcription factor genes. Commun Biol 2019; 2:237. [PMID: 31263781 PMCID: PMC6588583 DOI: 10.1038/s42003-019-0469-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 05/17/2019] [Indexed: 12/18/2022] Open
Abstract
The LFY transcription factor gene family are important in the promotion of cell proliferation and floral development. Understanding their evolution offers an insight into floral development in plant evolution. Though a promiscuous transition intermediate and a gene duplication event within the LFY family had been identified previously, the early evolutionary path of this family remained elusive. Here, we reconstructed the LFY family phylogeny using maximum-likelihood and Bayesian inference methods incorporating LFY genes from all major lineages of streptophytes. The well-resolved phylogeny unveiled a high-confidence duplication event before the functional divergence of types I and II LFY genes in the ancestry of liverworts, mosses and tracheophytes, supporting sub-functionalization of an ancestral promiscuous gene. The identification of promiscuous genes in Osmunda suggested promiscuous LFY genes experienced an ancient transient duplication. Genomic synteny comparisons demonstrated a deep genomic positional conservation of LFY genes and an ancestral lineage-specific transposition activity in grasses.
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Affiliation(s)
- Bei Gao
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Moxian Chen
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Xiaoshuang Li
- Key Laboratory of Biogeography and Bioresource, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011 China
| | - Jianhua Zhang
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
- Department of Biology, Faculty of Science, Hong Kong Baptist University, Hong Kong, China
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22
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Lai X, Daher H, Galien A, Hugouvieux V, Zubieta C. Structural Basis for Plant MADS Transcription Factor Oligomerization. Comput Struct Biotechnol J 2019; 17:946-953. [PMID: 31360333 PMCID: PMC6639411 DOI: 10.1016/j.csbj.2019.06.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 06/06/2019] [Accepted: 06/11/2019] [Indexed: 10/26/2022] Open
Abstract
MADS transcription factors (TFs) are DNA binding proteins found in almost all eukaryotes that play essential roles in diverse biological processes. While present in animals and fungi as a small TF family, the family has dramatically expanded in plants over the course of evolution, with the model flowering plant, Arabidopsis thaliana, possessing over 100 type I and type II MADS TFs. All MADS TFs contain a core and highly conserved DNA binding domain called the MADS or M domain. Plant MADS TFs have diversified this domain with plant-specific auxiliary domains. Plant type I MADS TFs have a highly diverse and largely unstructured Carboxy-terminal (C domain), whereas type II MADS have added oligomerization domains, called Intervening (I domain) and Keratin-like (K domain), in addition to the C domain. In this mini review, we describe the overall structure of the type II "MIKC" type MADS TFs in plants, with a focus on the K domain, a critical oligomerization module. We summarize the determining factors for oligomerization and provide mechanistic insights on how secondary structural elements are required for oligomerization capability and specificity. Using MADS TFs that are involved in flower organ specification as an example, we provide case studies and homology modeling of MADS TFs complex formation. Finally, we highlight outstanding questions in the field.
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Affiliation(s)
- Xuelei Lai
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, Univ. Grenoble Alpes, CEA, INRA, IRIG, Grenoble, France
| | - Hussein Daher
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, Univ. Grenoble Alpes, CEA, INRA, IRIG, Grenoble, France
| | - Antonin Galien
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, Univ. Grenoble Alpes, CEA, INRA, IRIG, Grenoble, France
| | - Veronique Hugouvieux
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, Univ. Grenoble Alpes, CEA, INRA, IRIG, Grenoble, France
| | - Chloe Zubieta
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, Univ. Grenoble Alpes, CEA, INRA, IRIG, Grenoble, France
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23
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Guo J, Zhang G, Song Y, Li Z, Ma S, Niu N, Wang J. Comparative proteomic analysis of multi-ovary wheat under heterogeneous cytoplasm suppression. BMC PLANT BIOLOGY 2019; 19:175. [PMID: 31046676 PMCID: PMC6498644 DOI: 10.1186/s12870-019-1778-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Accepted: 04/15/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND DUOII is a multi-ovary wheat (Triticum aestivum L.) line with two or three pistils and three stamens in each floret. The multi-ovary trait of DUOII is controlled by a dominant gene, whose expression can be suppressed by the heterogeneous cytoplasm of TeZhiI (TZI), a line with the nucleus of common wheat and the cytoplasm of Aegilops. Crosses between female DUOII plants and male TZI plants resulted in multi-ovary F1s; whereas, the reciprocal crosses resulted in mono-ovary F1s. Although the multi-ovary trait is inherited as single trait controlled by a dominant allele in lines with a Triticum cytoplasm, the mechanism by which the special heterogeneous cytoplasm suppresses the expression of multi-ovary is not well understood. RESULTS Observing the developmental process, we found that the critical stage of additional pistil primordium development was when the young spikes were 2-6 mm long. Then, we compared the quantitative proteomic profiles of 2-6 mm long young spikes obtained from the reciprocal crosses between DUOII and TZI. A total of 90 differentially expressed proteins were identified and analyzed based on their biological functions. These proteins had obvious functional pathways mainly implicated in chloroplast metabolism, nuclear and cell division, plant respiration, protein metabolism, and flower development. Importantly, we identified two key proteins, Flowering Locus K Homology Domain and PEPPER, which are known to play an essential role in the specification of pistil organ identity. By drawing relationships between the 90 differentially expressed proteins, we found that these proteins revealed a complex network which is associated with multi-ovary gene expression under heterogeneous cytoplasmic suppression. CONCLUSIONS Our proteomic analysis has identified certain differentially expressed proteins in 2-6 mm long young spikes, which was the critical stage of additional primordium development. This paper provided a universal proteomic profiling involved in the cytoplasmic suppression of wheat floral meristems; and our findings have laid a solid foundation for further mechanistic studies on the underlying mechanisms that control the heterogeneous cytoplasm-induced suppression of the nuclear multi-ovary gene in wheat.
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Affiliation(s)
- Jialin Guo
- College of Agronomy, National Yangling Agriculture Biotechnology & Breeding Center, Yangling Branch of State Wheat Improvement Centre, Wheat Breeding Engineering Research Center, Ministry of Education, Key Laboratory of Crop Heterosis of Shaanxi Province, Northwest A & F University, Yangling, 712100 Shaanxi China
| | - Gaisheng Zhang
- College of Agronomy, National Yangling Agriculture Biotechnology & Breeding Center, Yangling Branch of State Wheat Improvement Centre, Wheat Breeding Engineering Research Center, Ministry of Education, Key Laboratory of Crop Heterosis of Shaanxi Province, Northwest A & F University, Yangling, 712100 Shaanxi China
| | - Yulong Song
- College of Agronomy, National Yangling Agriculture Biotechnology & Breeding Center, Yangling Branch of State Wheat Improvement Centre, Wheat Breeding Engineering Research Center, Ministry of Education, Key Laboratory of Crop Heterosis of Shaanxi Province, Northwest A & F University, Yangling, 712100 Shaanxi China
| | - Zheng Li
- College of Agronomy, National Yangling Agriculture Biotechnology & Breeding Center, Yangling Branch of State Wheat Improvement Centre, Wheat Breeding Engineering Research Center, Ministry of Education, Key Laboratory of Crop Heterosis of Shaanxi Province, Northwest A & F University, Yangling, 712100 Shaanxi China
| | - Shoucai Ma
- College of Agronomy, National Yangling Agriculture Biotechnology & Breeding Center, Yangling Branch of State Wheat Improvement Centre, Wheat Breeding Engineering Research Center, Ministry of Education, Key Laboratory of Crop Heterosis of Shaanxi Province, Northwest A & F University, Yangling, 712100 Shaanxi China
| | - Na Niu
- College of Agronomy, National Yangling Agriculture Biotechnology & Breeding Center, Yangling Branch of State Wheat Improvement Centre, Wheat Breeding Engineering Research Center, Ministry of Education, Key Laboratory of Crop Heterosis of Shaanxi Province, Northwest A & F University, Yangling, 712100 Shaanxi China
| | - Junwei Wang
- College of Agronomy, National Yangling Agriculture Biotechnology & Breeding Center, Yangling Branch of State Wheat Improvement Centre, Wheat Breeding Engineering Research Center, Ministry of Education, Key Laboratory of Crop Heterosis of Shaanxi Province, Northwest A & F University, Yangling, 712100 Shaanxi China
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24
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Sheng XG, Zhao ZQ, Wang JS, Yu HF, Shen YS, Zeng XY, Gu HH. Genome wide analysis of MADS-box gene family in Brassica oleracea reveals conservation and variation in flower development. BMC PLANT BIOLOGY 2019; 19:106. [PMID: 30890145 PMCID: PMC6425688 DOI: 10.1186/s12870-019-1717-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 03/12/2019] [Indexed: 05/26/2023]
Abstract
BACKGROUND MADS-box genes play important roles in vegetative growth and reproductive development and are essential for the correct development of plants (particularly inflorescences, flowers, and fruits). However, this gene family has not been identified nor their functions analyzed in Brassica oleracea. RESULTS In this study, we performed a whole-genome survey of the complete set of MADS-box genes in B. oleracea. In total, 91 MADS-box transcription factors (TFs) were identified and categorized as type I (Mα, Mβ, Mγ) and type II (MIKCC, MIKC*) groups according to the phylogeny and gene structure analysis. Among these genes, 59 were randomly distributed on 9 chromosomes, while the other 23 were assigned to 19 scaffolds and 9 genes from NCBI had no location information. Both RNA-sequencing and quantitative real-time-PCR analysis suggested that MIKC genes had more active and complex expression patterns than M type genes and most type II genes showed high flowering-related expression profiles. Additional quantitative real-time-PCR analysis of pedicel and four flower whorls revealed that the structure of the B.oleracea MIKC genes was conserved, but their homologues showed variable expression patterns compared to those in Arabidopsis thaliana. CONCLUSION This paper gives a detailed overview of the BolMADS genes and their expression patterns. The results obtained in this study provide useful information for understanding the molecular regulation of flower development and further functional characterization of MADS-box genes in B. oleracea.
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Affiliation(s)
- Xiao-Guang Sheng
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021 China
| | - Zhen-Qing Zhao
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021 China
| | - Jian-Sheng Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021 China
| | - Hui-Fang Yu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021 China
| | - Yu-Sen Shen
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021 China
| | - Xiao-Yuan Zeng
- Agricultural Technology Promotion Station of Taizhou, Taizhou, 318000 China
| | - Hong-Hui Gu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021 China
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25
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Theune ML, Bloss U, Brand LH, Ladwig F, Wanke D. Phylogenetic Analyses and GAGA-Motif Binding Studies of BBR/BPC Proteins Lend to Clues in GAGA-Motif Recognition and a Regulatory Role in Brassinosteroid Signaling. FRONTIERS IN PLANT SCIENCE 2019; 10:466. [PMID: 31057577 PMCID: PMC6477699 DOI: 10.3389/fpls.2019.00466] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 03/28/2019] [Indexed: 05/21/2023]
Abstract
Plant GAGA-motif binding factors are encoded by the BARLEY B RECOMBINANT / BASIC PENTACYSTEINE (BBR/BPC) family, which fulfill indispensable functions in growth and development. BBR/BPC proteins control flower development, size of the stem cell niche and seed development through transcriptional regulation of homeotic transcription factor genes. They are responsible for the context dependent recruitment of Polycomb repressive complexes (PRC) or other repressive proteins to GAGA-motifs, which are contained in Polycomb repressive DNA-elements (PREs). Hallmark of the protein family is the highly conserved BPC domain, which is required for DNA binding. Here we study the evolution and diversification of the BBR/BPC family and its DNA-binding domain. Our analyses supports a further division of the family into four main groups (I-IV) and several subgroups, to resolve a strict monophyletic descent of the BPC domain. We prove a polyphyletic origin for group III proteins, which evolved from group I and II members through extensive loss of domains in the N-terminus. Conserved motif searches lend to the identification of a WAR/KHGTN consensus and a TIR/K motif at the very C-terminus of the BPC-domain. We could show by DPI-ELISA that this signature is required for DNA-binding in AtBPC1. Additional binding studies with AtBPC1, AtBPC6 and mutated oligonucleotides consolidated the binding to GAGA tetramers. To validate these findings, we used previously published ChIP-seq data from GFP-BPC6. We uncovered that many genes of the brassinosteroid signaling pathway are targeted by AtBPC6. Consistently, bpc6, bpc4 bpc6, and lhp1 bpc4 bpc4 mutants display brassinosteroid-dependent root growth phenotypes. Both, a function in brassinosteroid signaling and our phylogenetic data supports a link between BBR/BPC diversification in the land plant lineage and the complexity of flower and seed plant evolution.
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Affiliation(s)
- Marius L. Theune
- Molecular Plant Biology, Saarland University, Saarbrücken, Germany
| | - Ulrich Bloss
- ZMBP-Plant Physiology, Tübingen University, Tübingen, Germany
| | - Luise H. Brand
- ZMBP-Plant Physiology, Tübingen University, Tübingen, Germany
| | | | - Dierk Wanke
- Molecular Plant Biology, Saarland University, Saarbrücken, Germany
- ZMBP-Plant Physiology, Tübingen University, Tübingen, Germany
- *Correspondence: Dierk Wanke,
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26
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Feltes BC, Grisci BI, Poloni JDF, Dorn M. Perspectives and applications of machine learning for evolutionary developmental biology. Mol Omics 2018; 14:289-306. [PMID: 30168572 DOI: 10.1039/c8mo00111a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Evolutionary Developmental Biology (Evo-Devo) is an ever-expanding field that aims to understand how development was modulated by the evolutionary process. In this sense, "omic" studies emerged as a powerful ally to unravel the molecular mechanisms underlying development. In this scenario, bioinformatics tools become necessary to analyze the growing amount of information. Among computational approaches, machine learning stands out as a promising field to generate knowledge and trace new research perspectives for bioinformatics. In this review, we aim to expose the current advances of machine learning applied to evolution and development. We draw clear perspectives and argue how evolution impacted machine learning techniques.
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Affiliation(s)
- Bruno César Feltes
- Institute of Informatics, Federal University of Rio Grande do Sul, Porto Alegre, Brazil.
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27
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Hugouvieux V, Zubieta C. MADS transcription factors cooperate: complexities of complex formation. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:1821-1823. [PMID: 29635482 PMCID: PMC6019057 DOI: 10.1093/jxb/ery099] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
This article comments on: Rümpler F, Theißen G, Melzer R. 2018. A conserved leucine zipper-like motif accounts for strong tetramerization capabilities of SEPALLATA-like MADS-domain transcription factors. Journal of Experimental Botany 69, 1943–1954.
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Affiliation(s)
- Veronique Hugouvieux
- Laboratoire de Physiologie Cellulaire & Végétale, CEA, Univ. Grenoble Alpes, CNRS, INRA, BIG, Grenoble, France
| | - Chloe Zubieta
- Laboratoire de Physiologie Cellulaire & Végétale, CEA, Univ. Grenoble Alpes, CNRS, INRA, BIG, Grenoble, France
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28
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Schilling S, Pan S, Kennedy A, Melzer R. MADS-box genes and crop domestication: the jack of all traits. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:1447-1469. [PMID: 29474735 DOI: 10.1093/jxb/erx479] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 01/10/2018] [Indexed: 05/25/2023]
Abstract
MADS-box genes are key regulators of virtually every aspect of plant reproductive development. They play especially prominent roles in flowering time control, inflorescence architecture, floral organ identity determination, and seed development. The developmental and evolutionary importance of MADS-box genes is widely acknowledged. However, their role during flowering plant domestication is less well recognized. Here, we provide an overview illustrating that MADS-box genes have been important targets of selection during crop domestication and improvement. Numerous examples from a diversity of crop plants show that various developmental processes have been shaped by allelic variations in MADS-box genes. We propose that new genomic and genome editing resources provide an excellent starting point for further harnessing the potential of MADS-box genes to improve a variety of reproductive traits in crops. We also suggest that the biophysics of MADS-domain protein-protein and protein-DNA interactions, which is becoming increasingly well characterized, makes them especially suited to exploit coding sequence variations for targeted breeding approaches.
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Affiliation(s)
- Susanne Schilling
- School of Biology and Environmental Science, University College Dublin, Irel
| | - Sirui Pan
- School of Biology and Environmental Science, University College Dublin, Irel
| | - Alice Kennedy
- School of Biology and Environmental Science, University College Dublin, Irel
| | - Rainer Melzer
- School of Biology and Environmental Science, University College Dublin, Irel
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29
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Theißen G, Melzer R, Rümpler F. MADS-domain transcription factors and the floral quartet model of flower development: linking plant development and evolution. Development 2017; 143:3259-71. [PMID: 27624831 DOI: 10.1242/dev.134080] [Citation(s) in RCA: 238] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The floral quartet model of floral organ specification poses that different tetramers of MIKC-type MADS-domain transcription factors control gene expression and hence the identity of floral organs during development. Here, we provide a brief history of the floral quartet model and review several lines of recent evidence that support the model. We also describe how the model has been used in contemporary developmental and evolutionary biology to shed light on enigmatic topics such as the origin of land and flowering plants. Finally, we suggest a novel hypothesis describing how floral quartet-like complexes may interact with chromatin during target gene activation and repression.
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Affiliation(s)
- Günter Theißen
- Department of Genetics, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Rainer Melzer
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Florian Rümpler
- Department of Genetics, Friedrich Schiller University Jena, 07743 Jena, Germany
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30
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MacKintosh C, Ferrier DEK. Recent advances in understanding the roles of whole genome duplications in evolution. F1000Res 2017; 6:1623. [PMID: 28928963 PMCID: PMC5590085 DOI: 10.12688/f1000research.11792.2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/23/2018] [Indexed: 01/21/2023] Open
Abstract
Ancient whole-genome duplications (WGDs)- paleopolyploidy events-are key to solving Darwin's 'abominable mystery' of how flowering plants evolved and radiated into a rich variety of species. The vertebrates also emerged from their invertebrate ancestors via two WGDs, and genomes of diverse gymnosperm trees, unicellular eukaryotes, invertebrates, fishes, amphibians and even a rodent carry evidence of lineage-specific WGDs. Modern polyploidy is common in eukaryotes, and it can be induced, enabling mechanisms and short-term cost-benefit assessments of polyploidy to be studied experimentally. However, the ancient WGDs can be reconstructed only by comparative genomics: these studies are difficult because the DNA duplicates have been through tens or hundreds of millions of years of gene losses, mutations, and chromosomal rearrangements that culminate in resolution of the polyploid genomes back into diploid ones (rediploidisation). Intriguing asymmetries in patterns of post-WGD gene loss and retention between duplicated sets of chromosomes have been discovered recently, and elaborations of signal transduction systems are lasting legacies from several WGDs. The data imply that simpler signalling pathways in the pre-WGD ancestors were converted via WGDs into multi-stranded parallelised networks. Genetic and biochemical studies in plants, yeasts and vertebrates suggest a paradigm in which different combinations of sister paralogues in the post-WGD regulatory networks are co-regulated under different conditions. In principle, such networks can respond to a wide array of environmental, sensory and hormonal stimuli and integrate them to generate phenotypic variety in cell types and behaviours. Patterns are also being discerned in how the post-WGD signalling networks are reconfigured in human cancers and neurological conditions. It is fascinating to unpick how ancient genomic events impact on complexity, variety and disease in modern life.
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Affiliation(s)
- Carol MacKintosh
- Division of Cell and Developmental Biology, University of Dundee, Dundee, Scotland, DD1 5EH, UK
| | - David E K Ferrier
- The Scottish Oceans Institute, University of St Andrews, Scotland, KY16 8LB, UK
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31
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Protein interaction evolution from promiscuity to specificity with reduced flexibility in an increasingly complex network. Sci Rep 2017; 7:44948. [PMID: 28337996 PMCID: PMC5364480 DOI: 10.1038/srep44948] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 02/16/2017] [Indexed: 12/27/2022] Open
Abstract
A key question regarding protein evolution is how proteins adapt to the dynamic environment in which they function and how in turn their evolution shapes the protein interaction network. We used extant and resurrected ancestral plant MADS-domain transcription factors to understand how SEPALLATA3, a protein with hub and glue properties, evolved and takes part in network organization. Although the density of dimeric interactions was saturated in the network, many new interactions became mediated by SEPALLATA3 after a whole genome triplication event. By swapping SEPALLATA3 and its ancestors between dimeric networks of different ages, we found that the protein lost the capacity of promiscuous interaction and acquired specificity in evolution. This was accompanied with constraints on conformations through proline residue accumulation, which made the protein less flexible. SHORT VEGETATIVE PHASE on the other hand (non-hub) was able to gain protein-protein interactions due to a C-terminal domain insertion, allowing for a larger interaction interface. These findings illustrate that protein interaction evolution occurs at the level of conformational dynamics, when the binding mechanism concerns an induced fit or conformational selection. Proteins can evolve towards increased specificity with reduced flexibility when the complexity of the protein interaction network requires specificity.
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32
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Yang T, Du MF, Guo YH, Liu X. Two LEAFY homologs ILFY1 and ILFY2 control reproductive and vegetative developments in Isoetes L. Sci Rep 2017; 7:225. [PMID: 28331204 PMCID: PMC5412651 DOI: 10.1038/s41598-017-00297-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 02/17/2017] [Indexed: 11/09/2022] Open
Abstract
LEAFY (LFY) is a plant-specific transcription factor, which is found in algae and all land plants. LFY homologs exert ancestral roles in regulating cell division and obtain novel functions to control floral identity. Isoetes L. is an ancient genus of heterosporous lycophytes. However, characters about LFY homologs in lycophytes remain poorly investigated. In this study, two LFY homologs, ILFY1 and ILFY2, were cloned from five Isoetes species, including I. hypsophila, I. yunguiensis, I. sinensis, I. orientalis, and I. taiwanensis. The full length of ILFY1 was 1449-1456 bp with an open reading frame (ORF) of 927-936 bp. The full length of ILFY2 was 1768 bp with ORF of 726 bp. Phylogenetic tree revealed that ILFY1 and ILFY2 were separated into two clades, and I. hypsophila were separated with the others. Expression analysis demonstrated that IsLFY1 and IsLFY2 for I. sinensis did not show functional diversity. The two transcripts were similarly accumulated in both vegetative and reproductive tissues and highly expressed in juvenile tissues. In addition, the IsLFY1 and IsLFY2 transgenic Arabidopsis similarly did not promote precocious flowering, and they were inactive to rescue lfy mutants. The results facilitate general understandings about the characteristics of LFY in Isoetes and evolutionary process.
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Affiliation(s)
- Tao Yang
- Laboratory of Plant Systematics and Evolutionary Biology, College of Life Science, Wuhan University, Wuhan, Hubei, China
| | - Ming-Fang Du
- Laboratory of Plant Systematics and Evolutionary Biology, College of Life Science, Wuhan University, Wuhan, Hubei, China
| | - You-Hao Guo
- Laboratory of Plant Systematics and Evolutionary Biology, College of Life Science, Wuhan University, Wuhan, Hubei, China.
| | - Xing Liu
- Laboratory of Plant Systematics and Evolutionary Biology, College of Life Science, Wuhan University, Wuhan, Hubei, China.
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33
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Lombardo F, Kuroki M, Yao S, Shimizu H, Ikegaya T, Kimizu M, Ohmori S, Akiyama T, Hayashi T, Yamaguchi T, Koike S, Yatou O, Yoshida H. The superwoman1-cleistogamy2 mutant is a novel resource for gene containment in rice. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:97-106. [PMID: 27336225 PMCID: PMC5253472 DOI: 10.1111/pbi.12594] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 06/09/2016] [Accepted: 06/18/2016] [Indexed: 05/31/2023]
Abstract
Outcrossing between cultivated plants and their related wild species may result in the loss of favourable agricultural traits in the progeny or escape of transgenes in the environment. Outcrossing can be physically prevented by using cleistogamous (i.e. closed-flower) plants. In rice, flower opening is dependent on the mechanical action of fleshy organs called lodicules, which are generally regarded as the grass petal equivalents. Lodicule identity and development are specified by the action of protein complexes involving the SPW1 and OsMADS2 transcription factors. In the superwoman1-cleistogamy1 (spw1-cls1) mutant, SPW1 is impaired for heterodimerization with OsMADS2 and consequently spw1-cls1 shows thin, ineffective lodicules. However, low temperatures help stabilise the mutated SPW1/OsMADS2 heterodimer and lodicule development is restored when spw1-cls1 is grown in a cold environment, resulting in the loss of the cleistogamous phenotype. To identify a novel, temperature-stable cleistogamous allele of SPW1, targeted and random mutations were introduced into the SPW1 sequence and their effects over SPW1/OsMADS2 dimer formation were assessed in yeast two-hybrid experiments. In parallel, a novel cleistogamous allele of SPW1 called spw1-cls2 was isolated from a forward genetic screen. In spw1-cls2, a mutation leading to a change of an amino acid involved in DNA binding by the transcription factor was identified. Fertility of spw1-cls2 is somewhat decreased under low temperatures but unlike for spw1-cls1, the cleistogamous phenotype is maintained, making the line a safer and valuable genetic resource for gene containment.
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Affiliation(s)
- Fabien Lombardo
- Division of Applied GeneticsInstitute of Agrobiological SciencesNational Agriculture and Food Research Organization (NARO)IbarakiJapan
| | - Makoto Kuroki
- Division of Crop Breeding ResearchHokkaido Agricultural Research CenterNAROHokkaidoJapan
- Division of Rice ResearchInstitute of Crop ScienceNAROIbarakiJapan
| | - Shan‐Guo Yao
- Division of Crop DevelopmentCentral Region Agricultural Research CenterNARONiigataJapan
- Present address: Center for Genome BiologyInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing100101China
| | - Hiroyuki Shimizu
- Division of Crop Breeding ResearchHokkaido Agricultural Research CenterNAROHokkaidoJapan
| | - Tomohito Ikegaya
- Division of Crop Breeding ResearchHokkaido Agricultural Research CenterNAROHokkaidoJapan
| | - Mayumi Kimizu
- Division of Crop DevelopmentCentral Region Agricultural Research CenterNARONiigataJapan
| | - Shinnosuke Ohmori
- Division of Crop DevelopmentCentral Region Agricultural Research CenterNARONiigataJapan
| | - Takashi Akiyama
- Division of Applied GeneticsInstitute of Agrobiological SciencesNational Agriculture and Food Research Organization (NARO)IbarakiJapan
| | - Takami Hayashi
- Division of Crop Breeding ResearchHokkaido Agricultural Research CenterNAROHokkaidoJapan
- Division of Agro‐Production Technologies and Management ResearchTohoku Agricultural Research CenterNAROIwateJapan
| | - Tomoya Yamaguchi
- Division of Agro‐Production Technologies and Management ResearchTohoku Agricultural Research CenterNAROIwateJapan
- Present address: Agriculture, Forestry and Fisheries Research CouncilMinistry of Agriculture, Forestry and Fisheries of JapanTokyo100‐8950Japan
| | - Setsuo Koike
- Division of Agro‐Production Technologies and Management ResearchTohoku Agricultural Research CenterNAROIwateJapan
| | - Osamu Yatou
- Division of Crop DevelopmentCentral Region Agricultural Research CenterNARONiigataJapan
| | - Hitoshi Yoshida
- Division of Applied GeneticsInstitute of Agrobiological SciencesNational Agriculture and Food Research Organization (NARO)IbarakiJapan
- Division of Crop DevelopmentCentral Region Agricultural Research CenterNARONiigataJapan
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34
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Ren Z, Yu D, Yang Z, Li C, Qanmber G, Li Y, Li J, Liu Z, Lu L, Wang L, Zhang H, Chen Q, Li F, Yang Z. Genome-Wide Identification of the MIKC-Type MADS-Box Gene Family in Gossypium hirsutum L. Unravels Their Roles in Flowering. FRONTIERS IN PLANT SCIENCE 2017; 8:384. [PMID: 28382045 PMCID: PMC5360754 DOI: 10.3389/fpls.2017.00384] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2016] [Accepted: 03/06/2017] [Indexed: 05/22/2023]
Abstract
Cotton is one of the major world oil crops. Cottonseed oil meets the increasing demand of fried food, ruminant feed, and renewable bio-fuels. MADS intervening keratin-like and C-terminal (MIKC)-type MADS-box genes encode transcription factors that have crucial roles in various plant developmental processes. Nevertheless, this gene family has not been characterized, nor its functions investigated, in cotton. Here, we performed a comprehensive analysis of MIKC-type MADS genes in the tetraploid Gossypium hirsutum L., which is the most widely cultivated cotton species. In total, 110 GhMIKC genes were identified and phylogenetically classified into 13 subfamilies. The Flowering locus C (FLC) subfamily was absent in the Gossypium hirsutum L. genome but is found in Arabidopsis and Vitis vinifera L. Among the genes, 108 were distributed across the 13 A and 12 of the D genome's chromosomes, while two were located in scaffolds. GhMIKCs within subfamilies displayed similar exon/intron characteristics and conserved motif compositions. According to RNA-sequencing, most MIKC genes exhibited high flowering-associated expression profiles. A quantitative real-time PCR analysis revealed that some crucial MIKC genes determined the identities of the five flower organs. Furthermore, the overexpression of GhAGL17.9 in Arabidopsis caused an early flowering phenotype. Meanwhile, the expression levels of the flowering-related genes CONSTANS (CO), LEAFY (LFY) and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1) were significantly increased in these lines. These results provide useful information for future studies of GhMIKCs' regulation of cotton flowering.
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Affiliation(s)
- Zhongying Ren
- Xinjiang Research Base, State Key Laboratory of Cotton Biology, Xinjiang Agriculture UniversityUrumqi, China
- Institute of Cotton Research, Chinese Academy of Agricultural SciencesAnyang, China
| | - Daoqian Yu
- Xinjiang Research Base, State Key Laboratory of Cotton Biology, Xinjiang Agriculture UniversityUrumqi, China
- Institute of Cotton Research, Chinese Academy of Agricultural SciencesAnyang, China
| | - Zhaoen Yang
- Xinjiang Research Base, State Key Laboratory of Cotton Biology, Xinjiang Agriculture UniversityUrumqi, China
- Institute of Cotton Research, Chinese Academy of Agricultural SciencesAnyang, China
| | - Changfeng Li
- Institute of Cotton Research, Chinese Academy of Agricultural SciencesAnyang, China
- Cotton Research Institute, Anhui Academy of Agricultural SciencesHefei, China
| | - Ghulam Qanmber
- Institute of Cotton Research, Chinese Academy of Agricultural SciencesAnyang, China
| | - Yi Li
- Institute of Cotton Research, Chinese Academy of Agricultural SciencesAnyang, China
| | - Jie Li
- Institute of Cotton Research, Chinese Academy of Agricultural SciencesAnyang, China
| | - Zhao Liu
- Institute of Cotton Research, Chinese Academy of Agricultural SciencesAnyang, China
| | - Lili Lu
- Institute of Cotton Research, Chinese Academy of Agricultural SciencesAnyang, China
| | - Lingling Wang
- Institute of Cotton Research, Chinese Academy of Agricultural SciencesAnyang, China
| | - Hua Zhang
- Xinjiang Research Base, State Key Laboratory of Cotton Biology, Xinjiang Agriculture UniversityUrumqi, China
| | - Quanjia Chen
- Xinjiang Research Base, State Key Laboratory of Cotton Biology, Xinjiang Agriculture UniversityUrumqi, China
| | - Fuguang Li
- Xinjiang Research Base, State Key Laboratory of Cotton Biology, Xinjiang Agriculture UniversityUrumqi, China
- Institute of Cotton Research, Chinese Academy of Agricultural SciencesAnyang, China
- *Correspondence: Zuoren Yang
| | - Zuoren Yang
- Xinjiang Research Base, State Key Laboratory of Cotton Biology, Xinjiang Agriculture UniversityUrumqi, China
- Institute of Cotton Research, Chinese Academy of Agricultural SciencesAnyang, China
- Fuguang Li
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35
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Thomson B, Zheng B, Wellmer F. Floral Organogenesis: When Knowing Your ABCs Is Not Enough. PLANT PHYSIOLOGY 2017; 173:56-64. [PMID: 27789738 PMCID: PMC5210729 DOI: 10.1104/pp.16.01288] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 10/24/2016] [Indexed: 05/18/2023]
Abstract
The use of new experimental approaches enhances the understanding of floral organogenesis.
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Affiliation(s)
- Bennett Thomson
- Smurfit Institute of Genetics, Trinity College, Dublin 2, Ireland
| | - Beibei Zheng
- Smurfit Institute of Genetics, Trinity College, Dublin 2, Ireland
| | - Frank Wellmer
- Smurfit Institute of Genetics, Trinity College, Dublin 2, Ireland
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36
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Davis TL, Rebay I. Master regulators in development: Views from the Drosophila retinal determination and mammalian pluripotency gene networks. Dev Biol 2016; 421:93-107. [PMID: 27979656 DOI: 10.1016/j.ydbio.2016.12.005] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 12/03/2016] [Accepted: 12/03/2016] [Indexed: 02/07/2023]
Abstract
Among the mechanisms that steer cells to their correct fate during development, master regulatory networks are unique in their sufficiency to trigger a developmental program outside of its normal context. In this review we discuss the key features that underlie master regulatory potency during normal and ectopic development, focusing on two examples, the retinal determination gene network (RDGN) that directs eye development in the fruit fly and the pluripotency gene network (PGN) that maintains cell fate competency in the early mammalian embryo. In addition to the hierarchical transcriptional activation, extensive positive transcriptional feedback, and cooperative protein-protein interactions that enable master regulators to override competing cellular programs, recent evidence suggests that network topology must also be dynamic, with extensive rewiring of the interactions and feedback loops required to navigate the correct sequence of developmental transitions to reach a final fate. By synthesizing the in vivo evidence provided by the RDGN with the extensive mechanistic insight gleaned from the PGN, we highlight the unique regulatory capabilities that continual reorganization into new hierarchies confers on master control networks. We suggest that deeper understanding of such dynamics should be a priority, as accurate spatiotemporal remodeling of network topology will undoubtedly be essential for successful stem cell based therapeutic efforts.
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Affiliation(s)
- Trevor L Davis
- Committee on Development, Regeneration, and Stem Cell Biology, University of Chicago, Chicago, IL 60637, USA
| | - Ilaria Rebay
- Committee on Development, Regeneration, and Stem Cell Biology, University of Chicago, Chicago, IL 60637, USA; Ben May Department for Cancer Research, University of Chicago, Chicago, IL 60637, USA.
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