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Kong X, Xiong Y, Song X, Wadey S, Yu S, Rao J, Lale A, Lombardi M, Fusi R, Bhosale R, Huang G. Ethylene regulates auxin-mediated root gravitropic machinery and controls root angle in cereal crops. PLANT PHYSIOLOGY 2024; 195:1969-1980. [PMID: 38446735 DOI: 10.1093/plphys/kiae134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 01/18/2024] [Accepted: 02/01/2024] [Indexed: 03/08/2024]
Abstract
Root angle is a critical factor in optimizing the acquisition of essential resources from different soil depths. The regulation of root angle relies on the auxin-mediated root gravitropism machinery. While the influence of ethylene on auxin levels is known, its specific role in governing root gravitropism and angle remains uncertain, particularly when Arabidopsis (Arabidopsis thaliana) core ethylene signaling mutants show no gravitropic defects. Our research, focusing on rice (Oryza sativa L.) and maize (Zea mays), clearly reveals the involvement of ethylene in root angle regulation in cereal crops through the modulation of auxin biosynthesis and the root gravitropism machinery. We elucidated the molecular components by which ethylene exerts its regulatory effect on auxin biosynthesis to control root gravitropism machinery. The ethylene-insensitive mutants ethylene insensitive2 (osein2) and ethylene insensitive like1 (oseil1), exhibited substantially shallower crown root angle compared to the wild type. Gravitropism assays revealed reduced root gravitropic response in these mutants. Hormone profiling analysis confirmed decreased auxin levels in the root tips of the osein2 mutant, and exogenous auxin (NAA) application rescued root gravitropism in both ethylene-insensitive mutants. Additionally, the auxin biosynthetic mutant mao hu zi10 (mhz10)/tryptophan aminotransferase2 (ostar2) showed impaired gravitropic response and shallow crown root angle phenotypes. Similarly, maize ethylene-insensitive mutants (zmein2) exhibited defective gravitropism and root angle phenotypes. In conclusion, our study highlights that ethylene controls the auxin-dependent root gravitropism machinery to regulate root angle in rice and maize, revealing a functional divergence in ethylene signaling between Arabidopsis and cereal crops. These findings contribute to a better understanding of root angle regulation and have implications for improving resource acquisition in agricultural systems.
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Affiliation(s)
- Xiuzhen Kong
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, SJTU-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Shanghai Collaborative Innovation Center of Agri-Seeds/School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yali Xiong
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, SJTU-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaoyun Song
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, SJTU-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Samuel Wadey
- Future Food Beacon and School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK
| | - Suhang Yu
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, SJTU-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jinliang Rao
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, SJTU-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Aneesh Lale
- Future Food Beacon and School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK
| | - Marco Lombardi
- Future Food Beacon and School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK
| | - Riccardo Fusi
- Future Food Beacon and School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK
| | - Rahul Bhosale
- Future Food Beacon and School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru 502324, Hyderabad, India
| | - Guoqiang Huang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, SJTU-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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Li X, Dong J, Zhu W, Zhao J, Zhou L. Progress in the study of functional genes related to direct seeding of rice. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:46. [PMID: 37309311 PMCID: PMC10248684 DOI: 10.1007/s11032-023-01388-y] [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: 09/22/2022] [Accepted: 04/20/2023] [Indexed: 06/14/2023]
Abstract
Rice is a major food crop in the world. Owing to the shortage of rural labor and the development of agricultural mechanization, direct seeding has become the main method of rice cultivation. At present, the main problems faced by direct seeding of rice are low whole seedling rate, serious weeds, and easy lodging of rice in the middle and late stages of growth. Along with the rapid development of functional genomics, the functions of a large number of genes have been confirmed, including seed vigor, low-temperature tolerance germination, low oxygen tolerance growth, early seedling vigor, early root vigor, resistance to lodging, and other functional genes related to the direct seeding of rice. A review of the related functional genes has not yet been reported. In this study, the genes related to direct seeding of rice are summarized to comprehensively understand the genetic basis and mechanism of action in direct seeding of rice and to lay the foundation for further basic theoretical research and breeding application research in direct seeding of rice.
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Affiliation(s)
- Xuezhong Li
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225 Guangdong China
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory, Guangzhou, 510640 China
| | - Jingfang Dong
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory, Guangzhou, 510640 China
| | - Wen Zhu
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225 Guangdong China
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory, Guangzhou, 510640 China
| | - Junliang Zhao
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory, Guangzhou, 510640 China
| | - Lingyan Zhou
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225 Guangdong China
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Shelden MC, Munns R. Crop root system plasticity for improved yields in saline soils. FRONTIERS IN PLANT SCIENCE 2023; 14:1120583. [PMID: 36909408 PMCID: PMC9999379 DOI: 10.3389/fpls.2023.1120583] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
Crop yields must increase to meet the demands of a growing world population. Soil salinization is increasing due to the impacts of climate change, reducing the area of arable land for crop production. Plant root systems are plastic, and their architecture can be modulated to (1) acquire nutrients and water for growth, and (2) respond to hostile soil environments. Saline soils inhibit primary root growth and alter root system architecture (RSA) of crop plants. In this review, we explore how crop root systems respond and adapt to salinity, focusing predominately on the staple cereal crops wheat, maize, rice, and barley, that all play a major role in global food security. Cereal crops are classified as glycophytes (salt-sensitive) however salt-tolerance can differ both between species and within a species. In the past, due to the inherent difficulties associated with visualising and measuring root traits, crop breeding strategies have tended to focus on optimising shoot traits. High-resolution phenotyping techniques now make it possible to visualise and measure root traits in soil systems. A steep, deep and cheap root ideotype has been proposed for water and nitrogen capture. Changes in RSA can be an adaptive strategy to avoid saline soils whilst optimising nutrient and water acquisition. In this review we propose a new model for designing crops with a salt-tolerant root ideotype. The proposed root ideotype would exhibit root plasticity to adapt to saline soils, root anatomical changes to conserve energy and restrict sodium (Na+) uptake, and transport mechanisms to reduce the amount of Na+ transported to leaves. In the future, combining high-resolution root phenotyping with advances in crop genetics will allow us to uncover root traits in complex crop species such as wheat, that can be incorporated into crop breeding programs for yield stability in saline soils.
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Affiliation(s)
- Megan C. Shelden
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA, Australia
| | - Rana Munns
- Australian Research Council (ARC) Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, University of Western Australia, Crawley, WA, Australia
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Verma PK, Verma S, Pandey N. Root system architecture in rice: impacts of genes, phytohormones and root microbiota. 3 Biotech 2022; 12:239. [PMID: 36016841 PMCID: PMC9395555 DOI: 10.1007/s13205-022-03299-9] [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: 03/14/2022] [Accepted: 08/01/2022] [Indexed: 11/28/2022] Open
Abstract
To feed the continuously expanding world's population, new crop varieties have been generated, which significantly contribute to the world's food security. However, the growth of these improved plant varieties relies primarily on synthetic fertilizers, which negatively affect the environment and human health; therefore, continuous improvement is needed for sustainable agriculture. Several plants, including cereal crops, have the adaptive capability to combat adverse environmental changes by altering physiological and molecular mechanisms and modifying their root system to improve nutrient uptake efficiency. These plants operate distinct pathways at various developmental stages to optimally establish their root system. These processes include changes in the expression profile of genes, changes in phytohormone level, and microbiome-induced root system architecture (RSA) modification. Several studies have been performed to understand microbial colonization and their involvement in RSA improvement through changes in phytohormone and transcriptomic levels. This review highlights the impact of genes, phytohormones, and particularly root microbiota in influencing RSA and provides new insights resulting from recent studies on rice root as a model system and summarizes the current knowledge about biochemical and central molecular mechanisms.
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Affiliation(s)
- Pankaj Kumar Verma
- Department of Botany, University of Lucknow, Lucknow, India
- Present Address: French Associates Institute for Agriculture and Biotechnology of Drylands, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Israel
| | - Shikha Verma
- Present Address: French Associates Institute for Agriculture and Biotechnology of Drylands, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Israel
| | - Nalini Pandey
- Department of Botany, University of Lucknow, Lucknow, India
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Hanzawa E, Kitomi Y, Uga Y, Sato T. Quantification of Soil-surface Roots in Seedlings and Mature Rice Plants. Bio Protoc 2022; 12:e4409. [PMID: 35800462 PMCID: PMC9090522 DOI: 10.21769/bioprotoc.4409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 03/21/2022] [Indexed: 12/29/2022] Open
Abstract
Soil-surface roots (SORs) in rice are primary roots that elongate over or near the soil surface. SORs help avoid excessive reduction of stress that occurs in paddy, such as in saline conditions. SORs may also be beneficial for rice growth in phosphorus-deficient paddy fields. Thus, SOR is a useful trait for crop adaptation to certain environmental stresses. To identify a promising genetic material showing SOR, we established methods for evaluating SOR under different growth conditions. We introduced procedures to evaluate the genetic diversity of SOR in various growth stages and conditions: the Cup method allowed us to quantify SOR at the seedling stage, and the Basket method, using a basket buried in a pot or field, is useful in quantifying SOR at the adult stage. These protocols are expected to contribute not only to the evaluation of the genetic diversity of SOR, but also the isolation of related genes in rice.
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Affiliation(s)
- Eiko Hanzawa
- Graduate School of Life Sciences, Tohoku University, 980-8577 Sendai, Miyagi, Japan
| | - Yuka Kitomi
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 305-8518 Tsukuba, Ibaraki, Japan
| | - Yusaku Uga
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 305-8518 Tsukuba, Ibaraki, Japan
| | - Tadashi Sato
- Graduate School of Agricultural Science, Tohoku University, 980-8572 Sendai, Miyagi, Japan
,
*For correspondence: or
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Vinarao R, Proud C, Zhang X, Snell P, Fukai S, Mitchell J. Stable and Novel Quantitative Trait Loci (QTL) Confer Narrow Root Cone Angle in an Aerobic Rice (Oryza sativa L.) Production System. RICE (NEW YORK, N.Y.) 2021; 14:28. [PMID: 33677700 PMCID: PMC7937586 DOI: 10.1186/s12284-021-00471-2] [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: 01/10/2021] [Accepted: 03/01/2021] [Indexed: 05/27/2023]
Abstract
BACKGROUND Aerobic rice production (AP) may be a solution to the looming water crisis by utilising less water compared to traditional flooded culture. As such, development of genotypes with narrow root cone angle (RCA) is considered a key AP adaptation trait as it could lead to deeper rooting and ensure water uptake at depth. Quantitative trait loci (QTL) and genes associated with rooting angle have been identified in rice, but usually in conventional transplanted systems or in upland and drought conditions. This study aimed to identify QTL associated with RCA in AP systems using a recombinant inbred line population derived from IRAT109. RESULTS Four experiments conducted in glasshouse and aerobic field conditions revealed significant genotypic variation existed for RCA in the population. Single and multiple QTL models identified the presence of eight QTL distributed in chromosomes 1, 2, 3, 4, and 11. Combined, these QTL explained 36.7-51.2% of the genotypic variance in RCA present in the population. Two QTL, qRCA1.1 and qRCA1.3, were novel and may be new targets for improvement of RCA. Genotypes with higher number of favourable QTL alleles tended to have narrower RCA. qRCA4 was shown to be a major and stable QTL explaining up to 24.3% of the genotypic variation, and the presence of the target allele resulted in as much as 8.6° narrower RCA. Several genes related to abiotic stress stimulus response were found in the qRCA4 region. CONCLUSION Stable and novel genomic regions associated with RCA have been identified. Genotypes which had combinations of these QTL, resulted in a narrower RCA phenotype. Allele mining, gene cloning, and physiological dissection should aid in understanding the molecular function and mechanisms underlying RCA and these QTL. Ultimately, our work provides an opportunity for breeding programs to develop genotypes with narrow RCA and deep roots for improved adaptation in an AP system for sustainable rice production.
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Affiliation(s)
- Ricky Vinarao
- The University of Queensland, School of Agriculture and Food Sciences, Brisbane, QLD, 4072, Australia
| | - Christopher Proud
- The University of Queensland, School of Agriculture and Food Sciences, Brisbane, QLD, 4072, Australia
| | - Xiaolu Zhang
- The University of Queensland, School of Agriculture and Food Sciences, Brisbane, QLD, 4072, Australia
| | - Peter Snell
- Department of Primary Industries, Yanco Agricultural Institute, Yanco, NSW, 2703, Australia
| | - Shu Fukai
- The University of Queensland, School of Agriculture and Food Sciences, Brisbane, QLD, 4072, Australia
| | - Jaquie Mitchell
- The University of Queensland, School of Agriculture and Food Sciences, Brisbane, QLD, 4072, Australia.
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Zhao J, Yang B, Li W, Sun S, Peng L, Feng D, Li L, Di H, He Y, Wang Z. A genome-wide association study reveals that the glucosyltransferase OsIAGLU regulates root growth in rice. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:1119-1134. [PMID: 33130882 DOI: 10.1093/jxb/eraa512] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 10/26/2020] [Indexed: 05/18/2023]
Abstract
Good root growth in the early post-germination stages is an important trait for direct seeding in rice, but its genetic control is poorly understood. In this study, we examined the genetic architecture of variation in primary root length using a diverse panel of 178 accessions. Four QTLs for root length (qRL3, qRL6, qRL7, and qRL11) were identified using genome-wide association studies. One candidate gene was validated for the major QTL qRL11, namely the glucosyltransferase OsIAGLU. Disruption of this gene in Osiaglu mutants reduced the primary root length and the numbers of lateral and crown roots. The natural allelic variations of OsIAGLU contributing to root growth were identified. Functional analysis revealed that OsIAGLU regulates root growth mainly via modulating multiple hormones in the roots, including levels of auxin, jasmonic acid, abscisic acid, and cytokinin. OsIAGLU also influences the expression of multiple hormone-related genes associated with root growth. The regulation of root growth through multiple hormone pathways by OsIAGLU makes it a potential target for future rice breeding for crop improvement.
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Affiliation(s)
- Jia Zhao
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, People's Republic of China
| | - Bin Yang
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, People's Republic of China
| | - Wenjun Li
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, People's Republic of China
| | - Shan Sun
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, People's Republic of China
| | - Liling Peng
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, People's Republic of China
| | - Defeng Feng
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, People's Republic of China
| | - Li Li
- Huzhou Agricultural Science and Technology Development Center, Huzhou, People's Republic of China
| | - Hong Di
- Northeast Agricultural University, Harbin, People's Republic of China
| | - Yongqi He
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, People's Republic of China
| | - Zhoufei Wang
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, People's Republic of China
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Root angle modifications by the DRO1 homolog improve rice yields in saline paddy fields. Proc Natl Acad Sci U S A 2020; 117:21242-21250. [PMID: 32817523 PMCID: PMC7474696 DOI: 10.1073/pnas.2005911117] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The root system architecture (RSA) of crops can affect their production, particularly in abiotic stress conditions, such as with drought, waterlogging, and salinity. Salinity is a growing problem worldwide that negatively impacts on crop productivity, and it is believed that yields could be improved if RSAs that enabled plants to avoid saline conditions were identified. Here, we have demonstrated, through the cloning and characterization of qSOR1 (quantitative trait locus for SOIL SURFACE ROOTING 1), that a shallower root growth angle (RGA) could enhance rice yields in saline paddies. qSOR1 is negatively regulated by auxin, predominantly expressed in root columella cells, and involved in the gravitropic responses of roots. qSOR1 was found to be a homolog of DRO1 (DEEPER ROOTING 1), which is known to control RGA. CRISPR-Cas9 assays revealed that other DRO1 homologs were also involved in RGA. Introgression lines with combinations of gain-of-function and loss-of-function alleles in qSOR1 and DRO1 demonstrated four different RSAs (ultra-shallow, shallow, intermediate, and deep rooting), suggesting that natural alleles of the DRO1 homologs could be utilized to control RSA variations in rice. In saline paddies, near-isogenic lines carrying the qSOR1 loss-of-function allele had soil-surface roots (SOR) that enabled rice to avoid the reducing stresses of saline soils, resulting in increased yields compared to the parental cultivars without SOR. Our findings suggest that DRO1 homologs are valuable targets for RSA breeding and could lead to improved rice production in environments characterized by abiotic stress.
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Xu P, Yang J, Ma Z, Yu D, Zhou J, Tao D, Li Z. Identification and Validation of Aerobic Adaptation QTLs in Upland Rice. Life (Basel) 2020; 10:life10050065. [PMID: 32423169 PMCID: PMC7281610 DOI: 10.3390/life10050065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/30/2020] [Accepted: 05/13/2020] [Indexed: 12/23/2022] Open
Abstract
The aerobic adaptation of upland rice is considered as the key genetic difference between upland rice and lowland rice. Genetic dissection of the aerobic adaptation is important as the basis for improving drought tolerance and terrestrial adaptation by using the upland rice. We raised BC1-BC3 introgression lines (ILs) in lowland rice Minghui 63 (MH63) background. The QTLs of yield and yield-related traits were detected based on ILs under the aerobic and lowland environments, and then the yield-related QTLs were identified in a backcrossed inbred population of BC4F5 under aerobic condition. We further verified phenotypes of QTL near-isogenic lines. Finally, three QTLs responsible for increasing yield in aerobic environment were detected by multiple locations and generations, which were designated as qAER1, qAER3, and qAER9 (QTL of aerobic adaptation). The qAER1 and qAER9 were fine-mapped. We found that qAER1 and qAER9 controlled plant height and heading date, respectively; while both of them increased yields simultaneously by suitable plant height and heading date without delay in the aerobic environment. The phenotypic differences between lowland rice and upland rice in the aerobic environment further supported the above results. We pyramided the two QTLs as corresponding molecular modules in the irrigated lowland rice MH63 background, and successfully developed a new upland rice variety named as Zhongkexilu 2. This study will lay the foundation for using aerobic adaptation QTLs in rice breeding programs and for further cloning the key genes involved in aerobic adaptation.
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Affiliation(s)
- Peng Xu
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China;
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China; (J.Y.); (Z.M.); (D.Y.)
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650200, China;
| | - Jun Yang
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China; (J.Y.); (Z.M.); (D.Y.)
| | - Zhenbing Ma
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China; (J.Y.); (Z.M.); (D.Y.)
| | - Diqiu Yu
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China; (J.Y.); (Z.M.); (D.Y.)
| | - Jiawu Zhou
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650200, China;
| | - Dayun Tao
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650200, China;
- Correspondence: (D.T.); (Z.L.); Tel.: +86-871-6589-3754 (D.T.); +86-10-6273-1414 (Z.L.)
| | - Zichao Li
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China;
- Correspondence: (D.T.); (Z.L.); Tel.: +86-871-6589-3754 (D.T.); +86-10-6273-1414 (Z.L.)
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10
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Lee JS, Velasco-Punzalan M, Pacleb M, Valdez R, Kretzschmar T, McNally KL, Ismail AM, Cruz PCS, Sackville Hamilton NR, Hay FR. Variation in seed longevity among diverse Indica rice varieties. ANNALS OF BOTANY 2019; 124:447-460. [PMID: 31180503 PMCID: PMC6798842 DOI: 10.1093/aob/mcz093] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 05/24/2019] [Indexed: 05/20/2023]
Abstract
BACKGROUND AND AIMS Understanding variation in seed longevity, especially within closely related germplasm, will lead to better understanding of the molecular basis of this trait, which is particularly important for seed genebanks, but is also relevant to anyone handling seeds. We therefore set out to determine the relative seed longevity of diverse Indica rice accessions through storage experiments. Since antioxidants are purported to play a role in seed storability, the antioxidant activity and phenolic content of caryopses were determined. METHODS Seeds of 299 Indica rice accessions harvested at 31, 38 and 45 d after heading (DAH) between March and May 2015 and differing in harvest moisture content (MC) were subsequently stored at 10.9 % MC and 45 °C. Samples were taken at regular intervals and sown for germination. Germination data were subjected to probit analysis and the resulting parameters that describe the loss of viability during storage were used for genome-wide association (GWA) analysis. KEY RESULTS The seed longevity parameters, Ki [initial viability in normal equivalent deviates (NED)], -σ-1 (σ is the time for viability to fall by 1 NED in experimental storage) and p50 [time for viability to fall to 50 % (0 NED)], varied considerably across the 299 Indica accessions. Seed longevity tended to increase as harvest MC decreased and to decrease as harvest MC increased. Eight major loci associated with seed longevity parameters were identified through GWA analysis. The favourable haplotypes on chromosomes 1, 3, 4, 9 and 11 enhanced p50 by ratios of 0.22-1.86. CONCLUSIONS This is the first study to describe the extent of variation in σ within a species' variety group. A priori candidate genes selected based on rice genome annotation and gene network ontology databases suggested that the mechanisms conferring high seed longevity might be related to DNA repair and transcription, sugar metabolism, reactive oxygen species scavenging and embryonic/root development.
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Affiliation(s)
- Jae-Sung Lee
- International Rice Research Institute, Los Baños, College, Laguna, Philippines
| | | | - Myrish Pacleb
- International Rice Research Institute, Los Baños, College, Laguna, Philippines
| | - Rocel Valdez
- International Rice Research Institute, Los Baños, College, Laguna, Philippines
- Institute of Crop Science, University of the Philippines Los Baños, College, Laguna, Philippines
| | - Tobias Kretzschmar
- International Rice Research Institute, Los Baños, College, Laguna, Philippines
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW, Australia
| | - Kenneth L McNally
- International Rice Research Institute, Los Baños, College, Laguna, Philippines
| | - Abdel M Ismail
- International Rice Research Institute, Los Baños, College, Laguna, Philippines
| | - Pompe C Sta Cruz
- Institute of Crop Science, University of the Philippines Los Baños, College, Laguna, Philippines
| | | | - Fiona R Hay
- International Rice Research Institute, Los Baños, College, Laguna, Philippines
- Department of Agroecology, Aarhus University, Forsøgsvej, Slagelse, Denmark
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Zhao Y, Zhang H, Xu J, Jiang C, Yin Z, Xiong H, Xie J, Wang X, Zhu X, Li Y, Zhao W, Rashid MAR, Li J, Wang W, Fu B, Ye G, Guo Y, Hu Z, Li Z, Li Z. Loci and natural alleles underlying robust roots and adaptive domestication of upland ecotype rice in aerobic conditions. PLoS Genet 2018; 14:e1007521. [PMID: 30096145 PMCID: PMC6086435 DOI: 10.1371/journal.pgen.1007521] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 06/27/2018] [Indexed: 12/21/2022] Open
Abstract
A robust (long and thick) root system is characteristic of upland japonica rice adapted to drought conditions. Using deep sequencing and large scale phenotyping data of 795 rice accessions and an integrated strategy combining results from high resolution mapping by GWAS and linkage mapping, comprehensive analyses of genomic, transcriptomic and haplotype data, we identified large numbers of QTLs affecting rice root length and thickness (RL and RT) and shortlisted relatively few candidate genes for many of the identified small-effect QTLs. Forty four and 97 QTL candidate genes for RL and RT were identified, and five of the RL QTL candidates were validated by T-DNA insertional mutation; all have diverse functions and are involved in root development. This work demonstrated a powerful strategy for highly efficient cloning of moderate- and small-effect QTLs that is difficult using the classical map-based cloning approach. Population analyses of the 795 accessions, 202 additional upland landraces, and 446 wild rice accessions based on random SNPs and SNPs within robust loci suggested that there could be much less diversity in robust-root candidate genes among upland japonica accessions than in other ecotypes. Further analysis of nucleotide diversity and allele frequency in the robust loci among different ecotypes and wild rice accessions showed that almost all alleles could be detected in wild rice, and pyramiding of robust-root alleles could be an important genetic characteristic of upland japonica. Given that geographical distribution of upland landraces, we suggest that during domestication of upland japonica, the strongest pyramiding of robust-root alleles makes it a unique ecotype adapted to aerobic conditions. Asian cultivated rice is well-known for its rich-within-species diversity with two major subspecies, indica and japonica and subpopulation differentiation. A robust (long and thick) root system that is characteristic of upland japonica rice represents a predominant ecotype grown under aerobic and rain-fed conditions. In this study, we identified candidate genes for root length and root thickness, and validated five root length candidates by T-DNA insertional mutations. Further analyses of an Asian cultivated and wild rice population were performed based on random SNPs and SNPs within robust loci. The findings hold promise for application in improving drought resistance and also reveal the adaptive domestication history of upland rice as a unique Asian cultivated rice ecotype.
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Affiliation(s)
- Yan Zhao
- Key Lab of Crop Heterosis and Utilization of Ministry of Education and Beijing Key Lab of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Hongliang Zhang
- Key Lab of Crop Heterosis and Utilization of Ministry of Education and Beijing Key Lab of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Jianlong Xu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Shenzhen Institute for Innovative Breeding, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Conghui Jiang
- Key Lab of Crop Heterosis and Utilization of Ministry of Education and Beijing Key Lab of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Zhigang Yin
- Key Lab of Crop Heterosis and Utilization of Ministry of Education and Beijing Key Lab of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Haiyan Xiong
- Key Lab of Crop Heterosis and Utilization of Ministry of Education and Beijing Key Lab of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Jianyin Xie
- Key Lab of Crop Heterosis and Utilization of Ministry of Education and Beijing Key Lab of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Xueqiang Wang
- Key Lab of Crop Heterosis and Utilization of Ministry of Education and Beijing Key Lab of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Xiaoyang Zhu
- Key Lab of Crop Heterosis and Utilization of Ministry of Education and Beijing Key Lab of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Yang Li
- Key Lab of Crop Heterosis and Utilization of Ministry of Education and Beijing Key Lab of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Weipeng Zhao
- Key Lab of Crop Heterosis and Utilization of Ministry of Education and Beijing Key Lab of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Muhammad Abdul Rehman Rashid
- Key Lab of Crop Heterosis and Utilization of Ministry of Education and Beijing Key Lab of Crop Genetic Improvement, China Agricultural University, Beijing, China
- University of Agriculture Faisalabad, Sub-campus Burewala-Vehari, Pakistan
| | - Jinjie Li
- Key Lab of Crop Heterosis and Utilization of Ministry of Education and Beijing Key Lab of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Wensheng Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Binying Fu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guoyou Ye
- Shenzhen Institute for Innovative Breeding, Chinese Academy of Agricultural Sciences, Shenzhen, China
- International Rice Research Institute, Manila, Philippines
| | - Yan Guo
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Zhiqiang Hu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhikang Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Shenzhen Institute for Innovative Breeding, Chinese Academy of Agricultural Sciences, Shenzhen, China
- * E-mail: (ZhL); (ZL)
| | - Zichao Li
- Key Lab of Crop Heterosis and Utilization of Ministry of Education and Beijing Key Lab of Crop Genetic Improvement, China Agricultural University, Beijing, China
- * E-mail: (ZhL); (ZL)
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12
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E3 ubiquitin ligase SOR1 regulates ethylene response in rice root by modulating stability of Aux/IAA protein. Proc Natl Acad Sci U S A 2018; 115:4513-4518. [PMID: 29632179 PMCID: PMC5924906 DOI: 10.1073/pnas.1719387115] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Auxin signaling components participate in ethylene-mediated inhibition of root elongation. However, the interplay between TIR1/AFB2-auxin-Aux/indole acetic acid (IAA) signaling and ethylene response remains to be elucidated in detail. In this study, we report an E3 ubiquitin ligase soil-surface rooting 1 (SOR1), which targets a noncanonical Aux/IAA protein OsIAA26 for 26S proteasome-mediated degradation. The E3 ligase activity of SOR1 can be repressed by the canonical Aux/IAA protein OsIAA9, which is the target of OsTIR1/AFB2. Our study identifies a potential regulator that modulates auxin-mediated ethylene response at the auxin signaling level. Plant hormones ethylene and auxin synergistically regulate plant root growth and development. Ubiquitin-mediated proteolysis of Aux/IAA transcriptional repressors by the E3 ubiquitin ligase SCFTIR1/AFB triggers a transcription-based auxin signaling. Here we show that rice (Oryza sativa L.) soil-surface rooting 1 (SOR1), which is a RING finger E3 ubiquitin ligase identified from analysis of a rice ethylene-insensitive mutant mhz2/sor1-2, controls root-specific ethylene responses by modulating Aux/IAA protein stability. SOR1 physically interacts with OsIAA26 and OsIAA9, which are atypical and canonical Aux/IAA proteins, respectively. SOR1 targets OsIAA26 for ubiquitin/26S proteasome-mediated degradation, whereas OsIAA9 protects the OsIAA26 protein from degradation by inhibiting the E3 activity of SOR1. Auxin promotes SOR1-dependent degradation of OsIAA26 by facilitating SCFOsTIR1/AFB2-mediated and SOR1-assisted destabilization of OsIAA9 protein. Our study provides a candidate mechanism by which the SOR1-OsIAA26 module acts downstream of the OsTIR1/AFB2-auxin-OsIAA9 signaling to modulate ethylene inhibition of root growth in rice seedlings.
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Bettembourg M, Dal-Soglio M, Bureau C, Vernet A, Dardoux A, Portefaix M, Bes M, Meynard D, Mieulet D, Cayrol B, Perin C, Courtois B, Ma JF, Dievart A. Root cone angle is enlarged in docs1 LRR-RLK mutants in rice. RICE (NEW YORK, N.Y.) 2017; 10:50. [PMID: 29247303 PMCID: PMC5732118 DOI: 10.1186/s12284-017-0190-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 11/30/2017] [Indexed: 05/24/2023]
Abstract
BACKGROUND The DEFECTIVE IN OUTER CELL LAYER SPECIFICATION 1 (DOCS1) gene belongs to the Leucine-Rich Repeat Receptor-Like Kinase (LRR-RLK) subfamily. It has been discovered few years ago in Oryza sativa (rice) in a screen to isolate mutants with defects in sensitivity to aluminum. The c68 (docs1-1) mutant possessed a nonsense mutation in the C-terminal part of the DOCS1 kinase domain. FINDINGS We have generated a new loss-of-function mutation in the DOCS1 gene (docs1-2) using the CRISPR-Cas9 technology. This new loss-of-function mutant and docs1-1 present similar phenotypes suggesting the original docs1-1 was a null allele. Besides the aluminum sensitivity phenotype, both docs1 mutants shared also several root phenotypes described previously: less root hairs and mixed identities of the outer cell layers. Moreover, our new results suggest that DOCS1 could also play a role in root cap development. We hypothesized these docs1 root phenotypes may affect gravity responses. As expected, in seedlings, the early gravitropic response was delayed. Furthermore, at adult stage, the root gravitropic set angle of docs1 mutants was also affected since docs1 mutant plants displayed larger root cone angles. CONCLUSIONS All these observations add new insights into the DOCS1 gene function in gravitropic responses at several stages of plant development.
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Affiliation(s)
- M. Bettembourg
- CIRAD, UMR AGAP, F34398 Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - M. Dal-Soglio
- CIRAD, UMR AGAP, F34398 Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - C. Bureau
- CIRAD, UMR AGAP, F34398 Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - A. Vernet
- CIRAD, UMR AGAP, F34398 Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - A. Dardoux
- CIRAD, UMR AGAP, F34398 Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - M. Portefaix
- CIRAD, UMR AGAP, F34398 Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - M. Bes
- CIRAD, UMR AGAP, F34398 Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - D. Meynard
- CIRAD, UMR AGAP, F34398 Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - D. Mieulet
- CIRAD, UMR AGAP, F34398 Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - B. Cayrol
- CIRAD, UMR AGAP, F34398 Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - C. Perin
- CIRAD, UMR AGAP, F34398 Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - B. Courtois
- CIRAD, UMR AGAP, F34398 Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - J. F. Ma
- Institute of Plant Science and Resources, Okayama University, Chuo 2-20-1, Kurashiki, 710-0046 Japan
| | - A. Dievart
- CIRAD, UMR AGAP, F34398 Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
- Present address: Shanghai Jiao Tong University (SJTU), School of Life Sciences and Biotechnology, Shanghai, 200240 China
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14
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Bettembourg M, Dardou A, Audebert A, Thomas E, Frouin J, Guiderdoni E, Ahmadi N, Perin C, Dievart A, Courtois B. Genome-wide association mapping for root cone angle in rice. RICE (NEW YORK, N.Y.) 2017; 10:45. [PMID: 28971382 PMCID: PMC5624858 DOI: 10.1186/s12284-017-0184-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 09/19/2017] [Indexed: 05/24/2023]
Abstract
BACKGROUND Plant root systems play a major role in anchoring and in water and nutrient uptake from the soil. The root cone angle is an important parameter of the root system architecture because, combined with root depth, it helps to determine the volume of soil explored by the plant. Two genes, DRO1 and SOR1, and several QTLs for root cone angle have been discovered in the last 5 years. RESULTS To find other QTLs linked to root cone angle, a genome-wide association mapping study was conducted on two panels of 162 indica and 169 japonica rice accessions genotyped with two sets of SNP markers (genotyping-by-sequencing set with approximately 16,000 markers and high-density-rice-array set with approximately 300,000 markers). The root cone angle of all accessions was measured using a screen protractor on images taken after 1 month of plant growth in the Rhizoscope phenotyping system. The distribution of the root cone angle in the indica panel was Gaussian, but several accessions of the japonica panel (all the bulus from Indonesia and three temperate japonicas from Nepal or India) appeared as outliers with a very wide root cone angle. The data were submitted to association mapping using a mixed model with control of structure and kinship. A total of 15 QTLs for the indica panel and 40 QTLs for the japonica panel were detected. Genes underlying these QTLs (+/-50 kb from the significant markers) were analyzed. We focused our analysis on auxin-related genes, kinases, and genes involved in root developmental processes and identified 8 particularly interesting genes. CONCLUSIONS The present study identifies new sources of wide root cone angle in rice, proposes ways to bypass some drawbacks of association mapping to further understand the genetics of the trait and identifies candidate genes deserving further investigation.
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Affiliation(s)
| | | | - Alain Audebert
- Cirad, UMR AGAP, F34398 Montpellier Cedex 5, France
- Cirad / ISRA-Ceraas, BP 3320 Thies, Senegal
| | | | | | | | | | | | - Anne Dievart
- Cirad, UMR AGAP, F34398 Montpellier Cedex 5, France
- Shanghai Jiao Tong University (SJTU), School of Life Sciences and Biotechnology, Shanghai, 200240 China
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15
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Ghneim-Herrera T, Selvaraj MG, Meynard D, Fabre D, Peña A, Ben Romdhane W, Ben Saad R, Ogawa S, Rebolledo MC, Ishitani M, Tohme J, Al-Doss A, Guiderdoni E, Hassairi A. Expression of the Aeluropus littoralis AlSAP Gene Enhances Rice Yield under Field Drought at the Reproductive Stage. FRONTIERS IN PLANT SCIENCE 2017; 8:994. [PMID: 28659945 PMCID: PMC5466986 DOI: 10.3389/fpls.2017.00994] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 05/26/2017] [Indexed: 05/03/2023]
Abstract
We evaluated the yields of Oryza sativa L. 'Nipponbare' rice lines expressing a gene encoding an A20/AN1 domain stress-associated protein, AlSAP, from the halophyte grass Aeluropus littoralis under the control of different promoters. Three independent field trials were conducted, with drought imposed at the reproductive stage. In all trials, the two transgenic lines, RN5 and RN6, consistently out-performed non-transgenic (NT) and wild-type (WT) controls, providing 50-90% increases in grain yield (GY). Enhancement of tillering and panicle fertility contributed to this improved GY under drought. In contrast with physiological records collected during previous greenhouse dry-down experiments, where drought was imposed at the early tillering stage, we did not observe significant differences in photosynthetic parameters, leaf water potential, or accumulation of antioxidants in flag leaves of AlSAP-lines subjected to drought at flowering. However, AlSAP expression alleviated leaf rolling and leaf drying induced by drought, resulting in increased accumulation of green biomass. Therefore, the observed enhanced performance of the AlSAP-lines subjected to drought at the reproductive stage can be tentatively ascribed to a primed status of the transgenic plants, resulting from a higher accumulation of biomass during vegetative growth, allowing reserve remobilization and maintenance of productive tillering and grain filling. Under irrigated conditions, the overall performance of AlSAP-lines was comparable with, or even significantly better than, the NT and WT controls. Thus, AlSAP expression inflicted no penalty on rice yields under optimal growth conditions. Our results support the use of AlSAP transgenics to reduce rice GY losses under drought conditions.
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Affiliation(s)
| | | | - Donaldo Meynard
- UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, Centre de Coopération Internationale en Recherche Agronomique pour le DéveloppementMontpellier, France
| | - Denis Fabre
- UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, Centre de Coopération Internationale en Recherche Agronomique pour le DéveloppementMontpellier, France
| | - Alexandra Peña
- Departamento de Ciencias Biológicas, Universidad IcesiCali, Colombia
| | - Walid Ben Romdhane
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud UniversityRiyadh, Saudi Arabia
| | - Rania Ben Saad
- Biotechnology and Plant Improvement Laboratory, Centre of Biotechnology of Sfax, University of SfaxSfax, Tunisia
| | - Satoshi Ogawa
- International Center for Tropical AgricultureCali, Colombia
- Graduate School of Agricultural and Life Science, Department of Global Agricultural Science, The University of TokyoTokyo, Japan
| | | | | | - Joe Tohme
- International Center for Tropical AgricultureCali, Colombia
| | - Abdullah Al-Doss
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud UniversityRiyadh, Saudi Arabia
| | - Emmanuel Guiderdoni
- UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, Centre de Coopération Internationale en Recherche Agronomique pour le DéveloppementMontpellier, France
| | - Afif Hassairi
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud UniversityRiyadh, Saudi Arabia
- Centre of Biotechnology of SfaxSfax, Tunisia
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16
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Tomita A, Sato T, Uga Y, Obara M, Fukuta Y. Genetic variation of root angle distribution in rice ( Oryza sativa L.) seedlings. BREEDING SCIENCE 2017; 67:181-190. [PMID: 28744171 PMCID: PMC5515312 DOI: 10.1270/jsbbs.16185] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 12/29/2016] [Indexed: 05/19/2023]
Abstract
We developed a new method of using seedling trays to evaluate root angle distribution in rice (Oryza sativa. L), and found a wide genetic variation among cultivars. The seedling tray method can be used to evaluate in detail the growth angles of rice crown roots at the seedling stage by allocating nine scores (10° to 90°). Unlike basket methods, it can handle large plant populations over a short growth period (only 14 days). By using the method, we characterized the root angle distributions of 97 accessions into two cluster groups: A and B. The numbers of accessions in group A were limited, and these were categorized as shallow rooting types including soil-surface root. Group B included from shallow to deep rooting types; both included Indica and Japonica Group cultivars, lowland and upland cultivars, and landraces and improved types. No relationship between variation in root vertical angle and total root number was found. The variation in root angle distribution was not related to differentiation between the Japonica and Indica Groups, among ecosystems used for rice cultivation, or among degrees of genetic improvement. The new evaluation method and associated information on genetic variation of rice accessions will be useful in root architecture breeding of rice.
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Affiliation(s)
- Asami Tomita
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Tadashi Sato
- Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi 981-8555, Japan
| | - Yusaku Uga
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8602, Japan
| | - Mitsuhiro Obara
- Biological Resources Division, Japan International Research Center for Agricultural Sciences, Tsukuba, Ibaraki 305-8686, Japan
| | - Yoshimichi Fukuta
- Tropical Agriculture Research Front, Japan International Research Center for Agricultural Sciences, Ishigaki, Okinawa 907-0002, Japan
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17
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Mustafiz A, Kumari S, Karan R. Ascribing Functions to Genes: Journey Towards Genetic Improvement of Rice Via Functional Genomics. Curr Genomics 2016; 17:155-76. [PMID: 27252584 PMCID: PMC4869004 DOI: 10.2174/1389202917666160202215135] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 07/01/2015] [Accepted: 07/06/2015] [Indexed: 11/22/2022] Open
Abstract
Rice, one of the most important cereal crops for mankind, feeds more than half the world population. Rice has been heralded as a model cereal owing to its small genome size, amenability to easy transformation, high synteny to other cereal crops and availability of complete genome sequence. Moreover, sequence wealth in rice is getting more refined and precise due to resequencing efforts. This humungous resource of sequence data has confronted research fraternity with a herculean challenge as well as an excellent opportunity to functionally validate expressed as well as regulatory portions of the genome. This will not only help us in understanding the genetic basis of plant architecture and physiology but would also steer us towards developing improved cultivars. No single technique can achieve such a mammoth task. Functional genomics through its diverse tools viz. loss and gain of function mutants, multifarious omics strategies like transcriptomics, proteomics, metabolomics and phenomics provide us with the necessary handle. A paradigm shift in technological advances in functional genomics strategies has been instrumental in generating considerable amount of information w.r.t functionality of rice genome. We now have several databases and online resources for functionally validated genes but despite that we are far from reaching the desired milestone of functionally characterizing each and every rice gene. There is an urgent need for a common platform, for information already available in rice, and collaborative efforts between researchers in a concerted manner as well as healthy public-private partnership, for genetic improvement of rice crop better able to handle the pressures of climate change and exponentially increasing population.
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Affiliation(s)
- Ananda Mustafiz
- South Asian University, Akbar Bhawan, Chanakyapuri, New Delhi
| | - Sumita Kumari
- Sher-e-Kashmir University of Agriculture Sciences and Technology, Jammu 180009, India
| | - Ratna Karan
- Agronomy Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville - 32611, Florida, USA
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18
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Phung NTP, Mai CD, Hoang GT, Truong HTM, Lavarenne J, Gonin M, Nguyen KL, Ha TT, Do VN, Gantet P, Courtois B. Genome-wide association mapping for root traits in a panel of rice accessions from Vietnam. BMC PLANT BIOLOGY 2016; 16:64. [PMID: 26964867 PMCID: PMC4785749 DOI: 10.1186/s12870-016-0747-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 02/26/2016] [Indexed: 05/05/2023]
Abstract
BACKGROUND Despite recent sequencing efforts, local genetic resources remain underexploited, even though they carry alleles that can bring agronomic benefits. Taking advantage of the recent genotyping with 22,000 single-nucleotide polymorphism markers of a core collection of 180 Vietnamese rice varieties originating from provinces from North to South Vietnam and from different agrosystems characterized by contrasted water regimes, we have performed a genome-wide association study for different root parameters. Roots contribute to water stress avoidance and are a still underexploited target for breeding purpose due to the difficulty to observe them. RESULTS The panel of 180 rice varieties was phenotyped under greenhouse conditions for several root traits in an experimental design with 3 replicates. The phenotyping system consisted of long plastic bags that were filled with sand and supplemented with fertilizer. Root length, root mass in different layers, root thickness, and the number of crown roots, as well as several derived root parameters and shoot traits, were recorded. The results were submitted to association mapping using a mixed model involving structure and kinship to enable the identification of significant associations. The analyses were conducted successively on the whole panel and on its indica (115 accessions) and japonica (64 accessions) subcomponents. The two associations with the highest significance were for root thickness on chromosome 2 and for crown root number on chromosome 11. No common associations were detected between the indica and japonica subpanels, probably because of the polymorphism repartition between the subspecies. Based on orthology with Arabidopsis, the possible candidate genes underlying the quantitative trait loci are reviewed. CONCLUSIONS Some of the major quantitative trait loci we detected through this genome-wide association study contain promising candidate genes encoding regulatory elements of known key regulators of root formation and development.
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Affiliation(s)
- Nhung Thi Phuong Phung
- />Agricultural Genetics Institute, National Key Laboratory for Plant Cell Biotechnology, LMI RICE, 00000 Hanoi, Vietnam
| | - Chung Duc Mai
- />Agricultural Genetics Institute, National Key Laboratory for Plant Cell Biotechnology, LMI RICE, 00000 Hanoi, Vietnam
- />University of Science and Technology of Hanoi, LMI RICE, 00000 Hanoi, Vietnam
| | - Giang Thi Hoang
- />Agricultural Genetics Institute, National Key Laboratory for Plant Cell Biotechnology, LMI RICE, 00000 Hanoi, Vietnam
- />University of Science and Technology of Hanoi, LMI RICE, 00000 Hanoi, Vietnam
| | - Hue Thi Minh Truong
- />Agricultural Genetics Institute, National Key Laboratory for Plant Cell Biotechnology, LMI RICE, 00000 Hanoi, Vietnam
- />University of Science and Technology of Hanoi, LMI RICE, 00000 Hanoi, Vietnam
| | - Jeremy Lavarenne
- />University of Science and Technology of Hanoi, LMI RICE, 00000 Hanoi, Vietnam
- />IRD, LMI RICE, 00000 Hanoi, Vietnam
| | | | - Khanh Le Nguyen
- />University of Science and Technology of Hanoi, LMI RICE, 00000 Hanoi, Vietnam
- />IRD, LMI RICE, 00000 Hanoi, Vietnam
| | - Thuy Thi Ha
- />Agricultural Genetics Institute, National Key Laboratory for Plant Cell Biotechnology, LMI RICE, 00000 Hanoi, Vietnam
| | - Vinh Nang Do
- />Agricultural Genetics Institute, National Key Laboratory for Plant Cell Biotechnology, LMI RICE, 00000 Hanoi, Vietnam
| | - Pascal Gantet
- />University of Science and Technology of Hanoi, LMI RICE, 00000 Hanoi, Vietnam
- />IRD, LMI RICE, 00000 Hanoi, Vietnam
- />Université de Montpellier, UMR DIADE, 34095 Montpellier, France
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