1
|
Li J, Xu C, Tian Y, Chen G, Chi W, Dai Z, Li J, Wang C, Cheng X, Liu Y, Sun Z, Li J, Wang B, Xu D, Sun X, Zhang H, Zhu C, Wang C, Wan J. Genome-wide association and selection studies reveal genomic insight into saline-alkali tolerance in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2025; 121:e70056. [PMID: 40084738 DOI: 10.1111/tpj.70056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2024] [Revised: 01/13/2025] [Accepted: 02/08/2025] [Indexed: 03/16/2025]
Abstract
Saline-alkali stress has detrimental effects on growth and development of rice (Oryza sativa L.). Domesticated rice cultivars with high saline-alkali tolerance (SAT) are essential for sustainable agriculture. To explore the genomic basis underlying SAT in rice, we integrate genome-wide association study (GWAS) with selective sweep analysis using a core population consisting of 234 cultivars grown in the saline and normal fields across three consecutive years and identify 70 genes associated with SAT with signals of selection and evolution between subpopulations of tolerance and sensitivity. We detected and subsequently characterized GATA19 trans-regulated SAT1/OsCYL4 that regulated SAT through reactive oxygen species (ROS) scavenging pathway. Our results provide a comprehensive insight into genome-wide natural variants and selection sweep underlying saline-alkali tolerance and pave avenues for SAT breeding through genome editing and genomic selection in rice.
Collapse
Affiliation(s)
- Jin Li
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Zhongshan Biological Breeding Laboratory, Nanjing, 210014, China
| | - Chen Xu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Zhongshan Biological Breeding Laboratory, Nanjing, 210014, China
| | - Yunlu Tian
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Zhongshan Biological Breeding Laboratory, Nanjing, 210014, China
| | - Gaoming Chen
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Zhongshan Biological Breeding Laboratory, Nanjing, 210014, China
| | - Wenchao Chi
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Zhongshan Biological Breeding Laboratory, Nanjing, 210014, China
| | - Zhaoyang Dai
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Zhongshan Biological Breeding Laboratory, Nanjing, 210014, China
| | - Jing Li
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Zhongshan Biological Breeding Laboratory, Nanjing, 210014, China
| | - Chunyuan Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Zhongshan Biological Breeding Laboratory, Nanjing, 210014, China
| | - Xinran Cheng
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Zhongshan Biological Breeding Laboratory, Nanjing, 210014, China
| | - Yan Liu
- Lianyungang Academy of Agricultural Science, Lianyungang, 222000, Jiangsu, China
| | - Zhiguang Sun
- Lianyungang Academy of Agricultural Science, Lianyungang, 222000, Jiangsu, China
| | - Jingfang Li
- Lianyungang Academy of Agricultural Science, Lianyungang, 222000, Jiangsu, China
| | - Baoxiang Wang
- Lianyungang Academy of Agricultural Science, Lianyungang, 222000, Jiangsu, China
| | - Dayong Xu
- Lianyungang Academy of Agricultural Science, Lianyungang, 222000, Jiangsu, China
| | - Xianjun Sun
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hui Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chengsong Zhu
- Department of Immunology, The University of Texas Southwestern Medical Centre, Dallas, 75390, Texas, USA
| | - Chunming Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Zhongshan Biological Breeding Laboratory, Nanjing, 210014, China
- Southern Japonica Rice R&D Corporation Ltd, Nanjing, 210095, China
| | - Jianmin Wan
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Zhongshan Biological Breeding Laboratory, Nanjing, 210014, China
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| |
Collapse
|
2
|
Liu J, Zhu L, Cao D, Zhu X, Zhang H, Zhang Y, Liu J. Identification of Drought Stress-Responsive Genes in Rice by Random Walk with Multi-Restart Probability on MultiPlex Biological Networks. Int J Mol Sci 2024; 25:9216. [PMID: 39273165 PMCID: PMC11395135 DOI: 10.3390/ijms25179216] [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: 08/12/2024] [Revised: 08/22/2024] [Accepted: 08/23/2024] [Indexed: 09/15/2024] Open
Abstract
Exploring drought stress-responsive genes in rice is essential for breeding drought-resistant varieties. Rice drought resistance is controlled by multiple genes, and mining drought stress-responsive genes solely based on single omics data lacks stability and accuracy. Multi-omics correlation analysis and biological molecular network analysis provide robust solutions. This study proposed a random walk with a multi-restart probability (RWMRP) algorithm, based on the Restarted Random Walk (RWR) algorithm, to operate on rice MultiPlex biological networks. It explores the interactions between biological molecules across various levels and ranks potential genes. RWMRP uses eigenvector centrality to evaluate node importance in the network and adjusts the restart probabilities accordingly, diverging from the uniform restart probability employed in RWR. In the random walk process, it can be better to consider the global relationships in the network. Firstly, we constructed a MultiPlex biological network by integrating the rice protein-protein interaction, gene pathway, and gene co-expression network. Then, we employed RWMRP to predict the potential genes associated with rice tolerance to drought stress. Enrichment and correlation analyses resulted in the identification of 12 drought-related genes. We further conducted quantitative real-time polymerase chain reaction (qRT-PCR) analysis on these 12 genes, ultimately identifying 10 genes responsive to drought stress.
Collapse
Affiliation(s)
- Jiacheng Liu
- College of Information and Intelligence, Hunan Agricultural University, Changsha 410128, China
| | - Liu Zhu
- College of Information and Intelligence, Hunan Agricultural University, Changsha 410128, China
| | - Dan Cao
- College of Science, Central South University of Forestry and Technology, Changsha 410004, China
| | - Xinghui Zhu
- College of Information and Intelligence, Hunan Agricultural University, Changsha 410128, China
| | - Hongyan Zhang
- College of Information and Intelligence, Hunan Agricultural University, Changsha 410128, China
| | - Yinqiong Zhang
- College of Information and Intelligence, Hunan Agricultural University, Changsha 410128, China
| | - Jing Liu
- College of Information and Intelligence, Hunan Agricultural University, Changsha 410128, China
| |
Collapse
|
3
|
Characterization of Transposon-Derived Accessible Chromatin Regions in Rice (Oryza Sativa). Int J Mol Sci 2022; 23:ijms23168947. [PMID: 36012213 PMCID: PMC9408979 DOI: 10.3390/ijms23168947] [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: 07/05/2022] [Revised: 08/05/2022] [Accepted: 08/08/2022] [Indexed: 11/17/2022] Open
Abstract
Growing evidence indicates that transposons or transposable elements (TEs)-derived accessible chromatin regions (ACRs) play essential roles in multiple biological processes by interacting with trans-acting factors. However, the function of TE-derived ACRs in the regulation of gene expression in the rice genome has not been well characterized. In this study, we examined the chromatin dynamics in six types of rice tissues and found that ~8% of ACRs were derived from TEs and exhibited distinct levels of accessibility and conservation as compared to those without TEs. TEs exhibited a TE subtype-dependent impact on ACR formation, which can be mediated by changes in the underlying DNA methylation levels. Moreover, we found that tissue-specific TE-derived ACRs might function in the tissue development through the modulation of nearby gene expression. Interestingly, many genes in domestication sweeps were found to overlap with TE-derived ACRs, suggesting their potential functions in the rice domestication. In addition, we found that the expression divergence of 1070 duplicate gene pairs were associated with TE-derived ACRs and had distinct distributions of TEs and ACRs around the transcription start sites (TSSs), which may experience different selection pressures. Thus, our study provides some insights into the biological implications of TE-derived ACRs in the rice genome. Our results imply that these ACRs are likely involved in the regulation of tissue development, rice domestication and functional divergence of duplicated genes.
Collapse
|
4
|
Ortiz D, Salas-Fernandez MG. Dissecting the genetic control of natural variation in sorghum photosynthetic response to drought stress. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3251-3267. [PMID: 34791180 PMCID: PMC9126735 DOI: 10.1093/jxb/erab502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 11/12/2021] [Indexed: 06/13/2023]
Abstract
Drought stress causes crop yield losses worldwide. Sorghum is a C4 species tolerant to moderate drought stress, and its extensive natural variation for photosynthetic traits under water-limiting conditions can be exploited for developing cultivars with enhanced stress tolerance. The objective of this study was to discover genes/genomic regions that control the sorghum photosynthetic capacity under pre-anthesis water-limiting conditions. We performed a genome-wide association study for seven photosynthetic gas exchange and chlorophyll fluorescence traits during three periods of contrasting soil volumetric water content (VWC): control (30% VWC), drought (15% VWC), and recovery (30% VWC). Water stress was imposed with an automated irrigation system that generated a controlled dry-down period for all plants, to perform an unbiased genotypic comparison. A total of 60 genomic regions were associated with natural variation in one or more photosynthetic traits in a particular treatment or with derived variables. We identified 33 promising candidate genes with predicted functions related to stress signaling, oxidative stress protection, hormonal response to stress, and dehydration protection. Our results provide new knowledge about the natural variation and genetic control of sorghum photosynthetic response to drought with the ultimate goal of improving its adaptation and productivity under water stress scenarios.
Collapse
Affiliation(s)
- Diego Ortiz
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA
- Instituto Nacional de Tecnologia Agropecuaria, Manfredi, Cordoba 5988, Argentina
| | | |
Collapse
|
5
|
Wu T, Zhang H, Bi Y, Yu Y, Liu H, Yang H, Yuan B, Ding X, Chu Z. Tal2c Activates the Expression of OsF3H04g to Promote Infection as a Redundant TALE of Tal2b in Xanthomonas oryzae pv. oryzicola. Int J Mol Sci 2021; 22:ijms222413628. [PMID: 34948428 PMCID: PMC8707247 DOI: 10.3390/ijms222413628] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 12/11/2022] Open
Abstract
Xanthomonas oryzae delivers transcription activator-like effectors (TALEs) into plant cells to facilitate infection. Following economic principles, the redundant TALEs are rarely identified in Xanthomonas. Previously, we identified the Tal2b, which activates the expression of the rice 2-oxoglutarate-dependent dioxygenase gene OsF3H03g to promote infection in the highly virulent strain of X. oryzae pv. oryzicola HGA4. Here, we reveal that another clustered TALE, Tal2c, also functioned as a virulence factor to target rice OsF3H04g, a homologue of OsF3H03g. Transferring Tal2c into RS105 induced expression of OsF3H04g to coincide with increased susceptibility in rice. Overexpressing OsF3H04g caused higher susceptibility and less salicylic acid (SA) production compared to wild-type plants. Moreover, CRISPR–Cas9 system-mediated editing of the effector-binding element in the promoters of OsF3H03g or OsF3H04g was found to specifically enhance resistance to Tal2b- or Tal2c-transferring strains, but had no effect on resistance to either RS105 or HGA4. Furthermore, transcriptome analysis revealed that several reported SA-related and defense-related genes commonly altered expression in OsF3H04g overexpression line compared with those identified in OsF3H03g overexpression line. Overall, our results reveal a functional redundancy mechanism of pathogenic virulence in Xoc in which tandem Tal2b and Tal2c specifically target homologues of host genes to interfere with rice immunity by reducing SA.
Collapse
Affiliation(s)
- Tao Wu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China; (T.W.); (H.Z.); (Y.Y.); (H.L.)
- State Key Laboratory of Hybrid Rice, Hubei Hongshan Laboratory, College of Life Sciences, Wuhan University, Wuhan 430072, China;
| | - Haimiao Zhang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China; (T.W.); (H.Z.); (Y.Y.); (H.L.)
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai’an 271018, China
| | - Yunya Bi
- State Key Laboratory of Hybrid Rice, Hubei Hongshan Laboratory, College of Life Sciences, Wuhan University, Wuhan 430072, China;
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China;
| | - Yue Yu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China; (T.W.); (H.Z.); (Y.Y.); (H.L.)
| | - Haifeng Liu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China; (T.W.); (H.Z.); (Y.Y.); (H.L.)
| | - Hong Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China;
| | - Bin Yuan
- Institute of Plant Protection and Soil Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan 430064, China;
| | - Xinhua Ding
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China; (T.W.); (H.Z.); (Y.Y.); (H.L.)
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai’an 271018, China
- Correspondence: (X.D.); (Z.C.); Tel.: +86-538-8245569 (X.D.); +86-27-68752095 (Z.C.)
| | - Zhaohui Chu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China; (T.W.); (H.Z.); (Y.Y.); (H.L.)
- State Key Laboratory of Hybrid Rice, Hubei Hongshan Laboratory, College of Life Sciences, Wuhan University, Wuhan 430072, China;
- Correspondence: (X.D.); (Z.C.); Tel.: +86-538-8245569 (X.D.); +86-27-68752095 (Z.C.)
| |
Collapse
|
6
|
Lu X, Zhou Y, Fan F, Peng J, Zhang J. Coordination of light, circadian clock with temperature: The potential mechanisms regulating chilling tolerance in rice. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:737-760. [PMID: 31243851 DOI: 10.1111/jipb.12852] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 06/19/2019] [Indexed: 06/09/2023]
Abstract
Rice (Oryza sativa L.) is a major staple food crop for over half of the world's population. As a crop species originated from the subtropics, rice production is hampered by chilling stress. The genetic mechanisms of rice responses to chilling stress have attracted much attention, focusing on chilling-related gene mining and functional analyses. Plants have evolved sophisticated regulatory systems to respond to chilling stress in coordination with light signaling pathway and internal circadian clock. However, in rice, information about light-signaling pathways and circadian clock regulation and their roles in chilling tolerance remains elusive. Further investigation into the regulatory network of chilling tolerance in rice is needed, as knowledge of the interaction between temperature, light, and circadian clock dynamics is limited. Here, based on phenotypic analysis of transgenic and mutant rice lines, we delineate the relevant genes with important regulatory roles in chilling tolerance. In addition, we discuss the potential coordination mechanism among temperature, light, and circadian clock in regulating chilling response and tolerance of rice, and provide perspectives for the ongoing chilling signaling network research in rice.
Collapse
Affiliation(s)
- Xuedan Lu
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, School of Agriculture, Hunan Agricultural University, Changsha, 410128, China
| | - Yan Zhou
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, School of Agriculture, Hunan Agricultural University, Changsha, 410128, China
| | - Fan Fan
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, School of Agriculture, Hunan Agricultural University, Changsha, 410128, China
| | - JunHua Peng
- Huazhi Rice Bio-tech Company Ltd., Changsha, 410128, China
| | - Jian Zhang
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, School of Agriculture, Hunan Agricultural University, Changsha, 410128, China
- Huazhi Rice Bio-tech Company Ltd., Changsha, 410128, China
| |
Collapse
|
7
|
Gao S, Song T, Han J, He M, Zhang Q, Zhu Y, Zhu Z. A calcium-dependent lipid binding protein, OsANN10, is a negative regulator of osmotic stress tolerance in rice. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 293:110420. [PMID: 32081268 DOI: 10.1016/j.plantsci.2020.110420] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 01/16/2020] [Accepted: 01/18/2020] [Indexed: 05/21/2023]
Abstract
Annexin, a multi-gene family in plants, is essential for plant growth and stress responses. Recent studies demonstrated a positive effect of annexin in abiotic stress responses. Interestingly, we found OsANN10, a putative annexin gene in rice, negatively regulated plant responses to osmotic stress. Knocking down OsANN10 significantly decreased the content of H2O2 by increasing Peroxidase (POD) and Catalase (CAT) activities, further reducing oxidative damage in rice leaves, suggesting a negative regulation of OsANN10 in protecting cell membrane against oxidative damage via scavenging ROS under osmotic stress.
Collapse
Affiliation(s)
- Shuxin Gao
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of the Ministry of Education, College of Life Science, Hebei Normal University, Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, Hebei, 050024, China
| | - Tao Song
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of the Ministry of Education, College of Life Science, Hebei Normal University, Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, Hebei, 050024, China
| | - Jianbo Han
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of the Ministry of Education, College of Life Science, Hebei Normal University, Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, Hebei, 050024, China
| | - Mengli He
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of the Ministry of Education, College of Life Science, Hebei Normal University, Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, Hebei, 050024, China
| | - Qian Zhang
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of the Ministry of Education, College of Life Science, Hebei Normal University, Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, Hebei, 050024, China
| | - Ying Zhu
- The Institute of Viral and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Zhengge Zhu
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of the Ministry of Education, College of Life Science, Hebei Normal University, Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, Hebei, 050024, China.
| |
Collapse
|
8
|
Li N, Liu H, Sun J, Zheng H, Wang J, Yang L, Zhao H, Zou D. Transcriptome analysis of two contrasting rice cultivars during alkaline stress. Sci Rep 2018; 8:9586. [PMID: 29941956 PMCID: PMC6018505 DOI: 10.1038/s41598-018-27940-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 06/13/2018] [Indexed: 12/26/2022] Open
Abstract
Soil alkalinity greatly affects plant growth and crop productivity. Although RNA-Seq analyses have been conducted to investigate genome-wide gene expression in response to alkaline stress in many plants, the expressions of alkali-responsive genes in rice have not been previously investigated. In this study, the transcriptomic data between an alkaline-tolerant (WD20342) and an alkaline-sensitive (Caidao) rice cultivar were compared under alkaline stress conditions. A total of 962 important alkali-responsive (IAR) genes from highly differentially expressed genes (DEGs) were identified, including 28 alkaline-resistant cultivar-related genes, 771 alkaline-sensitive cultivar-related genes and 163 cultivar-non-specific genes. Gene ontology (GO) analysis indicated the enrichment of IAR genes involved in various stimulus or stress responses. According to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, the IAR genes were related primarily to plant hormone signal transduction and biosynthesis of secondary metabolites. Additionally, among these 962 IAR genes, 74 were transcription factors and 15 occurred with differential alternative splicing between the different samples after alkaline treatment. Our results provide a valuable resource on alkali-responsive genes and should benefit the improvement of alkaline stress tolerance in rice.
Collapse
Affiliation(s)
- Ning Li
- Rice Research Institute, College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Hualong Liu
- Rice Research Institute, College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Jian Sun
- Rice Research Institute, College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Hongliang Zheng
- Rice Research Institute, College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Jingguo Wang
- Rice Research Institute, College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Luomiao Yang
- Rice Research Institute, College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Hongwei Zhao
- Rice Research Institute, College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Detang Zou
- Rice Research Institute, College of Agriculture, Northeast Agricultural University, Harbin, China.
| |
Collapse
|
9
|
Genome-Wide Identification of the Alba Gene Family in Plants and Stress-Responsive Expression of the Rice Alba Genes. Genes (Basel) 2018; 9:genes9040183. [PMID: 29597290 PMCID: PMC5924525 DOI: 10.3390/genes9040183] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 01/26/2018] [Accepted: 01/29/2018] [Indexed: 11/17/2022] Open
Abstract
Architectural proteins play key roles in genome construction and regulate the expression of many genes, albeit the modulation of genome plasticity by these proteins is largely unknown. A critical screening of the architectural proteins in five crop species, viz., Oryza sativa, Zea mays, Sorghum bicolor, Cicer arietinum, and Vitis vinifera, and in the model plant Arabidopsis thaliana along with evolutionary relevant species such as Chlamydomonas reinhardtii, Physcomitrella patens, and Amborella trichopoda, revealed 9, 20, 10, 7, 7, 6, 1, 4, and 4 Alba (acetylation lowers binding affinity) genes, respectively. A phylogenetic analysis of the genes and of their counterparts in other plant species indicated evolutionary conservation and diversification. In each group, the structural components of the genes and motifs showed significant conservation. The chromosomal location of the Alba genes of rice (OsAlba), showed an unequal distribution on 8 of its 12 chromosomes. The expression profiles of the OsAlba genes indicated a distinct tissue-specific expression in the seedling, vegetative, and reproductive stages. The quantitative real-time PCR (qRT-PCR) analysis of the OsAlba genes confirmed their stress-inducible expression under multivariate environmental conditions and phytohormone treatments. The evaluation of the regulatory elements in 68 Alba genes from the 9 species studied led to the identification of conserved motifs and overlapping microRNA (miRNA) target sites, suggesting the conservation of their function in related proteins and a divergence in their biological roles across species. The 3D structure and the prediction of putative ligands and their binding sites for OsAlba proteins offered a key insight into the structure-function relationship. These results provide a comprehensive overview of the subtle genetic diversification of the OsAlba genes, which will help in elucidating their functional role in plants.
Collapse
|
10
|
Wang D, Liu J, Li C, Kang H, Wang Y, Tan X, Liu M, Deng Y, Wang Z, Liu Y, Zhang D, Xiao Y, Wang GL. Genome-wide Association Mapping of Cold Tolerance Genes at the Seedling Stage in Rice. RICE (NEW YORK, N.Y.) 2016; 9:61. [PMID: 27848161 PMCID: PMC5110459 DOI: 10.1186/s12284-016-0133-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Accepted: 11/03/2016] [Indexed: 05/17/2023]
Abstract
BACKGROUND Rice is a temperature-sensitive crop and its production is severely affected by low temperature in temperate and sub-tropical regions. To understand the genetic basis of cold tolerance in rice, we evaluated the cold tolerance at the seedling stage (CTS) of 295 rice cultivars in the rice diversity panel 1 (RDP1), these cultivars were collected from 82 countries. RESULTS The evaluations revealed that both temperate and tropical japonica rice cultivars are more tolerant to cold stress than indica and AUS cultivars. Using the cold tolerance phenotypes and 44 K SNP chip dataset of RDP1, we performed genome-wide association mapping of quantitative trait loci (QTLs) for CTS. The analysis identified 67 QTLs for CTS that are located on 11 chromosomes. Fifty-six of these QTLs are located in regions without known cold tolerance-related QTLs. CONCLUSION Our study has provided new information on the genetic architecture of rice cold tolerance and has also identified highly cold tolerant cultivars and CTS-associated SNP markers that will be useful rice improvement.
Collapse
Affiliation(s)
- Dan Wang
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China and College of Agronomy, Hunan Agricultural University, Changsha, Hunan, 410128, China
| | - Jinling Liu
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China and College of Agronomy, Hunan Agricultural University, Changsha, Hunan, 410128, China
| | - Chengang Li
- Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, Hunan, 410128, 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
| | - Yue Wang
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China and College of Agronomy, Hunan Agricultural University, Changsha, Hunan, 410128, China
| | - Xinqiu Tan
- Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, Hunan, 410128, China
| | - Minghao Liu
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China and College of Agronomy, Hunan Agricultural University, Changsha, Hunan, 410128, China
| | - Yufei Deng
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China and College of Agronomy, Hunan Agricultural University, Changsha, Hunan, 410128, China
| | - Zhilong Wang
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China and College of Agronomy, Hunan Agricultural University, Changsha, Hunan, 410128, China
| | - Yong Liu
- Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, Hunan, 410128, China
| | - Deyong Zhang
- Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, Hunan, 410128, China
| | - Yinghui Xiao
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China and College of Agronomy, Hunan Agricultural University, Changsha, Hunan, 410128, China.
| | - Guo-Liang Wang
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China and College of Agronomy, Hunan Agricultural University, Changsha, Hunan, 410128, China.
- Department of Plant Pathology, Ohio State University, Columbus, OH, 43210, USA.
| |
Collapse
|
11
|
Metabolic Pathway Involved in 6-Chloro-2-Benzoxazolinone Degradation by Pigmentiphaga sp. Strain DL-8 and Identification of the Novel Metal-Dependent Hydrolase CbaA. Appl Environ Microbiol 2016; 82:4169-4179. [PMID: 27208123 DOI: 10.1128/aem.00532-16] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 04/27/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED 6-Chloro-2-benzoxazolinone (CDHB) is a precursor of herbicide, insecticide, and fungicide synthesis and has a broad spectrum of biological activity. Pigmentiphaga sp. strain DL-8 can transform CDHB into 2-amino-5-chlorophenol (2A5CP), which it then utilizes as a carbon source for growth. The CDHB hydrolase (CbaA) was purified from strain DL-8, which can also hydrolyze 2-benzoxazolinone (BOA), 5-chloro-2-BOA, and benzamide. The specific activity of purified CbaA was 5,900 U · mg protein(-1) for CDHB, with Km and kcat values of 0.29 mM and 8,500 s(-1), respectively. The optimal pH for purified CbaA was 9.0, the highest activity was observed at 55°C, and the inactive metal-free enzyme could be reactivated by Mg(2+), Ni(2+), Ca(2+), or Zn(2+) Based on the results obtained for the CbaA peptide mass fingerprinting and draft genome sequence of strain DL-8, cbaA (encoding 339 amino acids) was cloned and expressed in Escherichia coli BL21(DE3). CbaA shared 18 to 21% identity with some metal-dependent hydrolases of the PF01499 family and contained the signature metal-binding motif Q127XXXQ131XD133XXXH137 The conserved amino acid residues His288 and Glu301 served as the proton donor and acceptor. E. coli BL21(DE3-pET-cbaA) resting cells could transform 0.2 mM CDHB into 2A5CP. The mutant strain DL-8ΔcbaA lost the ability to degrade CDHB but retained the ability to degrade 2A5CP, consistent with strain DL-8. These results indicated that cbaA was the key gene responsible for CDHB degradation by strain DL-8. IMPORTANCE 2-Benzoxazolinone (BOA) derivatives are widely used as synthetic intermediates and are also an important group of allelochemicals acting in response to tissue damage or pathogen attack in gramineous plants. However, the degradation mechanism of BOA derivatives by microorganisms is not clear. In the present study, we reported the identification of CbaA and metabolic pathway responsible for the degradation of CDHB in Pigmentiphaga sp. DL-8. This will provide microorganism and gene resources for the bioremediation of the environmental pollution caused by BOA derivatives.
Collapse
|
12
|
Wang Z, Wang Y, Yang J, Hu K, An B, Deng X, Li Y. Reliable Selection and Holistic Stability Evaluation of Reference Genes for Rice Under 22 Different Experimental Conditions. Appl Biochem Biotechnol 2016; 179:753-75. [PMID: 26940571 DOI: 10.1007/s12010-016-2029-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Accepted: 02/22/2016] [Indexed: 01/26/2023]
Abstract
Stable and uniform expression of reference genes across samples plays a key role in accurate normalization of gene expression by reverse-transcription quantitative polymerase chain reaction (RT-qPCR). For rice study, there is still a lack of validation and recommendation of appropriate reference genes with high stability depending on experimental conditions. Eleven candidate reference genes potentially owning high stability were evaluated by geNorm and NormFinder for their expression stability in 22 various experimental conditions. Best combinations of multiple reference genes were recommended depending on experimental conditions, and the holistic stability of reference genes was also evaluated. Reference genes would become more variable and thus needed to be critically selected in experimental groups of tissues, heat, 6-benzylamino purine, and drought, but they were comparatively stable under cold, wound, and ultraviolet-B stresses. Triosephosphate isomerase (TI), profilin-2 (Profilin-2), ubiquitin-conjugating enzyme E2 (UBC), endothelial differentiation factor (Edf), and ADP-ribosylation factor (ARF) were stable in most of our experimental conditions. No universal reference gene showed good stability in all experimental conditions. To get accurate expression result, suitable combination of multiple reference genes for a specific experimental condition would be a better choice. This study provided an application guideline to select stable reference genes for rice gene expression study.
Collapse
Affiliation(s)
- Zhaohai Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Hubei, 430072, People's Republic of China
| | - Ya Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Hubei, 430072, People's Republic of China
| | - Jing Yang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Hubei, 430072, People's Republic of China
| | - Keke Hu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Hubei, 430072, People's Republic of China
| | - Baoguang An
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Hubei, 430072, People's Republic of China
| | - Xiaolong Deng
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Hubei, 430072, People's Republic of China
| | - Yangsheng Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Hubei, 430072, People's Republic of China. .,State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, Ministry of Agriculture, College of Life Sciences, Wuhan University, Hubei, 430072, People's Republic of China.
| |
Collapse
|