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Daryani P, Amirbakhtiar N, Soorni J, Loni F, Darzi Ramandi H, Shobbar ZS. Uncovering the Genomic Regions Associated with Yield Maintenance in Rice Under Drought Stress Using an Integrated Meta-Analysis Approach. RICE (NEW YORK, N.Y.) 2024; 17:7. [PMID: 38227151 DOI: 10.1186/s12284-024-00684-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 01/03/2024] [Indexed: 01/17/2024]
Abstract
The complex trait of yield is controlled by several quantitative trait loci (QTLs). Given the global water deficit issue, the development of rice varieties suitable for non-flooded cultivation holds significant importance in breeding programs. The powerful approach of Meta-QTL (MQTL) analysis can be used for the genetic dissection of complicated quantitative traits. In the current study, a comprehensive MQTL analysis was conducted to identify consistent QTL regions associated with drought tolerance and yield-related traits under water deficit conditions in rice. In total, 1087 QTLs from 134 rice populations, published between 2000 to 2021, were utilized in the analysis. Distinct MQTL analysis of the relevant traits resulted in the identification of 213 stable MQTLs. The confidence interval (CI) for the detected MQTLs was between 0.12 and 19.7 cM. The average CI of the identified MQTLs (4.68 cM) was 2.74 times narrower compared to the average CI of the initial QTLs. Interestingly, 63 MQTLs coincided with SNP peak positions detected by genome-wide association studies for yield and drought tolerance-associated traits under water deficit conditions in rice. Considering the genes located both in the QTL-overview peaks and the SNP peak positions, 19 novel candidate genes were introduced, which are associated with drought response index, plant height, panicle number, biomass, and grain yield. Moreover, an inclusive MQTL analysis was performed on all the traits to obtain "Breeding MQTLs". This analysis resulted in the identification of 96 MQTLs with a CI ranging from 0.01 to 9.0 cM. The mean CI of the obtained MQTLs (2.33 cM) was 4.66 times less than the mean CI of the original QTLs. Thirteen MQTLs fulfilling the criteria of having more than 10 initial QTLs, CI < 1 cM, and an average phenotypic variance explained greater than 10%, were designated as "Breeding MQTLs". These findings hold promise for assisting breeders in enhancing rice yield under drought stress conditions.
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Affiliation(s)
- Parisa Daryani
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Nazanin Amirbakhtiar
- National Plant Gene Bank of Iran, Seed and Plant Improvement Institute (SPII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Jahad Soorni
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Fatemeh Loni
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Hadi Darzi Ramandi
- Department of Plant Production and Genetics, Faculty of Agriculture, Bu-Ali Sina University, Hamedan, Iran.
| | - Zahra-Sadat Shobbar
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran.
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Cheng Q, Wang P, Wu G, Wang Y, Tan J, Li C, Zhang X, Liu S, Huang S, Huang T, Yang M, He H, Bian J. Coordination of m 6A mRNA methylation and gene transcriptome in rice response to cadmium stress. RICE (NEW YORK, N.Y.) 2021; 14:62. [PMID: 34224034 PMCID: PMC8257850 DOI: 10.1186/s12284-021-00502-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 06/08/2021] [Indexed: 05/19/2023]
Abstract
N6-methyladenosine (m6A) is the most prevalent internal modification present in the mRNAs of all higher eukaryotes. However, the role of the m6A methylomes in rice is still poorly understood. With the development of the MeRIP-seq technique, the in-depth identification of mRNAs with m6A modification has become feasible. A study suggested that m6A modification is crucial for posttranscriptional regulation related to Cd2+-induced malignant transformation, but the association between m6A modification in plants and Cd tolerance has not been reported. We investigated the m6A methylomes in the roots of a cadmium (Cd)-treated group and compared them with the roots in the control (CK) group by m6A sequencing of cv. 9311 and cv. Nipponbare (NIP) plants. The results indicated that Cd leads to an altered modification profile in 3,406 differential m6A peaks in cv. 9311 and 2,065 differential m6A peaks in cv. NIP. KEGG pathway analysis of the genes with differentially modified m6A peaks indicated that the "phenylalanine", "tyrosine and tryptophan biosynthesis", "glycine", "adherens junctions", "glycerophospholipid metabolism" and "threonine metabolism" signalling pathways may be associated with the abnormal root development of cv. 9311 rice due to exposure to Cd. The "arginine", "proline metabolism", "glycerolipid", and "protein processing in endoplasmic reticulum" metabolism pathways were significantly enriched in genes with differentially modified m6A peaks in cv. NIP. Unlike that in Arabidopsis, the m6A-modified nucleotide position on mRNAs (m6A peak) distribution in rice exhibited a preference towards both the stop codon and 3' untranslated regions (3' UTRs). These findings provide a resource for plant RNA epitranscriptomic studies and further increase our knowledge on the function of m6A modification in RNA in plants.
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Affiliation(s)
- Qin Cheng
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, 330045 Nanchang, China
- College of Agronomy, Jiangxi Agricultural University, 330045 Nanchang, China
| | - Peng Wang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, 330045 Nanchang, China
- College of Agronomy, Jiangxi Agricultural University, 330045 Nanchang, China
| | - Guangliang Wu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, 330045 Nanchang, China
- College of Agronomy, Jiangxi Agricultural University, 330045 Nanchang, China
| | - Yanning Wang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, 330045 Nanchang, China
- College of Agronomy, Jiangxi Agricultural University, 330045 Nanchang, China
| | - Jingai Tan
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, 330045 Nanchang, China
- College of Agronomy, Jiangxi Agricultural University, 330045 Nanchang, China
| | - Caijing Li
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, 330045 Nanchang, China
- College of Agronomy, Jiangxi Agricultural University, 330045 Nanchang, China
| | - Xiangyu Zhang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, 330045 Nanchang, China
- College of Agronomy, Jiangxi Agricultural University, 330045 Nanchang, China
| | - Shilei Liu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, 330045 Nanchang, China
- College of Agronomy, Jiangxi Agricultural University, 330045 Nanchang, China
| | - Shiying Huang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, 330045 Nanchang, China
- College of Agronomy, Jiangxi Agricultural University, 330045 Nanchang, China
| | - Tao Huang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, 330045 Nanchang, China
- College of Agronomy, Jiangxi Agricultural University, 330045 Nanchang, China
| | - Mengmeng Yang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, 330045 Nanchang, China
- College of Agronomy, Jiangxi Agricultural University, 330045 Nanchang, China
| | - Haohua He
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, 330045 Nanchang, China
- College of Agronomy, Jiangxi Agricultural University, 330045 Nanchang, China
| | - Jianmin Bian
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, 330045 Nanchang, China
- College of Agronomy, Jiangxi Agricultural University, 330045 Nanchang, China
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Lucob-Agustin N, Sugiura D, Kano-Nakata M, Hasegawa T, Suralta RR, Niones JM, Inari-Ikeda M, Yamauchi A, Inukai Y. The promoted lateral root 1 (plr1) mutation is involved in reduced basal shoot starch accumulation and increased root sugars for enhanced lateral root growth in rice. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 301:110667. [PMID: 33218634 DOI: 10.1016/j.plantsci.2020.110667] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 09/03/2020] [Accepted: 09/05/2020] [Indexed: 06/11/2023]
Abstract
Lateral roots (LRs) are indispensable for plant growth, adaptability and productivity. We previously reported a rice mutant, exhibiting a high density of thick and long LRs (L-type LRs) with long parental roots and herein referred to as promoted lateral root1 (plr1). In this study, we describe that the mutant exhibited decreased basal shoot starch accumulation, suggesting that carbohydrates might regulate the mutant root phenotype. Further analysis revealed that plr1 mutation gene regulated reduced starch accumulation resulting in increased root sugars for the regulation of promoted LR development. This was supported by the exogenous glucose application that promoted L-type LRs. Moreover, nitrogen (N) application was found to reduce basal shoot starch accumulation in both plr1 mutant and wild-type seedlings, which was due to the repressed expression of starch biosynthesis genes. However, unlike the wild-type that responded to N treatment only at seedling stage, the plr1 mutant regulated LR development under low to increasing N levels, both at seedling and higher growth stages. These results suggest that plr1 mutation gene is involved in reduced basal shoot starch accumulation and increased root sugar level for the promotion of L-type LR development, and thus would be very useful in improving rice root architecture.
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Affiliation(s)
- Nonawin Lucob-Agustin
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan.
| | - Daisuke Sugiura
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan.
| | - Mana Kano-Nakata
- International Center for Research and Education in Agriculture, Nagoya University, Nagoya, Aichi 464-8601, Japan.
| | - Tomomi Hasegawa
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan.
| | - Roel R Suralta
- Philippine Rice Research Institute, Central Experiment Station, Science City of Muñoz, Nueva Ecija 3119, Philippines.
| | - Jonathan M Niones
- Philippine Rice Research Institute, Central Experiment Station, Science City of Muñoz, Nueva Ecija 3119, Philippines.
| | - Mayuko Inari-Ikeda
- International Center for Research and Education in Agriculture, Nagoya University, Nagoya, Aichi 464-8601, Japan.
| | - Akira Yamauchi
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan.
| | - Yoshiaki Inukai
- International Center for Research and Education in Agriculture, Nagoya University, Nagoya, Aichi 464-8601, Japan.
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Xu X, Ye J, Yang Y, Zhang M, Xu Q, Feng Y, Yuan X, Yu H, Wang Y, Yang Y, Wei X. Genome-Wide Association Study of Rice Rooting Ability at the Seedling Stage. RICE (NEW YORK, N.Y.) 2020; 13:59. [PMID: 32833069 PMCID: PMC7445215 DOI: 10.1186/s12284-020-00420-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 08/10/2020] [Indexed: 05/15/2023]
Abstract
BACKGROUND Rice rooting ability is a complex agronomical trait that displays heterosis and plays an important role in rice growth and production. Only a few quantitative trait loci (QTLs) have been identified by bi-parental population. More genes or QTLs are required to dissect the genetic architecture of rice rooting ability. RESULTS To characterize the genetic basis for rice rooting ability, we used a natural rice population, genotyped by a 90 K single nucleotide polymorphism (SNP) array, to identify the loci associated with rooting-related traits through the genome-wide association study (GWAS). Population structure analysis divided the natural population into two subgroups: indica and japonica. We measured four traits for evaluating rice rooting ability, namely root growth ability (RGA), maximum root length (MRL), root length (RL), and root number (RN). Using the association study in three panels consisting of one for the full population, one for indica, and one for japonica, 24 SNPs associated with rooting ability-related traits were identified. Through comparison of the relative expression levels and DNA sequences between germplasm with extreme phenotypes, results showed that LOC_Os05g11810 had non-synonymous variations at the coding region, which may cause differences in root number, and that the expression levels of LOC_Os04g09900 and LOC_Os04g10060 are closely associated with root length variation. CONCLUSIONS Through evaluation of the rice rooting ability-related traits and the association mapping, we provided useful information for understanding the genetic basis of rice rooting ability and also identified some candidate genes and molecular markers for rice root breeding.
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Affiliation(s)
- Xin Xu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Junhua Ye
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Yingying Yang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Mengchen Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Qun Xu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Yue Feng
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Xiaoping Yuan
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Hanyong Yu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Yiping Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Yaolong Yang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China.
| | - Xinghua Wei
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China.
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Gluconacetobacter diazotrophicus Changes The Molecular Mechanisms of Root Development in Oryza sativa L. Growing Under Water Stress. Int J Mol Sci 2020; 21:ijms21010333. [PMID: 31947822 PMCID: PMC6981854 DOI: 10.3390/ijms21010333] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 12/31/2019] [Accepted: 01/02/2020] [Indexed: 01/19/2023] Open
Abstract
Background: Inoculation with Gluconacetobacter diazotrophicus has shown to influence root development in red rice plants, and more recently, the induced systemic tolerance (IST) response to drought was also demonstrated. The goal of this study was to evaluate the inoculation effect of G. diazotrophicus strain Pal5 on the amelioration of drought stress and root development in red rice (Oryza sativa L.). Methods: The experimental treatments consist of red rice plants inoculated with and without strain Pal5 in presence and absence of water restriction. Physiological, biochemical, and molecular analyses of plant roots were carried out, along with measurements of growth and biochemical components. Results: The plants showed a positive response to the bacterial inoculation, with root growth promotion and induction of tolerance to drought. An increase in the root area and higher levels of osmoprotectant solutes were observed in roots. Bacterial inoculation increased the drought tolerance and positively regulated certain root development genes against the water deficit in plants. Conclusion: G. diazotrophicus Pal5 strain inoculation favored red rice plants by promoting various root growth and developmental mechanisms against drought stress, enabling root development and improving biochemical composition.
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Meng F, Xiang D, Zhu J, Li Y, Mao C. Molecular Mechanisms of Root Development in Rice. RICE (NEW YORK, N.Y.) 2019; 12:1. [PMID: 30631971 PMCID: PMC6328431 DOI: 10.1186/s12284-018-0262-x] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 12/27/2018] [Indexed: 05/20/2023]
Abstract
Roots are fundamentally important for growth and development, anchoring the plant to its growth substrate, facilitating water and nutrient uptake from the soil, and sensing and responding to environmental signals such as biotic and abiotic stresses. Understanding the molecular mechanisms controlling root architecture is essential for improving nutrient uptake efficiency and crop yields. In this review, we describe the progress being made in the identification of genes and regulatory pathways involved in the development of root systems in rice (Oryza sativa L.), including crown roots, lateral roots, root hairs, and root length. Genes involved in the adaptation of roots to the environmental nutrient status are reviewed, and strategies for further study and agricultural applications are discussed. The growth and development of rice roots are controlled by both genetic factors and environmental cues. Plant hormones, especially auxin and cytokinin, play important roles in root growth and development. Understanding the molecular mechanisms regulating root architecture and response to environmental signals can contribute to the genetic improvement of crop root systems, enhancing their adaptation to stressful environmental conditions.
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Affiliation(s)
- Funing Meng
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Dan Xiang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jianshu Zhu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yong Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Chuanzao Mao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
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Ding W, Lin L, Zhang B, Xiang X, Wu J, Pan Z, Zhu S. OsKASI, a β-ketoacyl-[acyl carrier protein] synthase I, is involved in root development in rice (Oryza sativa L.). PLANTA 2015; 242:203-13. [PMID: 25893869 DOI: 10.1007/s00425-015-2296-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 03/30/2015] [Indexed: 05/08/2023]
Abstract
The involvement of OsKASI in FA synthesis is found to play a critical role in root development of rice. The root system plays important roles in plant nutrient and water acquisition. However, mechanisms of root development and molecular regulation in rice are still poorly understood. Here, we characterized a rice (Oryza sativa L.) mutant with shortened roots due to a defect in cell elongation. Map-based cloning revealed that the mutation occurred in a putative 3-oxoacyl-synthase, an ortholog of β-ketoacyl-[acyl carrier protein] synthase I (KASI) in Arabidopsis, thus designated as OsKASI. OsKASI was found to be ubiquitously expressed in various tissues throughout the plant and OsKASI protein was localized in the plastid. In addition, OsKASI deficiency resulted in reduced fertility and a remarkable change in fatty acid (FA) composition and contents in roots and seeds. Our results demonstrate that involvement of OsKASI in FA synthesis is required for root development in rice.
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Affiliation(s)
- Wona Ding
- College of Science and Technology, Ningbo University, Ningbo, 315211, People's Republic of China
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Meister R, Rajani MS, Ruzicka D, Schachtman DP. Challenges of modifying root traits in crops for agriculture. TRENDS IN PLANT SCIENCE 2014; 19:779-88. [PMID: 25239776 DOI: 10.1016/j.tplants.2014.08.005] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 08/05/2014] [Accepted: 08/21/2014] [Indexed: 05/20/2023]
Abstract
Roots play an essential role in the acquisition of water and minerals from soils. Measuring crop root architecture and assaying for changes in function can be challenging, but examples have emerged showing that modifications to roots result in higher yield and increased stress tolerance. In this review, we focus mainly on the molecular genetic advances that have been made in altering root system architecture and function in crop plants, as well as phenotyping methods. The future for the modification of crop plant roots looks promising based on recent advances, but there are also important challenges ahead.
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Affiliation(s)
- Robert Meister
- Monsanto Company, 700 Chesterfield Parkway, Chesterfield, MO 63017, USA
| | - M S Rajani
- Monsanto Company, 700 Chesterfield Parkway, Chesterfield, MO 63017, USA
| | - Daniel Ruzicka
- Monsanto Company, 700 Chesterfield Parkway, Chesterfield, MO 63017, USA
| | - Daniel P Schachtman
- University of Nebraska Lincoln, Center for Plant Science Innovation, E243 Beadle, Lincoln, NE 68588-0660, USA.
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