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Liu X, Deng M, Shi B, Zhu K, Chen J, Xu S, Bie X, Zhang X, Lin X, Xiao J. Distinct roles of H3K27me3 and H3K36me3 in vernalization response, maintenance, and resetting in winter wheat. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-024-2664-0. [PMID: 38987431 DOI: 10.1007/s11427-024-2664-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Accepted: 06/25/2024] [Indexed: 07/12/2024]
Abstract
Winter plants rely on vernalization, a crucial process for adapting to cold conditions and ensuring successful reproduction. However, understanding the role of histone modifications in guiding the vernalization process in winter wheat remains limited. In this study, we investigated the transcriptome and chromatin dynamics in the shoot apex throughout the life cycle of winter wheat in the field. Two core histone modifications, H3K27me3 and H3K36me3, exhibited opposite patterns on the key vernalization gene VERNALIZATION1 (VRN1), correlating with its induction during cold exposure. Moreover, the H3K36me3 level remained high at VRN1 after cold exposure, which may maintain its active state. Mutations in FERTILIZATION-INDEPENDENT ENDOSPERM (TaFIE) and SET DOMAIN GROUP 8/EARLY FLOWERING IN SHORT DAYS (TaSDG8/TaEFS), components of the writer complex for H3K27me3 and H3K36me3, respectively, affected flowering time. Intriguingly, VRN1 lost its high expression after the cold exposure memory in the absence of H3K36me3. During embryo development, VRN1 was silenced with the removal of active histone modifications in both winter and spring wheat, with selective restoration of H3K27me3 in winter wheat. The mutant of Tafie-cr-87, a component of H3K27me3 "writer" complex, did not influence the silence of VRN1 during embryo development, but rather attenuated the cold exposure requirement of winter wheat. Integrating gene expression with H3K27me3 and H3K36me3 patterns identified potential regulators of flowering. This study unveils distinct roles of H3K27me3 and H3K36me3 in controlling vernalization response, maintenance, and resetting in winter wheat.
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Affiliation(s)
- Xuemei Liu
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Min Deng
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bingxin Shi
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Kehui Zhu
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jinchao Chen
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shujuan Xu
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, 3400, Austria
| | - Xiaomin Bie
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Xiansheng Zhang
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Xuelei Lin
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Jun Xiao
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Centre of Excellence for Plant and Microbial Science (CEPAMS), JIC-CAS, Beijing, 100101, China.
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Dong K, Wu F, Cheng S, Li S, Zhang F, Xing X, Jin X, Luo S, Feng M, Miao R, Chang Y, Zhang S, You X, Wang P, Zhang X, Lei C, Ren Y, Zhu S, Guo X, Wu C, Yang DL, Lin Q, Cheng Z, Wan J. OsPRMT6a-mediated arginine methylation of OsJAZ1 regulates jasmonate signaling and spikelet development in rice. MOLECULAR PLANT 2024; 17:900-919. [PMID: 38704640 DOI: 10.1016/j.molp.2024.04.014] [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: 12/07/2023] [Revised: 04/04/2024] [Accepted: 04/29/2024] [Indexed: 05/06/2024]
Abstract
Although both protein arginine methylation (PRMT) and jasmonate (JA) signaling are crucial for regulating plant development, the relationship between these processes in the control of spikelet development remains unclear. In this study, we used the CRISPR/Cas9 technology to generate two OsPRMT6a loss-of-function mutants that exhibit various abnormal spikelet structures. Interestingly, we found that OsPRMT6a can methylate arginine residues in JA signal repressors OsJAZ1 and OsJAZ7. We showed that arginine methylation of OsJAZ1 enhances the binding affinity of OsJAZ1 with the JA receptors OsCOI1a and OsCOI1b in the presence of JAs, thereby promoting the ubiquitination of OsJAZ1 by the SCFOsCOI1a/OsCOI1b complex and degradation via the 26S proteasome. This process ultimately releases OsMYC2, a core transcriptional regulator in the JA signaling pathway, to activate or repress JA-responsive genes, thereby maintaining normal plant (spikelet) development. However, in the osprmt6a-1 mutant, reduced arginine methylation of OsJAZ1 impaires the interaction between OsJAZ1 and OsCOI1a/OsCOI1b in the presence of JAs. As a result, OsJAZ1 proteins become more stable, repressing JA responses, thus causing the formation of abnormal spikelet structures. Moreover, we discovered that JA signaling reduces the OsPRMT6a mRNA level in an OsMYC2-dependent manner, thereby establishing a negative feedback loop to balance JA signaling. We further found that OsPRMT6a-mediated arginine methylation of OsJAZ1 likely serves as a switch to tune JA signaling to maintain normal spikelet development under harsh environmental conditions such as high temperatures. Collectively, our study establishes a direct molecular link between arginine methylation and JA signaling in rice.
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Affiliation(s)
- Kun Dong
- State Key Laboratory of Crop Gene Resources and Breeding, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Fuqing Wu
- State Key Laboratory of Crop Gene Resources and Breeding, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Siqi Cheng
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Shuai Li
- State Key Laboratory of Crop Gene Resources and Breeding, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Feng Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xinxin Xing
- State Key Laboratory of Crop Gene Resources and Breeding, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xin Jin
- State Key Laboratory of Crop Gene Resources and Breeding, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Sheng Luo
- State Key Laboratory of Crop Gene Resources and Breeding, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Miao Feng
- State Key Laboratory of Crop Gene Resources and Breeding, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Rong Miao
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Yanqi Chang
- State Key Laboratory of Crop Gene Resources and Breeding, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shuang Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaoman You
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Peiran Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Xin Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Cailin Lei
- State Key Laboratory of Crop Gene Resources and Breeding, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yulong Ren
- State Key Laboratory of Crop Gene Resources and Breeding, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shanshan Zhu
- State Key Laboratory of Crop Gene Resources and Breeding, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiuping Guo
- State Key Laboratory of Crop Gene Resources and Breeding, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chuanyin Wu
- State Key Laboratory of Crop Gene Resources and Breeding, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Dong-Lei Yang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Qibing Lin
- State Key Laboratory of Crop Gene Resources and Breeding, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Zhijun Cheng
- State Key Laboratory of Crop Gene Resources and Breeding, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Jianmin Wan
- State Key Laboratory of Crop Gene Resources and Breeding, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.
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Usai G, Fambrini M, Pugliesi C, Simoni S. Exploring the patterns of evolution: Core thoughts and focus on the saltational model. Biosystems 2024; 238:105181. [PMID: 38479653 DOI: 10.1016/j.biosystems.2024.105181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/29/2024] [Accepted: 03/08/2024] [Indexed: 03/18/2024]
Abstract
The Modern Synthesis, a pillar in biological thought, united Darwin's species origin concepts with Mendel's laws of character heredity, providing a comprehensive understanding of evolution within species. Highlighting phenotypic variation and natural selection, it elucidated the environment's role as a selective force, shaping populations over time. This framework integrated additional mechanisms, including genetic drift, random mutations, and gene flow, predicting their cumulative effects on microevolution and the emergence of new species. Beyond the Modern Synthesis, the Extended Evolutionary Synthesis expands perspectives by recognizing the role of developmental plasticity, non-genetic inheritance, and epigenetics. We suggest that these aspects coexist in the plant evolutionary process; in this context, we focus on the saltational model, emphasizing how saltation events, such as dichotomous saltation, chromosomal mutations, epigenetic phenomena, and polyploidy, contribute to rapid evolutionary changes. The saltational model proposes that certain evolutionary changes, such as the rise of new species, may result suddenly from single macromutations rather than from gradual changes in DNA sequences and allele frequencies within a species over time. These events, observed in domesticated and wild higher plants, provide well-defined mechanistic bases, revealing their profound impact on plant diversity and rapid evolutionary events. Notably, next-generation sequencing exposes the likely crucial role of allopolyploidy and autopolyploidy (saltational events) in generating new plant species, each characterized by distinct chromosomal complements. In conclusion, through this review, we offer a thorough exploration of the ongoing dissertation on the saltational model, elucidating its implications for our understanding of plant evolutionary processes and paving the way for continued research in this intriguing field.
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Affiliation(s)
- Gabriele Usai
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Marco Fambrini
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Claudio Pugliesi
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy.
| | - Samuel Simoni
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
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Lin X, Xu Y, Wang D, Yang Y, Zhang X, Bie X, Gui L, Chen Z, Ding Y, Mao L, Zhang X, Lu F, Zhang X, Uauy C, Fu X, Xiao J. Systematic identification of wheat spike developmental regulators by integrated multi-omics, transcriptional network, GWAS, and genetic analyses. MOLECULAR PLANT 2024; 17:438-459. [PMID: 38310351 DOI: 10.1016/j.molp.2024.01.010] [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: 08/14/2023] [Revised: 11/29/2023] [Accepted: 01/30/2024] [Indexed: 02/05/2024]
Abstract
The spike architecture of wheat plays a crucial role in determining grain number, making it a key trait for optimization in wheat breeding programs. In this study, we used a multi-omic approach to analyze the transcriptome and epigenome profiles of the young spike at eight developmental stages, revealing coordinated changes in chromatin accessibility and H3K27me3 abundance during the flowering transition. We constructed a core transcriptional regulatory network (TRN) that drives wheat spike formation and experimentally validated a multi-layer regulatory module involving TaSPL15, TaAGLG1, and TaFUL2. By integrating the TRN with genome-wide association studies, we identified 227 transcription factors, including 42 with known functions and 185 with unknown functions. Further investigation of 61 novel transcription factors using multiple homozygous mutant lines revealed 36 transcription factors that regulate spike architecture or flowering time, such as TaMYC2-A1, TaMYB30-A1, and TaWRKY37-A1. Of particular interest, TaMYB30-A1, downstream of and repressed by WFZP, was found to regulate fertile spikelet number. Notably, the excellent haplotype of TaMYB30-A1, which contains a C allele at the WFZP binding site, was enriched during wheat breeding improvement in China, leading to improved agronomic traits. Finally, we constructed a free and open access Wheat Spike Multi-Omic Database (http://39.98.48.156:8800/#/). Our study identifies novel and high-confidence regulators and offers an effective strategy for dissecting the genetic basis of wheat spike development, with practical value for wheat breeding.
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Affiliation(s)
- Xuelei Lin
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yongxin Xu
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dongzhi Wang
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Yiman Yang
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Xiaoyu Zhang
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaomin Bie
- Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Lixuan Gui
- Department of Life Science, Tcuni Inc., Chengdu, Sichuan 610000, China
| | - Zhongxu Chen
- Department of Life Science, Tcuni Inc., Chengdu, Sichuan 610000, China
| | - Yiliang Ding
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Long Mao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xueyong Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Fei Lu
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, CAS, Beijing 100101, China
| | - Xiansheng Zhang
- Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Xiangdong Fu
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Xiao
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, CAS, Beijing 100101, China.
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Peng G, Liu M, Luo Z, Deng S, Wang Q, Wang M, Chen H, Xiao Y, Zhang Y, Hong H, Zhu L, Liu Z, Zhou L, Wang Y, Zhuang C, Zhou H. An E3 ubiquitin ligase CSIT2 controls critical sterility-inducing temperature of thermo-sensitive genic male sterile rice. THE NEW PHYTOLOGIST 2024; 241:2059-2074. [PMID: 38197218 DOI: 10.1111/nph.19520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 12/08/2023] [Indexed: 01/11/2024]
Abstract
Thermo-sensitive genic male sterile (TGMS) lines are the core of two-line hybrid rice (Oryza sativa). However, elevated or unstable critical sterility-inducing temperatures (CSITs) of TGMS lines are bottlenecks that restrict the development of two-line hybrid rice. However, the genes and molecular mechanisms controlling CSIT remain unknown. Here, we report the CRITICAL STERILITY-INDUCING TEMPERATURE 2 (CSIT2) that encodes a really interesting new gene (RING) type E3 ligase, controlling the CSIT of thermo-sensitive male sterility 5 (tms5)-based TGMS lines through ribosome-associated protein quality control (RQC). CSIT2 binds to the large and small ribosomal subunits and ubiquitinates 80S ribosomes for dissociation, and may also ubiquitinate misfolded proteins for degradation. Mutation of CSIT2 inhibits the possible damage to ubiquitin system and protein translation, which allows more proteins such as catalases to accumulate for anther development and inhibits abnormal accumulation of reactive oxygen species (ROS) and premature programmed cell death (PCD) in anthers, partly rescuing male sterility and raised the CSIT of tms5-based TGMS lines. These findings reveal a mechanism controlling CSIT and provide a strategy for solving the elevated or unstable CSITs of tms5-based TGMS lines in two-line hybrid rice.
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Affiliation(s)
- Guoqing Peng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
- College of Agriculture & Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Minglong Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Ziliang Luo
- Agronomy Department, University of Florida, Gainesville, FL, 32610, USA
| | - Shuangfan Deng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Qinghua Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Mumei Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Huiqiong Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yueping Xiao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yongjie Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Haona Hong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Liya Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Zhenlan Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Lingyan Zhou
- College of Agriculture & Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Yingxiang Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Chuxiong Zhuang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Hai Zhou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
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Fang H, Chen H, Wang J, Li N, Zhang L, Wei C. G1 Interacts with OsMADS1 to Regulate the Development of the Sterile Lemma in Rice. PLANTS (BASEL, SWITZERLAND) 2024; 13:505. [PMID: 38498476 PMCID: PMC10892649 DOI: 10.3390/plants13040505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 02/04/2024] [Accepted: 02/08/2024] [Indexed: 03/20/2024]
Abstract
Flower development, as the basis for plant seed development, is principally conserved in angiosperms. At present, a number of genes regulating flower organ differentiation have been identified, and an ABCDE model has also been proposed. In contrast, the mechanism that regulates the development of the sterile lemma remains unclear. In this study, we identified and characterized a rice floral organ mutant, M15, in which the sterile lemma transformed into a lemma-like organ. Positional cloning combined with a complementary experiment demonstrated that the mutant phenotype was restored by LONG STERILE LEMMA1/(G1). G1 was expressed constitutively in various tissues, with the highest expression levels detected in the sterile lemma and young panicle. G1 is a nucleus-localized protein and functions as a homomer. Biochemical assays showed that G1 physically interacted with OsMADS1 both in vitro and in vivo. Interestingly, the expression of G1 in M15 decreased, while the expression level of OsMADS1 increased compared with the wild type. We demonstrate that G1 plays a key role in sterile lemma development through cooperating with OsMADS1. The above results have implications for further research on the molecular mechanisms underlying flower development and may have potential applications in crop improvement strategies.
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Affiliation(s)
- Huimin Fang
- Guangling College, Yangzhou University, Yangzhou 225000, China; (H.F.); (J.W.)
| | - Hualan Chen
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China; (H.C.); (N.L.); (L.Z.)
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Joint International Research Laboratory of Agriculture & Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Jianing Wang
- Guangling College, Yangzhou University, Yangzhou 225000, China; (H.F.); (J.W.)
| | - Ning Li
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China; (H.C.); (N.L.); (L.Z.)
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Joint International Research Laboratory of Agriculture & Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Long Zhang
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China; (H.C.); (N.L.); (L.Z.)
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Joint International Research Laboratory of Agriculture & Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Cunxu Wei
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China; (H.C.); (N.L.); (L.Z.)
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Joint International Research Laboratory of Agriculture & Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
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Zhang Y, Shen C, Li G, Shi J, Yuan Y, Ye L, Song Q, Shi J, Zhang D. MADS1-regulated lemma and awn development benefits barley yield. Nat Commun 2024; 15:301. [PMID: 38182608 PMCID: PMC10770128 DOI: 10.1038/s41467-023-44457-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 12/14/2023] [Indexed: 01/07/2024] Open
Abstract
Floral organ shape and size in cereal crops can affect grain size and yield, so genes that regulate their development are promising breeding targets. The lemma, which protects inner floral organs, can physically constrain grain growth; while the awn, a needle-like extension of the lemma, creates photosynthate to developing grain. Although several genes and modules controlling grain size and awn/lemma growth in rice have been characterized, these processes, and the relationships between them, are not well understood for barley and wheat. Here, we demonstrate that the barley E-class gene HvMADS1 positively regulates awn length and lemma width, affecting grain size and weight. Cytological data indicates that HvMADS1 promotes awn and lemma growth by promoting cell proliferation, while multi-omics data reveals that HvMADS1 target genes are associated with cell cycle, phytohormone signaling, and developmental processes. We define two potential targets of HvMADS1 regulation, HvSHI and HvDL, whose knockout mutants mimic awn and/or lemma phenotypes of mads1 mutants. Additionally, we demonstrate that HvMADS1 interacts with APETALA2 (A-class) to synergistically activate downstream genes in awn/lemma development in barley. Notably, we find that MADS1 function remains conserved in wheat, promoting cell proliferation to increase awn length. These findings extend our understanding of MADS1 function in floral organ development and provide insights for Triticeae crop improvement strategies.
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Affiliation(s)
- Yueya Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Chaoqun Shen
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- School of Agriculture, Food and Wine, The University of Adelaide, Waite Campus, Adelaide, SA, 5064, Australia
| | - Gang Li
- School of Agriculture, Food and Wine, The University of Adelaide, Waite Campus, Adelaide, SA, 5064, Australia.
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Jin Shi
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yajing Yuan
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Lingzhen Ye
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Qingfeng Song
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Jianxin Shi
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, 572025, China.
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- School of Agriculture, Food and Wine, The University of Adelaide, Waite Campus, Adelaide, SA, 5064, Australia
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, 572025, China
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8
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Shen C, Zhang Y, Li G, Shi J, Wang D, Zhu W, Yang X, Dreni L, Tucker MR, Zhang D. MADS8 is indispensable for female reproductive development at high ambient temperatures in cereal crops. THE PLANT CELL 2023; 36:65-84. [PMID: 37738656 PMCID: PMC10734617 DOI: 10.1093/plcell/koad246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 07/25/2023] [Accepted: 07/27/2023] [Indexed: 09/24/2023]
Abstract
Temperature is a major factor that regulates plant growth and phenotypic diversity. To ensure reproductive success at a range of temperatures, plants must maintain developmental stability of their sexual organs when exposed to temperature fluctuations. However, the mechanisms integrating plant floral organ development and temperature responses are largely unknown. Here, we generated barley and rice loss-of-function mutants in the SEPALLATA-like MADS-box gene MADS8. The mutants in both species form multiple carpels that lack ovules at high ambient temperatures. Tissue-specific markers revealed that HvMADS8 is required to maintain floral meristem determinacy and ovule initiation at high temperatures, and transcriptome analyses confirmed that temperature-dependent differentially expressed genes in Hvmads8 mutants predominantly associate with floral organ and meristem regulation. HvMADS8 temperature-responsive activity relies on increased binding to promoters of downstream targets, as revealed by a cleavage under targets and tagmentation (CUT&Tag) analysis. We also demonstrate that HvMADS8 directly binds to 2 orthologs of D-class floral homeotic genes to activate their expression. Overall, our findings revealed a new, conserved role for MADS8 in maintaining pistil number and ovule initiation in cereal crops, extending the known function of plant MADS-box proteins in floral organ regulation.
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Affiliation(s)
- Chaoqun Shen
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 20040, China
- Waite Research Institute, School of Agriculture, Food and Wine, The University of Adelaide, Waite campus, Adelaide, South Australia 5064, Australia
| | - Yueya Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 20040, China
| | - Gang Li
- Waite Research Institute, School of Agriculture, Food and Wine, The University of Adelaide, Waite campus, Adelaide, South Australia 5064, Australia
| | - Jin Shi
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 20040, China
| | - Duoxiang Wang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 20040, China
| | - Wanwan Zhu
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 20040, China
| | - Xiujuan Yang
- Waite Research Institute, School of Agriculture, Food and Wine, The University of Adelaide, Waite campus, Adelaide, South Australia 5064, Australia
| | - Ludovico Dreni
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 20040, China
| | - Matthew R Tucker
- Waite Research Institute, School of Agriculture, Food and Wine, The University of Adelaide, Waite campus, Adelaide, South Australia 5064, Australia
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 20040, China
- Waite Research Institute, School of Agriculture, Food and Wine, The University of Adelaide, Waite campus, Adelaide, South Australia 5064, Australia
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9
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Wang W, Chen W, Wang J. FRIZZLE PANICLE (FZP) regulates rice spikelets development through modulating cytokinin metabolism. BMC PLANT BIOLOGY 2023; 23:650. [PMID: 38102566 PMCID: PMC10724965 DOI: 10.1186/s12870-023-04671-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 12/07/2023] [Indexed: 12/17/2023]
Abstract
BACKGROUND The number of grains per panicle is an important factor in determining rice yield. The DST-OsCKX2 module has been demonstrated to regulate panicle development in rice by controlling cytokinin content. However, to date, how the function of DST-OsCKX2 module is regulated during panicle development remains obscure. RESULT In this study, the ABNORMAL PANICLE 1 (ABP1), a severely allele of FRIZZY PANICLE (FZP), exhibits abnormal spikelets morphology. We show that FZP can repress the expression of DST via directly binding to its promotor. Consistently, the expression level of OsCKX2 increased and the cytokinin content decreased in the fzp mutant, suggesting that the FZP acts upstream of the DST-OsCKX2 to maintain cytokinin homeostasis in the inflorescence meristem. CONCLUSIONS Our results indicate that FZP plays an important role in regulating spikelet development and grain number through mediating cytokinin metabolism.
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Affiliation(s)
- Wei Wang
- Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Wenqiang Chen
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/College of Agriculture, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Junmin Wang
- Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
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10
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Qu K, Liu A, Yin M, Mu W, Wu S, Hu H, Chen J, Su X, Dou Q, Ren G. A genome assembly for Orinus kokonorica provides insights into the origin, adaptive evolution and further diversification of two closely related grass genera. Commun Biol 2023; 6:1223. [PMID: 38042963 PMCID: PMC10693610 DOI: 10.1038/s42003-023-05620-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 11/21/2023] [Indexed: 12/04/2023] Open
Abstract
Ancient whole-genome duplication (WGD) or polyploidization is prevalent in plants and has played a crucial role in plant adaptation. However, the underlying genomic basis of ecological adaptation and subsequent diversification after WGD are still poorly understood in most plants. Here, we report a chromosome-scale genome assembly for the genus Orinus (Orinus kokonorica as representative) and preform comparative genomics with its closely related genus Cleistogenes (Cleistogenes songorica as representative), both belonging to a newly named subtribe Orininae of the grass subfamily Chloridoideae. The two genera may share one paleo-allotetraploidy event before 10 million years ago, and the two subgenomes of O. kokonorica display neither fractionation bias nor global homoeolog expression dominance. We find substantial genome rearrangements and extensive structural variations (SVs) between the two species. With comparative transcriptomics, we demonstrate that functional innovations of orthologous genes may have played an important role in promoting adaptive evolution and diversification of the two genera after polyploidization. In addition, copy number variations and extensive SVs between orthologs of flower and rhizome related genes may contribute to the morphological differences between the two genera. Our results provide new insights into the adaptive evolution and subsequent diversification of the two genera after polyploidization.
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Affiliation(s)
- Kunjing Qu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Ai Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Mou Yin
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Wenjie Mu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Shuang Wu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Hongyin Hu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Jinyuan Chen
- Key Laboratory of Biodiversity Formation Mechanism and Comprehensive Utilization of the Qinghai-Tibet Plateau in Qinghai Province, Qinghai Normal University, Xining, 810008, China
- Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining, 810016, China
| | - Xu Su
- Key Laboratory of Biodiversity Formation Mechanism and Comprehensive Utilization of the Qinghai-Tibet Plateau in Qinghai Province, Qinghai Normal University, Xining, 810008, China
- Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining, 810016, China
| | - Quanwen Dou
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Guangpeng Ren
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China.
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11
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Ming L, Fu D, Wu Z, Zhao H, Xu X, Xu T, Xiong X, Li M, Zheng Y, Li G, Yang L, Xia C, Zhou R, Liao K, Yu Q, Chai W, Li S, Liu Y, Wu X, Mao J, Wei J, Li X, Wang L, Wu C, Xie W. Transcriptome-wide association analyses reveal the impact of regulatory variants on rice panicle architecture and causal gene regulatory networks. Nat Commun 2023; 14:7501. [PMID: 37980346 PMCID: PMC10657423 DOI: 10.1038/s41467-023-43077-6] [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: 02/17/2023] [Accepted: 10/30/2023] [Indexed: 11/20/2023] Open
Abstract
Panicle architecture is a key determinant of rice grain yield and is mainly determined at the 1-2 mm young panicle stage. Here, we investigated the transcriptome of the 1-2 mm young panicles from 275 rice varieties and identified thousands of genes whose expression levels were associated with panicle traits. Multimodel association studies suggested that many small-effect genetic loci determine spikelet per panicle (SPP) by regulating the expression of genes associated with panicle traits. We found that alleles at cis-expression quantitative trait loci of SPP-associated genes underwent positive selection, with a strong preference for alleles increasing SPP. We further developed a method that integrates the associations of cis- and trans-expression components of genes with traits to identify causal genes at even small-effect loci and construct regulatory networks. We identified 36 putative causal genes of SPP, including SDT (MIR156j) and OsMADS17, and inferred that OsMADS17 regulates SDT expression, which was experimentally validated. Our study reveals the impact of regulatory variants on rice panicle architecture and provides new insights into the gene regulatory networks of panicle traits.
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Affiliation(s)
- Luchang Ming
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Debao Fu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Zhaona Wu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Hu Zhao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xingbing Xu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Tingting Xu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xiaohu Xiong
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Mu Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yi Zheng
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Ge Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Ling Yang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Chunjiao Xia
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Rongfang Zhou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Keyan Liao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Qian Yu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Wenqi Chai
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Sijia Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yinmeng Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xiaokun Wu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Jianquan Mao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Julong Wei
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA
| | - Xu Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Lei Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Changyin Wu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China.
| | - Weibo Xie
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China.
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China.
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China.
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12
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Chen G, Mishina K, Wang Q, Zhu H, Tagiri A, Kikuchi S, Sassa H, Oono Y, Komatsuda T. Organ-enriched gene expression during floral morphogenesis in wild barley. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:887-902. [PMID: 37548103 DOI: 10.1111/tpj.16416] [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: 05/31/2023] [Revised: 07/19/2023] [Accepted: 07/23/2023] [Indexed: 08/08/2023]
Abstract
Floral morphology varies considerably between dicots and monocots. The ABCDE model explaining how floral organ development is controlled was formulated using core eudicots and applied to grass crops. Barley (Hordeum. vulgare) has unique floral morphogenesis. Wild barley (H. vulgare ssp. spontaneum), which is the immediate ancestor of cultivated barley (H. vulgare ssp. vulgare), contains a rich reservoir of genetic diversity. However, the wild barley genes involved in floral organ development are still relatively uncharacterized. In this study, we generated an organ-specific transcriptome atlas for wild barley floral organs. Genome-wide transcription profiles indicated that 22 838 protein-coding genes were expressed in at least one organ. These genes were grouped into seven clusters according to the similarities in their expression patterns. Moreover, 5619 genes exhibited organ-enriched expression, 677 of which were members of 47 transcription factor families. Gene ontology analyses suggested that the functions of the genes with organ-enriched expression influence the biological processes in floral organs. The co-expression regulatory network showed that the expression of 690 genes targeted by MADS-box proteins was highly positively correlated with the expression of ABCDE model genes during floral morphogenesis. Furthermore, the expression of 138 genes was specific to the wild barley OUH602 genome and not the Morex genome; most of these genes were highly expressed in the glume, awn, lemma, and palea. This study revealed the global gene expression patterns underlying floral morphogenesis in wild barley. On the basis of the study findings, a molecular mechanism controlling floral morphology in barley was proposed.
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Affiliation(s)
- Gang Chen
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba, 271-8510, Japan
| | - Kohei Mishina
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
| | - Qi Wang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, 100141, China
| | - Hongjing Zhu
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba, 271-8510, Japan
| | - Akemi Tagiri
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
| | - Shinji Kikuchi
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba, 271-8510, Japan
| | - Hidenori Sassa
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba, 271-8510, Japan
| | - Youko Oono
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba, 271-8510, Japan
| | - Takao Komatsuda
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba, 271-8510, Japan
- Crop Research Institute, Shandong Academy of Agricultural Sciences/National Engineering Research Center of Wheat and Maize/Shandong Technology Innovation Center of Wheat, Jinan, 252100, China
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13
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Liu E, Zhu S, Du M, Lyu H, Zeng S, Liu Q, Wu G, Jiang J, Dang X, Dong Z, Hong D. LAX1, functioning with MADS-box genes, determines normal palea development in rice. Gene 2023; 883:147635. [PMID: 37442304 DOI: 10.1016/j.gene.2023.147635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 06/19/2023] [Accepted: 07/10/2023] [Indexed: 07/15/2023]
Abstract
Normal floral organ development in rice is necessary for grain formation. Many MADS-box family genes that belong to ABCDE model have been widely implicated in rice flower development. The LAX1 allele encodes a plant-specific basic helix-loop-helix (bHLH) transcription factor, which is the main regulator of axillary meristem formation in rice. However, the molecular mechanisms of LAX1 allele together with MADS-box family genes underlying palea development have not been reported. We found a short palea mutant plant in a population of indica rice variety 9311 treated with cobalt 60. We report the map-based cloning and characterization of lax1-7, identified as a new mutant allele of the LAX1 locus, and the role of its wild-type allele LAX1 in rice palea development. Through complementary experiments, combined with genetic and molecular biological analyses, the function of the LAX1 allele was determined. We showed that LAX1 allele is expressed specifically in young spikelets and encodes a nucleus-localized protein. In vitro and in vivo experiments revealed that the LAX1 protein physically interacts with OsMADS1, OsMADS6 and OsMADS7. The LAX1 allele is pleiotropic for the maintenance of rice palea identity via cooperation with MADS-box genes and other traits, including axillary meristem initiation, days to heading, plant height, panicle length and spikelet fertility.
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Affiliation(s)
- Erbao Liu
- College of Agriculture, Anhui Agricultural University, Hefei 230036, China
| | - Shangshang Zhu
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Mingyu Du
- College of Agriculture, Anhui Agricultural University, Hefei 230036, China
| | - Huineng Lyu
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Siyuan Zeng
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Qiangming Liu
- Chongqing Academy of Agricultural Sciences, Chongqing 401329, China
| | - Guocan Wu
- Ningde Institute of Agricultural Sciences, Ningde 355017, China
| | - Jianhua Jiang
- Anhui Academy of Agricultural Sciences, Hefei 230001, China
| | - Xiaojing Dang
- Anhui Academy of Agricultural Sciences, Hefei 230001, China
| | - Zhiyao Dong
- College of Life Sciences, Jilin Normal University, Jilin 136000, China
| | - Delin Hong
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China.
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14
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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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15
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Lin ZY, Zhu GF, Lu CQ, Gao J, Li J, Xie Q, Wei YL, Jin JP, Wang FL, Yang FX. Functional conservation and divergence of SEPALLATA-like genes in floral development in Cymbidium sinense. FRONTIERS IN PLANT SCIENCE 2023; 14:1209834. [PMID: 37711312 PMCID: PMC10498475 DOI: 10.3389/fpls.2023.1209834] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 08/08/2023] [Indexed: 09/16/2023]
Abstract
Cymbidium sinense is one of the most important traditional Chinese Orchids due to its unique and highly ornamental floral organs. Although the ABCDE model for flower development is well-established in model plant species, the precise roles of these genes in C. sinense are not yet fully understood. In this study, four SEPALLATA-like genes were isolated and identified from C. sinense. CsSEP1 and CsSEP3 were grouped into the AGL9 clade, while CsSEP2 and CsSEP4 were included in the AGL2/3/4 clade. The expression pattern of CsSEP genes showed that they were significantly accumulated in reproductive tissues and expressed during flower bud development but only mildly detected or even undetected in vegetative organs. Subcellular localization revealed that CsSEP1 and CsSEP4 were localized to the nucleus, while CsSEP2 and CsSEP3 were located at the nuclear membrane. Promoter sequence analysis predicted that CsSEP genes contained a number of hormone response elements (HREs) and MADS-box binding sites. The early flowering phenotype observed in transgenic Arabidopsis plants expressing four CsSEP genes, along with the expression profiles of endogenous genes, such as SOC1, LFY, AG, FT, SEP3 and TCPs, in both transgenic Arabidopsis and C. sinense protoplasts, suggested that the CsSEP genes played a regulatory role in the flowering transition by influencing downstream genes related to flowering. However, only transgenic plants overexpressing CsSEP3 and CsSEP4 caused abnormal phenotypes of floral organs, while CsSEP1 and CsSEP2 had no effect on floral organs. Protein-protein interaction assays indicated that CsSEPs formed a protein complex with B-class CsAP3-2 and CsSOC1 proteins, affecting downstream genes to regulate floral organs and flowering time. Our findings highlighted both the functional conservation and divergence of SEPALLATA-like genes in C. sinense floral development. These results provided a valuable foundation for future studies of the molecular network underlying floral development in C. sinense.
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Affiliation(s)
- Zeng-Yu Lin
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Institute of Environmental Horticulture, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Gen-Fa Zhu
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Institute of Environmental Horticulture, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Chu-Qiao Lu
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Institute of Environmental Horticulture, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Jie Gao
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Institute of Environmental Horticulture, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Jie Li
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Institute of Environmental Horticulture, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Qi Xie
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Institute of Environmental Horticulture, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Yong-Lu Wei
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Institute of Environmental Horticulture, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Jian-Peng Jin
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Institute of Environmental Horticulture, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Feng-Lan Wang
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Feng-Xi Yang
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Institute of Environmental Horticulture, Guangdong Academy of Agricultural Sciences, Guangzhou, China
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16
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Shalmani A, Ullah U, Tai L, Zhang R, Jing XQ, Muhammd I, Bhanbhro N, Liu WT, Li WQ, Chen KM. OsBBX19-OsBTB97/OsBBX11 module regulates spikelet development and yield production in rice. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023:111779. [PMID: 37355232 DOI: 10.1016/j.plantsci.2023.111779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 05/09/2023] [Accepted: 06/20/2023] [Indexed: 06/26/2023]
Abstract
Spikelet and floral-related organs are important agronomic traits for rice grain yield. BTB (broad-complex, tram track, and bric-abrac) proteins control various developmental functions in plants; however, the molecular mechanism of BTB proteins underlying grain development and yield production is still unknown. Here, we evaluated the molecular mechanism of a previously unrecognized functional gene, namely OsBTB97 that regulates the floral and spikelet-related organs which greatly affect the final grain yield. We found that the knockdown of the OsBTB97 gene had significant impacts on the development of spikelet-related organs and grain size, resulting in a decrease in yield, by altering the transcript levels of various spikelet- and grain-related genes. Furthermore, we found that the knockout mutants of two BBX genes, OsBBX11 and OsBBX19, which interact with the OsBTB97 protein at translation and transcriptional level, respectively, displayed lower OsBTB97 expression, suggesting the genetic relationship between the BTB protein and the BBX transcription factors in rice. Taken together, our study dissects the function of the novel OsBTB97 by interacting with two BBX proteins and an OsBBX19-OsBTB97/OsBBX11 module might function in the spikelet development and seed production in rice. The outcome of the present study provides promising knowledge about BTB proteins in the improvement of crop production in plants.
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Affiliation(s)
- Abdullah Shalmani
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, China
| | - Uzair Ullah
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, China
| | - Li Tai
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, China
| | - Ran Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, China
| | - Xiu-Qing Jing
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, China
| | - Izhar Muhammd
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, China
| | - Nadeem Bhanbhro
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, China
| | - Wen-Ting Liu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, China
| | - Wen-Qiang Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, China
| | - Kun-Ming Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, China.
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17
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Li W, Wang D, Hong X, Shi J, Hong J, Su S, Loaiciga CR, Li J, Liang W, Shi J, Zhang D. Identification and validation of new MADS-box homologous genes in 3010 rice pan-genome. PLANT CELL REPORTS 2023; 42:975-988. [PMID: 37016094 DOI: 10.1007/s00299-023-03006-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 03/17/2023] [Indexed: 05/12/2023]
Abstract
KEY MESSAGE Identification and validation of ten new MADS-box homologous genes in 3010 rice pan-genome for rice breeding. The functional genome is significant for rice breeding. MADS-box genes encode transcription factors that are indispensable for rice growth and development. The reported 15,362 novel genes in the rice pan-genome (RPAN) of Asian cultivated rice accessions provided a useful gene reservoir for the identification of more MADS-box candidates to overcome the limitation for the usage of only 75 MADS-box genes identified in Nipponbare for rice breeding. Here, we report the identification and validation of ten MADS-box homologous genes in RPAN. Origin and identity analysis indicated that they are originated from different wild rice accessions and structure of motif analysis revealed high variations in their amino acid sequences. Phylogenetic results with 277 MADS-box genes in 41 species showed that all these ten MADS-box homologous genes belong to type I (SRF-like, M-type). Gene expression analysis confirmed the existence of these ten MADS-box genes in IRIS_313-10,394, all of them were expressed in flower tissues, and six of them were highly expressed during seed development. Altogether, we identified and validated experimentally, for the first time, ten novel MADS-box genes in RPAN, which provides new genetic sources for rice improvement.
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Affiliation(s)
- Weihua Li
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Duoxiang Wang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiaokun Hong
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jin Shi
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jun Hong
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Su Su
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, 572024, China
| | - Cristopher Reyes Loaiciga
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jing Li
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wanqi Liang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, 572024, China
| | - Jianxin Shi
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, 572024, China.
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, 572024, China
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, Adelaide, 5064, Australia
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18
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Robinson R, Sprott D, Couroux P, Routly E, Labbé N, Xing T, Robert LS. The triticale mature pollen and stigma proteomes - assembling the proteins for a productive encounter. J Proteomics 2023; 278:104867. [PMID: 36870675 DOI: 10.1016/j.jprot.2023.104867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/13/2023] [Accepted: 02/20/2023] [Indexed: 03/06/2023]
Abstract
Triticeae crops are major contributors to global food production and ensuring their capacity to reproduce and generate seeds is critical. However, despite their importance our knowledge of the proteins underlying Triticeae reproduction is severely lacking and this is not only true of pollen and stigma development, but also of their pivotal interaction. When the pollen grain and stigma are brought together they have each accumulated the proteins required for their intended meeting and accordingly studying their mature proteomes is bound to reveal proteins involved in their diverse and complex interactions. Using triticale as a Triticeae representative, gel-free shotgun proteomics was used to identify 11,533 and 2977 mature stigma and pollen proteins respectively. These datasets, by far the largest to date, provide unprecedented insights into the proteins participating in Triticeae pollen and stigma development and interactions. The study of the Triticeae stigma has been particularly neglected. To begin filling this knowledge gap, a developmental iTRAQ analysis was performed revealing 647 proteins displaying differential abundance as the stigma matures in preparation for pollination. An in-depth comparison to an equivalent Brassicaceae analysis divulged both conservation and diversification in the makeup and function of proteins involved in the pollen and stigma encounter. SIGNIFICANCE: Successful pollination brings together the mature pollen and stigma thus initiating an intricate series of molecular processes vital to crop reproduction. In the Triticeae crops (e.g. wheat, barley, rye, triticale) there persists a vast deficit in our knowledge of the proteins involved which needs to be addressed if we are to face the many upcoming challenges to crop production such as those associated with climate change. At maturity, both the pollen and stigma have acquired the protein complement necessary for their forthcoming encounter and investigating their proteomes will inevitably provide unprecedented insights into the proteins enabling their interactions. By combining the analysis of the most comprehensive Triticeae pollen and stigma global proteome datasets to date with developmental iTRAQ investigations, proteins implicated in the different phases of pollen-stigma interaction enabling pollen adhesion, recognition, hydration, germination and tube growth, as well as those underlying stigma development were revealed. Extensive comparisons between equivalent Triticeae and Brassiceae datasets highlighted both the conservation of biological processes in line with the shared goal of activating the pollen grain and promoting pollen tube invasion of the pistil to effect fertilization, as well as the significant distinctions in their proteomes consistent with the considerable differences in their biochemistry, physiology and morphology.
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Affiliation(s)
- Reneé Robinson
- Ottawa Research and Development Centre, 960 Carling Ave., Ottawa, Ontario K1A 0C6, Canada; Carleton University, Department of Biology, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada
| | - David Sprott
- Ottawa Research and Development Centre, 960 Carling Ave., Ottawa, Ontario K1A 0C6, Canada
| | - Philippe Couroux
- Ottawa Research and Development Centre, 960 Carling Ave., Ottawa, Ontario K1A 0C6, Canada
| | - Elizabeth Routly
- Ottawa Research and Development Centre, 960 Carling Ave., Ottawa, Ontario K1A 0C6, Canada
| | - Natalie Labbé
- Ottawa Research and Development Centre, 960 Carling Ave., Ottawa, Ontario K1A 0C6, Canada
| | - Tim Xing
- Carleton University, Department of Biology, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada
| | - Laurian S Robert
- Ottawa Research and Development Centre, 960 Carling Ave., Ottawa, Ontario K1A 0C6, Canada.
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19
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Li C, Zhang S, Yan X, Cheng P, Yu H. Single-nucleus sequencing deciphers developmental trajectories in rice pistils. Dev Cell 2023; 58:694-708.e4. [PMID: 37028425 DOI: 10.1016/j.devcel.2023.03.004] [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: 09/17/2022] [Revised: 01/25/2023] [Accepted: 03/07/2023] [Indexed: 04/08/2023]
Abstract
Angiosperms possess a life cycle with an alternation of sporophyte and gametophyte generations, which happens in plant organs like pistils. Rice pistils contain ovules and receive pollen for successful fertilization to produce grains. The cellular expression profile in rice pistils is largely unknown. Here, we show a cell census of rice pistils before fertilization through the use of droplet-based single-nucleus RNA sequencing. The ab initio marker identification validated by in situ hybridization assists with cell-type annotation, revealing cell heterogeneity between ovule- and carpel-originated cells. A comparison of 1N (gametophyte) and 2N (sporophyte) nuclei identifies the developmental path of germ cells in ovules with typical resetting of pluripotency before the sporophyte-gametophyte transition, while trajectory analysis of carpel-originated cells suggests previously neglected features of epidermis specification and style function. These findings gain a systems-level view of cellular differentiation and development of rice pistils before flowering and lay a foundation for understanding female reproductive development in plants.
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Affiliation(s)
- Chengxiang Li
- Department of Biological Sciences and Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117543, Singapore
| | - Songyao Zhang
- Department of Biological Sciences and Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117543, Singapore
| | - Xingying Yan
- Department of Biological Sciences and Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117543, Singapore; Biotechnology Research Center, Southwest University, Chongqing 400716, China
| | - Peng Cheng
- Department of Biological Sciences and Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117543, Singapore
| | - Hao Yu
- Department of Biological Sciences and Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117543, Singapore.
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20
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Zhao L, Yang Y, Chen J, Lin X, Zhang H, Wang H, Wang H, Bie X, Jiang J, Feng X, Fu X, Zhang X, Du Z, Xiao J. Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat. Genome Biol 2023; 24:7. [PMID: 36639687 PMCID: PMC9837924 DOI: 10.1186/s13059-022-02844-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 12/31/2022] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Plant and animal embryogenesis have conserved and distinct features. Cell fate transitions occur during embryogenesis in both plants and animals. The epigenomic processes regulating plant embryogenesis remain largely elusive. RESULTS Here, we elucidate chromatin and transcriptomic dynamics during embryogenesis of the most cultivated crop, hexaploid wheat. Time-series analysis reveals stage-specific and proximal-distal distinct chromatin accessibility and dynamics concordant with transcriptome changes. Following fertilization, the remodeling kinetics of H3K4me3, H3K27ac, and H3K27me3 differ from that in mammals, highlighting considerable species-specific epigenomic dynamics during zygotic genome activation. Polycomb repressive complex 2 (PRC2)-mediated H3K27me3 deposition is important for embryo establishment. Later H3K27ac, H3K27me3, and chromatin accessibility undergo dramatic remodeling to establish a permissive chromatin environment facilitating the access of transcription factors to cis-elements for fate patterning. Embryonic maturation is characterized by increasing H3K27me3 and decreasing chromatin accessibility, which likely participates in restricting totipotency while preventing extensive organogenesis. Finally, epigenomic signatures are correlated with biased expression among homeolog triads and divergent expression after polyploidization, revealing an epigenomic contributor to subgenome diversification in an allohexaploid genome. CONCLUSIONS Collectively, we present an invaluable resource for comparative and mechanistic analysis of the epigenomic regulation of crop embryogenesis.
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Affiliation(s)
- Long Zhao
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Yiman Yang
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.,Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Jinchao Chen
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuelei Lin
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Hao Zhang
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hao Wang
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hongzhe Wang
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaomin Bie
- Shandong Agricultural University, Tai'an, Shandong, China
| | - Jiafu Jiang
- Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Xiaoqi Feng
- John Innes Centre, Colney Lane, Norwich, NR4 7UH, UK
| | - Xiangdong Fu
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | | | - Zhuo Du
- University of Chinese Academy of Sciences, Beijing, 100049, China.,State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jun Xiao
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China. .,CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
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21
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Liu H, Liu X, Chang X, Chen F, Lin Z, Zhang L. Large-scale analyses of angiosperm Flowering Locus T genes reveal duplication and functional divergence in monocots. FRONTIERS IN PLANT SCIENCE 2023; 13:1039500. [PMID: 36684773 PMCID: PMC9847362 DOI: 10.3389/fpls.2022.1039500] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 11/29/2022] [Indexed: 06/17/2023]
Abstract
FLOWERING LOCUS T (FT) are well-known key genes for initiating flowering in plants. Delineating the evolutionary history and functional diversity of FT genes is important for understanding the diversification of flowering time and how plants adapt to the changing surroundings. We performed a comprehensive phylogenetic analysis of FT genes in 47 sequenced flowering plants and the 1,000 Plant Transcriptomes (1KP) database with a focus on monocots, especially cereals. We revealed the evolutionary history of FT genes. The FT genes in monocots can be divided into three clades (I, II, and III), whereas only one monophyletic group was detected in early angiosperms, magnoliids, and eudicots. Multiple rounds of whole-genome duplications (WGD) events followed by gene retention contributed to the expansion and variation of FT genes in monocots. Amino acid sites in the clade II and III genes were preferentially under high positive selection, and some sites located in vital domain regions are known to change functions when mutated. Clade II and clade III genes exhibited high variability in important regions and functional divergence compared with clade I genes; thus, clade I is more conserved than clade II and III. Genes in clade I displayed higher expression levels in studied organs and tissues than the clade II and III genes. The co-expression modules showed that some of the FT genes might have experienced neofunctionalization and subfunctionalization, such as the acquisition of environmental resistance. Overall, FT genes in monocots might form three clades by the ancient gene duplication, and each clade was subsequently subjected to different selection pressures and amino acid substitutions, which eventually led to different expression patterns and functional diversification. Our study provides a global picture of FT genes' evolution in monocots, paving a road for investigating FT genes' function in future.
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Affiliation(s)
- Hongling Liu
- Hainan Institute of Zhejiang University, Sanya, China
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Xing Liu
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaojun Chang
- Laboratory of Medicinal Plant Biotechnology, School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Fei Chen
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
| | - Zhenguo Lin
- Department of Biology, Saint Louis University, St Louis, MO, United States
| | - Liangsheng Zhang
- Hainan Institute of Zhejiang University, Sanya, China
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
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22
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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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23
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Zhou G, Yin H, Chen F, Wang Y, Gao Q, Yang F, He C, Zhang L, Wan Y. The genome of Areca catechu provides insights into sex determination of monoecious plants. THE NEW PHYTOLOGIST 2022; 236:2327-2343. [PMID: 36089819 DOI: 10.1111/nph.18471] [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: 05/21/2022] [Accepted: 08/25/2022] [Indexed: 06/15/2023]
Abstract
The areca palm (Areca catechu) has a monoecious spadix, with male flowers on the apical side and females on the basal side. Here, we applied multiomics analysis to investigate sex determination and floral organ development in areca palms. We generated a chromosome-level reference genome of A. catechu with 16 pseudochromosomes, composed of 2.73 Gb and encoding 31 406 genes. Data from RNA-seq and ATAC-seq (assay for transposase accessible chromatin sequencing) suggested that jasmonic acid (JA) synthesis and signal transduction-related genes were differentially expressed between female and male flowers via epigenetic modifications. JA concentration in female flowers was c. 10 times than that in males on the same inflorescence, while JA concentration in hermaphroditic flowers of abnormal inflorescences was about twice that in male flowers of normal inflorescences. JA promotes the development of female flower organs by decreasing the expression of B-function genes, including AGL16, AP3, PIb and PIc. There is also a region on pseudochromosome 15 harboring sex-related genes, including CYP703, LOG, GPAT, AMS and BiP. Among them, CYP703, AMS and BiP were specifically expressed in male flowers.
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Affiliation(s)
- Guangzhen Zhou
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Hongyan Yin
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Fei Chen
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, China
- Hainan Yazhou Bay Seed Laboratory, College of Tropical Crops, Sanya Nanfan Research Institute, Hainan University, Sanya, 572025, China
| | - Yicheng Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Qiang Gao
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Fusun Yang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Chaozhu He
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Liangsheng Zhang
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- Hainan Institute of Zhejiang University, Sanya, 572025, China
| | - Yinglang Wan
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, China
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Chen L, Yan Y, Ke H, Zhang Z, Meng C, Ma L, Sun Z, Chen B, Liu Z, Wang G, Yang J, Wu J, Li Z, Wu L, Zhang G, Zhang Y, Wang X, Ma Z. SEP-like genes of Gossypium hirsutum promote flowering via targeting different loci in a concentration-dependent manner. FRONTIERS IN PLANT SCIENCE 2022; 13:990221. [PMID: 36531379 PMCID: PMC9752867 DOI: 10.3389/fpls.2022.990221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 11/02/2022] [Indexed: 06/17/2023]
Abstract
SEP genes are famous for their function in the morphological novelty of bisexual flowers. Although the diverse functions of SEP genes were reported, only the regulatory mechanisms underlying floral organ development have been addressed. In this study, we identified SEP-like genes in Gossypium and found that SEP3 genes were duplicated in diploid cotton varieties. GhSEP4.1 and GhSEP4.2 were abundantly transcribed in the shoot apical meristem (SAM), but only GhSEP4.2 was expressed in the leaf vasculature. The expression pattern of GhSEPs in floral organs was conserved with that of homologs in Arabidopsis, except for GhSEP2 that was preponderantly expressed in ovules and fibers. The overexpression and silencing of each single GhSEP gene suggested their distinct role in promoting flowering via direct binding to GhAP1 and GhLFY genomic regions. The curly leaf and floral defects in overexpression lines with a higher expression of GhSEP genes revealed the concentration-dependent target gene regulation of GhSEP proteins. Moreover, GhSEP proteins were able to dimerize and interact with flowering time regulators. Together, our results suggest the dominant role of GhSEP4.2 in leaves to promote flowering via GhAP1-A04, and differently accumulated GhSEP proteins in the SAM alternately participate in forming the dynamic tetramer complexes to target at the different loci of GhAP1 and GhLFY to maintain reproductive growth. The regulatory roles of cotton SEP genes reveal their conserved and diversified functions.
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25
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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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26
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Han Y, Hu M, Ma X, Yan G, Wang C, Jiang S, Lai J, Zhang M. Exploring key developmental phases and phase-specific genes across the entirety of anther development in maize. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:1394-1410. [PMID: 35607822 PMCID: PMC10360140 DOI: 10.1111/jipb.13276] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
Anther development from stamen primordium to pollen dispersal is complex and essential to sexual reproduction. How this highly dynamic and complex developmental process is controlled genetically is not well understood, especially for genes involved in specific key developmental phases. Here we generated RNA sequencing libraries spanning 10 key stages across the entirety of anther development in maize (Zea mays). Global transcriptome analyses revealed distinct phases of cell division and expansion, meiosis, pollen maturation, and mature pollen, for which we detected 50, 245, 42, and 414 phase-specific marker genes, respectively. Phase-specific transcription factor genes were significantly enriched in the phase of meiosis. The phase-specific expression of these marker genes was highly conserved among the maize lines Chang7-2 and W23, indicating they might have important roles in anther development. We explored a desiccation-related protein gene, ZmDRP1, which was exclusively expressed in the tapetum from the tetrad to the uninucleate microspore stage, by generating knockout mutants. Notably, mutants in ZmDRP1 were completely male-sterile, with abnormal Ubisch bodies and defective pollen exine. Our work provides a glimpse into the gene expression dynamics and a valuable resource for exploring the roles of key phase-specific genes that regulate anther development.
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Affiliation(s)
- Yingjia Han
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
| | - Mingjian Hu
- State Key Laboratory of Plant Physiology and Biochemistry & National Maize Improvement Center of China Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Xuxu Ma
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
| | - Ge Yan
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chunyu Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Siqi Jiang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jinsheng Lai
- State Key Laboratory of Plant Physiology and Biochemistry & National Maize Improvement Center of China Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Mei Zhang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
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27
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Cheng H, Xie X, Ren M, Yang S, Zhao X, Mahna N, Liu Y, Xu Y, Xiang Y, Chai H, Zheng L, Ge H, Jia R. Characterization of Three SEPALLATA-Like MADS-Box Genes Associated With Floral Development in Paphiopedilum henryanum (Orchidaceae). FRONTIERS IN PLANT SCIENCE 2022; 13:916081. [PMID: 35693163 PMCID: PMC9178235 DOI: 10.3389/fpls.2022.916081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 05/03/2022] [Indexed: 06/15/2023]
Abstract
Paphiopedilum (Orchidaceae) is one of the world's most popular orchids that is found in tropical and subtropical forests and has an enormous ornamental value. SEPALLATA-like (SEP-like) MADS-box genes are responsible for floral organ specification. In this study, three SEP-like MADS-box genes, PhSEP1, PhSEP2, and PhSEP3, were identified in Paphiopedilum henryanum. These genes were 732-916 bp, with conserved SEPI and SEPII motifs. Phylogenetic analysis revealed that PhSEP genes were evolutionarily closer to the core eudicot SEP3 lineage, whereas none of them belonged to core eudicot SEP1/2/4 clades. PhSEP genes displayed non-ubiquitous expression, which was detectable across all floral organs at all developmental stages of the flower buds. Furthermore, subcellular localization experiments revealed the localization of PhSEP proteins in the nucleus. Yeast two-hybrid assays revealed no self-activation of PhSEPs. The protein-protein interactions revealed that PhSEPs possibly interact with B-class DEFICIENS-like and E-class MADS-box proteins. Our study suggests that the three SEP-like genes may play key roles in flower development in P. henryanum, which will improve our understanding of the roles of the SEP-like MADS-box gene family and provide crucial insights into the mechanisms underlying floral development in orchids.
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Affiliation(s)
- Hao Cheng
- Key Laboratory of Biology and Genetic Improvement of Flower Crops (North China), Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- National Agricultural Science & Technology Center, Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, China
| | - Xiulan Xie
- National Agricultural Science & Technology Center, Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, China
| | - Maozhi Ren
- National Agricultural Science & Technology Center, Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, China
| | - Shuhua Yang
- Key Laboratory of Biology and Genetic Improvement of Flower Crops (North China), Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xin Zhao
- Key Laboratory of Biology and Genetic Improvement of Flower Crops (North China), Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Nasser Mahna
- Department of Horticultural Sciences, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| | - Yi Liu
- National Agricultural Science & Technology Center, Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, China
| | - Yufeng Xu
- Key Laboratory of Biology and Genetic Improvement of Flower Crops (North China), Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yukai Xiang
- Department of High-Performance Computing, National Supercomputing Center in Chengdu, Chengdu, China
| | - Hua Chai
- Department of High-Performance Computing, National Supercomputing Center in Chengdu, Chengdu, China
| | - Liang Zheng
- Department of High-Performance Computing, National Supercomputing Center in Chengdu, Chengdu, China
| | - Hong Ge
- Key Laboratory of Biology and Genetic Improvement of Flower Crops (North China), Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ruidong Jia
- Key Laboratory of Biology and Genetic Improvement of Flower Crops (North China), Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
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28
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Kitazawa Y, Iwabuchi N, Maejima K, Sasano M, Matsumoto O, Koinuma H, Tokuda R, Suzuki M, Oshima K, Namba S, Yamaji Y. A phytoplasma effector acts as a ubiquitin-like mediator between floral MADS-box proteins and proteasome shuttle proteins. THE PLANT CELL 2022; 34:1709-1723. [PMID: 35234248 PMCID: PMC9048881 DOI: 10.1093/plcell/koac062] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 02/14/2022] [Indexed: 06/01/2023]
Abstract
Plant pathogenic bacteria have developed effectors to manipulate host cell functions to facilitate infection. A certain number of effectors use the conserved ubiquitin-proteasome system in eukaryotic to proteolyze targets. The proteasome utilization mechanism is mainly mediated by ubiquitin interaction with target proteins destined for degradation. Phyllogens are a family of protein effectors produced by pathogenic phytoplasmas that transform flowers into leaves in diverse plants. Here, we present a noncanonical mechanism for phyllogen action that involves the proteasome and is ubiquitin-independent. Phyllogens induce proteasomal degradation of floral MADS-box transcription factors (MTFs) in the presence of RADIATION-SENSITIVE23 (RAD23) shuttle proteins, which recruit ubiquitinated proteins to the proteasome. Intracellular localization analysis revealed that phyllogen induced colocalization of MTF with RAD23. The MTF/phyllogen/RAD23 ternary protein complex was detected not only in planta but also in vitro in the absence of ubiquitin, showing that phyllogen directly mediates interaction between MTF and RAD23. A Lys-less nonubiquitinated phyllogen mutant induced degradation of MTF or a Lys-less mutant of MTF. Furthermore, the method of sequential formation of the MTF/phyllogen/RAD23 protein complex was elucidated, first by MTF/phyllogen interaction and then RAD23 recruitment. Phyllogen recognized both the evolutionarily conserved tetramerization region of MTF and the ubiquitin-associated domain of RAD23. Our findings indicate that phyllogen functionally mimics ubiquitin as a mediator between MTF and RAD23.
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Affiliation(s)
- Yugo Kitazawa
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Nozomu Iwabuchi
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | | | - Momoka Sasano
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Oki Matsumoto
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Hiroaki Koinuma
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Ryosuke Tokuda
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Masato Suzuki
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Kenro Oshima
- Faculty of Bioscience and Applied Chemistry, Hosei University, Tokyo 184-8584, Japan
| | - Shigetou Namba
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Yasuyuki Yamaji
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
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Feng T, Wang L, Li L, Liu Y, Chong K, Theißen G, Meng Z. OsMADS14 and NF-YB1 cooperate in the direct activation of OsAGPL2 and Waxy during starch synthesis in rice endosperm. THE NEW PHYTOLOGIST 2022; 234:77-92. [PMID: 35067957 DOI: 10.1111/nph.17990] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 01/03/2022] [Indexed: 05/02/2023]
Abstract
Starch synthesis makes a dramatic contribution to the yield and nutritional value of cereal crops. Although several starch synthesis enzymes and related regulators have been reported, the underlying regulatory mechanisms of starch synthesis remain largely unknown. OsMADS14 is a FRUITFULL (FUL)-like MADS-box gene in rice (Oryza sativa). Here we show that two null mutations of OsMADS14 result in a shrunken and chalky grain phenotype. It is caused by obviously defective compound starch granules and a significantly reduced content of both total starch and amylose in the endosperm. Transcriptomic profiling analyses revealed that the loss-of-function of OsMADS14 leads to significantly downregulated expression of many core starch synthesis genes, including OsAGPL2 and Waxy. Both in vitro and in vivo assays demonstrate that the OsMADS14 protein directly binds to stretches of DNA with a CArG-box consensus in the putative regulatory regions of OsAGPL2 and Waxy. Protein-protein interaction experiments also suggest that OsMADS14 interacts with nuclear factor NF-YB1 to promote the transcription of OsAGPL2 and Waxy. Our study thus demonstrates that OsMADS14 plays an essential role in the synthesis of storage starch and provides novel insights into the underlying molecular mechanism that may be used to improve rice cultivars by molecular breeding.
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Affiliation(s)
- Tingting Feng
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lili Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Laiyun Li
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuan Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Kang Chong
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Günter Theißen
- Matthias Schleiden Institute/Genetics, Friedrich Schiller University Jena, Jena, D-07743, Germany
| | - Zheng Meng
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
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30
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Su Q, Zhang F, Xiao Y, Zhang P, Xing H, Chen F. An efficient screening system to identify protein-protein or protein-DNA interaction partners of rice transcription factors. J Genet Genomics 2022; 49:979-981. [PMID: 35218975 DOI: 10.1016/j.jgg.2022.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 01/18/2022] [Accepted: 02/06/2022] [Indexed: 10/19/2022]
Affiliation(s)
- Qingmei Su
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fang Zhang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; OE biotech Co., Ltd. Shanghai, China
| | | | | | | | - Fan Chen
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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31
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Zhan P, Ma S, Xiao Z, Li F, Wei X, Lin S, Wang X, Ji Z, Fu Y, Pan J, Zhou M, Liu Y, Chang Z, Li L, Bu S, Liu Z, Zhu H, Liu G, Zhang G, Wang S. Natural variations in grain length 10 (GL10) regulate rice grain size. J Genet Genomics 2022; 49:405-413. [DOI: 10.1016/j.jgg.2022.01.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/23/2022] [Accepted: 01/24/2022] [Indexed: 10/19/2022]
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32
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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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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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Kaur A, Nijhawan A, Yadav M, Khurana JP. OsbZIP62/OsFD7, a functional ortholog of FLOWERING LOCUS D, regulates floral transition and panicle development in rice. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:7826-7845. [PMID: 34459895 DOI: 10.1093/jxb/erab396] [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: 03/13/2021] [Accepted: 08/30/2021] [Indexed: 05/04/2023]
Abstract
We have characterized a rice bZIP protein-coding gene OsbZIP62/OsFD7 that is expressed preferentially in the shoot apical meristem and during early panicle developmental stages in comparison with other OsFD genes characterized to date. Surprisingly, unlike OsFD1, OsFD7 interacts directly and more efficiently with OsFTLs; the interaction is strongest with OsFTL1 followed by Hd3a and RFT1, as confirmed by fluorescence lifetime imaging-Förster resonant energy transfer (FLIM-FRET) analysis. In addition, OsFD7 is phosphorylated at its C-terminal end by OsCDPK41 and OsCDPK49 in vitro, and this phosphorylated moiety is recognized by OsGF14 proteins. OsFD7 RNAi transgenics were late flowering; the transcript levels of some floral meristem identity genes (e.g. OsMADS14, OsMADS15, and OsMADS18) were also down-regulated. RNAi lines also exhibited dense panicle morphology with an increase in the number of primary and secondary branches resulting in longer panicles and more seeds, probably due to down-regulation of SEPALLATA family genes. In comparison with other FD-like proteins previously characterized in rice, it appears that OsFD7 may have undergone diversification during evolution, resulting in the acquisition of newer functions and thus playing a dual role in floral transition and panicle development in rice.
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Affiliation(s)
- Amarjot Kaur
- Interdisciplinary Centre for Plant Genomics, University of Delhi South Campus, New Delhi-110021, India
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi-110021, India
| | - Aashima Nijhawan
- Interdisciplinary Centre for Plant Genomics, University of Delhi South Campus, New Delhi-110021, India
| | - Mahesh Yadav
- Interdisciplinary Centre for Plant Genomics, University of Delhi South Campus, New Delhi-110021, India
| | - Jitendra P Khurana
- Interdisciplinary Centre for Plant Genomics, University of Delhi South Campus, New Delhi-110021, India
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi-110021, India
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Zhou L, Zhu C, Fang X, Liu H, Zhong S, Li Y, Liu J, Song Y, Jian X, Lin Z. Gene duplication drove the loss of awn in sorghum. MOLECULAR PLANT 2021; 14:1831-1845. [PMID: 34271177 DOI: 10.1016/j.molp.2021.07.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 06/18/2021] [Accepted: 07/08/2021] [Indexed: 06/13/2023]
Abstract
Loss of the awn in some cereals, including sorghum, is a key transition during cereal domestication or improvement that has facilitated grain harvest and storage. The genetic basis of awn loss in sorghum during domestication or improvement remains unknown. Here, we identified the awn1 gene encoding a transcription factor with the ALOG domain that is responsible for awn loss during sorghum domestication or improvement. awn1 arose from a gene duplication on chromosome 10 that translocated to chromosome 3, recruiting a new promoter from the neighboring intergenic region filled with "noncoding DNA" and recreating the first exon and intron. awn1 acquired high expression after duplication and represses the elongation of awns in domesticated sorghum. Comparative mapping revealed high collinearity at the awn1 paralog locus on chromosome 10 across cereals, and awn growth and development were successfully reactivated on the rice spikelet by inactivating the rice awn1 ortholog. RNA-seq and DAP-seq revealed that as a transcriptional repressor, AWN1 bound directly to a motif in the regulatory regions of three MADS genes related to flower development and two genes, DL and LKS2, involved in awn development. AWN1 downregulates the expression of these genes, thereby repressing awn elongation. The preexistence of regulatory elements in the neighboring intergenic region of awn1 before domestication implicates that noncoding DNA may serve as a treasure trove for evolution during sorghum adaptation to a changing world. Taken together, our results suggest that gene duplication can rapidly drive the evolution of gene regulatory networks in plants.
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Affiliation(s)
- Leina Zhou
- National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, China Agricultural University, Beijing 100193, China
| | - Can Zhu
- National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, China Agricultural University, Beijing 100193, China
| | - Xiaojian Fang
- National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, China Agricultural University, Beijing 100193, China
| | - Hangqin Liu
- National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, China Agricultural University, Beijing 100193, China
| | - Shuyang Zhong
- National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, China Agricultural University, Beijing 100193, China
| | - Yan Li
- National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, China Agricultural University, Beijing 100193, China
| | - Jiacheng Liu
- National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, China Agricultural University, Beijing 100193, China
| | - Yang Song
- National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, China Agricultural University, Beijing 100193, China
| | - Xing Jian
- National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, China Agricultural University, Beijing 100193, China
| | - Zhongwei Lin
- National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, China Agricultural University, Beijing 100193, China.
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Kuijer HNJ, Shirley NJ, Khor SF, Shi J, Schwerdt J, Zhang D, Li G, Burton RA. Transcript Profiling of MIKCc MADS-Box Genes Reveals Conserved and Novel Roles in Barley Inflorescence Development. FRONTIERS IN PLANT SCIENCE 2021; 12:705286. [PMID: 34539699 PMCID: PMC8442994 DOI: 10.3389/fpls.2021.705286] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 08/04/2021] [Indexed: 05/26/2023]
Abstract
MADS-box genes have a wide range of functions in plant reproductive development and grain production. The ABCDE model of floral organ development shows that MADS-box genes are central players in these events in dicotyledonous plants but the applicability of this model remains largely unknown in many grass crops. Here, we show that transcript analysis of all MIKCc MADS-box genes through barley (Hordeum vulgare L.) inflorescence development reveals co-expression groups that can be linked to developmental events. Thirty-four MIKCc MADS-box genes were identified in the barley genome and single-nucleotide polymorphism (SNP) scanning of 22,626 barley varieties revealed that the natural variation in the coding regions of these genes is low and the sequences have been extremely conserved during barley domestication. More detailed transcript analysis showed that MADS-box genes are generally expressed at key inflorescence developmental phases and across various floral organs in barley, as predicted by the ABCDE model. However, expression patterns of some MADS genes, for example HvMADS58 (AGAMOUS subfamily) and HvMADS34 (SEPALLATA subfamily), clearly deviate from predicted patterns. This places them outside the scope of the classical ABCDE model of floral development and demonstrates that the central tenet of antagonism between A- and C-class gene expression in the ABC model of other plants does not occur in barley. Co-expression across three correlation sets showed that specifically grouped members of the barley MIKCc MADS-box genes are likely to be involved in developmental events driving inflorescence meristem initiation, floral meristem identity and floral organ determination. Based on these observations, we propose a potential floral ABCDE working model in barley, where the classic model is generally upheld, but that also provides new insights into the role of MIKCc MADS-box genes in the developing barley inflorescence.
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Affiliation(s)
- Hendrik N. J. Kuijer
- School of Agriculture Food and Wine, University of Adelaide, Glen Osmond, SA, Australia
| | - Neil J. Shirley
- School of Agriculture Food and Wine, University of Adelaide, Glen Osmond, SA, Australia
| | - Shi F. Khor
- School of Agriculture Food and Wine, University of Adelaide, Glen Osmond, SA, Australia
| | - Jin Shi
- 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
| | - Julian Schwerdt
- School of Agriculture Food and Wine, University of Adelaide, Glen Osmond, SA, Australia
| | - Dabing Zhang
- School of Agriculture Food and Wine, University of Adelaide, Glen Osmond, SA, Australia
- 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
| | - Gang Li
- School of Agriculture Food and Wine, University of Adelaide, Glen Osmond, SA, Australia
- School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, China
| | - Rachel A. Burton
- School of Agriculture Food and Wine, University of Adelaide, Glen Osmond, SA, Australia
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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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38
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Adal AM, Binson E, Remedios L, Mahmoud SS. Expression of lavender AGAMOUS-like and SEPALLATA3-like genes promote early flowering and alter leaf morphology in Arabidopsis thaliana. PLANTA 2021; 254:54. [PMID: 34410495 DOI: 10.1007/s00425-021-03703-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 08/09/2021] [Indexed: 06/13/2023]
Abstract
The expression of full-length cDNAs encoding lavender AGAMOUS-like (LaAG-like) and SEPALLATA3-like (LaSEP3-like) transcription factors induces early flowering and impacts the leaf morphology at a strong expression level in Arabidopsis. Lavandula angustifolia is widely cultivated as an ornamental plant due to its attractive flower structure, and as a source of valuable essential oils for use in cosmetics, alternative medicines, and culinary products. We recently employed RNA-Seq and transcript profiling to describe a number of transcription factors (TFs) that potentially control flower development in this plant. In this study, we investigated the roles of two TFs, LaAGAMOUS-like (LaAG-like) and LaSEPALLATA3-like (LaSEP3-like), that exhibited substantial homology to Arabidopsis thaliana floral development genes, AGAMOUS and SEPALLATA3, respectively, in flowering initiation in Arabidopsis. We stably and constitutively expressed LaAG-like and LaSEP3-like cDNAs in separate Arabidopsis plants. All transgenic plants flowered earlier than the wild-type controls. However, plants that modestly overexpressed the gene were phenotypically normal, while those that strongly expressed the transgene developed curly leaves. We also assessed the expression of five endogenous flowering time regulating genes, from which high expression of Flowering Locus T (AtFT) mRNA in both LaAG-like (type-I and -II) and LaSEP3-like (type-I), and Leafy (AtLFY) mRNAs in LaSEP3-like (type-I) transgenic plants were detected, compared to wild-type controls. Our results suggest that with controlled expression, lavender AG-like and SEP3-like genes are potentially useful for the regulation of flowering time in commercial lavender species, and could be used for plant improvement studies through molecular genetics and targeted breeding programs.
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Affiliation(s)
- Ayelign M Adal
- Department of Biology, The University of British Columbia, Kelowna, BC, V1V 1V7, Canada
| | - Elinor Binson
- Department of Biology, The University of British Columbia, Kelowna, BC, V1V 1V7, Canada
| | - Lisa Remedios
- Department of Biology, The University of British Columbia, Kelowna, BC, V1V 1V7, Canada
| | - Soheil S Mahmoud
- Department of Biology, The University of British Columbia, Kelowna, BC, V1V 1V7, Canada.
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Li G, Kuijer HNJ, Yang X, Liu H, Shen C, Shi J, Betts N, Tucker MR, Liang W, Waugh R, Burton RA, Zhang D. MADS1 maintains barley spike morphology at high ambient temperatures. NATURE PLANTS 2021; 7:1093-1107. [PMID: 34183784 DOI: 10.1038/s41477-021-00957-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 06/02/2021] [Indexed: 05/05/2023]
Abstract
Temperature stresses affect plant phenotypic diversity. The developmental stability of the inflorescence, required for reproductive success, is tightly regulated by the interplay of genetic and environmental factors. However, the mechanisms underpinning how plant inflorescence architecture responds to temperature are largely unknown. We demonstrate that the barley SEPALLATA MADS-box protein HvMADS1 is responsible for maintaining an unbranched spike architecture at high temperatures, while the loss-of-function mutant forms a branched inflorescence-like structure. HvMADS1 exhibits increased binding to target promoters via A-tract CArG-box motifs, which change conformation with temperature. Target genes for high-temperature-dependent HvMADS1 activation are predominantly associated with inflorescence differentiation and phytohormone signalling. HvMADS1 directly regulates the cytokinin-degrading enzyme HvCKX3 to integrate temperature response and cytokinin homeostasis, which is required to repress meristem cell cycle/division. Our findings reveal a mechanism by which genetic factors direct plant thermomorphogenesis, extending the recognized role of plant MADS-box proteins in floral development.
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Affiliation(s)
- Gang Li
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Waite Campus, Glen Osmond, South Australia, Australia.
- School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, China.
| | - Hendrik N J Kuijer
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Waite Campus, Glen Osmond, South Australia, Australia
| | - Xiujuan Yang
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Waite Campus, Glen Osmond, South Australia, Australia
| | - Huiran Liu
- Joint International Research Laboratory of Metabolic and 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
| | - Chaoqun Shen
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Waite Campus, Glen Osmond, South Australia, Australia
- Joint International Research Laboratory of Metabolic and 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
| | - Jin Shi
- Joint International Research Laboratory of Metabolic and 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
| | - Natalie Betts
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Waite Campus, Glen Osmond, South Australia, Australia
| | - Matthew R Tucker
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Waite Campus, Glen Osmond, South Australia, Australia
| | - Wanqi Liang
- Joint International Research Laboratory of Metabolic and 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
| | - Robbie Waugh
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Waite Campus, Glen Osmond, South Australia, Australia
- James Hutton Institute, Dundee, UK
- Division of Plant Sciences, School of Life Sciences, University of Dundee, Dundee, UK
| | - Rachel A Burton
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Waite Campus, Glen Osmond, South Australia, Australia
| | - Dabing Zhang
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Waite Campus, Glen Osmond, South Australia, Australia.
- Joint International Research Laboratory of Metabolic and 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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40
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Liu T, Jiang GQ, Yao XF, Liu CM. The leucine-rich repeat receptor-like kinase OsERL plays a critical role in anther lobe formation in rice. Biochem Biophys Res Commun 2021; 563:85-91. [PMID: 34062391 DOI: 10.1016/j.bbrc.2021.05.059] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 05/17/2021] [Indexed: 11/16/2022]
Abstract
In Arabidopsis, ERECTA (ER) subfamily of leucine-rich repeat (LRR) receptor kinases (LRR-RKs) play important roles in cell division and cell elongation. However, the functions of OsER genes in rice are still very much unknown. In this study, sixty-seven TILLING and four gene-edited mutants were identified for one of the three OsERs, OsERL, and used for functional analyses. Results showed that mutations in OsERL led to striking defects in anther development. Compete male sterility and reduced numbers of anther lobes, more severe than knockout mutants, were observed in mutants with amino acid substitutions in the kinase domain. Among alleles with amino acid changes in LRRs, only one mutation in the 16th LRR showed evident phenotype, suggesting a role of the LRR in ligand sensing. OsERL is expressed in shoot apcies, internodes and anthers, and within the anther OsERL is expressed in sporophytic and tapetal cells. Cell biological analyses revealed that mutations in OsERL led to defected periclinal division in archesporial cells in anthers, suggesting a critical role of OsERL in rice anther development.
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Affiliation(s)
- Ting Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guo-Qiang Jiang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China; Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xue-Feng Yao
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Chun-Ming Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
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41
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Fei H, Yang Z, Lu Q, Wen X, Zhang Y, Zhang A, Lu C. OsSWEET14 cooperates with OsSWEET11 to contribute to grain filling in rice. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 306:110851. [PMID: 33775358 DOI: 10.1016/j.plantsci.2021.110851] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 02/08/2021] [Accepted: 02/11/2021] [Indexed: 06/12/2023]
Abstract
The grain-filling process is crucial for cereal crop yields, but how the caryopsis of such plants is supplied with sugars, which are produced by photosynthesis in leaves and then transported long distance, is largely unknown. In rice (Oryza sativa), various SWEET family sucrose transporters are thought to have important roles in grain filling. Here, we report that OsSWEET14 plays a crucial part in this process in rice. ossweet14 knockout mutants did not show any detectable phenotypic differences from the wild type, whereas ossweet14;ossweet11 double-knockout mutants had much more severe phenotypes than ossweet11 single-knockout mutants, including strongly reduced grain weight and yield, reduced grain-filling rate, and increased starch accumulation in the pericarp. Both OsSWEET14 and OsSWEET11 exhibited distinct spatiotemporal expression patterns between the early stage of caryopsis development and the rapid grain-filling stage. During the rapid grain-filling stage, OsSWEET14 and OsSWEET11 localized to four key sites: vascular parenchyma cells, the nucellar projection, the nucellar epidermis, and cross cells. These results demonstrate that OsSWEET14 plays an important role in grain filling, and they suggest that four major apoplasmic pathways supply sucrose to the endosperm during the rapid grain-filling stage via the sucrose effluxers SWEET14 and SWEET11.
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Affiliation(s)
- Honghong Fei
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Zhipan Yang
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Qingtao Lu
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
| | - Xiaogang Wen
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
| | - Yi Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, China.
| | - Aihong Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, China.
| | - Congming Lu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, China.
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42
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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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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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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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45
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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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46
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Hu J, Chang X, Zhang Y, Yu X, Qin Y, Sun Y, Zhang L. The pineapple MADS-box gene family and the evolution of early monocot flower. Sci Rep 2021; 11:849. [PMID: 33441609 PMCID: PMC7806820 DOI: 10.1038/s41598-020-79163-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 11/27/2020] [Indexed: 11/23/2022] Open
Abstract
Unlike the flower of the model monocot rice, which has diverged greatly from the ancestral monocot flower, the pineapple (Ananas comosus) flower is more typical of monocot flowers. Here, we identified 43 pineapple genes containing MADS-box domains, including 11 type I and 32 type II genes. RNA-seq expression data generated from five pineapple floral organs (sepals, petals, stamens, pistils, and ovules) and quantitative real-time PCR revealed tissue-specific expression patterns for some genes. We found that AcAGL6 and AcFUL1 were mainly expressed in sepals and petals, suggesting their involvement in the regulation of these floral organs. A pineapple ‘ABCDE’ model was proposed based on the phylogenetic analysis and expression patterns of MADS-box genes. Unlike rice and orchid with frequent species-specific gene duplication and subsequent expression divergence, the composition and expression of the ABCDE genes were conserved in pineapple. We also found that AcSEP1/3, AcAG, AcAGL11a/b/c, and AcFUL1 were highly expressed at different stages of fruit development and have similar expression profiles, implicating these genes’ role in fruit development and ripening processes. We propose that the pineapple flower can be used as a model for studying the ancestral form of monocot flowers to investigate their development and evolutionary history.
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Affiliation(s)
- Juan Hu
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiaojun Chang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ying Zhang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xianxian Yu
- School of Urban-Rural Planning and Landscape Architecture, Xuchang University, Xuchang, 461000, China
| | - Yuan Qin
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yun Sun
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Liangsheng Zhang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China.
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47
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Chen Z, Shen Z, Xu L, Zhao D, Zou Q. Regulator Network Analysis of Rice and Maize Yield-Related Genes. Front Cell Dev Biol 2021; 8:621464. [PMID: 33425929 PMCID: PMC7793993 DOI: 10.3389/fcell.2020.621464] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 11/12/2020] [Indexed: 11/13/2022] Open
Abstract
Rice and maize are the principal food crop species worldwide. The mechanism of gene regulation for the yield of rice and maize is still the research focus at present. Seed size, weight and shape are important traits of crop yield in rice and maize. Most members of three gene families, APETALA2/ethylene response factor, auxin response factors and MADS, were identified to be involved in yield traits in rice and maize. Analysis of molecular regulation mechanisms related to yield traits provides theoretical support for the improvement of crop yield. Genetic regulatory network analysis can provide new insights into gene families with the improvement of sequencing technology. Here, we analyzed the evolutionary relationships and the genetic regulatory network for the gene family members to predicted genes that may be involved in yield-related traits in rice and maize. The results may provide some theoretical and application guidelines for future investigations of molecular biology, which may be helpful for developing new rice and maize varieties with high yield traits.
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Affiliation(s)
- Zheng Chen
- School of Applied Chemistry and Biological Technology, Shenzhen Polytechnic, Shenzhen, China.,Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
| | - Zijie Shen
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
| | - Lei Xu
- School of Electronic and Communication Engineering, Shenzhen Polytechnic, Shenzhen, China
| | - Da Zhao
- School of Applied Chemistry and Biological Technology, Shenzhen Polytechnic, Shenzhen, China.,Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
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48
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Jensen E, Shafiei R, Ma X, Serba DD, Smith DP, Slavov GT, Robson P, Farrar K, Thomas Jones S, Swaller T, Flavell R, Clifton‐Brown J, Saha MC, Donnison I. Linkage mapping evidence for a syntenic QTL associated with flowering time in perennial C 4 rhizomatous grasses Miscanthus and switchgrass. GLOBAL CHANGE BIOLOGY. BIOENERGY 2021; 13:98-111. [PMID: 33381230 PMCID: PMC7756372 DOI: 10.1111/gcbb.12755] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 08/10/2020] [Indexed: 06/12/2023]
Abstract
Flowering in perennial species is directed via complex signalling pathways that adjust to developmental regulations and environmental cues. Synchronized flowering in certain environments is a prerequisite to commercial seed production, and so the elucidation of the genetic architecture of flowering time in Miscanthus and switchgrass could aid breeding in these underdeveloped species. In this context, we assessed a mapping population in Miscanthus and two ecologically diverse switchgrass mapping populations over 3 years from planting. Multiple flowering time quantitative trait loci (QTL) were identified in both species. Remarkably, the most significant Miscanthus and switchgrass QTL proved to be syntenic, located on linkage groups 4 and 2, with logarithm of odds scores of 17.05 and 21.8 respectively. These QTL regions contained three flowering time transcription factors: Squamosa Promoter-binding protein-Like, MADS-box SEPELLATA2 and gibberellin-responsive bHLH137. The former is emerging as a key component of the age-related flowering time pathway.
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Affiliation(s)
- Elaine Jensen
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Reza Shafiei
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
- University of Dundee at JHIDundeeUK
| | - Xue‐Feng Ma
- Ceres, Inc.Thousand OaksCAUSA
- Noble Research Institute, LLC.ArdmoreOKUSA
| | - Desalegn D. Serba
- Noble Research Institute, LLC.ArdmoreOKUSA
- Agricultural Research Center‐HaysKansas State UniversityHaysKSUSA
| | - Daniel P. Smith
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
- ScionRotoruaNew Zealand
| | - Gancho T. Slavov
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
- ScionRotoruaNew Zealand
| | - Paul Robson
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Kerrie Farrar
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Sian Thomas Jones
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Timothy Swaller
- Ceres, Inc.Thousand OaksCAUSA
- Genomics Institute of the Novartis Research FoundationSan DiegoCAUSA
| | - Richard Flavell
- Ceres, Inc.Thousand OaksCAUSA
- International Wheat Yield PartnershipTexas A&M UniversityCollege StationTXUSA
| | - John Clifton‐Brown
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | | | - Iain Donnison
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
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49
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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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50
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Yuan J, Jiao W, Liu Y, Ye W, Wang X, Liu B, Song Q, Chen ZJ. Dynamic and reversible DNA methylation changes induced by genome separation and merger of polyploid wheat. BMC Biol 2020; 18:171. [PMID: 33218336 PMCID: PMC7679994 DOI: 10.1186/s12915-020-00909-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 10/28/2020] [Indexed: 02/07/2023] Open
Abstract
Background Wheat is a powerful genetic model for studying polyploid evolution and crop domestication. Hexaploid bread wheat was formed by two rounds of interspecific hybridization and polyploidization, processes which are often accompanied by genetic and epigenetic changes, including DNA methylation. However, the extent and effect of such changes during wheat evolution, particularly from tetraploid-to-hexaploid wheat, are currently elusive. Results Here we report genome-wide DNA methylation landscapes in extracted tetraploid wheat (ETW, AABB), natural hexaploid wheat (NHW, AABBDD), resynthesized hexaploid wheat (RHW, AABBDD), natural tetraploid wheat (NTW, AABB), and diploid (DD). In the endosperm, levels of DNA methylation, especially in CHG (H=A, T, or C) context, were dramatically decreased in the ETW relative to natural hexaploid wheat; hypo-differentially methylated regions (DMRs) (850,832) were 24-fold more than hyper-DMRs (35,111). Interestingly, those demethylated regions in ETW were remethylated in the resynthesized hexaploid wheat after the addition of the D genome. In ETW, hypo-DMRs correlated with gene expression, and TEs were demethylated and activated, which could be silenced in the hexaploid wheat. In NHW, groups of TEs were dispersed in genic regions of three subgenomes, which may regulate the expression of TE-associated genes. Further, hypo-DMRs in ETW were associated with reduced H3K9me2 levels and increased expression of histone variant genes, suggesting concerted epigenetic changes after separation from the hexaploid. Conclusion Genome merger and separation provoke dynamic and reversible changes in chromatin and DNA methylation. These changes correlate with altered gene expression and TE activity, which may provide insights into polyploid genome and wheat evolution.
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Affiliation(s)
- Jingya Yuan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, China
| | - Wu Jiao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, China
| | - Yanfeng Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, China
| | - Wenxue Ye
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, China
| | - Xiue Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchu, 130024, China
| | - Qingxin Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, China.
| | - Z Jeffrey Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, China. .,Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA.
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