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Salama EAA, Kambale R, Gnanapanditha Mohan SV, Premnath A, Fathy Yousef A, Moursy ARA, Abdelsalam NR, Abd El Moneim D, Muthurajan R, Manikanda Boopathi N. Empowering rice breeding with NextGen genomics tools for rapid enhancement nitrogen use efficiency. Gene 2024; 927:148715. [PMID: 38909967 DOI: 10.1016/j.gene.2024.148715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 06/17/2024] [Accepted: 06/19/2024] [Indexed: 06/25/2024]
Abstract
As rice has no physiological capacity of fixing nitrogen in the soil, its production had always been reliant on the external application of nitrogen (N) to ensure enhanced productivity. In the light of improving nitrogen use efficiency (NUE) in rice, several advanced agronomic strategies have been proposed. However, the soared increase of the prices of N fertilizers and subsequent environmental downfalls caused by the excessive use of N fertilizers, reinforces the prerequisite adaptation of other sustainable, affordable, and globally acceptable strategies. An appropriate alternative approach would be to develop rice cultivars with better NUE. Conventional breeding techniques, however, have had only sporadic success in improving NUE, and hence, this paper proposes a new schema that employs the wholesome benefits of the recent advancements in omics technologies. The suggested approach promotes multidisciplinary research, since such cooperation enables the synthesis of many viewpoints, approaches, and data that result in a comprehensive understanding of NUE in rice. Such collaboration also encourages innovation that leads to developing rice varieties that use nitrogen more effectively, facilitate smart technology transfer, and promotes the adoption of NUE practices by farmers and stakeholders to minimize ecological impact and contribute to a sustainable agricultural future.
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Affiliation(s)
- Ehab A A Salama
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India; Agricultural Botany Department (Genetics), Faculty of Agriculture Saba Basha, Alexandria University, Alexandria 21531, Egypt.
| | - Rohit Kambale
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India.
| | - Shobhana V Gnanapanditha Mohan
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India.
| | - Ameena Premnath
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India.
| | - Ahmed Fathy Yousef
- Department of Horticulture, College of Agriculture, University of Al-Azhar (Branch Assiut), Assiut 71524, Egypt.
| | - Ali R A Moursy
- Soil and Water Department, Faculty of Agriculture, Sohag University, Sohag 82524, Egypt.
| | - Nader R Abdelsalam
- Agricultural Botany Department (Genetics), Faculty of Agriculture Saba Basha, Alexandria University, Alexandria 21531, Egypt.
| | - Diaa Abd El Moneim
- Department of Plant Production (Genetic Branch), Faculty of Environmental Agricultural Sciences, Arish University, El-Arish 45511, Egypt.
| | - Raveendran Muthurajan
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India.
| | - Narayanan Manikanda Boopathi
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India.
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Sisharmini A, Wihardjaka A, Enggarini W, Apriana A, Hairmansis A, Amirhusin B. Field performance and nitrous oxide emissions of transgenic nitrogen use efficient rice lines cultivated in tropical paddy fields. Transgenic Res 2024:10.1007/s11248-024-00410-z. [PMID: 39266882 DOI: 10.1007/s11248-024-00410-z] [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: 06/20/2024] [Accepted: 08/30/2024] [Indexed: 09/14/2024]
Abstract
Nitrogen (N) fertilizers make up the majority of the input used in rice production, and their excess application leads to significant environmental pollution. Developing rice varieties with improved nitrogen use efficiency (NUE) is essential to maintain the sustainability of rice production. This study aims to evaluate the performance of transgenic Oryza sativa japonica cv. Kitaake expressing the barley (Hordeum vulgare) alanine aminotransferase (HvAlaAT) gene in response to different levels of N fertilizer application under tropical paddy field conditions. Results from this study demonstrate that transgenic nitrogen use efficient Kitaake rice (Kitaake NUE) displays a grain yield increase of up to 41% compared to Kitaake null. Transgenic Kitaake NUE expressing the HvAlaAT gene displays a higher N uptake and achieves a higher nitrogen use efficiency compared to control plants while maintaining lower nitrous oxide (N2O) fluxes. The reduction in N2O emissions in Kitaake NUE compared to Kitaake null ranges from 37.5 to 96.3%. The transgenic Kitaake NUE used in this study has potential as a donor to improve the nitrogen use efficiency of indica rice for better adaptability to tropical conditions.
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Affiliation(s)
- Atmitri Sisharmini
- Research Center for Food Crops, Research Organization for Agriculture and Food, National Research and Innovation Agency, Jl. Raya Bogor Km 46, Cibinong, Bogor, West Java, Indonesia
| | - Anicetus Wihardjaka
- Research Center for Food Crops, Research Organization for Agriculture and Food, National Research and Innovation Agency, Jl. Raya Bogor Km 46, Cibinong, Bogor, West Java, Indonesia
| | - Wening Enggarini
- Research Center for Genetic Engineering, Research Organization for Life Sciences and Environment, National Research and Innovation Agency, Jl. Raya Bogor Km 46, Cibinong, Bogor, West Java, Indonesia
| | - Aniversari Apriana
- Research Center for Food Crops, Research Organization for Agriculture and Food, National Research and Innovation Agency, Jl. Raya Bogor Km 46, Cibinong, Bogor, West Java, Indonesia
| | - Aris Hairmansis
- Research Center for Food Crops, Research Organization for Agriculture and Food, National Research and Innovation Agency, Jl. Raya Bogor Km 46, Cibinong, Bogor, West Java, Indonesia
| | - Bahagiawati Amirhusin
- Research Center for Food Crops, Research Organization for Agriculture and Food, National Research and Innovation Agency, Jl. Raya Bogor Km 46, Cibinong, Bogor, West Java, Indonesia.
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Haelterman L, Louvieaux J, Chiodi C, Bouchet AS, Kupcsik L, Stahl A, Rousseau-Gueutin M, Snowdon R, Laperche A, Nesi N, Hermans C. Genetic control of root morphology in response to nitrogen across rapeseed diversity. PHYSIOLOGIA PLANTARUM 2024; 176:e14315. [PMID: 38693794 DOI: 10.1111/ppl.14315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 04/03/2024] [Accepted: 04/11/2024] [Indexed: 05/03/2024]
Abstract
Rapeseed (Brassica napus L.) is an oil-containing crop of great economic value but with considerable nitrogen requirement. Breeding root systems that efficiently absorb nitrogen from the soil could be a driver to ensure genetic gains for more sustainable rapeseed production. The aim of this study is to identify genomic regions that regulate root morphology in response to nitrate availability. The natural variability offered by 300 inbred lines was screened at two experimental locations. Seedlings grew hydroponically with low or elevated nitrate levels. Fifteen traits related to biomass production and root morphology were measured. On average across the panel, a low nitrate level increased the root-to-shoot biomass ratio and the lateral root length. A large phenotypic variation was observed, along with important heritability values and genotypic effects, but low genotype-by-nitrogen interactions. Genome-wide association study and bulk segregant analysis were used to identify loci regulating phenotypic traits. The first approach nominated 319 SNPs that were combined into 80 QTLs. Three QTLs identified on the A07 and C07 chromosomes were stable across nitrate levels and/or experimental locations. The second approach involved genotyping two groups of individuals from an experimental F2 population created by crossing two accessions with contrasting lateral root lengths. These individuals were found in the tails of the phenotypic distribution. Co-localized QTLs found in both mapping approaches covered a chromosomal region on the A06 chromosome. The QTL regions contained some genes putatively involved in root organogenesis and represent selection targets for redesigning the root morphology of rapeseed.
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Affiliation(s)
- Loïc Haelterman
- Crop Production and Biostimulation Laboratory (CPBL), Brussels Bioengineering School, Université libre de Bruxelles (ULB), Brussels, Belgium
| | - Julien Louvieaux
- Crop Production and Biostimulation Laboratory (CPBL), Brussels Bioengineering School, Université libre de Bruxelles (ULB), Brussels, Belgium
- Laboratory of Applied Plant Ecophysiology, Haute Ecole Provinciale de Hainaut Condorcet, Centre pour l'Agronomie et l'Agro-industrie de la Province de Hainaut (CARAH), Belgium
| | - Claudia Chiodi
- Crop Production and Biostimulation Laboratory (CPBL), Brussels Bioengineering School, Université libre de Bruxelles (ULB), Brussels, Belgium
| | - Anne-Sophie Bouchet
- Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Institut Agro, Université de Rennes, Le Rheu, France
| | - Laszlo Kupcsik
- Crop Production and Biostimulation Laboratory (CPBL), Brussels Bioengineering School, Université libre de Bruxelles (ULB), Brussels, Belgium
| | - Andreas Stahl
- Julius Kühn Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
| | - Mathieu Rousseau-Gueutin
- Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Institut Agro, Université de Rennes, Le Rheu, France
| | - Rod Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Germany
| | - Anne Laperche
- Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Institut Agro, Université de Rennes, Le Rheu, France
| | - Nathalie Nesi
- Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Institut Agro, Université de Rennes, Le Rheu, France
| | - Christian Hermans
- Crop Production and Biostimulation Laboratory (CPBL), Brussels Bioengineering School, Université libre de Bruxelles (ULB), Brussels, Belgium
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Liao Z, Xia X, Zhang Z, Nong B, Guo H, Feng R, Chen C, Xiong F, Qiu Y, Li D, Yang X. Genome-wide association study using specific-locus amplified fragment sequencing identifies new genes influencing nitrogen use efficiency in rice landraces. FRONTIERS IN PLANT SCIENCE 2023; 14:1126254. [PMID: 37521918 PMCID: PMC10375723 DOI: 10.3389/fpls.2023.1126254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 04/28/2023] [Indexed: 08/01/2023]
Abstract
Nitrogen is essential for crop production. It is a critical macronutrient for plant growth and development. However, excessive application of nitrogen fertilizer is not only a waste of resources but also pollutes the environment. An effective approach to solving this problem is to breed rice varieties with high nitrogen use efficiency (NUE). In this study, we performed a genome-wide association study (GWAS) on 419 rice landraces using 208,993 single nucleotide polymorphisms (SNPs). With the mixed linear model (MLM) in the Tassel software, we identified 834 SNPs associated with root surface area (RSA), root length (RL), root branch number (RBN), root number (RN), plant dry weight (PDW), plant height (PH), root volume (RL), plant fresh weight (PFW), root fractal dimension (RFD), number of root nodes (NRN), and average root diameter (ARD), with a significant level of p < 2.39×10-7. In addition, we found 49 SNPs that were correlated with RL, RBN, RN, PDW, PH, PFW, RFD, and NRN using genome-wide efficient mixed-model association (GEMMA), with a significant level of p < 1×10-6. Additionally, the final results for eight traits associated with 193 significant SNPs by using multi-locus random-SNP-effect mixed linear model (mrMLM) model and 272 significant SNPs associated with 11 traits by using IIIVmrMLM. Within the linkage intervals of significantly associated SNP, we identified eight known related genes to NUE in rice, namely, OsAMT2;3, OsGS1, OsNR2, OsNPF7.4, OsPTR9, OsNRT1.1B, OsNRT2.3, and OsNRT2.2. According to the linkage disequilibrium (LD) decay value of this population, there were 75 candidate genes within the 150-kb regions upstream and downstream of the most significantly associated SNP (Chr5_29804690, Chr5_29956584, and Chr10_17540654). These candidate genes included 22 transposon genes, 25 expressed genes, and 28 putative functional genes. The expression levels of these candidate genes were measured by real-time quantitative PCR (RT-qPCR), and the expression levels of LOC_Os05g51700 and LOC_Os05g51710 in C347 were significantly lower than that in C117; the expression levels of LOC_Os05g51740, LOC_Os05g51780, LOC_Os05g51960, LOC_Os05g51970, and LOC_Os10g33210 were significantly higher in C347 than C117. Among them, LOC_Os10g33210 encodes a peptide transporter, and LOC_Os05g51690 encodes a CCT domain protein and responds to NUE in rice. This study identified new loci related to NUE in rice, providing new genetic resources for the molecular breeding of rice landraces with high NUE.
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Affiliation(s)
- Zuyu Liao
- College of Agriculture, Guangxi University, Nanning, China
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Xiuzhong Xia
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Zongqiong Zhang
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Baoxuan Nong
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Hui Guo
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Rui Feng
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Can Chen
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Faqian Xiong
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Yongfu Qiu
- College of Agriculture, Guangxi University, Nanning, China
| | - Danting Li
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Xinghai Yang
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
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Gajardo HA, Gómez-Espinoza O, Boscariol Ferreira P, Carrer H, Bravo LA. The Potential of CRISPR/Cas Technology to Enhance Crop Performance on Adverse Soil Conditions. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091892. [PMID: 37176948 PMCID: PMC10181257 DOI: 10.3390/plants12091892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/22/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023]
Abstract
Worldwide food security is under threat in the actual scenery of global climate change because the major staple food crops are not adapted to hostile climatic and soil conditions. Significant efforts have been performed to maintain the actual yield of crops, using traditional breeding and innovative molecular techniques to assist them. However, additional strategies are necessary to achieve the future food demand. Clustered regularly interspaced short palindromic repeat/CRISPR-associated protein (CRISPR/Cas) technology, as well as its variants, have emerged as alternatives to transgenic plant breeding. This novelty has helped to accelerate the necessary modifications in major crops to confront the impact of abiotic stress on agriculture systems. This review summarizes the current advances in CRISPR/Cas applications in crops to deal with the main hostile soil conditions, such as drought, flooding and waterlogging, salinity, heavy metals, and nutrient deficiencies. In addition, the potential of extremophytes as a reservoir of new molecular mechanisms for abiotic stress tolerance, as well as their orthologue identification and edition in crops, is shown. Moreover, the future challenges and prospects related to CRISPR/Cas technology issues, legal regulations, and customer acceptance will be discussed.
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Affiliation(s)
- Humberto A Gajardo
- Laboratorio de Fisiología y Biología Molecular Vegetal, Instituto de Agroindustria, Departamento de Ciencias Agronómicas y Recursos Naturales, Facultad de Ciencias Agropecuarias y Medioambiente & Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 1145, Chile
| | - Olman Gómez-Espinoza
- Laboratorio de Fisiología y Biología Molecular Vegetal, Instituto de Agroindustria, Departamento de Ciencias Agronómicas y Recursos Naturales, Facultad de Ciencias Agropecuarias y Medioambiente & Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 1145, Chile
- Centro de Investigación en Biotecnología, Escuela de Biología, Instituto Tecnológico de Costa Rica, Cartago 30101, Costa Rica
| | - Pedro Boscariol Ferreira
- Department of Biological Sciences, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Piracicaba 13418-900, Brazil
| | - Helaine Carrer
- Department of Biological Sciences, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Piracicaba 13418-900, Brazil
| | - León A Bravo
- Laboratorio de Fisiología y Biología Molecular Vegetal, Instituto de Agroindustria, Departamento de Ciencias Agronómicas y Recursos Naturales, Facultad de Ciencias Agropecuarias y Medioambiente & Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 1145, Chile
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