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Zhang X, He W, Wang X, Duan Y, Li Y, Wang Y, Jiang Q, Liao B, Zhou S, Li Y. Genome-Wide Analyses of MADS-Box Genes Reveal Their Involvement in Seed Development and Oil Accumulation of Tea-Oil Tree ( Camellia oleifera). Int J Genomics 2024; 2024:3375173. [PMID: 39105136 PMCID: PMC11300058 DOI: 10.1155/2024/3375173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 07/05/2024] [Accepted: 07/08/2024] [Indexed: 08/07/2024] Open
Abstract
The seeds of Camellia oleifera produce high amount of oil, which can be broadly used in the fields of food, industry, and medicine. However, the molecular regulation mechanisms of seed development and oil accumulation in C. oleifera are unclear. In this study, evolutionary and expression analyses of the MADS-box gene family were performed across the C. oleifera genome for the first time. A total of 86 MADS-box genes (ColMADS) were identified, including 60 M-type and 26 MIKC members. More gene duplication events occurred in M-type subfamily (6) than that in MIKC subfamily (2), and SEP-like genes were lost from the MIKCC clade. Furthermore, 8, 15, and 17 differentially expressed ColMADS genes (DEGs) were detected between three developmental stages of seed (S1/S2, S2/S3, and S1/S3), respectively. Among these DEGs, the STK-like ColMADS12 and TT16-like ColMADS17 were highly expressed during the seed formation (S1 and S2), agreeing with their predicted functions to positively regulate the seed organogenesis and oil accumulation. While ColMADS57 and ColMADS07 showed increasing expression level with the seed maturation (S2 and S3), conforming to their potential roles in promoting the seed ripening. In all, these results revealed a critical role of MADS-box genes in the C. oleifera seed development and oil accumulation, which will contribute to the future molecular breeding of C. oleifera.
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Affiliation(s)
- Xianzhi Zhang
- College of Horticulture and Landscape ArchitectureZhongkai University of Agriculture and Engineering, Guangzhou 510225, China
- Heyuan Branch CenterGuangdong Laboratory for Lingnan Modern Agriculture, Heyuan 517500, China
| | - Wenliang He
- College of Horticulture and Landscape ArchitectureZhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Xinyi Wang
- College of Horticulture and Landscape ArchitectureZhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Yongliang Duan
- College of Horticulture and Landscape ArchitectureZhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Yongjuan Li
- College of Horticulture and Landscape ArchitectureZhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Yi Wang
- School of Mechanic and Electronic EngineeringZhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Qingbin Jiang
- Research Institute of Tropical ForestryChinese Academy of Forestry, Guangzhou 510520, China
| | - Boyong Liao
- College of Horticulture and Landscape ArchitectureZhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Sheng Zhou
- College of Horticulture and Landscape ArchitectureZhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Yongquan Li
- College of Horticulture and Landscape ArchitectureZhongkai University of Agriculture and Engineering, Guangzhou 510225, China
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Hu Z, Huang X, Xia H, Zhang Z, Lu H, Wang X, Sun Y, Cui M, Yang S, Kant S, Xu G, Sun S. Transcription factor OsSHR2 regulates rice architecture and yield per plant in response to nitrogen. PLANTA 2024; 259:148. [PMID: 38717679 DOI: 10.1007/s00425-024-04400-7] [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: 12/27/2023] [Accepted: 03/28/2024] [Indexed: 05/23/2024]
Abstract
MAIN CONCLUSION Mutation of OsSHR2 adversely impacted root and shoot growth and impaired plant response to N conditions, further reducing the yield per plant. Nitrogen (N) is a crucial factor that regulates the plant architecture. There is still a lack of research on it. In our study, it was observed that the knockout of the SHORTROOT 2 (OsSHR2) which was induced by N deficiency, can significantly affect the regulation of plant architecture response to N in rice. Under N deficiency, the mutation of OsSHR2 significantly reduced root growth, and impaired the sensitivity of the root meristem length to N deficiency. The mutants were found to have approximately a 15% reduction in plant height compared to wild type. But mutants showed a significant increase in tillering at post-heading stage, approximately 26% more than the wild type, particularly in high N conditions. In addition, due to reduced seed setting rate and 1000-grain weight, mutant yield was significantly decreased by approximately 33% under low N fertilizer supply. The mutation also changed the distribution of N between the vegetative and reproductive organs. Our findings suggest that the transcription factor OsSHR2 plays a regulatory role in the response of plant architecture and yield per plant to N in rice.
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Affiliation(s)
- Zhi Hu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xu Huang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Huihuang Xia
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhantian Zhang
- Yantai Academy of Agricultural Sciences, Yantai, 265500, China
| | - Huixin Lu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaowen Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yafei Sun
- Institute of Eco-Environment and Plant Protection, Shanghai Academy of Agriculture Science, Shanghai, 201403, China
| | - Mengyuan Cui
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shanshan Yang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Surya Kant
- Agriculture Victoria, Grains Innovation Park, Horsham, VIC, 3400, Australia
| | - Guohua Xu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shubin Sun
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
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3
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Zhang H, Liu M, Yin K, Liu H, Liu J, Yan Z. A novel OsHB5-OsAPL-OsMADS27/OsWRKY102 regulatory module regulates grain size in rice. JOURNAL OF PLANT PHYSIOLOGY 2024; 295:154210. [PMID: 38460401 DOI: 10.1016/j.jplph.2024.154210] [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: 01/15/2024] [Revised: 02/17/2024] [Accepted: 02/29/2024] [Indexed: 03/11/2024]
Abstract
Grain size, a crucial trait that determines rice yield and quality, is typically regulated by multiple genes. Although numerous genes controlling grain size have been identified, the precise and dynamic regulatory network governing grain size is still not fully understood. In this study, we unveiled a novel regulatory module composed of OsHB5, OsAPL and OsMADS27/OsWRKY102, which plays a crucial role in modulating grain size in rice. As a positive regulator of grain size, OsAPL has been found to interact with OsHB5 both in vitro and in vivo. Through chromatin immunoprecipitation-sequencing, we successfully mapped two potential targets of OsAPL, namely OsMADS27, a positive regulator in grain size and OsWRKY102, a negative regulator in lignification that is also associated with grain size control. Further evidence from EMSA and chromatin immunoprecipitation-quantitative PCR experiments has shown that OsAPL acts as an upstream transcription factor that directly binds to the promoters of OsMADS27 and OsWRKY102. Moreover, EMSA and dual-luciferase reporter assays have indicated that the interaction between OsAPL and OsHB5 enhances the repressive effect of OsAPL on OsMADS27 and OsWRKY102. Collectively, our findings discovered a novel regulatory module, OsHB5-OsAPL-OsMADS27/OsWRKY102, which plays a significant role in controlling grain size in rice. These discoveries provide potential targets for breeding high-yield and high-quality rice varieties.
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Affiliation(s)
- Han Zhang
- Key Laboratory for Bio-resources and Eco-environment & State Key Lab of Hydraulics & Mountain River Engineering, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Meng Liu
- Key Laboratory for Bio-resources and Eco-environment & State Key Lab of Hydraulics & Mountain River Engineering, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Kangqun Yin
- Key Laboratory for Bio-resources and Eco-environment & State Key Lab of Hydraulics & Mountain River Engineering, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Huanhuan Liu
- Key Laboratory for Bio-resources and Eco-environment & State Key Lab of Hydraulics & Mountain River Engineering, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, China; National Demonstration Center for Experimental Biology Education (Sichuan University), Chengdu, 610064, China
| | - Jianquan Liu
- Key Laboratory for Bio-resources and Eco-environment & State Key Lab of Hydraulics & Mountain River Engineering, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, China; State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems and College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Zhen Yan
- Key Laboratory for Bio-resources and Eco-environment & State Key Lab of Hydraulics & Mountain River Engineering, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, China; National Demonstration Center for Experimental Biology Education (Sichuan University), Chengdu, 610064, China.
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Almeida-Silva F, Pedrosa-Silva F, Venancio TM. The Soybean Expression Atlas v2: A comprehensive database of over 5000 RNA-seq samples. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1041-1051. [PMID: 37681739 DOI: 10.1111/tpj.16459] [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: 04/28/2023] [Revised: 07/04/2023] [Accepted: 08/28/2023] [Indexed: 09/09/2023]
Abstract
Soybean is a crucial crop worldwide, used as a source of food, feed, and industrial products due to its high protein and oil content. Previously, the rapid accumulation of soybean RNA-seq data in public databases and the computational challenges of processing raw RNA-seq data motivated us to develop the Soybean Expression Atlas, a gene expression database of over a thousand RNA-seq samples. Over the past few years, our database has allowed researchers to explore the expression profiles of important gene families, discover genes associated with agronomic traits, and understand the transcriptional dynamics of cellular processes. Here, we present the Soybean Expression Atlas v2, an updated version of our database with a fourfold increase in the number of samples, featuring transcript- and gene-level transcript abundance matrices for 5481 publicly available RNA-seq samples. New features in our database include the availability of transcript-level abundance estimates and equivalence classes to explore differential transcript usage, abundance estimates in bias-corrected counts to increase the accuracy of differential gene expression analyses, a new web interface with improved data visualization and user experience, and a reproducible and scalable pipeline available as an R package. The Soybean Expression Atlas v2 is available at https://soyatlas.venanciogroup.uenf.br/, and it will accelerate soybean research, empowering researchers with high-quality and easily accessible gene expression data.
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Affiliation(s)
- Fabricio Almeida-Silva
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | - Francisnei Pedrosa-Silva
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Thiago M Venancio
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
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Chen J, Yang Y, Li C, Chen Q, Liu S, Qin B. Genome-Wide Identification of MADS-Box Genes in Taraxacum kok-saghyz and Taraxacum mongolicum: Evolutionary Mechanisms, Conserved Functions and New Functions Related to Natural Rubber Yield Formation. Int J Mol Sci 2023; 24:10997. [PMID: 37446175 DOI: 10.3390/ijms241310997] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 06/27/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023] Open
Abstract
MADS-box transcription regulators play important roles in plant growth and development. However, very few MADS-box genes have been isolated in the genus Taraxacum, which consists of more than 3000 species. To explore their functions in the promising natural rubber (NR)-producing plant Taraxacum kok-saghyz (TKS), MADS-box genes were identified in the genome of TKS and the related species Taraxacum mongolicum (TM; non-NR-producing) via genome-wide screening. In total, 66 TkMADSs and 59 TmMADSs were identified in the TKS and TM genomes, respectively. From diploid TKS to triploid TM, the total number of MADS-box genes did not increase, but expansion occurred in specific subfamilies. Between the two genomes, a total of 11 duplications, which promoted the expansion of MADS-box genes, were identified in the two species. TkMADS and TmMADS were highly conserved, and showed good collinearity. Furthermore, most TkMADS genes exhibiting tissue-specific expression patterns, especially genes associated with the ABCDE model, were preferentially expressed in the flowers, suggesting their conserved and dominant functions in flower development in TKS. Moreover, by comparing the transcriptomes of different TKS lines, we identified 25 TkMADSs related to biomass formation and 4 TkMADSs related to NR content, which represented new targets for improving the NR yield of TKS.
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Affiliation(s)
- Jiaqi Chen
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture and Rural Affairs, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Institute of Tropical Crops, Hainan University, Haikou 570228, China
| | - Yushuang Yang
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture and Rural Affairs, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Chuang Li
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture and Rural Affairs, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Institute of Tropical Crops, Hainan University, Haikou 570228, China
| | - Qiuhui Chen
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture and Rural Affairs, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Shizhong Liu
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture and Rural Affairs, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Bi Qin
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture and Rural Affairs, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
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6
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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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7
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Mahto A, Yadav A, P V A, Parida SK, Tyagi AK, Agarwal P. Cytological, transcriptome and miRNome temporal landscapes decode enhancement of rice grain size. BMC Biol 2023; 21:91. [PMID: 37076907 PMCID: PMC10116700 DOI: 10.1186/s12915-023-01577-3] [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: 05/12/2022] [Accepted: 03/27/2023] [Indexed: 04/21/2023] Open
Abstract
BACKGROUND Rice grain size (GS) is an essential agronomic trait. Though several genes and miRNA modules influencing GS are known and seed development transcriptomes analyzed, a comprehensive compendium connecting all possible players is lacking. This study utilizes two contrasting GS indica rice genotypes (small-grained SN and large-grained LGR). Rice seed development involves five stages (S1-S5). Comparative transcriptome and miRNome atlases, substantiated with morphological and cytological studies, from S1-S5 stages and flag leaf have been analyzed to identify GS proponents. RESULTS Histology shows prolonged endosperm development and cell enlargement in LGR. Stand-alone and comparative RNAseq analyses manifest S3 (5-10 days after pollination) stage as crucial for GS enhancement, coherently with cell cycle, endoreduplication, and programmed cell death participating genes. Seed storage protein and carbohydrate accumulation, cytologically and by RNAseq, is shown to be delayed in LGR. Fourteen transcription factor families influence GS. Pathway genes for four phytohormones display opposite patterns of higher expression. A total of 186 genes generated from the transcriptome analyses are located within GS trait-related QTLs deciphered by a cross between SN and LGR. Fourteen miRNA families express specifically in SN or LGR seeds. Eight miRNA-target modules display contrasting expressions amongst SN and LGR, while 26 (SN) and 43 (LGR) modules are differentially expressed in all stages. CONCLUSIONS Integration of all analyses concludes in a "Domino effect" model for GS regulation highlighting chronology and fruition of each event. This study delineates the essence of GS regulation, providing scope for future exploits. The rice grain development database (RGDD) ( www.nipgr.ac.in/RGDD/index.php ; https://doi.org/10.5281/zenodo.7762870 ) has been developed for easy access of data generated in this paper.
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Affiliation(s)
- Arunima Mahto
- National Institute of Plant Genome Research, New Delhi, India
| | - Antima Yadav
- National Institute of Plant Genome Research, New Delhi, India
| | - Aswathi P V
- National Institute of Plant Genome Research, New Delhi, India
| | - Swarup K Parida
- National Institute of Plant Genome Research, New Delhi, India
| | - Akhilesh K Tyagi
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Pinky Agarwal
- National Institute of Plant Genome Research, New Delhi, India.
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8
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Hong Y, Zhang M, Xu R. Genetic Localization and Homologous Genes Mining for Barley Grain Size. Int J Mol Sci 2023; 24:ijms24054932. [PMID: 36902360 PMCID: PMC10003025 DOI: 10.3390/ijms24054932] [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: 01/29/2023] [Revised: 02/27/2023] [Accepted: 02/27/2023] [Indexed: 03/08/2023] Open
Abstract
Grain size is an important agronomic trait determining barley yield and quality. An increasing number of QTLs (quantitative trait loci) for grain size have been reported due to the improvement in genome sequencing and mapping. Elucidating the molecular mechanisms underpinning barley grain size is vital for producing elite cultivars and accelerating breeding processes. In this review, we summarize the achievements in the molecular mapping of barley grain size over the past two decades, highlighting the results of QTL linkage analysis and genome-wide association studies. We discuss the QTL hotspots and predict candidate genes in detail. Moreover, reported homologs that determine the seed size clustered into several signaling pathways in model plants are also listed, providing the theoretical basis for mining genetic resources and regulatory networks of barley grain size.
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Affiliation(s)
- Yi Hong
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225127, China
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou 225127, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225127, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Mengna Zhang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225127, China
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou 225127, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225127, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Rugen Xu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225127, China
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou 225127, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225127, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Correspondence:
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Liu G, Zhang R, Li S, Ullah R, Yang F, Wang Z, Guo W, You M, Li B, Xie C, Wang L, Liu J, Ni Z, Sun Q, Liang R. TaMADS29 interacts with TaNF-YB1 to synergistically regulate early grain development in bread wheat. SCIENCE CHINA. LIFE SCIENCES 2023:10.1007/s11427-022-2286-0. [PMID: 36802319 DOI: 10.1007/s11427-022-2286-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 01/18/2023] [Indexed: 02/23/2023]
Abstract
Grain development is a crucial determinant of yield and quality in bread wheat (Triticum aestivum L.). However, the regulatory mechanisms underlying wheat grain development remain elusive. Here we report how TaMADS29 interacts with TaNF-YB1 to synergistically regulate early grain development in bread wheat. The tamads29 mutants generated by CRISPR/Cas9 exhibited severe grain filling deficiency, coupled with excessive accumulation of reactive oxygen species (ROS) and abnormal programmed cell death that occurred in early developing grains, while overexpression of TaMADS29 increased grain width and 1,000-kernel weight. Further analysis revealed that TaMADS29 interacted directly with TaNF-YB1; null mutation in TaNF-YB1 caused grain developmental deficiency similar to tamads29 mutants. The regulatory complex composed of TaMADS29 and TaNF-YB1 exercises its possible function that inhibits the excessive accumulation of ROS by regulating the genes involved in chloroplast development and photosynthesis in early developing wheat grains and prevents nucellar projection degradation and endosperm cell death, facilitating transportation of nutrients into the endosperm and wholly filling of developing grains. Collectively, our work not only discloses the molecular mechanism of MADS-box and NF-Y TFs in facilitating bread wheat grain development, but also indicates that caryopsis chloroplast might be a central regulator of grain development rather than merely a photosynthesis organelle. More importantly, our work offers an innovative way to breed high-yield wheat cultivars by controlling the ROS level in developing grains.
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Affiliation(s)
- Guoyu Liu
- Frontiers Science Center for Molecular Design Breeding (MOE), State Key Laboratory for Agrobiotechnology, State Key Laboratory of Plant Physiology and Biochemistry, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Runqi Zhang
- Frontiers Science Center for Molecular Design Breeding (MOE), State Key Laboratory for Agrobiotechnology, State Key Laboratory of Plant Physiology and Biochemistry, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Sen Li
- Frontiers Science Center for Molecular Design Breeding (MOE), State Key Laboratory for Agrobiotechnology, State Key Laboratory of Plant Physiology and Biochemistry, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Rehmat Ullah
- Frontiers Science Center for Molecular Design Breeding (MOE), State Key Laboratory for Agrobiotechnology, State Key Laboratory of Plant Physiology and Biochemistry, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Fengping Yang
- Frontiers Science Center for Molecular Design Breeding (MOE), State Key Laboratory for Agrobiotechnology, State Key Laboratory of Plant Physiology and Biochemistry, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zihao Wang
- Frontiers Science Center for Molecular Design Breeding (MOE), State Key Laboratory for Agrobiotechnology, State Key Laboratory of Plant Physiology and Biochemistry, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Weilong Guo
- Frontiers Science Center for Molecular Design Breeding (MOE), State Key Laboratory for Agrobiotechnology, State Key Laboratory of Plant Physiology and Biochemistry, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Mingshan You
- Frontiers Science Center for Molecular Design Breeding (MOE), State Key Laboratory for Agrobiotechnology, State Key Laboratory of Plant Physiology and Biochemistry, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Baoyun Li
- Frontiers Science Center for Molecular Design Breeding (MOE), State Key Laboratory for Agrobiotechnology, State Key Laboratory of Plant Physiology and Biochemistry, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Chaojie Xie
- Frontiers Science Center for Molecular Design Breeding (MOE), State Key Laboratory for Agrobiotechnology, State Key Laboratory of Plant Physiology and Biochemistry, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Liangsheng Wang
- Frontiers Science Center for Molecular Design Breeding (MOE), State Key Laboratory for Agrobiotechnology, State Key Laboratory of Plant Physiology and Biochemistry, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Jie Liu
- Frontiers Science Center for Molecular Design Breeding (MOE), State Key Laboratory for Agrobiotechnology, State Key Laboratory of Plant Physiology and Biochemistry, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zhongfu Ni
- Frontiers Science Center for Molecular Design Breeding (MOE), State Key Laboratory for Agrobiotechnology, State Key Laboratory of Plant Physiology and Biochemistry, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Qixin Sun
- Frontiers Science Center for Molecular Design Breeding (MOE), State Key Laboratory for Agrobiotechnology, State Key Laboratory of Plant Physiology and Biochemistry, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Rongqi Liang
- Frontiers Science Center for Molecular Design Breeding (MOE), State Key Laboratory for Agrobiotechnology, State Key Laboratory of Plant Physiology and Biochemistry, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China.
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10
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Yang D, Yang J, Wan J, Xu Y, Li L, Rong J, Chen L, He T, Zheng Y. Genome-Wide Identification of MIKCc-Type MADS-Box Family Gene and Floral Organ Transcriptome Characterization in Ma Bamboo ( Dendrocalamus latiflorus Munro). Genes (Basel) 2022; 14:genes14010078. [PMID: 36672819 PMCID: PMC9859424 DOI: 10.3390/genes14010078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/21/2022] [Accepted: 12/23/2022] [Indexed: 12/28/2022] Open
Abstract
Most bamboos die after flowering, and the molecular mechanisms responsible for flowering is poorly understood. The MIKCc-type MADS-box family gene is involved in the flowering process. To explore the mechanism of the MIKCc-type MADS-box gene and phytohormone regulation in the flowering of Dendrocalamus latiflorus Munro (D. latiflorus), characterized by extremely rapid growth and widely cultivated woody bamboo, we initially did a genome-wide analysis of the MIKCc-type MADS-box gene in D. latiflorus. In the meantime, transcriptome analysis was performed using the floral organs. A total of 170 MIKCc-Type MADS-Box genes were identified and divided into 15 categories. The cis-acting element analysis in promoters regions revealed that MIKC-type MADS-box family genes were associated with hormones, including auxin, abscisic acid (ABA), gibberellin (GA) and jasmonic acid (JA), which was found at 79, 476, 96, 486 sites and cover 61, 103, 73, 128 genes. Genome synteny analysis showed subgenome AA and BB were better than CC and obtained 49, 40, 39 synteny genes compared with Oryza sativa (O. sativa). In transcriptome analysis of floral organs, the enriched pathway from DEGs included circadian, vernalization and gibberellin pathways associated with the flowering process. We found that the jasmonic acid synthesis gene is highly expressed in the pistil, which may be the cause of Ma bamboo pollen abortion. The expression profile showed that most MIKC-type MADS-box genes exhibited high expression in flower organs. The consequences of this study will provide insight into the irregular flowering and low pollen counts of Ma bamboo.
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Affiliation(s)
- Deming Yang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jing Yang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jiayi Wan
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yanping Xu
- College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lei Li
- College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jundong Rong
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lingyan Chen
- College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Tianyou He
- College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yushan Zheng
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence:
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11
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Sun Q, Li Y, Gong D, Hu A, Zhong W, Zhao H, Ning Q, Tan Z, Liang K, Mu L, Jackson D, Zhang Z, Yang F, Qiu F. A NAC-EXPANSIN module enhances maize kernel size by controlling nucellus elimination. Nat Commun 2022; 13:5708. [PMID: 36175574 PMCID: PMC9522829 DOI: 10.1038/s41467-022-33513-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 09/21/2022] [Indexed: 11/17/2022] Open
Abstract
Maize early endosperm development is initiated in coordination with elimination of maternal nucellar tissues. However, the underlying mechanisms are largely unknown. Here, we characterize a major quantitative trait locus for maize kernel size and weight that encodes an EXPANSIN gene, ZmEXPB15. The encoded β-expansin protein is expressed specifically in nucellus, and positively controls kernel size and weight by promoting nucellus elimination. We further show that two nucellus-enriched transcription factors (TFs), ZmNAC11 and ZmNAC29, activate ZmEXPB15 expression. Accordingly, these two TFs also promote kernel size and weight through nucellus elimination regulation, and genetic analyses support their interaction with ZmEXPB15. Importantly, hybrids derived from a ZmEXPB15 overexpression line have increased kernel weight, demonstrates its potential value in breeding. Together, we reveal a pathway modulating the cellular processes of maternal nucellus elimination and early endosperm development, and an approach to improve kernel weight. Current studies of maize kernel development mostly focus on endosperm and embryo development, and little is known about the control of the nucellus tissue. Here, the authors report a NAC-EXPB15 pathway that regulate maize kernel size by modulating nucellus elimination and early endosperm development.
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Affiliation(s)
- Qin Sun
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Yunfu Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Dianming Gong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Aoqing Hu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Wanshun Zhong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Hailiang Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Qiang Ning
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Zengdong Tan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Kun Liang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Luyao Mu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - David Jackson
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China.,Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, 11724, USA
| | - Zuxin Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China.,Hubei Hongshan Laboratory, 430070, Wuhan, Hubei, China
| | - Fang Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China. .,Hubei Hongshan Laboratory, 430070, Wuhan, Hubei, China.
| | - Fazhan Qiu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China. .,Hubei Hongshan Laboratory, 430070, Wuhan, Hubei, China.
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12
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Li W, Yu Y, Chen X, Fang Q, Yang A, Chen X, Wu L, Wang C, Wu D, Ye S, Wu D, Sun G. N6-Methyladenosine dynamic changes and differential methylation in wheat grain development. PLANTA 2022; 255:125. [PMID: 35567638 DOI: 10.1007/s00425-022-03893-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 04/02/2022] [Indexed: 06/15/2023]
Abstract
More methylation changes occur in late interval than in early interval of wheat seed development with protein and the starch synthesis-related pathway enriched in the later stages. Wheat seed development is a critical process to determining wheat yield and quality, which is controlled by genetics, epigenetics and environments. The N6-methyladenosine (m6A) modification is a reversible and dynamic process and plays regulatory role in plant development and stress responses. To better understand the role of m6A in wheat grain development, we characterized the m6A modification at 10 day post-anthesis (DPA), 20 DPA and 30 DPA in wheat grain development. m6A-seq identified 30,615, 30,326, 27,676 high confidence m6A peaks from the 10DPA, 20DPA, and 30DPA, respectively, and enriched at 3'UTR. There were 29,964, 29,542 and 26,834 unique peaks identified in AN0942_10d, AN0942_20d and AN0942_30d. One hundred and forty-two genes were methylated by m6A throughout seed development, 940 genes methylated in early grain development (AN0942_20d vs AN0942_10d), 1542 genes in late grain development (AN0942_30d vs AN0942_20d), and 1190 genes between early and late development stage (AN0942_30d vs AN0942_10d). KEGG enrichment analysis found that protein-related pathways and the starch synthesis-related pathway were significantly enriched in the later stages of seed development. Our results provide novel knowledge on m6A dynamic changes and its roles in wheat grain development.
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Affiliation(s)
- Wenxiang Li
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Yi Yu
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Xuanrong Chen
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Qian Fang
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Anqi Yang
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Xinyu Chen
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Lei Wu
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Chengyu Wang
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, Anhui, China
- Key Laboratory of Wheat Biology and Genetic Improvement on South Yellow and Huai River Valley, Ministry of Agriculture, Hefei, 230036, China
| | - Dechuan Wu
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Sihong Ye
- Cotton Institute, Anhui Academy of Agricultural Sciences, Hefei, 230001, Anhui, China.
| | - Dexiang Wu
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, Anhui, China.
| | - Genlou Sun
- Biology Department, Saint Mary's University, Halifax, NS, B3H 3C3, Canada.
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13
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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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14
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Htwe YM, Shi P, Zhang D, Li Z, Xiao Y, Yang Y, Lei X, Wang Y. Programmed Cell Death May Be Involved in the Seedless Phenotype Formation of Oil Palm. FRONTIERS IN PLANT SCIENCE 2022; 13:832017. [PMID: 35401608 PMCID: PMC8984474 DOI: 10.3389/fpls.2022.832017] [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: 12/09/2021] [Accepted: 02/22/2022] [Indexed: 06/14/2023]
Abstract
Oil palm (Elaeis guineensis Jacq.) is a well-known vegetable oil-yielding crop. Seedlessness is one of the most prominent traits in oil palm due to its low processing costs and high oil content. Nevertheless, an extensive study on molecular mechanisms regulating seedless phenotype formation in oil palm is very limited so far. In this study, stigma, style, and ovary from seedless and seeded (Tenera and Pisifera) oil palm trees were used to investigate the possible mechanism. Results showed that non-pollination resulted in no fruits, and self- and cross-pollinations resulted in seedless fruits, while boron treatment had no effect on seedless phenotype formation, implying that seedless trees have incomplete self and outcrossing incompatibility. Furthermore, the transcriptome data analysis highlighted eight programmed cell death (PCD) genes and three groups of PCD-related genes: 4-coumarate-CoA ligase (4CL), S-RNase, and MADS-box. The majority of these genes were significantly up-regulated in the stigma and style of Seedless palm trees compared to Tenera and Pisifera. In addition, the co-expression network analysis confirmed the significant correlation among these genes. Moreover, two simple sequence repeats (SSR) markers (S41 and S44) were developed to identify the seedless phenotype. The up-regulation of 4CL and MADS-box TFs activated the expression of PCD genes; on the other hand, S-RNase resulted in pollen tube RNA degradation and triggered PCD. While the link between PCD and seedless phenotype formation in oil palm has not been extensively studied to date, these findings suggest a role of PCD in pollen tube lethality, leading to double fertilization failure and the seedless phenotype.
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Affiliation(s)
- Yin Min Htwe
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions/Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Peng Shi
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions/Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Dapeng Zhang
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions/Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Zhiying Li
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions/Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Yong Xiao
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions/Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Yaodong Yang
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Xintao Lei
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
- Tropical Crops Genetic Resources Institute of Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Yong Wang
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions/Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, China
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15
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Genome-wide identification, phylogenetic and expression pattern analysis of MADS-box family genes in foxtail millet (Setaria italica). Sci Rep 2022; 12:4979. [PMID: 35322041 PMCID: PMC8943164 DOI: 10.1038/s41598-022-07103-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 02/10/2022] [Indexed: 11/28/2022] Open
Abstract
Foxtail millet (Setaria italica) is rich in nutrients and extremely beneficial to human health. We identified and comprehensively analyzed 89 MADS-box genes in the foxtail millet genome. According to the classification of MADS-box genes in Arabidopsis thaliana and rice, the SiMADS-box genes were divided into M-type (37) and MIKC-type (52). During evolution, the differentiation of MIKC-type MADS-box genes occurred before that of monocotyledons and dicotyledons. The SiMADS-box gene structure has undergone much differentiation, and the number of introns in the MIKC-type subfamily is much greater than that in the M-type subfamily. Analysis of gene duplication events revealed that MIKC-type MADS-box gene segmental duplication accounted for the vast majority of gene duplication events, and MIKC-type MADS-box genes played a major role in the amplification of SiMADS-box genes. Collinearity analysis showed highest collinearity between foxtail millet and maize MADS-box genes. Analysis of tissue-specific expression showed that SiMADS-box genes are highly expressed throughout the grain-filling process. Expression analysis of SiMADS-box genes under eight different abiotic stresses revealed many stress-tolerant genes, with induced expression of SiMADS33 and SiMADS78 under various stresses warranting further attention. Further, some SiMADS-box proteins may interact under external stress. This study provides insights for MADS-box gene mining and molecular breeding of foxtail millet in the future.
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16
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Li W, Guo X, Wu W, Yu W, Li S, Luo D, Wang T, Zhu Q, Chen L, Lee D. Construction of a Novel Female Sterility System for Hybrid Rice. FRONTIERS IN PLANT SCIENCE 2022; 12:815401. [PMID: 35185963 PMCID: PMC8850283 DOI: 10.3389/fpls.2021.815401] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 12/27/2021] [Indexed: 06/14/2023]
Abstract
The main constraints of current hybrid rice technology using male sterility (MS) are the low yield and high labor costs of hybrid rice seed (HRS) production. Therefore, there is an urgent need for innovative new hybrid rice technology. Fortunately, we discovered a unique spontaneous sporophytic female-sterile rice mutant controlled by a single recessive locus in the nucleus. Because female-sterile mutant lines cannot produce any selfed-seeds but their pollen has totally normal functions, female sterility (FS) lines may be considered ideal pollen donors to replace the female-fertile pollen donor parent lines currently used in the HRS production. In this study, a genetically engineered FS-based system was constructed to propagate a pure transgene-free FS line using a bentazon herbicide screening. Additionally, the ability of the FS + MS (FM)-line system, with mixed plantings of FS and MS lines, to produce HRS was tested. The pilot field experiment results showed that HRS of the FM-line system was more efficient compared with the conventional FS to MS strip planting control mode. Thus, this study provides new insights into genetic engineering technology and a promising strategy for the utilization of FS in hybrid rice.
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Affiliation(s)
- Wei Li
- Rice Research Institute, Yunnan Agriculture University, Kunming, China
| | - Xiaoqiong Guo
- Rice Research Institute, Yunnan Agriculture University, Kunming, China
| | - Wenbin Wu
- Rice Research Institute, Yunnan Agriculture University, Kunming, China
| | - Weilin Yu
- Rice Research Institute, Yunnan Agriculture University, Kunming, China
| | - Shichuan Li
- Rice Research Institute, Yunnan Agriculture University, Kunming, China
| | - Di Luo
- Rice Research Institute, Yunnan Agriculture University, Kunming, China
| | - Tianjie Wang
- Rice Research Institute, Yunnan Agriculture University, Kunming, China
| | - Qian Zhu
- Rice Research Institute, Yunnan Agriculture University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- The Key Laboratory for Crop Production and Smart Agriculture of Yunnan Province, Yunnan Agricultural University, Kunming, China
| | - Lijuan Chen
- Rice Research Institute, Yunnan Agriculture University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- The Key Laboratory for Crop Production and Smart Agriculture of Yunnan Province, Yunnan Agricultural University, Kunming, China
| | - Dongsun Lee
- Rice Research Institute, Yunnan Agriculture University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- The Key Laboratory for Crop Production and Smart Agriculture of Yunnan Province, Yunnan Agricultural University, Kunming, China
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17
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Jiang H, Guo D, Ye J, Gao Y, Liu H, Wang Y, Xue M, Yan Q, Chen J, Duan L, Li G, Li X, Xie L. Genome-wide analysis of genomic imprinting in the endosperm and allelic variation in flax. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:1697-1710. [PMID: 34228847 DOI: 10.1111/tpj.15411] [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: 11/24/2020] [Accepted: 06/30/2021] [Indexed: 06/13/2023]
Abstract
Genomic imprinting is an epigenetic phenomenon that causes biased expression of maternally and paternally inherited alleles. In flowering plants, genomic imprinting predominantly occurs in the triploid endosperm and plays a vital role in seed development. In this study, we identified 248 candidate imprinted genes including 114 maternally expressed imprinted genes (MEGs) and 134 paternally expressed imprinted genes (PEGs) in flax (Linum usitatissimum L.) endosperm using deep RNA sequencing. These imprinted genes were neither clustered in specific chromosomal regions nor well conserved among flax and other plant species. MEGs tended to be expressed specifically in the endosperm, whereas the expression of PEGs was not tissue-specific. Imprinted single nucleotide polymorphisms differentiated 200 flax cultivars into the oil flax, oil-fiber dual purpose flax and fiber flax subgroups, suggesting that genomic imprinting contributed to intraspecific variation in flax. The nucleotide diversity of imprinted genes in the oil flax subgroup was significantly higher than that in the fiber flax subgroup, indicating that some imprinted genes underwent positive selection during flax domestication from oil flax to fiber flax. Moreover, imprinted genes that underwent positive selection were related to flax functions. Thirteen imprinted genes related to flax seed size and weight were identified using a candidate gene-based association study. Therefore, our study provides information for further exploration of the function and genomic variation of imprinted genes in the flax population.
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Affiliation(s)
- Haixia Jiang
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Dongliang Guo
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Jiali Ye
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Yanfang Gao
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Huiqing Liu
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Yue Wang
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Min Xue
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Qingcheng Yan
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Jiaxun Chen
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Lepeng Duan
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Gongze Li
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Xiao Li
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Liqiong Xie
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
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18
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Saada S, Solomon CU, Drea S. Programmed Cell Death in Developing Brachypodium distachyon Grain. Int J Mol Sci 2021; 22:ijms22169086. [PMID: 34445790 PMCID: PMC8396479 DOI: 10.3390/ijms22169086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/14/2021] [Accepted: 08/19/2021] [Indexed: 01/01/2023] Open
Abstract
The normal developmental sequence in a grass grain entails the death of several maternal and filial tissues in a genetically regulated process termed programmed cell death (PCD). The progression and molecular aspects of PCD in developing grains have been reported for domesticated species such as barley, rice, maize and wheat. Here, we report a detailed investigation of PCD in the developing grain of the wild model species Brachypodium distachyon. We detected PCD in developing Brachypodium grains using molecular and histological approaches. We also identified in Brachypodium the orthologs of protease genes known to contribute to grain PCD and surveyed their expression. We found that, similar to cereals, PCD in the Brachypodium nucellus occurs in a centrifugal pattern following anthesis. However, compared to cereals, the rate of post-mortem clearance in the Brachypodium nucellus is slower. However, compared to wheat and barley, mesocarp PCD in Brachypodium proceeds more rapidly in lateral cells. Remarkably, Brachypodium mesocarp PCD is not coordinated with endosperm development. Phylogenetic analysis suggests that barley and wheat possess more vacuolar processing enzymes that drive nucellar PCD compared to Brachypodium and rice. Our expression analysis highlighted putative grain-specific PCD proteases in Brachypodium. Combined with existing knowledge on grain PCD, our study suggests that the rate of nucellar PCD moderates grain size and that the pattern of mesocarp PCD influences grain shape.
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Affiliation(s)
- Safia Saada
- Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester LE1 7RH, UK; (S.S.); (S.D.)
| | - Charles Ugochukwu Solomon
- Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester LE1 7RH, UK; (S.S.); (S.D.)
- Department of Plant Science and Biotechnology, Abia State University, Uturu PMB 2000, Nigeria
- Correspondence:
| | - Sinéad Drea
- Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester LE1 7RH, UK; (S.S.); (S.D.)
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19
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Sandhu J, Irvin L, Liu K, Staswick P, Zhang C, Walia H. Endoplasmic reticulum stress pathway mediates the early heat stress response of developing rice seeds. PLANT, CELL & ENVIRONMENT 2021; 44:2604-2624. [PMID: 34036580 DOI: 10.1111/pce.14103] [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: 02/20/2021] [Accepted: 05/16/2021] [Indexed: 06/12/2023]
Abstract
A transient heat stress occurring during early seed development in rice (Oryza sativa) reduces seed size by altering endosperm development. However, the relationship between the timing of the stress and specific developmental stage on heat sensitivity is not well-understood. To address this, we imposed a series of non-overlapping heat stress treatments and found that young seeds are most sensitive during the first two days after flowering. Temporal transcriptome analysis of developing, heat stressed (35°C) seeds during this window shows that Inositol-requiring enzyme 1 (IRE1)-mediated endoplasmic reticulum (ER) stress response and jasmonic acid (JA) pathways are the early (1-3 h) drivers of heat stress response. We propose that increased JA levels under heat stress may precede ER stress response as JA application promotes the spliced form of OsbZIP50, an ER response marker gene linked to IRE1-specific pathway. This study presents temporal and mechanistic insights into the role of JA and ER stress signalling during early heat stress response of rice seeds that impact both grain size and quality. Modulating the heat sensitivity of the early sensing pathways and downstream endosperm development genes can enhance rice resilience to transient heat stress events.
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Affiliation(s)
- Jaspreet Sandhu
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Larissa Irvin
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Kan Liu
- School of Biological Science, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Paul Staswick
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Chi Zhang
- School of Biological Science, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Harkamal Walia
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
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20
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Ye LX, Zhang JX, Hou XJ, Qiu MQ, Wang WF, Zhang JX, Hu CG, Zhang JZ. A MADS-Box Gene CiMADS43 Is Involved in Citrus Flowering and Leaf Development through Interaction with CiAGL9. Int J Mol Sci 2021; 22:ijms22105205. [PMID: 34069068 PMCID: PMC8156179 DOI: 10.3390/ijms22105205] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 05/10/2021] [Accepted: 05/12/2021] [Indexed: 11/16/2022] Open
Abstract
MADS-box genes are involved in various developmental processes including vegetative development, flower architecture, flowering, pollen formation, seed and fruit development. However, the function of most MADS-box genes and their regulation mechanism are still unclear in woody plants compared with model plants. In this study, a MADS-box gene (CiMADS43) was identified in citrus. Phylogenetic and sequence analysis showed that CiMADS43 is a GOA-like Bsister MADS-box gene. It was localized in the nucleus and as a transcriptional activator. Overexpression of CiMADS43 promoted early flowering and leaves curling in transgenic Arabidopsis. Besides, overexpression or knockout of CiMADS43 also showed leaf curl phenotype in citrus similar to that of CiMADS43 overexpressed in Arabidopsis. Protein–protein interaction found that a SEPALLATA (SEP)-like protein (CiAGL9) interacted with CiMADS43 protein. Interestingly, CiAGL9 also can bind to the CiMADS43 promoter and promote its transcription. Expression analysis also showed that these two genes were closely related to seasonal flowering and the development of the leaf in citrus. Our findings revealed the multifunctional roles of CiMADS43 in the vegetative and reproductive development of citrus. These results will facilitate our understanding of the evolution and molecular mechanisms of MADS-box genes in citrus.
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21
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Lu J, Le Hir R, Gómez-Páez DM, Coen O, Péchoux C, Jasinski S, Magnani E. The nucellus: between cell elimination and sugar transport. PLANT PHYSIOLOGY 2021; 185:478-490. [PMID: 33721907 PMCID: PMC8133628 DOI: 10.1093/plphys/kiaa045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 11/10/2020] [Indexed: 05/29/2023]
Abstract
The architecture of the seed is shaped by the processes of tissue partitioning, which determines the volume ratio of maternal and zygotic tissues, and nutrient partitioning, which regulates nutrient distribution among tissues. In angiosperms, early seed development is characterized by antagonistic development of the nucellus maternal tissue and the endosperm fertilization product to become the main sugar sink. This process marked the evolution of angiosperms and outlines the most ancient seed architectures. In Arabidopsis, the endosperm partially eliminates the nucellus and imports sugars from the seed coat. Here, we show that the nucellus is symplasmically connected to the chalaza, the seed nutrient unloading zone, and works as both a sugar sink and source alongside the seed coat. After fertilization, the transient nucellus accumulates starch early on and releases it in the apoplasmic space during its elimination. By contrast, the persistent nucellus exports sugars toward the endosperm through the SWEET4 hexose facilitator. Finally, we analyzed sugar metabolism and transport in the transparent testa 16 mutant, which fails to undergo nucellus cell elimination, which shed light on the coordination between tissue and nutrient partitioning. Overall, this study identifies a path of sugar transport in the Arabidopsis seed and describes a link between sugar redistribution and the nucellus cell-elimination program.
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Affiliation(s)
- Jing Lu
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, CNRS, University of Paris-Saclay, Route de St-Cyr (RD10), 78026 Versailles Cedex, France
- École Doctorale 567 Sciences du Végétal, University Paris-Sud, University of Paris-Saclay, bat 360, 91405 Orsay Cedex, France
| | - Rozenn Le Hir
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, CNRS, University of Paris-Saclay, Route de St-Cyr (RD10), 78026 Versailles Cedex, France
| | - Dennys-Marcela Gómez-Páez
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, CNRS, University of Paris-Saclay, Route de St-Cyr (RD10), 78026 Versailles Cedex, France
| | - Olivier Coen
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, CNRS, University of Paris-Saclay, Route de St-Cyr (RD10), 78026 Versailles Cedex, France
- École Doctorale 567 Sciences du Végétal, University Paris-Sud, University of Paris-Saclay, bat 360, 91405 Orsay Cedex, France
| | - Christine Péchoux
- INRAE, Génétique Animale et Biologie Intégrative, Domaine de Vilvert, 78352 Jouy-en-Josas Cedex, France
| | - Sophie Jasinski
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, CNRS, University of Paris-Saclay, Route de St-Cyr (RD10), 78026 Versailles Cedex, France
| | - Enrico Magnani
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, CNRS, University of Paris-Saclay, Route de St-Cyr (RD10), 78026 Versailles Cedex, France
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22
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Shoesmith JR, Solomon CU, Yang X, Wilkinson LG, Sheldrick S, van Eijden E, Couwenberg S, Pugh LM, Eskan M, Stephens J, Barakate A, Drea S, Houston K, Tucker MR, McKim SM. APETALA2 functions as a temporal factor together with BLADE-ON-PETIOLE2 and MADS29 to control flower and grain development in barley. Development 2021; 148:dev.194894. [DOI: 10.1242/dev.194894] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 01/25/2021] [Indexed: 11/20/2022]
Abstract
ABSTRACT
Cereal grain develops from fertilised florets. Alterations in floret and grain development greatly influence grain yield and quality. Despite this, little is known about the underlying genetic control of these processes, especially in key temperate cereals such as barley and wheat. Using a combination of near-isogenic mutant comparisons, gene editing and genetic analyses, we reveal that HvAPETALA2 (HvAP2) controls floret organ identity, floret boundaries, and maternal tissue differentiation and elimination during grain development. These new roles of HvAP2 correlate with changes in grain size and HvAP2-dependent expression of specific HvMADS-box genes, including the B-sister gene, HvMADS29. Consistent with this, gene editing demonstrates that HvMADS29 shares roles with HvAP2 in maternal tissue differentiation. We also discovered that a gain-of-function HvAP2 allele masks changes in floret organ identity and grain size due to loss of barley LAXATUM.A/BLADE-ON-PETIOLE2 (HvBOP2) gene function. Taken together, we reveal novel pleiotropic roles and regulatory interactions for an AP2-like gene controlling floret and grain development in a temperate cereal.
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Affiliation(s)
- Jennifer R. Shoesmith
- Division of Plant Sciences, School of Life Sciences, University of Dundee at the James Hutton Institute, Invergowrie DD2 5DA, UK
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie DD2 5DA, UK
| | - Charles Ugochukwu Solomon
- Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester LE1 7RH, UK
- Department of Plant Science and Biotechnology, Abia State University, PMB 2000, Uturu, Nigeria
| | - Xiujuan Yang
- Waite Research Institute, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA, 5064, Australia
| | - Laura G. Wilkinson
- Waite Research Institute, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA, 5064, Australia
- Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Scott Sheldrick
- Division of Plant Sciences, School of Life Sciences, University of Dundee at the James Hutton Institute, Invergowrie DD2 5DA, UK
| | - Ewan van Eijden
- Division of Plant Sciences, School of Life Sciences, University of Dundee at the James Hutton Institute, Invergowrie DD2 5DA, UK
| | - Sanne Couwenberg
- Division of Plant Sciences, School of Life Sciences, University of Dundee at the James Hutton Institute, Invergowrie DD2 5DA, UK
| | - Laura M. Pugh
- Division of Plant Sciences, School of Life Sciences, University of Dundee at the James Hutton Institute, Invergowrie DD2 5DA, UK
| | - Mhmoud Eskan
- Division of Plant Sciences, School of Life Sciences, University of Dundee at the James Hutton Institute, Invergowrie DD2 5DA, UK
| | - Jennifer Stephens
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie DD2 5DA, UK
| | - Abdellah Barakate
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie DD2 5DA, UK
| | - Sinéad Drea
- Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Kelly Houston
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie DD2 5DA, UK
| | - Matthew R. Tucker
- Waite Research Institute, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA, 5064, Australia
| | - Sarah M. McKim
- Division of Plant Sciences, School of Life Sciences, University of Dundee at the James Hutton Institute, Invergowrie DD2 5DA, UK
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23
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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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24
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Orchid B sister gene PeMADS28 displays conserved function in ovule integument development. Sci Rep 2021; 11:1205. [PMID: 33441740 PMCID: PMC7806631 DOI: 10.1038/s41598-020-79877-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 12/14/2020] [Indexed: 11/21/2022] Open
Abstract
The ovules and egg cells are well developed to be fertilized at anthesis in many flowering plants. However, ovule development is triggered by pollination in most orchids. In this study, we characterized the function of a Bsister gene, named PeMADS28, isolated from Phalaenopsis equestris, the genome-sequenced orchid. Spatial and temporal expression analysis showed PeMADS28 predominantly expressed in ovules between 32 and 48 days after pollination, which synchronizes with integument development. Subcellular localization and protein–protein interaction analyses revealed that PeMADS28 could form a homodimer as well as heterodimers with D-class and E-class MADS-box proteins. In addition, ectopic expression of PeMADS28 in Arabidopsis thaliana induced small curled rosette leaves, short silique length and few seeds, similar to that with overexpression of other species’ Bsister genes in Arabidopsis. Furthermore, complementation test revealed that PeMADS28 could rescue the phenotype of the ABS/TT16 mutant. Together, these results indicate the conserved function of BsisterPeMADS28 associated with ovule integument development in orchid.
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25
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Verma A, Prakash G, Ranjan R, Tyagi AK, Agarwal P. Silencing of an Ubiquitin Ligase Increases Grain Width and Weight in indica Rice. Front Genet 2021; 11:600378. [PMID: 33510769 PMCID: PMC7835794 DOI: 10.3389/fgene.2020.600378] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 11/27/2020] [Indexed: 11/18/2022] Open
Abstract
Many quantitative trait loci (QTLs) have been identified by molecular genetic studies which control grain size by regulating grain width, length, and/or thickness. Grain width 2 (GW2) is one such QTL that codes for a RING-type E3 ubiquitin ligase and increases grain size by regulating grain width through ubiquitin-mediated degradation of unknown substrates. A natural variation (single-nucleotide polymorphism at the 346th position) in the functional domain-coding region of OsGW2 in japonica rice genotypes has been shown to cause an increase in grain width/weight in rice. However, this variation is absent in indica rice genotypes. In this study, we report that reduced expression of OsGW2 can alter grain size, even though natural sequence variation is not responsible for increased grain size in indica rice genotypes. OsGW2 shows high expression in seed development stages and the protein localizes to the nucleus and cytoplasm. Downregulation of OsGW2 by RNAi technology results in wider and heavier grains. Microscopic observation of grain morphology suggests that OsGW2 determines grain size by influencing both cell expansion and cell proliferation in spikelet hull. Using transcriptome analysis, upregulated genes related to grain size regulation have been identified among 1,426 differentially expressed genes in an OsGW2_RNAi transgenic line. These results reveal that OsGW2 is a negative regulator of grain size in indica rice and affects both cell number and cell size in spikelet hull.
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Affiliation(s)
- Ankit Verma
- National Institute of Plant Genome Research, New Delhi, India
| | - Geeta Prakash
- National Institute of Plant Genome Research, New Delhi, India.,Department of Botany, Gargi College, University of Delhi, New Delhi, India
| | - Rajeev Ranjan
- National Institute of Plant Genome Research, New Delhi, India.,Department of Plant Molecular Biology, University of Delhi, New Delhi, India
| | - Akhilesh K Tyagi
- National Institute of Plant Genome Research, New Delhi, India.,Department of Plant Molecular Biology, University of Delhi, New Delhi, India
| | - Pinky Agarwal
- National Institute of Plant Genome Research, New Delhi, India
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26
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Niu B, Deng H, Li T, Sharma S, Yun Q, Li Q, E Z, Chen C. OsbZIP76 interacts with OsNF-YBs and regulates endosperm cellularization in rice (Oryza sativa). JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:1983-1996. [PMID: 32621654 DOI: 10.1111/jipb.12989] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 07/03/2020] [Indexed: 05/23/2023]
Abstract
Following double fertilization, plant endosperm nuclei undergo syncytial divisions, followed by synchronous cellularization. Cellularization is a key event during endosperm development, but our understanding of its regulation is limited to Arabidopsis. In this study we show that OsbZIP76 regulates cellularization in rice (Oryza sativa). Activation of OsbZIP76 coincided with the initiation of cellularization, and its knockdown or knockout mutants exhibited precocious cellularization. Genes involved in endosperm development or starch biosynthesis were prematurely activated in the osbzip76 caryopsis. As a putative transcription factor, OsbZIP76 alone lacked transcriptional activation activity; however, it interacted with the nuclear factor Y (NF-Y) family transcription factors OsNF-YB9 and OsNF-YB1 in yeast and in planta. OsbZIP76 and OsNF-YB9 were predominantly expressed in the endosperm and the proteins colocalized. Seeds of osnf-yb1 and osbzip76 mutants showed reduced size and reduced apparent amylose content. The parent-of-origin-dependent expression of OsbZIP76 is variable in different rice accessions. In summary, OsbZIP76 is an endosperm-expressed imprinted gene that regulates endosperm development in rice.
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Affiliation(s)
- Baixiao Niu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Hui Deng
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Tingting Li
- Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310000, China
| | - Sandeep Sharma
- Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, BHU, Varanasi, 221005, India
| | - Qianbin Yun
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Qianru Li
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Zhiguo E
- Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310000, China
| | - Chen Chen
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, 225009, China
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Wu TY, Müller M, Gruissem W, Bhullar NK. Genome Wide Analysis of the Transcriptional Profiles in Different Regions of the Developing Rice Grains. RICE (NEW YORK, N.Y.) 2020; 13:62. [PMID: 32894395 PMCID: PMC7477059 DOI: 10.1186/s12284-020-00421-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 08/20/2020] [Indexed: 05/14/2023]
Abstract
BACKGROUND Rice is an important food source for humans worldwide. Because of its nutritional and agricultural significance, a number of studies addressed various aspects of rice grain development and grain filling. Nevertheless, the molecular processes underlying grain filling and development, and in particular the contributions of different grain tissues to these processes, are not understood. MAIN TEXT Using RNA-sequencing, we profiled gene expression activity in grain tissues comprised of cross cells (CC), the nucellar epidermis (NE), ovular vascular trace (OVT), endosperm (EN) and the aleurone layer (AL). These tissues were dissected using laser capture microdissection (LCM) at three distinct grain development stages. The mRNA expression datasets offer comprehensive and new insights into the gene expression patterns in different rice grain tissues and their contributions to grain development. Comparative analysis of the different tissues revealed their similar and/or unique functions, as well as the spatio-temporal regulation of common and tissue-specific genes. The expression patterns of genes encoding hormones and transporters indicate an important role of the OVT tissue in metabolite transport during grain development. Gene co-expression network prediction on OVT-specific genes identified several distinct and common development-specific transcription factors. Further analysis of enriched DNA sequence motifs proximal to OVT-specific genes revealed known and novel DNA sequence motifs relevant to rice grain development. CONCLUSION Together, the dataset of gene expression in rice grain tissues is a novel and useful resource for further work to dissect the molecular and metabolic processes during rice grain development.
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Affiliation(s)
- Ting-Ying Wu
- Department of Biology, Plant Biotechnology, Institute of Molecular Plant Biology, ETH Zurich, 8092, Zurich, Switzerland
- Present address: Temasek Life Science Laboratory, 1 Research Link, Singapore, 117604, Singapore
| | - Marlen Müller
- Department of Biology, Plant Biotechnology, Institute of Molecular Plant Biology, ETH Zurich, 8092, Zurich, Switzerland
- Present address: Roche Glycart AG, Wagistrasse 10, 8952, Schlieren, Switzerland
| | - Wilhelm Gruissem
- Department of Biology, Plant Biotechnology, Institute of Molecular Plant Biology, ETH Zurich, 8092, Zurich, Switzerland
- Advanced Plant Biotechnology Center, National Chung Hsing University, 145 Xingda Road, Taichung, 40227, Taiwan
| | - Navreet K Bhullar
- Department of Biology, Plant Biotechnology, Institute of Molecular Plant Biology, ETH Zurich, 8092, Zurich, Switzerland.
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Doronina TV, Sheval EV, Lazareva EM. Programmed Cell Death during Formation of the Embryo Sac and Seed. Russ J Dev Biol 2020. [DOI: 10.1134/s1062360420030029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Pretty crowds are happy crowds: the influence of attractiveness on mood perception. PSYCHOLOGICAL RESEARCH 2020; 85:1823-1836. [PMID: 32451630 PMCID: PMC8289770 DOI: 10.1007/s00426-020-01360-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 05/13/2020] [Indexed: 11/07/2022]
Abstract
Empirical findings predominantly support a happiness superiority effect in visual search and emotion categorization paradigms and reveal that social cues, like sex and race, moderate this advantage. A more recent study showed that the facial attribute attractiveness also influences the accuracy and speed of emotion perception. In the current study, we investigated whether the influence of attractiveness on emotion perception translates into a more general evaluation of moods when more than one emotional target is presented. In two experiments, we used the mood-of-the-crowd (MoC) task to investigate whether attractive crowds are perceived more positively compared to less attractive crowds. The task was to decide whether an array of faces included more angry or more happy faces. Furthermore, we recorded gaze movements to test the assumption that fixations on happy expressions occur more often in attractive crowds. Thirty-four participants took part in experiment 1 as well as in experiment 2. In both experiments, crowds presenting attractive faces were judged as being happy more frequently whereas the reverse pattern was found for unattractive crowds of faces. Moreover, participants were faster and more accurate when evaluating attractive crowds containing more happy faces as well as when judging unattractive crowds composed of more angry expressions. Additionally, in experiment 1, there were more fixations on happy compared to angry expressions in attractive crowds. Overall, the present findings support the assumption that attractiveness moderates emotion perception.
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Tang Y, Wang J, Bao X, Wu Q, Yang T, Li H, Wang W, Zhang Y, Bai N, Guan Y, Dai J, Xie Y, Li S, Huo R, Cheng W. Genome-wide analysis of Jatropha curcas MADS-box gene family and functional characterization of the JcMADS40 gene in transgenic rice. BMC Genomics 2020; 21:325. [PMID: 32345214 PMCID: PMC7187513 DOI: 10.1186/s12864-020-6741-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 04/16/2020] [Indexed: 11/17/2022] Open
Abstract
Background Physic nut (Jatropha curcas), an inedible oilseed plant, is among the most promising alternative energy sources because of its high oil content, rapid growth and extensive adaptability. Proteins encoded by MADS-box family genes are important transcription factors participated in regulating plant growth, seed development and responses to abiotic stress. However, there has been no in-depth research on the MADS-box genes and their roles in physic nut. Results In our study, 63 MADS-box genes (JcMADSs) were identified in the physic nut genome, and classed into five groups (MIKCC, Mα, Mβ, Mγ, MIKC*) according to phylogenetic comparison with Arabidopsis homologs. Expression profile analysis based on RNA-seq suggested that many JcMADS genes had the strongest expression in seeds, and seven of them responded in leaves to at least one abiotic stressor (drought and/or salinity) at one or more time points. Transient expression analysis and a transactivation assay indicated that JcMADS40 is a nucleus-localized transcriptional activator. Plants overexpressing JcMADS40 did not show altered plant growth, but the overexpressing plants did exhibit reductions in grain size, grain length, grain width, 1000-seed weight and yield per plant. Further data on the reduced grain size in JcMADS40-overexpressing plants supported the putative role of JcMADS genes in seed development. Conclusions This study will be useful in order to further understand the process of MADS-box genes involved in regulating growth and development in addition to their functions in abiotic stress resistance, and will eventually provide a theoretical basis for the functional investigation and the exploitation of candidate genes for the molecular improvement of physic nut.
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Affiliation(s)
- Yuehui Tang
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Henan, Zhoukou, China. .,Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, Henan, Zhoukou, China.
| | - Jian Wang
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Henan, Zhoukou, China.,Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, Henan, Zhoukou, China
| | - Xinxin Bao
- School of Journalism and Communication, Zhoukou Normal University, Henan, Zhoukou, China
| | - Qian Wu
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Henan, Zhoukou, China
| | - Tongwen Yang
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Henan, Zhoukou, China
| | - Han Li
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Henan, Zhoukou, China
| | - Wenxia Wang
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Henan, Zhoukou, China
| | - Yizhen Zhang
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Henan, Zhoukou, China
| | - Nannan Bai
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Henan, Zhoukou, China
| | - Yaxin Guan
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Henan, Zhoukou, China
| | - Jiaxi Dai
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Henan, Zhoukou, China
| | - Yanjie Xie
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Henan, Zhoukou, China
| | - Shen Li
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Henan, Zhoukou, China
| | - Rui Huo
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Henan, Zhoukou, China
| | - Wei Cheng
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Henan, Zhoukou, China
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Ram H, Gandass N, Sharma A, Singh A, Sonah H, Deshmukh R, Pandey AK, Sharma TR. Spatio-temporal distribution of micronutrients in rice grains and its regulation. Crit Rev Biotechnol 2020; 40:490-507. [DOI: 10.1080/07388551.2020.1742647] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Hasthi Ram
- Department of Agri-Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali, India
| | - Nishu Gandass
- Department of Agri-Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali, India
| | - Ankita Sharma
- Department of Agri-Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali, India
| | - Anmol Singh
- Department of Agri-Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali, India
| | - Humira Sonah
- Department of Agri-Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali, India
| | - Rupesh Deshmukh
- Department of Agri-Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali, India
| | - Ajay Kumar Pandey
- Department of Agri-Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali, India
| | - Tilak Raj Sharma
- Department of Agri-Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali, India
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Guo Y, Gao M, Liang X, Xu M, Liu X, Zhang Y, Liu X, Liu J, Gao Y, Qu S, Luan F. Quantitative Trait Loci for Seed Size Variation in Cucurbits - A Review. FRONTIERS IN PLANT SCIENCE 2020; 11:304. [PMID: 32265957 PMCID: PMC7099056 DOI: 10.3389/fpls.2020.00304] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 03/03/2020] [Indexed: 05/17/2023]
Abstract
Cucurbits (Cucurbitaceae family) include many economically important fruit vegetable crops such as watermelon, pumpkin/squash, cucumber, and melon. Seed size (SS) is an important trait in cucurbits breeding, which is controlled by quantitative trait loci (QTL). Recent advances have deciphered several signaling pathways underlying seed size variation in model plants such as Arabidopsis and rice, but little is known on the genetic basis of SS variation in cucurbits. Here we conducted literature review on seed size QTL identified in watermelon, pumpkin/squash, cucumber and melon, and inferred 14, 9 and 13 consensus SS QTL based on their physical positions in respective draft genomes. Among them, four from watermelon (ClSS2.2, ClSS6.1, ClSS6.2, and ClSS8.2), two from cucumber (CsSS4.1 and CsSS5.1), and one from melon (CmSS11.1) were major-effect, stable QTL for seed size and weight. Whole genome sequence alignment revealed that these major-effect QTL were located in syntenic regions across different genomes suggesting possible structural and functional conservation of some important genes for seed size control in cucurbit crops. Annotation of genes in the four watermelon consensus SS QTL regions identified genes that are known to play important roles in seed size control including members of the zinc finger protein and the E3 ubiquitin-protein ligase families. The present work highlights the utility of comparative analysis in understanding the genetic basis of seed size variation, which may help future mapping and cloning of seed size QTL in cucurbits.
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Affiliation(s)
- Yu Guo
- College of Life Sciences, Agriculture and Forestry, Qiqihar University, Qiqihar, China
- Heilongjiang Provincial Key Laboratory of Resistance Gene Engineering and Preservation of Biodiversity in Cold Areas, Qiqihar, China
| | - Meiling Gao
- College of Life Sciences, Agriculture and Forestry, Qiqihar University, Qiqihar, China
- Heilongjiang Provincial Key Laboratory of Resistance Gene Engineering and Preservation of Biodiversity in Cold Areas, Qiqihar, China
| | - Xiaoxue Liang
- College of Life Sciences, Agriculture and Forestry, Qiqihar University, Qiqihar, China
| | - Ming Xu
- College of Life Sciences, Agriculture and Forestry, Qiqihar University, Qiqihar, China
| | - Xiaosong Liu
- College of Life Sciences, Agriculture and Forestry, Qiqihar University, Qiqihar, China
| | - Yanling Zhang
- College of Life Sciences, Agriculture and Forestry, Qiqihar University, Qiqihar, China
| | - Xiujie Liu
- Qiqihar Horticultural Research Institute, Qiqihar, China
| | - Jixiu Liu
- Qiqihar Horticultural Research Institute, Qiqihar, China
| | - Yue Gao
- Qiqihar Horticultural Research Institute, Qiqihar, China
| | - Shuping Qu
- College of Horticulture, Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Feishi Luan
- College of Horticulture, Landscape Architecture, Northeast Agricultural University, Harbin, China
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Schilling S, Kennedy A, Pan S, Jermiin LS, Melzer R. Genome-wide analysis of MIKC-type MADS-box genes in wheat: pervasive duplications, functional conservation and putative neofunctionalization. THE NEW PHYTOLOGIST 2020; 225:511-529. [PMID: 31418861 DOI: 10.1111/nph.16122] [Citation(s) in RCA: 129] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 08/06/2019] [Indexed: 05/21/2023]
Abstract
Wheat (Triticum aestivum) is one of the most important crops worldwide. Given a growing global population coupled with increasingly challenging cultivation conditions, facilitating wheat breeding by fine-tuning important traits is of great importance. MADS-box genes are prime candidates for this, as they are involved in virtually all aspects of plant development. Here, we present a detailed overview of phylogeny and expression of 201 wheat MIKC-type MADS-box genes. Homoeolog retention is significantly above the average genome-wide retention rate for wheat genes, indicating that many MIKC-type homoeologs are functionally important and not redundant. Gene expression is generally in agreement with the expected subfamily-specific expression pattern, indicating broad conservation of function of MIKC-type genes during wheat evolution. We also found extensive expansion of some MIKC-type subfamilies, especially those potentially involved in adaptation to different environmental conditions like flowering time genes. Duplications are especially prominent in distal telomeric regions. A number of MIKC-type genes show novel expression patterns and respond, for example, to biotic stress, pointing towards neofunctionalization. We speculate that conserved, duplicated and neofunctionalized MIKC-type genes may have played an important role in the adaptation of wheat to a diversity of conditions, hence contributing to the importance of wheat as a global staple food.
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Affiliation(s)
- Susanne Schilling
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Dublin, Ireland
| | - Alice Kennedy
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Dublin, Ireland
| | - Sirui Pan
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Dublin, Ireland
| | - Lars S Jermiin
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Dublin, Ireland
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Rainer Melzer
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Dublin, Ireland
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Genome-wide identification and expression profile of the MADS-box gene family in Erigeron breviscapus. PLoS One 2019; 14:e0226599. [PMID: 31860684 PMCID: PMC6924644 DOI: 10.1371/journal.pone.0226599] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Accepted: 11/29/2019] [Indexed: 12/30/2022] Open
Abstract
The MADS-box gene family encodes transcription factors with many biological functions that extensively regulate plant growth, development and reproduction. Erigeron breviscapus is a medicinal herb used widely in traditional Chinese medicine, and is believed to improve blood circulation and ameliorate platelet coagulation. In order to gain a detailed understanding of how transcription factor expression may regulate the growth of this potentially important medicinal plant, a genome-wide analysis of the MADS-box gene family of E. breviscapus is needed. In the present study, 44 MADS-box genes were identified in E. breviscapus and categorized into five subgroups (MIKC, Mα, Mβ, Mγ and Mδ) according to their phylogenetic relationships with the Arabidopsis MADS-box genes. Additionally, the functional domain, subcellular location and motif compositions of the E. breviscapus MADS-box gene products were characterized. The expression levels for each of the E. breviscapus MADS-box (EbMADS) genes were analyzed in flower, leaf, stem and root organs, and showed that the majority of EbMADS genes were expressed in flowers. Meanwhile, some MADS genes were found to express high levels in leaf, stem and root, indicating that the MADS-box genes are involved in various aspects of the physiological and developmental processes of the E. breviscapus. The results from gene expression analysis under different pollination treatments revealed that the MADS-box genes were highly expressed after non-pollinated treatment. To the best of our knowledge, this study describes the first genome-wide analysis of the E. breviscapus MADS-box gene family, and the results provide valuable information for understanding of the classification, cloning and putative functions of the MADS-box family.
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Yin X, Liu X, Xu B, Lu P, Dong T, Yang D, Ye T, Feng YQ, Wu Y. OsMADS18, a membrane-bound MADS-box transcription factor, modulates plant architecture and the abscisic acid response in rice. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:3895-3909. [PMID: 31034557 PMCID: PMC6685668 DOI: 10.1093/jxb/erz198] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 04/16/2019] [Indexed: 05/18/2023]
Abstract
The APETALA1 (AP1)/FRUITFULL (FUL)-like transcription factor OsMADS18 plays diverse functions in rice development, but the underlying molecular mechanisms are far from fully understood. Here, we report that down-regulation of OsMADS18 expression in RNAi lines caused a delay in seed germination and young seedling growth, whereas the overexpression of OsMADS18 produced plants with fewer tillers. In targeted OsMADS18 genome-edited mutants (osmads18-cas9), an increased number of tillers, altered panicle size, and reduced seed setting were observed. The EYFP-OsMADS18 (full-length) protein was localized to the nucleus and plasma membrane but the EYFP-OsMADS18-N (N-terminus) protein mainly localized to the nucleus. The expression of OsMADS18 could be stimulated by abscisic acid (ABA), and ABA stimulation triggered the cleavage of HA-OsMADS18 and the translocation of OsMADS18 from the plasma membrane to the nucleus. The inhibitory effect of ABA on seedling growth was less effective in the OsMADS18-overexpressing plants. The expression of a set of ABA-responsive genes was significantly reduced in the overexpressing plants. The phenotypes of transgenic plants expressing EYFP-OsMADS18-N resembled those observed in the osmads18-cas9 mutants. Analysis of the interaction of OsMADS18 with OsMADS14, OsMADS15, and OsMADS57 strongly suggests an essential role for OsMADS18 in rice development.
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Affiliation(s)
- Xiaoming Yin
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Xiong Liu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Buxian Xu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Piaoyin Lu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Tian Dong
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Di Yang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Tiantian Ye
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan, China
| | - Yu-Qi Feng
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan, China
| | - Yan Wu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
- Correspondence:
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Hoffmeier A, Gramzow L, Bhide AS, Kottenhagen N, Greifenstein A, Schubert O, Mummenhoff K, Becker A, Theißen G. A Dead Gene Walking: Convergent Degeneration of a Clade of MADS-Box Genes in Crucifers. Mol Biol Evol 2019; 35:2618-2638. [PMID: 30053121 DOI: 10.1093/molbev/msy142] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Genes are "born," and eventually they "die." These processes shape the phenotypic evolution of organisms and are hence of great biological interest. If genes die in plants, they generally do so quite rapidly. Here, we describe the fate of GOA-like genes that evolve in a dramatically different manner. GOA-like genes belong to the subfamily of Bsister genes of MIKC-type MADS-box genes. Typical MIKC-type genes encode conserved transcription factors controlling plant development. We show that ABS-like genes, a clade of Bsister genes, are indeed highly conserved in crucifers (Brassicaceae) maintaining the ancestral function of Bsister genes in ovule and seed development. In contrast, their closest paralogs, the GOA-like genes, have been undergoing convergent gene death in Brassicaceae. Intriguingly, erosion of GOA-like genes occurred after millions of years of coexistence with ABS-like genes. We thus describe Delayed Convergent Asymmetric Degeneration, a so far neglected but possibly frequent pattern of duplicate gene evolution that does not fit classical scenarios. Delayed Convergent Asymmetric Degeneration of GOA-like genes may have been initiated by a reduction in the expression of an ancestral GOA-like gene in the stem group of Brassicaceae and driven by dosage subfunctionalization. Our findings have profound implications for gene annotations in genomics, interpreting patterns of gene evolution and using genes in phylogeny reconstructions of species.
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Affiliation(s)
- Andrea Hoffmeier
- Genetics, Matthias Schleiden Institute, Friedrich-Schiller-University Jena, Jena, Germany
| | - Lydia Gramzow
- Genetics, Matthias Schleiden Institute, Friedrich-Schiller-University Jena, Jena, Germany
| | - Amey S Bhide
- Plant Developmental Biology Group, Institute of Botany, Justus-Liebig-University Giessen, Giessen, Germany
| | - Nina Kottenhagen
- Genetics, Matthias Schleiden Institute, Friedrich-Schiller-University Jena, Jena, Germany
| | - Andreas Greifenstein
- Genetics, Matthias Schleiden Institute, Friedrich-Schiller-University Jena, Jena, Germany
| | - Olesia Schubert
- Plant Developmental Biology Group, Institute of Botany, Justus-Liebig-University Giessen, Giessen, Germany
| | - Klaus Mummenhoff
- Department of Biology/Botany, University of Osnabrück, Osnabrück, Germany
| | - Annette Becker
- Plant Developmental Biology Group, Institute of Botany, Justus-Liebig-University Giessen, Giessen, Germany
| | - Günter Theißen
- Genetics, Matthias Schleiden Institute, Friedrich-Schiller-University Jena, Jena, Germany
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Ali Z, Raza Q, Atif RM, Aslam U, Ajmal M, Chung G. Genetic and Molecular Control of Floral Organ Identity in Cereals. Int J Mol Sci 2019; 20:E2743. [PMID: 31167420 PMCID: PMC6600504 DOI: 10.3390/ijms20112743] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 05/25/2019] [Accepted: 05/28/2019] [Indexed: 12/22/2022] Open
Abstract
Grasses represent a major family of monocots comprising mostly cereals. When compared to their eudicot counterparts, cereals show a remarkable morphological diversity. Understanding the molecular basis of floral organ identity and inflorescence development is crucial to gain insight into the grain development for yield improvement purposes in cereals, however, the exact genetic mechanism of floral organogenesis remains elusive due to their complex inflorescence architecture. Extensive molecular analyses of Arabidopsis and other plant genera and species have established the ABCDE floral organ identity model. According to this model, hierarchical combinatorial activities of A, B, C, D, and E classes of homeotic genes regulate the identity of different floral organs with partial conservation and partial diversification between eudicots and cereals. Here, we review the developmental role of A, B, C, D, and E gene classes and explore the recent advances in understanding the floral development and subsequent organ specification in major cereals with reference to model plants. Furthermore, we discuss the evolutionary relationships among known floral organ identity genes. This comparative overview of floral developmental genes and associated regulatory factors, within and between species, will provide a thorough understanding of underlying complex genetic and molecular control of flower development and floral organ identity, which can be helpful to devise innovative strategies for grain yield improvement in cereals.
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Affiliation(s)
- Zulfiqar Ali
- Institute of Plant Breeding and Biotechnology, Muhammad Nawaz Sharif University of Agriculture, Multan 66000, Pakistan.
| | - Qasim Raza
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan.
- Molecular Breeding Laboratory, Division of Plant Breeding and Genetics, Rice Research Institute, Kala Shah Kaku 39020, Pakistan.
| | - Rana Muhammad Atif
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan.
- Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture, Faisalabad 38000, Pakistan.
| | - Usman Aslam
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan.
| | - Muhammad Ajmal
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan.
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Chonnam 59626, Korea.
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Kumpeangkeaw A, Tan D, Fu L, Han B, Sun X, Hu X, Ding Z, Zhang J. Asymmetric birth and death of type I and type II MADS-box gene subfamilies in the rubber tree facilitating laticifer development. PLoS One 2019; 14:e0214335. [PMID: 30934009 PMCID: PMC6443149 DOI: 10.1371/journal.pone.0214335] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Accepted: 03/11/2019] [Indexed: 01/13/2023] Open
Abstract
The rubber tree (Hevea brasiliensis Muell. Arg.) is a rubber producing crop and contains specialized laticifers. MADS-box genes are a family of transcription factor genes that regulate plant development, especially floral organ and gametophyte development. 97 MADS-box genes were identified in the rubber tree through transcriptomes and genome mining. 93.8% of the genes were mapped onto the genome scaffolds in correspondence to the coverage (93.8%) of current version of sequenced genome. Phylogenetic analysis indicates that type II MADS-box genes have been more actively duplicated than their orthologous genes in Arabidopsis and rice, so that most (70, 72.2%) of the MADS-box genes in the rubber tree belong to type II subfamily. This is a high percentage compared to those in Arabidopsis (43.7%) and rice (56.8%). Moreover, 69 out of 70 type II genes in the rubber tree are transcribed, and they are mostly predominantly expressed in flowers, but some genes are predominantly expressed in laticifers, suggesting their roles in both flower and laticifer development. The number of type I genes in the rubber tree is only 27 (27.8%), a much smaller number compared to their orthologous genes in Arabidopsis (56.3%) and rice (43.2%). At the same time, most of the type I genes (55.6%, 15) in the rubber tree are silent and are probably pseudogenes. The high birth rate and low death rate of type II genes and low birth rate and high death rate of type I genes may corresponds to special developmental requirements in the rubber tree, e.g. the development of laticifer system for biosynthesis of cis-polyisoprene, the rubber. Moreover, atypical MIKC* factors (e.g. HbMADS1 in S-clade, and HbMADS20 in P-clade) are identified. These genes are diverged to typical MIKC* genes in sequences and facilitate functions required in laticifer development and rubber biosynthesis, which is not necessary in Arabidopsis and rice.
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Affiliation(s)
- Anuwat Kumpeangkeaw
- International College, Huazhong Agricultural University, Lion Mountain, Wuhan, China
- Institute of Tropical Bioscience and Biotechnology, MOA Key Laboratory of Tropical Crops Biology and Genetic Resources, Hainan Bioenergy Center, CATAS, Haikou, Hainan Province, China
- Song Khla Rubber Research Centre, Department of Agriculture, Ministry of Agriculture and Cooperatives, Had Yai, Song Khla, Thailand
| | - Deguan Tan
- Institute of Tropical Bioscience and Biotechnology, MOA Key Laboratory of Tropical Crops Biology and Genetic Resources, Hainan Bioenergy Center, CATAS, Haikou, Hainan Province, China
| | - Lili Fu
- Institute of Tropical Bioscience and Biotechnology, MOA Key Laboratory of Tropical Crops Biology and Genetic Resources, Hainan Bioenergy Center, CATAS, Haikou, Hainan Province, China
| | - Bingying Han
- Institute of Tropical Bioscience and Biotechnology, MOA Key Laboratory of Tropical Crops Biology and Genetic Resources, Hainan Bioenergy Center, CATAS, Haikou, Hainan Province, China
| | - Xuepiao Sun
- Institute of Tropical Bioscience and Biotechnology, MOA Key Laboratory of Tropical Crops Biology and Genetic Resources, Hainan Bioenergy Center, CATAS, Haikou, Hainan Province, China
| | - Xiaowen Hu
- Zhanjiang Experimental Station, CATAS, Zhanjiang, Guangdong Province, China
| | - Zehong Ding
- Institute of Tropical Bioscience and Biotechnology, MOA Key Laboratory of Tropical Crops Biology and Genetic Resources, Hainan Bioenergy Center, CATAS, Haikou, Hainan Province, China
| | - Jiaming Zhang
- Institute of Tropical Bioscience and Biotechnology, MOA Key Laboratory of Tropical Crops Biology and Genetic Resources, Hainan Bioenergy Center, CATAS, Haikou, Hainan Province, China
- * E-mail:
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Shchennikova AV, Shulga OA, Skryabin KG. Diversification of the Homeotic AP3 Clade MADS-Box Genes in Asteraceae Species Chrysanthemum morifolium L. and Helianthus annuus L. DOKL BIOCHEM BIOPHYS 2018; 483:348-354. [PMID: 30607737 DOI: 10.1134/s1607672918060145] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Indexed: 11/23/2022]
Abstract
The structure and phylogeny of MADS-box genes HAM91 of sunflower (Helianthus annuus) and CDM115 of chrysanthemum (Chrysanthemum morifolium) were characterized. It is shown that these genes encode MADS-domain transcription factors, which are orthologs of TM6 (Solanum lycopersicum) and APETALA3 (Arabidopsis thaliana), respectively. We obtained two types of transgenic tobacco plants (Nicotiana tabacum) with constitutive expression of HAM91 and CDM115 genes. Both types of plants flowered later than the control plants and formed more flowers and seed pods. The weight of seeds of 35S::CDM115 plants was significantly lower than in the control and 35S::HAM91 plants, which may indicate to a change in the identity of ovules in 35S::CDM115.
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Affiliation(s)
- A V Shchennikova
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia.
| | - O A Shulga
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, 127550, Russia
| | - K G Skryabin
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia
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Lu J, Magnani E. Seed tissue and nutrient partitioning, a case for the nucellus. PLANT REPRODUCTION 2018; 31:309-317. [PMID: 29869727 PMCID: PMC6105262 DOI: 10.1007/s00497-018-0338-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 04/25/2018] [Indexed: 05/18/2023]
Abstract
Flowering plants display a large spectrum of seed architectures. The volume ratio of maternal versus zygotic seed tissues changes considerably among species and underlies different nutrient-storing strategies. Such diversity arose through the evolution of cell elimination programs that regulate the relative growth of one tissue over another to become the major storage compartment. The elimination of the nucellus maternal tissue is regulated by developmental programs that marked the origin of angiosperms and outlined the most ancient seed architectures. This review focuses on such a defining mechanism for seed evolution and discusses the role of nucellus development in seed tissues and nutrient partitioning at the light of novel discoveries on its molecular regulation.
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Affiliation(s)
- Jing Lu
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, University of Paris-Saclay, Route de St-Cyr (RD10), 78026, Versailles Cedex, France
- Ecole Doctorale 567 Sciences du Végétal, University Paris-Sud, University of Paris-Saclay, Bat 360, 91405, Orsay Cedex, France
| | - Enrico Magnani
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, University of Paris-Saclay, Route de St-Cyr (RD10), 78026, Versailles Cedex, France.
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41
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Long W, Wang Y, Zhu S, Jing W, Wang Y, Ren Y, Tian Y, Liu S, Liu X, Chen L, Wang D, Zhong M, Zhang Y, Hu T, Zhu J, Hao Y, Zhu X, Zhang W, Wang C, Zhang W, Wan J. FLOURY SHRUNKEN ENDOSPERM1 Connects Phospholipid Metabolism and Amyloplast Development in Rice. PLANT PHYSIOLOGY 2018; 177:698-712. [PMID: 29717019 PMCID: PMC6001332 DOI: 10.1104/pp.17.01826] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 04/11/2018] [Indexed: 05/03/2023]
Abstract
Starch synthesized and stored in amyloplasts serves as the major energy storage molecule in cereal endosperm. To elucidate the molecular mechanisms underlying amyloplast development and starch synthesis, we isolated a series of floury endosperm mutants in rice (Oryza sativa). We identified the rice mutant floury shrunken endosperm1 (fse1), which exhibited obvious defects in the development of compound starch grains, decreased starch content, and altered starch physicochemical features. Map-based cloning showed that FSE1 encodes a phospholipase-like protein homologous to phosphatidic acid-preferring phospholipase A1FSE1 was expressed ubiquitously with abundant levels observed in developing seeds and roots. FSE1 was localized to both the cytosol and intracellular membranes. Lipid profiling indicated that total extra-plastidic lipids and phosphatidic acid were increased in fse1 plants, suggesting that FSE1 may exhibit in vivo phospholipase A1 activity on phosphatidylcholine, phosphatidylinositol, phosphatidyl-Ser, phosphatidylethanolamine, and, in particular, phosphatidic acid. Additionally, the total galactolipid content in developing fse1 endosperm was significantly reduced, which may cause abnormal amyloplast development. Our results identify FSE1 as a phospholipase-like protein that controls the synthesis of galactolipids in rice endosperm and provide a novel connection between lipid metabolism and starch synthesis in rice grains during endosperm development.
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Affiliation(s)
- Wuhua Long
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, P.R. China
- Guizhou Rice Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550006, P.R. China
| | - Yunlong Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Susong Zhu
- Guizhou Rice Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550006, P.R. China
| | - Wen Jing
- College of Life Sciences, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Yihua Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Yulong Ren
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R. China
| | - Yunlu Tian
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Shijia Liu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Xi Liu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Liangming Chen
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Di Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Mingsheng Zhong
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Yuanyan Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Tingting Hu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Jianping Zhu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Yuanyuan Hao
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Xiaopin Zhu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Wenwei Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Chunming Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Wenhua Zhang
- College of Life Sciences, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Jianmin Wan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, P.R. China
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R. China
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Callens C, Tucker MR, Zhang D, Wilson ZA. Dissecting the role of MADS-box genes in monocot floral development and diversity. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:2435-2459. [PMID: 29718461 DOI: 10.1093/jxb/ery086] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 03/16/2018] [Indexed: 05/05/2023]
Abstract
Many monocot plants have high social and economic value. These include grasses such as rice (Oryza sativa), wheat (Triticum aestivum), and barley (Hordeum vulgare), which produce soft commodities for many food and beverage industries, and ornamental flowers such ase lily (Lilium longiflorum) and orchid (Oncidium Gower Ramsey), which represent an important component of international flower markets. There is constant pressure to improve the development and diversity of these species, with a significant emphasis on flower development, and this is particularly relevant considering the impact of changing environments on reproduction and thus yield. MADS-box proteins are a family of transcription factors that contain a conserved 60 amino acid MADS-box motif. In plants, attention has been devoted to characterization of this family due to their roles in inflorescence and flower development, which holds promise for the modification of floral architecture for plant breeding. This has been explored in diverse angiosperms, but particularly the dicot model Arabidopsis thaliana. The focus of this review is on the less well characterized roles of the MADS-box proteins in monocot flower development and how changes in MADS-box proteins throughout evolution may have contributed to creating a diverse range of flowers. Examining these changes within the monocots can identify the importance of certain genes and pinpoint those which might be useful in future crop improvement and breeding strategies.
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Affiliation(s)
- Cindy Callens
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, UK
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA, Australia
| | - Matthew R Tucker
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA, Australia
| | - Dabing Zhang
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA, Australia
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Zoe A Wilson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, UK
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43
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Zhang H, Xu H, Feng M, Zhu Y. Suppression of OsMADS7 in rice endosperm stabilizes amylose content under high temperature stress. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:18-26. [PMID: 28429576 PMCID: PMC5785353 DOI: 10.1111/pbi.12745] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 04/06/2017] [Accepted: 04/11/2017] [Indexed: 05/03/2023]
Abstract
High temperature significantly alters the amylose content of rice, resulting in mature grains with poor eating quality. However, only few genes and/or quantitative trait loci involved in this process have been isolated and the molecular mechanisms of this effect remain unclear. Here, we describe a floral organ identity gene, OsMADS7, involved in stabilizing rice amylose content at high temperature. OsMADS7 is greatly induced by high temperature at the early filling stage. Constitutive suppression of OsMADS7 stabilizes amylose content under high temperature stress but results in low spikelet fertility. However, rice plants with both stable amylose content at high temperature and normal spikelet fertility can be obtained by specifically suppressing OsMADS7 in endosperm. GBSSI is the major enzyme responsible for amylose biosynthesis. A low filling rate and high expression of GBSSI were detected in OsMADS7 RNAi plants at high temperature, which may be correlated with stabilized amylose content in these transgenic seeds under high temperature. Thus, specific suppression of OsMADS7 in endosperm could improve the stability of rice amylose content at high temperature, and such transgenic materials may be a valuable genetic resource for breeding rice with elite thermal resilience.
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Affiliation(s)
- Hua Zhang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease ControlKey Laboratory of Creative AgricultureMinistry of AgricultureInstitute of Virology and BiotechnologyZhejiang Academy of Agricultural SciencesHangzhouZhejiangChina
| | - Heng Xu
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease ControlKey Laboratory of Creative AgricultureMinistry of AgricultureInstitute of Virology and BiotechnologyZhejiang Academy of Agricultural SciencesHangzhouZhejiangChina
| | - Mengjie Feng
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease ControlKey Laboratory of Creative AgricultureMinistry of AgricultureInstitute of Virology and BiotechnologyZhejiang Academy of Agricultural SciencesHangzhouZhejiangChina
| | - Ying Zhu
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease ControlKey Laboratory of Creative AgricultureMinistry of AgricultureInstitute of Virology and BiotechnologyZhejiang Academy of Agricultural SciencesHangzhouZhejiangChina
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Huang J, Deng J, Shi T, Chen Q, Liang C, Meng Z, Zhu L, Wang Y, Zhao F, Yu S, Chen Q. Global transcriptome analysis and identification of genes involved in nutrients accumulation during seed development of rice tartary buckwheat (Fagopyrum Tararicum). Sci Rep 2017; 7:11792. [PMID: 28924217 PMCID: PMC5603606 DOI: 10.1038/s41598-017-11929-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 08/31/2017] [Indexed: 12/20/2022] Open
Abstract
Tartary buckwheat seeds are rich in various nutrients, such as storage proteins, starch, and flavonoids. To get a good knowledge of the transcriptome dynamics and gene regulatory mechanism during the process of seed development and nutrients accumulation, we performed a comprehensive global transcriptome analysis using rice tartary buckwheat seeds at different development stages, namely pre-filling stage, filling stage, and mature stage. 24 819 expressed genes, including 108 specifically expressed genes, and 11 676 differentially expressed genes (DEGs) were identified. qRT-PCR analysis was performed on 34 DEGs to validate the transcriptome data, and a good consistence was obtained. Based on their expression patterns, the identified DEGs were classified to eight clusters, and the enriched GO items in each cluster were analyzed. In addition, 633 DEGs related to plant hormones were identified. Furthermore, genes in the biosynthesis pathway of nutrients accumulation were analyzed, including 10, 20, and 23 DEGs corresponding to the biosynthesis of seed storage proteins, flavonoids, and starch, respectively. This is the first transcriptome analysis during seed development of tartary buckwheat. It would provide us a comprehensive understanding of the complex transcriptome dynamics during seed development and gene regulatory mechanism of nutrients accumulation.
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Affiliation(s)
- Juan Huang
- Research Center of Guizhou Buckwheat Engineering and Technology, Research Center of Buckwheat Industry Technology, Guizhou Normal University, Baoshan Beilu 116, Guiyang, 550001, Guizhou, P.R. China
| | - Jiao Deng
- Research Center of Guizhou Buckwheat Engineering and Technology, Research Center of Buckwheat Industry Technology, Guizhou Normal University, Baoshan Beilu 116, Guiyang, 550001, Guizhou, P.R. China
| | - Taoxiong Shi
- Research Center of Guizhou Buckwheat Engineering and Technology, Research Center of Buckwheat Industry Technology, Guizhou Normal University, Baoshan Beilu 116, Guiyang, 550001, Guizhou, P.R. China
| | - Qijiao Chen
- Research Center of Guizhou Buckwheat Engineering and Technology, Research Center of Buckwheat Industry Technology, Guizhou Normal University, Baoshan Beilu 116, Guiyang, 550001, Guizhou, P.R. China
| | - Chenggang Liang
- Research Center of Guizhou Buckwheat Engineering and Technology, Research Center of Buckwheat Industry Technology, Guizhou Normal University, Baoshan Beilu 116, Guiyang, 550001, Guizhou, P.R. China
| | - Ziye Meng
- Research Center of Guizhou Buckwheat Engineering and Technology, Research Center of Buckwheat Industry Technology, Guizhou Normal University, Baoshan Beilu 116, Guiyang, 550001, Guizhou, P.R. China
| | - Liwei Zhu
- Research Center of Guizhou Buckwheat Engineering and Technology, Research Center of Buckwheat Industry Technology, Guizhou Normal University, Baoshan Beilu 116, Guiyang, 550001, Guizhou, P.R. China
| | - Yan Wang
- Research Center of Guizhou Buckwheat Engineering and Technology, Research Center of Buckwheat Industry Technology, Guizhou Normal University, Baoshan Beilu 116, Guiyang, 550001, Guizhou, P.R. China
| | - Fengli Zhao
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Pengfei Road No. 7, Dapeng New District, Shenzhen, 518120, Guangdong, P.R. China
| | - Shizhou Yu
- Guizhou Academy of Tobacco Science, Longbatan Road 29, Guanshanhu District, Guiyang, 550081, Guizhou, P.R. China
| | - Qingfu Chen
- Research Center of Guizhou Buckwheat Engineering and Technology, Research Center of Buckwheat Industry Technology, Guizhou Normal University, Baoshan Beilu 116, Guiyang, 550001, Guizhou, P.R. China.
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Cheng Z, Ge W, Li L, Hou D, Ma Y, Liu J, Bai Q, Li X, Mu S, Gao J. Analysis of MADS-Box Gene Family Reveals Conservation in Floral Organ ABCDE Model of Moso Bamboo ( Phyllostachys edulis). FRONTIERS IN PLANT SCIENCE 2017; 8:656. [PMID: 28515730 PMCID: PMC5413564 DOI: 10.3389/fpls.2017.00656] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 04/10/2017] [Indexed: 05/05/2023]
Abstract
Mini chromosome maintenance 1, agamous, deficiens, and serum response factor (MADS)-box genes are transcription factors which play fundamental roles in flower development and regulation of floral organ identity. However, till date, identification and functions of MADS-box genes remain largely unclear in Phyllostachys edulis. In view of this, we performed a whole-genome survey and identified 34 MADS-box genes in P. edulis, and based on phylogeny, they were classified as MIKCC, MIKC∗, Mα, and Mβ. The detailed analysis about gene structure and motifs, phylogenetic classification, comparison of gene divergence and duplication are provided. Interestingly, expression patterns for most genes were found similar to those of Arabidopsis and rice, indicating that the well-established ABCDE model can be applied to P. edulis. Moreover, we overexpressed PheMADS15, an AP1-like gene, in Arabidopsis, and found that the transgenic plants have early flowering phenotype, suggesting that PheMADS15 might be a regulator of flowering transition in P. edulis. Taken together, this study provides not only insightful comprehension but also useful information for understanding the functions of MADS-box genes in P. edulis.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Jian Gao
- Key Laboratory of Bamboo and Rattan Science and Technology of the State Forestry Administration, International Centre for Bamboo and RattanBeijing, China
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46
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Ingram GC. Dying to live: cell elimination as a developmental strategy in angiosperm seeds. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:785-796. [PMID: 27702990 DOI: 10.1093/jxb/erw364] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The complete elimination of unwanted cells during development is a repeated theme in both multicellular animals and in plants. In plants, such events have been extensively studied and reviewed in terms of their molecular regulation, of marker genes and proteins expressed, and in terms of cellular changes associated with their progression. This review will take a slightly different view of developmental cell elimination and will concentrate specifically on the numerous elimination events that occur during ovule and seed development (here grouped together as seed development). It asks why this cell elimination occurs in specific seed tissues, in order to understand something about the commonalities underlying how seemingly disparate events are triggered and regulated. Finally, by placing the seed in its broader evolutionary context, the question of why cell elimination may have emerged as such a key component of the seed developmental toolbox will be considered.
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Affiliation(s)
- Gwyneth C Ingram
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, CNRS (UMR 5667), INRA (UMR 0879), UCB Lyon 1, Ecole Normale Supérieure de Lyon, F-69342 Lyon, France
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Ehlers K, Bhide AS, Tekleyohans DG, Wittkop B, Snowdon RJ, Becker A. The MADS Box Genes ABS, SHP1, and SHP2 Are Essential for the Coordination of Cell Divisions in Ovule and Seed Coat Development and for Endosperm Formation in Arabidopsis thaliana. PLoS One 2016; 11:e0165075. [PMID: 27776173 PMCID: PMC5077141 DOI: 10.1371/journal.pone.0165075] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 10/05/2016] [Indexed: 01/07/2023] Open
Abstract
Seed formation is a pivotal process in plant reproduction and dispersal. It begins with megagametophyte development in the ovule, followed by fertilization and subsequently coordinated development of embryo, endosperm, and maternal seed coat. Two closely related MADS-box genes, SHATTERPROOF 1 and 2 (SHP1 and SHP2) are involved in specifying ovule integument identity in Arabidopsis thaliana. The MADS box gene ARABIDOPSIS BSISTER (ABS or TT16) is required, together with SEEDSTICK (STK) for the formation of endothelium, part of the seed coat and innermost tissue layer formed by the maternal plant. Little is known about the genetic interaction of SHP1 and SHP2 with ABS and the coordination of endosperm and seed coat development. In this work, mutant and expression analysis shed light on this aspect of concerted development. Triple tt16 shp1 shp2 mutants produce malformed seedlings, seed coat formation defects, fewer seeds, and mucilage reduction. While shp1 shp2 mutants fail to coordinate the timely development of ovules, tt16 mutants show less peripheral endosperm after fertilization. Failure in coordinated division of the innermost integument layer in early ovule stages leads to inner seed coat defects in tt16 and tt16 shp1 shp2 triple mutant seeds. An antagonistic action of ABS and SHP1/SHP2 is observed in inner seed coat layer formation. Expression analysis also indicates that ABS represses SHP1, SHP2, and FRUITFUL expression. Our work shows that the evolutionary conserved Bsister genes are required not only for endothelium but also for endosperm development and genetically interact with SHP1 and SHP2 in a partially antagonistic manner.
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Affiliation(s)
- Katrin Ehlers
- Justus Liebig University, Institute of Botany, Heinrich-Buff-Ring 38, D-35392, Gießen, Germany
| | - Amey S. Bhide
- Justus Liebig University, Institute of Botany, Heinrich-Buff-Ring 38, D-35392, Gießen, Germany
| | - Dawit G. Tekleyohans
- Justus Liebig University, Institute of Botany, Heinrich-Buff-Ring 38, D-35392, Gießen, Germany
| | - Benjamin Wittkop
- Justus Liebig University, Department of Plant Breeding, Heinrich-Buff-Ring 26-32, D 35392, Gießen, Germany
| | - Rod J. Snowdon
- Justus Liebig University, Department of Plant Breeding, Heinrich-Buff-Ring 26-32, D 35392, Gießen, Germany
| | - Annette Becker
- Justus Liebig University, Institute of Botany, Heinrich-Buff-Ring 38, D-35392, Gießen, Germany
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Wu X, Liu J, Li D, Liu CM. Rice caryopsis development II: Dynamic changes in the endosperm. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2016; 58:786-98. [PMID: 0 DOI: 10.1111/jipb.12488] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 07/22/2016] [Indexed: 05/18/2023]
Affiliation(s)
- Xiaoba Wu
- Key Laboratory of Plant Molecular Physiology; Institute of Botany; Chinese Academy of Sciences; Beijing 100093 China
| | - Jinxin Liu
- Key Laboratory of Plant Molecular Physiology; Institute of Botany; Chinese Academy of Sciences; Beijing 100093 China
| | - Dongqi Li
- 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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Wu X, Liu J, Li D, Liu CM. Rice caryopsis development I: Dynamic changes in different cell layers. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2016; 58:772-85. [PMID: 26472484 PMCID: PMC5064628 DOI: 10.1111/jipb.12440] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 10/09/2015] [Indexed: 05/18/2023]
Abstract
Rice caryopsis as one of the most important food sources for humans has a complex structure that is composed of maternal tissues including the pericarp and testa and filial tissues including the endosperm and embryo. Although rice caryopsis studies have been conducted previously, a systematic characterization throughout the entire developmental process is still lacking. In this study, detailed morphological examinations of caryopses were made during the entire 30-day developmental process. We observed some rapid changes in cell differentiation events and cataloged how cellular degeneration processes occurred in maternal tissues. The differentiations of tube cells and cross cells were achieved by 9 days after pollination (DAP). In the testa, the outer integument was degenerated by 3 DAP, while the outer layer of the inner integument degenerated by 7 DAP. In the nucellus, all tissues with the exception of the nucellar projection and the nucellar epidermis degenerated in the first 5 DAP. By 21 DAP, all maternal tissues, including vascular bundles, the nucellar projection and the nucellar epidermal cells were degenerated. In summary, this study provides a complete atlas of the dynamic changes in cell differentiation and degeneration for individual maternal cell layers of rice caryopsis.
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Affiliation(s)
- Xiaoba Wu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Jinxin Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Dongqi Li
- 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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Xu W, Fiume E, Coen O, Pechoux C, Lepiniec L, Magnani E. Endosperm and Nucellus Develop Antagonistically in Arabidopsis Seeds. THE PLANT CELL 2016; 28:1343-60. [PMID: 27233529 PMCID: PMC4944409 DOI: 10.1105/tpc.16.00041] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 05/26/2016] [Indexed: 05/06/2023]
Abstract
In angiosperms, seed architecture is shaped by the coordinated development of three genetically different components: embryo, endosperm, and maternal tissues. The relative contribution of these tissues to seed mass and nutrient storage varies considerably among species. The development of embryo, endosperm, or nucellus maternal tissue as primary storage compartments defines three main typologies of seed architecture. It is still debated whether the ancestral angiosperm seed accumulated nutrients in the endosperm or the nucellus. During evolution, plants shifted repeatedly between these two storage strategies through molecular mechanisms that are largely unknown. Here, we characterize the regulatory pathway underlying nucellus and endosperm tissue partitioning in Arabidopsis thaliana We show that Polycomb-group proteins repress nucellus degeneration before fertilization. A signal initiated in the endosperm by the AGAMOUS-LIKE62 MADS box transcription factor relieves this Polycomb-mediated repression and therefore allows nucellus degeneration. Further downstream in the pathway, the TRANSPARENT TESTA16 (TT16) and GORDITA MADS box transcription factors promote nucellus degeneration. Moreover, we demonstrate that TT16 mediates the crosstalk between nucellus and seed coat maternal tissues. Finally, we characterize the nucellus cell death program and its feedback role in timing endosperm development. Altogether, our data reveal the antagonistic development of nucellus and endosperm, in coordination with seed coat differentiation.
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Affiliation(s)
- Wenjia Xu
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, University of Paris-Saclay, 78026 Versailles Cedex, France
| | - Elisa Fiume
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, University of Paris-Saclay, 78026 Versailles Cedex, France
| | - Olivier Coen
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, University of Paris-Saclay, 78026 Versailles Cedex, France Ecole Doctorale 145 Sciences du Végétal, University Paris-Sud, University of Paris-Saclay, 91405 Orsay Cedex, France
| | - Christine Pechoux
- INRA, Génétique Animale et Biologie Intégrative, Domaine de Vilvert, 78352 Jouy-en-Josas Cedex, France
| | - Loïc Lepiniec
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, University of Paris-Saclay, 78026 Versailles Cedex, France
| | - Enrico Magnani
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, University of Paris-Saclay, 78026 Versailles Cedex, France
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