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Aloryi KD, Okpala NE, Guo H, Karikari B, Amo A, Bello SF, Saini DK, Akaba S, Tian X. Integrated meta-analysis and transcriptomics pinpoint genomic loci and novel candidate genes associated with submergence tolerance in rice. BMC Genomics 2024; 25:338. [PMID: 38575927 PMCID: PMC10993490 DOI: 10.1186/s12864-024-10219-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 03/13/2024] [Indexed: 04/06/2024] Open
Abstract
BACKGROUND Due to rising costs, water shortages, and labour shortages, farmers across the globe now prefer a direct seeding approach. However, submergence stress remains a major bottleneck limiting the success of this approach in rice cultivation. The merger of accumulated rice genetic resources provides an opportunity to detect key genomic loci and candidate genes that influence the flooding tolerance of rice. RESULTS In the present study, a whole-genome meta-analysis was conducted on 120 quantitative trait loci (QTL) obtained from 16 independent QTL studies reported from 2004 to 2023. These QTL were confined to 18 meta-QTL (MQTL), and ten MQTL were successfully validated by independent genome-wide association studies from diverse natural populations. The mean confidence interval (CI) of the identified MQTL was 3.44 times narrower than the mean CI of the initial QTL. Moreover, four core MQTL loci with genetic distance less than 2 cM were obtained. By combining differentially expressed genes (DEG) from two transcriptome datasets with 858 candidate genes identified in the core MQTL regions, we found 38 common differentially expressed candidate genes (DECGs). In silico expression analysis of these DECGs led to the identification of 21 genes with high expression in embryo and coleoptile under submerged conditions. These DECGs encode proteins with known functions involved in submergence tolerance including WRKY, F-box, zinc fingers, glycosyltransferase, protein kinase, cytochrome P450, PP2C, hypoxia-responsive family, and DUF domain. By haplotype analysis, the 21 DECGs demonstrated distinct genetic differentiation and substantial genetic distance mainly between indica and japonica subspecies. Further, the MQTL7.1 was successfully validated using flanked marker S2329 on a set of genotypes with phenotypic variation. CONCLUSION This study provides a new perspective on understanding the genetic basis of submergence tolerance in rice. The identified MQTL and novel candidate genes lay the foundation for marker-assisted breeding/engineering of flooding-tolerant cultivars conducive to direct seeding.
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Grants
- 2023AFA022 Hubei Provincial Natural Science Foundation of China
- 2023AFA022 Hubei Provincial Natural Science Foundation of China
- 2023AFA022 Hubei Provincial Natural Science Foundation of China
- 2023AFA022 Hubei Provincial Natural Science Foundation of China
- 2023AFA022 Hubei Provincial Natural Science Foundation of China
- 2023AFA022 Hubei Provincial Natural Science Foundation of China
- 2023AFA022 Hubei Provincial Natural Science Foundation of China
- 2023AFA022 Hubei Provincial Natural Science Foundation of China
- 2023AFA022 Hubei Provincial Natural Science Foundation of China
- 2020BBB060 Key R&D Project in Hubei Province, China
- 2020BBB060 Key R&D Project in Hubei Province, China
- 2020BBB060 Key R&D Project in Hubei Province, China
- 2020BBB060 Key R&D Project in Hubei Province, China
- 2020BBB060 Key R&D Project in Hubei Province, China
- 2020BBB060 Key R&D Project in Hubei Province, China
- 2020BBB060 Key R&D Project in Hubei Province, China
- 2020BBB060 Key R&D Project in Hubei Province, China
- 2020BBB060 Key R&D Project in Hubei Province, China
- 2018YFD0301306 the National Key Research and Development Program of China
- 2018YFD0301306 the National Key Research and Development Program of China
- 2018YFD0301306 the National Key Research and Development Program of China
- 2018YFD0301306 the National Key Research and Development Program of China
- 2018YFD0301306 the National Key Research and Development Program of China
- 2018YFD0301306 the National Key Research and Development Program of China
- 2018YFD0301306 the National Key Research and Development Program of China
- 2018YFD0301306 the National Key Research and Development Program of China
- 2018YFD0301306 the National Key Research and Development Program of China
- Key R&D Project in Hubei Province, China
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Affiliation(s)
- Kelvin Dodzi Aloryi
- Hubei Collaborative Innovation Centre for Grain Industry, College of Agriculture, Yangtze University, Jingzhou, China
| | - Nnaemeka Emmanuel Okpala
- Hubei Collaborative Innovation Centre for Grain Industry, College of Agriculture, Yangtze University, Jingzhou, China
| | - Hong Guo
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Benjamin Karikari
- Département de phytologie, Université Laval, Québec, QC, Canada
- Department of Agricultural Biotechnology, Faculty of Agriculture, Food and Consumer Sciences, University for Development Studies, Tamale, Ghana
| | - Aduragbemi Amo
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, USA
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX, USA
| | - Semiu Folaniyi Bello
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
| | - Dinesh Kumar Saini
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, USA
| | - Selorm Akaba
- School of Agriculture, University of Cape Coast, Cape Coast, Ghana
| | - Xiaohai Tian
- Hubei Collaborative Innovation Centre for Grain Industry, College of Agriculture, Yangtze University, Jingzhou, China.
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Pandey S. Agronomic potential of plant-specific Gγ proteins. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:337-347. [PMID: 38623166 PMCID: PMC11016034 DOI: 10.1007/s12298-024-01428-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 01/17/2024] [Accepted: 02/28/2024] [Indexed: 04/17/2024]
Abstract
The vascular plant-specific type III Gγ proteins have emerged as important targets for biotechnological applications. These proteins are exemplified by Arabidopsis AGG3, rice Grain Size 3 (GS3), Dense and Erect Panicle 1 (DEP1), and GGC2 and regulate plant stature, seed size, weight and quality, nitrogen use efficiency, and multiple stress responses. These Gγ proteins are an integral component of the plant heterotrimeric G-protein complex and differ from the canonical Gγ proteins due to the presence of a long, cysteine-rich C-terminal region. Most cereal genomes encode three or more of these proteins, which have similar N-terminal Gγ domains but varying lengths of the C-terminal domain. The C-terminal domain is hypothesized to give specificity to the protein function. Intriguingly, many accessions of cultivated cereals have natural deletion of this region in one or more proteins, but the mechanistic details of protein function remain perplexing. Distinct, sometimes contrasting, effects of deletion of the C-terminal region have been reported in different crops or under varying environmental conditions. This review summarizes the known roles of type III Gγ proteins, the possible action mechanisms, and a perspective on what is needed to comprehend their full agronomic potential.
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Affiliation(s)
- Sona Pandey
- Donald Danforth Plant Science Center, 975 N. Warson Road, St. Louis, MO 63132 USA
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3
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Phukan UJ, Jindal S, Laldinsangi C, Singh PK, Longchar B. A microscopic scenario on recovery mechanisms under waterlogging and submergence stress in rice. PLANTA 2023; 259:9. [PMID: 38030751 DOI: 10.1007/s00425-023-04285-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 11/08/2023] [Indexed: 12/01/2023]
Abstract
MAIN CONCLUSION Adaptive traits in rice responding to flooding, a compound stress, are associated with morpho-anatomical and physiological changes which are regulated at the genetic level. Therefore, understanding submergence stress tolerance in rice will help development of adapted cultivars that can help mitigate agricultural losses. Rice is an important dietary component of daily human consumption and is cultivated as a staple crop worldwide. Flooding is a compound stress which imposes significant financial losses to farmers. Flood-affected rainfed rice ecosystems led to the development of various adaptive traits in different cultivars for their optimal growth and survival. Some cultivars can tolerate hypoxia by temporarily arresting elongation and conserving their energy sources, which they utilize to regrow after the stress conditions subside. However, few other cultivars rapidly elongate to escape hypoxia using carbohydrate resources. These contrasting characters are regulated at the genetic level through different quantitative trait loci that contain ERF transcription factors (TFs), Submergence and Snorkels. TFs can simultaneously activate the transcription of various genes involved in stress and development responses. These TFs are of prime importance because the introgressed and near-isogenic lines showed promising results with increased submergence tolerance without affecting yield or quality. However, the entire landscape of submergence tolerance is not entirely depicted, and further exploration in the field is necessary to understand the mechanism in rice completely. Therefore, this review will highlight the significant adaptive traits observed in flooded rice varieties and how they are regulated mechanistically.
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Affiliation(s)
- Ujjal J Phukan
- School of Plant Sciences, University of Arizona, Tucson, AZ, 85721-0036, USA
| | - Sunita Jindal
- Institute of Plant Molecular Biology, Biology Centre, Czech Academy of Sciences, 37005, České Budějovice, Czech Republic
| | - C Laldinsangi
- Department of Life Sciences, Pachhunga University College, Mizoram University, Aizawl, 796001, Mizoram, India
| | - Prashant Kumar Singh
- Department of Biotechnology, Pachhunga University College, Mizoram University, Aizawl, 796001, Mizoram, India
- Institute of Plant Sciences, Agricultural Research Organization (ARO), Volcani Center, 68 HaMacabim Road, 7505101, Rishon Lezion, Israel
| | - Bendangchuchang Longchar
- Department of Life Sciences, Pachhunga University College, Mizoram University, Aizawl, 796001, Mizoram, India.
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Geng S, Lin Z, Xie S, Xiao J, Wang H, Zhao X, Zhou Y, Duan L. Ethylene enhanced waterlogging tolerance by changing root architecture and inducing aerenchyma formation in maize seedlings. JOURNAL OF PLANT PHYSIOLOGY 2023; 287:154042. [PMID: 37348450 DOI: 10.1016/j.jplph.2023.154042] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/11/2023] [Accepted: 06/15/2023] [Indexed: 06/24/2023]
Abstract
Waterlogging negatively affects maize growth and yield. In this study, we found that ethylene played a vital role in plant adaptation to waterlogging. ET promotes better growth in seedlings under waterlogging conditions by altering root architecture and increasing lateral root formation by 42.1%. What's more, plants with high endogenous ethylene levels exhibited reduced sensitivity to waterlogging stress. ET also induced the formation of aerenchyma, a specialized tissue that facilitates gas exchange, in a different pattern compared to aerenchyma formed under waterlogging. Aerenchyma induced by ET was mainly located in the medial cortex of the roots and was not prone to decay. ethylene inhibited root elongation under normal conditions, but this inhibition was not alleviated under waterlogging stress. Upon activation of the ET signaling pathway, the transcription factor EREB90 promoted aerenchyma formation by enhancing the programmed cell death process. Overexpression of EREB90 resulted in increased waterlogging tolerance compared to wild type plants. Our findings suggest that pre-treatment of maize seedlings with ET before waterlogging stress can trigger the programmed cell death process and induce aerenchyma formation, thus improving waterlogging resistance.
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Affiliation(s)
- Shiying Geng
- Engineering Research Center of Plant Growth Regulator, Ministry of Education & College of Agronomy and Biotechnology, China Agricultural University, No. 2 Yuanmingyuan Xi Lu, Haidian District, Beijing, 100193, China; State Key Laboratory of Plant Environmental Resilience, China Agricultural University, No. 2 Yuanmingyuan Xi Lu, Haidian District, Beijing, 100193, China
| | - Ziqing Lin
- Engineering Research Center of Plant Growth Regulator, Ministry of Education & College of Agronomy and Biotechnology, China Agricultural University, No. 2 Yuanmingyuan Xi Lu, Haidian District, Beijing, 100193, China; State Key Laboratory of Plant Environmental Resilience, China Agricultural University, No. 2 Yuanmingyuan Xi Lu, Haidian District, Beijing, 100193, China
| | - Shipeng Xie
- Engineering Research Center of Plant Growth Regulator, Ministry of Education & College of Agronomy and Biotechnology, China Agricultural University, No. 2 Yuanmingyuan Xi Lu, Haidian District, Beijing, 100193, China; State Key Laboratory of Plant Environmental Resilience, China Agricultural University, No. 2 Yuanmingyuan Xi Lu, Haidian District, Beijing, 100193, China
| | - Jinzhong Xiao
- Engineering Research Center of Plant Growth Regulator, Ministry of Education & College of Agronomy and Biotechnology, China Agricultural University, No. 2 Yuanmingyuan Xi Lu, Haidian District, Beijing, 100193, China; State Key Laboratory of Plant Environmental Resilience, China Agricultural University, No. 2 Yuanmingyuan Xi Lu, Haidian District, Beijing, 100193, China
| | - Haiyan Wang
- Engineering Research Center of Plant Growth Regulator, Ministry of Education & College of Agronomy and Biotechnology, China Agricultural University, No. 2 Yuanmingyuan Xi Lu, Haidian District, Beijing, 100193, China
| | - Xi Zhao
- Engineering Research Center of Plant Growth Regulator, Ministry of Education & College of Agronomy and Biotechnology, China Agricultural University, No. 2 Yuanmingyuan Xi Lu, Haidian District, Beijing, 100193, China
| | - Yuyi Zhou
- Engineering Research Center of Plant Growth Regulator, Ministry of Education & College of Agronomy and Biotechnology, China Agricultural University, No. 2 Yuanmingyuan Xi Lu, Haidian District, Beijing, 100193, China; State Key Laboratory of Plant Environmental Resilience, China Agricultural University, No. 2 Yuanmingyuan Xi Lu, Haidian District, Beijing, 100193, China.
| | - Liusheng Duan
- Engineering Research Center of Plant Growth Regulator, Ministry of Education & College of Agronomy and Biotechnology, China Agricultural University, No. 2 Yuanmingyuan Xi Lu, Haidian District, Beijing, 100193, China; State Key Laboratory of Plant Environmental Resilience, China Agricultural University, No. 2 Yuanmingyuan Xi Lu, Haidian District, Beijing, 100193, China; College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
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5
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Aung KM, Oo WH, Maung TZ, Min MH, Somsri A, Nam J, Kim KW, Nawade B, Lee CY, Chu SH, Park YJ. Genomic landscape of the OsTPP7 gene in its haplotype diversity and association with anaerobic germination tolerance in rice. FRONTIERS IN PLANT SCIENCE 2023; 14:1225445. [PMID: 37560030 PMCID: PMC10407808 DOI: 10.3389/fpls.2023.1225445] [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: 05/19/2023] [Accepted: 07/07/2023] [Indexed: 08/11/2023]
Abstract
Early season flooding is a major constraint in direct-seeded rice, as rice genotypes vary in their coleoptile length during anoxia. Trehalose-6-phosphate phosphatase 7 (OsTPP7, Os09g0369400) has been identified as the genetic determinant for anaerobic germination (AG) and coleoptile elongation during flooding. We evaluated the coleoptile length of a diverse rice panel under normal and flooded conditions and investigated the Korean rice collection of 475 accessions to understand its genetic variation, population genetics, evolutionary relationships, and haplotypes in the OsTPP7 gene. Most accessions displayed enhanced flooded coleoptile lengths, with the temperate japonica ecotype exhibiting the highest average values for normal and flooded conditions. Positive Tajima's D values in indica, admixture, and tropical japonica ecotypes suggested balancing selection or population expansion. Haplotype analysis revealed 18 haplotypes, with three in cultivated accessions, 13 in the wild type, and two in both. Hap_1 was found mostly in japonica, while Hap-2 and Hap_3 were more prevalent in indica accessions. Further phenotypic performance of major haplotypes showed significant differences in flooded coleoptile length, flooding tolerance index, and shoot length between Hap_1 and Hap_2/3. These findings could be valuable for future selective rice breeding and the development of efficient haplotype-based breeding strategies for improving flood tolerance.
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Affiliation(s)
- Kyaw Myo Aung
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan, Republic of Korea
| | - Win Htet Oo
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan, Republic of Korea
| | - Thant Zin Maung
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan, Republic of Korea
| | - Myeong-Hyeon Min
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan, Republic of Korea
| | - Aueangporn Somsri
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan, Republic of Korea
| | - Jungrye Nam
- Center for Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan, Republic of Korea
| | - Kyu-Won Kim
- Center for Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan, Republic of Korea
| | - Bhagwat Nawade
- Center for Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan, Republic of Korea
| | - Chang-Yong Lee
- Department of Industrial and Systems Engineering, College of Engineering, Kongju National University, Cheonan, Republic of Korea
| | - Sang-Ho Chu
- Center for Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan, Republic of Korea
| | - Yong-Jin Park
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan, Republic of Korea
- Center for Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan, Republic of Korea
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6
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Naithani S, Mohanty B, Elser J, D’Eustachio P, Jaiswal P. Biocuration of a Transcription Factors Network Involved in Submergence Tolerance during Seed Germination and Coleoptile Elongation in Rice ( Oryza sativa). PLANTS (BASEL, SWITZERLAND) 2023; 12:2146. [PMID: 37299125 PMCID: PMC10255735 DOI: 10.3390/plants12112146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/19/2023] [Accepted: 05/23/2023] [Indexed: 06/12/2023]
Abstract
Modeling biological processes and genetic-regulatory networks using in silico approaches provides a valuable framework for understanding how genes and associated allelic and genotypic differences result in specific traits. Submergence tolerance is a significant agronomic trait in rice; however, the gene-gene interactions linked with this polygenic trait remain largely unknown. In this study, we constructed a network of 57 transcription factors involved in seed germination and coleoptile elongation under submergence. The gene-gene interactions were based on the co-expression profiles of genes and the presence of transcription factor binding sites in the promoter region of target genes. We also incorporated published experimental evidence, wherever available, to support gene-gene, gene-protein, and protein-protein interactions. The co-expression data were obtained by re-analyzing publicly available transcriptome data from rice. Notably, this network includes OSH1, OSH15, OSH71, Sub1B, ERFs, WRKYs, NACs, ZFP36, TCPs, etc., which play key regulatory roles in seed germination, coleoptile elongation and submergence response, and mediate gravitropic signaling by regulating OsLAZY1 and/or IL2. The network of transcription factors was manually biocurated and submitted to the Plant Reactome Knowledgebase to make it publicly accessible. We expect this work will facilitate the re-analysis/re-use of OMICs data and aid genomics research to accelerate crop improvement.
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Affiliation(s)
- Sushma Naithani
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA; (J.E.); (P.J.)
| | - Bijayalaxmi Mohanty
- NUS Environmental Research Institute, National University of Singapore, Singapore 117411, Singapore;
| | - Justin Elser
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA; (J.E.); (P.J.)
| | - Peter D’Eustachio
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA; (J.E.); (P.J.)
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Wang X, Komatsu S. The Role of Phytohormones in Plant Response to Flooding. Int J Mol Sci 2022; 23:6383. [PMID: 35742828 PMCID: PMC9223812 DOI: 10.3390/ijms23126383] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 06/05/2022] [Accepted: 06/06/2022] [Indexed: 02/07/2023] Open
Abstract
Climatic variations influence the morphological, physiological, biological, and biochemical states of plants. Plant responses to abiotic stress include biochemical adjustments, regulation of proteins, molecular mechanisms, and alteration of post-translational modifications, as well as signal transduction. Among the various abiotic stresses, flooding stress adversely affects the growth of plants, including various economically important crops. Biochemical and biological techniques, including proteomic techniques, provide a thorough understanding of the molecular mechanisms during flooding conditions. In particular, plants can cope with flooding conditions by embracing an orchestrated set of morphological adaptations and physiological adjustments that are regulated by an elaborate hormonal signaling network. With the help of these findings, the main objective is to identify plant responses to flooding and utilize that information for the development of flood-tolerant plants. This review provides an insight into the role of phytohormones in plant response mechanisms to flooding stress, as well as different mitigation strategies that can be successfully administered to improve plant growth during stress exposure. Ultimately, this review will expedite marker-assisted genetic enhancement studies in crops for developing high-yield lines or varieties with flood tolerance.
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Affiliation(s)
- Xin Wang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China;
| | - Setsuko Komatsu
- Faculty of Environmental and Information Sciences, Fukui University of Technology, Fukui 910-8505, Japan
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Shin NH, Han JH, Vo KTX, Seo J, Navea IP, Yoo SC, Jeon JS, Chin JH. Development of a Temperate Climate-Adapted indica Multi-stress Tolerant Rice Variety by Pyramiding Quantitative Trait Loci. RICE (NEW YORK, N.Y.) 2022; 15:22. [PMID: 35397732 PMCID: PMC8994804 DOI: 10.1186/s12284-022-00568-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 03/27/2022] [Indexed: 06/14/2023]
Abstract
Successful cultivation of rice (Oryza sativa L.) in many Asian countries requires submergence stress tolerance at the germination and early establishment stages. Two quantitative trait loci, Sub1 (conferring submergence tolerance) and AG1 (conferring anaerobic germination), were recently pyramided into a single genetic background, without compromising any desirable agronomic traits, leading to the development of Ciherang-Sub1 + AG1 (CSA). However, little research has been conducted to enhance plant tolerance to abiotic stress (submergence) and biotic stress (rice blast), which occur in a damp climate following flooding. The BC2F5 breeding line was phenotypically characterized using the AvrPi9 isolate. The biotic and abiotic stress tolerance of selected lines was tested under submergence stress and anaerobic germination conditions, and lines tolerant to each stress condition were identified through phenotypic and gene expression analyses. The Ciherang-Sub1 + AG1 + Pi9 (CSA-Pi9) line showed similar agronomic performance to its recurrent parent, CSA, but had significantly reduced chalkiness in field trials conducted in temperate regions. Unexpectedly, the CSA-Pi9 line also showed salinity tolerance. Thus, the breeding line newly developed in this study, CSA-Pi9, functioned under stress conditions, in which Sub1, AG1, and Pi9 play a role and had superior grain quality traits compared to its recurrent parent in temperate regions. We speculate that CSA-Pi9 will enable the establishment of climate-resilient rice cropping systems, particularly in East Asia.
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Affiliation(s)
- Na-Hyun Shin
- Department of Integrative Biological Sciences and Industry, College of Life Sciences, Sejong University, Seoul, 05006, Korea
| | - Jae-Hyuk Han
- Department of Integrative Biological Sciences and Industry, College of Life Sciences, Sejong University, Seoul, 05006, Korea
| | - Kieu Thi Xuan Vo
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, Gyeonggi-do, 17104, Korea
| | - Jeonghwan Seo
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang, 50463, Korea
- Life and Industry Convergence Research Institute, Pusan National University, Miryang, 50463, Korea
| | - Ian Paul Navea
- Department of Integrative Biological Sciences and Industry, College of Life Sciences, Sejong University, Seoul, 05006, Korea
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, Los Banos, Philippines
| | - Soo-Cheul Yoo
- Department of Plant Life and Environmental Science, Hankyong National University, Anseong, Gyeonggi-do, 17579, Korea
| | - Jong-Seong Jeon
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, Gyeonggi-do, 17104, Korea.
| | - Joong Hyoun Chin
- Department of Integrative Biological Sciences and Industry, College of Life Sciences, Sejong University, Seoul, 05006, Korea.
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Transcriptomics View over the Germination Landscape in Biofortified Rice. Genes (Basel) 2021; 12:genes12122013. [PMID: 34946962 PMCID: PMC8700799 DOI: 10.3390/genes12122013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/14/2021] [Accepted: 12/15/2021] [Indexed: 12/29/2022] Open
Abstract
Hidden hunger, or micronutrient deficiency, is a worldwide problem. Several approaches are employed to alleviate its effects (e.g., promoting diet diversity, use of dietary supplements, chemical fortification of processed food), and among these, biofortification is considered as one of the most cost-effective and highly sustainable. Rice is one of the best targets for biofortification since it is a staple food for almost half of the world’s population as a high-energy source but with low nutritional value. Multiple biofortified rice lines have been produced during the past decades, while few studies also reported modifications in germination behavior (in terms of enhanced or decreased germination percentage or speed). It is important to underline that rapid, uniform germination, and seedling establishment are essential prerequisites for crop productivity. Combining the two traits, biofortified, highly-nutritious seeds with improved germination behavior can be envisaged as a highly-desired target for rice breeding. To this purpose, information gathered from transcriptomics studies can reveal useful insights to unveil the molecular players governing both traits. The present review aims to provide an overview of transcriptomics studies applied at the crossroad between biofortification and seed germination, pointing out potential candidates for trait pyramiding.
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Anwar K, Joshi R, Dhankher OP, Singla-Pareek SL, Pareek A. Elucidating the Response of Crop Plants towards Individual, Combined and Sequentially Occurring Abiotic Stresses. Int J Mol Sci 2021. [PMID: 34204152 DOI: 10.3390/ijms221161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023] Open
Abstract
In nature, plants are exposed to an ever-changing environment with increasing frequencies of multiple abiotic stresses. These abiotic stresses act either in combination or sequentially, thereby driving vegetation dynamics and limiting plant growth and productivity worldwide. Plants' responses against these combined and sequential stresses clearly differ from that triggered by an individual stress. Until now, experimental studies were mainly focused on plant responses to individual stress, but have overlooked the complex stress response generated in plants against combined or sequential abiotic stresses, as well as their interaction with each other. However, recent studies have demonstrated that the combined and sequential abiotic stresses overlap with respect to the central nodes of their interacting signaling pathways, and their impact cannot be modelled by swimming in an individual extreme event. Taken together, deciphering the regulatory networks operative between various abiotic stresses in agronomically important crops will contribute towards designing strategies for the development of plants with tolerance to multiple stress combinations. This review provides a brief overview of the recent developments in the interactive effects of combined and sequentially occurring stresses on crop plants. We believe that this study may improve our understanding of the molecular and physiological mechanisms in untangling the combined stress tolerance in plants, and may also provide a promising venue for agronomists, physiologists, as well as molecular biologists.
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Affiliation(s)
- Khalid Anwar
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Rohit Joshi
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
- Division of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, India
| | - Om Parkash Dhankher
- Stockbridge School of Agriculture, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Sneh L Singla-Pareek
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
- National Agri-Food Biotechnology Institute (NABI), Mohali 140306, India
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Anwar K, Joshi R, Dhankher OP, Singla-Pareek SL, Pareek A. Elucidating the Response of Crop Plants towards Individual, Combined and Sequentially Occurring Abiotic Stresses. Int J Mol Sci 2021; 22:6119. [PMID: 34204152 PMCID: PMC8201344 DOI: 10.3390/ijms22116119] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/30/2021] [Accepted: 05/31/2021] [Indexed: 12/11/2022] Open
Abstract
In nature, plants are exposed to an ever-changing environment with increasing frequencies of multiple abiotic stresses. These abiotic stresses act either in combination or sequentially, thereby driving vegetation dynamics and limiting plant growth and productivity worldwide. Plants' responses against these combined and sequential stresses clearly differ from that triggered by an individual stress. Until now, experimental studies were mainly focused on plant responses to individual stress, but have overlooked the complex stress response generated in plants against combined or sequential abiotic stresses, as well as their interaction with each other. However, recent studies have demonstrated that the combined and sequential abiotic stresses overlap with respect to the central nodes of their interacting signaling pathways, and their impact cannot be modelled by swimming in an individual extreme event. Taken together, deciphering the regulatory networks operative between various abiotic stresses in agronomically important crops will contribute towards designing strategies for the development of plants with tolerance to multiple stress combinations. This review provides a brief overview of the recent developments in the interactive effects of combined and sequentially occurring stresses on crop plants. We believe that this study may improve our understanding of the molecular and physiological mechanisms in untangling the combined stress tolerance in plants, and may also provide a promising venue for agronomists, physiologists, as well as molecular biologists.
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Affiliation(s)
- Khalid Anwar
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India; (K.A.); (R.J.)
| | - Rohit Joshi
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India; (K.A.); (R.J.)
- Division of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, India
| | - Om Parkash Dhankher
- Stockbridge School of Agriculture, University of Massachusetts Amherst, Amherst, MA 01003, USA;
| | - Sneh L. Singla-Pareek
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India;
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India; (K.A.); (R.J.)
- National Agri-Food Biotechnology Institute (NABI), Mohali 140306, India
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Genetic Mapping by Sequencing More Precisely Detects Loci Responsible for Anaerobic Germination Tolerance in Rice. PLANTS 2021; 10:plants10040705. [PMID: 33917499 PMCID: PMC8067528 DOI: 10.3390/plants10040705] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 04/01/2021] [Accepted: 04/04/2021] [Indexed: 11/16/2022]
Abstract
Direct seeded rice (DSR) is a mainstay for planting rice in the Americas, and it is rapidly becoming more popular in Asia. It is essential to develop rice varieties that are suitable for this type of production system. ASD1, a landrace from India, possesses several traits desirable for direct-seeded fields, including tolerance to anaerobic germination (AG). To map the genetic basis of its tolerance, we examined a population of 200 F2:3 families derived from a cross between IR64 and ASD1 using the restriction site-associated DNA sequencing (RAD-seq) technology. This genotyping platform enabled the identification of 1921 single nucleotide polymorphism (SNP) markers to construct a high-resolution genetic linkage map with an average interval of 0.9 cM. Two significant quantitative trait loci (QTLs) were detected on chromosomes 7 and 9, qAG7 and qAG9, with LOD scores of 7.1 and 15.0 and R2 values of 15.1 and 29.4, respectively. Here, we obtained more precise locations of the QTLs than traditional simple sequence repeat and low-density SNP genotyping methods and may help further dissect the genetic factors of these QTLs.
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Schaarschmidt S, Fischer A, Lawas LMF, Alam R, Septiningsih EM, Bailey-Serres J, Jagadish SVK, Huettel B, Hincha DK, Zuther E. Utilizing PacBio Iso-Seq for Novel Transcript and Gene Discovery of Abiotic Stress Responses in Oryza sativa L. Int J Mol Sci 2020; 21:ijms21218148. [PMID: 33142722 PMCID: PMC7663775 DOI: 10.3390/ijms21218148] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 10/20/2020] [Accepted: 10/30/2020] [Indexed: 01/05/2023] Open
Abstract
The wide natural variation present in rice is an important source of genes to facilitate stress tolerance breeding. However, identification of candidate genes from RNA-Seq studies is hampered by the lack of high-quality genome assemblies for the most stress tolerant cultivars. A more targeted solution is the reconstruction of transcriptomes to provide templates to map RNA-seq reads. Here, we sequenced transcriptomes of ten rice cultivars of three subspecies on the PacBio Sequel platform. RNA was isolated from different organs of plants grown under control and abiotic stress conditions in different environments. Reconstructed de novo reference transcriptomes resulted in 37,500 to 54,600 plant-specific high-quality isoforms per cultivar. Isoforms were collapsed to reduce sequence redundancy and evaluated, e.g., for protein completeness (BUSCO). About 40% of all identified transcripts were novel isoforms compared to the Nipponbare reference transcriptome. For the drought/heat tolerant aus cultivar N22, 56 differentially expressed genes in developing seeds were identified at combined heat and drought in the field. The newly generated rice transcriptomes are useful to identify candidate genes for stress tolerance breeding not present in the reference transcriptomes/genomes. In addition, our approach provides a cost-effective alternative to genome sequencing for identification of candidate genes in highly stress tolerant genotypes.
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Affiliation(s)
- Stephanie Schaarschmidt
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany; (A.F.); (L.M.F.L.); (D.K.H.)
- Correspondence: (S.S.); (E.Z.)
| | - Axel Fischer
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany; (A.F.); (L.M.F.L.); (D.K.H.)
| | - Lovely Mae F. Lawas
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany; (A.F.); (L.M.F.L.); (D.K.H.)
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Rejbana Alam
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USA; (R.A.); (J.B.-S.)
| | - Endang M. Septiningsih
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA;
| | - Julia Bailey-Serres
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USA; (R.A.); (J.B.-S.)
| | - S. V. Krishna Jagadish
- International Rice Research Institute, DAPO Box 7777, Metro Manila 1301, Philippines;
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA
| | - Bruno Huettel
- Max Planck Genome Centre Cologne, Carl-von-Linné-Weg 10, 50829 Cologne, Germany;
| | - Dirk K. Hincha
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany; (A.F.); (L.M.F.L.); (D.K.H.)
| | - Ellen Zuther
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany; (A.F.); (L.M.F.L.); (D.K.H.)
- Correspondence: (S.S.); (E.Z.)
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