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Jyoti SD, Singh G, Pradhan AK, Tarpley L, Septiningsih EM, Talukder SK. Rice breeding for low input agriculture. FRONTIERS IN PLANT SCIENCE 2024; 15:1408356. [PMID: 38974981 PMCID: PMC11224470 DOI: 10.3389/fpls.2024.1408356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 05/24/2024] [Indexed: 07/09/2024]
Abstract
A low-input-based farming system can reduce the adverse effects of modern agriculture through proper utilization of natural resources. Modern varieties often need to improve in low-input settings since they are not adapted to these systems. In addition, rice is one of the most widely cultivated crops worldwide. Enhancing rice performance under a low input system will significantly reduce the environmental concerns related to rice cultivation. Traits that help rice to maintain yield performance under minimum inputs like seedling vigor, appropriate root architecture for nutrient use efficiency should be incorporated into varieties for low input systems through integrated breeding approaches. Genes or QTLs controlling nutrient uptake, nutrient assimilation, nutrient remobilization, and root morphology need to be properly incorporated into the rice breeding pipeline. Also, genes/QTLs controlling suitable rice cultivars for sustainable farming. Since several variables influence performance under low input conditions, conventional breeding techniques make it challenging to work on many traits. However, recent advances in omics technologies have created enormous opportunities for rapidly improving multiple characteristics. This review highlights current research on features pertinent to low-input agriculture and provides an overview of alternative genomics-based breeding strategies for enhancing genetic gain in rice suitable for low-input farming practices.
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Affiliation(s)
- Subroto Das Jyoti
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
| | - Gurjeet Singh
- Texas A&M AgriLife Research Center, Beaumont, TX, United States
| | | | - Lee Tarpley
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
- Texas A&M AgriLife Research Center, Beaumont, TX, United States
| | - Endang M. Septiningsih
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
| | - Shyamal K. Talukder
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
- Texas A&M AgriLife Research Center, Beaumont, TX, United States
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Hu Q, Wu Y, Hong T, Wu D, Wang L. OsMED16, a tail subunit of Mediator complex, interacts with OsE2Fa to synergistically regulate rice leaf development and blast resistance. Int J Biol Macromol 2023; 253:126728. [PMID: 37678689 DOI: 10.1016/j.ijbiomac.2023.126728] [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: 06/28/2023] [Revised: 08/20/2023] [Accepted: 09/03/2023] [Indexed: 09/09/2023]
Abstract
Mediator, a universal eukaryotic coactivator, is a multiprotein complex to transduce information from the DNA-bound transcription factors to the RNA polymerase II transcriptional machinery. In this study, the biofunctions of a rice mediator subunit OsMED16 in leaf development and blast resistance were characterized. OsMED16 encodes a putative protein of 1170 amino acids, which is 393 bp shorted than the version in Rice Genome Annotation Project databases. Overexpression of OsMED16 plants exhibited wider leaves with larger and more numerous cells in lateral axis, and enhanced resistance to M. oryzae with hyperaccumulated salicylic acid. Further analysis revealed that OsMED16 interacts with OsE2Fa in nuclei, and the complex could directly regulate the transcriptional levels of several genes involved in cell cycle regulation and SA mediated blast resistance, such as OsCC52A1, OsCDKA1, OsCDKB2;2, OsICS1 and OsWRKY45. Altogether, this study proved that OsMED16 is a positive regulator of rice leaf development and blast resistance, and providing new insights into the crosstalk between cell cycle regulation and immunity.
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Affiliation(s)
- Qin Hu
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources, Guangxi University, Daxue East Road 100, Nanning 530004, China; College of Agriculture, Guangxi University, Daxue East Road 100, Nanning 530004, China.
| | - Yanfei Wu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Youyi Avenue 368, Wuhan 430062, China
| | - Tianshu Hong
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources, Guangxi University, Daxue East Road 100, Nanning 530004, China; College of Agriculture, Guangxi University, Daxue East Road 100, Nanning 530004, China
| | - Deng Wu
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources, Guangxi University, Daxue East Road 100, Nanning 530004, China; College of Agriculture, Guangxi University, Daxue East Road 100, Nanning 530004, China
| | - Lulu Wang
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources, Guangxi University, Daxue East Road 100, Nanning 530004, China; College of Agriculture, Guangxi University, Daxue East Road 100, Nanning 530004, China
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Prasanna JA, Mandal VK, Kumar D, Chakraborty N, Raghuram N. Nitrate-responsive transcriptome analysis of rice RGA1 mutant reveals the role of G-protein alpha subunit in negative regulation of nitrogen-sensitivity and use efficiency. PLANT CELL REPORTS 2023; 42:1987-2010. [PMID: 37874341 DOI: 10.1007/s00299-023-03078-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 09/19/2023] [Indexed: 10/25/2023]
Abstract
KEY MESSAGE Nitrate-responsive transcriptomic, phenotypic and physiological analyses of rice RGA1 mutant revealed many novel RGA1-regulated genes/processes/traits related to nitrogen use efficiency, and provided robust genetic evidence of RGA1-regulation of NUE. Nitrogen (N) use efficiency (NUE) is important for sustainable agriculture. G-protein signalling was implicated in N-response/NUE in rice, but needed firm genetic characterization of the role of alpha subunit (RGA1). The knock-out mutant of RGA1 in japonica rice exhibited lesser nitrate-dose sensitivity than the wild type (WT), in yield and NUE. We, therefore, investigated its genomewide nitrate-response relative to WT. It revealed 3416 differentially expressed genes (DEGs), including 719 associated with development, grain yield and phenotypic traits for NUE. The upregulated DEGs were related to photosynthesis, chlorophyll, tetrapyrrole and porphyrin biosynthesis, while the downregulated DEGs belonged to cellular protein metabolism and transport, small GTPase signalling, cell redox homeostasis, etc. We validated 26 nitrate-responsive DEGs across functional categories by RT-qPCR. Physiological validation of nitrate-response in the mutant and the WT at 1.5 and 15 mM doses revealed higher chlorophyll and stomatal length but decreased stomatal density, conductance and transpiration. The consequent increase in photosynthesis and water use efficiency may have contributed to better yield and NUE in the mutant, whereas the WT was N-dose sensitive. The mutant was not as N-dose-responsive as the WT in shoot/root growth, productive tillers and heading date, but equally responsive as WT in total N and protein content. The RGA1 mutant was less impacted by higher N-dose or salt stress in terms of yield, protein content, photosynthetic performance, relative water content, water use efficiency and catalase activity. PPI network analyses revealed known NUE-related proteins as RGA1 interactors. Therefore, RGA1 negatively regulates N-dose sensitivity and NUE in rice.
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Affiliation(s)
- Jangam Annie Prasanna
- Centre for Sustainable Nitrogen and Nutrient Management, School of Biotechnology, Guru Gobind Singh Indraprastha University, Sector 16C, Dwarka, New Delhi, 110078, India
| | - Vikas Kumar Mandal
- Centre for Sustainable Nitrogen and Nutrient Management, School of Biotechnology, Guru Gobind Singh Indraprastha University, Sector 16C, Dwarka, New Delhi, 110078, India
- Prof. H.S. Srivastava Foundation for Science and Society, 10B/7, Madan Mohan Malviya Marg, Lucknow, India
| | - Dinesh Kumar
- Division of Agronomy, ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi, India
| | - Navjyoti Chakraborty
- Centre for Sustainable Nitrogen and Nutrient Management, School of Biotechnology, Guru Gobind Singh Indraprastha University, Sector 16C, Dwarka, New Delhi, 110078, India.
| | - Nandula Raghuram
- Centre for Sustainable Nitrogen and Nutrient Management, School of Biotechnology, Guru Gobind Singh Indraprastha University, Sector 16C, Dwarka, New Delhi, 110078, India.
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Ma S, Zhong Y, Zheng S, He Y, Yang S, Wang L, Traw MB, Zhang Q, Zhang X. Rapid Identification by Resequencing-Based QTL Mapping of a Novel Allele RGA1-FH Decreasing Grain Length in a Rice Restorer Line 'Fuhui212'. Int J Mol Sci 2023; 24:10746. [PMID: 37445924 DOI: 10.3390/ijms241310746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/21/2023] [Accepted: 06/25/2023] [Indexed: 07/15/2023] Open
Abstract
Grain size is one of the most frequently selected traits during domestication and modern breeding. The continued discovery and characterization of new genes and alleles in controlling grain size are important in safeguarding the food supply for the world's growing population. Previously, a small grain size was observed in a rice restorer line 'Fuhui212', while the underlying genetic factors controlling this trait were unknown. In this study, by combining QTL mapping, variant effect prediction, and complementation experiments, we recovered a novel allele RGA1-FH that explains most of the phenotypic changes. The RGA1-FH allele contains an A-to-T splicing site variant that disrupts the normal function of RGA1. While population analysis suggests extremely strong artificial selection in maintaining a functional allele of RGA1, our study is the first, to the best of our knowledge, to prove that a dysfunctional RGA1 allele can also be beneficial in real agricultural production. Future breeding programs would benefit from paying more attention to the rational utilization of those overlooked 'unfavored' alleles.
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Affiliation(s)
- Shiying Ma
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Yifan Zhong
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Shuyi Zheng
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Ying He
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Sihai Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Long Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Milton Brian Traw
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Qijun Zhang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Xiaohui Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
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Wang J, Xu J, Wang L, Zhou M, Nian J, Chen M, Lu X, Liu X, Wang Z, Cen J, Liu Y, Zhang Z, Zeng D, Hu J, Zhu L, Dong G, Ren D, Gao Z, Shen L, Zhang Q, Li Q, Guo L, Yu S, Qian Q, Zhang G. SEMI-ROLLED LEAF 10 stabilizes catalase isozyme B to regulate leaf morphology and thermotolerance in rice (Oryza sativa L.). PLANT BIOTECHNOLOGY JOURNAL 2023; 21:819-838. [PMID: 36597711 PMCID: PMC10037157 DOI: 10.1111/pbi.13999] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 12/18/2022] [Accepted: 12/25/2022] [Indexed: 06/17/2023]
Abstract
Plant architecture and stress tolerance play important roles in rice breeding. Specific leaf morphologies and ideal plant architecture can effectively improve both abiotic stress resistance and rice grain yield. However, the mechanism by which plants simultaneously regulate leaf morphogenesis and stress resistance remains elusive. Here, we report that SRL10, which encodes a double-stranded RNA-binding protein, regulates leaf morphology and thermotolerance in rice through alteration of microRNA biogenesis. The srl10 mutant had a semi-rolled leaf phenotype and elevated sensitivity to high temperature. SRL10 directly interacted with catalase isozyme B (CATB), and the two proteins mutually increased one other's stability to enhance hydrogen peroxide (H2 O2 ) scavenging, thereby contributing to thermotolerance. The natural Hap3 (AGC) type of SRL10 allele was found to be present in the majority of aus rice accessions, and was identified as a thermotolerant allele under high temperature stress in both the field and the growth chamber. Moreover, the seed-setting rate was 3.19 times higher and grain yield per plant was 1.68 times higher in near-isogenic line (NIL) carrying Hap3 allele compared to plants carrying Hap1 allele under heat stress. Collectively, these results reveal a new locus of interest and define a novel SRL10-CATB based regulatory mechanism for developing cultivars with high temperature tolerance and stable yield. Furthermore, our findings provide a theoretical basis for simultaneous breeding for plant architecture and stress resistance.
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Affiliation(s)
- Jiajia Wang
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene ResearchCollege of Plant Science and Technology, Huazhong Agricultural UniversityWuhanChina
| | - Jing Xu
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding of Zhejiang ProvinceResearch Institute of Subtropical Forestry, Chinese Academy of ForestryHangzhouChina
| | - Li Wang
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Mengyu Zhou
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Jinqiang Nian
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Minmin Chen
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Xueli Lu
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Xiong Liu
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Zian Wang
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Jiangsu Cen
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Yiting Liu
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Zhihai Zhang
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Dali Zeng
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Jiang Hu
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Li Zhu
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Guojun Dong
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Deyong Ren
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Zhenyu Gao
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Lan Shen
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Qiang Zhang
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Qing Li
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Longbiao Guo
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Sibin Yu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene ResearchCollege of Plant Science and Technology, Huazhong Agricultural UniversityWuhanChina
| | - Qian Qian
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
- Hainan Yazhou Bay Seed LaboratorySanyaChina
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural SciencesSanyaChina
| | - Guangheng Zhang
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
- Hainan Yazhou Bay Seed LaboratorySanyaChina
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural SciencesSanyaChina
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Sharma N, Jaiswal DK, Kumari S, Dash GK, Panda S, Anandan A, Raghuram N. Genome-Wide Urea Response in Rice Genotypes Contrasting for Nitrogen Use Efficiency. Int J Mol Sci 2023; 24:ijms24076080. [PMID: 37047052 PMCID: PMC10093866 DOI: 10.3390/ijms24076080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 01/12/2023] [Accepted: 01/13/2023] [Indexed: 04/14/2023] Open
Abstract
Rice is an ideal crop for improvement of nitrogen use efficiency (NUE), especially with urea, its predominant fertilizer. There is a paucity of studies on rice genotypes contrasting for NUE. We compared low urea-responsive transcriptomes of contrasting rice genotypes, namely Nidhi (low NUE) and Panvel1 (high NUE). Transcriptomes of whole plants grown with media containing normal (15 mM) and low urea (1.5 mM) revealed 1497 and 2819 differentially expressed genes (DEGs) in Nidhi and Panvel1, respectively, of which 271 were common. Though 1226 DEGs were genotype-specific in Nidhi and 2548 in Panvel1, there was far higher commonality in underlying processes. High NUE is associated with the urea-responsive regulation of other nutrient transporters, miRNAs, transcription factors (TFs) and better photosynthesis, water use efficiency and post-translational modifications. Many of their genes co-localized to NUE-QTLs on chromosomes 1, 3 and 9. A field evaluation under different doses of urea revealed better agronomic performance including grain yield, transport/uptake efficiencies and NUE of Panvel1. Comparison of our urea-based transcriptomes with our previous nitrate-based transcriptomes revealed many common processes despite large differences in their expression profiles. Our model proposes that differential involvement of transporters and TFs, among others, contributes to better urea uptake, translocation, utilization, flower development and yield for high NUE.
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Affiliation(s)
- Narendra Sharma
- Centre for Sustainable Nitrogen and Nutrient Management, University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sector 16C, Dwarka, New Delhi 110078, India
| | - Dinesh Kumar Jaiswal
- Centre for Sustainable Nitrogen and Nutrient Management, University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sector 16C, Dwarka, New Delhi 110078, India
| | - Supriya Kumari
- Centre for Sustainable Nitrogen and Nutrient Management, University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sector 16C, Dwarka, New Delhi 110078, India
| | - Goutam Kumar Dash
- Crop Improvement Division, Indian Council of Agricultural Research (ICAR)-National Rice Research Institute (NRRI), Cuttack 753006, India
| | - Siddharth Panda
- Crop Improvement Division, Indian Council of Agricultural Research (ICAR)-National Rice Research Institute (NRRI), Cuttack 753006, India
- Institute of Agricultural Sciences, SOA (DU), Bhubaneswar 751003, India
| | - Annamalai Anandan
- Crop Improvement Division, Indian Council of Agricultural Research (ICAR)-National Rice Research Institute (NRRI), Cuttack 753006, India
- Regional Station, Indian Council of Agricultural Research (ICAR)-Indian Institute of Seed Science, Bengaluru 560065, India
| | - Nandula Raghuram
- Centre for Sustainable Nitrogen and Nutrient Management, University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sector 16C, Dwarka, New Delhi 110078, India
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Bowman CS, Traband R, Wang X, Knowles SP, Lo S, Jia Z, Vorsa N, Herniter IA. Multiple Leaf Sample Extraction System (MuLES): A tool to improve automated morphometric leaf studies. APPLICATIONS IN PLANT SCIENCES 2023; 11:e11513. [PMID: 37051583 PMCID: PMC10083438 DOI: 10.1002/aps3.11513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 11/13/2022] [Accepted: 11/29/2022] [Indexed: 06/19/2023]
Abstract
PREMISE The measurement of leaf morphometric parameters from digital images can be time-consuming or restrictive when using digital image analysis softwares. The Multiple Leaf Sample Extraction System (MuLES) is a new tool that enables high-throughput leaf shape analysis with minimal user input or prerequisites, such as coding knowledge or image modification. METHODS AND RESULTS MuLES uses contrasting pixel color values to distinguish between leaf objects and their background area, eliminating the need for color threshold-based methods or color correction cards typically required in other software methods. The leaf morphometric parameters measured by this software, especially leaf aspect ratio, were able to distinguish between large populations of different accessions for the same species in a high-throughput manner. CONCLUSIONS MuLES provides a simple method for the rapid measurement of leaf morphometric parameters in large plant populations from digital images and demonstrates the ability of leaf aspect ratio to distinguish between closely related plant types.
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Affiliation(s)
- Christian S. Bowman
- Department of Botany and Plant SciencesUniversity of CaliforniaRiverside, 2142 Batchelor HallRiversideCalifornia92521USA
| | - Ryan Traband
- Department of Botany and Plant SciencesUniversity of CaliforniaRiverside, 2142 Batchelor HallRiversideCalifornia92521USA
| | - Xuesong Wang
- Department of Botany and Plant SciencesUniversity of CaliforniaRiverside, 2142 Batchelor HallRiversideCalifornia92521USA
| | - Sara P. Knowles
- Department of Plant BiologyRutgers University59 Dudley RoadNew BrunswickNew Jersey08901USA
| | - Sassoum Lo
- Department of Plant SciencesUniversity of California, Davis, One Shields AvenueDavisCalifornia95616USA
| | - Zhenyu Jia
- Department of Botany and Plant SciencesUniversity of CaliforniaRiverside, 2142 Batchelor HallRiversideCalifornia92521USA
| | - Nicholi Vorsa
- Department of Plant BiologyRutgers University59 Dudley RoadNew BrunswickNew Jersey08901USA
| | - Ira A. Herniter
- Department of Plant BiologyRutgers University59 Dudley RoadNew BrunswickNew Jersey08901USA
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8
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Wang J, Liu H, Zhao C, Tang H, Mu Y, Xu Q, Deng M, Jiang Q, Chen G, Qi P, Wang J, Jiang Y, Chen S, Wei Y, Zheng Y, Lan X, Ma J. Mapping and validation of major and stable QTL for flag leaf size from tetraploid wheat. THE PLANT GENOME 2022; 15:e20252. [PMID: 35929379 DOI: 10.1002/tpg2.20252] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 06/28/2022] [Indexed: 06/15/2023]
Abstract
The flag leaf is an important photosynthetic organ of wheat (Triticum aestivum L.). Appropriate flag leaf size can effectively increase grain yield. In this study, a tetraploid wheat population of recombinant inbred lines (RILs) and a genetic map constructed based on a wheat 55K single-nucleotide polymorphism (SNP) array were used to identify quantitative trait loci (QTL) for flag leaf length (FLL), flag leaf width (FLW), flag leaf area (FLA), and the flag leaf length/width ratio (FLR). A novel and major interval flanked by markers AX-111633224 and AX-109317229 was identified. This interval includes QTL for FLL (QFll.sau-AM-4B.2), for FLW (QFlw.sau-AM-4B.4), for FLA (QFla.sau-AM-4B), and for FLR (QFlr.sau-AM-4B). Based on the genotypes of the closely linked KASP (Kompetitive allele-specific polymerase chain reaction [PCR]) marker (KASP-AX-108756198), QFlw.sau-AM-4B.4 and QFla.sau-AM-4B were successfully verified in two F3 populations with different genetic backgrounds. Genetic associations between flag leaf-related traits and other agronomic traits were detected and analyzed. Four genes in this interval were likely involved in the growth and development of the flag leaf size. In conclusion, this study provides clues for excavating genes related to flag leaf size and breeding variety with ideal plant structure.
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Affiliation(s)
- Jian Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural Univ., Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural Univ., Chengdu, 611130, China
| | - Hang Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural Univ., Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural Univ., Chengdu, 611130, China
| | - Conghao Zhao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural Univ., Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural Univ., Chengdu, 611130, China
| | - Huaping Tang
- Triticeae Research Institute, Sichuan Agricultural Univ., Chengdu, 611130, China
| | - Yang Mu
- Triticeae Research Institute, Sichuan Agricultural Univ., Chengdu, 611130, China
| | - Qiang Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural Univ., Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural Univ., Chengdu, 611130, China
| | - Mei Deng
- Triticeae Research Institute, Sichuan Agricultural Univ., Chengdu, 611130, China
| | - Qiantao Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural Univ., Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural Univ., Chengdu, 611130, China
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural Univ., Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural Univ., Chengdu, 611130, China
| | - Pengfei Qi
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural Univ., Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural Univ., Chengdu, 611130, China
| | - Jirui Wang
- Triticeae Research Institute, Sichuan Agricultural Univ., Chengdu, 611130, China
| | - Yunfeng Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural Univ., Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural Univ., Chengdu, 611130, China
| | - Shisheng Chen
- Institute of Advanced Agricultural Sciences, Peking Univ., Weifang, 262113, China
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural Univ., Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural Univ., Chengdu, 611130, China
| | - Youliang Zheng
- Triticeae Research Institute, Sichuan Agricultural Univ., Chengdu, 611130, China
| | - Xiujin Lan
- Triticeae Research Institute, Sichuan Agricultural Univ., Chengdu, 611130, China
| | - Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural Univ., Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural Univ., Chengdu, 611130, China
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Wang J, Liu Y, Hu S, Xu J, Nian J, Cao X, Chen M, Cen J, Liu X, Zhang Z, Liu D, Zhu L, Hu J, Ren D, Gao Z, Shen L, Dong G, Zhang Q, Li Q, Yu S, Qian Q, Zhang G. LEAF TIP RUMPLED 1 Regulates Leaf Morphology and Salt Tolerance in Rice. Int J Mol Sci 2022; 23:8818. [PMID: 35955949 PMCID: PMC9369171 DOI: 10.3390/ijms23158818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/04/2022] [Accepted: 08/06/2022] [Indexed: 12/02/2022] Open
Abstract
Leaf morphology is one of the important traits related to ideal plant architecture and is an important factor determining rice stress resistance, which directly affects yield. Wax layers form a barrier to protect plants from different environmental stresses. However, the regulatory effect of wax synthesis genes on leaf morphology and salt tolerance is not well-understood. In this study, we identified a rice mutant, leaf tip rumpled 1 (ltr1), in a mutant library of the classic japonica variety Nipponbare. Phenotypic investigation of NPB and ltr1 suggested that ltr1 showed rumpled leaf with uneven distribution of bulliform cells and sclerenchyma cells, and disordered vascular bundles. A decrease in seed-setting rate in ltr1 led to decreased per-plant grain yield. Moreover, ltr1 was sensitive to salt stress, and LTR1 was strongly induced by salt stress. Map-based cloning of LTR1 showed that there was a 2-bp deletion in the eighth exon of LOC_Os02g40784 in ltr1, resulting in a frameshift mutation and early termination of transcription. Subsequently, the candidate gene was confirmed using complementation, overexpression, and knockout analysis of LOC_Os02g40784. Functional analysis of LTR1 showed that it was a wax synthesis gene and constitutively expressed in entire tissues with higher relative expression level in leaves and panicles. Moreover, overexpression of LTR1 enhanced yield in rice and LTR1 positively regulates salt stress by affecting water and ion homeostasis. These results lay a theoretical foundation for exploring the molecular mechanism of leaf morphogenesis and stress response, providing a new potential strategy for stress-tolerance breeding.
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Affiliation(s)
- Jiajia Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yiting Liu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
- Research Center of Plant Functional Genes and Tissue Culture Technology, College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China
| | - Songping Hu
- Research Center of Plant Functional Genes and Tissue Culture Technology, College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China
| | - Jing Xu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Jinqiang Nian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Xiaoping Cao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Minmin Chen
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Jiangsu Cen
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Xiong Liu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Zhihai Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Dan Liu
- Research Center of Plant Functional Genes and Tissue Culture Technology, College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China
| | - Li Zhu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Jiang Hu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Deyong Ren
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Zhenyu Gao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Lan Shen
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Guojun Dong
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Qiang Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Qing Li
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Sibin Yu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Guangheng Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China
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10
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Ren Y, Zhu J, Zhang H, Lin B, Hao P, Hua S. Leaf Carbohydrate Metabolism Variation Caused by Late Planting in Rapeseed (Brassica napus L.) at Reproductive Stage. PLANTS 2022; 11:plants11131696. [PMID: 35807649 PMCID: PMC9268982 DOI: 10.3390/plants11131696] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 11/16/2022]
Abstract
Delayed planting date of rapeseed is an important factor affecting seed yield. However, regulation of the leaf carbohydrate metabolism in rapeseed by a late planting date at the reproductive stage is scarcely investigated. A two-year field experiment was conducted to assess the effect of planting dates, including early (15 September), optimal (1 October), late (15 October), and very late (30 October), on leaf growth and carbohydrate biosynthetic and catabolic metabolism at the reproductive stage. The results showed that leaf dry matter decreased linearly on average from 7.48 to 0.62 g plant−1 with an early planting date, whereas it increased at first and peaked at 14 days after anthesis (DAA) with other planting dates. Leaf dry matter was the lowest at the very late planting date during the reproductive stage. For leaf chlorophyll content, rapeseed planted at an optimal date maximized at 14 DAA with an average content of 1.51 mg g−1 fresh weight, whereas it kept high and stable at a very late planting date after 28 DAA. For the carbohydrate catabolic system, acid and neutral invertase (AI and NI, respectively) showed higher activity before 14 DAA, whereas both sucrose synthase (SS) and starch phosphorylase (SP) showed higher activity after 14 DAA. For the carbohydrate biosynthetic system, the activity of sucrose phosphate synthase (SPS) was the highest at the late planting date after 14 DAA, whereas it was at the lowest at the very late planting date. However, the activity of ADP-glucose pyrophosphorylase (AGPase) at the late and very late planting dates was significantly higher than that of the early and optimal plant dates after 21 DAA, which is in accordance with the leaf total soluble sugar content, suggesting that leaf carbohydrate metabolism is governed by a biosynthetic system. The current study provides new insights on leaf carbohydrate metabolism regulation by late planting in rapeseed at the reproductive stage.
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Affiliation(s)
- Yun Ren
- Huzhou Agricultural Science and Technology Development Center, Huzhou Academy of Agricultural Sciences, Huzhou 313000, China; (Y.R.); (J.Z.)
| | - Jianfang Zhu
- Huzhou Agricultural Science and Technology Development Center, Huzhou Academy of Agricultural Sciences, Huzhou 313000, China; (Y.R.); (J.Z.)
| | - Hui Zhang
- Zhejiang Agro-Tech Extension and Service Center, Hangzhou 310020, China;
| | - Baogang Lin
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (B.L.); (P.H.)
| | - Pengfei Hao
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (B.L.); (P.H.)
| | - Shuijin Hua
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (B.L.); (P.H.)
- Correspondence:
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11
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Sathee L, Jagadhesan B, Pandesha PH, Barman D, Adavi B S, Nagar S, Krishna GK, Tripathi S, Jha SK, Chinnusamy V. Genome Editing Targets for Improving Nutrient Use Efficiency and Nutrient Stress Adaptation. Front Genet 2022; 13:900897. [PMID: 35774509 PMCID: PMC9237392 DOI: 10.3389/fgene.2022.900897] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 05/17/2022] [Indexed: 11/22/2022] Open
Abstract
In recent years, the development of RNA-guided genome editing (CRISPR-Cas9 technology) has revolutionized plant genome editing. Under nutrient deficiency conditions, different transcription factors and regulatory gene networks work together to maintain nutrient homeostasis. Improvement in the use efficiency of nitrogen (N), phosphorus (P) and potassium (K) is essential to ensure sustainable yield with enhanced quality and tolerance to stresses. This review outlines potential targets suitable for genome editing for understanding and improving nutrient use (NtUE) efficiency and nutrient stress tolerance. The different genome editing strategies for employing crucial negative and positive regulators are also described. Negative regulators of nutrient signalling are the potential targets for genome editing, that may improve nutrient uptake and stress signalling under resource-poor conditions. The promoter engineering by CRISPR/dead (d) Cas9 (dCas9) cytosine and adenine base editing and prime editing is a successful strategy to generate precise changes. CRISPR/dCas9 system also offers the added advantage of exploiting transcriptional activators/repressors for overexpression of genes of interest in a targeted manner. CRISPR activation (CRISPRa) and CRISPR interference (CRISPRi) are variants of CRISPR in which a dCas9 dependent transcription activation or interference is achieved. dCas9-SunTag system can be employed to engineer targeted gene activation and DNA methylation in plants. The development of nutrient use efficient plants through CRISPR-Cas technology will enhance the pace of genetic improvement for nutrient stress tolerance of crops and improve the sustainability of agriculture.
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Affiliation(s)
- Lekshmy Sathee
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - B. Jagadhesan
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Pratheek H. Pandesha
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
- Roy and Diana Vagelos Division of Biology and Biomedical Sciences, Washington University in St. Louis, St. Louis, MO, United States
| | - Dipankar Barman
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Sandeep Adavi B
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Shivani Nagar
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - G. K. Krishna
- Department of Plant Physiology, College of Agriculture, KAU, Thrissur, India
| | - Shailesh Tripathi
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Shailendra K. Jha
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Viswanathan Chinnusamy
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
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12
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Wang F, Tang Z, Wang Y, Fu J, Yang W, Wang S, Wang Y, Bai T, Huang Z, Yin H, Wang Z. Leaf Mutant 7 Encoding Heat Shock Protein OsHSP40 Regulates Leaf Size in Rice. Int J Mol Sci 2022; 23:ijms23084446. [PMID: 35457263 PMCID: PMC9027358 DOI: 10.3390/ijms23084446] [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: 03/22/2022] [Revised: 04/09/2022] [Accepted: 04/12/2022] [Indexed: 02/01/2023] Open
Abstract
Leaf size is an important agronomic trait directly affecting yield in rice, and thus understanding the genes determining leaf size is important in breeding. In this study, one Leaf Mutant 7 (lm7) with small leaf size was isolated using ethyl methane sulphonate (EMS) mutagenesis from the japonica Zhenggeng 1925. MutMap by whole genome resequencing of phenotypic bulks revealed that LM7 is likely located in the 133 kb region on chromosome 7 using F2 population from a cross between lm7 and wild-type (WT) Zhenggeng 1925. The candidate gene encoding heat shock protein OsHSP40 for LM7 was functionally validated. Disruption of this gene in Oshsp40 mutants significantly reduced the leaf size compared with that of WT in rice. Microscopic examination showed that OsHSP40 modulated leaf size via regulating the veins formation and cell size/cell number. Nucleotide diversity analysis indicated that a single nucleotide polymorphism (SNP) variation of C to T in the coding region of OsHSP40 may cause small leaves among rice accessions. Therefore, the natural variation of OsHSP40 contributing to leaf size might be useful for rice breeding.
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Affiliation(s)
- Fuhua Wang
- Institute of Cereal Crop, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (F.W.); (Y.W.); (J.F.); (W.Y.); (S.W.); (Y.W.); (T.B.)
| | - Zhengbin Tang
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China; (Z.T.); (Z.H.)
| | - Ya Wang
- Institute of Cereal Crop, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (F.W.); (Y.W.); (J.F.); (W.Y.); (S.W.); (Y.W.); (T.B.)
| | - Jing Fu
- Institute of Cereal Crop, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (F.W.); (Y.W.); (J.F.); (W.Y.); (S.W.); (Y.W.); (T.B.)
| | - Wenbo Yang
- Institute of Cereal Crop, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (F.W.); (Y.W.); (J.F.); (W.Y.); (S.W.); (Y.W.); (T.B.)
| | - Shengxuan Wang
- Institute of Cereal Crop, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (F.W.); (Y.W.); (J.F.); (W.Y.); (S.W.); (Y.W.); (T.B.)
| | - Yuetao Wang
- Institute of Cereal Crop, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (F.W.); (Y.W.); (J.F.); (W.Y.); (S.W.); (Y.W.); (T.B.)
| | - Tao Bai
- Institute of Cereal Crop, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (F.W.); (Y.W.); (J.F.); (W.Y.); (S.W.); (Y.W.); (T.B.)
| | - Zhibo Huang
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China; (Z.T.); (Z.H.)
| | - Haiqing Yin
- Institute of Cereal Crop, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (F.W.); (Y.W.); (J.F.); (W.Y.); (S.W.); (Y.W.); (T.B.)
- Correspondence: (H.Y.); (Z.W.)
| | - Zhoufei Wang
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China; (Z.T.); (Z.H.)
- Correspondence: (H.Y.); (Z.W.)
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