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Cai Z, Ruan L, Wei W, He W, Yang H, Chen H, Liang Z, Huang Z, Lan X, Zhang X, Huang R, Zhao C, Li T, He L, Li H. Morphological, anatomical, and transcriptomics analysis reveals the regulatory mechanisms of cassava plant height development. BMC Genomics 2024; 25:699. [PMID: 39020298 PMCID: PMC11253480 DOI: 10.1186/s12864-024-10599-2] [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: 03/21/2024] [Accepted: 07/08/2024] [Indexed: 07/19/2024] Open
Abstract
BACKGROUND Cassava is one of three major potato crops and the sixth most important food crop globally. Improving yield remains a primary aim in cassava breeding. Notably, plant height significantly impacts the yield and quality of crops; however, the mechanisms underlying cassava plant height development are yet to be elucidated. RESULTS In this study, we investigated the mechanisms responsible for cassava plant height development using phenotypic, anatomical, and transcriptomic analyses. Phenotypic and anatomical analysis revealed that compared to the high-stem cassava cultivar, the dwarf-stem cassava cultivar exhibited a significant reduction in plant height and a notable increase in internode tissue xylem area. Meanwhile, physiological analysis demonstrated that the lignin content of dwarf cassava was significantly higher than that of high cassava. Notably, transcriptome analysis of internode tissues identified several differentially expressed genes involved in cell wall synthesis and expansion, plant hormone signal transduction, phenylpropanoid biosynthesis, and flavonoid biosynthesis between the two cassava cultivars. CONCLUSIONS Our findings suggest that internode tissue cell division, secondary wall lignification, and hormone-related gene expression play important roles in cassava plant height development. Ultimately, this study provides new insights into the mechanisms of plant height morphogenesis in cassava and identifies candidate regulatory genes associated with plant height that can serve as valuable genetic resources for future crop dwarfing breeding.
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Affiliation(s)
- Zhaoqin Cai
- Guangxi South Subtropical Agricultural Science Research Institute, Nanning, 530007, PR China
| | - Lixia Ruan
- Guangxi South Subtropical Agricultural Science Research Institute, Nanning, 530007, PR China
| | - Wanling Wei
- Guangxi South Subtropical Agricultural Science Research Institute, Nanning, 530007, PR China
| | - Wen He
- Guangxi South Subtropical Agricultural Science Research Institute, Nanning, 530007, PR China
| | - Haixia Yang
- Guangxi South Subtropical Agricultural Science Research Institute, Nanning, 530007, PR China
| | - Huixian Chen
- Guangxi South Subtropical Agricultural Science Research Institute, Nanning, 530007, PR China
| | - Zhenhua Liang
- Guangxi South Subtropical Agricultural Science Research Institute, Nanning, 530007, PR China
| | - Zhenling Huang
- Guangxi South Subtropical Agricultural Science Research Institute, Nanning, 530007, PR China
| | - Xiu Lan
- Guangxi South Subtropical Agricultural Science Research Institute, Nanning, 530007, PR China
| | - Xiufen Zhang
- Guangxi South Subtropical Agricultural Science Research Institute, Nanning, 530007, PR China
| | - Ruolan Huang
- Guangxi South Subtropical Agricultural Science Research Institute, Nanning, 530007, PR China
| | - Chunhui Zhao
- Guangxi South Subtropical Agricultural Science Research Institute, Nanning, 530007, PR China
| | - Tianyuan Li
- Guangxi South Subtropical Agricultural Science Research Institute, Nanning, 530007, PR China
| | - Longfei He
- National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, 530004, PR China.
| | - Hengrui Li
- Guangxi South Subtropical Agricultural Science Research Institute, Nanning, 530007, PR China.
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Ruan B, Jiang Y, Ma Y, Zhou M, Chen F, Zhang Y, Yu Y, Wu L. Characterization of the ddt1 Mutant in Rice and Its Impact on Plant Height Reduction and Water Use Efficiency. Int J Mol Sci 2024; 25:7629. [PMID: 39062872 PMCID: PMC11277124 DOI: 10.3390/ijms25147629] [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: 06/04/2024] [Revised: 07/05/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024] Open
Abstract
Rice (Oryza sativa L.), a fundamental global staple, nourishes over half of the world's population. The identification of the ddt1 mutant in rice through EMS mutagenesis of the indica cultivar Shuhui527 revealed a dwarf phenotype, characterized by reduced plant height, smaller grain size, and decreased grain weight. Detailed phenotypic analysis and map-based cloning pinpointed the mutation to a single-base transversion in the LOC_Os03g04680 gene, encoding a cytochrome P450 enzyme, which results in a premature termination of the protein. Functional complementation tests confirmed LOC_Os03g04680 as the DDT1 gene responsible for the observed phenotype. We further demonstrated that the ddt1 mutation leads to significant alterations in gibberellic acid (GA) metabolism and signal transduction, evidenced by the differential expression of key GA-related genes such as OsGA20OX2, OsGA20OX3, and SLR1. The mutant also displayed enhanced drought tolerance, as indicated by higher survival rates, reduced water loss, and rapid stomatal closure under drought conditions. This increased drought resistance was linked to the mutant's improved antioxidant capacity, with elevated activities of antioxidant enzymes and higher expression levels of related genes. Our findings suggest that DDT1 plays a crucial role in regulating both plant height and drought stress responses. The potential for using gene editing of DDT1 to mitigate the dwarf phenotype while retaining improved drought resistance offers promising avenues for rice improvement.
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Affiliation(s)
| | | | | | | | | | | | | | - Limin Wu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; (B.R.); (Y.J.); (Y.M.); (M.Z.); (F.C.); (Y.Z.); (Y.Y.)
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Park JR, Jang YH, Kim EG, Hur SS, Kim KM. Quantitative Trait Loci Mapping Identified Candidate Genes Involved in Plant Height Regulation in Rice. Int J Mol Sci 2023; 24:16895. [PMID: 38069217 PMCID: PMC10706376 DOI: 10.3390/ijms242316895] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 11/24/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
Rice plant height is an agricultural trait closely related to biomass, lodging tolerance, and yield. Identifying quantitative trait loci (QTL) regions related to plant height regulation and developing strategies to screen potential candidate genes can improve agricultural traits in rice. In this study, a double haploid population (CNDH), derived by crossing 'Cheongcheong' and 'Nagdong' individuals, was used, and a genetic map was constructed with 222 single-sequence repeat markers. In the RM3482-RM212 region on chromosome 1, qPh1, qPh1-1, qPh1-3, qPh1-5, and qPh1-6 were identified for five consecutive years. The phenotypic variance explained ranged from 9.3% to 13.1%, and the LOD score ranged between 3.6 and 17.6. OsPHq1, a candidate gene related to plant height regulation, was screened in RM3482-RM212. OsPHq1 is an ortholog of gibberellin 20 oxidase 2, and its haplotype was distinguished by nine SNPs. Plants were divided into two groups based on their height, and tall and short plants were distinguished and clustered according to the expression level of OsPHq1. QTLs and candidate genes related to plant height regulation, and thus, biomass regulation, were screened and identified in this study, but the molecular mechanism of the regulation remains poorly known. The information obtained in this study will help develop molecular markers for marker-assisted selection and breeding through rice plant height control.
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Affiliation(s)
- Jae-Ryoung Park
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju 55365, Republic of Korea;
- Coastal Agriculture Research Institute, Kyungpook National University, Daegu 41566, Republic of Korea;
| | - Yoon-Hee Jang
- Coastal Agriculture Research Institute, Kyungpook National University, Daegu 41566, Republic of Korea;
| | - Eun-Gyeong Kim
- Coastal Agriculture Research Institute, Kyungpook National University, Daegu 41566, Republic of Korea;
| | - Sang-Sun Hur
- Division of Health and Welfare, Department of BioFood Science, Joongbu University, Geunmsan 32713, Republic of Korea;
| | - Kyung-Min Kim
- Coastal Agriculture Research Institute, Kyungpook National University, Daegu 41566, Republic of Korea;
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
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4
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Jing L, Wei X, Song Q, Wang F. Research on Estimating Rice Canopy Height and LAI Based on LiDAR Data. SENSORS (BASEL, SWITZERLAND) 2023; 23:8334. [PMID: 37837163 PMCID: PMC10575206 DOI: 10.3390/s23198334] [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: 08/14/2023] [Revised: 10/06/2023] [Accepted: 10/08/2023] [Indexed: 10/15/2023]
Abstract
Rice canopy height and density are directly usable crop phenotypic traits for the direct estimation of crop biomass. Therefore, it is crucial to rapidly and accurately estimate these phenotypic parameters. To achieve the non-destructive detection and estimation of these essential parameters in rice, a platform based on LiDAR (Light Detection and Ranging) point cloud data for rice phenotypic parameter detection was established. Data collection of rice canopy layers was performed across multiple plots. The LiDAR-detected canopy-top point clouds were selected using a method based on the highest percentile, and a surface model of the canopy was calculated. The canopy height estimation was the difference between the ground elevation and the percentile value. To determine the optimal percentile that would define the rice canopy top, testing was conducted incrementally at percentile values from 0.8 to 1, with increments of 0.005. The optimal percentile value was found to be 0.975. The root mean square error (RMSE) between the LiDAR-detected and manually measured canopy heights for each case was calculated. The prediction model based on canopy height (R2 = 0.941, RMSE = 0.019) exhibited a strong correlation with the actual canopy height. Linear regression analysis was conducted between the gap fractions of different plots, and the average rice canopy Leaf Area Index (LAI) was manually detected. Prediction models of canopy LAIs based on ground return counts (R2 = 0.24, RMSE = 0.1) and ground return intensity (R2 = 0.28, RMSE = 0.09) showed strong correlations but had lower correlations with rice canopy LAIs. Regression analysis was performed between LiDAR-detected canopy heights and manually measured rice canopy LAIs. The results thereof indicated that the prediction model based on canopy height (R2 = 0.77, RMSE = 0.03) was more accurate.
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Affiliation(s)
| | - Xinhua Wei
- Key Laboratory of Modern Agricultural Equipment and Technology, Ministry of Education of the People’s Republic of China, Institute of Agricultural Engineering, Jiangsu University, Zhenjiang 212013, China
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Wang H, Ouyang J, Jian W, Li M, Zhong J, Yan X, Gao J, Wang X, Li S. Rice miR5504 regulates plant height by affecting cell proliferation and expansion. PHYSIOLOGIA PLANTARUM 2023; 175:e14023. [PMID: 37882316 DOI: 10.1111/ppl.14023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 08/26/2023] [Accepted: 08/29/2023] [Indexed: 10/27/2023]
Abstract
miRNAs play critical roles in the regulation of plant growth and development by cleaving mRNA or repressing transcription. In our previous study, miR5504 with unknown functions was captured by small RNA sequencing. Here, the function and characters of miR5504 were extensively analyzed using CRISPR/Cas9, overexpression strategy, Northern blot, cytological analysis, and transcriptomics analysis. We found that the dwarf phenotype of mir5504 mutants (mir5504-1 and mir5504-2) appeared on 35-day seedlings and became more apparent at the mature stage. The cytological results showed a substantial decrease in the vascular bundle number, cell number and cell length in the mir5504 mutant compared with NIP. In addition, we found that miR5504 regulated plant height by targeting LOC_Os08g16914. The results of RNA-seq revealed that numerous biological processes were mainly enriched, including DNA-binding transcription factor activity, transferase activity, regulation of transcription, metabolic process, and protein binding. Meanwhile, KEEG analysis showed that numerous proteins were associated with cellular processes and metabolism pathways. Taken together, miR5504 may be involved in the regulation of plant height by affecting cell expansion and division of internode in rice.
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Affiliation(s)
- Huihui Wang
- Key Laboratory of Molecular Biology and Genetic Engineering of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang, China
| | - Jiexiu Ouyang
- Key Laboratory of Molecular Biology and Genetic Engineering of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang, China
| | - Wenjia Jian
- Key Laboratory of Molecular Biology and Genetic Engineering of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang, China
| | - Meng Li
- Key Laboratory of Molecular Biology and Genetic Engineering of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang, China
| | - Jiancong Zhong
- Key Laboratory of Molecular Biology and Genetic Engineering of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang, China
| | - Xin Yan
- Key Laboratory of Molecular Biology and Genetic Engineering of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang, China
| | - Jiadong Gao
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Guangzhou, China
- Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Xin Wang
- Key Laboratory of Molecular Biology and Genetic Engineering of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang, China
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Shaobo Li
- Key Laboratory of Molecular Biology and Genetic Engineering of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang, China
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6
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Jiang X, Hong WJ, Lee SK, Jung KH. Genome-Wide Identification and Analysis of Collar Region-Preferential Genes in Rice. PLANTS (BASEL, SWITZERLAND) 2023; 12:2959. [PMID: 37631170 PMCID: PMC10458737 DOI: 10.3390/plants12162959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/13/2023] [Accepted: 08/13/2023] [Indexed: 08/27/2023]
Abstract
The collar region plays a crucial role in leaf angle formation and plant architecture, which is important for improving crop yield given the challenges of diminishing arable land and changing environmental conditions. To determine collar region-preferential genes (CRPGs) affecting plant architecture and crop yield, we conducted genome-wide transcriptomic analysis. By integrating our RNA sequencing data with public rice anatomical expression data, we identified 657 CRPGs. Verification involved testing six randomly selected CRPGs, all of which exhibited collar-preferential expression. The functional significance of CRPGs was assessed via Gene Ontology enrichment analysis, utilizing MapMan and KEGG, and literature analysis provided additional information for characterized CRPGs. Our findings revealed links between manipulating leaf angle and phytohormone-related pathways and stress responses. Moreover, based on the CRPGs, five transcription factors downstream of the liguleless 1 (LG1) gene were identified. Overall, the identified CRPGs provide potential targets for further research and breeding applications aimed at improving crop productivity by manipulating leaf architecture.
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Affiliation(s)
- Xu Jiang
- Graduate School of Green-Bio Science and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea; (X.J.); (S.-K.L.)
| | - Woo-Jong Hong
- Department of Smart Farm Science, Kyung Hee University, Yongin 17104, Republic of Korea;
| | - Su-Kyoung Lee
- Graduate School of Green-Bio Science and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea; (X.J.); (S.-K.L.)
| | - Ki-Hong Jung
- Graduate School of Green-Bio Science and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea; (X.J.); (S.-K.L.)
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7
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Castanera R, Morales-Díaz N, Gupta S, Purugganan M, Casacuberta JM. Transposons are important contributors to gene expression variability under selection in rice populations. eLife 2023; 12:RP86324. [PMID: 37467142 PMCID: PMC10393045 DOI: 10.7554/elife.86324] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2023] Open
Abstract
Transposable elements (TEs) are an important source of genome variability. Here, we analyze their contribution to gene expression variability in rice by performing a TE insertion polymorphism expression quantitative trait locus mapping using expression data from 208 varieties from the Oryza sativa ssp. indica and O. sativa ssp. japonica subspecies. Our data show that TE insertions are associated with changes of expression of many genes known to be targets of rice domestication and breeding. An important fraction of these insertions were already present in the rice wild ancestors, and have been differentially selected in indica and japonica rice populations. Taken together, our results show that small changes of expression in signal transduction genes induced by TE insertions accompany the domestication and adaptation of rice populations.
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Affiliation(s)
- Raúl Castanera
- Centre for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Cerdanyola del Vallès, Barcelona, Spain
| | - Noemia Morales-Díaz
- Centre for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Cerdanyola del Vallès, Barcelona, Spain
| | - Sonal Gupta
- Center for Genomics and Systems Biology, New York University, New York, United States
| | - Michael Purugganan
- Center for Genomics and Systems Biology, New York University, New York, United States
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates
| | - Josep M Casacuberta
- Centre for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Cerdanyola del Vallès, Barcelona, Spain
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8
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Peng S, Liu Y, Xu Y, Zhao J, Gao P, Liu Q, Yan S, Xiao Y, Zuo SM, Kang H. Genome-Wide Association Study Identifies a Plant-Height-Associated Gene OsPG3 in a Population of Commercial Rice Varieties. Int J Mol Sci 2023; 24:11454. [PMID: 37511211 PMCID: PMC10380248 DOI: 10.3390/ijms241411454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/05/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
Plant height is one of the most crucial components of plant structure. However, due to its complexity, the genetic architecture of rice plant height has not been fully elucidated. In this study, we performed a genome-wide association study (GWAS) to determine rice plant height using 178 commercial rice varieties and identified 37 loci associated with rice plant height (LAPH). Among these loci, in LAPH2, we identified a polygalacturonase gene, OsPG3, which was genetically and functionally associated with rice plant height. The rice plant exhibits a super dwarf phenotype when the knockout of the OsPG3 gene occurs via CRISPR-Cas9 gene-editing technology. RNA-Seq analysis indicated that OsPG3 modulates the expression of genes involved in phytohormone metabolism and cell-wall-biosynthesis pathways. Our findings suggest that OsPG3 plays a vital role in controlling rice plant height by regulating cell wall biosynthesis. Given that rice architecture is one of the most critical phenotypes in rice breeding, OsPG3 has potential in rice's molecular design breeding toward an ideal plant height.
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Affiliation(s)
- Shasha Peng
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yanchen Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yuchen Xu
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jianhua Zhao
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou 225009, China
| | - Peng Gao
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou 225009, China
| | - Qi Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Shuangyong Yan
- Tianjin Key Laboratory of Crop Genetic Breeding, Tianjin Crop Research Institute, Tianjin Academy of Agriculture Sciences, Tianjin 300112, China
| | - Yinghui Xiao
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Shi-Min Zuo
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou 225009, China
| | - Houxiang Kang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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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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Xu Z, Wang R, Kong K, Begum N, Almakas A, Liu J, Li H, Liu B, Zhao T, Zhao T. An APETALA2/ethylene responsive factor transcription factor GmCRF4a regulates plant height and auxin biosynthesis in soybean. FRONTIERS IN PLANT SCIENCE 2022; 13:983650. [PMID: 36147224 PMCID: PMC9485679 DOI: 10.3389/fpls.2022.983650] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/17/2022] [Indexed: 06/01/2023]
Abstract
Plant height is one of the key agronomic traits affecting soybean yield. The cytokinin response factors (CRFs), as a branch of the APETALA2/ethylene responsive factor (AP2/ERF) super gene family, have been reported to play important roles in regulating plant growth and development. However, their functions in soybean remain unknown. This study characterized a soybean CRF gene named GmCRF4a by comparing the performance of the homozygous Gmcrf4a-1 mutant, GmCRF4a overexpression (OX) and co-silencing (CS) lines. Phenotypic analysis showed that overexpression of GmCRF4a resulted in taller hypocotyls and epicotyls, more main stem nodes, and higher plant height. While down-regulation of GmCRF4a conferred shorter hypocotyls and epicotyls, as well as a reduction in plant height. The histological analysis results demonstrated that GmCRF4a promotes epicotyl elongation primarily by increasing cell length. Furthermore, GmCRF4a is required for the expression of GmYUCs genes to elevate endogenous auxin levels, which may subsequently enhance stem elongation. Taken together, these observations describe a novel regulatory mechanism in soybean, and provide the basis for elucidating the function of GmCRF4a in auxin biosynthesis pathway and plant heigh regulation in plants.
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Affiliation(s)
- Zhiyong Xu
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ruikai Wang
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Keke Kong
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Naheeda Begum
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Aisha Almakas
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Jun Liu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongyu Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Bin Liu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tuanjie Zhao
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Tao Zhao
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
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Tong L, Yan M, Zhu M, Yang J, Li Y, Xu M. ZmCCT haplotype H5 improves yield, stalk-rot resistance, and drought tolerance in maize. FRONTIERS IN PLANT SCIENCE 2022; 13:984527. [PMID: 36046586 PMCID: PMC9421135 DOI: 10.3389/fpls.2022.984527] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 07/27/2022] [Indexed: 05/30/2023]
Abstract
The ZmCCT locus underlies both stalk-rot resistance and photoperiod sensitivity in maize (Zea mays L.). We previously introduced nine resistant ZmCCT haplotypes into seven elite but susceptible maize inbred lines (containing the haplotype H1) to generate 63 backcross families. Here, we continued backcrossing, followed by selfing, to develop 63 near-isogenic lines (NILs). We evaluated 22 of these NILs for stalk-rot resistance and flowering time under long-day conditions. Lines harboring the haplotype H5 outperformed the others, steadily reducing disease severity, while showing less photoperiod sensitivity. To demonstrate the value of haplotype H5 for maize production, we selected two pairs of NILs, 83B28 H1 /83B28 H5 and A5302 H1 /A5302 H5 , and generated F1 hybrids with the same genetic backgrounds but different ZmCCT alleles: 83B28 H1 × A5302 H1 , 83B28 H1 × A5302 H5 , 83B28 H5 × A5302 H1 , and 83B28 H5 × A5302 H5 . We performed field trials to investigate yield/yield-related traits, stalk-rot resistance, flowering time, and drought/salt tolerance in these four hybrids. 83B28 H5 × A5302 H1 performed the best, with significantly improved yield, stalk-rot resistance, and drought tolerance compared to the control (83B28 H1 × A5302 H1 ). Therefore, the ZmCCT haplotype H5 has great value for breeding maize varieties with high yield potential, stalk-rot resistance, and drought tolerance.
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Affiliation(s)
- Lixiu Tong
- State Key Laboratory of Plant Physiology and Biochemistry, College of Agronomy and Biotechnology, National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, China
| | - Mingzhu Yan
- State Key Laboratory of Plant Physiology and Biochemistry, College of Agronomy and Biotechnology, National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, China
| | - Mang Zhu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Agronomy and Biotechnology, National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, China
| | - Jie Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Agronomy and Biotechnology, National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, China
- Food Crops Research Institute, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Yipu Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Agronomy and Biotechnology, National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, China
- Agricultural College, Inner Mongolia Agricultural University, Hohhot, China
| | - Mingliang Xu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Agronomy and Biotechnology, National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, China
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12
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Singh L, Dhillon GS, Kaur S, Dhaliwal SK, Kaur A, Malik P, Kumar A, Gill RK, Kaur S. Genome-wide Association Study for Yield and Yield-Related Traits in Diverse Blackgram Panel (Vigna mungo L. Hepper) Reveals Novel Putative Alleles for Future Breeding Programs. Front Genet 2022; 13:849016. [PMID: 35899191 PMCID: PMC9310006 DOI: 10.3389/fgene.2022.849016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 06/20/2022] [Indexed: 11/29/2022] Open
Abstract
Blackgram (Vigna mungo L. Hepper) is an important tropical and sub-tropical short-duration legume that is rich in dietary protein and micronutrients. Producing high-yielding blackgram varieties is hampered by insufficient genetic variability, absence of suitable ideotypes, low harvest index and susceptibility to biotic-abiotic stresses. Seed yield, a complex trait resulting from the expression and interaction of multiple genes, necessitates the evaluation of diverse germplasm for the identification of novel yield contributing traits. Henceforth, a panel of 100 blackgram genotypes was evaluated at two locations (Ludhiana and Gurdaspur) across two seasons (Spring 2019 and Spring 2020) for 14 different yield related traits. A wide range of variability, high broad-sense heritability and a high correlation of grain yield were observed for 12 out of 14 traits studied among all environments. Investigation of population structure in the panel using a set of 4,623 filtered SNPs led to identification of four sub-populations based on ad-hoc delta K and Cross entropy value. Using Farm CPU model and Mixed Linear Model algorithms, a total of 49 significant SNP associations representing 42 QTLs were identified. Allelic effects were found to be statistically significant at 37 out of 42 QTLs and 50 known candidate genes were identified in 24 of QTLs.
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Affiliation(s)
- Lovejit Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | | | - Sarabjit Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Sandeep Kaur Dhaliwal
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Amandeep Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Palvi Malik
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Ashok Kumar
- Regional Research Station, Punjab Agricultural University, Gurdaspur, India
| | - Ranjit Kaur Gill
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Satinder Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
- *Correspondence: Satinder Kaur,
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Mishra M, Rathore RS, Joshi R, Pareek A, Singla-Pareek SL. DTH8 overexpression induces early flowering, boosts yield, and improves stress recovery in rice cv IR64. PHYSIOLOGIA PLANTARUM 2022; 174:e13691. [PMID: 35575899 DOI: 10.1111/ppl.13691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 04/17/2022] [Accepted: 04/27/2022] [Indexed: 06/15/2023]
Abstract
Rice yield and heading date are the two discrete traits controlled by quantitative trait loci (QTLs). Both traits are influenced by the genetic make-up of the plant as well as the environmental factors where it thrives. Drought and salinity adversely affect crop productivity in many parts of the world. Tolerance to these stresses is multigenic and complex in nature. In this study, we have characterized a QTL, DTH8 (days to heading) from Oryza sativa L. cv IR64 that encodes a putative HAP3/NF-YB/CBF subunit of CCAAT-box binding protein (HAP complex). We demonstrate DTH8 to be positively influencing the yield, heading date, and stress tolerance in IR64. DTH8 up-regulates the transcription of RFT1, Hd3a, GHD7, MOC1, and RCN1 in IR64 at the pre-flowering stage and plays a role in early flowering, increased number of tillers, enhanced panicle branching, and improved tolerance towards drought and salinity stress at the reproductive stage. The presence of DTH8 binding elements (CCAAT) in the promoter regions of all of these genes, predicted by in silico analysis of the promoter region, indicates the regulation of their expression by DTH8. In addition, DTH8 overexpressing transgenic lines showed favorable physiological parameters causing less yield penalty under stress than the WT plants. Taken together, DTH8 is a positive regulator of the network of genes related to early flowering/heading, higher yield, as well as salinity and drought stress tolerance, thus, enabling the crops to adapt to a wide range of climatic conditions.
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Affiliation(s)
- Manjari Mishra
- Plant Stress Biology, International Center for Genetic Engineering and Biotechnology, New Delhi, India
| | - Ray Singh Rathore
- Plant Stress Biology, International Center for Genetic Engineering and Biotechnology, New Delhi, India
| | - Rohit Joshi
- Plant Stress Biology, International Center for Genetic Engineering and Biotechnology, New Delhi, India
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Sneh Lata Singla-Pareek
- Plant Stress Biology, International Center for Genetic Engineering and Biotechnology, New Delhi, India
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Javed T, I I, Singhal RK, Shabbir R, Shah AN, Kumar P, Jinger D, Dharmappa PM, Shad MA, Saha D, Anuragi H, Adamski R, Siuta D. Recent Advances in Agronomic and Physio-Molecular Approaches for Improving Nitrogen Use Efficiency in Crop Plants. FRONTIERS IN PLANT SCIENCE 2022; 13:877544. [PMID: 35574130 PMCID: PMC9106419 DOI: 10.3389/fpls.2022.877544] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 03/11/2022] [Indexed: 05/05/2023]
Abstract
The efficiency with which plants use nutrients to create biomass and/or grain is determined by the interaction of environmental and plant intrinsic factors. The major macronutrients, especially nitrogen (N), limit plant growth and development (1.5-2% of dry biomass) and have a direct impact on global food supply, fertilizer demand, and concern with environmental health. In the present time, the global consumption of N fertilizer is nearly 120 MT (million tons), and the N efficiency ranges from 25 to 50% of applied N. The dynamic range of ideal internal N concentrations is extremely large, necessitating stringent management to ensure that its requirements are met across various categories of developmental and environmental situations. Furthermore, approximately 60 percent of arable land is mineral deficient and/or mineral toxic around the world. The use of chemical fertilizers adds to the cost of production for the farmers and also increases environmental pollution. Therefore, the present study focused on the advancement in fertilizer approaches, comprising the use of biochar, zeolite, and customized nano and bio-fertilizers which had shown to be effective in improving nitrogen use efficiency (NUE) with lower soil degradation. Consequently, adopting precision farming, crop modeling, and the use of remote sensing technologies such as chlorophyll meters, leaf color charts, etc. assist in reducing the application of N fertilizer. This study also discussed the role of crucial plant attributes such as root structure architecture in improving the uptake and transport of N efficiency. The crosstalk of N with other soil nutrients plays a crucial role in nutrient homeostasis, which is also discussed thoroughly in this analysis. At the end, this review highlights the more efficient and accurate molecular strategies and techniques such as N transporters, transgenes, and omics, which are opening up intriguing possibilities for the detailed investigation of the molecular components that contribute to nitrogen utilization efficiency, thus expanding our knowledge of plant nutrition for future global food security.
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Affiliation(s)
- Talha Javed
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Department of Agronomy, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Indu I
- Indian Council of Agricultural Research (ICAR)-Indian Grassland and Fodder Research Institute, Jhansi, India
| | - Rajesh Kumar Singhal
- Indian Council of Agricultural Research (ICAR)-Indian Grassland and Fodder Research Institute, Jhansi, India
| | - Rubab Shabbir
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Department of Plant Breeding and Genetics, Seed Science and Technology, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Adnan Noor Shah
- Department of Agricultural Engineering, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, Pakistan
| | - Pawan Kumar
- Indian Council of Agricultural Research (ICAR)-Central Institute for Arid Horticulture, Bikaner, India
| | - Dinesh Jinger
- Research Centre, Indian Council of Agricultural Research (ICAR)-Indian Institute of Soil and Water Conservation, Anand, India
| | - Prathibha M. Dharmappa
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Horticultural Research, Bengaluru, India
| | - Munsif Ali Shad
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene, Hubei Hongshan Laboratory, Wuhan, China
| | - Debanjana Saha
- Centurion University of Technology and Management, Jatni, India
| | - Hirdayesh Anuragi
- Indian Council of Agricultural Research (ICAR)- Central Agroforestry Research Institute, Jhansi, India
| | - Robert Adamski
- Faculty of Process and Environmental Engineering, Łódź University of Technology, Łódź, Poland
| | - Dorota Siuta
- Faculty of Process and Environmental Engineering, Łódź University of Technology, Łódź, Poland
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15
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Phenotypic and Molecular Characterization of Rice Genotypes’ Tolerance to Cold Stress at the Seedling Stage. SUSTAINABILITY 2022. [DOI: 10.3390/su14094871] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Rice plants are affected by low-temperature stress during germination, vegetative growth, and reproductive stages. Thirty-nine rice genotypes including 36 near-isogenic lines (NILs) of BRRI dhan29 were evaluated to investigate the level of cold tolerance under artificially induced low temperature at the seedling stage. Three cold-related traits, leaf discolouration (LD), survivability, and recovery rate, were measured to determine the level of cold tolerance. Highly significant variation among the genotypes was observed for LD, survivability, and recovery rate. Three NILs, IR90688-74-1-1-1-1-1, IR90688-81-1-1-1-1-1, and IR90688-103-1-1-1-1-1, showed tolerance in all three traits, while IR90688-118-1-1-1-1-1 showed cold tolerance with LD and recovery rate. IR90688-92-1-1-1-1-1, IR90688-125-1-1-1-1-1, IR90688-104-1-1-1-1-1, IR90688-124-1-1-1-1-P2, IR90688-15-1-1-1-1-1, and IR90688-27-1-1-1-1-1 showed significantly higher yield coupled with short growth duration and good grain quality. Genetic analysis with SSRs markers revealed that the high-yielding NILs were genetically 67% similar to BRRI dhan28 and possessed cold tolerance at the seedling stage. These cold-tolerant NILs could be used as potential resources to broaden the genetic base of the breeding germplasm to develop high-yielding cold-tolerant rice varieties.
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Detection of QTLs for Plant Height Architecture Traits in Rice (Oryza sativa L.) by Association Mapping and the RSTEP-LRT Method. PLANTS 2022; 11:plants11070999. [PMID: 35406978 PMCID: PMC9002822 DOI: 10.3390/plants11070999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 03/26/2022] [Accepted: 03/30/2022] [Indexed: 11/23/2022]
Abstract
Plant height (PH) and its component traits are critical determinants of lodging resistance and strongly influence yield in rice. The genetic architecture of PH and its component traits were mined in two mapping populations. In the natural population composed of 504 accessions, a total of forty simple sequence repeat (SSR) markers associated with PH and its component traits were detected across two environments via association mapping. Allele RM305-210 bp on chromosome 5 for PH had the largest phenotypic effect value (PEV) (−51.42 cm) with a reducing effect. Allele RM3533-220 bp on chromosome 9 for panicle length and allele RM264-120 bp on chromosome 8 for the length of upper first elongated internode (1IN) showed the highest positive PEV. Among the elongated internodes with negative effects being desirable, the allele RM348-130 bp showed the largest PEV (−7.48 cm) for the length of upper second elongated internode. In the chromosome segment substitution line population consisting of 53 lines, a total of nine QTLs were detected across two environments, with the phenotypic variance explained (PVE) ranging 10.07–28.42%. Among the detected QTLs, q1IN-7 explained the largest PVE (28.42%) for the 1IN, with an additive of 5.31 cm. The favorable allele RM257-125 bp on chromosome 9 for the 1IN increasing was detected in both populations. The favorable alleles provided here could be used to shape PH architecture against lodging.
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Global N 6-Methyladenosine Profiling Revealed the Tissue-Specific Epitranscriptomic Regulation of Rice Responses to Salt Stress. Int J Mol Sci 2022; 23:ijms23042091. [PMID: 35216209 PMCID: PMC8875919 DOI: 10.3390/ijms23042091] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/29/2022] [Accepted: 02/10/2022] [Indexed: 12/13/2022] Open
Abstract
N6-methyladenosine (m6A) methylation represents a new layer of the epitranscriptomic regulation of plant development and growth. However, the effects of m6A on rice responses to environmental stimuli remain unclear. In this study, we performed a methylated-RNA immunoprecipitation sequencing analysis and compared the changes in m6A methylation and gene expression in rice under salt stress conditions. Salt stress significantly increased the m6A methylation in the shoots (p value < 0.05). Additionally, 2537 and 2304 differential m6A sites within 2134 and 1997 genes were identified in the shoots and roots, respectively, under salt stress and control conditions. These differential m6A sites were largely regulated in a tissue-specific manner. A unique set of genes encoding transcription factors, antioxidants, and auxin-responsive proteins had increased or decreased m6A methylation levels only in the shoots or roots under salt stress, implying m6A may mediate salt tolerance by regulating transcription, ROS homeostasis, and auxin signaling in a tissue-specific manner. Integrating analyses of m6A modifications and gene expression changes revealed that m6A changes regulate the expression of genes controlling plant growth, stress responses, and ion transport under saline conditions. These findings may help clarify the regulatory effects of m6A modifications on rice salt tolerance.
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18
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A New RING Finger Protein, PLANT ARCHITECTURE and GRAIN NUMBER 1, Affects Plant Architecture and Grain Yield in Rice. Int J Mol Sci 2022; 23:ijms23020824. [PMID: 35055011 PMCID: PMC8777624 DOI: 10.3390/ijms23020824] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/09/2022] [Accepted: 01/10/2022] [Indexed: 12/21/2022] Open
Abstract
Developing methods for increasing the biomass and improving the plant architecture is important for crop improvement. We herein describe a gene belonging to the RING_Ubox (RING (Really Interesting New Gene) finger domain and U-box domain) superfamily, PLANT ARCHITECTURE and GRAIN NUMBER 1 (PAGN1), which regulates the number of grains per panicle, the plant height, and the number of tillers. We used the CRISPR/Cas9 system to introduce loss-of-function mutations to OsPAGN1. Compared with the control plants, the resulting pagn1 mutant plants had a higher grain yield because of increases in the plant height and in the number of tillers and grains per panicle. Thus, OsPAGN1 may be useful for the genetic improvement of plant architecture and yield. An examination of evolutionary relationships revealed that OsPAGN1 is highly conserved in rice. We demonstrated that OsPAGN1 can interact directly with OsCNR10 (CELL NUMBER REGULATOR10), which negatively regulates the number of rice grains per panicle. A transcriptome analysis indicated that silencing OsPAGN1 affects the levels of active cytokinins in rice. Therefore, our findings have clarified the OsPAGN1 functions related to rice growth and grain development.
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Management for Paddy, Oil Palm, and Pineapple Plantations in Malaysia: Current Status and Reviews. JOURNAL OF APPLIED SCIENCE & PROCESS ENGINEERING 2021. [DOI: 10.33736/jaspe.3438.2021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Heavy rainfall causes a loss of fertiliser to the environment, and it leads to environmental issues such as eutrophication. Replenishment of fertiliser to replace the loss imposes a financial impact since frequent applications are costly and labour intensive. Therefore, investigations on proper fertiliser application in maintaining good soil pH, improving plant growth, and increasing crop yield from various plantations across Malaysia are of paramount importance. Meanwhile, limited agricultural-related studies about crop management in Malaysia have been done. This study presents a state-of-the-art review of Malaysia’s paddy, oil palm, pineapple plantations, and the existing nutrient management and fertilisation practices throughout the crop cycle. A systematic study of the existing crop management in terms of farming practices, nutrient management, and fertiliser application on the plantations of paddy, oil palm, and pineapple in Malaysia was carried out. Industry overviews for these three crop types based on past situations and future directions are also included. Recommendations on how to better manage these plantations are also outlined to promote a better understanding of the past, current, and future direction of the agricultural activities and management for principal edible crops like paddy, oil palm, and pineapple in Malaysia.
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Saini DK, Chopra Y, Pal N, Chahal A, Srivastava P, Gupta PK. Meta-QTLs, ortho-MQTLs and candidate genes for nitrogen use efficiency and root system architecture in bread wheat ( Triticum aestivum L.). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:2245-2267. [PMID: 34744364 PMCID: PMC8526679 DOI: 10.1007/s12298-021-01085-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 09/26/2021] [Accepted: 09/27/2021] [Indexed: 05/04/2023]
Abstract
In wheat, meta-QTLs (MQTLs), ortho-MQTLs, and candidate genes (CGs) were identified for nitrogen use efficiency and root system architecture. For this purpose, 1788 QTLs were available from 24 studies published during 2006-2020. Of these, 1098 QTLs were projected onto the consensus map resulting in 118 MQTLs. The average confidence interval (CI) of MQTLs was reduced up to 8.56 folds in comparison to the average CI of QTLs. Of the 118 MQTLs, 112 were anchored to the physical map of the wheat reference genome. The physical interval of MQTLs ranged from 0.02 to 666.18 Mb with a mean of 94.36 Mb. Eighty-eight of these 112 MQTLs were verified by marker-trait associations (MTAs) identified in published genome-wide association studies (GWAS); the MQTLs that were verified using GWAS also included 9 most robust MQTLs, which are particularly useful for breeders; we call them 'Breeder's QTLs'. Some selected wheat MQTLs were further utilized for the identification of ortho-MQTLs for wheat and maize; 9 such ortho-MQTLs were available. As many as 1991 candidate genes (CGs) were also detected, which included 930 CGs with an expression level of > 2 transcripts per million in relevant organs/tissues. Among the CGs, 97 CGs with functions previously reported as important for the traits under study were selected. Based on homology analysis and expression patterns, 49 orthologues of 35 rice genes were also identified in MQTL regions. The results of the present study may prove useful for the improvement of selection strategy for yield potential, stability, and performance under N-limiting conditions. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01085-0.
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Affiliation(s)
- Dinesh Kumar Saini
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004 India
| | - Yuvraj Chopra
- College of Agriculture, Punjab Agricultural University, Ludhiana, 141004 India
- Present Address: Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583 USA
| | - Neeraj Pal
- Department of Molecular Biology and Genetic Engineering, G. B. Pant, University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - Amneek Chahal
- College of Agriculture, Punjab Agricultural University, Ludhiana, 141004 India
| | - Puja Srivastava
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004 India
| | - Pushpendra Kumar Gupta
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004 India
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21
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Roy NS, Ban YW, Yoo H, Ramekar RV, Cheong EJ, Park NI, Na JK, Park KC, Choi IY. Analysis of genome variants in dwarf soybean lines obtained in F6 derived from cross of normal parents (cultivated and wild soybean). Genomics Inform 2021; 19:e19. [PMID: 34261303 PMCID: PMC8261272 DOI: 10.5808/gi.21024] [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: 04/08/2021] [Accepted: 04/21/2021] [Indexed: 11/20/2022] Open
Abstract
Plant height is an important component of plant architecture and significantly affects crop breeding practices and yield. We studied DNA variations derived from F5 recombinant inbred lines (RILs) with 96.8% homozygous genotypes. Here, we report DNA variations between the normal and dwarf members of four lines harvested from a single seed parent in an F6 RIL population derived from a cross between Glycine max var. Peking and Glycine soja IT182936. Whole genome sequencing was carried out, and the DNA variations in the whole genome were compared between the normal and dwarf samples. We found a large number of DNA variations in both the dwarf and semi-dwarf lines, with one single nucleotide polymorphism (SNP) per at least 3.68 kb in the dwarf lines and 1 SNP per 11.13 kb of the whole genome. This value is 2.18 times higher than the expected DNA variation in the F6 population. A total of 186 SNPs and 241 SNPs were discovered in the coding regions of the dwarf lines 1282 and 1303, respectively, and we discovered 33 homogeneous nonsynonymous SNPs that occurred at the same loci in each set of dwarf and normal soybean. Of them, five SNPs were in the same positions between lines 1282 and 1303. Our results provide important information for improving our understanding of the genetics of soybean plant height and crop breeding. These polymorphisms could be useful genetic resources for plant breeders, geneticists, and biologists for future molecular biology and breeding projects.
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Affiliation(s)
- Neha Samir Roy
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon 24341, Korea
| | - Yong-Wook Ban
- Department of Forest Environmental System, Kangwon National University, Chuncheon 24341, Korea
| | - Hana Yoo
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon 24341, Korea
| | - Rahul Vasudeo Ramekar
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon 24341, Korea
| | - Eun Ju Cheong
- Department of Forest Environmental System, Kangwon National University, Chuncheon 24341, Korea
| | - Nam-Il Park
- Department of Plant Science, Gangneung-Wonju National University, Gangneung 25457, Korea
| | - Jong Kuk Na
- Department of Controlled Agriculture, Kangwon National University, Chuncheon 24341, Korea
| | - Kyong-Cheul Park
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon 24341, Korea
| | - Ik-Young Choi
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon 24341, Korea
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Dey S, Paul S, Nag A, Banerjee R, Gopal G, Mukherjee A, Kundu R. Iron-pulsing, a novel seed invigoration technique to enhance crop yield in rice: A journey from lab to field aiming towards sustainable agriculture. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 769:144671. [PMID: 33482554 DOI: 10.1016/j.scitotenv.2020.144671] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 12/18/2020] [Accepted: 12/18/2020] [Indexed: 06/12/2023]
Abstract
Bulk fertilizer application is one of the easiest means of improving yield of crops however it comes with several environmental impediments and consumer health menace. In the wake of this situation, sustainable agricultural practices stand as pertinent agronomic tool to increase yield and ensure sufficient food supply from farm to fork. In the present study, efficacy of iron-pulsing in improving the rice yield has been elucidated. This technique involves seed treatment with different concentrations (2.5, 5 and 10 mM) of iron salts (FeCl3 and FeSO4) during germination. FeCl3 or FeSO4 was used to treat the sets and depending on the concentration of the salts, the sets were named as C2.5, C5, C10 and S2.5, S5, S10 (where C and S stands for FeCl3 and FeSO4 respectively and the numbers succeeding them denotes the concentration of salt in mM). Our investigation identified 72 h of treatment as ideal duration for iron-pulsing. At this time point, the seedling emergence attributes and activities of α-amylase and protease increased. The relative water uptake of the seeds also increased through upregulation of aquaporin expression. The treatment efficiently maintained the ROS balance with the aid of antioxidant enzymes and increased the iron content within the treated seeds. After transplantation in field, photosynthetic rate and chlorophyll content enhanced in the treated plants. Finally, the post-harvest agro-morphological traits (represented through panicle morphology, 1000 seed weight, harvest index) and yield showed significant improvement with treatment. Sets C5 and S5 showed optimum efficiency in terms of yield improvement. To our best knowledge, this study is the first report deciphering the efficacy of iron-pulsing as a safe, cost effective and promising technique to escalate the yield of rice crops without incurring an environmental cost. Thus, iron-pulsing is expected to serve as a potential tool to address global food security in years to come.
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Affiliation(s)
- Swarnali Dey
- Centre of Advance Study, Department of Botany, University of Calcutta, Kolkata 700019, India
| | - Subhabrata Paul
- School of Biotechnology, Presidency University (2nd Campus), Kolkata 700156, India
| | - Anish Nag
- Department of Life Sciences, CHRIST (Deemed to be University), Bangalore 560029, India
| | - Ritesh Banerjee
- Centre of Advance Study, Department of Botany, University of Calcutta, Kolkata 700019, India
| | - Geetha Gopal
- Centre for Nano Biotechnology, VIT University, Vellore 632014, Tamil Nadu, India
| | - Amitava Mukherjee
- Centre for Nano Biotechnology, VIT University, Vellore 632014, Tamil Nadu, India
| | - Rita Kundu
- Centre of Advance Study, Department of Botany, University of Calcutta, Kolkata 700019, India.
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Adak A, Conrad C, Chen Y, Wilde SC, Murray SC, Anderson S, Subramanian NK. Validation of Functional Polymorphisms Affecting Maize Plant Height by Unoccupied Aerial Systems (UAS) Discovers Novel Temporal Phenotypes. G3-GENES GENOMES GENETICS 2021; 11:6211193. [PMID: 33822935 PMCID: PMC8495742 DOI: 10.1093/g3journal/jkab075] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 02/28/2021] [Indexed: 11/14/2022]
Abstract
Plant height (PHT) in maize (Zea mays L.) has been scrutinized genetically and phenotypically due to relationship with other agronomically valuable traits (e.g. yield). Heritable variation of PHT is determined by many discovered quantitative trait loci (QTLs); however, phenotypic effects of such loci often lack validation across environments and genetic backgrounds, especially in the hybrid state grown by farmers rather than the inbred state more often used by geneticists. A previous genome wide association study using a topcrossed hybrid diversity panel identified two novel quantitative trait variants (QTVs) controlling both PHT and grain yield. Here, heterogeneous inbred families demonstrated that these two loci, characterized by two single nucleotide polymorphisms (SNPs), cause phenotypic variation in inbred lines, but that size of these effects were variable across four different genetic backgrounds, ranging from 1 to 10 cm. Weekly unoccupied aerial system flights demonstrated the two SNPs had larger effects, varying from 10 to 25 cm, in early growth while effects decreased towards the end of the season. These results show that allelic effect sizes of economically valuable loci are both dynamic in temporal growth and dynamic across genetic backgrounds, resulting in informative phenotypic variability overlooked following traditional phenotyping methods. Public genotyping data shows recent favorable allele selection in elite temperate germplasm with little change across tropical backgrounds. As these loci remain rarer in tropical germplasm, with effects most visible early in growth, they are useful for breeding and selection to expand the genetic basis of maize.
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Affiliation(s)
- Alper Adak
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Clarissa Conrad
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuanyuan Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.,Department of Environmental Horticulture, Institute of Food and Agricultural Sciences, Mid-Florida Research and Education Center, University of Florida, Apopka, FL, 32703, USA
| | - Scott C Wilde
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Seth C Murray
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Steven Anderson
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.,Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843-2474, USA
| | - Nithya K Subramanian
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
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24
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Yang Q, Lin G, Lv H, Wang C, Yang Y, Liao H. Environmental and genetic regulation of plant height in soybean. BMC PLANT BIOLOGY 2021; 21:63. [PMID: 33494700 PMCID: PMC7836565 DOI: 10.1186/s12870-021-02836-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 01/11/2021] [Indexed: 05/27/2023]
Abstract
BACKGROUND Shoot architecture is fundamentally crucial to crop growth and productivity. As a key component of shoot architecture, plant height is known to be controlled by both genetic and environmental factors, though specific details remain scarce. RESULTS In this study, 308 representative soybean lines from a core collection and 168 F9 soybean progeny were planted at distinct field sites. The results demonstrated the presence of significant genotype × environment interaction (G × E) effects on traits associated with plant height in a natural soybean population. In total, 19 loci containing 51 QTLs (quantitative trait locus) for plant height were identified across four environments, with 23, 13 and 15 being QTLs for SH (shoot height), SNN (stem node number) and AIL (average internode length), respectively. Significant LOD ranging from 2.50 to 16.46 explained 2.80-26.10% of phenotypic variation. Intriguingly, only two loci, Loc11 and Loc19-1, containing 20 QTLs, were simultaneously detected across all environments. Results from Pearson correlation analysis and PCA (principal component analysis) revealed that each of the five agro-meteorological factors and four soil properties significantly affected soybean plant height traits, and that the corresponding QTLs had additive effects. Among significant environmental factors, AD (average day-length), AMaT (average maximum temperature), pH, and AN (available nitrogen) had the largest impacts on soybean plant height. Therefore, in spite of uncontrollable agro-meteorological factors, soybean shoot architecture might be remolded through combined efforts to produce superior soybean genetic materials while also optimizing soil properties. CONCLUSIONS Overall, the comprehensive set of relationships outlined herein among environment factors, soybean genotypes and QTLs in effects on plant height opens new avenues to explore in work aiming to increase soybean yield through improvements in shoot architecture.
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Affiliation(s)
- Qing Yang
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Gaoming Lin
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Huiyong Lv
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Cunhu Wang
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yongqing Yang
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Hong Liao
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
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25
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López-Marqués RL, Nørrevang AF, Ache P, Moog M, Visintainer D, Wendt T, Østerberg JT, Dockter C, Jørgensen ME, Salvador AT, Hedrich R, Gao C, Jacobsen SE, Shabala S, Palmgren M. Prospects for the accelerated improvement of the resilient crop quinoa. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5333-5347. [PMID: 32643753 PMCID: PMC7501820 DOI: 10.1093/jxb/eraa285] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 06/11/2020] [Indexed: 05/04/2023]
Abstract
Crops tolerant to drought and salt stress may be developed by two approaches. First, major crops may be improved by introducing genes from tolerant plants. For example, many major crops have wild relatives that are more tolerant to drought and high salinity than the cultivated crops, and, once deciphered, the underlying resilience mechanisms could be genetically manipulated to produce crops with improved tolerance. Secondly, some minor (orphan) crops cultivated in marginal areas are already drought and salt tolerant. Improving the agronomic performance of these crops may be an effective way to increase crop and food diversity, and an alternative to engineering tolerance in major crops. Quinoa (Chenopodium quinoa Willd.), a nutritious minor crop that tolerates drought and salinity better than most other crops, is an ideal candidate for both of these approaches. Although quinoa has yet to reach its potential as a fully domesticated crop, breeding efforts to improve the plant have been limited. Molecular and genetic techniques combined with traditional breeding are likely to change this picture. Here we analyse protein-coding sequences in the quinoa genome that are orthologous to domestication genes in established crops. Mutating only a limited number of such genes by targeted mutagenesis appears to be a promising route for accelerating the improvement of quinoa and generating a nutritious high-yielding crop that can meet the future demand for food production in a changing climate.
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Affiliation(s)
- Rosa L López-Marqués
- NovoCrops Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
- Correspondence: or
| | - Anton F Nørrevang
- NovoCrops Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Peter Ache
- Institute for Molecular Plant Physiology and Biophysics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Max Moog
- NovoCrops Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Davide Visintainer
- NovoCrops Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Toni Wendt
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, Copenhagen V, Denmark
| | - Jeppe T Østerberg
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, Copenhagen V, Denmark
| | - Christoph Dockter
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, Copenhagen V, Denmark
| | - Morten E Jørgensen
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, Copenhagen V, Denmark
| | - Andrés Torres Salvador
- The Quinoa Company, Wageningen, The Netherlands
- Plant Biotechnology Laboratory (COCIBA), Universidad San Francisco de Quito USFQ, Cumbayá, Ecuador
| | - Rainer Hedrich
- Institute for Molecular Plant Physiology and Biophysics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | | | - Sergey Shabala
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan, China
- Tasmanian Institute for Agriculture, College of Science and Engineering, University of Tasmania, Hobart, Tasmania, Australia
| | - Michael Palmgren
- NovoCrops Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan, China
- Correspondence: or
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26
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Phenotypic Characterization of Tiger Nuts ( Cyperus esculentus L.) from Major Growing Areas in Ghana. ScientificWorldJournal 2020; 2020:7232591. [PMID: 32831807 PMCID: PMC7428959 DOI: 10.1155/2020/7232591] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 07/01/2020] [Accepted: 07/16/2020] [Indexed: 11/17/2022] Open
Abstract
Tigernut (Cyperus esculentus Lativum) is an important but understudied and underutilized crop in Ghana. The tubers are highly appreciated for their health benefits and nutritive value. To contribute to the conservation process of tiger nut and identify elite genotypes, this study was conducted to assess phenotypic variability in tiger nut genotypes in Ghana. Sixty-four (64) genotypes were collected from major tiger nut growing areas in Ghana. The genotypes were field-grown and characterized based on phenotypic and yield traits. Similarity coefficient (Bray-Curtis) was between 0.82 and 0.98, indicating low variability in both qualitative and quantitative characters. The cophenetic correlation coefficient was 0.64. The genotypes were mainly brown with only a few black (6) tubers from the central region. Materials collected from parts of the eastern region (Aduamoah) generally recorded the highest tuber weight. Tuber weight depended on plant height and number of tillers. There were high tillering genetic materials among the genotypes. Tubers were categorised as oval (10), ovoid (33), or oblong (15). The genotypes clustered into two groups based on shoot and tuber characteristics, rather than on geographical origin. The low genetic diversity among the genotypes suggested either the possible existence of a network among tiger nut farmers in Ghana in circulating the planting material or some form of seed sorting for uniform and homogenous planting materials has been carried out over the years. Our results point to the imperativeness to expand the genetic base of the tiger nuts to facilitate its improvement in Ghana.
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27
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Liu N, Cheng F. Association mapping for yield traits in Paeonia rockii based on SSR markers within transcription factors of comparative transcriptome. BMC PLANT BIOLOGY 2020; 20:245. [PMID: 32487017 PMCID: PMC7265254 DOI: 10.1186/s12870-020-02449-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 05/18/2020] [Indexed: 05/30/2023]
Abstract
BACKGROUND Allelic variation underlying the quantitative traits in plants is caused by the extremely complex regulation process. Tree peony originated in China is a peculiar ornamental, medicinal and oil woody plant. Paeonia rockii, one of tree peony species, is a precious emerging woody oil crop. However, in this valuable plant, the study of functional loci associated with yield traits has rarely been identified. Therefore, to explore the genetic architecture of 24 yield quantitative traits, the association mapping was first reported in 420 unrelated cultivated P. rockii individuals based on the next-generation sequencing (NGS) and single-molecule long-read sequencing (SMLRS). RESULTS The developed 58 pairs of polymorphic expressed sequence tag-simple sequence repeat (EST-SSR) markers from 959 candidate transcription factors (TFs) associated with yield were used for genotyping the 420 P. rockii accessions. We observed a high level of genetic diversity (polymorphic information content, PIC = 0.514) and low linkage disequilibrium (LD) between EST-SSRs. Moreover, four subpopulations in the association population were revealed by STRUCTURE analyses. Further, single-marker association analysis identified 141 significant associations, involving 17 quantitative traits and 41 EST-SSRs. These loci were mainly from AP2, TCP, MYB, HSF, bHLH, GATA, and B3 gene families and showed a small proportion of the phenotypic variance (3.79 to 37.45%). CONCLUSIONS Our results summarize a valuable collection of functional loci associated with yield traits in P. rockii, and provide a precious resource that reveals allelic variation underlying quantitative traits in Paeonia and other woody oil crops.
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Affiliation(s)
- Na Liu
- Peony International Institute, Beijing Advanced Innovation Center of Tree Breeding by Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Fangyun Cheng
- Peony International Institute, Beijing Advanced Innovation Center of Tree Breeding by Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China.
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28
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Park SI, Kim JJ, Shin SY, Kim YS, Yoon HS. ASR Enhances Environmental Stress Tolerance and Improves Grain Yield by Modulating Stomatal Closure in Rice. FRONTIERS IN PLANT SCIENCE 2020; 10:1752. [PMID: 32117337 PMCID: PMC7033646 DOI: 10.3389/fpls.2019.01752] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 12/13/2019] [Indexed: 05/24/2023]
Abstract
Abscisic acid-, stress-, and ripening-induced (ASR) genes are involved in responding to abiotic stresses, but their precise roles in enhancing grain yield under stress conditions remain to be determined. We cloned a rice (Oryza sativa) ASR gene, OsASR1, and characterized its function in rice plants. OsASR1 expression was induced by abscisic acid (ABA), salt, and drought treatments. Transgenic rice plants overexpressing OsASR1 displayed improved water regulation under salt and drought stresses, which was associated with osmolyte accumulation, improved modulation of stomatal closure, and reduced transpiration rates. OsASR1-overexpressing plants were hypersensitive to exogenous ABA and accumulated higher endogenous ABA levels under salt and drought stresses, indicating that OsASR1 is a positive regulator of the ABA signaling pathway. The growth of OsASR1-overexpressing plants was superior to that of wild-type (WT) plants under paddy field conditions when irrigation was withheld, likely due to improved modulation of stomatal closure via modified ABA signaling. The transgenic plants had higher grain yields than WT plants for four consecutive generations. We conclude that OsASR1 has a crucial role in ABA-mediated regulation of stomatal closure to conserve water under salt- and drought-stress conditions, and OsASR1 overexpression can enhance salinity and drought tolerance, resulting in improved crop yields.
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Affiliation(s)
- Seong-Im Park
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, South Korea
- School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu, South Korea
| | - Jin-Ju Kim
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, South Korea
- School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu, South Korea
| | - Sun-Young Shin
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, South Korea
| | - Young-Saeng Kim
- Research Institute for Dok-do and Ulleung-do, Kyungpook National University, Daegu, South Korea
| | - Ho-Sung Yoon
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, South Korea
- School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu, South Korea
- Advanced Bio-Resource Research Center, Kyungpook National University, Daegu, South Korea
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29
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Improving grain yield, stress resilience and quality of bread wheat using large-scale genomics. Nat Genet 2019; 51:1530-1539. [DOI: 10.1038/s41588-019-0496-6] [Citation(s) in RCA: 126] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 08/13/2019] [Indexed: 01/11/2023]
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30
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Li R, Li M, Ashraf U, Liu S, Zhang J. Exploring the Relationships Between Yield and Yield-Related Traits for Rice Varieties Released in China From 1978 to 2017. FRONTIERS IN PLANT SCIENCE 2019; 10:543. [PMID: 31134107 PMCID: PMC6514245 DOI: 10.3389/fpls.2019.00543] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 04/09/2019] [Indexed: 05/20/2023]
Abstract
Despite evidence from previous case studies showing that agronomic traits partially determine the resulting yield of different rice (Oryza sativa L.) varieties, it remains unclear whether this is true at the ecotype level. Here, an extensive dataset of the traits of 7686 rice varieties, released in China from 1978 to 2017, was used to study the relationship between yield and other agronomic traits. We assessed the association between yield and other agronomic traits for four different rice ecotypes, i.e., indica inbred, indica hybrid, japonica inbred, and japonica hybrid. We found that associations between agronomic traits and yield were ecotype-dependent. For both the indica inbred and indica hybrid ecotypes, we found that greater values of certain traits, including the filled grain number per panicle, 1000-grain-weight, plant height, panicle length, grains per panicle, seed setting rate, long growth period, low panicle number per unit area, and low seed length/width ratio, have accounted for high grain yield. In the japonica inbred and japonica hybrid ecotypes, we found that only high panicle number per unit area and long growth period led to high grain yield. Indirectly, growth period consistently had a positive effect on yield in all ecotypes, and plant height had a positive effect on yield for the indicas and japonica inbred only. Plant height had a negative effect for the japonica hybrid. Altogether, our findings potentially have valuable implications for improving the breeds of rice ecotypes.
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Affiliation(s)
- Ronghua Li
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
- Key Laboratory of Agro-Environment in the Tropics, Ministry of Agriculture, South China Agricultural University, Guangzhou, China
| | - Meijuan Li
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
- Key Laboratory of Agro-Environment in the Tropics, Ministry of Agriculture, South China Agricultural University, Guangzhou, China
| | - Umair Ashraf
- Department of Botany, University of Education (Lahore), Faisalabad-Campus, Faisalabad, Pakistan
- College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Shiwei Liu
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
- Key Laboratory of Agro-Environment in the Tropics, Ministry of Agriculture, South China Agricultural University, Guangzhou, China
| | - Jiaen Zhang
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
- Key Laboratory of Agro-Environment in the Tropics, Ministry of Agriculture, South China Agricultural University, Guangzhou, China
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31
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Chen X, Xu P, Zhou J, Tao D, Yu D. Mapping and breeding value evaluation of a semi-dominant semi-dwarf gene in upland rice. PLANT DIVERSITY 2018; 40:238-244. [PMID: 30740570 PMCID: PMC6224660 DOI: 10.1016/j.pld.2018.09.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 08/29/2018] [Accepted: 09/03/2018] [Indexed: 06/01/2023]
Abstract
Plant height is an important trait related to yield potential and plant architecture. A suitable plant height plays a crucial role in improvement of rice yield and lodging resistance. In this study, we found that the traditional upland landrace 'Kaowenghan' (KWH) showed a special semi-dwarf phenotype. To identify the semi-dwarf gene from KWH, we raised BC2F4 semi-dwarf introgression lines (IL) by hybridization of the japonica rice cultivar 'Dianjingyou1' (DJY1) and KWH in a DJY1 background. The plant height of the homozygous semi-dwarf IL (IL-87) was significantly reduced compared with that of DJY1. The phenotype of the F1 progeny of the semi-dwarf IL-87 and DJY1 showed that the semi-dwarf phenotype was semi-dominant. QTL mapping indicated that the semi-dwarf phenotype was controlled by a major QTL qDH1 and was localized between the markers RM6696 and RM12047 on chromosome 1. We also developed near-isogenic lines (NIL) from the BC3F3 population, and found that the yield of homozygous NIL (NIL-2) was not significantly different compared to DJY1. Breeding value evaluation through investigation of the plant height of the progeny of NIL (NIL-2) and cultivars from different genetic background indicate that the novel semi-dwarf gene shows potential as a genetic resource for rice breeding.
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Affiliation(s)
- Xiaoqian Chen
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Peng Xu
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Jiawu Zhou
- Food Crops Research Institute, Yunnan Academy of Agricultural Sciences (YAAS), Kunming, 650200, China
| | - Dayun Tao
- Food Crops Research Institute, Yunnan Academy of Agricultural Sciences (YAAS), Kunming, 650200, China
| | - Diqiu Yu
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
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32
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Sim JS, Kesawat MS, Kumar M, Kim SY, Mani V, Subramanian P, Park S, Lee CM, Kim SR, Hahn BS. Lack of the α1,3-Fucosyltransferase Gene ( Osfuct) Affects Anther Development and Pollen Viability in Rice. Int J Mol Sci 2018; 19:ijms19041225. [PMID: 29670011 PMCID: PMC5979348 DOI: 10.3390/ijms19041225] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 04/11/2018] [Accepted: 04/16/2018] [Indexed: 12/04/2022] Open
Abstract
N-linked glycosylation is one of the key post-translational modifications. α1,3-Fucosyltransferase (OsFucT) is responsible for transferring α1,3-linked fucose residues to the glycoprotein N-glycan in plants. We characterized an Osfuct mutant that displayed pleiotropic developmental defects, such as impaired anther and pollen development, diminished growth, shorter plant height, fewer tillers, and shorter panicle length and internodes under field conditions. In addition, the anthers were curved, the pollen grains were shriveled, and pollen viability and pollen number per anther decreased dramatically in the mutant. Matrix-assisted laser desorption/ionization time-of-flight analyses of the N-glycans revealed that α1,3-fucose was lacking in the N-glycan structure of the mutant. Mutant complementation revealed that the phenotype was caused by loss of Osfuct function. Transcriptome profiling also showed that several genes essential for plant developmental processes were significantly altered in the mutant, including protein kinases, transcription factors, genes involved in metabolism, genes related to protein synthesis, and hypothetical proteins. Moreover, the mutant exhibited sensitivity to an increased concentration of salt. This study facilitates a further understanding of the function of genes mediating N-glycan modification and anther and pollen development in rice.
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Affiliation(s)
- Joon-Soo Sim
- Metabolic Engineering Division, Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea.
| | - Mahipal Singh Kesawat
- Metabolic Engineering Division, Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea.
| | - Manu Kumar
- Department of Life Sciences, Sogang University, Seoul 121-742, Korea.
| | - Su-Yeon Kim
- Metabolic Engineering Division, Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea.
| | - Vimalraj Mani
- Metabolic Engineering Division, Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea.
| | - Parthiban Subramanian
- Metabolic Engineering Division, Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea.
| | - Soyoung Park
- Metabolic Engineering Division, Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea.
| | - Chang-Muk Lee
- Metabolic Engineering Division, Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea.
| | - Seong-Ryong Kim
- Department of Life Sciences, Sogang University, Seoul 121-742, Korea.
| | - Bum-Soo Hahn
- Metabolic Engineering Division, Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea.
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