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Jain R, Dhaka N, Krishnan K, Yadav G, Priyam P, Sharma MK, Sharma RA. Temporal Gene Expression Profiles From Pollination to Seed Maturity in Sorghum Provide Core Candidates for Engineering Seed Traits. PLANT, CELL & ENVIRONMENT 2024. [PMID: 39248611 DOI: 10.1111/pce.15134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 08/12/2024] [Accepted: 08/19/2024] [Indexed: 09/10/2024]
Abstract
Sorghum (Sorghum bicolor (L.) Moench) is a highly nutritional multipurpose millet crop. However, the genetic and molecular regulatory mechanisms governing sorghum grain development and the associated agronomic traits remain unexplored. In this study, we performed a comprehensive transcriptomic analysis of pistils collected 1-2 days before pollination, and developing seeds collected -2, 10, 20 and 30 days after pollination of S. bicolor variety M35-1. Out of 31 337 genes expressed in these stages, 12 804 were differentially expressed in the consecutive stages of seed development. These exhibited 10 dominant expression patterns correlated with the distinct pathways and gene functions. Functional analysis, based on the pathway mapping, transcription factor enrichment and orthology, delineated the key patterns associated with pollination, fertilization, early seed development, grain filling and seed maturation. Furthermore, colocalization with previously reported quantitative trait loci (QTLs) for grain weight/size revealed 48 differentially expressed genes mapping to these QTL regions. Comprehensive literature mining integrated with QTL mapping and expression data shortlisted 25, 17 and 8 core candidates for engineering grain size, starch and protein content, respectively.
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Affiliation(s)
- Rubi Jain
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Namrata Dhaka
- Department of Biotechnology, School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendergarh, Haryana, India
| | - Kushagra Krishnan
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Garima Yadav
- Department of Biotechnology, School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendergarh, Haryana, India
| | - Prachi Priyam
- Department of Biotechnology, School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendergarh, Haryana, India
| | | | - Rita A Sharma
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS) Pilani, Pilani, Rajasthan, India
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
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2
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Pal AK, Gandhivel VHS, Nambiar AB, Shivaprasad PV. Upstream regulator of genomic imprinting in rice endosperm is a small RNA-associated chromatin remodeler. Nat Commun 2024; 15:7807. [PMID: 39242590 PMCID: PMC11379814 DOI: 10.1038/s41467-024-52239-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 08/29/2024] [Indexed: 09/09/2024] Open
Abstract
Genomic imprinting is observed in endosperm, a placenta-like seed tissue, where transposable elements (TEs) and repeat-derived small RNAs (sRNAs) mediate epigenetic changes in plants. In imprinting, uniparental gene expression arises due to parent-specific epigenetic marks on one allele but not on the other. The importance of sRNAs and their regulation in endosperm development or in imprinting is poorly understood in crops. Here we show that a previously uncharacterized CLASSY (CLSY)-family chromatin remodeler named OsCLSY3 is essential for rice endosperm development and imprinting, acting as an upstream player in the sRNA pathway. Comparative transcriptome and genetic analysis indicated its endosperm-preferred expression and its likely paternal imprinted nature. These important features are modulated by RNA-directed DNA methylation (RdDM) of tandemly arranged TEs in its promoter. Upon perturbation of OsCLSY3 in transgenic lines, we observe defects in endosperm development and a loss of around 70% of all sRNAs. Interestingly, well-conserved endosperm-specific sRNAs (siren) that are vital for reproductive fitness in angiosperms are also dependent on OsCLSY3. We observed that many imprinted genes and seed development-associated genes are under the control of OsCLSY3. These results support an essential role of OsCLSY3 in rice endosperm development and imprinting, and propose similar regulatory strategies involving CLSY3 homologs among other cereals.
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Affiliation(s)
- Avik Kumar Pal
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, India
| | - Vivek Hari-Sundar Gandhivel
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, India
| | - Amruta B Nambiar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, India
| | - P V Shivaprasad
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, India.
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3
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Prusty A, Mehra P, Sharma S, Malik N, Agarwal P, Parida SK, Kapoor S, Tyagi AK. OsMED14_2, a tail module subunit of Mediator complex, controls rice development and involves jasmonic acid. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 346:112146. [PMID: 38848769 DOI: 10.1016/j.plantsci.2024.112146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 05/15/2024] [Accepted: 05/31/2024] [Indexed: 06/09/2024]
Abstract
The Mediator complex is essential for eukaryotic transcription, yet its role and the function of its individual subunits in plants, especially in rice, remain poorly understood. Here, we investigate the function of OsMED14_2, a subunit of the Mediator tail module, in rice development. Overexpression and knockout of OsMED14_2 resulted in notable changes in panicle morphology and grain size. Microscopic analysis revealed impact of overexpression on pollen maturation, reflected by reduced viability, irregular shapes, and aberrant intine development. OsMED14_2 was found to interact with proteins involved in pollen development, namely, OsMADS62, OsMADS63 and OsMADS68, and its overexpression negatively affected the expression of OsMADS68 and the expression of other genes involved in intine development, including OsCAP1, OsGCD1, OsRIP1, and OsCPK29. Additionally, we found that OsMED14_2 overexpression influences jasmonic acid (JA) homeostasis, affecting bioactive JA levels, and expression of OsJAZ genes. Our data suggest OsMED14_2 may act as a regulator of JA-responsive genes through its interactions with OsHDAC6 and OsJAZ repressors. These findings contribute to better understanding of the Mediator complex's role in plant traits regulation.
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Affiliation(s)
- Ankita Prusty
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus (UDSC), New Delhi 110021, India
| | - Poonam Mehra
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus (UDSC), New Delhi 110021, India; Plant and Crop Sciences, School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK
| | - Shivam Sharma
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus (UDSC), New Delhi 110021, India
| | - Naveen Malik
- National Institute of Plant Genome Research, New Delhi 110067, India; Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur 303002, India
| | - Pinky Agarwal
- National Institute of Plant Genome Research, New Delhi 110067, India
| | | | - Sanjay Kapoor
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus (UDSC), New Delhi 110021, India
| | - Akhilesh Kumar Tyagi
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus (UDSC), New Delhi 110021, India.
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Dong N, Jiao G, Cao R, Li S, Zhao S, Duan Y, Ma L, Li X, Lu F, Wang H, Wang S, Shao G, Sheng Z, Hu S, Tang S, Wei X, Hu P. OsLESV and OsESV1 promote transitory and storage starch biosynthesis to determine rice grain quality and yield. PLANT COMMUNICATIONS 2024; 5:100893. [PMID: 38581128 PMCID: PMC11287174 DOI: 10.1016/j.xplc.2024.100893] [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: 01/22/2024] [Revised: 03/07/2024] [Accepted: 04/01/2024] [Indexed: 04/08/2024]
Abstract
Transitory starch is an important carbon source in leaves, and its biosynthesis and metabolism are closely related to grain quality and yield. The molecular mechanisms controlling leaf transitory starch biosynthesis and degradation and their effects on rice (Oryza sativa) quality and yield remain unclear. Here, we show that OsLESV and OsESV1, the rice orthologs of AtLESV and AtESV1, are associated with transitory starch biosynthesis in rice. The total starch and amylose contents in leaves and endosperms are significantly reduced, and the final grain quality and yield are compromised in oslesv and osesv1 single and oslesv esv1 double mutants. Furthermore, we found that OsLESV and OsESV1 bind to starch, and this binding depends on a highly conserved C-terminal tryptophan-rich region that acts as a starch-binding domain. Importantly, OsLESV and OsESV1 also interact with the key enzymes of starch biosynthesis, granule-bound starch synthase I (GBSSI), GBSSII, and pyruvate orthophosphote dikiase (PPDKB), to maintain their protein stability and activity. OsLESV and OsESV1 also facilitate the targeting of GBSSI and GBSSII from plastid stroma to starch granules. Overexpression of GBSSI, GBSSII, and PPDKB can partly rescue the phenotypic defects of the oslesv and osesv1 mutants. Thus, we demonstrate that OsLESV and OsESV1 play a key role in regulating the biosynthesis of both leaf transitory starch and endosperm storage starch in rice. These findings deepen our understanding of the molecular mechanisms underlying transitory starch biosynthesis in rice leaves and reveal how the transitory starch metabolism affects rice grain quality and yield, providing useful information for the genetic improvement of rice grain quality and yield.
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Affiliation(s)
- Nannan Dong
- State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Guiai Jiao
- State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Ruijie Cao
- State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Sanfeng Li
- State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Shaolu Zhao
- State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Yingqing Duan
- State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Liuyang Ma
- State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Xinwei Li
- State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Feifei Lu
- State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Hong Wang
- State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Shiwen Wang
- State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Gaoneng Shao
- State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Zhonghua Sheng
- State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Shikai Hu
- State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Shaoqing Tang
- State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Xiangjin Wei
- State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China.
| | - Peisong Hu
- State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China.
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5
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He J, Wang J, Zhang Z. Toward unveiling transcriptome dynamics and regulatory modules at the maternal/filial interface of developing maize kernel. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:2124-2140. [PMID: 38551088 DOI: 10.1111/tpj.16733] [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: 11/07/2023] [Revised: 02/21/2024] [Accepted: 03/12/2024] [Indexed: 06/14/2024]
Abstract
The basal region of maize (Zea mays) kernels, which includes the pedicel, placenta-chalazal, and basal endosperm transfer layers, serves as the maternal/filial interface for nutrient transfer from the mother plant to the developing seed. However, transcriptome dynamics of this maternal/filial interface remain largely unexplored. To address this gap, we conducted high-temporal-resolution RNA sequencing of the basal and upper kernel regions between 4 and 32 days after pollination and deeply analyzed transcriptome dynamics of the maternal/filial interface. Utilizing 790 specifically and highly expressed genes in the basal region, we performed the gene ontology (GO) term and weighted gene co-expression network analyses. In the early-stage basal region, we identified five MADS-box transcription factors (TFs) as hubs. Their homologs have been demonstrated as pivotal regulators at the maternal/filial interface of rice or Arabidopsis, suggesting their potential roles in maize kernel development. In the filling-stage basal region, numerous GO terms associated with transcriptional regulation and transporters are significantly enriched. Furthermore, we investigated the molecular function of three hub TFs. Through genome-wide DNA affinity purification sequencing combined with promoter transactivation assays, we suggested that these three TFs act as regulators of 10 basal-specific transporter genes involved in the transfer of sugars, amino acids, and ions. This study provides insights into transcriptomic dynamic and regulatory modules of the maternal/filial interface. In the future, genetic investigation of these hub regulators must advance our understanding of maternal/filial interface development and function.
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Affiliation(s)
- Juan He
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Jincang Wang
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Zhiyong Zhang
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
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6
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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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7
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Sharma E, Bhatnagar A, Bhaskar A, Majee SM, Kieffer M, Kepinski S, Khurana P, Khurana JP. Stress-induced F-Box protein-coding gene OsFBX257 modulates drought stress adaptations and ABA responses in rice. PLANT, CELL & ENVIRONMENT 2023; 46:1207-1231. [PMID: 36404527 DOI: 10.1111/pce.14496] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 10/15/2022] [Accepted: 11/16/2022] [Indexed: 06/16/2023]
Abstract
F-box (FB) proteins that form part of SKP1-CUL1-F-box (SCF) type of E3 ubiquitin ligases are important components of plant growth and development. Here we characterized OsFBX257, a rice FB protein-coding gene that is differentially expressed under drought conditions and other abiotic stresses. Population genomics analysis suggest that OsFBX257 shows high allelic diversity in aus accessions and has been under positive selection in some japonica, aromatic and indica cultivars. Interestingly, allelic variation at OsFBX257 in aus cultivar Nagina22 is associated with an alternatively spliced transcript. Conserved among land plants, OsFBX257 is a component of the SCF complex, can form homomers and interact molecularly with the 14-3-3 rice proteins GF14b and GF14c. OsFBX257 is co-expressed in a network involving protein kinases and phosphatases. We show that OsFBX257 can bind the kinases OsCDPK1 and OsSAPK2, and that its phosphorylation can be reversed by phosphatase OsPP2C08. OsFBX257 expression level modulates root architecture and drought stress tolerance in rice. OsFBX257 knockdown (OsFBX257KD ) lines show reduced total root length and depth, crown root number, panicle size and survival under stress. In contrast, its overexpression (OsFBX257OE ) increases root depth, leaf and grain length, number of panicles, and grain yield in rice. OsFBX257 is a promising breeding target for alleviating drought stress-induced damage in rice.
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Affiliation(s)
- Eshan Sharma
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Akanksha Bhatnagar
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Avantika Bhaskar
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Susmita M Majee
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Martin Kieffer
- Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Stefan Kepinski
- Faculty of Biological Sciences, University of Leeds, Leeds, UK
- Global Food and Environment Institute, University of Leeds, Leeds, UK
| | - Paramjit Khurana
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Jitendra P Khurana
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
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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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9
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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] [Key Words] [MESH Headings] [Grants] [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.
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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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10
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Wu C, Cui K, Fahad S. Heat Stress Decreases Rice Grain Weight: Evidence and Physiological Mechanisms of Heat Effects Prior to Flowering. Int J Mol Sci 2022; 23:10922. [PMID: 36142833 PMCID: PMC9504709 DOI: 10.3390/ijms231810922] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/02/2022] [Accepted: 09/15/2022] [Indexed: 11/16/2022] Open
Abstract
Heat stress during the preflowering panicle initiation stage seriously decreases rice grain weight in an invisible way and has not been given enough attention. The current review aims to (i) specify the heat effects on rice grain weight during the panicle initiation stage compared with the most important grain-filling stage; and (ii) discuss the physiological mechanisms of the decreased rice grain weight induced by heat during panicle initiation in terms of assimilate supply and phytohormone regulation, which are key physiological processes directly regulating rice grain weight. We emphasize that the effect of heat during the panicle initiation stage on rice grain weight is more serious than that during the grain-filling stage. Heat stress during the panicle initiation stage induces alterations in endogenous phytohormones, leading to the inhibition of the photosynthesis of functional leaves (source) and the formation of vascular bundles (flow), thus reducing the accumulation and transport of nonstructural carbohydrates and the growth of lemmata and paleae. The disruptions in the "flow" and restrictions in the preanthesis "source" tissue reduce grain size directly and decrease grain plumpness indirectly, resulting in a reduction in the final grain weight, which could be the direct physiological causes of the lower rice grain weight induced by heat during the panicle initiation stage. We highlight the seriousness of preflowering heat stress on rice grain weight, which can be regarded as an invisible disaster. The physiological mechanisms underlying the lower grain weight induced by heat during panicle initiation show a certain novelty because they distinguish this stage from the grain-filling stage. Additionally, a number of genes that control grain size through phytohormones have been summarized, but their functions have not yet been fully tested under heat conditions, except for the Grain Size and Abiotic stress tolerance 1 (GSA1) and BRASSINOSTEROID INSENSITIVE1 (OsBRI1) genes, which are reported to respond rapidly to heat stress. The mechanisms of reduced rice grain weight induced by heat during the panicle initiation stage should be studied in more depth in terms of molecular pathways.
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Affiliation(s)
- Chao Wu
- Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin 541006, China
| | - Kehui Cui
- National Key Laboratory of Crop Genetic Improvement, MOA Key Laboratory of Crop Ecophysiology and Farming Systems in the Middle Reaches of the Yangtze River, Huazhong Agricultural University, Wuhan 430070, China
| | - Shah Fahad
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou 570228, China
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11
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Transcriptome Analysis and Gene Expression Profiling of the Peanut Small Seed Mutant Identified Genes Involved in Seed Size Control. Int J Mol Sci 2022; 23:ijms23179726. [PMID: 36077124 PMCID: PMC9456316 DOI: 10.3390/ijms23179726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/23/2022] [Accepted: 08/24/2022] [Indexed: 11/17/2022] Open
Abstract
Seed size is a key factor affecting crop yield and a major agronomic trait concerned in peanut (Arachis hypogaea L.) breeding. However, little is known about the regulation mechanism of peanut seed size. In the present study, a peanut small seed mutant1 (ssm1) was identified through irradiating peanut cultivar Luhua11 (LH11) using 60Coγ ray. Since the globular embryo stage, the embryo size of ssm1 was significantly smaller than that of LH11. The dry seed weight of ssm1 was only 39.69% of the wild type LH14. The seeds were wrinkled with darker seed coat. The oil content of ssm1 seeds were also decreased significantly. Seeds of ssm1 and LH11 were sampled 10, 20, and 40 days after pegging (DAP) and were used for RNA-seq. The results revealed that genes involved in plant hormones and several transcription factors related to seed development were differentially expressed at all three stages, especially at DAP10 and DAP20. Genes of fatty acid biosynthesis and late embryogenesis abundant protein were significantly decreased to compare with LH11. Interestingly, the gene profiling data suggested that PKp2 and/or LEC1 could be the key candidate genes leading to the small seed phenotype of the mutant. Our results provide valuable clues for further understanding the mechanisms underlying seed size control in peanut.
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12
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Zhu Y, Chen L, Hong X, Shi H, Li X. Revealing the novel complexity of plant long non-coding RNA by strand-specific and whole transcriptome sequencing for evolutionarily representative plant species. BMC Genomics 2022; 23:381. [PMID: 35590257 PMCID: PMC9118565 DOI: 10.1186/s12864-022-08602-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 05/03/2022] [Indexed: 12/02/2022] Open
Abstract
Background Previous studies on plant long noncoding RNAs (lncRNAs) lacked consistency and suffered from many factors like heterogeneous data sources and experimental protocols, different plant tissues, inconsistent bioinformatics pipelines, etc. For example, the sequencing of RNAs with poly(A) tails excluded a large portion of lncRNAs without poly(A), and use of regular RNA-sequencing technique did not distinguish transcripts’ direction for lncRNAs. The current study was designed to systematically discover and analyze lncRNAs across eight evolutionarily representative plant species, using strand-specific (directional) and whole transcriptome sequencing (RiboMinus) technique. Results A total of 39,945 lncRNAs (25,350 lincRNAs and 14,595 lncNATs) were identified, which showed molecular features of lncRNAs that are consistent across divergent plant species but different from those of mRNA. Further, transposable elements (TEs) were found to play key roles in the origination of lncRNA, as significantly large number of lncRNAs were found to contain TEs in gene body and promoter region, and transcription of many lncRNAs was driven by TE promoters. The lncRNA sequences were divergent even in closely related species, and most plant lncRNAs were genus/species-specific, amid rapid turnover in evolution. Evaluated with PhastCons scores, plant lncRNAs showed similar conservation level to that of intergenic sequences, suggesting that most lincRNAs were young and with short evolutionary age. INDUCED BY PHOSPHATE STARVATION (IPS) was found so far to be the only plant lncRNA group with conserved motifs, which may play important roles in the adaptation of terrestrial life during migration from aquatic to terrestrial. Most highly and specially expressed lncRNAs formed co-expression network with coding genes, and their functions were believed to be closely related to their co-expression genes. Conclusion The study revealed novel features and complexity of lncRNAs in plants through systematic analysis, providing important insights into the origination and evolution of plant lncRNAs. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08602-9.
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Affiliation(s)
- Yan Zhu
- Key Laboratory of Synthetic Biology, Center for Excellence in Molecular Plant Sciences/Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Longxian Chen
- Key Laboratory of Synthetic Biology, Center for Excellence in Molecular Plant Sciences/Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiangna Hong
- Key Laboratory of Synthetic Biology, Center for Excellence in Molecular Plant Sciences/Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,Henan University, Kaifeng, China
| | - Han Shi
- Key Laboratory of Synthetic Biology, Center for Excellence in Molecular Plant Sciences/Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xuan Li
- Key Laboratory of Synthetic Biology, Center for Excellence in Molecular Plant Sciences/Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China. .,University of Chinese Academy of Sciences, Beijing, China.
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13
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Mehra P, Pandey BK, Verma L, Prusty A, Singh AP, Sharma S, Malik N, Bennett MJ, Parida SK, Giri J, Tyagi AK. OsJAZ11 regulates spikelet and seed development in rice. PLANT DIRECT 2022; 6:e401. [PMID: 35582630 PMCID: PMC9090556 DOI: 10.1002/pld3.401] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 04/10/2022] [Accepted: 04/20/2022] [Indexed: 06/15/2023]
Abstract
Seed size is one of the major determinants of seed weight and eventually, crop yield. As the global population is increasing beyond the capacity of current food production, enhancing seed size is a key target for crop breeders. Despite the identification of several genes and QTLs, current understanding about the molecular regulation of seed size/weight remains fragmentary. In the present study, we report novel role of a jasmonic acid (JA) signaling repressor, OsJAZ11 controlling rice seed width and weight. Transgenic rice lines overexpressing OsJAZ11 exhibited up to a 14% increase in seed width and ~30% increase in seed weight compared to wild type (WT). Constitutive expression of OsJAZ11 dramatically influenced spikelet morphogenesis leading to extra glume-like structures, open hull, and abnormal numbers of floral organs. Furthermore, overexpression lines accumulated higher JA levels in spikelets and developing seeds. Expression studies uncovered altered expression of JA biosynthesis/signaling and MADS box genes in overexpression lines compared to WT. Yeast two-hybrid and pull-down assays revealed that OsJAZ11 interacts with OsMADS29 and OsMADS68. Remarkably, expression of OsGW7, a key negative regulator of grain size, was significantly reduced in overexpression lines. We propose that OsJAZ11 participates in the regulation of seed size and spikelet development by coordinating the expression of JA-related, OsGW7 and MADS genes.
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Affiliation(s)
- Poonam Mehra
- Department of Plant Molecular BiologyUniversity of Delhi South CampusNew DelhiIndia
- National Institute of Plant Genome ResearchNew DelhiIndia
- Plant and Crop Sciences, School of BiosciencesUniversity of NottinghamSutton BoningtonUK
| | - Bipin K. Pandey
- National Institute of Plant Genome ResearchNew DelhiIndia
- Plant and Crop Sciences, School of BiosciencesUniversity of NottinghamSutton BoningtonUK
| | - Lokesh Verma
- National Institute of Plant Genome ResearchNew DelhiIndia
| | - Ankita Prusty
- Department of Plant Molecular BiologyUniversity of Delhi South CampusNew DelhiIndia
| | - Ajit Pal Singh
- National Institute of Plant Genome ResearchNew DelhiIndia
| | - Shivam Sharma
- Department of Plant Molecular BiologyUniversity of Delhi South CampusNew DelhiIndia
| | - Naveen Malik
- National Institute of Plant Genome ResearchNew DelhiIndia
| | - Malcolm J. Bennett
- Plant and Crop Sciences, School of BiosciencesUniversity of NottinghamSutton BoningtonUK
| | | | - Jitender Giri
- National Institute of Plant Genome ResearchNew DelhiIndia
| | - Akhilesh K. Tyagi
- Department of Plant Molecular BiologyUniversity of Delhi South CampusNew DelhiIndia
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14
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Khurana R, Bhimrajka S, Sivakrishna Rao G, Verma V, Boora N, Gawande G, Kapoor M, Rao KV, Kapoor S. Characterization of Transcription Regulatory Domains of OsMADS29: Identification of Proximal Auxin-Responsive Domains and a Strong Distal Negative Element. FRONTIERS IN PLANT SCIENCE 2022; 13:850956. [PMID: 35557721 PMCID: PMC9085466 DOI: 10.3389/fpls.2022.850956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 03/02/2022] [Indexed: 06/15/2023]
Abstract
OsMADS29 (M29) is a seed-specific MADS-box transcription factor involved in programmed cell death of nucellar tissue and maintaining auxin:cytokinin homeostasis. It affects embryo and endosperm development and starch filling during seed development in rice. Its expression seems to be tightly regulated by developmental, spatial, and temporal cues; however, cis- and trans-regulatory factors that affect its expression are largely unknown. In silico analysis of the 1.7 kb upstream regulatory region (URR) consisting of 1,290 bp promoter and 425 bp 5'-UTR regions revealed several auxin-responsive and seed-specific cis-regulatory elements distributed across the URR. In this study, the analysis of four URR deletions fused to a downstream β-glucuronidase (GUS) reporter in transgenic rice has revealed the presence of several proximal positive elements and a strong distal negative element (NE). The promoter regions containing auxin-responsive elements responded positively to the exogenous application of auxins to transgenic seedlings. The proximal positive elements are capable of driving reporter expression in both vegetative and reproductive tissues. In contrast, the NE strongly suppresses reporter gene expression in both vegetative and reproductive tissues. In a transient onion peel assay system, the NE could reduce the efficacy of a 2x CaMV 35S promoter by ∼90%. Our results indicate the existence of a complex array of positive and negative regulatory regions along with auxin-responsive elements guiding the development-dependent and spatial expression of M29.
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Affiliation(s)
- Ridhi Khurana
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Sanchi Bhimrajka
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | | | - Vibha Verma
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Neelima Boora
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Gautam Gawande
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Meenu Kapoor
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi, India
| | | | - Sanjay Kapoor
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
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15
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Li P, Chen YH, Lu J, Zhang CQ, Liu QQ, Li QF. Genes and Their Molecular Functions Determining Seed Structure, Components, and Quality of Rice. RICE (NEW YORK, N.Y.) 2022; 15:18. [PMID: 35303197 PMCID: PMC8933604 DOI: 10.1186/s12284-022-00562-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 03/01/2022] [Indexed: 05/14/2023]
Abstract
With the improvement of people's living standards and rice trade worldwide, the demand for high-quality rice is increasing. Therefore, breeding high quality rice is critical to meet the market demand. However, progress in improving rice grain quality lags far behind that of rice yield. This might be because of the complexity of rice grain quality research, and the lack of consensus definition and evaluation standards for high quality rice. In general, the main components of rice grain quality are milling quality (MQ), appearance quality (AQ), eating and cooking quality (ECQ), and nutritional quality (NQ). Importantly, all these quality traits are determined directly or indirectly by the structure and composition of the rice seeds. Structurally, rice seeds mainly comprise the spikelet hull, seed coat, aleurone layer, embryo, and endosperm. Among them, the size of spikelet hull is the key determinant of rice grain size, which usually affects rice AQ, MQ, and ECQ. The endosperm, mainly composed of starch and protein, is the major edible part of the rice seed. Therefore, the content, constitution, and physicochemical properties of starch and protein are crucial for multiple rice grain quality traits. Moreover, the other substances, such as lipids, minerals, vitamins, and phytochemicals, included in different parts of the rice seed, also contribute significantly to rice grain quality, especially the NQ. Rice seed growth and development are precisely controlled by many genes; therefore, cloning and dissecting these quality-related genes will enhance our knowledge of rice grain quality and will assist with the breeding of high quality rice. This review focuses on summarizing the recent progress on cloning key genes and their functions in regulating rice seed structure and composition, and their corresponding contributions to rice grain quality. This information will facilitate and advance future high quality rice breeding programs.
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Affiliation(s)
- Pei Li
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology/State Key Laboratory of Hybrid Rice, College of Agriculture, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Yu-Hao Chen
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology/State Key Laboratory of Hybrid Rice, College of Agriculture, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Jun Lu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology/State Key Laboratory of Hybrid Rice, College of Agriculture, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Chang-Quan Zhang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology/State Key Laboratory of Hybrid Rice, College of Agriculture, Yangzhou University, Yangzhou, 225009, Jiangsu, China
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Qiao-Quan Liu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology/State Key Laboratory of Hybrid Rice, College of Agriculture, Yangzhou University, Yangzhou, 225009, Jiangsu, China.
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, Jiangsu, China.
| | - Qian-Feng Li
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology/State Key Laboratory of Hybrid Rice, College of Agriculture, Yangzhou University, Yangzhou, 225009, Jiangsu, China.
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, Jiangsu, China.
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16
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Wu Q, Liu Y, Huang J. CRISPR-Cas9 Mediated Mutation in OsPUB43 Improves Grain Length and Weight in Rice by Promoting Cell Proliferation in Spikelet Hull. Int J Mol Sci 2022; 23:ijms23042347. [PMID: 35216463 PMCID: PMC8877319 DOI: 10.3390/ijms23042347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/14/2022] [Accepted: 02/15/2022] [Indexed: 12/27/2022] Open
Abstract
Grain weight, a crucial trait that determines the grain yield in rice, is influenced by grain size. Although a series of regulators that control grain size have been identified in rice, the mechanisms underlying grain development are not yet well understood. In this study, we identified OsPUB43, a U-box E3 ubiquitin ligase, as an important negative regulator determining the gain size and grain weight in rice. Phenotypes of large grain are observed in ospub43 mutants, whereas overexpression of OsPUB43 results in short grains. Scanning electron microscopy analysis reveals that OsPUB43 modulates the grain size mainly by inhibiting cell proliferation in the spikelet hull. The OsPUB43 protein is localized in the cytoplasm and nucleus. The ospub43 mutants display high sensitivity to exogenous BR, while OsPUB43-OE lines are hyposensitive to BR. Furthermore, the transient transcriptional activity assay shows that OsBZR1 can activate the expression of OsPUB43. Collectively, our results indicate that OsPUB43 negatively controls the gain size by modulating the expression of BR-responsive genes as well as MADS-box genes that are required for lemma/palea specification, suggesting that OsPUB43 has a potential valuable application in the enlargement of grain size in rice.
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17
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Zhan P, Ma S, Xiao Z, Li F, Wei X, Lin S, Wang X, Ji Z, Fu Y, Pan J, Zhou M, Liu Y, Chang Z, Li L, Bu S, Liu Z, Zhu H, Liu G, Zhang G, Wang S. Natural variations in grain length 10 (GL10) regulate rice grain size. J Genet Genomics 2022; 49:405-413. [DOI: 10.1016/j.jgg.2022.01.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/23/2022] [Accepted: 01/24/2022] [Indexed: 10/19/2022]
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18
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Zhang H, Xu H, Jiang Y, Zhang H, Wang S, Wang F, Zhu Y. Genetic Control and High Temperature Effects on Starch Biosynthesis and Grain Quality in Rice. FRONTIERS IN PLANT SCIENCE 2021; 12:757997. [PMID: 34975940 PMCID: PMC8718882 DOI: 10.3389/fpls.2021.757997] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 11/23/2021] [Indexed: 05/29/2023]
Abstract
Grain quality is one of the key targets to be improved for rice breeders and covers cooking, eating, nutritional, appearance, milling, and sensory properties. Cooking and eating quality are mostly of concern to consumers and mainly determined by starch structure and composition. Although many starch synthesis enzymes have been identified and starch synthesis system has been established for a long time, novel functions of some starch synthesis genes have continually been found, and many important regulatory factors for seed development and grain quality control have recently been identified. Here, we summarize the progress in this field as comprehensively as possible and hopefully reveal some underlying molecular mechanisms controlling eating quality in rice. The regulatory network of amylose content (AC) determination is emphasized, as AC is the most important index for rice eating quality (REQ). Moreover, the regulatory mechanism of REQ, especially AC influenced by high temperature which is concerned as a most harmful environmental factor during grain filling is highlighted in this review.
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Affiliation(s)
- Hua Zhang
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Science, Hangzhou, China
| | - Heng Xu
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Science, Hangzhou, China
| | - Yingying Jiang
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Science, Hangzhou, China
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, China
| | - Heng Zhang
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Science, Hangzhou, China
| | - Shiyu Wang
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Science, Hangzhou, China
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, China
| | - Fulin Wang
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Science, Hangzhou, China
| | - Ying Zhu
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Science, Hangzhou, China
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19
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Cheng K, Pan YF, Liu LM, Zhang HQ, Zhang YM. Integrated Transcriptomic and Bioinformatics Analyses Reveal the Molecular Mechanisms for the Differences in Seed Oil and Starch Content Between Glycine max and Cicer arietinum. FRONTIERS IN PLANT SCIENCE 2021; 12:743680. [PMID: 34764968 PMCID: PMC8576049 DOI: 10.3389/fpls.2021.743680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 09/23/2021] [Indexed: 06/13/2023]
Abstract
The seed oil and starch content of soybean are significantly different from that of chickpea. However, there are limited studies on its molecular mechanisms. To address this issue, we conducted integrated transcriptomic and bioinformatics analyses for species-specific genes and acyl-lipid-, starch-, and carbon metabolism-related genes. Among seven expressional patterns of soybean-specific genes, four were highly expressed at the middle- and late oil accumulation stages; these genes significantly enriched fatty acid synthesis and carbon metabolism, and along with common acetyl CoA carboxylase (ACCase) highly expressed at soybean middle seed development stage, common starch-degrading enzyme beta-amylase-5 (BAM5) was highly expressed at soybean early seed development stage and oil synthesis-related genes ACCase, KAS, KAR, ACP, and long-chain acyl-CoA synthetase (LACS) were co-expressed with WRI1, which may result in high seed oil content and low seed starch content in soybean. The common ADP-glucose pyrophosphorylase (AGPase) was highly expressed at chickpea middle seed development stage, along with more starch biosynthesis genes co-expressed with four-transcription-factor homologous genes in chickpea than in soybean, and the common WRI1 was not co-expressed with oil synthesis genes in chickpea, which may result in high seed starch content and low seed oil content in chickpea. The above results may be used to improve chickpea seed oil content in two ways. One is to edit CaWRI1 to co-express with oil synthesis-related genes, which may increase carbon metabolites flowing to oil synthesis, and another is to increase the expression levels of miRNA159 and miRNA319 to inhibit the expression of MYB33, which may downregulate starch synthesis-related genes, making more carbon metabolites flow into oil synthesis. Our study will provide a basis for future breeding efforts to increase the oil content of chickpea seeds.
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20
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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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21
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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: 11] [Impact Index Per Article: 3.7] [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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22
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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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23
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Shoesmith JR, Solomon CU, Yang X, Wilkinson LG, Sheldrick S, van Eijden E, Couwenberg S, Pugh LM, Eskan M, Stephens J, Barakate A, Drea S, Houston K, Tucker MR, McKim SM. APETALA2 functions as a temporal factor together with BLADE-ON-PETIOLE2 and MADS29 to control flower and grain development in barley. Development 2021; 148:dev.194894. [DOI: 10.1242/dev.194894] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 01/25/2021] [Indexed: 11/20/2022]
Abstract
ABSTRACT
Cereal grain develops from fertilised florets. Alterations in floret and grain development greatly influence grain yield and quality. Despite this, little is known about the underlying genetic control of these processes, especially in key temperate cereals such as barley and wheat. Using a combination of near-isogenic mutant comparisons, gene editing and genetic analyses, we reveal that HvAPETALA2 (HvAP2) controls floret organ identity, floret boundaries, and maternal tissue differentiation and elimination during grain development. These new roles of HvAP2 correlate with changes in grain size and HvAP2-dependent expression of specific HvMADS-box genes, including the B-sister gene, HvMADS29. Consistent with this, gene editing demonstrates that HvMADS29 shares roles with HvAP2 in maternal tissue differentiation. We also discovered that a gain-of-function HvAP2 allele masks changes in floret organ identity and grain size due to loss of barley LAXATUM.A/BLADE-ON-PETIOLE2 (HvBOP2) gene function. Taken together, we reveal novel pleiotropic roles and regulatory interactions for an AP2-like gene controlling floret and grain development in a temperate cereal.
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Affiliation(s)
- Jennifer R. Shoesmith
- Division of Plant Sciences, School of Life Sciences, University of Dundee at the James Hutton Institute, Invergowrie DD2 5DA, UK
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie DD2 5DA, UK
| | - Charles Ugochukwu Solomon
- Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester LE1 7RH, UK
- Department of Plant Science and Biotechnology, Abia State University, PMB 2000, Uturu, Nigeria
| | - Xiujuan Yang
- Waite Research Institute, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA, 5064, Australia
| | - Laura G. Wilkinson
- Waite Research Institute, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA, 5064, Australia
- Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Scott Sheldrick
- Division of Plant Sciences, School of Life Sciences, University of Dundee at the James Hutton Institute, Invergowrie DD2 5DA, UK
| | - Ewan van Eijden
- Division of Plant Sciences, School of Life Sciences, University of Dundee at the James Hutton Institute, Invergowrie DD2 5DA, UK
| | - Sanne Couwenberg
- Division of Plant Sciences, School of Life Sciences, University of Dundee at the James Hutton Institute, Invergowrie DD2 5DA, UK
| | - Laura M. Pugh
- Division of Plant Sciences, School of Life Sciences, University of Dundee at the James Hutton Institute, Invergowrie DD2 5DA, UK
| | - Mhmoud Eskan
- Division of Plant Sciences, School of Life Sciences, University of Dundee at the James Hutton Institute, Invergowrie DD2 5DA, UK
| | - Jennifer Stephens
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie DD2 5DA, UK
| | - Abdellah Barakate
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie DD2 5DA, UK
| | - Sinéad Drea
- Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Kelly Houston
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie DD2 5DA, UK
| | - Matthew R. Tucker
- Waite Research Institute, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA, 5064, Australia
| | - Sarah M. McKim
- Division of Plant Sciences, School of Life Sciences, University of Dundee at the James Hutton Institute, Invergowrie DD2 5DA, UK
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24
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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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25
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Mathew IE, Priyadarshini R, Mahto A, Jaiswal P, Parida SK, Agarwal P. SUPER STARCHY1/ONAC025 participates in rice grain filling. PLANT DIRECT 2020; 4:e00249. [PMID: 32995698 PMCID: PMC7507516 DOI: 10.1002/pld3.249] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 06/10/2020] [Accepted: 07/10/2020] [Indexed: 05/04/2023]
Abstract
NAC transcription factors (TFs) are known for their role in development and stress. This article attempts to functionally validate the role of rice SS1/ ONAC025 (LOC_Os11g31330) during seed development. The gene is seed-specific and its promoter directs reporter expression in the developing endosperm and embryo in rice transgenic plants. Furthermore, rice transgenic plants ectopically expressing SS1/ ONAC025 have a plantlet lethal phenotype with hampered vegetative growth, but increased tillers and an altered shoot apical meristem structure. The vegetative cells of these plantlets are filled with distinct starch granules. RNAseq analysis of two independent plantlets reveals the differential expression of reproductive and photosynthetic genes. A comparison with seed development transcriptome indicates differential regulation of many seed-related genes by SS1/ ONAC025. Genes involved in starch biosynthesis, especially amylopectin and those encoding seed storage proteins, and regulating seed size are also differentially expressed. In conjunction, SS1/ ONAC025 shows highest expression in japonica rice. As a TF, SS1/ ONAC025 is a transcriptional repressor localized to endoplasmic reticulum and nucleus. The article shows that SS1/ ONAC025 is a seed-specific gene promoting grain filling in rice, and negatively affecting vegetative growth.
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Affiliation(s)
| | | | - Arunima Mahto
- National Institute of Plant Genome ResearchNew DelhiIndia
| | - Priya Jaiswal
- National Institute of Plant Genome ResearchNew DelhiIndia
| | | | - Pinky Agarwal
- National Institute of Plant Genome ResearchNew DelhiIndia
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26
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Corrigendum. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:1634. [PMID: 32531140 PMCID: PMC7292535 DOI: 10.1111/pbi.13418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
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27
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Chen L, Zhao J, Song J, Jameson PE. Cytokinin dehydrogenase: a genetic target for yield improvement in wheat. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:614-630. [PMID: 31782596 PMCID: PMC7004901 DOI: 10.1111/pbi.13305] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 11/19/2019] [Indexed: 05/04/2023]
Abstract
The plant hormone group, the cytokinins, is implicated in both qualitative and quantitative components of yield. Cytokinins have opposing actions in shoot and root growth-actions shown to involve cytokinin dehydrogenase (CKX), the enzyme that inactivates cytokinin. We revise and provide unambiguous names for the CKX gene family members in wheat, based on the most recently released wheat genome database, IWGSC RefSeq v1.0 & v2.0. We review expression data of CKX gene family members in wheat, revealing tissue-specific gene family member expression as well as sub-genome-specific expression. Manipulation of CKX in cereals shows clear impacts on yield, root growth and orientation, and Zn nutrition, but this also emphasizes the necessity to unlink promotive effects on grain yield from negative effects of cytokinin on root growth and uptake of mineral nutrients, particularly Zn and Fe. Wheat is the most widely grown cereal crop globally, yet is under-research compared with rice and maize. We highlight gaps in our knowledge of the involvement of CKX for wheat. We also highlight the necessity for accurate analysis of endogenous cytokinins, acknowledging why this is challenging, and provide examples where inadequate analyses of endogenous cytokinins have led to unjustified conclusions. We acknowledge that the allohexaploid nature of bread wheat poses challenges in terms of uncovering useful mutations. However, we predict TILLING followed by whole-exome sequencing will uncover informative mutations and we indicate the potential for stacking mutations within the three genomes to modify yield components. We model a wheat ideotype based on CKX manipulation.
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Affiliation(s)
- Lei Chen
- School of Life SciencesYantai UniversityYantaiChina
| | - Jiqiang Zhao
- School of Life SciencesYantai UniversityYantaiChina
| | | | - Paula E. Jameson
- School of Life SciencesYantai UniversityYantaiChina
- School of Biological SciencesUniversity of CanterburyChristchurchNew Zealand
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28
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Malik N, Ranjan R, Parida SK, Agarwal P, Tyagi AK. Mediator subunit OsMED14_1 plays an important role in rice development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:1411-1429. [PMID: 31702850 DOI: 10.1111/tpj.14605] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 10/14/2019] [Accepted: 10/30/2019] [Indexed: 05/06/2023]
Abstract
Mediator, a multisubunit co-activator complex, regulates transcription in eukaryotes and is involved in diverse processes in Arabidopsis through its different subunits. Here, we have explored developmental aspects of one of the rice Mediator subunit gene OsMED14_1. We analyzed its expression pattern through RNA in situ hybridization and pOsMED14_1:GUS transgenics that showed its expression in roots, leaves, anthers and seeds prominently at younger stages, indicating possible involvement of this subunit in multiple aspects of rice development. To understand the developmental roles of OsMED14_1 in rice, we generated and studied RNAi-based knockdown rice plants that showed multiple effects including less height, narrower leaves and culms with reduced vasculature, lesser lateral root branching, defective microspore development, reduced panicle branching and seed set, and smaller seeds. Histological analyses showed that slender organs were caused by reduction in both cell number and cell size in OsMED14_1 knockdown plants. Flow cytometric analyses and expression analyses of cell cycle-related genes revealed that defective cell-cycle progression led to these defects. Expression analyses of auxin-related genes and indole-3-acetic acid (IAA) immunolocalization study indicated altered auxin level in these knockdown plants. Reduction of lateral root branching in knockdown plants was corrected by exogenous IAA supplement. OsMED14_1 physically interacts with transcription factors YABBY5, TAPETUM DEGENERATION RETARDATION (TDR) and MADS29, possibly regulating auxin homeostasis and ultimately leading to lateral organ/leaf, microspore and seed development.
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Affiliation(s)
- Naveen Malik
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Rajeev Ranjan
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Marg, New Delhi, 110021, India
| | - Swarup K Parida
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Pinky Agarwal
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Akhilesh K Tyagi
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Marg, New Delhi, 110021, India
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29
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Najeeb S, Ali J, Mahender A, Pang Y, Zilhas J, Murugaiyan V, Vemireddy LR, Li Z. Identification of main-effect quantitative trait loci (QTLs) for low-temperature stress tolerance germination- and early seedling vigor-related traits in rice ( Oryza sativa L.). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2020; 40:10. [PMID: 31975784 PMCID: PMC6944268 DOI: 10.1007/s11032-019-1090-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 12/12/2019] [Indexed: 05/09/2023]
Abstract
An attempt was made in the current study to identify the main-effect and co-localized quantitative trait loci (QTLs) for germination and early seedling growth traits under low-temperature stress (LTS) conditions in rice. The plant material used in this study was an early backcross population of 230 introgression lines (ILs) in BCIF7 generation derived from the Weed Tolerant Rice-1 (WTR-1) (as the recipient) and Haoannong (HNG) (as the donor). Genetic analyses of LTS tolerance revealed a total of 27 main-effect quantitative trait loci (M-QTLs) mapped on 12 chromosomes. These QTLs explained more than 10% of phenotypic variance (PV), and average PV of 12.71% while employing 704 high-quality SNP markers. Of these 27 QTLs distributed on 12 chromosomes, 11 were associated with low-temperature germination (LTG), nine with low-temperature germination stress index (LTGS), five with root length stress index (RLSI), and two with biomass stress index (BMSI) QTLs, shoot length stress index (SLSI) and root length stress index (RLSI), seven with seed vigor index (SVI), and single QTL with root length (RL). Among them, five significant major QTLs (qLTG(I) 1 , qLTGS(I) 1-2 , qLTG(I) 5 , qLTGS(I) 5 , and qLTG(I) 7 ) mapped on chromosomes 1, 5, and 7 were associated with LTG and LTGS traits and the PV explained ranged from 16 to 23.3%. The genomic regions of these QTLs were co-localized with two to six QTLs. Most of the QTLs were growth stage-specific and found to harbor QTLs governing multiple traits. Eight chromosomes had more than four QTLs and were clustered together and designated as promising LTS tolerance QTLs (qLTTs), as qLTT 1 , qLTT 2 , qLTT 3 , qLTT 5 , qLTT 6 , qLTT 8 , qLTT 9 , and qLTT 11 . A total of 16 putative candidate genes were identified in the major M-QTLs and co-localized QTL regions distributed on different chromosomes. Overall, these significant genomic regions of M-QTLs are responsible for multiple traits and this suggested that these could serve as the best predictors of LTS tolerance at germination and early seedling growth stages. Furthermore, it is necessary to fine-map these regions and to find functional markers for marker-assisted selection in rice breeding programs for cold tolerance.
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Affiliation(s)
- S. Najeeb
- Rice Breeding Platform, International Rice Research Institute (IRRI), 4031 Los Baños, Laguna Philippines
- Mountain Research Centre for Field Crops, Sher-e-Kashmir University of Agricultural Science & Technology (SKAUST), Khudwani, Kashmir 190025 India
| | - J. Ali
- Rice Breeding Platform, International Rice Research Institute (IRRI), 4031 Los Baños, Laguna Philippines
| | - A. Mahender
- Rice Breeding Platform, International Rice Research Institute (IRRI), 4031 Los Baños, Laguna Philippines
| | - Y.L. Pang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, 271018 People’s Republic of China
| | - J. Zilhas
- Rice Breeding Platform, International Rice Research Institute (IRRI), 4031 Los Baños, Laguna Philippines
| | - V. Murugaiyan
- Rice Breeding Platform, International Rice Research Institute (IRRI), 4031 Los Baños, Laguna Philippines
- Plant Nutrition, Institute of Crop Sciences and Resource Conservation (INRES), University of Bonn, 53012 Bonn, Germany
| | - Lakshminarayana R. Vemireddy
- Department of Genetics and Plant Breeding, Sri Venkateswara Agricultural College, Acharya NG Ranga Agricultural University, Tirupati, Andhra Pradesh 517502 India
| | - Z. Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081 People’s Republic of China
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30
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Wu C, Tang S, Li G, Wang S, Fahad S, Ding Y. Roles of phytohormone changes in the grain yield of rice plants exposed to heat: a review. PeerJ 2019; 7:e7792. [PMID: 31763066 PMCID: PMC6873875 DOI: 10.7717/peerj.7792] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 08/29/2019] [Indexed: 11/23/2022] Open
Abstract
During its reproductive phase, rice is susceptible to heat stress. Heat events will occur at all stages during the reproductive phase of rice as a result of global warming. Moreover, rice yield traits respond differently to heat stress during panicle initiation, flowering and grain filling. The reduction in the number of spikelets per panicle of heat-stressed plants is due to the attenuated differentiation of secondary branches and their attached florets as well as the promotion of their degradation during the panicle-initiation stage but is not affected by heat stress thereafter. Spikelet sterility as a result of heat stress is attributed not only to physiological abnormalities in the reproductive organs during the flowering stage but also to structural and morphological abnormalities in reproductive organs during the panicle-initiation stage. The reduced grain weight of heat-stressed plants is due to a reduction in nonstructural carbohydrates, undeveloped vascular bundles, and a reduction in glume size during the panicle-initiation stage, while a shortened grain-filling duration, reduced grain-filling rate, and decreased grain width contribute to reduced grain weight during the grain-filling stage. Thus, screening and breeding rice varieties that have comprehensive tolerance to heat stress at all time points during their reproductive stage may be possible to withstand unpredictable heat events in the future. The responses of yield traits to heat stress are regulated by phytohormone levels, which are determined by phytohormone homeostasis. Currently, the biosynthesis and transport of phytohormones are the key processes that determine phytohormone levels in and grain yield of rice under heat stress. Studies on phytohormone homeostatic responses are needed to further reveal the key processes that determine phytohormone levels under heat conditions.
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Affiliation(s)
- Chao Wu
- College of Agronomy, Nanjing Agricultural University, Nanjing, Jiangsu, China.,Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, Jiangsu, China
| | - She Tang
- College of Agronomy, Nanjing Agricultural University, Nanjing, Jiangsu, China.,Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, Jiangsu, China
| | - Ganghua Li
- College of Agronomy, Nanjing Agricultural University, Nanjing, Jiangsu, China.,Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, Jiangsu, China
| | - Shaohua Wang
- College of Agronomy, Nanjing Agricultural University, Nanjing, Jiangsu, China.,Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, Jiangsu, China
| | - Shah Fahad
- Department of Agronomy, University of Swabi, Swabi Kyber Paktunkhwa, Pakistan
| | - Yanfeng Ding
- College of Agronomy, Nanjing Agricultural University, Nanjing, Jiangsu, China.,Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, Jiangsu, China
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31
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Ji X, Du Y, Li F, Sun H, Zhang J, Li J, Peng T, Xin Z, Zhao Q. The basic helix-loop-helix transcription factor, OsPIL15, regulates grain size via directly targeting a purine permease gene OsPUP7 in rice. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:1527-1537. [PMID: 30628157 PMCID: PMC6662305 DOI: 10.1111/pbi.13075] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 12/02/2018] [Accepted: 12/21/2018] [Indexed: 05/18/2023]
Abstract
As members of the basic helix-loop-helix transcription factor families, phytochrome-interacting factors regulate an array of developmental responses ranging from seed germination to plant growth. However, little is known about their roles in modulating grain development. Here, we firstly analyzed the expression pattern of rice OsPIL genes in grains and found that OsPIL15 may play an important role in grain development. We then generated knockout (KO) OsPIL15 lines in rice using CRISPR/Cas9 technology, the silencing expression of OsPIL15 led to increased numbers of cells, which thus enhanced grain size and weight. Moreover, overexpression and suppression of OsPIL15 in the rice endosperm resulted in brown rice showing grain sizes and weights that were decreased and increased respectively. Further studies indicated that OsPIL15 binds to N1-box (CACGCG) motifs of the purine permease gene OsPUP7 promoter. Measurement of isopentenyl adenosine, a bioactive form of cytokinin (CTK), revealed increased contents in the OsPIL15-KO spikelets compared with the wild-type. Overall, our results demonstrate a possible pathway whereby OsPIL15 directly targets OsPUP7, affecting CTK transport and thereby influencing cell division and subsequent grain size. These findings provide a valuable insight into the molecular functions of OsPIL15 in rice grains, highlighting a useful genetic improvement leading to increased rice yield.
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Affiliation(s)
- Xin Ji
- Henan Key Laboratory of Rice BiologyCollaborative Innovation Center of Henan Grain CropsHenan Agricultural UniversityZhengzhouChina
| | - Yanxiu Du
- Henan Key Laboratory of Rice BiologyCollaborative Innovation Center of Henan Grain CropsHenan Agricultural UniversityZhengzhouChina
| | - Fei Li
- Henan Key Laboratory of Rice BiologyCollaborative Innovation Center of Henan Grain CropsHenan Agricultural UniversityZhengzhouChina
| | - Hongzheng Sun
- Henan Key Laboratory of Rice BiologyCollaborative Innovation Center of Henan Grain CropsHenan Agricultural UniversityZhengzhouChina
| | - Jing Zhang
- Henan Key Laboratory of Rice BiologyCollaborative Innovation Center of Henan Grain CropsHenan Agricultural UniversityZhengzhouChina
| | - Junzhou Li
- Henan Key Laboratory of Rice BiologyCollaborative Innovation Center of Henan Grain CropsHenan Agricultural UniversityZhengzhouChina
| | - Ting Peng
- Henan Key Laboratory of Rice BiologyCollaborative Innovation Center of Henan Grain CropsHenan Agricultural UniversityZhengzhouChina
| | - Zeyu Xin
- Henan Key Laboratory of Rice BiologyCollaborative Innovation Center of Henan Grain CropsHenan Agricultural UniversityZhengzhouChina
| | - Quanzhi Zhao
- Henan Key Laboratory of Rice BiologyCollaborative Innovation Center of Henan Grain CropsHenan Agricultural UniversityZhengzhouChina
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Chen Y, Shen Q, Lyu P, Lin R, Sun C. Identification and expression profiling of selected MADS-box family genes in Dendrobium officinale. Genetica 2019; 147:303-313. [PMID: 31292836 DOI: 10.1007/s10709-019-00071-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 07/05/2019] [Indexed: 11/24/2022]
Abstract
Dendrobium officinale, a herb with highly medicinal and ornamental value, is widely distributed in China. MADS-box genes encode transcription factors that regulate various growth and developmental processes in plants, particular in flowering. However, the MADS-box genes in D. officinale are largely unknown. In our study, expression profiling analyses of selected MADS-box genes in D. officinale were performed. In total, 16 DnMADS-box genes with full-length ORF were identified and named according to their phylogenetic relationships with model plants. The transient expression of eight selected MADS-box genes in the epidermal cells of tobacco leaves showed that these DnMADS-box proteins localized to the nucleus. Tissue-specific expression analysis pointed out eight flower-specific expressed MADS-box genes in D. officinale. Furthermore, expression patterns of DnMADS-box genes were investigated during the floral transition process. DnMADS3, DnMADS8 and DnMADS22 were significantly up-regulated in the reproductive phase compared with the vegetative phase, suggesting putative roles of these DnMADS-box genes in flowering. Our data showed that the expressions of MADS-box genes in D. officinale were controlled by diverse exogenous phytohormones. Together, these findings will facilitate further studies of MADS-box genes in Orchids and broaden our understanding of the genetics of flowering.
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Affiliation(s)
- Yue Chen
- Institute of Horticulture, Zhejiang Academy of Agriculture Science, Hangzhou, Zhejiang, People's Republic of China.,Key laboratory of creative Agriculture, Ministry of Agriculture, Hangzhou, People's Republic of China
| | - Qi Shen
- Plant Protection and Microbiology, Zhejiang Academy of Agricultural Science, Hangzhou, Zhejiang, People's Republic of China
| | - Ping Lyu
- Lin'an Agricultural & Forestry Technology Extension Center, Hangzhou, Zhejiang, People's Republic of China
| | - Renan Lin
- Yueqing Forestry Varieties Tech Center, Yueqing, Zhejiang, People's Republic of China
| | - Chongbo Sun
- Institute of Horticulture, Zhejiang Academy of Agriculture Science, Hangzhou, Zhejiang, People's Republic of China. .,Key laboratory of creative Agriculture, Ministry of Agriculture, Hangzhou, People's Republic of China.
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Bernardi J, Battaglia R, Bagnaresi P, Lucini L, Marocco A. Transcriptomic and metabolomic analysis of ZmYUC1 mutant reveals the role of auxin during early endosperm formation in maize. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 281:133-145. [PMID: 30824046 DOI: 10.1016/j.plantsci.2019.01.027] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Revised: 01/22/2019] [Accepted: 01/30/2019] [Indexed: 05/22/2023]
Abstract
Kernel size in cereal is an important agronomic trait controlled by the interaction of genetic and environmental factors. The endosperm occupies most of the kernel area; for this reason, the endosperm cells dimension, number and metabolic content strongly influence kernel properties. This paper presents the transcriptomic and metabolomic analysis of the maize defective endosperm 18 (de18) mutant, where auxin accumulation in the endosperm is impaired. This mutation, involving the ZmYuc1 gene, leads to a reduced kernel size compared to the wild-type line B37. Our results mainly indicate that IAA concentration controls sugar and protein metabolism during kernel differentiation and it is necessary for BETL formation. Furthermore, a fine tuning of different auxin conjugates is reported as the main mechanism to counteract the auxin deficit. Some candidates as master regulators of endosperm transcriptional regulation mediated by auxin are found between MYB and MADS-box gene families. A link between auxin and storage protein accumulation is highlighted, suggesting that IAA directly or indirectly, through CK or ABA, regulates the transcription of zein coding genes. This study represents a move forward with respect to the current knowledge about the role of auxin during maize endosperm differentiation thus revealing the genes that are modulated by auxin and that control agronomic traits as kernel size and metabolic composition.
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Affiliation(s)
- Jamila Bernardi
- Department of Sustainable Crop Production, Università Cattolica del Sacro Cuore, Piacenza, Italy.
| | - Raffaella Battaglia
- Department of Sustainable Crop Production, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Paolo Bagnaresi
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Piacenza, Italy
| | - Luigi Lucini
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Adriano Marocco
- Department of Sustainable Crop Production, Università Cattolica del Sacro Cuore, Piacenza, Italy.
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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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35
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Ke S, Liu XJ, Luan X, Yang W, Zhu H, Liu G, Zhang G, Wang S. Genome-wide transcriptome profiling provides insights into panicle development of rice (Oryza sativa L.). Gene 2018; 675:285-300. [PMID: 29969697 DOI: 10.1016/j.gene.2018.06.105] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 04/26/2018] [Accepted: 06/28/2018] [Indexed: 12/19/2022]
Abstract
Panicle architecture is an important component of agronomic trait in rice, which is also a key ingredient that could influence yield and quality of rice. In the panicle growth and development process, there are a series of complicated molecular and cellular events which are regulated by many interlinking genes. In this study, to explore the potential mechanism and identify genes and pathways involved in the formation of rice panicle, we compared the transcriptional profile of rice panicles (NIL-GW8 and NIL-gw8Amol) at three different stages of panicle development: In5 (formation of higher-order branches), In6 (differentiation of glumes) and In7 (differentiation of floral organs). A range of 40.5 to 54.1 million clean reads was aligned to 31,209 genes in our RNA-Seq analysis. In addition, we investigated transcriptomic changes between the two rice lines during different stages. A total of 726, 1121 and 2584 differentially expressed genes (DEGs) were identified at stages 1, 2 and 3, respectively. Based on an impact analysis of the DEGs, we hypothesize that MADS-box gene family, cytochrome P450 (CYP) and pentatricopeptide repeat (PPR) protein and various transcription factors may be involved in regulation of panicle development. Further, we also explored the functional properties of DEGs by gene ontology analysis, and the results showed that different numbers of DEGs genes were associated with 53 GO groups. In KEGG pathway enrichment analysis, many DEGs related to biosynthesis of secondary metabolites and plant hormone signal transduction, suggesting their important roles during panicle development. This study provides the first examination of changes in gene expression between different panicle development stages in rice. Our results of transcriptomic characterization provide important information to elucidate the complex molecular and cellular events about the panicle formation in rice or other cereal crops. Also, the findings will be helpful for the further identification of the genes related to panicle development.
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Affiliation(s)
- Shanwen Ke
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Xin-Jiang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Xin Luan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Weifeng Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Haitao Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Guifu Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Guiquan Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China..
| | - Shaokui Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China..
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Singh B, Khurana P, Khurana JP, Singh P. Gene encoding vesicle-associated membrane protein-associated protein from Triticum aestivum (TaVAP) confers tolerance to drought stress. Cell Stress Chaperones 2018; 23:411-428. [PMID: 29116579 PMCID: PMC5904086 DOI: 10.1007/s12192-017-0854-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 10/08/2017] [Accepted: 10/13/2017] [Indexed: 12/21/2022] Open
Abstract
Abiotic stresses like drought, salinity, high and low temperature, and submergence are major factors that limit the crop productivity. Hence, identification of genes associated with stress response in crops is a prerequisite for improving their tolerance to adverse environmental conditions. In an earlier study, we had identified a drought-inducible gene, vesicle-associated membrane protein-associated protein (TaVAP), in developing grains of wheat. In this study, we demonstrate that TaVAP is able to complement yeast and Arabidopsis mutants, which are impaired in their respective orthologs, signifying functional conservation. Constitutive expression of TaVAP in Arabidopsis imparted tolerance to water stress conditions without any apparent yield penalty. Enhanced tolerance to water stress was associated with maintenance of higher relative water content, photosynthetic efficiency, and antioxidant activities. Compared to wild type, the TaVAP-overexpressing plants showed enhanced lateral root proliferation that was attributed to higher endogenous levels of IAA. These studies are the first to demonstrate that TaVAP plays a critical role in growth and development in plants, and is a potential candidate for improving the abiotic stress tolerance in crop plants.
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Affiliation(s)
- Brinderjit Singh
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, Punjab, 143005, India
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Paramjit Khurana
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Jitendra P Khurana
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Prabhjeet Singh
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, Punjab, 143005, India.
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Joshi R, Sahoo KK, Tripathi AK, Kumar R, Gupta BK, Pareek A, Singla-Pareek SL. Knockdown of an inflorescence meristem-specific cytokinin oxidase - OsCKX2 in rice reduces yield penalty under salinity stress condition. PLANT, CELL & ENVIRONMENT 2018; 41:936-946. [PMID: 28337744 DOI: 10.1111/pce.12947] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 02/14/2017] [Accepted: 02/19/2017] [Indexed: 05/04/2023]
Abstract
Cytokinins play a significant role in determining grain yield in plants. Cytokinin oxidases catalyse irreversible degradation of cytokinins and hence modulate cellular cytokinin levels. Here, we studied the role of an inflorescence meristem-specific rice cytokinin oxidase - OsCKX2 - in reducing yield penalty under salinity stress conditions. We utilized an RNAi-based approach to study the function of OsCKX2 in maintaining grain yield under salinity stress condition. Ultra-performance liquid chromatography-based estimation revealed a significant increase in cytokinins in the inflorescence meristem of OsCKX2-knockdown plants. To determine if there exists a correlation between OsCKX2 levels and yield under salinity stress condition, we assessed the growth, physiology and grain yield of OsCKX2-knockdown plants vis-à-vis the wild type. OsCKX2-knockdown plants showed better vegetative growth, higher relative water content and photosynthetic efficiency and reduced electrolyte leakage as compared with the wild type under salinity stress. Importantly, we found a negative correlation between OsCKX2 expression and plant productivity as evident by assessment of agronomical parameters such as panicle branching, filled grains per plant and harvest index both under control and salinity stress conditions. These results suggest that OsCKX2, via controlling cytokinin levels, regulates floral primordial activity modulating rice grain yield under normal as well as abiotic stress conditions.
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Affiliation(s)
- Rohit Joshi
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110 067, India
| | - Khirod Kumar Sahoo
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110 067, India
| | - Amit Kumar Tripathi
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110 067, India
| | - Ritesh Kumar
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110 067, India
| | - Brijesh Kumar Gupta
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110 067, India
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Sneh Lata Singla-Pareek
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110 067, India
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38
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Gianinetti A, Finocchiaro F, Bagnaresi P, Zechini A, Faccioli P, Cattivelli L, Valè G, Biselli C. Seed Dormancy Involves a Transcriptional Program That Supports Early Plastid Functionality during Imbibition. PLANTS 2018; 7:plants7020035. [PMID: 29671830 PMCID: PMC6026906 DOI: 10.3390/plants7020035] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 04/05/2018] [Accepted: 04/11/2018] [Indexed: 01/18/2023]
Abstract
Red rice fully dormant seeds do not germinate even under favorable germination conditions. In several species, including rice, seed dormancy can be removed by dry-afterripening (warm storage); thus, dormant and non-dormant seeds can be compared for the same genotype. A weedy (red) rice genotype with strong dormancy was used for mRNA expression profiling, by RNA-Seq, of dormant and non-dormant dehulled caryopses (here addressed as seeds) at two temperatures (30 °C and 10 °C) and two durations of incubation in water (8 h and 8 days). Aim of the study was to highlight the differences in the transcriptome of dormant and non-dormant imbibed seeds. Transcript data suggested important differences between these seeds (at least, as inferred by expression-based metabolism reconstruction): dry-afterripening seems to impose a respiratory impairment onto non-dormant seeds, thus glycolysis is deduced to be preferentially directed to alcoholic fermentation in non-dormant seeds but to alanine production in dormant ones; phosphoenolpyruvate carboxykinase, pyruvate phosphate dikinase and alanine aminotransferase pathways appear to have an important gluconeogenetic role associated with the restoration of plastid functions in the dormant seed following imbibition; correspondingly, co-expression analysis pointed out a commitment to guarantee plastid functionality in dormant seeds. At 8 h of imbibition, as inferred by gene expression, dormant seeds appear to preferentially use carbon and nitrogen resources for biosynthetic processes in the plastid, including starch and proanthocyanidins accumulation. Chromatin modification appears to be a possible mechanism involved in the transition from dormancy to germination. Non-dormant seeds show higher expression of genes related to cell wall modification, suggesting they prepare for acrospire/radicle elongation.
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Affiliation(s)
- Alberto Gianinetti
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, via S. Protaso 302, 29017 Fiorenzuola d'Arda (PC), Italy.
| | - Franca Finocchiaro
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, via S. Protaso 302, 29017 Fiorenzuola d'Arda (PC), Italy.
| | - Paolo Bagnaresi
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, via S. Protaso 302, 29017 Fiorenzuola d'Arda (PC), Italy.
| | - Antonella Zechini
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, via S. Protaso 302, 29017 Fiorenzuola d'Arda (PC), Italy.
| | - Primetta Faccioli
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, via S. Protaso 302, 29017 Fiorenzuola d'Arda (PC), Italy.
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, via S. Protaso 302, 29017 Fiorenzuola d'Arda (PC), Italy.
| | - Giampiero Valè
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, via S. Protaso 302, 29017 Fiorenzuola d'Arda (PC), Italy.
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, s.s. 11 to Torino, km 2.5, 13100 Vercelli, Italy.
| | - Chiara Biselli
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, via S. Protaso 302, 29017 Fiorenzuola d'Arda (PC), Italy.
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Bakshi A, Moin M, Datla R, Kirti PB. Expression profiling of development related genes in rice plants ectopically expressing AtTOR. PLANT SIGNALING & BEHAVIOR 2017; 12:e1362519. [PMID: 28816596 PMCID: PMC5640186 DOI: 10.1080/15592324.2017.1362519] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 07/27/2017] [Indexed: 05/19/2023]
Abstract
Expression analysis of genes associated with development at different growth stages such as shoot apical meristem (SAM), root apical meristem (RAM), shoot and root tissues 10 DAG, flowers and grains of 2 high expression transgenic lines of rice ectopically expressing AtTOR revealed the involvement of AtTOR in transcriptional regulation of these genes. We have observed that in the SAM of these 2 selected lines, TR-2.24 and TR-15.1, OsFON1 and OsFON4 (orthologs of AtCLV1 and AtCLV3, respectively), OsKNOX2, OsKNOX3 and OsWOX3 became upregulated. The upregulation of OsFON1 and OsFON4 is likely to be involved in the maintenance of effective meristem size of the inflorescence and phyllotaxis. The grains and spikes of transgenic plants exhibited enhanced transcript levels of OsMADS1, OsMADS6, and OsMADS29 further implicating the role of TOR in modulating the expression of the genes in rice grain formation and development. Moreover, the upregulation of auxin transporter, PIN1c in RAM and roots derived from seedlings 10 DAG showed the involvement of TOR in root development. The seeds of 2 high expression lines also showed increased expression of OSE2 and GAMYB transcription factors involved in seed development. In summary, the present study, by heterologous expression of AtTOR in rice, demonstrated the involvement of TOR in regulating genes involved in various growth and developmental stages of rice plant and also in photosynthesis, productivity related functions and water-use efficiency.
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Affiliation(s)
- Achala Bakshi
- Department of Plant Sciences, University of Hyderabad, Hyderabad
| | - Mazahar Moin
- Department of Plant Sciences, University of Hyderabad, Hyderabad
| | - Raju Datla
- National Research Council of Canada, Saskatoon, Saskatchewan, Canada
| | - P. B. Kirti
- Department of Plant Sciences, University of Hyderabad, Hyderabad
- CONTECT P. B. Kirti Department of Plant Sciences, University of Hyderabad, Hyderabad-500046, TelanganaIndia
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40
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Affiliation(s)
- Yasunori Nakamura
- Akita Natural Science Laboratory; Tennoh, Katagami, Akita Japan
- Faculty of Bioresource Sciences; Akita Prefectural University; Shimoshinjo-Nakano, Akita Japan
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Ranjan R, Khurana R, Malik N, Badoni S, Parida SK, Kapoor S, Tyagi AK. bHLH142 regulates various metabolic pathway-related genes to affect pollen development and anther dehiscence in rice. Sci Rep 2017; 7:43397. [PMID: 28262713 PMCID: PMC5338287 DOI: 10.1038/srep43397] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 01/20/2017] [Indexed: 01/14/2023] Open
Abstract
Apposite development of anther and its dehiscence are important for the reproductive success of the flowering plants. Recently, bHLH142, a bHLH transcription factor encoding gene of rice has been found to show anther-specific expression and mutant analyses suggest its functions in regulating tapetum differentiation and degeneration during anther development. However, our study on protein level expression and gain-of-function phenotype revealed novel aspects of its regulation and function during anther development. Temporally dissimilar pattern of bHLH142 transcript and polypeptide accumulation suggested regulation of its expression beyond transcriptional level. Overexpression of bHLH142 in transgenic rice resulted in indehiscent anthers and aborted pollen grains. Defects in septum and stomium rupture caused anther indehiscence while pollen abortion phenotype attributed to abnormal degeneration of the tapetum. Furthermore, RNA-Seq-based transcriptome analysis of tetrad and mature pollen stage anthers of wild type and bHLH142OEplants suggested that it might regulate carbohydrate and lipid metabolism, cell wall modification, reactive oxygen species (ROS) homeostasis and cell death-related genes during rice anther development. Thus, bHLH142 is an anther-specific gene whose expression is regulated at transcriptional and post-transcriptional/translational levels. It plays a role in pollen maturation and anther dehiscence by regulating expression of various metabolic pathways-related genes.
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Affiliation(s)
- Rajeev Ranjan
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Reema Khurana
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Marg, New Delhi 110021, India
| | - Naveen Malik
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Saurabh Badoni
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Swarup K. Parida
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Sanjay Kapoor
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Marg, New Delhi 110021, India
| | - Akhilesh K. Tyagi
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Marg, New Delhi 110021, India
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42
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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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43
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Agarwal P, Parida SK, Raghuvanshi S, Kapoor S, Khurana P, Khurana JP, Tyagi AK. Rice Improvement Through Genome-Based Functional Analysis and Molecular Breeding in India. RICE (NEW YORK, N.Y.) 2016; 9:1. [PMID: 26743769 PMCID: PMC4705060 DOI: 10.1186/s12284-015-0073-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 12/22/2015] [Indexed: 05/05/2023]
Abstract
Rice is one of the main pillars of food security in India. Its improvement for higher yield in sustainable agriculture system is also vital to provide energy and nutritional needs of growing world population, expected to reach more than 9 billion by 2050. The high quality genome sequence of rice has provided a rich resource to mine information about diversity of genes and alleles which can contribute to improvement of useful agronomic traits. Defining the function of each gene and regulatory element of rice remains a challenge for the rice community in the coming years. Subsequent to participation in IRGSP, India has continued to contribute in the areas of diversity analysis, transcriptomics, functional genomics, marker development, QTL mapping and molecular breeding, through national and multi-national research programs. These efforts have helped generate resources for rice improvement, some of which have already been deployed to mitigate loss due to environmental stress and pathogens. With renewed efforts, Indian researchers are making new strides, along with the international scientific community, in both basic research and realization of its translational impact.
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Affiliation(s)
- Pinky Agarwal
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Swarup K Parida
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Saurabh Raghuvanshi
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Sanjay Kapoor
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Paramjit Khurana
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Jitendra P Khurana
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Akhilesh K Tyagi
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India.
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India.
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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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Petla BP, Kamble NU, Kumar M, Verma P, Ghosh S, Singh A, Rao V, Salvi P, Kaur H, Saxena SC, Majee M. Rice PROTEIN l-ISOASPARTYL METHYLTRANSFERASE isoforms differentially accumulate during seed maturation to restrict deleterious isoAsp and reactive oxygen species accumulation and are implicated in seed vigor and longevity. THE NEW PHYTOLOGIST 2016; 211:627-45. [PMID: 26987457 DOI: 10.1111/nph.13923] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Accepted: 02/03/2016] [Indexed: 05/03/2023]
Abstract
PROTEIN l-ISOASPARTYL O-METHYLTRANSFERASE (PIMT) is a protein-repairing enzyme involved in seed vigor and longevity. However, the regulation of PIMT isoforms during seed development and the mechanism of PIMT-mediated improvement of seed vigor and longevity are largely unknown. In this study in rice (Oryza sativa), we demonstrate the dynamics and correlation of isoaspartyl (isoAsp)-repairing demands and PIMT activity, and their implications, during seed development, germination and aging, through biochemical, molecular and genetic studies. Molecular and biochemical analyses revealed that rice possesses various biochemically active and inactive PIMT isoforms. Transcript and western blot analyses clearly showed the seed development stage and tissue-specific accumulation of active isoforms. Immunolocalization studies revealed distinct isoform expression in embryo and aleurone layers. Further analyses of transgenic lines for each OsPIMT isoform revealed a clear role in the restriction of deleterious isoAsp and age-induced reactive oxygen species (ROS) accumulation to improve seed vigor and longevity. Collectively, our data suggest that a PIMT-mediated, protein repair mechanism is initiated during seed development in rice, with each isoform playing a distinct, yet coordinated, role. Our results also raise the intriguing possibility that PIMT repairs antioxidative enzymes and proteins which restrict ROS accumulation, lipid peroxidation, etc. in seed, particularly during aging, thus contributing to seed vigor and longevity.
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Affiliation(s)
- Bhanu Prakash Petla
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, Delhi, 110067, India
| | - Nitin Uttam Kamble
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, Delhi, 110067, India
| | - Meenu Kumar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, Delhi, 110067, India
| | - Pooja Verma
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, Delhi, 110067, India
| | - Shraboni Ghosh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, Delhi, 110067, India
| | - Ajeet Singh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, Delhi, 110067, India
| | - Venkateswara Rao
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, Delhi, 110067, India
| | - Prafull Salvi
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, Delhi, 110067, India
| | - Harmeet Kaur
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, Delhi, 110067, India
| | - Saurabh Chandra Saxena
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, Delhi, 110067, India
| | - Manoj Majee
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, Delhi, 110067, India
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46
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Chen C, Begcy K, Liu K, Folsom JJ, Wang Z, Zhang C, Walia H. Heat stress yields a unique MADS box transcription factor in determining seed size and thermal sensitivity. PLANT PHYSIOLOGY 2016; 171:606-22. [PMID: 26936896 PMCID: PMC4854699 DOI: 10.1104/pp.15.01992] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 03/02/2016] [Indexed: 05/19/2023]
Abstract
Early seed development events are highly sensitive to increased temperature. This high sensitivity to a short-duration temperature spike reduces seed viability and seed size at maturity. The molecular basis of heat stress sensitivity during early seed development is not known. We selected rice (Oryza sativa), a highly heat-sensitive species, to explore this phenomenon. Here, we elucidate the molecular pathways that contribute to the heat sensitivity of a critical developmental window during which the endosperm transitions from syncytium to the cellularization stage in young seeds. A transcriptomic comparison of seeds exposed to moderate (35°C) and severe (39°C) heat stress with control (28°C) seeds identified a set of putative imprinted genes, which were down-regulated under severe heat stress. Several type I MADS box genes specifically expressed during the syncytial stage were differentially regulated under moderate and severe heat stress. The suppression and overaccumulation of these genes are associated with precocious and delayed cellularization under moderate and severe stress, respectively. We show that modulating the expression of OsMADS87, one of the heat-sensitive, imprinted genes associated with syncytial stage endosperm, regulates rice seed size. Transgenic seeds deficient in OsMADS87 exhibit accelerated endosperm cellularization. These seeds also have lower sensitivity to a moderate heat stress in terms of seed size reduction compared with seeds from wild-type plants and plants overexpressing OsMADS87 Our findings suggest that OsMADS87 and several other genes identified in this study could be potential targets for improving the thermal resilience of rice during reproductive development.
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Affiliation(s)
- Chen Chen
- Department of Agronomy and Horticulture (C.C., K.B., J.J.F., Z.W., H.W.) and School of Biological Sciences (K.L., C.Z.), University of Nebraska, Lincoln, Nebraska 68583; andKey Laboratory of Crop Genetics and Physiology of Jiangsu Province and Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, China (C.C.)
| | - Kevin Begcy
- Department of Agronomy and Horticulture (C.C., K.B., J.J.F., Z.W., H.W.) and School of Biological Sciences (K.L., C.Z.), University of Nebraska, Lincoln, Nebraska 68583; andKey Laboratory of Crop Genetics and Physiology of Jiangsu Province and Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, China (C.C.)
| | - Kan Liu
- Department of Agronomy and Horticulture (C.C., K.B., J.J.F., Z.W., H.W.) and School of Biological Sciences (K.L., C.Z.), University of Nebraska, Lincoln, Nebraska 68583; andKey Laboratory of Crop Genetics and Physiology of Jiangsu Province and Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, China (C.C.)
| | - Jing J Folsom
- Department of Agronomy and Horticulture (C.C., K.B., J.J.F., Z.W., H.W.) and School of Biological Sciences (K.L., C.Z.), University of Nebraska, Lincoln, Nebraska 68583; andKey Laboratory of Crop Genetics and Physiology of Jiangsu Province and Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, China (C.C.)
| | - Zhen Wang
- Department of Agronomy and Horticulture (C.C., K.B., J.J.F., Z.W., H.W.) and School of Biological Sciences (K.L., C.Z.), University of Nebraska, Lincoln, Nebraska 68583; andKey Laboratory of Crop Genetics and Physiology of Jiangsu Province and Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, China (C.C.)
| | - Chi Zhang
- Department of Agronomy and Horticulture (C.C., K.B., J.J.F., Z.W., H.W.) and School of Biological Sciences (K.L., C.Z.), University of Nebraska, Lincoln, Nebraska 68583; andKey Laboratory of Crop Genetics and Physiology of Jiangsu Province and Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, China (C.C.)
| | - Harkamal Walia
- Department of Agronomy and Horticulture (C.C., K.B., J.J.F., Z.W., H.W.) and School of Biological Sciences (K.L., C.Z.), University of Nebraska, Lincoln, Nebraska 68583; andKey Laboratory of Crop Genetics and Physiology of Jiangsu Province and Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, China (C.C.)
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Dreni L, Zhang D. Flower development: the evolutionary history and functions of the AGL6 subfamily MADS-box genes. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:1625-1638. [PMID: 26956504 DOI: 10.1093/jxb/erw046] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
AGL6 is an ancient subfamily of MADS-box genes found in both gymnosperms and angiosperms. Its functions remained elusive despite the fact that the MADS-box genes and the ABC model have been studied for >20 years. Nevertheless, recent discoveries in petunia, rice, and maize support its involvement in the 'E' function of floral development, very similar to the closely related AGL2 (SEPALLATA) subfamily which has been well characterized. The known functions of AGL6 span from ancient conserved roles to new functions acquired in specific plant families. The AGL6 genes are involved in floral meristem regulation, in floral organs, and ovule (integument) and seed development, and have possible roles in both male and female germline and gametophyte development. In grasses, they are also important for the development of the first whorl of the flower, whereas in Arabidopsis they may play additional roles before floral meristem formation. This review covers these recent insights and some other aspects that are not yet fully elucidated, which deserve more studies in the future.
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Affiliation(s)
- Ludovico Dreni
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University (SJTU)-University of Adelaide Joint Centre for Agriculture and Health, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University (SJTU)-University of Adelaide Joint Centre for Agriculture and Health, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China School of Agriculture, Food, and Wine, University of Adelaide, South Australia 5064, Australia
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48
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Sui Z, Wang T, Li H, Zhang M, Li Y, Xu R, Xing G, Ni Z, Xin M. Overexpression of Peptide-Encoding OsCEP6.1 Results in Pleiotropic Effects on Growth in Rice (O. sativa). FRONTIERS IN PLANT SCIENCE 2016; 7:228. [PMID: 26973672 PMCID: PMC4773640 DOI: 10.3389/fpls.2016.00228] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Accepted: 02/11/2016] [Indexed: 05/19/2023]
Abstract
Plant peptide hormones play an important role in regulating plant developmental programs via cell-to-cell communication in a non-cell autonomous manner. To characterize the biological relevance of C-TERMINALLY ENCODED PEPTIDE (CEP) genes in rice, we performed a genome-wide search against public databases using a bioinformatics approach and identified six additional CEP members. Expression analysis revealed a spatial-temporal pattern of OsCEP6.1 gene in different tissues and at different developmental stages of panicle. Interestingly, the expression level of the OsCEP6.1 was also significantly up-regulated by exogenous cytokinin. Application of a chemically synthesized 15-amino acid OsCEP6.1 peptide showed that OsCEP6.1 had a negative role in regulating root and seedling growth, which was further confirmed by transgenic lines. Furthermore, the constitutive expression of OsCEP6.1 was sufficient to lead to panicle architecture and grain size variations. Scanning electron microscopy analysis revealed that the phenotypic variation of OsCEP6.1 overexpression lines resulted from decreased cell size but not reduced cell number. Moreover, starch accumulation was not significantly affected. Taken together, these data suggest that the OsCEP6.1 peptide might be involved in regulating the development of panicles and grains in rice.
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Affiliation(s)
- Zhipeng Sui
- Key Laboratory of Crop Heterosis and Utilization (MOE) and State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural UniversityBeijing, China
- National Center for Plant Gene Research–BeijingBeijing, China
| | - Tianya Wang
- Key Laboratory of Crop Heterosis and Utilization (MOE) and State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural UniversityBeijing, China
- National Center for Plant Gene Research–BeijingBeijing, China
| | - Hongjian Li
- Key Laboratory of Crop Heterosis and Utilization (MOE) and State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural UniversityBeijing, China
- National Center for Plant Gene Research–BeijingBeijing, China
| | - Ming Zhang
- Key Laboratory of Crop Heterosis and Utilization (MOE) and State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural UniversityBeijing, China
- National Center for Plant Gene Research–BeijingBeijing, China
| | - Yangyang Li
- Key Laboratory of Crop Heterosis and Utilization (MOE) and State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural UniversityBeijing, China
- National Center for Plant Gene Research–BeijingBeijing, China
| | - Ruibin Xu
- Qingdao Agricultural UniversityQingdao, China
| | | | - Zhongfu Ni
- Key Laboratory of Crop Heterosis and Utilization (MOE) and State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural UniversityBeijing, China
- National Center for Plant Gene Research–BeijingBeijing, China
- *Correspondence: Zhongfu Ni
| | - Mingming Xin
- Key Laboratory of Crop Heterosis and Utilization (MOE) and State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural UniversityBeijing, China
- National Center for Plant Gene Research–BeijingBeijing, China
- Mingming Xin
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Mathew IE, Das S, Mahto A, Agarwal P. Three Rice NAC Transcription Factors Heteromerize and Are Associated with Seed Size. FRONTIERS IN PLANT SCIENCE 2016; 7:1638. [PMID: 27872632 PMCID: PMC5098391 DOI: 10.3389/fpls.2016.01638] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 10/17/2016] [Indexed: 05/18/2023]
Abstract
NACs are plant-specific transcription factors (TFs) involved in multiple aspects of development and stress. In rice, three NAC TF encoding genes, namely ONAC020, ONAC026, and ONAC023 express specifically during seed development, at extremely high levels. They exhibit significantly strong association with seed size/weight with the sequence variations located in the upstream regulatory region. Concomitantly, their expression pattern/levels during seed development vary amongst different accessions with variation in seed size. The alterations in the promoter sequences of the three genes, amongst the five rice accessions, correlate with the expression levels to a certain extent only. In terms of transcriptional properties, the three NAC TFs can activate and/or suppress downstream genes, though to different extents. Only ONAC026 is localized to the nucleus while ONAC020 and ONAC023 are targeted to the ER and cytoplasm, respectively. Interestingly, these two proteins interact with ONAC026 and the dimers localize in the nucleus. Trans-splicing between ONAC020 and ONAC026 results in three additional forms of ONAC020. The transcriptional properties including activation, repression, subcellular localization and heterodimerization of trans-spliced forms of ONAC020 and ONAC026 are different, indicating toward their role as competitors. The analysis presented in this paper helps to conclude that the three NAC genes, which are associated with seed size, have independent as well as overlapping roles during the process and can be exploited as potential targets for crop improvement.
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50
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Radchuk V, Borisjuk L. Physical, metabolic and developmental functions of the seed coat. FRONTIERS IN PLANT SCIENCE 2014; 5:510. [PMID: 25346737 PMCID: PMC4193196 DOI: 10.3389/fpls.2014.00510] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 09/11/2014] [Indexed: 05/04/2023]
Abstract
The conventional understanding of the role of the seed coat is that it provides a protective layer for the developing zygote. Recent data show that the picture is more nuanced. The seed coat certainly represents a first line of defense against adverse external factors, but it also acts as channel for transmitting environmental cues to the interior of the seed. The latter function primes the seed to adjust its metabolism in response to changes in its external environment. The purpose of this review is to provide the reader with a comprehensive view of the structure and functionality of the seed coat, and to expose its hidden interaction with both the endosperm and embryo. Any breeding and/or biotechnology intervention seeking to increase seed size or modify seed features will have to consider the implications on this tripartite interaction.
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Affiliation(s)
| | - Ljudmilla Borisjuk
- Heterosis, Molecular Genetics, Leibniz-Institut für Pflanzengenetik und KulturpflanzenforschungGatersleben, Germany
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