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Cui Z, Wang X, Dai Y, Li Y, Ban Y, Tian W, Zhang X, Feng X, Zhang X, Jia L, He G, Sang X. Transcription factor OsNF-YC1 regulates grain size by coordinating the transcriptional activation of OsMADS1 in Oryza sativa L. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 38887937 DOI: 10.1111/tpj.16868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 04/23/2024] [Accepted: 05/23/2024] [Indexed: 06/20/2024]
Abstract
Grain weight, grain number per panicle, and the number of panicles are the three factors that determine rice (Oryza sativa L.) yield. Of these, grain weight, which not only directly determines rice yield but also influences appearance and quality, is often considered the most important for rice production. Here, we describe OsNF-YC1, a member of the NF-Y transcription factor family that regulates rice grain size. OsNF-YC1 knockout plants (osnf-yc1), obtained using CRISPR-Cas9 technology, showed reduced grain weight due to reduced width and thickness, with no change in grain length, leading to a slenderer grain shape. Downregulation of OsNF-YC1 using RNA interference resulted in similar grain phenotypes as osnf-yc1. OsNF-YC1 affects grain formation by regulating both cell proliferation and cell expansion. OsNF-YC1 localizes in both the nucleus and cytoplasm, has transcriptional activation activity at both the N-terminus and C-terminus, and is highly expressed in young panicles. OsNF-YC1 interacts with OsMADS1 both in vivo and in vitro. Further analysis showed that the histone-like structural CBFD-NFYB-HMF domain of OsNF-YC1 conserved in the OsNF-YC transcription factor family can directly interact with the MADS-box domain of OsMADS1 to enhance its transcriptional activation activity. This interaction positively regulates the expression of OsMADS55, the direct downstream target of OsMADS1. Therefore, this paper reveals a potential grain size regulation pathway controlled by an OsNF-YC1-OsMADS1-OsMADS55 module in rice.
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Affiliation(s)
- Zhibo Cui
- Chongqing Key Laboratory of Crop Molecular Improvement, Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Xiaowen Wang
- Chongqing Key Laboratory of Crop Molecular Improvement, Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Yongdong Dai
- Chongqing Key Laboratory of Crop Molecular Improvement, Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Yangyang Li
- Chongqing Key Laboratory of Crop Molecular Improvement, Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Yijie Ban
- Chongqing Key Laboratory of Crop Molecular Improvement, Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Weijiang Tian
- Chongqing Key Laboratory of Crop Molecular Improvement, Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Xiaobo Zhang
- Chongqing Key Laboratory of Crop Molecular Improvement, Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Xinyu Feng
- Chongqing Key Laboratory of Crop Molecular Improvement, Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Xuefei Zhang
- Chongqing Key Laboratory of Crop Molecular Improvement, Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Luqi Jia
- Chongqing Key Laboratory of Crop Molecular Improvement, Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Guanghua He
- Chongqing Key Laboratory of Crop Molecular Improvement, Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Xianchun Sang
- Chongqing Key Laboratory of Crop Molecular Improvement, Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, 400715, China
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2
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Zhang X, Meng W, Liu D, Pan D, Yang Y, Chen Z, Ma X, Yin W, Niu M, Dong N, Liu J, Shen W, Liu Y, Lu Z, Chu C, Qian Q, Zhao M, Tong H. Enhancing rice panicle branching and grain yield through tissue-specific brassinosteroid inhibition. Science 2024; 383:eadk8838. [PMID: 38452087 DOI: 10.1126/science.adk8838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 01/29/2024] [Indexed: 03/09/2024]
Abstract
Crop yield potential is constrained by the inherent trade-offs among traits such as between grain size and number. Brassinosteroids (BRs) promote grain size, yet their role in regulating grain number is unclear. By deciphering the clustered-spikelet rice germplasm, we show that activation of the BR catabolic gene BRASSINOSTEROID-DEFICIENT DWARF3 (BRD3) markedly increases grain number. We establish a molecular pathway in which the BR signaling inhibitor GSK3/SHAGGY-LIKE KINASE2 phosphorylates and stabilizes OsMADS1 transcriptional factor, which targets TERMINAL FLOWER1-like gene RICE CENTRORADIALIS2. The tissue-specific activation of BRD3 in the secondary branch meristems enhances panicle branching, minimizing negative effects on grain size, and improves grain yield. Our study showcases the power of tissue-specific hormonal manipulation in dismantling the trade-offs among various traits and thus unleashing crop yield potential in rice.
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Affiliation(s)
- Xiaoxing Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wenjing Meng
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Dapu Liu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Dezhuo Pan
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350018, China
| | - Yanzhao Yang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhuo Chen
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaoding Ma
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wenchao Yin
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Mei Niu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Nana Dong
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jihong Liu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Weifeng Shen
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350018, China
| | - Yuqin Liu
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350018, China
| | - Zefu Lu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chengcai Chu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qian Qian
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Mingfu Zhao
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350018, China
| | - Hongning Tong
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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3
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Wang X, Jia C, An L, Zeng J, Ren A, Han X, Wang Y, Wu S. Genome-wide identification and expression characterization of the GH3 gene family of tea plant (Camellia sinensis). BMC Genomics 2024; 25:120. [PMID: 38280985 PMCID: PMC10822178 DOI: 10.1186/s12864-024-10004-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 01/10/2024] [Indexed: 01/29/2024] Open
Abstract
To comprehensively understand the characteristics of the GH3 gene family in tea plants (Camellia sinensis), we identified 17 CsGH3 genes and analyzed their physicochemical properties, phylogenetic relationships, gene structures, promoters, and expression patterns in different tissues. The study showed that the 17 CsGH3 genes are distributed on 9 chromosomes, and based on evolutionary analysis, the CsGH3 members were divided into three subgroups. Gene duplication analysis revealed that segmental duplications have a significant impact on the amplification of CsGH3 genes. In addition, we identified and classified cis-elements in the CsGH3 gene promoters and detected elements related to plant hormone responses and non-biotic stress responses. Through expression pattern analysis, we observed tissue-specific expression of CsGH3.3 and CsGH3.10 in flower buds and roots. Moreover, based on predictive analysis of upstream regulatory transcription factors of CsGH3, we identified the potential transcriptional regulatory role of gibberellin response factor CsDELLA in CsGH3.14 and CsGH3.15. In this study, we found that CsGH3 genes are involved in a wide range of activities, such as growth and development, stress response, and transcription. This is the first report on CsGH3 genes and their potential roles in tea plants. In conclusion, these results provide a theoretical basis for elucidating the role of GH3 genes in the development of perennial woody plants and offer new insights into the synergistic effects of multiple hormones on plant growth and development in tea plants.
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Affiliation(s)
- Xinge Wang
- School of Life Science and Agriculture, Qiannan Normal University for Nationalities, Duyun, Guizhou, 558000, China
| | - Chunyu Jia
- School of Life Science and Agriculture, Qiannan Normal University for Nationalities, Duyun, Guizhou, 558000, China
| | - Lishuang An
- School of Life Science and Agriculture, Qiannan Normal University for Nationalities, Duyun, Guizhou, 558000, China
| | - Jiangyan Zeng
- School of Life Science and Agriculture, Qiannan Normal University for Nationalities, Duyun, Guizhou, 558000, China
| | - Aixia Ren
- School of Life Science and Agriculture, Qiannan Normal University for Nationalities, Duyun, Guizhou, 558000, China
| | - Xin Han
- School of Life Science and Agriculture, Qiannan Normal University for Nationalities, Duyun, Guizhou, 558000, China
| | - Yiqing Wang
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, Guizhou, 550025, China.
| | - Shuang Wu
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, Guizhou, 550025, China.
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Yao P, Zhang C, Qin T, Liu Y, Liu Z, Xie X, Bai J, Sun C, Bi Z. Comprehensive Analysis of GH3 Gene Family in Potato and Functional Characterization of StGH3.3 under Drought Stress. Int J Mol Sci 2023; 24:15122. [PMID: 37894803 PMCID: PMC10606756 DOI: 10.3390/ijms242015122] [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: 08/23/2023] [Revised: 10/05/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
As an important hormone response gene, Gretchen Hagen 3 (GH3) maintains hormonal homeostasis by conjugating excess auxin with amino acids during plant stress-related signaling pathways. GH3 genes have been characterized in many plant species, but they are rarely reported in potato. Here, 19 StGH3 genes were isolated and characterized. Phylogenetic analysis indicated that StGH3s were divided into two categories (group I and group III). Analyses of gene structure and motif composition showed that the members of a specific StGH3 subfamily are relatively conserved. Collinearity analysis of StGH3 genes in potato and other plants laid a foundation for further exploring the evolutionary characteristics of the StGH3 genes. Promoter analysis showed that most StGH3 promoters contained hormone and abiotic stress response elements. Multiple transcriptome studies indicated that some StGH3 genes were responsive to ABA, water deficits, and salt treatments. Moreover, qRT-PCR analysis indicated that StGH3 genes could be induced by phytohormones (ABA, SA, and MeJA) and abiotic stresses (water deficit, high salt, and low temperature), although with different patterns. Furthermore, transgenic tobacco with transient overexpression of the StGH3.3 gene showed positive regulation in response to water deficits by increasing proline accumulation and reducing the leaf water loss rate. These results suggested that StGH3 genes may be involved in the response to abiotic stress through hormonal signal pathways. Overall, this study provides useful insights into the evolution and function of StGH3s and lays a foundation for further study on the molecular mechanisms of StGH3s in the regulation of potato drought resistance.
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Affiliation(s)
- Panfeng Yao
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (P.Y.); (C.Z.); (T.Q.); (Y.L.); (Z.L.); (X.X.); (J.B.); (C.S.)
| | - Chunli Zhang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (P.Y.); (C.Z.); (T.Q.); (Y.L.); (Z.L.); (X.X.); (J.B.); (C.S.)
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Tianyuan Qin
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (P.Y.); (C.Z.); (T.Q.); (Y.L.); (Z.L.); (X.X.); (J.B.); (C.S.)
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Yuhui Liu
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (P.Y.); (C.Z.); (T.Q.); (Y.L.); (Z.L.); (X.X.); (J.B.); (C.S.)
| | - Zhen Liu
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (P.Y.); (C.Z.); (T.Q.); (Y.L.); (Z.L.); (X.X.); (J.B.); (C.S.)
| | - Xiaofei Xie
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (P.Y.); (C.Z.); (T.Q.); (Y.L.); (Z.L.); (X.X.); (J.B.); (C.S.)
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Jiangping Bai
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (P.Y.); (C.Z.); (T.Q.); (Y.L.); (Z.L.); (X.X.); (J.B.); (C.S.)
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Chao Sun
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (P.Y.); (C.Z.); (T.Q.); (Y.L.); (Z.L.); (X.X.); (J.B.); (C.S.)
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Zhenzhen Bi
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (P.Y.); (C.Z.); (T.Q.); (Y.L.); (Z.L.); (X.X.); (J.B.); (C.S.)
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
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5
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Adam H, Gutiérrez A, Couderc M, Sabot F, Ntakirutimana F, Serret J, Orjuela J, Tregear J, Jouannic S, Lorieux M. Genomic introgressions from African rice (Oryza glaberrima) in Asian rice (O. sativa) lead to the identification of key QTLs for panicle architecture. BMC Genomics 2023; 24:587. [PMID: 37794325 PMCID: PMC10548634 DOI: 10.1186/s12864-023-09695-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 09/21/2023] [Indexed: 10/06/2023] Open
Abstract
BACKGROUND Developing high yielding varieties is a major challenge for breeders tackling the challenges of climate change in agriculture. The panicle (inflorescence) architecture of rice is one of the key components of yield potential and displays high inter- and intra-specific variability. The genus Oryza features two different crop species: Asian rice (Oryza sativa L.) and the African rice (O. glaberrima Steud.). One of the main morphological differences between the two independently domesticated species is the structure (or complexity) of the panicle, with O. sativa displaying a highly branched panicle, which in turn produces a larger number of grains than that of O. glaberrima. The gene regulatory network that governs intra- and interspecific panicle diversity is still under-studied. RESULTS To identify genetic factors linked to panicle architecture diversity in the two species, we used a set of 60 Chromosome Segment Substitution Lines (CSSLs) issued from third generation backcross (BC3DH) and carrying genomic segments from O. glaberrima cv. MG12 in the genetic background of O. sativa Tropical Japonica cv. Caiapó. Phenotypic data were collected for rachis and primary branch length, primary, secondary and tertiary branch number and spikelet number. A total of 15 QTLs were localized on chromosomes 1, 2, 3, 7, 11 and 12, QTLs associated with enhanced secondary and tertiary branch numbers were detected in two CSSLs. Furthermore, BC4F3:5 lines carrying different combinations of substituted segments were produced to decipher the effects of the identified QTL regions on variations in panicle architecture. A detailed analysis of phenotypes versus genotypes was carried out between the two parental genomes within these regions in order to understand how O. glaberrima introgression events may lead to alterations in panicle traits. CONCLUSION Our analysis led to the detection of genomic variations between O. sativa cv. Caiapó and O. glaberrima cv. MG12 in regions associated with enhanced panicle traits in specific CSSLs. These regions contain a number of key genes that regulate panicle development in O. sativa and their interspecific genomic variations may explain the phenotypic effects observed.
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Affiliation(s)
- Hélène Adam
- UMR DIADE, University of Montpellier, IRD, Cirad, Montpellier, France.
| | | | - Marie Couderc
- UMR DIADE, University of Montpellier, IRD, Cirad, Montpellier, France
| | - François Sabot
- UMR DIADE, University of Montpellier, IRD, Cirad, Montpellier, France
| | | | - Julien Serret
- UMR DIADE, University of Montpellier, IRD, Cirad, Montpellier, France
| | - Julie Orjuela
- UMR DIADE, University of Montpellier, IRD, Cirad, Montpellier, France
| | - James Tregear
- UMR DIADE, University of Montpellier, IRD, Cirad, Montpellier, France
| | - Stefan Jouannic
- UMR DIADE, University of Montpellier, IRD, Cirad, Montpellier, France.
| | - Mathias Lorieux
- UMR DIADE, University of Montpellier, IRD, Cirad, Montpellier, France.
- Agrobiodiversity Unit, Alliance Bioversity-CIAT, Cali, Colombia.
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6
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Mao X, Zheng X, Chen W, Li C. Characterization and Gene Mapping of an Open-Glume Oryza sativa L. Mutant. Int J Mol Sci 2023; 24:12702. [PMID: 37628883 PMCID: PMC10454609 DOI: 10.3390/ijms241612702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/04/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
Floral organ development determines agricultural productivity by affecting seed development, seed quality, and final yield. In this study, we described the novel ogl mutant in rice (Oryza sativa L.), which is characterized by an open-glume phenotype, increased pistil number, reduced stamen number, decreased seed setting rate, and smaller rice grains. Genetic analysis showed that the open-glume phenotype might be controlled by a recessive qualitative trait locus. Employing bulked segregant analysis (BSA), one candidate region was identified on rice chromosome 1. The glume opening phenotype cosegregated with SNP (Chr1:1522703), which was located at the start codon of one transcript of OsJAG, resulting in partial loss of OsJAG function. cDNA analysis revealed that OsJAG encodes two transcript variants. Compared to normal plants, the expression of OsJAG.1 was upregulated in open-glume plants. When investigating the glume phenotype, we found that the expression of genes related to floral development changed greatly in open-glume plants. Taken together, this work increases our understanding of the developmental role of OsJAG in rice floral development.
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Affiliation(s)
- Xingxue Mao
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
| | - Xiaoyu Zheng
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
| | - Wenfeng Chen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
| | - Chen Li
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
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7
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Ahmed HI, Heuberger M, Schoen A, Koo DH, Quiroz-Chavez J, Adhikari L, Raupp J, Cauet S, Rodde N, Cravero C, Callot C, Lazo GR, Kathiresan N, Sharma PK, Moot I, Yadav IS, Singh L, Saripalli G, Rawat N, Datla R, Athiyannan N, Ramirez-Gonzalez RH, Uauy C, Wicker T, Tiwari VK, Abrouk M, Poland J, Krattinger SG. Einkorn genomics sheds light on history of the oldest domesticated wheat. Nature 2023; 620:830-838. [PMID: 37532937 PMCID: PMC10447253 DOI: 10.1038/s41586-023-06389-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 06/29/2023] [Indexed: 08/04/2023]
Abstract
Einkorn (Triticum monococcum) was the first domesticated wheat species, and was central to the birth of agriculture and the Neolithic Revolution in the Fertile Crescent around 10,000 years ago1,2. Here we generate and analyse 5.2-Gb genome assemblies for wild and domesticated einkorn, including completely assembled centromeres. Einkorn centromeres are highly dynamic, showing evidence of ancient and recent centromere shifts caused by structural rearrangements. Whole-genome sequencing analysis of a diversity panel uncovered the population structure and evolutionary history of einkorn, revealing complex patterns of hybridizations and introgressions after the dispersal of domesticated einkorn from the Fertile Crescent. We also show that around 1% of the modern bread wheat (Triticum aestivum) A subgenome originates from einkorn. These resources and findings highlight the history of einkorn evolution and provide a basis to accelerate the genomics-assisted improvement of einkorn and bread wheat.
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Affiliation(s)
- Hanin Ibrahim Ahmed
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Matthias Heuberger
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Adam Schoen
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Dal-Hoe Koo
- Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | | | - Laxman Adhikari
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - John Raupp
- Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Stéphane Cauet
- INRAE, CNRGV French Plant Genomic Resource Center, Castanet-Tolosan, France
| | - Nathalie Rodde
- INRAE, CNRGV French Plant Genomic Resource Center, Castanet-Tolosan, France
| | - Charlotte Cravero
- INRAE, CNRGV French Plant Genomic Resource Center, Castanet-Tolosan, France
| | - Caroline Callot
- INRAE, CNRGV French Plant Genomic Resource Center, Castanet-Tolosan, France
| | - Gerard R Lazo
- Crop Improvement and Genetics Research Unit, Western Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Albany, CA, USA
| | - Nagarajan Kathiresan
- KAUST Supercomputing Core Lab (KSL), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Parva K Sharma
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Ian Moot
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Inderjit Singh Yadav
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Lovepreet Singh
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Gautam Saripalli
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Nidhi Rawat
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Raju Datla
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Naveenkumar Athiyannan
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | | | | | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Vijay K Tiwari
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA.
| | - Michael Abrouk
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
- Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
| | - Jesse Poland
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
- Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
| | - Simon G Krattinger
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
- Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
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8
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Zhao H, Fu Y, Zhang G, Luo Y, Yang W, Liang X, Yin L, Zheng Z, Wang Y, Li Z, Zhu H, Huang J, Tan Q, Bu S, Liu G, Wang S, Liu Z. GS6.1 controls kernel size and plant architecture in rice. PLANTA 2023; 258:42. [PMID: 37432475 DOI: 10.1007/s00425-023-04201-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 07/06/2023] [Indexed: 07/12/2023]
Abstract
MAIN CONCLUSION A novel QTL GS6.1 increases yield per plant by controlling kernel size, plant architecture, and kernel filling in rice. Kernel size and plant architecture are critical agronomic traits that greatly influence kernel yield in rice. Using the single-segment substitution lines (SSSLs) with an indica cultivar Huajingxian74 as a recipient parent and American Jasmine as a donor parent, we identified a novel quantitative trait locus (QTL), named GS6.1. Near isogenic line-GS6.1 (NIL-GS6.1) produces long and narrow kernels by regulating cell length and width in the spikelet hulls, thus increasing the 1000-kernel weight. Compared with the control, the plant height, panicles per plant, panicle length, kernels per plant, secondary branches per panicle, and yield per plant of NIL-GS6.1 are increased. In addition, GS6.1 regulates the kernel filling rate. GS6.1 controls kernel size by modulating the transcription levels of part of EXPANSINs, kernel filling-related genes, and kernel size-related genes. These results indicate that GS6.1 might be beneficial for improving kernel yield and plant architecture in rice breeding by molecular design.
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Affiliation(s)
- Hongyuan Zhao
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510630, Guangdong, China
| | - Yu Fu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510630, Guangdong, China
| | - Guiquan Zhang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510630, Guangdong, China
| | - Yingqin Luo
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510630, Guangdong, China
| | - Weifeng Yang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510630, Guangdong, China
| | - Xiaoya Liang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510630, Guangdong, China
| | - Lin Yin
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510630, Guangdong, China
| | - Zhenwu Zheng
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510630, Guangdong, China
| | - Yijun Wang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510630, Guangdong, China
| | - Zhan Li
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510630, Guangdong, China
| | - Haitao Zhu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510630, Guangdong, China
| | - Jinyan Huang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510630, Guangdong, China
| | - Quanya Tan
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510630, Guangdong, China
| | - Suhong Bu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510630, Guangdong, China
| | - Guifu Liu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510630, Guangdong, China
| | - Shaokui Wang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510630, Guangdong, China.
| | - Zupei Liu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510630, Guangdong, China.
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9
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Giaume F, Bono GA, Martignago D, Miao Y, Vicentini G, Toriba T, Wang R, Kong D, Cerise M, Chirivì D, Biancucci M, Khahani B, Morandini P, Tameling W, Martinotti M, Goretti D, Coupland G, Kater M, Brambilla V, Miki D, Kyozuka J, Fornara F. Two florigens and a florigen-like protein form a triple regulatory module at the shoot apical meristem to promote reproductive transitions in rice. NATURE PLANTS 2023; 9:525-534. [PMID: 36973415 DOI: 10.1038/s41477-023-01383-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 02/22/2023] [Indexed: 06/18/2023]
Abstract
Many plant species monitor and respond to changes in day length (photoperiod) for aligning reproduction with a favourable season. Day length is measured in leaves and, when appropriate, leads to the production of floral stimuli called florigens that are transmitted to the shoot apical meristem to initiate inflorescence development1. Rice possesses two florigens encoded by HEADING DATE 3a (Hd3a) and RICE FLOWERING LOCUS T 1 (RFT1)2. Here we show that the arrival of Hd3a and RFT1 at the shoot apical meristem activates FLOWERING LOCUS T-LIKE 1 (FT-L1), encoding a florigen-like protein that shows features partially differentiating it from typical florigens. FT-L1 potentiates the effects of Hd3a and RFT1 during the conversion of the vegetative meristem into an inflorescence meristem and organizes panicle branching by imposing increasing determinacy to distal meristems. A module comprising Hd3a, RFT1 and FT-L1 thus enables the initiation and balanced progression of panicle development towards determinacy.
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Affiliation(s)
- Francesca Giaume
- Department of Biosciences, University of Milan, Milan, Italy
- Department of Agricultural and Environmental Sciences-Production, Territory, Agroenergy, University of Milan, Milan, Italy
| | - Giulia Ave Bono
- Department of Biosciences, University of Milan, Milan, Italy
| | | | - Yiling Miao
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Giulio Vicentini
- Department of Agricultural and Environmental Sciences-Production, Territory, Agroenergy, University of Milan, Milan, Italy
| | - Taiyo Toriba
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Rui Wang
- Shanghai Center for Plant Stress Biology, Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Dali Kong
- Shanghai Center for Plant Stress Biology, Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Martina Cerise
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Daniele Chirivì
- Department of Biosciences, University of Milan, Milan, Italy
| | - Marco Biancucci
- Department of Biosciences, University of Milan, Milan, Italy
| | - Bahman Khahani
- Plant Biology Graduate Program, University of Massachusetts, Amherst, MA, USA
| | - Piero Morandini
- Department of Environmental Science and Policy, University of Milan, Milan, Italy
| | | | | | - Daniela Goretti
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - George Coupland
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Martin Kater
- Department of Biosciences, University of Milan, Milan, Italy
| | - Vittoria Brambilla
- Department of Agricultural and Environmental Sciences-Production, Territory, Agroenergy, University of Milan, Milan, Italy
| | - Daisuke Miki
- Shanghai Center for Plant Stress Biology, Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Junko Kyozuka
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Fabio Fornara
- Department of Biosciences, University of Milan, Milan, Italy.
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10
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Dreni L. The ABC of Flower Development in Monocots: The Model of Rice Spikelet. Methods Mol Biol 2023; 2686:59-82. [PMID: 37540354 DOI: 10.1007/978-1-0716-3299-4_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
The initial seminal studies of flower developmental genetics were made from observations in several eudicot model species, particularly Arabidopsis and Antirrhinum. However, an increasing amount of research in monocot model and crop species is finally giving the credit that monocots deserve for their position in the evolutionary history of Angiosperms, their astonishing diversification and adaptation, their diversified floral structures, their pivotal function in most ecosystems on Earth and, finally, their importance in agriculture and farming, economy, landscaping and feeding mankind. Rice is a staple crop and the major monocot model to study the reproductive phase and flower evolution. Inspired by this, this chapter reviews a story of highly conserved functions related to the ABC model of flower development. Nevertheless, this model is complicated in rice by cases of gene neofunctionalization, like the recruitment of MADS-box genes for the development of the unique organs known as lemma and palea, subfunctionalization, and rewiring of conserved molecular pathways.
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Affiliation(s)
- Ludovico Dreni
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Valencia, Spain
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11
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Dreni L, Ferrándiz C. Tracing the Evolution of the SEPALLATA Subfamily across Angiosperms Associated with Neo- and Sub-Functionalization for Reproductive and Agronomically Relevant Traits. PLANTS (BASEL, SWITZERLAND) 2022; 11:2934. [PMID: 36365387 PMCID: PMC9656651 DOI: 10.3390/plants11212934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/26/2022] [Accepted: 10/27/2022] [Indexed: 06/16/2023]
Abstract
SEPALLATA transcription factors (SEP TFs) have been extensively studied in angiosperms as pivotal components of virtually all the MADS-box tetrameric complex master regulators of floral organ identities. However, there are published reports that suggest that some SEP members also regulate earlier reproductive events, such as inflorescence meristem determinacy and inflorescence architecture, with potential for application in breeding programs in crops. The SEP subfamily underwent a quite complex pattern of duplications during the radiation of the angiosperms. Taking advantage of the many whole genomic sequences now available, we present a revised and expanded SEP phylogeny and link it to the known functions of previously characterized genes. This snapshot supports the evidence that the major SEP3 clade is highly specialized for the specification of the three innermost floral whorls, while its sister LOFSEP clade is functionally more versatile and has been recruited for diverse roles, such as the regulation of extra-floral bract formation and inflorescence determinacy and shape. This larger pool of angiosperm SEP genes confirms previous evidence that their evolution was driven by whole-genome duplications rather than small-scale duplication events. Our work may help to identify those SEP lineages that are the best candidates for the improvement of inflorescence traits, even in far distantly related crops.
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12
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Wang Y, Bi X, Zhong J. Revisiting the origin and identity specification of the spikelet: A structural innovation in grasses (Poaceae). PLANT PHYSIOLOGY 2022; 190:60-71. [PMID: 35640983 PMCID: PMC9434286 DOI: 10.1093/plphys/kiac257] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 05/03/2022] [Indexed: 05/06/2023]
Abstract
Spikelets are highly specialized and short-lived branches and function as a constitutional unit of the complex grass inflorescences. A series of genetic, genomic, and developmental studies across different clades of the family have called for and permitted a synthesis on the regulation and evolution of spikelets, and hence inflorescence diversity. Here, we have revisited the identity specification of a spikelet, focusing on the diagnostic features of a spikelet from morphological, developmental, and molecular perspectives. Particularly, recent studies on a collection of barley (Hordeum vulgare L.), wheat (Triticum spp.), and rice (Oryza sativa L.) mutants have highlighted a set of transcription factors that are important in the control of spikelet identity and the patterning of floral parts of a spikelet. In addition, we have endeavored to clarify some puzzling issues on the (in)determinacy and modifications of spikelets over the course of evolution. Meanwhile, genomes of two sister taxa of the remaining grass species have again demonstrated the importance of genome duplication and subsequent gene losses on the evolution of spikelets. Accordingly, we argue that changes in the orthologs of spikelet-related genes could be critical for the development and evolution of the spikelet, an evolutionary innovation in the grass family. Likewise, the conceptual discussions on the regulation of a fundamental unit of compound inflorescences could be translated into other organismal groups where compound structures are similarly formed, permitting a comparative perspective on the control of biological complexity.
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13
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Mehra P, Pandey BK, Verma L, Prusty A, Singh AP, Sharma S, Malik N, Bennett MJ, Parida SK, Giri J, Tyagi AK. OsJAZ11 regulates spikelet and seed development in rice. PLANT DIRECT 2022; 6:e401. [PMID: 35582630 PMCID: PMC9090556 DOI: 10.1002/pld3.401] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 04/10/2022] [Accepted: 04/20/2022] [Indexed: 06/15/2023]
Abstract
Seed size is one of the major determinants of seed weight and eventually, crop yield. As the global population is increasing beyond the capacity of current food production, enhancing seed size is a key target for crop breeders. Despite the identification of several genes and QTLs, current understanding about the molecular regulation of seed size/weight remains fragmentary. In the present study, we report novel role of a jasmonic acid (JA) signaling repressor, OsJAZ11 controlling rice seed width and weight. Transgenic rice lines overexpressing OsJAZ11 exhibited up to a 14% increase in seed width and ~30% increase in seed weight compared to wild type (WT). Constitutive expression of OsJAZ11 dramatically influenced spikelet morphogenesis leading to extra glume-like structures, open hull, and abnormal numbers of floral organs. Furthermore, overexpression lines accumulated higher JA levels in spikelets and developing seeds. Expression studies uncovered altered expression of JA biosynthesis/signaling and MADS box genes in overexpression lines compared to WT. Yeast two-hybrid and pull-down assays revealed that OsJAZ11 interacts with OsMADS29 and OsMADS68. Remarkably, expression of OsGW7, a key negative regulator of grain size, was significantly reduced in overexpression lines. We propose that OsJAZ11 participates in the regulation of seed size and spikelet development by coordinating the expression of JA-related, OsGW7 and MADS genes.
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Affiliation(s)
- Poonam Mehra
- Department of Plant Molecular BiologyUniversity of Delhi South CampusNew DelhiIndia
- National Institute of Plant Genome ResearchNew DelhiIndia
- Plant and Crop Sciences, School of BiosciencesUniversity of NottinghamSutton BoningtonUK
| | - Bipin K. Pandey
- National Institute of Plant Genome ResearchNew DelhiIndia
- Plant and Crop Sciences, School of BiosciencesUniversity of NottinghamSutton BoningtonUK
| | - Lokesh Verma
- National Institute of Plant Genome ResearchNew DelhiIndia
| | - Ankita Prusty
- Department of Plant Molecular BiologyUniversity of Delhi South CampusNew DelhiIndia
| | - Ajit Pal Singh
- National Institute of Plant Genome ResearchNew DelhiIndia
| | - Shivam Sharma
- Department of Plant Molecular BiologyUniversity of Delhi South CampusNew DelhiIndia
| | - Naveen Malik
- National Institute of Plant Genome ResearchNew DelhiIndia
| | - Malcolm J. Bennett
- Plant and Crop Sciences, School of BiosciencesUniversity of NottinghamSutton BoningtonUK
| | | | - Jitender Giri
- National Institute of Plant Genome ResearchNew DelhiIndia
| | - Akhilesh K. Tyagi
- Department of Plant Molecular BiologyUniversity of Delhi South CampusNew DelhiIndia
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14
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Prakash S, Rai R, Zamzam M, Ahmad O, Peesapati R, Vijayraghavan U. OsbZIP47 Is an Integrator for Meristem Regulators During Rice Plant Growth and Development. FRONTIERS IN PLANT SCIENCE 2022; 13:865928. [PMID: 35498659 PMCID: PMC9044032 DOI: 10.3389/fpls.2022.865928] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 03/09/2022] [Indexed: 06/14/2023]
Abstract
Stem cell homeostasis by the WUSCHEL-CLAVATA (WUS-CLV) feedback loop is generally conserved across species; however, its links with other meristem regulators can be species-specific, rice being an example. We characterized the role of rice OsbZIP47 in vegetative and reproductive development. The knockdown (KD) transgenics showed meristem size abnormality and defects in developmental progression. The size of the shoot apical meristem (SAM) in 25-day OsbZIP47KD plants was increased as compared to the wild-type (WT). Inflorescence of KD plants showed reduced rachis length, number of primary branches, and spikelets. Florets had defects in the second and third whorl organs and increased organ number. OsbZIP47KD SAM and panicles had abnormal expression for CLAVATA peptide-like signaling genes, such as FON2-LIKE CLE PROTEIN1 (FCP1), FLORAL ORGAN NUMBER 2 (FON2), and hormone pathway genes, such as cytokinin (CK) ISOPENTEYLTRANSFERASE1 (OsIPT1), ISOPENTEYLTRANSFERASE 8 (OsIPT8), auxin biosynthesis OsYUCCA6, OsYUCCA7 and gibberellic acid (GA) biosynthesis genes, such as GRAIN NUMBER PER PANICLE1 (GNP1/OsGA20OX1) and SHORTENED BASAL INTERNODE (SBI/OsGA2ox4). The effects on ABBERANT PANICLE ORGANIZATION1 (APO1), OsMADS16, and DROOPING LEAF (DL) relate to the second and third whorl floret phenotypes in OsbZIP47KD. Protein interaction assays showed OsbZIP47 partnerships with RICE HOMEOBOX1 (OSH1), RICE FLORICULA/LEAFY (RFL), and OsMADS1 transcription factors. The meta-analysis of KD panicle transcriptomes in OsbZIP47KD, OsMADS1KD, and RFLKD transgenics, combined with global OSH1 binding sites divulge potential targets coregulated by OsbZIP47, OsMADS1, OSH1, and RFL. Further, we demonstrate that OsbZIP47 redox status affects its DNA binding affinity to a cis element in FCP1, a target locus. Taken together, we provide insights on OsbZIP47 roles in SAM development, inflorescence branching, and floret development.
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15
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Wu Q, Liu Y, Huang J. CRISPR-Cas9 Mediated Mutation in OsPUB43 Improves Grain Length and Weight in Rice by Promoting Cell Proliferation in Spikelet Hull. Int J Mol Sci 2022; 23:ijms23042347. [PMID: 35216463 PMCID: PMC8877319 DOI: 10.3390/ijms23042347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/14/2022] [Accepted: 02/15/2022] [Indexed: 12/27/2022] Open
Abstract
Grain weight, a crucial trait that determines the grain yield in rice, is influenced by grain size. Although a series of regulators that control grain size have been identified in rice, the mechanisms underlying grain development are not yet well understood. In this study, we identified OsPUB43, a U-box E3 ubiquitin ligase, as an important negative regulator determining the gain size and grain weight in rice. Phenotypes of large grain are observed in ospub43 mutants, whereas overexpression of OsPUB43 results in short grains. Scanning electron microscopy analysis reveals that OsPUB43 modulates the grain size mainly by inhibiting cell proliferation in the spikelet hull. The OsPUB43 protein is localized in the cytoplasm and nucleus. The ospub43 mutants display high sensitivity to exogenous BR, while OsPUB43-OE lines are hyposensitive to BR. Furthermore, the transient transcriptional activity assay shows that OsBZR1 can activate the expression of OsPUB43. Collectively, our results indicate that OsPUB43 negatively controls the gain size by modulating the expression of BR-responsive genes as well as MADS-box genes that are required for lemma/palea specification, suggesting that OsPUB43 has a potential valuable application in the enlargement of grain size in rice.
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16
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Zhu W, Yang L, Wu D, Meng Q, Deng X, Huang G, Zhang J, Chen X, Ferrándiz C, Liang W, Dreni L, Zhang D. Rice SEPALLATA genes OsMADS5 and OsMADS34 cooperate to limit inflorescence branching by repressing the TERMINAL FLOWER1-like gene RCN4. THE NEW PHYTOLOGIST 2022; 233:1682-1700. [PMID: 34767634 DOI: 10.1111/nph.17855] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 10/31/2021] [Indexed: 06/13/2023]
Abstract
The spatiotemporal control of meristem identity is critical for determining inflorescence architecture, and thus yield, of cereal plants. However, the precise mechanisms underlying inflorescence and spikelet meristem determinacy in cereals are still largely unclear. We have generated loss-of-function and overexpression mutants of the paralogous OsMADS5 and OsMADS34 genes in rice (Oryza sativa), and analysed their panicle phenotypes. Using chromatin immunoprecipitation, electrophoretic mobility-shift and dual-luciferase assays, we have also identified RICE CENTRORADIALIS 4 (RCN4), a TFL1-like gene, as a direct downstream target of both OsMADS proteins, and have analysed RCN4 mutants. The osmads5 osmads34 mutant lines had significantly enhanced panicle branching with increased secondary, and even tertiary and quaternary, branches, compared to wild-type (WT) and osmads34 plants. The osmads34 mutant phenotype could largely be rescued by also knocking out RCN4. Moreover, transgenic panicles overexpressing RCN4 had significantly increased branching, and initiated development of c. 7× more spikelets than WT. Our results reveal a role for OsMADS5 in panicle development, and show that OsMADS5 and OsMADS34 play similar functions in limiting branching and promoting the transition to spikelet meristem identity, in part by repressing RCN4 expression. These findings provide new insights to better understand the molecular regulation of rice inflorescence architecture.
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Affiliation(s)
- Wanwan Zhu
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Liu Yang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Di Wu
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Qingcai Meng
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiao Deng
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Guoqiang Huang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jiao Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiaofei Chen
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Cristina Ferrándiz
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Valencia, 46022, Spain
| | - Wanqi Liang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ludovico Dreni
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Valencia, 46022, Spain
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA, 5064, Australia
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17
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Kim SH, Ji SD, Lee HS, Jeon YA, Shim KC, Adeva C, Luong NH, Yuan P, Kim HJ, Tai TH, Ahn SN. A Novel Embryo Phenotype Associated With Interspecific Hybrid Weakness in Rice Is Controlled by the MADS-Domain Transcription Factor OsMADS8. FRONTIERS IN PLANT SCIENCE 2022; 12:778008. [PMID: 35069634 PMCID: PMC8769243 DOI: 10.3389/fpls.2021.778008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 12/03/2021] [Indexed: 05/27/2023]
Abstract
A novel hybrid weakness gene, DTE9, associated with a dark tip embryo (DTE) trait, was observed in CR6078, an introgression line derived from a cross between the Oryza sativa spp. japonica "Hwayeong" (HY) and the wild relative Oryza rufipogon. CR6078 seeds exhibit protruding embryos and flowers have altered inner floral organs. DTE9 was also associated with several hybrid weakness symptoms including decreased grain weight. Map-based cloning and transgenic approaches revealed that DTE9 is an allele of OsMADS8, a MADS-domain transcription factor. Genetic analysis indicated that two recessive complementary genes were responsible for the expression of the DTE trait. No sequence differences were observed between the two parental lines in the OsMADS8 coding region; however, numerous single nucleotide polymorphisms were detected in the promoter and intronic regions. We generated overexpression (OX) and RNA interference (RNAi) transgenic lines of OsMADS8 in HY and CR6078, respectively. The OsMADS8-OX lines showed the dark tip embryo phenotype, whereas OsMADS8-RNAi recovered the normal embryo phenotype. Changes in gene expression, including of ABCDE floral homeotic genes, were observed in the OsMADS8-OX and OsMADS8-RNAi lines. Overexpression of OsMADS8 led to decreased expression of OsEMF2b and ABA signaling-related genes including OsVP1/ABI3. HY seeds showed higher ABA content than CR6078 seeds, consistent with OsMADS8/DTE9 regulating the expression of genes related ABA catabolism in CR6078. Our results suggest that OsMADS8 is critical for floral organ determination and seed germination and that these effects are the result of regulation of the expression of OsEMF2b and its role in ABA signaling and catabolism.
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Affiliation(s)
- Sun Ha Kim
- Department of Agronomy, College of Agriculture & Life Sciences, Chungnam National University, Daejeon, South Korea
| | - Shi-Dong Ji
- Department of Agronomy, College of Agriculture & Life Sciences, Chungnam National University, Daejeon, South Korea
| | - Hyun-Sook Lee
- Department of Agronomy, College of Agriculture & Life Sciences, Chungnam National University, Daejeon, South Korea
| | - Yun-A Jeon
- Department of Agronomy, College of Agriculture & Life Sciences, Chungnam National University, Daejeon, South Korea
| | - Kyu-Chan Shim
- Department of Agronomy, College of Agriculture & Life Sciences, Chungnam National University, Daejeon, South Korea
| | - Cheryl Adeva
- Department of Agronomy, College of Agriculture & Life Sciences, Chungnam National University, Daejeon, South Korea
| | - Ngoc Ha Luong
- Department of Agronomy, College of Agriculture & Life Sciences, Chungnam National University, Daejeon, South Korea
| | - Pingrong Yuan
- Department of Agronomy, College of Agriculture & Life Sciences, Chungnam National University, Daejeon, South Korea
| | | | - Thomas H. Tai
- Crops Pathology and Genetics Research Unit, USDA-ARS, Davis, CA, United States
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Sang-Nag Ahn
- Department of Agronomy, College of Agriculture & Life Sciences, Chungnam National University, Daejeon, South Korea
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Genome-Wide Analysis and the Expression Pattern of the MADS-Box Gene Family in Bletilla striata. PLANTS 2021; 10:plants10102184. [PMID: 34685993 PMCID: PMC8539064 DOI: 10.3390/plants10102184] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 10/07/2021] [Accepted: 10/10/2021] [Indexed: 02/04/2023]
Abstract
Bletilla striata (Thunb. ex A. Murray) Rchb. f., a species of the perennial herb Orchidaceae, has potent anti-inflammatory and antiviral biological activities. MADS-box transcription factors play critical roles in the various developmental processes of plants. Although this gene family has been extensively investigated in many species, it has not been analyzed for B. striata. In total, 45 MADS-box genes were identified from B. striata in this study, which were classified into five subfamilies (Mδ, MIKC, Mα, Mβ, and Mγ). Meanwhile, the highly correlated protein domains, motif compositions, and exon-intron structures of BsMADSs were investigated according to local B. striata databases. Chromosome distribution and synteny analyses revealed that segmental duplication and homologous exchange were the main BsMADSs expansion mechanisms. Further, RT-qPCR analysis revealed that BsMADSs had different expression patterns in response to various stress treatments. Our results provide a potential theoretical basis for further investigation of the functions of MADS genes during the growth of B. striata.
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Wu T, Ali A, Wang J, Song J, Fang Y, Zhou T, Luo Y, Zhang H, Chen X, Liao Y, Liu Y, Xu P, Wu X. A homologous gene of OsREL2/ASP1, ASP-LSL regulates pleiotropic phenotype including long sterile lemma in rice. BMC PLANT BIOLOGY 2021; 21:390. [PMID: 34418975 PMCID: PMC8379857 DOI: 10.1186/s12870-021-03163-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 08/06/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Panicle is a harvesting organ of rice, and its morphology and development are closely associated with grain yield. The current study was carried on a mutant screened through an EMS (ethyl-methane sulphonate) mutagenized population of a Japonica cultivar Kitaake (WT). RESULTS A mutant, named as asp-lsl (aberrant spikelet-long sterile lemma), showed a significant decrease in plant height, number of tillers, thousand-grains weight, seed setting rate, spikelet length, kernel length and effective number of grains per panicle as compared to WT. Asp-lsl showed a pleiotropic phenotype coupled with the obvious presence of a long sterile lemma. Cross-sections of lemma showed an increase in the cell volume rather than the number of cells. Genetic segregation analysis revealed its phenotypic trait is controlled by a single recessive nuclear gene. Primary and fine mapping indicated that candidate gene controlling the phenotype of asp-lsl was located in an interval of 212 kb on the short arm of chromosome 8 between RM22445 and RM22453. Further sequencing and indels markers analysis revealed LOC_Os08g06480 harbors a single base substitution (G→A), resulting in a change of 521st amino acid(Gly→Glu. The homology comparison and phylogenetic tree analysis revealed mutation was occurred in a highly conserved domain and had a high degree of similarity in Arabidopsis, corn, and sorghum. The CRISPR/Cas9 mutant line of ASP-LSL produced a similar phenotype as that of asp-lsl. Subcellular localization of ASP-LSL revealed that its protein is localized in the nucleus. Relative expression analysis revealed ASP-LSL was preferentially expressed in panicle, stem, and leaves. The endogenous contents of GA, CTK, and IAA were found significantly decreased in asp-lsl as compared to WT. CONCLUSIONS Current study presents the novel phenotype of asp-lsl and also validate the previously reported function of OsREL2 (ROMOSA ENHANCER LOCI2), / ASP1(ABERRANT SPIKELET AND PANICLE 1).
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Affiliation(s)
- Tingkai Wu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Asif Ali
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Jinhao Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Jiahe Song
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Yongqiong Fang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Tingting Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Yi Luo
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Hongyu Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Xiaoqiong Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Yongxiang Liao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Yutong Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Peizhou Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Xianjun Wu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, China.
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20
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INTERMEDIUM-M encodes an HvAP2L-H5 ortholog and is required for inflorescence indeterminacy and spikelet determinacy in barley. Proc Natl Acad Sci U S A 2021; 118:2011779118. [PMID: 33593903 PMCID: PMC7923579 DOI: 10.1073/pnas.2011779118] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Meristem determinacy/indeterminacy influences flower number and seed production in crops. Two closely related cool-season cereals, barley and wheat, produce variable and defined numbers of spikelets in their inflorescences, respectively. In this study, we identify a series of allelic barley mutants named intermedium-m and double seed1 that develop wheat-like determinate inflorescences producing a terminal spikelet and a reduced number of spikelets. INT-M/DUB1 is an APETALA2-like transcription factor that promotes an active inflorescence meristem via suppression of spikelet initiation and the maintenance of meristem identity. Our work has identified key regulators that may prolong meristem activities and could be genetically engineered in barley, wheat, and other cereals to improve grain yield. Inflorescence architecture dictates the number of flowers and, ultimately, seeds. The architectural discrepancies between two related cereals, barley and wheat, are controlled by differences in determinacy of inflorescence and spikelet meristems. Here, we characterize two allelic series of mutations named intermedium-m (int-m) and double seed1 (dub1) that convert barley indeterminate inflorescences into wheat-like determinate inflorescences bearing a multifloreted terminal spikelet and spikelets with additional florets. INT-M/DUB1 encodes an APETALA2-like transcription factor (HvAP2L-H5) that suppresses ectopic and precocious spikelet initiation signals and maintains meristem activity. HvAP2L-H5 inhibits the identity shift of an inflorescence meristem (IM) to a terminal spikelet meristem (TSM) in barley. Null mutations in AP2L-5 lead to fewer spikelets per inflorescence but extra florets per spikelet. In wheat, prolonged and elevated AP2L-A5 activity in rAP2L-A5 mutants delays but does not suppress the IM−TSM transition. We hypothesize that the regulation of AP2L-5 orthologs and downstream genes contributes to the different inflorescence determinacy in barley and wheat. We show that AP2L-5 proteins are evolutionarily conserved in grasses, promote IM activity, and restrict floret number per spikelet. This study provides insights into the regulation of spikelet and floret number, and hence grain yield in barley and wheat.
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21
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Gene duplication at the Fascicled ear1 locus controls the fate of inflorescence meristem cells in maize. Proc Natl Acad Sci U S A 2021; 118:2019218118. [PMID: 33579824 PMCID: PMC7896288 DOI: 10.1073/pnas.2019218118] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The maize ear is unbranched and terminates in a single point. The ear and tassel inflorescences of Fascicled ear mutants fail to grow as a single point and instead are branched. This phenotype results from the misexpression of duplicated transcription factors, ZMM8 and DRL2. We hypothesize that these gene rearrangements create regulatory sequences that cause misexpression in early inflorescence meristems, thus activating a laminar program, ablating the meristem, and producing branches. This work demonstrates that zmm8 and drl2 must be restricted from the inflorescence meristem to maintain its terminal point, and conversely, a mechanism by which branching may be imposed. Manipulation of these genes can be used to alter plant architecture, potentially to improve agronomic traits. Plant meristems are self-renewing groups of pluripotent stem cells that produce lateral organs in a stereotypical pattern. Of interest is how the radially symmetrical meristem produces laminar lateral organs. Both the male and female inflorescence meristems of the dominant Fascicled ear (Fas1) mutant fail to grow as a single point and instead show deep branching. Positional cloning of two independent Fas1 alleles identified an ∼160 kb region containing two floral genes, the MADS-box gene, zmm8, and the YABBY gene, drooping leaf2 (drl2). Both genes are duplicated within the Fas1 locus and spatiotemporally misexpressed in the mutant inflorescence meristems. Increased zmm8 expression alone does not affect inflorescence development; however, combined misexpression of zmm8, drl2, and their syntenic paralogs zmm14 and drl1, perturbs meristem organization. We hypothesize that misexpression of the floral genes in the inflorescence and their potential interaction cause ectopic activation of a laminar program, thereby disrupting signaling necessary for maintenance of radially symmetrical inflorescence meristems. Consistent with this hypothesis, RNA sequencing and in situ analysis reveal altered expression patterns of genes that define distinct zones of the meristem and developing leaf. Our findings highlight the importance of strict spatiotemporal patterns of expression for both zmm8 and drl2 and provide an example of phenotypes arising from tandem gene duplications.
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22
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Hu Y, Wang L, Jia R, Liang W, Zhang X, Xu J, Chen X, Lu D, Chen M, Luo Z, Xie J, Cao L, Xu B, Yu Y, Persson S, Zhang D, Yuan Z. Rice transcription factor MADS32 regulates floral patterning through interactions with multiple floral homeotic genes. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:2434-2449. [PMID: 33337484 DOI: 10.1093/jxb/eraa588] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 12/15/2020] [Indexed: 06/12/2023]
Abstract
Floral patterning is regulated by intricate networks of floral identity genes. The peculiar MADS32 subfamily genes, absent in eudicots but prevalent in monocots, control floral organ identity. However, how the MADS32 family genes interact with other floral homeotic genes during flower development is mostly unknown. We show here that the rice homeotic transcription factor OsMADS32 regulates floral patterning by interacting synergistically with E class protein OsMADS6 in a dosage-dependent manner. Furthermore, our results indicate important roles for OsMADS32 in defining stamen, pistil, and ovule development through physical and genetic interactions with OsMADS1, OsMADS58, and OsMADS13, and in specifying floral meristem identity with OsMADS6, OsMADS3, and OsMADS58, respectively. Our findings suggest that OsMADS32 is an important factor for floral meristem identity maintenance and that it integrates the action of other MADS-box homeotic proteins to sustain floral organ specification and development in rice. Given that OsMADS32 is an orphan gene and absent in eudicots, our data substantially expand our understanding of flower development in plants.
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Affiliation(s)
- Yun Hu
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Li Wang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ru Jia
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Wanqi Liang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xuelian Zhang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jie Xu
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaofei Chen
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Dan Lu
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Mingjiao Chen
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Zhijing Luo
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jiayang Xie
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Liming Cao
- Crop Breeding & Cultivation Research Institute, Shanghai Academy of Agriculture Sciences, Shanghai, China
| | - Ben Xu
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Yu Yu
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Staffan Persson
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- School of Biosciences, University of Melbourne, Parkville VIC, Melbourne, Australia
- Department for Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
- Copenhagen Plant Science Center, University of Copenhagen, Frederiksberg C, Denmark
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, South Australia, Australia
| | - Zheng Yuan
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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23
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Shoesmith JR, Solomon CU, Yang X, Wilkinson LG, Sheldrick S, van Eijden E, Couwenberg S, Pugh LM, Eskan M, Stephens J, Barakate A, Drea S, Houston K, Tucker MR, McKim SM. APETALA2 functions as a temporal factor together with BLADE-ON-PETIOLE2 and MADS29 to control flower and grain development in barley. Development 2021; 148:dev.194894. [DOI: 10.1242/dev.194894] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 01/25/2021] [Indexed: 11/20/2022]
Abstract
ABSTRACT
Cereal grain develops from fertilised florets. Alterations in floret and grain development greatly influence grain yield and quality. Despite this, little is known about the underlying genetic control of these processes, especially in key temperate cereals such as barley and wheat. Using a combination of near-isogenic mutant comparisons, gene editing and genetic analyses, we reveal that HvAPETALA2 (HvAP2) controls floret organ identity, floret boundaries, and maternal tissue differentiation and elimination during grain development. These new roles of HvAP2 correlate with changes in grain size and HvAP2-dependent expression of specific HvMADS-box genes, including the B-sister gene, HvMADS29. Consistent with this, gene editing demonstrates that HvMADS29 shares roles with HvAP2 in maternal tissue differentiation. We also discovered that a gain-of-function HvAP2 allele masks changes in floret organ identity and grain size due to loss of barley LAXATUM.A/BLADE-ON-PETIOLE2 (HvBOP2) gene function. Taken together, we reveal novel pleiotropic roles and regulatory interactions for an AP2-like gene controlling floret and grain development in a temperate cereal.
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Affiliation(s)
- Jennifer R. Shoesmith
- Division of Plant Sciences, School of Life Sciences, University of Dundee at the James Hutton Institute, Invergowrie DD2 5DA, UK
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie DD2 5DA, UK
| | - Charles Ugochukwu Solomon
- Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester LE1 7RH, UK
- Department of Plant Science and Biotechnology, Abia State University, PMB 2000, Uturu, Nigeria
| | - Xiujuan Yang
- Waite Research Institute, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA, 5064, Australia
| | - Laura G. Wilkinson
- Waite Research Institute, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA, 5064, Australia
- Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Scott Sheldrick
- Division of Plant Sciences, School of Life Sciences, University of Dundee at the James Hutton Institute, Invergowrie DD2 5DA, UK
| | - Ewan van Eijden
- Division of Plant Sciences, School of Life Sciences, University of Dundee at the James Hutton Institute, Invergowrie DD2 5DA, UK
| | - Sanne Couwenberg
- Division of Plant Sciences, School of Life Sciences, University of Dundee at the James Hutton Institute, Invergowrie DD2 5DA, UK
| | - Laura M. Pugh
- Division of Plant Sciences, School of Life Sciences, University of Dundee at the James Hutton Institute, Invergowrie DD2 5DA, UK
| | - Mhmoud Eskan
- Division of Plant Sciences, School of Life Sciences, University of Dundee at the James Hutton Institute, Invergowrie DD2 5DA, UK
| | - Jennifer Stephens
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie DD2 5DA, UK
| | - Abdellah Barakate
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie DD2 5DA, UK
| | - Sinéad Drea
- Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Kelly Houston
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie DD2 5DA, UK
| | - Matthew R. Tucker
- Waite Research Institute, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA, 5064, Australia
| | - Sarah M. McKim
- Division of Plant Sciences, School of Life Sciences, University of Dundee at the James Hutton Institute, Invergowrie DD2 5DA, UK
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24
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Shen C, Li G, Dreni L, Zhang D. Molecular Control of Carpel Development in the Grass Family. FRONTIERS IN PLANT SCIENCE 2021; 12:635500. [PMID: 33664762 PMCID: PMC7921308 DOI: 10.3389/fpls.2021.635500] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 01/04/2021] [Indexed: 05/26/2023]
Abstract
Carpel is the ovule-bearing female reproductive organ of flowering plants and is required to ensure its protection, an efficient fertilization, and the development of diversified types of fruits, thereby it is a vital element of most food crops. The origin and morphological changes of the carpel are key to the evolution and adaption of angiosperms. Progresses have been made in elucidating the developmental mechanisms of carpel establishment in the model eudicot plant Arabidopsis thaliana, while little and fragmentary information is known in grasses, a family that includes many important crops such as rice (Oryza sativa), maize (Zea mays), barley (Hordeum vulgare), and wheat (Triticum aestivum). Here, we highlight recent advances in understanding the mechanisms underlying potential pathways of carpel development in grasses, including carpel identity determination, morphogenesis, and floral meristem determinacy. The known role of transcription factors, hormones, and miRNAs during grass carpel formation is summarized and compared with the extensively studied eudicot model plant Arabidopsis. The genetic and molecular aspects of carpel development that are conserved or diverged between grasses and eudicots are therefore discussed.
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Affiliation(s)
- Chaoqun Shen
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA, Australia
| | - Gang Li
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA, Australia
| | - Ludovico Dreni
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Valencia, Spain
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA, Australia
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25
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Osnato M, Lacchini E, Pilatone A, Dreni L, Grioni A, Chiara M, Horner D, Pelaz S, Kater MM. Transcriptome analysis reveals rice MADS13 as an important repressor of the carpel development pathway in ovules. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:398-414. [PMID: 33035313 DOI: 10.1093/jxb/eraa460] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 10/03/2020] [Indexed: 06/11/2023]
Abstract
In angiosperms, floral homeotic genes encoding MADS-domain transcription factors regulate the development of floral organs. Specifically, members of the SEPALLATA (SEP) and AGAMOUS (AG) subfamilies form higher-order protein complexes to control floral meristem determinacy and to specify the identity of female reproductive organs. In rice, the AG subfamily gene OsMADS13 is intimately involved in the determination of ovule identity, since knock-out mutant plants develop carpel-like structures in place of ovules, resulting in female sterility. Little is known about the regulatory pathways at the base of rice gynoecium development. To investigate molecular mechanisms acting downstream of OsMADS13, we obtained transcriptomes of immature inflorescences from wild-type and Osmads13 mutant plants. Among a total of 476 differentially expressed genes (DEGs), a substantial overlap with DEGs from the SEP-family Osmads1 mutant was found, suggesting that OsMADS1 and OsMADS13 may act on a common set of target genes. Expression studies and preliminary analyses of two up-regulated genes encoding Zinc-finger transcription factors indicated that our dataset represents a valuable resource for the identification of both OsMADS13 target genes and novel players in rice ovule development. Taken together, our study suggests that OsMADS13 is an important repressor of the carpel pathway during ovule development.
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Affiliation(s)
- Michela Osnato
- Department of Biosciences, University of Milan, Milano, Italy
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Barcelona, Spain
| | - Elia Lacchini
- Department of Biosciences, University of Milan, Milano, Italy
- VIB Center for Plant System Biology, Ghent, BELGIUM
| | | | - Ludovico Dreni
- Department of Biosciences, University of Milan, Milano, Italy
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Valencia, Spain
| | - Andrea Grioni
- Department of Biosciences, University of Milan, Milano, Italy
| | - Matteo Chiara
- Department of Biosciences, University of Milan, Milano, Italy
| | - David Horner
- Department of Biosciences, University of Milan, Milano, Italy
| | - Soraya Pelaz
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Barcelona, Spain
| | - Martin M Kater
- Department of Biosciences, University of Milan, Milano, Italy
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Kannan P, Chongloi GL, Majhi BB, Basu D, Veluthambi K, Vijayraghavan U. Characterization of a new rice OsMADS1 null mutant generated by homologous recombination-mediated gene targeting. PLANTA 2021; 253:39. [PMID: 33474591 DOI: 10.1007/s00425-020-03547-3] [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: 08/18/2020] [Accepted: 12/22/2020] [Indexed: 06/12/2023]
Abstract
A new, stable, null mutant of OsMADS1 generated by homologous recombination-based gene targeting in an indica rice confirms its regulatory role for floral meristem identity, its determinate development and floral organ differentiation. OsMADS1, an E-class MADS-box gene, is an important regulator of rice flower development. Studies of several partial loss-of-function and knockdown mutants show varied floret organ defects and degrees of meristem indeterminacy. The developmental consequences of a true null mutant on floret meristem identity, its determinate development and differentiation of grass-specific organs such as the lemma and palea remain unclear. In this study, we generated an OsMADS1 null mutant by homologous recombination-mediated gene targeting by inserting a selectable marker gene (hpt) in OsMADS1 and replacing parts of its cis-regulatory and coding sequences. A binary vector was constructed with diphtheria toxin A chain gene (DT-A) as a negative marker to eliminate random integrations and the hpt marker for positive selection of homologous recombination. Precise disruption of the endogenous OsMADS1 locus in the rice genome was confirmed by Southern hybridization. The homozygous osmads1ko null mutant displayed severe defects in all floral organs including the lemma and palea. We also noticed striking instances of floral reversion to inflorescence and vegetative states which has not been reported for other mutant alleles of OsMADS1 and further reinforces the role of OsMADS1 in controlling floral meristem determinacy. Our data suggest, OsMADS1 commits and maintains determinate floret development by regulating floral meristem termination, carpel and ovule differentiation genes (OsMADS58, OsMADS13) while its modulation of genes such as OsMADS15, OsIG1 and OsMADS32 could be relevant in the differentiation and development of palea. Further, our study provides an important perspective on developmental stage-dependent modulation of some OsMADS1 target genes.
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Affiliation(s)
- Pachamuthu Kannan
- Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Madurai, Tamil Nadu, 625021, India
| | | | - Bharat Bhusan Majhi
- Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Madurai, Tamil Nadu, 625021, India
| | - Debjani Basu
- Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Madurai, Tamil Nadu, 625021, India
| | - Karuppannan Veluthambi
- Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Madurai, Tamil Nadu, 625021, India
| | - Usha Vijayraghavan
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, 560012, India.
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Yang D, He N, Zheng X, Zhen Y, Xie Z, Cheng C, Huang F. Cloning of long sterile lemma (lsl2), a single recessive gene that regulates spike germination in rice (Oryza sativa L.). BMC PLANT BIOLOGY 2020; 20:561. [PMID: 33308141 PMCID: PMC7733262 DOI: 10.1186/s12870-020-02776-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 12/02/2020] [Indexed: 05/26/2023]
Abstract
BACKGROUND Rice is a typical monocotyledonous plant and an important cereal crop. The structural units of rice flowers are spikelets and florets, and floral organ development and spike germination affect rice reproduction and yield. RESULTS In this study, we identified a novel long sterile lemma (lsl2) mutant from an EMS population. First, we mapped the lsl2 gene between the markers Indel7-22 and Indel7-27, which encompasses a 25-kb region. The rice genome annotation indicated the presence of four candidate genes in this region. Through gene prediction and cDNA sequencing, we confirmed that the target gene in the lsl2 mutant is allelic to LONG STERILE LEMMA1 (G1)/ELONGATED EMPTY GLUME (ELE), hereafter referred to as lsl2. Further analysis of the lsl2 and LSL2 proteins showed a one-amino-acid change, namely, the mutation of serine (Ser) 79 to proline (Pro) in lsl2 compared with LSL2, and this mutation might change the function of the protein. Knockout experiments showed that the lsl2 gene is responsible for the long sterile lemma phenotype. The lsl2 gene might reduce the damage induced by spike germination by decreasing the seed germination rate, but other agronomic traits of rice were not changed in the lsl2 mutant. Taken together, our results demonstrate that the lsl2 gene will have specific application prospects in future rice breeding. CONCLUSIONS The lsl2 gene is responsible for the long sterile lemma phenotype and might reduce the damage induced by spike germination by decreasing the seed germination rate.
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Affiliation(s)
- Dewei Yang
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fujian High Quality Rice Research & Development Center, Fuzhou, 350019, China.
| | - Niqing He
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fujian High Quality Rice Research & Development Center, Fuzhou, 350019, China
| | - Xianghua Zheng
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fujian High Quality Rice Research & Development Center, Fuzhou, 350019, China
| | - Yanmei Zhen
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fujian High Quality Rice Research & Development Center, Fuzhou, 350019, China
| | - Zhenxin Xie
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fujian High Quality Rice Research & Development Center, Fuzhou, 350019, China
| | - Chaoping Cheng
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fujian High Quality Rice Research & Development Center, Fuzhou, 350019, China
| | - Fenghuang Huang
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fujian High Quality Rice Research & Development Center, Fuzhou, 350019, China
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Yadav A, Garg T, Singh H, Yadav SR. Tissue-specific expression pattern of calcium-dependent protein kinases-related kinases (CRKs) in rice. PLANT SIGNALING & BEHAVIOR 2020; 15:1809846. [PMID: 32835584 PMCID: PMC7588190 DOI: 10.1080/15592324.2020.1809846] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/09/2020] [Accepted: 08/10/2020] [Indexed: 05/23/2023]
Abstract
Calcium-dependent protein kinases-related kinases (CDPK-related kinases; CRKs) are Ser/Thr kinases that bind with Ca2+/Calmodulin and play crucial roles in signal transduction pathways during plant growth, development, and responses to multiple stresses. In this study, we have studied detailed organ and tissue-specific expression patterns of rice CRK genes. Our organ-specific RT-PCR analyzes show the differential expression pattern of these genes in various organs of rice. Moreover, our RNA-RNA in situ hybridization study in rice stem base containing developing crown root primordia demonstrates that the expression of CRK genes is spatially restricted to the developing crown root primordia, suggesting their putative role in protein phosphorylation-dependent cellular signaling during rice crown root development. Furthermore, organ-specific differentially expression pattern of CRK genes during floral organogenesis further support for the organ-specific cell signaling during organogenesis. Thus, our study provides a developmentally regulated expression pattern of rice CRK genes, though they are broadly expressed and a basic foundation for functional characterizations of CRK gene members to unravel their specific functions during plant growth and development.
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Affiliation(s)
- Akhilesh Yadav
- Department of Biotechnology, Indian Institute of Technology, Roorkee, India
| | - Tushar Garg
- Department of Biotechnology, Indian Institute of Technology, Roorkee, India
| | - Harshita Singh
- Department of Biotechnology, Indian Institute of Technology, Roorkee, India
| | - Shri Ram Yadav
- Department of Biotechnology, Indian Institute of Technology, Roorkee, India
- CONTACT : Shri Ram Yadav Department of Biotechnology, Indian Institute of Technology, Roorkee247667, India
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Li P, Li H, Liu Z, Zhuang Y, Wei M, Gu Y, Liu Y, Sun X, Tang Y, Yue L, Lu L, Luo D, Huang W, Tu S, Wang S. Characterization of the 'Oat-Like Rice' Caused by a Novel Allele OsMADS1 Olr Reveals Vital Importance of OsMADS1 in Regulating Grain Shape in Oryza sativa L. RICE (NEW YORK, N.Y.) 2020; 13:73. [PMID: 33063229 PMCID: PMC7561663 DOI: 10.1186/s12284-020-00428-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 09/09/2020] [Indexed: 05/15/2023]
Abstract
BACKGROUND Grain shape is a critical agronomic trait affecting grain yield and quality. Exploration and functional characterization of grain shape-related genes will facilitate rice breeding for higher quality and yield. RESULTS Here, we characterized a recessive mutant named Oat-like rice for its unique grain shape which highly resembles oat grains. The Oat-like rice displayed abnormal floral organs, an open hull formed by remarkably elongated leafy lemmas and paleae, occasionally formed conjugated twin brown rice, an aberrant grain shape and a low seed setting rate. By map-based cloning, we discovered that Oat-like rice harbors a novel allele of OsMADS1 gene (OsMADS1Olr), which has a spontaneous point mutation that causes the substitution of an amino acid that is highly conserved in the MADS-box domain of the MADS-box family. Further linkage analysis indicated that the point mutation in the OsMADS1Olr is associated with Oat-like rice phenotype, and expression analysis of the OsMADS1 by qRT-PCR and GUS staining also indicated that it is highly expressed in flower organs as well as in the early stages of grain development. Furthermore, OsMADS1Olr-overexpressing plants showed similar phenotypes of Oat-like rice in grain shape, possibly due to the dominant negative effect. And OsMADS1-RNAi plants also displayed grain phenotypes like Oat-like rice. These results suggested that OsMADS1Olr is responsible for the Oat-like rice phenotype including aberrant grain shape. Moreover, the expression levels of representative genes related to grain shape regulation were apparently altered in Oat-like rice, OsMADS1Olr-overexpressing and OsMADS1-RNAi transgenic plants. Finally, compared with Oat-like rice, OsMADS1Olr-overexpressing and OsMADS1-RNAi plants, mild phenotype of seed-specific OsMADS1-RNAi transgenic plants indicated that OsMADS1 may has has a direct regulation role in grain development and the grain phenotypes of Oat-like rice, OsMADS1Olr-overexpressing and OsMADS1-RNAi plants are majorly caused by the abnormal lemma and palea development. CONCLUSIONS Altogether, our results showed that grain shape and a low seed setting rate of the notable 'Oat-like rice' are caused by a spontaneous point mutation in the novel allele OsMADS1Olr. Furthermore, our findings suggested that OsMADS1 mediates grain shape possibly by affecting the expression of representative genes related to grain shape regulation. Thus, this study not only revealed that OsMADS1 plays a vital role in regulating grain shape of rice but also highlighted the importance and value of OsMADS1 to improve the quality and yield of rice by molecular breeding.
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Affiliation(s)
- Penghui Li
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hui Li
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw, 05282, Myanmar.
| | - Zhijian Liu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yong Zhuang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ming Wei
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuanyang Gu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yangxuan Liu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiuqiang Sun
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuying Tang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lu Yue
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Longxiang Lu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dagang Luo
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
| | - Weizao Huang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw, 05282, Myanmar
| | - Shengbin Tu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw, 05282, Myanmar
| | - Songhu Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw, 05282, Myanmar.
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Wang R, Liu C, Li Q, Chen Z, Sun S, Wang X. Spatiotemporal Resolved Leaf Angle Establishment Improves Rice Grain Yield via Controlling Population Density. iScience 2020; 23:101489. [PMID: 32898833 PMCID: PMC7486458 DOI: 10.1016/j.isci.2020.101489] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 08/10/2020] [Accepted: 08/18/2020] [Indexed: 11/15/2022] Open
Abstract
Leaf angle is mainly determined by the lamina joint (LJ) and contributes to ideal crop architecture for high yield. Here, we dissected five successive stages with distinct cytological features of LJs spanning organogenesis to leaf angle formation and obtained the underlying stage-specific mRNAs and small RNAs, which well explained the cytological dynamics during LJ organogenesis and leaf angle plasticity. Combining the gene coexpression correlation with high-throughput promoter analysis, we identified a set of transcription factors (TFs) determining the stage- and/or cytological structure-specific profiles. The functional studies of these TFs demonstrated that cytological dynamics determined leaf angle and that the knockout rice of these TFs with erect leaves significantly enhanced yield by maintaining the proper tiller number under dense planting. This work revealed the high-resolution mechanisms of how the cytological dynamics of LJ determined leaf erectness and served as a valuable resource to remodel rice architecture for high yield by controlling population density.
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Affiliation(s)
- Rongna Wang
- National Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Science, Henan University, Kaifeng 475004, China
| | - Chang Liu
- National Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Science, Henan University, Kaifeng 475004, China
| | - Qinzhong Li
- National Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhina Chen
- National Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Shiyong Sun
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Science, Henan University, Kaifeng 475004, China.
| | - Xuelu Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Science, Henan University, Kaifeng 475004, China.
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Transcriptome Profiling Analysis Reveals Co-regulation of Hormone Pathways in Foxtail Millet during Sclerospora graminicola Infection. Int J Mol Sci 2020; 21:ijms21041226. [PMID: 32059399 PMCID: PMC7072888 DOI: 10.3390/ijms21041226] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 01/24/2020] [Accepted: 01/25/2020] [Indexed: 11/16/2022] Open
Abstract
Sclerospora graminicola (Sacc.) Schroeter is a biotrophic pathogen of foxtail millet (Setaria italica) and increasingly impacts crop production. We explored the main factors for symptoms such as dwarfing of diseased plants and the “hedgehog panicle” by determining panicle characteristics of varieties infected with S. graminicola and analyzing the endogenous hormone-related genes in leaves of Jingu 21. Results indicated that different varieties infected by S. graminicola exhibited various symptoms. Transcriptome analysis revealed that the ent-copalyl diphosphate synthetase (CPS) encoded by Seita.2G144900 and ent-kaurene synthase (KS) encoded by Seita.2G144400 were up-regulated 4.7-fold and 2.8-fold, respectively. Results showed that the biosynthesis of gibberellin might be increased, but the gibberellin signal transduction pathway might be blocked. The abscisic acid (ABA) 8′-hydroxylase encoded by Seita.6G181300 was continuously up-regulated by 4.2-fold, 2.7-fold, 14.3-fold, and 12.9-fold from TG1 to TG4 stage, respectively. Seita.2G144900 and Seita.2G144400 increased 79-fold and 51-fold, respectively, at the panicle development stage, promoting the formation of a “hedgehog panicle”. Jasmonic acid-related synthesis enzymes LOX2s, AOS, and AOC were up-regulated at the early stage of infection, indicating that jasmonic acid played an essential role in early response to S. graminicola infection. The expression of YUC-related genes of the auxin synthesis was lower than that of the control at TG3 and TG4 stages, but the amidase encoded by Seita.2G313400 was up-regulated by more than 30-fold, indicating that the main biosynthesis pathway of auxin had changed. The results suggest that there was co-regulation of the hormone pathways during the infection of foxtail millet by S. graminicola.
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ABNORMAL FLOWER AND GRAIN 1 encodes OsMADS6 and determines palea identity and affects rice grain yield and quality. SCIENCE CHINA-LIFE SCIENCES 2020; 63:228-238. [PMID: 31919631 DOI: 10.1007/s11427-019-1593-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 11/28/2019] [Indexed: 12/21/2022]
Abstract
The palea and lemma are floral organ structures unique to grasses; these structures form the hull and directly affect grain size and quality. However, the molecular mechanisms controlling the development of the hull are not well understood. In this study, we characterized the rice (Oryza sativa) abnormal flower and grain1 (afg1) mutant, a new allele of OsMADS6. Similar to previously characterized osmads6 alleles, in the afg1 floret, the palea lost its marginal region and acquired the lemma identity. However, in contrast to other osmads6 alleles, the afg1 mutant showed altered grain size and grain quality, with decreased total starch and amylose contents, and increased protein and soluble sugar contents. The analysis of transcriptional activity suggested that AFG1 is a transcriptional activator and may affect grain size by regulating the expression levels of several genes related to cell expansion and proliferation in the afg1 mutant. These results revealed that AFG1 plays an important role in determining palea identity and affecting grain yield and quality in rice.
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Huang D, Zheng Q, Melchkart T, Bekkaoui Y, Konkin DJF, Kagale S, Martucci M, You FM, Clarke M, Adamski NM, Chinoy C, Steed A, McCartney CA, Cutler AJ, Nicholson P, Feurtado JA. Dominant inhibition of awn development by a putative zinc-finger transcriptional repressor expressed at the B1 locus in wheat. THE NEW PHYTOLOGIST 2020; 225:340-355. [PMID: 31469444 PMCID: PMC6916588 DOI: 10.1111/nph.16154] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 08/16/2019] [Indexed: 05/22/2023]
Abstract
Awns, bristle-like structures extending from grass lemmas, provide protection against predators, contribute to photosynthesis and aid in grain dispersal. In wheat, selection of awns with minimal extension, termed awnletted, has occurred during domestication by way of loci that dominantly inhibit awn development, such as Tipped1 (B1), Tipped2 (B2), and Hooded (Hd). Here we identify and characterize the B1 gene. B1 was identified using bulked segregant RNA-sequencing of an F2 durum wheat population and through deletion mapping of awned bread wheat mutants. Functional characterization was accomplished by gene overexpression while haplotype analyses assessed B1 polymorphisms and genetic variation. Located on chromosome 5A, B1 is a C2H2 zinc finger encoding gene with ethylene-responsive element binding factor-associated amphiphilic repression (EAR) motifs. Constitutive overexpression of B1 in awned wheat produced an awnletted phenotype with pleiotropic effects on plant height and fertility. Transcriptome analysis of B1 overexpression plants suggests a role as transcriptional repressor, putatively targeting pathways involved in cell proliferation. Haplotype analysis revealed a conserved B1 coding region with proximal polymorphisms and supported the contention that B1 is mainly responsible for awnletted wheats globally. B1, predominantly responsible for awn inhibition in wheat, encodes a C2H2 zinc finger protein with EAR motifs which putatively functions as a transcriptional repressor.
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Affiliation(s)
- Daiqing Huang
- Aquatic and Crop Resource DevelopmentNational Research Council of CanadaSaskatoonSKS7N 0W9Canada
| | - Qian Zheng
- Aquatic and Crop Resource DevelopmentNational Research Council of CanadaSaskatoonSKS7N 0W9Canada
| | - Tancey Melchkart
- Aquatic and Crop Resource DevelopmentNational Research Council of CanadaSaskatoonSKS7N 0W9Canada
| | - Yasmina Bekkaoui
- Aquatic and Crop Resource DevelopmentNational Research Council of CanadaSaskatoonSKS7N 0W9Canada
| | - David J. F. Konkin
- Aquatic and Crop Resource DevelopmentNational Research Council of CanadaSaskatoonSKS7N 0W9Canada
| | - Sateesh Kagale
- Aquatic and Crop Resource DevelopmentNational Research Council of CanadaSaskatoonSKS7N 0W9Canada
| | - Martial Martucci
- Morden Research and Development CentreAgriculture and Agri‐Food Canada101 Route 100MordenMBR6M 1Y5Canada
| | - Frank M. You
- Ottawa Research and Development CentreAgriculture and Agri‐Food Canada960 Carling AvenueOttawaONK1A 0C6Canada
| | - Martha Clarke
- Department of Crop GeneticsJohn Innes CentreNorwich Research Park, Colney LaneNorwichNR4 7UHUK
| | - Nikolai M. Adamski
- Department of Crop GeneticsJohn Innes CentreNorwich Research Park, Colney LaneNorwichNR4 7UHUK
| | - Catherine Chinoy
- Department of Crop GeneticsJohn Innes CentreNorwich Research Park, Colney LaneNorwichNR4 7UHUK
| | - Andrew Steed
- Department of Crop GeneticsJohn Innes CentreNorwich Research Park, Colney LaneNorwichNR4 7UHUK
| | - Curt A. McCartney
- Morden Research and Development CentreAgriculture and Agri‐Food Canada101 Route 100MordenMBR6M 1Y5Canada
| | - Adrian J. Cutler
- Aquatic and Crop Resource DevelopmentNational Research Council of CanadaSaskatoonSKS7N 0W9Canada
| | - Paul Nicholson
- Department of Crop GeneticsJohn Innes CentreNorwich Research Park, Colney LaneNorwichNR4 7UHUK
| | - J. Allan Feurtado
- Aquatic and Crop Resource DevelopmentNational Research Council of CanadaSaskatoonSKS7N 0W9Canada
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Ren D, Cui Y, Hu H, Xu Q, Rao Y, Yu X, Zhang Y, Wang Y, Peng Y, Zeng D, Hu J, Zhang G, Gao Z, Zhu L, Chen G, Shen L, Zhang Q, Guo L, Qian Q. AH2 encodes a MYB domain protein that determines hull fate and affects grain yield and quality in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:813-824. [PMID: 31357245 DOI: 10.1111/tpj.14481] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 07/03/2019] [Accepted: 07/19/2019] [Indexed: 06/10/2023]
Abstract
The palea and lemma (hull) are grass-specific organs, and determine grain size and quality. In the study, AH2 encodes a MYB domain protein, and functions in the development of hull and grain. Mutation of AH2 produces smaller grains and alters grain quality including decreased amylose content and gel consistency, and increased protein content. Meantime, part of the hull lost the outer silicified cells, and induces a transformation of the outer rough epidermis to inner smooth epidermis cells, and the body of the palea was reduced in the ah2 mutant. We confirmed the function of AH2 by complementation, CRISPR-Cas9, and cytological and molecular tests. Additionally, AH2, as a repressor, repress transcription of the downstream genes. Our results revealed that AH2 plays an important role in the determination of hull epidermis development, palea identity, and grain size.
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Affiliation(s)
- Deyong Ren
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, People's Republic of China
| | - Yuanjiang Cui
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, People's Republic of China
| | - Haitao Hu
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, People's Republic of China
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, People's Republic of China
| | - Qiankun Xu
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, People's Republic of China
| | - Yuchun Rao
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, People's Republic of China
| | - Xiaoqi Yu
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, People's Republic of China
| | - Yu Zhang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, People's Republic of China
| | - Yuexing Wang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, People's Republic of China
| | - Youlin Peng
- Rice Research Institute, Southwest University of Science and Technology, Mianyang, 621010, People's Republic of China
| | - Dali Zeng
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, People's Republic of China
| | - Jiang Hu
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, People's Republic of China
| | - Guangheng Zhang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, People's Republic of China
| | - Zhenyu Gao
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, People's Republic of China
| | - Li Zhu
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, People's Republic of China
| | - Guang Chen
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, People's Republic of China
| | - Lan Shen
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, People's Republic of China
| | - Qiang Zhang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, People's Republic of China
| | - Longbiao Guo
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, People's Republic of China
| | - Qian Qian
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, People's Republic of China
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Yang C, Liu X, Li D, Zhu X, Wei Z, Feng Z, Zhang L, He J, Mou C, Jiang L, Wan J. OsLUGL is involved in the regulating auxin level and OsARFs expression in rice (Oryza sativa L.). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 288:110239. [PMID: 31521225 DOI: 10.1016/j.plantsci.2019.110239] [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: 05/06/2019] [Revised: 07/27/2019] [Accepted: 08/25/2019] [Indexed: 06/10/2023]
Abstract
Specification of floral organ identity is critical for floral morphology and inflorescence architecture. Floral organ identity in plants is controlled by floral homeotic A/B/C/D/E-class genes. Although multiple genes regulate floral organogenesis, our understanding of the regulatory network remains fragmentary. Here, we characterized a rice floral organ gene KAIKOUXIAO (KKX), mutation of which produces an uncharacteristic open hull, abnormal seed and semi-sterility. KKX encodes a putative LEUNIG-like (LUGL) transcriptional regulator OsLUGL. OsLUGL is preferentially expressed in young panicles and its protein can interact with OsSEU, which functions were reported as an adaptor for LEUNIG. OsLUGL-OsSEU functions together as a transcriptional co-regulatory complex to control organ identity. SEP3 (such as OsMADS8) and AP1 (such as OsMADS18) serve as the DNA-binding partner of OsLUGL-OsSEU complex. Further studies indicated that OsMADS8 and OsMADS18 could bind to the promoter of OsGH3-8. The altered expression of OsGH3-8 might cause the increased auxin level and the decreased expression of OsARFs. Overall, our results demonstrate a possible pathway whereby OsLUGL-OsSEU-OsAP1-OsSEP3 complex as a transcriptional co-regulator by targeting the promoter of OsGH3-8, then affecting auxin level, OsARFs expression and thereby influencing floral development. These findings provide a valuable insight into the molecular functions of OsLUGL in rice floral development.
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Affiliation(s)
- Chunyan Yang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xi Liu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Dianli Li
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xingjie Zhu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ziyao Wei
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhiming Feng
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Long Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jun He
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Changling Mou
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ling Jiang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Jianmin Wan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China; National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Neogy A, Garg T, Kumar A, Dwivedi AK, Singh H, Singh U, Singh Z, Prasad K, Jain M, Yadav SR. Genome-Wide Transcript Profiling Reveals an Auxin-Responsive Transcription Factor, OsAP2/ERF-40, Promoting Rice Adventitious Root Development. PLANT & CELL PHYSIOLOGY 2019; 60:2343-2355. [PMID: 31318417 DOI: 10.1093/pcp/pcz132] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 07/01/2019] [Indexed: 05/09/2023]
Abstract
Unlike dicots, the robust root system in grass species largely originates from stem base during postembryonic development. The mechanisms by which plant hormone signaling pathways control the architecture of adventitious root remain largely unknown. Here, we studied the modulations in global genes activity in developing rice adventitious root by genome-wide RNA sequencing in response to external auxin and cytokinin signaling cues. We further analyzed spatiotemporal regulations of key developmental regulators emerged from our global transcriptome analysis. Interestingly, some of the key cell fate determinants such as homeodomain transcription factor (TF), OsHOX12, no apical meristem protein, OsNAC39, APETALA2/ethylene response factor, OsAP2/ERF-40 and WUSCHEL-related homeobox, OsWOX6.1 and OsWOX6.2, specifically expressed in adventitious root primordia. Functional analysis of one of these regulators, an auxin-induced TF containing AP2/ERF domain, OsAP2/ERF-40, demonstrates its sufficiency to confer the adventitious root fate. The ability to trigger the root developmental program is largely attributed to OsAP2/ERF-40-mediated dose-dependent transcriptional activation of genes that can facilitate generating effective auxin response, and OsERF3-OsWOX11-OsRR2 pathway. Our studies reveal gene regulatory network operating in response to hormone signaling pathways and identify a novel TF regulating adventitious root developmental program, a key agronomically important quantitative trait, upstream of OsERF3-OsWOX11-OsRR2 pathway.
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Affiliation(s)
- Ananya Neogy
- Department of Biotechnology, Indian Institute of Technology, Roorkee, Uttarakhand, India
| | - Tushar Garg
- Department of Biotechnology, Indian Institute of Technology, Roorkee, Uttarakhand, India
| | - Anil Kumar
- Department of Biotechnology, Indian Institute of Technology, Roorkee, Uttarakhand, India
| | - Anuj K Dwivedi
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Harshita Singh
- Department of Biotechnology, Indian Institute of Technology, Roorkee, Uttarakhand, India
| | - Urminder Singh
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Zeenu Singh
- Department of Biotechnology, Indian Institute of Technology, Roorkee, Uttarakhand, India
| | - Kalika Prasad
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala, India
| | - Mukesh Jain
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Shri Ram Yadav
- Department of Biotechnology, Indian Institute of Technology, Roorkee, Uttarakhand, India
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Li Y, Zeng X, Zhuang H, Chen H, Zhang T, Zhang J, Zheng H, Tang J, Wang H, Ren S, Ling Y, He G. Characterization and fine mapping of nonstop glumes 2 ( nsg2) mutant in rice ( Oryza sativa L.). PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2019; 36:125-134. [PMID: 31768114 PMCID: PMC6854344 DOI: 10.5511/plantbiotechnology.19.0506a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 05/06/2019] [Indexed: 06/10/2023]
Abstract
In cereal crops, the grain number per panicle and the grain yield are greatly affected by the number of florets in a spikelet. In wild-type rice, a spikelet only produces one fertile floret and beneath the floret are a pair of sterile lemmas and a pair of rudimentary glumes. This study characterized a rice spikelet mutant nonstop glumes 2 (nsg2). In the nsg2 mutant, both the sterile lemmas and rudimentary glumes were elongated, and part of sterile lemma looked like a lemma in appearance, shape and size. Detailed histological analysis and qPCR analysis revealed that the sterile lemmas in the nsg2 mutant had homeotically transformed into lemma-like organs. This phenotype indicates that NSG2 is involved in the regulation of spikelet development and supports the long-held view that sterile lemmas were derived from the lemmas of the two lateral florets. This implies that the rice spikelet has the potential to be restored to the "three florets spikelet", which may have existed in its ancestors. Genetic analysis reveals that the nsg2 trait is controlled by a single recessive gene. The NSG2 gene was finally mapped between markers R-20 and R-39 on chromosome 7 with a physical region of 180 kb. The two MYB family factors LOC_Os07g44030 and LOC_Os07g44090 might be involved in the development of the spikelet and floral organ, and they were considered as candidate genes of NSG2. These results provide a foundation for map-based cloning and function analysis of NSG2, as well as evidence to support "three-florets spikelet" breeding in rice.
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Affiliation(s)
- Yunfeng Li
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Xiaoqin Zeng
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Hui Zhuang
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Huan Chen
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Ting Zhang
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Jun Zhang
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Hao Zheng
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Jun Tang
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Honglei Wang
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Suxian Ren
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Yinghua Ling
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Guanghua He
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
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Dissecting a heterotic gene through GradedPool-Seq mapping informs a rice-improvement strategy. Nat Commun 2019; 10:2982. [PMID: 31278256 PMCID: PMC6611799 DOI: 10.1038/s41467-019-11017-y] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 06/04/2019] [Indexed: 12/31/2022] Open
Abstract
Hybrid rice breeding for exploiting hybrid vigor, heterosis, has greatly increased grain yield. However, the heterosis-related genes associated with rice grain production remain largely unknown, partly because comprehensive mapping of heterosis-related traits is still labor-intensive and time-consuming. Here, we present a quantitative trait locus (QTL) mapping method, GradedPool-Seq, for rapidly mapping QTLs by whole-genome sequencing of graded-pool samples from F2 progeny via bulked-segregant analysis. We implement this method and map-based cloning to dissect the heterotic QTL GW3p6 from the female line. We then generate the near isogenic line NIL-FH676::GW3p6 by introgressing the GW3p6 allele from the female line Guangzhan63-4S into the male inbred line Fuhui676. The NIL-FH676::GW3p6 exhibits grain yield highly increased compared to Fuhui676. This study demonstrates that it may be possible to achieve a high level of grain production in inbred rice lines without the need to construct hybrids. Developing hybrid rice cultivars requires time consuming random crossing. Here, the authors develop a new next generation sequencing-based quantitative trait locus mapping method to dissect heterotic gene OsMADS1 and demonstrate the feasibility of pyramiding two genes to achieve large heterotic effect.
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Ghaemizadeh F, Dashti F, Shafeinia A. Expression pattern of ABCDE model genes in floral organs of bolting garlic clone. Gene Expr Patterns 2019; 34:119059. [PMID: 31201930 DOI: 10.1016/j.gep.2019.119059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 04/27/2019] [Accepted: 06/03/2019] [Indexed: 11/16/2022]
Abstract
A correct understanding of the ABCDE model genes expression, especially genes involved in the development of the reproductive floral organs, in bolting and fertile garlic clones improves the process of its fertilization and breeding programs. Therefore, Real-Time PCR was employed to evaluate the temporal and spatial expression patterns of some floral organ identity genes in the inflorescence and different floret organs in the two stages of green and purple florets of bolting garlic clone. Relative expression of the studied genes, except AsSTK, in the mature inflorescence increased significantly during the early stages of initiation and differentiation of floral organs. Relative expression of the AsAP1 in the tepal and carpel, and AsAP2 in the tepal, stamen and carpel increased significantly. The highest relative expression levels of the AsAP1 and AsAP2 were found in the tepal of green florets and in the carpel of purple florets, respectively. AsAP3 and AsPI expression increased significantly in the stamen and carpel, and the highest relative expression of these two genes were observed in the green floret tepal. Relative expression of the AsAG increased significantly only in the reproductive floral organs and decreased significantly both in the carpel and stamen at floret maturity. The AsSEP1, 3 were expressed in all floral organs, but the AsSTK was only expressed in the carpel and its relative expression increased significantly at floret maturity. Finally, since considerable expression levels of the above genes were observed in the floral organs, these genes seem to be influential in the formation of floral organs in bolting garlic.
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Affiliation(s)
| | - Farshad Dashti
- Department of Horticultural Science, Bu-Ali Sina University, Hamedan, Iran.
| | - Alireza Shafeinia
- Department of Agronomy and Plant Breeding, Ramin Agriculture and Natural University, Khuzestan, Iran.
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40
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Ali Z, Raza Q, Atif RM, Aslam U, Ajmal M, Chung G. Genetic and Molecular Control of Floral Organ Identity in Cereals. Int J Mol Sci 2019; 20:E2743. [PMID: 31167420 PMCID: PMC6600504 DOI: 10.3390/ijms20112743] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 05/25/2019] [Accepted: 05/28/2019] [Indexed: 12/22/2022] Open
Abstract
Grasses represent a major family of monocots comprising mostly cereals. When compared to their eudicot counterparts, cereals show a remarkable morphological diversity. Understanding the molecular basis of floral organ identity and inflorescence development is crucial to gain insight into the grain development for yield improvement purposes in cereals, however, the exact genetic mechanism of floral organogenesis remains elusive due to their complex inflorescence architecture. Extensive molecular analyses of Arabidopsis and other plant genera and species have established the ABCDE floral organ identity model. According to this model, hierarchical combinatorial activities of A, B, C, D, and E classes of homeotic genes regulate the identity of different floral organs with partial conservation and partial diversification between eudicots and cereals. Here, we review the developmental role of A, B, C, D, and E gene classes and explore the recent advances in understanding the floral development and subsequent organ specification in major cereals with reference to model plants. Furthermore, we discuss the evolutionary relationships among known floral organ identity genes. This comparative overview of floral developmental genes and associated regulatory factors, within and between species, will provide a thorough understanding of underlying complex genetic and molecular control of flower development and floral organ identity, which can be helpful to devise innovative strategies for grain yield improvement in cereals.
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Affiliation(s)
- Zulfiqar Ali
- Institute of Plant Breeding and Biotechnology, Muhammad Nawaz Sharif University of Agriculture, Multan 66000, Pakistan.
| | - Qasim Raza
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan.
- Molecular Breeding Laboratory, Division of Plant Breeding and Genetics, Rice Research Institute, Kala Shah Kaku 39020, Pakistan.
| | - Rana Muhammad Atif
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan.
- Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture, Faisalabad 38000, Pakistan.
| | - Usman Aslam
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan.
| | - Muhammad Ajmal
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan.
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Chonnam 59626, Korea.
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Chongloi GL, Prakash S, Vijayraghavan U. Regulation of meristem maintenance and organ identity during rice reproductive development. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:1719-1736. [PMID: 30753578 DOI: 10.1093/jxb/erz046] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 01/29/2019] [Indexed: 06/09/2023]
Abstract
Grasses have evolved complex inflorescences, where the primary unit is the specialized short branch called a spikelet. Detailed studies of the cumulative action of the genetic regulators that direct the progressive change in axillary meristem identity and their terminal differentiation are crucial to understanding the complexities of the inflorescence and the development of a determinate floret. Grass florets also pose interesting questions concerning the morphologies and functions of organs as compared to other monocots and eudicots. In this review, we summarize our current knowledge of the regulation of the transitions that occur in grass inflorescence meristems, and of the specification of floret meristems and their determinate development. We primarily use rice as a model, with appropriate comparisons to other crop models and to the extensively studied eudicot Arabidopsis. The role of MADS-domain transcription factors in floral organ patterning is well documented in many eudicots and in grasses. However, there is evidence to suggest that some of these rice floral regulators have evolved distinctive functions and that other grass species-specific factors and regulatory pathways occur - for example the LOFSEP 'E' class genes OsMADS1 and OsMAD34, and ramosa genes. A better understanding of these systems and the epigenetic regulators and hormone signaling pathways that interact with them will provide new insights into the rice inflorescence meristem and the differentiation of its floret organs, and should indicate genetic tools that can be used to control yield-related traits in both rice and other cereal crops.
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Affiliation(s)
- Grace L Chongloi
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Sandhan Prakash
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Usha Vijayraghavan
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
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Genome-Wide Identification and Characterization of the ALOG Domain Genes in Rice. Int J Genomics 2019; 2019:2146391. [PMID: 30923712 PMCID: PMC6409076 DOI: 10.1155/2019/2146391] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 01/06/2019] [Indexed: 11/17/2022] Open
Abstract
The ALOG domain genes, named after the Arabidopsis LSH1 and Oryza G1 (ALOG) proteins, have frequently been reported as key developmental regulators in rice and Arabidopsis. However, the investigation of the ALOG gene family is limited. Here, we conducted a genome-wide investigation of the ALOG gene family in rice and six other species. In total, eighty-four ALOG domain genes were identified from the seven species, of which fourteen ALOG domain genes (OsG1/G1Ls) were identified in the rice genome. The fourteen OsG1/G1Ls were unevenly distributed on eight chromosomes, and we found that eight segmental duplications contributed to the expansion of OsG1/G1Ls in the rice genome. The eighty-four ALOG family genes from seven species were classified into six clusters, and the ALOG domain-defined motifs 1, 2, and 3 were highly conserved across species according to the phylogenetic and structural analysis. However, the newly identified motifs 4 and 5 were only present in monocots, indicating a specified function in monocots. Moreover, OsG1/G1Ls exhibited tissue-specific expression patterns. Coexpression analysis suggested that OsG1 integrates OsMADS50 and the downstream MADS-box genes, such as OsMADS1, to regulate the development of rice inflorescence; OsG1L7 potentially associates with OsMADS22 and OsMADS55 to regulate stem elongation. In addition, comparative expression analysis revealed the conserved biological functions of ALOG family genes among rice, maize, and Arabidopsis. These results have shed light on the functional study of ALOG family genes in rice and other plants.
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Huang J, Liu H, Berberich T, Liu Y, Tao LZ, Liu T. Guanine Nucleotide Exchange Factor 7B (RopGEF7B) is involved in floral organ development in Oryza sativa. RICE (NEW YORK, N.Y.) 2018; 11:42. [PMID: 30062598 PMCID: PMC6066601 DOI: 10.1186/s12284-018-0235-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 07/10/2018] [Indexed: 05/22/2023]
Abstract
BACKGROUND RAC/ROP GTPase are versatile signaling molecules controlling diverse biological processes including cell polarity establishment, cell growth, morphogenesis, hormone responses and many other cellular processes in plants. The activities of ROPs are positively regulated by guanine nucleotide exchange factors (GEFs). Evidence suggests that RopGEFs regulate polar auxin transport and polar growth in pollen tube in Arabidopsis thaliana. However, the biological functions of rice RopGEFs during plant development remain largely unknown. RESULTS We investigated a member of the OsRopGEF family, namely OsRopGEF7B. OsRopGEF7Bpro:GUS analysis indicates that OsRopGEF7B is expressed in various tissues, especially in the floral meristem and floral organ primordia. Knock-out and -down of OsRopGEF7B by T-DNA insertion and RNA interference, respectively, predominantly caused an increase in the number of floral organs in the inner whorls (stamen and ovary), as well as abnormal paleae/lemmas and ectopic growth of lodicules, resulting in decline of rice seed setting. Bimolecular fluorescence complement (BiFC) assays as well as yeast two-hybrid assays indicate that OsRopGEF7B interacts with OsRACs. CONCLUSIONS OsRopGEF7B plays roles in floral organ development in rice, affecting rice seed setting rate. Manipulation of OsRopGEF7B has potential for application in genetically modified crops.
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Affiliation(s)
- Jiaqing Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Huili Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Thomas Berberich
- Senckenberg Biodiversity and Climate Research Center, Georg-Voigt-Str. 14-16, D-60325, Frankfurt am Main, Germany
| | - Yuting Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Li-Zhen Tao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642, China.
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
| | - Taibo Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642, China.
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
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Callens C, Tucker MR, Zhang D, Wilson ZA. Dissecting the role of MADS-box genes in monocot floral development and diversity. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:2435-2459. [PMID: 29718461 DOI: 10.1093/jxb/ery086] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 03/16/2018] [Indexed: 05/05/2023]
Abstract
Many monocot plants have high social and economic value. These include grasses such as rice (Oryza sativa), wheat (Triticum aestivum), and barley (Hordeum vulgare), which produce soft commodities for many food and beverage industries, and ornamental flowers such ase lily (Lilium longiflorum) and orchid (Oncidium Gower Ramsey), which represent an important component of international flower markets. There is constant pressure to improve the development and diversity of these species, with a significant emphasis on flower development, and this is particularly relevant considering the impact of changing environments on reproduction and thus yield. MADS-box proteins are a family of transcription factors that contain a conserved 60 amino acid MADS-box motif. In plants, attention has been devoted to characterization of this family due to their roles in inflorescence and flower development, which holds promise for the modification of floral architecture for plant breeding. This has been explored in diverse angiosperms, but particularly the dicot model Arabidopsis thaliana. The focus of this review is on the less well characterized roles of the MADS-box proteins in monocot flower development and how changes in MADS-box proteins throughout evolution may have contributed to creating a diverse range of flowers. Examining these changes within the monocots can identify the importance of certain genes and pinpoint those which might be useful in future crop improvement and breeding strategies.
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Affiliation(s)
- Cindy Callens
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, UK
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA, Australia
| | - Matthew R Tucker
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA, Australia
| | - Dabing Zhang
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA, Australia
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Zoe A Wilson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, UK
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Transcriptome Analysis of Litsea cubeba Floral Buds Reveals the Role of Hormones and Transcription Factors in the Differentiation Process. G3-GENES GENOMES GENETICS 2018; 8:1103-1114. [PMID: 29487185 PMCID: PMC5873901 DOI: 10.1534/g3.117.300481] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
BACKGROUND Litsea cubeba (Lour.) Pers. is an important economic plant that is rich in valuable essential oil. The essential oil is often used as a raw material for perfumes, food additives, insecticides and bacteriostats. Most of the essential oil is contained in the fruit, and the quantity and quality of fruit are dependent on the flowers. To explore the molecular mechanism of floral bud differentiation, high-throughput RNA sequencing was used to detect differences in the gene expression of L. cubeba female and male floral buds at three differentiation stages. RESULTS This study obtained 160.88 Gbp of clean data that were assembled into 100,072 unigenes, and a total of 38,658 unigenes were annotated. A total of 27,521 simple sequence repeats (SSRs) were identified after scanning the assembled transcriptome, and the mono-nucleotide repeats were predominant, followed by di-nucleotide and tri-nucleotide repeats. A total of 12,559 differentially expressed genes (DEGs) were detected from the female (F) and male (M) floral bud comparisons. The gene ontology (GO) databases revealed that these DEGs were primarily contained in "metabolic processes", "cellular processes", and "single-organism processes". The Kyoto Encyclopedia of Genes and Genomes (KEGG) databases suggested that the DEGs belonged to "plant hormone signal transduction" and accounted for a relatively large portion in all of these comparisons. We analyzed the expression level of plant hormone-related genes and detected the contents of several relevant plant hormones in different stages. The results revealed that the dynamic changes in each hormone content were almost consistent with the expression levels of relevant genes. The transcription factors selected from the DEGs were analyzed. Most DEGs of MADS-box were upregulated and most DEGs of bZIP were downregulated. The expression trends of the DEGs were nearly identical in female and male floral buds, and qRT-PCR analysis revealed consistency with the transcriptome data. CONCLUSIONS We sequenced and assembled a high-quality L. cubeba floral bud transcriptome, and the data appeared to be well replicated (n = 3) over three developmental time points during flower development. Our study explored the changes in the contents of several plant hormones during floral bud differentiation using biochemical and molecular biology techniques, and the changes in expression levels of several flower development related transcription factors. These results revealed the role of these factors (i.e., hormones and transcription factors) and may advance our understanding of their functions in flower development in L. cubeba.
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Liu Q, Han R, Wu K, Zhang J, Ye Y, Wang S, Chen J, Pan Y, Li Q, Xu X, Zhou J, Tao D, Wu Y, Fu X. G-protein βγ subunits determine grain size through interaction with MADS-domain transcription factors in rice. Nat Commun 2018; 9:852. [PMID: 29487282 PMCID: PMC5829230 DOI: 10.1038/s41467-018-03047-9] [Citation(s) in RCA: 154] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 01/12/2018] [Indexed: 01/16/2023] Open
Abstract
The simultaneous improvement of grain quality and yield of cereal crops is a major challenge for modern agriculture. Here we show that a rice grain yield quantitative trait locus qLGY3 encodes a MADS-domain transcription factor OsMADS1, which acts as a key downstream effector of G-protein βγ dimers. The presence of an alternatively spliced protein OsMADS1lgy3 is shown to be associated with formation of long and slender grains, resulting in increases in both grain quality and yield potential of rice. The Gγ subunits GS3 and DEP1 interact directly with the conserved keratin-like domain of MADS transcription factors, function as cofactors to enhance OsMADS1 transcriptional activity and promote the co-operative transactivation of common target genes, thereby regulating grain size and shape. We also demonstrate that combining OsMADS1 lgy3 allele with high-yield-associated dep1-1 and gs3 alleles represents an effective strategy for simultaneously improving both the productivity and end-use quality of rice.
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Affiliation(s)
- Qian Liu
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Ruixi Han
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China.,Development Center for Science and Technology, Ministry of Agriculture, 100122, Beijing, China
| | - Kun Wu
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China.,Institute of Technical Biology and Agriculture Engineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences, 230031, Hefei, China
| | - Jianqing Zhang
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Yafeng Ye
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Shuansuo Wang
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Jianfeng Chen
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Yajun Pan
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Qi Li
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Xiaopeng Xu
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China.,Root Biology Center, South China Agricultural University, 510642, Guangzhou, China
| | - Jiawu Zhou
- Food Crops Research, Institute Yunnan Academy of Agricultural Sciences, 650200, Kunming, China
| | - Dayun Tao
- Food Crops Research, Institute Yunnan Academy of Agricultural Sciences, 650200, Kunming, China
| | - Yuejin Wu
- Institute of Technical Biology and Agriculture Engineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences, 230031, Hefei, China
| | - Xiangdong Fu
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China. .,College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China.
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Yu J, Miao J, Zhang Z, Xiong H, Zhu X, Sun X, Pan Y, Liang Y, Zhang Q, Abdul Rehman RM, Li J, Zhang H, Li Z. Alternative splicing of OsLG3b controls grain length and yield in japonica rice. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:1667-1678. [PMID: 29479793 PMCID: PMC6097128 DOI: 10.1111/pbi.12903] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 12/31/2017] [Accepted: 02/03/2018] [Indexed: 05/18/2023]
Abstract
Grain size, one of the important components determining grain yield in rice, is controlled by the multiple quantitative trait loci (QTLs). Intensive artificial selection for grain size during domestication is evidenced in modern cultivars compared to their wild relatives. Here, we report the molecular cloning and characterization of OsLG3b, a QTL for grain length in tropical japonica rice that encodes MADS-box transcription factor 1 (OsMADS1). Six SNPs in the OsLG3b region led to alternative splicing, which were associated with grain length in an association analysis of candidate region. Quantitative PCR analysis indicated that OsLG3b expression was higher during the panicle and seed development stages. Analysis of haplotypes and introgression regions revealed that the long-grain allele of OsLG3b might have arisen after domestication of tropical japonica and spread to subspecies indica or temperate japonica by natural crossing and artificial selection. OsLG3b is therefore a target of human selection for adaptation to tropical regions during domestication and/or improvement of rice. Phylogenetic analysis and pedigree records showed that OsLG3b had been employed by breeders, but the gene still has much breeding potential for increasing grain length in indica. These findings will not only aid efforts to elucidate the molecular basis of grain development and domestication, but also facilitate the genetic improvement of rice yield.
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Affiliation(s)
- Jianping Yu
- Key Laboratory of Crop Heterosis and UtilizationMinistry of Education/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
| | - Jinli Miao
- Key Laboratory of Crop Heterosis and UtilizationMinistry of Education/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
| | - Zhanying Zhang
- Key Laboratory of Crop Heterosis and UtilizationMinistry of Education/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
| | - Haiyan Xiong
- Key Laboratory of Crop Heterosis and UtilizationMinistry of Education/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
| | - Xiaoyang Zhu
- Key Laboratory of Crop Heterosis and UtilizationMinistry of Education/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
| | - Xingming Sun
- Key Laboratory of Crop Heterosis and UtilizationMinistry of Education/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
| | - Yinghua Pan
- China/Guangxi Key Laboratory of Rice Genetics and BreedingRice Research InstituteGuangxi Academy of Agricultural SciencesNanningGuangxiChina
| | - Yuntao Liang
- China/Guangxi Key Laboratory of Rice Genetics and BreedingRice Research InstituteGuangxi Academy of Agricultural SciencesNanningGuangxiChina
| | - Qiang Zhang
- Key Laboratory of Crop Heterosis and UtilizationMinistry of Education/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
| | - Rashid Muhammad Abdul Rehman
- Key Laboratory of Crop Heterosis and UtilizationMinistry of Education/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
| | - Jinjie Li
- Key Laboratory of Crop Heterosis and UtilizationMinistry of Education/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
| | - Hongliang Zhang
- Key Laboratory of Crop Heterosis and UtilizationMinistry of Education/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
| | - Zichao Li
- Key Laboratory of Crop Heterosis and UtilizationMinistry of Education/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
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Ma X, Zheng Z, Lin F, Ge T, Sun H. Genetic analysis and gene mapping of a low stigma exposed mutant gene by high-throughput sequencing. PLoS One 2018; 13:e0186942. [PMID: 29298308 PMCID: PMC5751978 DOI: 10.1371/journal.pone.0186942] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Accepted: 10/10/2017] [Indexed: 12/02/2022] Open
Abstract
Rice is one of the main food crops and several studies have examined the molecular mechanism of the exposure of the rice plant stigma. The improvement in the exposure of the stigma in female parent hybrid combinations can enhance the efficiency of hybrid breeding. In the present study, a mutant plant with low exposed stigma (lesr) was discovered among the descendants of the indica thermo-sensitive sterile line 115S. The ES% rate of the mutant decreased by 70.64% compared with the wild type variety. The F2 population was established by genetic analysis considering the mutant as the female parent and the restorer line 93S as the male parent. The results indicated a normal F1 population, while a clear division was noted for the high and low exposed stigma groups, respectively. This process was possible only by a ES of 25% in the F2 population. This was in agreement with the ratio of 3:1, which indicated that the mutant was controlled by a recessive main-effect QTL locus, temporarily named as LESR. Genome-wide comparison of the SNP profiles between the early, high and low production bulks were constructed from F2 plants using bulked segregant analysis in combination with high-throughput sequencing technology. The results demonstrated that the candidate loci was located on the chromosome 10 of the rice. Following screening of the recombinant rice plants with newly developed molecular markers, the genetic region was narrowed down to 0.25 Mb. This region was flanked by InDel-2 and InDel-2 at the physical location from 13.69 to 13.94 Mb. Within this region, 7 genes indicated base differences between parents. A total of 2 genes exhibited differences at the coding region and upstream of the coding region, respectively. The present study aimed to further clone the LESR gene, verify its function and identify the stigma variation.
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Affiliation(s)
- Xiao Ma
- College of Life Science, Jinggangshan University, Ji’ an, China
| | - Zhuo Zheng
- College of Life Science, Jinggangshan University, Ji’ an, China
| | - Fanshu Lin
- College of Life Science, Jinggangshan University, Ji’ an, China
| | - Tingting Ge
- College of Life Science, Jinggangshan University, Ji’ an, China
| | - Huimin Sun
- College of Life Science, Jinggangshan University, Ji’ an, China
- * E-mail:
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Yoon H, Yang J, Liang W, Zhang D, An G. OsVIL2 Regulates Spikelet Development by Controlling Regulatory Genes in Oryza sativa. FRONTIERS IN PLANT SCIENCE 2018; 9:102. [PMID: 29467779 PMCID: PMC5808121 DOI: 10.3389/fpls.2018.00102] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Accepted: 01/18/2018] [Indexed: 05/08/2023]
Abstract
Flower organ patterning is accomplished by spatial and temporal functioning of various regulatory genes. We previously reported that Oryza sativa VIN3-LIKE 2 (OsVIL2) induces flowering by mediating the trimethylation of Histone H3 on LFL1 chromatin. In this study, we report that OsVIL2 also plays crucial roles during spikelet development. Two independent lines of T-DNA insertional mutants in the gene displayed altered organ numbers and abnormal morphology in all spikelet organs. Scanning electron microscopy showed that osvil2 affected organ primordia formation during early spikelet development. Expression analysis revealed that OsVIL2 is expressed in all stages of the spikelet developmental. Transcriptome analysis of developing spikelets revealed that several regulatory genes involved in that process and the formation of floral organs were down-regulated in osvil2. These results suggest that OsVIL2 is required for proper expression of the regulatory genes that control floral organ number and morphology.
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Affiliation(s)
- Hyeryung Yoon
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, South Korea
| | - Jungil Yang
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, South Korea
| | - Wanqi Liang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University–University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University–University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Gynheung An
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, South Korea
- *Correspondence: Gynheung An,
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