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Fan Y, Wan X, Zhang X, Zhang J, Zheng C, Yang Q, Yang L, Li X, Feng L, Zou L, Xiang D. GRAS gene family in rye (Secale cereale L.): genome-wide identification, phylogeny, evolutionary expansion and expression analyses. BMC PLANT BIOLOGY 2024; 24:46. [PMID: 38216860 PMCID: PMC10787399 DOI: 10.1186/s12870-023-04674-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 12/08/2023] [Indexed: 01/14/2024]
Abstract
BACKGROUND The GRAS transcription factor family plays a crucial role in various biological processes in different plants, such as tissue development, fruit maturation, and environmental stress. However, the GRAS family in rye has not been systematically analyzed yet. RESULTS In this study, 67 GRAS genes in S. cereale were identified and named based on the chromosomal location. The gene structures, conserved motifs, cis-acting elements, gene replications, and expression patterns were further analyzed. These 67 ScGRAS members are divided into 13 subfamilies. All members include the LHR I, VHIID, LHR II, PFYRE, and SAW domains, and some nonpolar hydrophobic amino acid residues may undergo cross-substitution in the VHIID region. Interested, tandem duplications may have a more important contribution, which distinguishes them from other monocotyledonous plants. To further investigate the evolutionary relationship of the GRAS family, we constructed six comparative genomic maps of homologous genes between rye and different representative monocotyledonous and dicotyledonous plants. The response characteristics of 19 ScGRAS members from different subfamilies to different tissues, grains at filling stages, and different abiotic stresses of rye were systematically analyzed. Paclobutrazol, a triazole-based plant growth regulator, controls plant tissue and grain development by inhibiting gibberellic acid (GA) biosynthesis through the regulation of DELLA proteins. Exogenous spraying of paclobutrazol significantly reduced the plant height but was beneficial for increasing the weight of 1000 grains of rye. Treatment with paclobutrazol, significantly reduced gibberellin levels in grain in the filling period, caused significant alteration in the expression of the DELLA subfamily gene members. Furthermore, our findings with respect to genes, ScGRAS46 and ScGRAS60, suggest that these two family members could be further used for functional characterization studies in basic research and in breeding programmes for crop improvement. CONCLUSIONS We identified 67 ScGRAS genes in rye and further analysed the evolution and expression patterns of the encoded proteins. This study will be helpful for further analysing the functional characteristics of ScGRAS genes.
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Affiliation(s)
- Yu Fan
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, College of Food and Biological engineering, Chengdu University, Longquanyi District, Chengdu, 610106, Sichuan Province, P.R. China
| | - Xianqi Wan
- Sichuan Academy of Agricultural Machinery Science, Chengdu, 610011, P.R. China
| | - Xin Zhang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, College of Food and Biological engineering, Chengdu University, Longquanyi District, Chengdu, 610106, Sichuan Province, P.R. China
| | - Jieyu Zhang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, College of Food and Biological engineering, Chengdu University, Longquanyi District, Chengdu, 610106, Sichuan Province, P.R. China
| | - Chunyu Zheng
- College of Food Science and Engineering, Xinjiang Institute of Technology, Aksu, 843100, P.R. China
| | - Qiaohui Yang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, College of Food and Biological engineering, Chengdu University, Longquanyi District, Chengdu, 610106, Sichuan Province, P.R. China
| | - Li Yang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, College of Food and Biological engineering, Chengdu University, Longquanyi District, Chengdu, 610106, Sichuan Province, P.R. China
| | - Xiaolong Li
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, College of Food and Biological engineering, Chengdu University, Longquanyi District, Chengdu, 610106, Sichuan Province, P.R. China
| | - Liang Feng
- Chengdu Institute of Food Inspection, Chengdu, 610000, P.R. China
| | - Liang Zou
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, College of Food and Biological engineering, Chengdu University, Longquanyi District, Chengdu, 610106, Sichuan Province, P.R. China.
| | - Dabing Xiang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, College of Food and Biological engineering, Chengdu University, Longquanyi District, Chengdu, 610106, Sichuan Province, P.R. China.
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Yang Y, Agassin RH, Ji K. Transcriptome-Wide Identification of the GRAS Transcription Factor Family in Pinus massoniana and Its Role in Regulating Development and Stress Response. Int J Mol Sci 2023; 24:10690. [PMID: 37445868 DOI: 10.3390/ijms241310690] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/20/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023] Open
Abstract
Pinus massoniana is a species used in afforestation and has high economic, ecological, and therapeutic significance. P. massoniana experiences a variety of biotic and abiotic stresses, and thus presents a suitable model for studying how woody plants respond to such stress. Numerous families of transcription factors are involved in the research of stress resistance, with the GRAS family playing a significant role in plant development and stress response. Though GRASs have been well explored in various plant species, much research remains to be undertaken on the GRAS family in P. massoniana. In this study, 21 PmGRASs were identified in the P. massoniana transcriptome. P. massoniana and Arabidopsis thaliana phylogenetic analyses revealed that the PmGRAS family can be separated into nine subfamilies. The results of qRT-PCR and transcriptome analyses under various stress and hormone treatments reveal that PmGRASs, particularly PmGRAS9, PmGRAS10 and PmGRAS17, may be crucial for stress resistance. The majority of PmGRASs were significantly expressed in needles and may function at multiple locales and developmental stages, according to tissue-specific expression analyses. Furthermore, the DELLA subfamily members PmGRAS9 and PmGRAS17 were nuclear localization proteins, while PmGRAS9 demonstrated transcriptional activation activity in yeast. The results of this study will help explore the relevant factors regulating the development of P. massoniana, improve stress resistance and lay the foundation for further identification of the biological functions of PmGRASs.
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Affiliation(s)
- Ye Yang
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Romaric Hippolyte Agassin
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Kongshu Ji
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
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Jardinaud MF, Carrere S, Gourion B, Gamas P. Symbiotic Nodule Development and Efficiency in the Medicago truncatula Mtefd-1 Mutant Is Highly Dependent on Sinorhizobium Strains. PLANT & CELL PHYSIOLOGY 2023; 64:27-42. [PMID: 36151948 DOI: 10.1093/pcp/pcac134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/22/2022] [Accepted: 09/23/2022] [Indexed: 06/16/2023]
Abstract
Symbiotic nitrogen fixation (SNF) can play a key role in agroecosystems to reduce the negative impact of nitrogen fertilizers. Its efficiency is strongly affected by the combination of bacterial and plant genotypes, but the mechanisms responsible for the differences in the efficiency of rhizobium strains are not well documented. In Medicago truncatula, SNF has been mostly studied using model systems, such as M. truncatula A17 in interaction with Sinorhizobium meliloti Sm2011. Here we analyzed both the wild-type (wt) A17 and the Mtefd-1 mutant in interaction with five S. meliloti and two Sinorhizobium medicae strains. ETHYLENE RESPONSE FACTOR REQUIRED FOR NODULE DIFFERENTIATION (MtEFD) encodes a transcription factor, which contributes to the control of nodule number and differentiation in M. truncatula. We found that, in contrast to Sm2011, four strains induce functional (Fix+) nodules in Mtefd-1, although less efficient for SNF than in wt A17. In contrast, the Mtefd-1 hypernodulation phenotype is not strain-dependent. We compared the plant nodule transcriptomes in response to SmBL225C, a highly efficient strain with A17, versus Sm2011, in wt and Mtefd-1 backgrounds. This revealed faster nodule development with SmBL225C and early nodule senescence with Sm2011. These RNA sequencing analyses allowed us to identify candidate plant factors that could drive the differential nodule phenotype. In conclusion, this work shows the value of having a set of rhizobium strains to fully evaluate the biological importance of a plant symbiotic gene.
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Affiliation(s)
- Marie-Françoise Jardinaud
- LIPME, INRAE, CNRS, Université de Toulouse, 24 Chemin de Borde Rouge, Auzeville-Tolosane 31320, France
| | - Sebastien Carrere
- LIPME, INRAE, CNRS, Université de Toulouse, 24 Chemin de Borde Rouge, Auzeville-Tolosane 31320, France
| | - Benjamin Gourion
- LIPME, INRAE, CNRS, Université de Toulouse, 24 Chemin de Borde Rouge, Auzeville-Tolosane 31320, France
| | - Pascal Gamas
- LIPME, INRAE, CNRS, Université de Toulouse, 24 Chemin de Borde Rouge, Auzeville-Tolosane 31320, France
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