1
|
Li X, Wang H, Xiao C, Huang J, Long Y, Lin C, Zhu Y, Wang M, Liu Y, Zhang Q. High-throughput selective sweep SNP-guided cloning of cold-tolerance genes in rice. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:2104-2106. [PMID: 38451603 PMCID: PMC11258967 DOI: 10.1111/pbi.14329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 10/16/2023] [Accepted: 02/24/2024] [Indexed: 03/08/2024]
Affiliation(s)
- Xiaoxia Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Hongmei Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Chujian Xiao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Juan Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Yuting Long
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Chuxin Lin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Yue Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Man Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Yao‐Guang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Qunyu Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| |
Collapse
|
2
|
Zhai M, Chen Y, Pan X, Chen Y, Zhou J, Jiang X, Zhang Z, Xiao G, Zhang H. OsEIN2-OsEIL1/2 pathway negatively regulates chilling tolerance by attenuating OsICE1 function in rice. PLANT, CELL & ENVIRONMENT 2024; 47:2561-2577. [PMID: 38518060 DOI: 10.1111/pce.14900] [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: 10/20/2023] [Revised: 02/27/2024] [Accepted: 03/11/2024] [Indexed: 03/24/2024]
Abstract
Low temperature severely affects rice development and yield. Ethylene signal is essential for plant development and stress response. Here, we reported that the OsEIN2-OsEIL1/2 pathway reduced OsICE1-dependent chilling tolerance in rice. The overexpressing plants of OsEIN2, OsEIL1 and OsEIL2 exhibited severe stress symptoms with excessive reactive oxygen species (ROS) accumulation under chilling, while the mutants (osein2 and oseil1) and OsEIL2-RNA interference plants (OsEIL2-Ri) showed the enhanced chilling tolerance. We validated that OsEIL1 and OsEIL2 could form a heterxodimer and synergistically repressed OsICE1 expression by binding to its promoter. The expression of OsICE1 target genes, ROS scavenging- and photosynthesis-related genes were downregulated by OsEIN2 and OsEIL1/2, which were activated by OsICE1, suggesting that OsEIN2-OsEIL1/2 pathway might mediate ROS accumulation and photosynthetic capacity under chilling by attenuating OsICE1 function. Moreover, the association analysis of the seedling chilling tolerance with the haplotype showed that the lower expression of OsEIL1 and OsEIL2 caused by natural variation might confer chilling tolerance on rice seedlings. Finally, we generated OsEIL2-edited rice with an enhanced chilling tolerance. Taken together, our findings reveal a possible mechanism integrating OsEIN2-OsEIL1/2 pathway with OsICE1-dependent cascade in regulating chilling tolerance, providing a practical strategy for breeding chilling-tolerant rice.
Collapse
Affiliation(s)
- Mingjuan Zhai
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yating Chen
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Xiaowu Pan
- Hunan Rice Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Ying Chen
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiahao Zhou
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaodan Jiang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhijin Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guiqing Xiao
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Haiwen Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| |
Collapse
|
3
|
Shahzad N, Nabi HG, Qiao L, Li W. The Molecular Mechanism of Cold-Stress Tolerance: Cold Responsive Genes and Their Mechanisms in Rice ( Oryza sativa L.). BIOLOGY 2024; 13:442. [PMID: 38927322 PMCID: PMC11200503 DOI: 10.3390/biology13060442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024]
Abstract
Rice (Oryza sativa L.) production is highly susceptible to temperature fluctuations, which can significantly reduce plant growth and development at different developmental stages, resulting in a dramatic loss of grain yield. Over the past century, substantial efforts have been undertaken to investigate the physiological, biochemical, and molecular mechanisms of cold stress tolerance in rice. This review aims to provide a comprehensive overview of the recent developments and trends in this field. We summarized the previous advancements and methodologies used for identifying cold-responsive genes and the molecular mechanisms of cold tolerance in rice. Integration of new technologies has significantly improved studies in this era, facilitating the identification of essential genes, QTLs, and molecular modules in rice. These findings have accelerated the molecular breeding of cold-resistant rice varieties. In addition, functional genomics, including the investigation of natural variations in alleles and artificially developed mutants, is emerging as an exciting new approach to investigating cold tolerance. Looking ahead, it is imperative for scientists to evaluate the collective impacts of these novel genes to develop rice cultivars resilient to global climate change.
Collapse
Affiliation(s)
- Nida Shahzad
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Life Sciences, Northwest A&F University, Xianyang 712100, China; (N.S.); (L.Q.)
| | - Hafiz Ghulam Nabi
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China;
| | - Lei Qiao
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Life Sciences, Northwest A&F University, Xianyang 712100, China; (N.S.); (L.Q.)
| | - Wenqiang Li
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Life Sciences, Northwest A&F University, Xianyang 712100, China; (N.S.); (L.Q.)
| |
Collapse
|
4
|
Xiong J, Wen G, Song J, Liu X, Chen Q, Zhang G, Xiao Y, Liu X, Deng H, Tang W, Wang F, Lu X. Knockout of the Chlorophyll a Oxygenase Gene OsCAO1 Reduces Chilling Tolerance in Rice Seedlings. Genes (Basel) 2024; 15:721. [PMID: 38927664 PMCID: PMC11202714 DOI: 10.3390/genes15060721] [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: 05/09/2024] [Revised: 05/27/2024] [Accepted: 05/28/2024] [Indexed: 06/28/2024] Open
Abstract
Chilling stress is one of the main abiotic factors affecting rice growth and yield. In rice, chlorophyllide a oxygenase encoded by OsCAO1 is responsible for converting chlorophyllide a to chlorophyllide b, playing a crucial role in photosynthesis and thus rice growth. However, little is known about the function of OsCAO1 in chilling stress responses. The presence of the cis-acting element involved in low-temperature responsiveness (LTR) in the OsCAO1 promoter implied that OsCAO1 probably is a cold-responsive gene. The gene expression level of OsCAO1 was usually inhibited by low temperatures during the day and promoted by low temperatures at night. The OsCAO1 knockout mutants generated by the CRISPR-Cas9 technology in rice (Oryza sativa L.) exhibited significantly weakened chilling tolerance at the seedling stage. OsCAO1 dysfunction led to the accumulation of reactive oxygen species and malondialdehyde, an increase in relative electrolyte leakage, and a reduction in antioxidant gene expression under chilling stress. In addition, the functional deficiency of OsCAO1 resulted in more severe damage to chloroplast morphology, such as abnormal grana thylakoid stacking, caused by low temperatures. Moreover, the rice yield was reduced in OsCAO1 knockout mutants. Therefore, the elevated expression of OsCAO1 probably has the potential to increase both rice yield and chilling tolerance simultaneously, providing a strategy to cultivate chilling-tolerant rice varieties with high yields.
Collapse
Affiliation(s)
- Jiayi Xiong
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China; (J.X.); (G.W.); (J.S.); (X.L.); (Q.C.); (G.Z.); (Y.X.); (X.L.); (H.D.); (F.W.)
- Yuelushan Laboratory, Changsha 410128, China;
| | - Genping Wen
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China; (J.X.); (G.W.); (J.S.); (X.L.); (Q.C.); (G.Z.); (Y.X.); (X.L.); (H.D.); (F.W.)
- Yuelushan Laboratory, Changsha 410128, China;
| | - Jin Song
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China; (J.X.); (G.W.); (J.S.); (X.L.); (Q.C.); (G.Z.); (Y.X.); (X.L.); (H.D.); (F.W.)
- Yuelushan Laboratory, Changsha 410128, China;
| | - Xiaoyi Liu
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China; (J.X.); (G.W.); (J.S.); (X.L.); (Q.C.); (G.Z.); (Y.X.); (X.L.); (H.D.); (F.W.)
- Yuelushan Laboratory, Changsha 410128, China;
| | - Qiuhong Chen
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China; (J.X.); (G.W.); (J.S.); (X.L.); (Q.C.); (G.Z.); (Y.X.); (X.L.); (H.D.); (F.W.)
- Yuelushan Laboratory, Changsha 410128, China;
| | - Guilian Zhang
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China; (J.X.); (G.W.); (J.S.); (X.L.); (Q.C.); (G.Z.); (Y.X.); (X.L.); (H.D.); (F.W.)
- Yuelushan Laboratory, Changsha 410128, China;
| | - Yunhua Xiao
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China; (J.X.); (G.W.); (J.S.); (X.L.); (Q.C.); (G.Z.); (Y.X.); (X.L.); (H.D.); (F.W.)
- Yuelushan Laboratory, Changsha 410128, China;
| | - Xiong Liu
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China; (J.X.); (G.W.); (J.S.); (X.L.); (Q.C.); (G.Z.); (Y.X.); (X.L.); (H.D.); (F.W.)
- Yuelushan Laboratory, Changsha 410128, China;
| | - Huabing Deng
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China; (J.X.); (G.W.); (J.S.); (X.L.); (Q.C.); (G.Z.); (Y.X.); (X.L.); (H.D.); (F.W.)
- Yuelushan Laboratory, Changsha 410128, China;
| | - Wenbang Tang
- Yuelushan Laboratory, Changsha 410128, China;
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Feng Wang
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China; (J.X.); (G.W.); (J.S.); (X.L.); (Q.C.); (G.Z.); (Y.X.); (X.L.); (H.D.); (F.W.)
- Yuelushan Laboratory, Changsha 410128, China;
| | - Xuedan Lu
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China; (J.X.); (G.W.); (J.S.); (X.L.); (Q.C.); (G.Z.); (Y.X.); (X.L.); (H.D.); (F.W.)
- Yuelushan Laboratory, Changsha 410128, China;
| |
Collapse
|
5
|
Hou XL, Han X, Meng Y, Wang L, Zhang W, Yang C, Li H, Tang S, Guo Z, Liu C, Qin Y, Zhang S, Shui G, Cao X, Song X. Acyl carrier protein OsMTACP2 confers rice cold tolerance at the booting stage. PLANT PHYSIOLOGY 2024; 195:1277-1292. [PMID: 38431526 DOI: 10.1093/plphys/kiae118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/19/2024] [Accepted: 01/21/2024] [Indexed: 03/05/2024]
Abstract
Low temperatures occurring at the booting stage in rice (Oryza sativa L.) often result in yield loss by impeding male reproductive development. However, the underlying mechanisms by which rice responds to cold at this stage remain largely unknown. Here, we identified MITOCHONDRIAL ACYL CARRIER PROTEIN 2 (OsMTACP2), the encoded protein of which mediates lipid metabolism involved in the cold response at the booting stage. Loss of OsMTACP2 function compromised cold tolerance, hindering anther cuticle and pollen wall development, resulting in abnormal anther morphology, lower pollen fertility, and seed setting. OsMTACP2 was highly expressed in tapetal cells and microspores during anther development, with the encoded protein localizing to both mitochondria and the cytoplasm. Comparative transcriptomic analysis revealed differential expression of genes related to lipid metabolism between the wild type and the Osmtacp2-1 mutant in response to cold. Through a lipidomic analysis, we demonstrated that wax esters, which are the primary lipid components of the anther cuticle and pollen walls, function as cold-responsive lipids. Their levels increased dramatically in the wild type but not in Osmtacp2-1 when exposed to cold. Additionally, mutants of two cold-induced genes of wax ester biosynthesis, ECERIFERUM1 and WAX CRYSTAL-SPARSE LEAF2, showed decreased cold tolerance. These results suggest that OsMTACP2-mediated wax ester biosynthesis is essential for cold tolerance in rice at the booting stage.
Collapse
Affiliation(s)
- Xiu-Li Hou
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiangyan Han
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Ying Meng
- Institute of Crop Cultivation and Tillage, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China
| | - Lizhi Wang
- Institute of Crop Cultivation and Tillage, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China
| | - Wenqi Zhang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chao Yang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hui Li
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shanjie Tang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhenhua Guo
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chunyan Liu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yongmei Qin
- College of Life Sciences, Peking University, Beijing 100871, China
| | - Shaohua Zhang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Guanghou Shui
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaofeng Cao
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xianwei Song
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- Key Laboratory of Seed Innovation, Chinese Academy of Sciences, Beijing 100101, China
| |
Collapse
|
6
|
Li R, Song Y, Wang X, Zheng C, Liu B, Zhang H, Ke J, Wu X, Wu L, Yang R, Jiang M. OsNAC5 orchestrates OsABI5 to fine-tune cold tolerance in rice. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:660-682. [PMID: 37968901 DOI: 10.1111/jipb.13585] [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: 08/31/2023] [Accepted: 11/14/2023] [Indexed: 11/17/2023]
Abstract
Due to its tropical origins, rice (Oryza sativa) is susceptible to cold stress, which poses severe threats to production. OsNAC5, a NAC-type transcription factor, participates in the cold stress response of rice, but the detailed mechanisms remain poorly understood. Here, we demonstrate that OsNAC5 positively regulates cold tolerance at germination and in seedlings by directly activating the expression of ABSCISIC ACID INSENSITIVE 5 (OsABI5). Haplotype analysis indicated that single nucleotide polymorphisms in a NAC-binding site in the OsABI5 promoter are strongly associated with cold tolerance. OsNAC5 also enhanced OsABI5 stability, thus regulating the expression of cold-responsive (COR) genes, enabling fine-tuned control of OsABI5 action for rapid, precise plant responses to cold stress. DNA affinity purification sequencing coupled with transcriptome deep sequencing identified several OsABI5 target genes involved in COR expression, including DEHYDRATION-RESPONSIVE ELEMENT BINDING FACTOR 1A (OsDREB1A), OsMYB20, and PEROXIDASE 70 (OsPRX70). In vivo and in vitro analyses suggested that OsABI5 positively regulates COR gene transcription, with marked COR upregulation in OsNAC5-overexpressing lines and downregulation in osnac5 and/or osabi5 knockout mutants. This study extends our understanding of cold tolerance regulation via OsNAC5 through the OsABI5-CORs transcription module, which may be used to ameliorate cold tolerance in rice via advanced breeding.
Collapse
Affiliation(s)
- Ruiqing Li
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Yue Song
- Hainan Institute, Yazhou Bay Sci-Tech City, Zhejiang University, Sanya, 572025, China
- National Key Laboratory of Rice Biology, Advanced Seed Institute, Zhejiang University, Hangzhou, 311225, China
| | - Xueqiang Wang
- Hainan Institute, Yazhou Bay Sci-Tech City, Zhejiang University, Sanya, 572025, China
- National Key Laboratory of Rice Biology, Advanced Seed Institute, Zhejiang University, Hangzhou, 311225, China
| | - Chenfan Zheng
- Hainan Institute, Yazhou Bay Sci-Tech City, Zhejiang University, Sanya, 572025, China
- National Key Laboratory of Rice Biology, Advanced Seed Institute, Zhejiang University, Hangzhou, 311225, China
| | - Bo Liu
- Hainan Institute, Yazhou Bay Sci-Tech City, Zhejiang University, Sanya, 572025, China
- National Key Laboratory of Rice Biology, Advanced Seed Institute, Zhejiang University, Hangzhou, 311225, China
| | - Huali Zhang
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 311401, China
| | - Jian Ke
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Xuejing Wu
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Liquan Wu
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Ruifang Yang
- Key Laboratory of Germplasm Innovation and Genetic Improvement of Grain and Oil Crops (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
| | - Meng Jiang
- Hainan Institute, Yazhou Bay Sci-Tech City, Zhejiang University, Sanya, 572025, China
- National Key Laboratory of Rice Biology, Advanced Seed Institute, Zhejiang University, Hangzhou, 311225, China
| |
Collapse
|
7
|
Deng H, Cao S, Zhang G, Xiao Y, Liu X, Wang F, Tang W, Lu X. OsVPE2, a Member of Vacuolar Processing Enzyme Family, Decreases Chilling Tolerance of Rice. RICE (NEW YORK, N.Y.) 2024; 17:5. [PMID: 38194166 PMCID: PMC10776553 DOI: 10.1186/s12284-023-00682-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 12/29/2023] [Indexed: 01/10/2024]
Abstract
Chilling is a major abiotic stress affecting rice growth, development and geographical distribution. Plant vacuolar processing enzymes (VPEs) contribute to the seed storage protein processing and mediate the programmed cell death by abiotic and biotic stresses. However, little is known about the roles of plant VPEs in cold stress responses and tolerance regulation. Here, we found that OsVPE2 was a chilling-responsive gene. The early-indica rice variety Xiangzaoxian31 overexpressing OsVPE2 was more sensitive to chilling stress, whereas the OsVPE2-knockout mutants generated by the CRISPR-Cas9 technology exhibited significantly enhanced chilling tolerance at the seedling stage without causing yield loss. Deficiency of OsVPE2 reduces relative electrolyte leakage, accumulation of toxic compounds such as reactive oxygen species and malondialdehyde, and promotes antioxidant enzyme activities under chilling stress conditions. It was indicated that OsVPE2 mediated the disintegration of vacuoles under chilling stress, accompanied by the entry of swollen mitochondria into vacuoles. OsVPE2 suppressed the expression of genes that have a positive regulatory role in antioxidant process. Moreover, haplotype analysis suggested that the natural variation in the OsVPE2 non-coding region may endow OsVPE2 with different expression levels, thereby probably conferring differences in cold tolerance between japonica and indica sub-population. Our results thus reveal a new biological function of the VPE family in regulating cold resistance, and suggest that the gene editing or natural variations of OsVPE2 can be used to create cold tolerant rice varieties with stable yield.
Collapse
Affiliation(s)
- Huabing Deng
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
- Yuelushan Laboratory, Changsha, 410128, China
| | - Sai Cao
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
- Yuelushan Laboratory, Changsha, 410128, China
| | - Guilian Zhang
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
- Yuelushan Laboratory, Changsha, 410128, China
| | - Yunhua Xiao
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
- Yuelushan Laboratory, Changsha, 410128, China
| | - Xiong Liu
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
- Yuelushan Laboratory, Changsha, 410128, China
| | - Feng Wang
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
- Yuelushan Laboratory, Changsha, 410128, China
| | - Wenbang Tang
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha, 410125, China.
- Yuelushan Laboratory, Changsha, 410128, China.
| | - Xuedan Lu
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China.
- Yuelushan Laboratory, Changsha, 410128, China.
| |
Collapse
|
8
|
Gan P, Luo X, Wei H, Hu Y, Li R, Luo J. Identification of hub genes that variate the qCSS12-mediated cold tolerance between indica and japonica rice using WGCNA. PLANT CELL REPORTS 2023; 43:24. [PMID: 38150036 DOI: 10.1007/s00299-023-03093-8] [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: 07/29/2023] [Accepted: 11/05/2023] [Indexed: 12/28/2023]
Abstract
KEY MESSAGE Cold-tolerant QTL qCSS12-regulated 14 hub genes are involved in the chloroplastic biological processes and in the protein synthesis and degradation processes in japonica rice. Low temperature is a main constraint factor for rice growth and production. To better understand the regulatory mechanisms underlying the cold tolerance phenotype in rice, here, we selected a cold-sensitive nearly isogenic line (NIL) NIL(qcss12) as materials to identify hub genes that are mediated by the cold-tolerant locus qCSS12 through weighted gene co-expression network analysis (WGCNA). Fourteen cold-responsive genes were identified, of which, 6 are involved in regulating biological processes in chloroplasts, including the reported EF-Tu, Prk, and ChlD, and 8 are involved in the protein synthesis and degradation processes. Differential expression of these genes between NIL(qcss12) and its controls under cold stress may be responsible for qCSS12-mediated cold tolerance in japonica rice. Moreover, natural variations in 12 of these hub genes are highly correlated with the cold tolerance divergence in two rice subspecies. The results provide deep insights into a better understanding of the molecular basis of cold adaptation in rice and provide a theoretical basis for molecular breeding.
Collapse
Affiliation(s)
- Ping Gan
- College of Life Science and Technology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, 530004, China
| | - Xianglan Luo
- College of Life Science and Technology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, 530004, China
| | - Hanxing Wei
- College of Life Science and Technology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, 530004, China
| | - Yunfei Hu
- College of Life Science and Technology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, 530004, China
| | - Rongbai Li
- College of Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, 530004, China
| | - Jijing Luo
- College of Life Science and Technology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, 530004, China.
| |
Collapse
|
9
|
Schläppi MR, Jessel AR, Jackson AK, Phan H, Jia MH, Edwards JD, Eizenga GC. Navigating rice seedling cold resilience: QTL mapping in two inbred line populations and the search for genes. FRONTIERS IN PLANT SCIENCE 2023; 14:1303651. [PMID: 38162313 PMCID: PMC10755946 DOI: 10.3389/fpls.2023.1303651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 11/20/2023] [Indexed: 01/03/2024]
Abstract
Due to global climate change resulting in extreme temperature fluctuations, it becomes increasingly necessary to explore the natural genetic variation in model crops such as rice to facilitate the breeding of climate-resilient cultivars. To uncover genomic regions in rice involved in managing cold stress tolerance responses and to identify associated cold tolerance genes, two inbred line populations developed from crosses between cold-tolerant and cold-sensitive parents were used for quantitative trait locus (QTL) mapping of two traits: degree of membrane damage after 1 week of cold exposure quantified as percent electrolyte leakage (EL) and percent low-temperature seedling survivability (LTSS) after 1 week of recovery growth. This revealed four EL QTL and 12 LTSS QTL, all overlapping with larger QTL regions previously uncovered by genome-wide association study (GWAS) mapping approaches. Within the QTL regions, 25 cold-tolerant candidate genes were identified based on genomic differences between the cold-tolerant and cold-sensitive parents. Of those genes, 20% coded for receptor-like kinases potentially involved in signal transduction of cold tolerance responses; 16% coded for transcription factors or factors potentially involved in regulating cold tolerance response effector genes; and 64% coded for protein chaperons or enzymes potentially serving as cold tolerance effector proteins. Most of the 25 genes were cold temperature regulated and had deleterious nucleotide variants in the cold-sensitive parent, which might contribute to its cold-sensitive phenotype.
Collapse
Affiliation(s)
- Michael R. Schläppi
- Department of Biological Sciences, Marquette University, Milwaukee, WI, United States
| | - Avery R. Jessel
- Department of Biological Sciences, Marquette University, Milwaukee, WI, United States
| | - Aaron K. Jackson
- Dale Bumpers National Rice Research Center, U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), Stuttgart, AR, United States
| | - Huy Phan
- Department of Biological Sciences, Marquette University, Milwaukee, WI, United States
| | - Melissa H. Jia
- Dale Bumpers National Rice Research Center, U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), Stuttgart, AR, United States
| | - Jeremy D. Edwards
- Dale Bumpers National Rice Research Center, U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), Stuttgart, AR, United States
| | - Georgia C. Eizenga
- Dale Bumpers National Rice Research Center, U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), Stuttgart, AR, United States
| |
Collapse
|
10
|
Baruah AR, Bannai H, Meija Y, Kimura A, Ueno H, Koide Y, Kishima Y, Palta J, Kasuga J, Yamamoto MP, Onishi K. Genetics of chilling response at early growth stage in rice: a recessive gene for tolerance and importance of acclimation. AOB PLANTS 2023; 15:plad075. [PMID: 38028749 PMCID: PMC10676198 DOI: 10.1093/aobpla/plad075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 11/06/2023] [Indexed: 12/01/2023]
Abstract
Low-temperature adaptation in rice is mediated by the ability of a genotype to tolerate chilling temperatures. A genetic locus on chromosome 11 was analysed for chilling tolerance at the plumule stage in rice. The tolerant allele of A58, a japonica landrace in Japan, was inherited as a recessive gene (ctp-1A58), whereas the susceptible alleles from wild rice (Ctp-1W107) and modern variety (Ctp-1HY) were the dominant genes. Another recessive tolerant allele (ctp-1Silewah) was found in a tropical japonica variety (Silewah). Fine-mapping revealed that a candidate gene for the ctp-1 locus encoded a protein similar to the nucleotide-binding domain and leucine-rich repeat (NLR) protein, in which frameshift mutation by a 73 bp-deletion might confer chilling tolerance in ctp-1A58. Analysis of near-isogenic lines demonstrated that ctp-1A58 imparted tolerance effects only at severe chilling temperatures of 0.5 °C and 2 °C, both at plumule and seedling stages. Chilling acclimation treatments at a wide range of temperatures (8 °C-16 °C) for 72 h concealed the susceptible phenotype of Ctp-1W107 and Ctp-1HY. Furthermore, short-term acclimation treatment of 12 h at 8 °C was enough to be fully acclimated. These results suggest that the NLR gene induces a susceptible response upon exposure to severe chilling stress, however, another interacting gene(s) for acclimation response could suppress the maladaptive phenotype caused by the Ctp-1 allele. This study provides new insights for the adaptation and breeding of rice in a low-temperature environment.
Collapse
Affiliation(s)
- Akhil Ranjan Baruah
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat-13, Assam, India
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
| | - Hiroaki Bannai
- Department of Agro-Environmental Science, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido 080-8555, Japan
| | - Yan Meija
- Department of Agro-Environmental Science, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido 080-8555, Japan
| | - Ayumi Kimura
- Department of Agro-Environmental Science, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido 080-8555, Japan
| | - Haruka Ueno
- Department of Agro-Environmental Science, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido 080-8555, Japan
| | - Yohei Koide
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
| | - Yuji Kishima
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
| | - Jiwan Palta
- Department of Horticulture, University of Wisconsin-Madison, 490 Moore Hall, 1575 Linden Drive, Madison, WI 53706, USA
| | - Jun Kasuga
- Department of Agro-Environmental Science, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido 080-8555, Japan
| | - Masayuki P Yamamoto
- Faculty of Science, Academic Assembly, University of Toyama, 3190 Gofuku, Toyama 930-8555, Japan
| | - Kazumitsu Onishi
- Department of Agro-Environmental Science, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido 080-8555, Japan
| |
Collapse
|
11
|
Mei C, Yang J, Mei Q, Jia D, Yan P, Feng B, Mamat A, Gong X, Guan Q, Mao K, Wang J, Ma F. MdNAC104 positively regulates apple cold tolerance via CBF-dependent and CBF-independent pathways. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:2057-2073. [PMID: 37387580 PMCID: PMC10502760 DOI: 10.1111/pbi.14112] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 06/15/2023] [Accepted: 06/17/2023] [Indexed: 07/01/2023]
Abstract
Low temperature is the main environmental factor affecting the yield, quality and geographical distribution of crops, which significantly restricts development of the fruit industry. The NAC (NAM, ATAF1/2 and CUC2) transcription factor (TF) family is involved in regulating plant cold tolerance, but the mechanisms underlying these regulatory processes remain unclear. Here, the NAC TF MdNAC104 played a positive role in modulating apple cold tolerance. Under cold stress, MdNAC104-overexpressing transgenic plants exhibited less ion leakage and lower ROS (reactive oxygen species) accumulation, but higher contents of osmoregulatory substances and activities of antioxidant enzymes. Transcriptional regulation analysis showed that MdNAC104 directly bound to the MdCBF1 and MdCBF3 promoters to promote expression. In addition, based on combined transcriptomic and metabolomic analyses, as well as promoter binding and transcriptional regulation analyses, we found that MdNAC104 stimulated the accumulation of anthocyanin under cold conditions by upregulating the expression of anthocyanin synthesis-related genes, including MdCHS-b, MdCHI-a, MdF3H-a and MdANS-b, and increased the activities of the antioxidant enzymes by promoting the expression of the antioxidant enzyme-encoding genes MdFSD2 and MdPRXR1.1. In conclusion, this study revealed the MdNAC104 regulatory mechanism of cold tolerance in apple via CBF-dependent and CBF-independent pathways.
Collapse
Affiliation(s)
- Chuang Mei
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of HorticultureNorthwest A & F UniversityYanglingShaanxiChina
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticulture CropsXinjiang Academy of Agricultural SciencesUrumqiChina
| | - Jie Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of HorticultureNorthwest A & F UniversityYanglingShaanxiChina
| | - Quanlin Mei
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of HorticultureNorthwest A & F UniversityYanglingShaanxiChina
| | - Dongfeng Jia
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of HorticultureNorthwest A & F UniversityYanglingShaanxiChina
| | - Peng Yan
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticulture CropsXinjiang Academy of Agricultural SciencesUrumqiChina
| | - Beibei Feng
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticulture CropsXinjiang Academy of Agricultural SciencesUrumqiChina
| | - Aisajan Mamat
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticulture CropsXinjiang Academy of Agricultural SciencesUrumqiChina
| | - Xiaoqing Gong
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of HorticultureNorthwest A & F UniversityYanglingShaanxiChina
| | - Qingmei Guan
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of HorticultureNorthwest A & F UniversityYanglingShaanxiChina
| | - Ke Mao
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of HorticultureNorthwest A & F UniversityYanglingShaanxiChina
| | - Jixun Wang
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticulture CropsXinjiang Academy of Agricultural SciencesUrumqiChina
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of HorticultureNorthwest A & F UniversityYanglingShaanxiChina
| |
Collapse
|
12
|
Cantos CF, dePamphilis CW, Assmann SM. Extra-large G proteins have extra-large effects on agronomic traits and stress tolerance in maize and rice. TRENDS IN PLANT SCIENCE 2023; 28:1033-1044. [PMID: 37156701 PMCID: PMC10524845 DOI: 10.1016/j.tplants.2023.04.005] [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: 07/04/2022] [Revised: 04/01/2023] [Accepted: 04/04/2023] [Indexed: 05/10/2023]
Abstract
Heterotrimeric G proteins - comprising Gα, Gβ, and Gγ subunits - are ubiquitous elements in eukaryotic cell signaling. Plant genomes contain both canonical Gα subunit genes and a family of plant-specific extra-large G protein genes (XLGs) that encode proteins consisting of a domain with Gα-like features downstream of a long N-terminal domain. In this review we summarize phenotypes modulated by the canonical Gα and XLG proteins of arabidopsis and highlight recent studies in maize and rice that reveal dramatic phenotypic consequences of XLG clustered regularly interspaced short palindromic repeats (CRISPR) mutagenesis in these important crop species. XLGs have both redundant and specific roles in the control of agronomically relevant plant architecture and resistance to both abiotic and biotic stresses. We also point out areas of current controversy, suggest future research directions, and propose a revised, phylogenetically-based nomenclature for XLG protein genes.
Collapse
Affiliation(s)
- Christian F Cantos
- Biology Department, Penn State University, University Park, State College, PA, USA; Intercollege Graduate Degree Program in Plant Biology, Penn State University, University Park, State College, PA, USA
| | - Claude W dePamphilis
- Biology Department, Penn State University, University Park, State College, PA, USA; Intercollege Graduate Degree Program in Plant Biology, Penn State University, University Park, State College, PA, USA
| | - Sarah M Assmann
- Biology Department, Penn State University, University Park, State College, PA, USA; Intercollege Graduate Degree Program in Plant Biology, Penn State University, University Park, State College, PA, USA.
| |
Collapse
|
13
|
Yu Y, Wu Y, Liu W, Liu J, Li P. Integration of Metabolome and Transcriptome Reveals the Major Metabolic Pathways and Potential Biomarkers in Response to Freeze-Stress Regulation in Apple ( Malus domestica). Metabolites 2023; 13:891. [PMID: 37623835 PMCID: PMC10456784 DOI: 10.3390/metabo13080891] [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: 06/14/2023] [Revised: 07/23/2023] [Accepted: 07/26/2023] [Indexed: 08/26/2023] Open
Abstract
Freezing stress is the main factor affecting the normal growth and distribution of plants. The safe overwintering of a perennial deciduous plant is a crucial link to ensuring its survival and yield. However, little is known about the molecular mechanism of its gene regulation metabolites as related to its freeze-tolerance. In order to enhance our comprehension of freeze-tolerance metabolites and gene expression in dormant apple trees, we examined the metabolic and transcriptomic differences between 'Ralls' and 'Fuji', two apple varieties with varying degrees of resistance to freezing. The results of the freezing treatment showed that 'Ralls' had stronger freeze-tolerance than 'Fuji'. We identified 302, 334, and 267 up-regulated differentially accumulated metabolites (DAMs) and 408, 387, and 497 down-regulated DAMs between 'Ralls' and 'Fuji' under -10, -15, and -20 °C treatment, respectively. A total of 359 shared metabolites were obtained in the upward trend modules, of which 62 metabolites were associated with 89 pathways. The number of up-regulated genes accounted for 50.2%, 45.6%, and 43.2% of the total number of differentially expressed genes (DEGs), respectively, at -10, -15, and -20 °C. Through combined transcriptome and metabolome analysis, we identified 12 pathways that included 16 DAMs and 65 DEGs. Meanwhile, we found that 20 DEGs were identified in the phenylpropanoid biosynthesis pathway and its related pathways, involving the metabolism of p-Coumaroyl-CoA, 7, 4'-Dihydroxyflavone, and scolymoside. These discoveries advance our comprehension of the molecular mechanism underlying apple freeze-tolerance and provide genetic material for breeding apple cultivars with enhanced freeze-tolerance.
Collapse
Affiliation(s)
- Yifei Yu
- Hebei Academy of Forestry and Grassland Sciences, Shijiazhuang 050061, China
| | - YaJing Wu
- Hebei Academy of Forestry and Grassland Sciences, Shijiazhuang 050061, China
| | - Wenfei Liu
- Hebei Academy of Forestry and Grassland Sciences, Shijiazhuang 050061, China
| | - Jun Liu
- Hebei Academy of Forestry and Grassland Sciences, Shijiazhuang 050061, China
| | - Ping Li
- College of Landscape and Tourism, Hebei Agricultural University, Baoding 071000, China
| |
Collapse
|
14
|
Yan T, Sun M, Su R, Wang X, Lu X, Xiao Y, Deng H, Liu X, Tang W, Zhang G. Transcriptomic Profiling of Cold Stress-Induced Differentially Expressed Genes in Seedling Stage of Indica Rice. PLANTS (BASEL, SWITZERLAND) 2023; 12:2675. [PMID: 37514289 PMCID: PMC10384097 DOI: 10.3390/plants12142675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/15/2023] [Accepted: 07/15/2023] [Indexed: 07/30/2023]
Abstract
Cold stress significantly constrains the growth, development, productivity, and distribution of rice, particularly the indica cultivar, known for its susceptibility to cold, limiting its cultivation to specific regions. This study investigated the genes associated with cold responsiveness in the roots of two indica cultivars, SQSL (cold-tolerant) and XZX45 (cold-susceptible), through transcriptome dynamics analysis during the seedling stage. The analysis identified 8144 and 6427 differentially expressed genes (DEGs) in XZX45 and SQSL, respectively. Among these DEGs, 4672 (G2) were shared by both cultivars, while 3472 DEGs (G1) were specific to XZX45, and 1755 DEGs (G3) were specific to SQSL. Additionally, 572 differentially expressed transcription factors (TFs) from 48 TF families, including WRKY, NAC, bHLH, ERF, bZIP, MYB, C2H2, and GRAS, were identified. Gene Ontology (GO) enrichment analysis revealed significant enrichment of DEGs in the G3 group, particularly in the "response to cold" category, highlighting the crucial role of these specific genes in response to cold stress in SQSL. Furthermore, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated pronounced enrichment of DEGs in the G3 group in metabolic pathways such as "Pyruvate metabolism", "Glycolysis/Gluconeogenesis", and "Starch and sucrose metabolism", contributing to cold tolerance mechanisms in SQSL. Overall, this study provides comprehensive insights into the molecular mechanisms underlying cold responses in the indica cultivar, informing future genetic improvement strategies to enhance cold tolerance in susceptible indica rice cultivars.
Collapse
Affiliation(s)
- Tao Yan
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410128, China
| | - Meng Sun
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410128, China
| | - Rui Su
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410128, China
| | - Xiaozhong Wang
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410128, China
| | - Xuedan Lu
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410128, China
| | - Yunhua Xiao
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410128, China
| | - Huabing Deng
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410128, China
| | - Xiong Liu
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410128, China
| | - Wenbang Tang
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410128, China
- Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410128, China
- State Key Laboratory of Hybrid Rice, Changsha 410128, China
| | - Guilian Zhang
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410128, China
| |
Collapse
|
15
|
Li N, Pu K, Ding D, Yang Y, Niu T, Li J, Xie J. Foliar Spraying of Glycine Betaine Alleviated Growth Inhibition, Photoinhibition, and Oxidative Stress in Pepper ( Capsicum annuum L.) Seedlings under Low Temperatures Combined with Low Light. PLANTS (BASEL, SWITZERLAND) 2023; 12:2563. [PMID: 37447123 DOI: 10.3390/plants12132563] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/30/2023] [Accepted: 07/03/2023] [Indexed: 07/15/2023]
Abstract
Low temperature combined with low light (LL stress) is a typical environmental stress that limits peppers' productivity, yield, and quality in northwestern China. Glycine betaine (GB), an osmoregulatory substance, has increasingly valuable effects on plant stress resistance. In this study, pepper seedlings were treated with different concentrations of GB under LL stress, and 20 mM of GB was the best treatment. To further explore the mechanism of GB in response to LL stress, four treatments, including CK (normal temperature and light, 28/18 °C, 300 μmol m-2 s-1), CB (normal temperature and light + 20 mM GB), LL (10/5 °C, 100 μmol m-2 s-1), and LB (10/5 °C, 100 μmol m-2 s-1 + 20 mM GB), were investigated in terms of pepper growth, biomass accumulation, photosynthetic capacity, expression levels of encoded proteins Capsb, cell membrane permeability, antioxidant enzyme gene expression and activity, and subcellular localization. The results showed that the pre-spraying of GB under LL stress significantly alleviated the growth inhibition of pepper seedlings; increased plant height by 4.64%; increased root activity by 63.53%; and decreased photoinhibition by increasing the chlorophyll content; upregulating the expression levels of encoded proteins Capsb A, Capsb B, Capsb C, Capsb D, Capsb S, Capsb P1, and Capsb P2 by 30.29%, 36.69%, 18.81%, 30.05%, 9.01%, 6.21%, and 16.45%, respectively; enhancing the fluorescence intensity (OJIP curves), the photochemical efficiency (Fv/Fm, Fv'/Fm'), qP, and NPQ; improving the light energy distribution of PSΠ (Y(II), Y(NPQ), and Y(NO)); and increasing the photochemical reaction fraction and reduced heat dissipation, thereby increasing plant height by 4.64% and shoot bioaccumulation by 13.55%. The pre-spraying of GB under LL stress also upregulated the gene expression of CaSOD, CaPOD, and CaCAT; increased the activity of the ROS-scavenging ability in the pepper leaves; and coordinately increased the SOD activity in the mitochondria, the POD activity in the mitochondria, chloroplasts, and cytosol, and the CAT activity in the cytosol, which improved the LL resistance of the pepper plants by reducing excess H2O2, O2-, MDA, and soluble protein levels in the leaf cells, leading to reduced biological membrane damage. Overall, pre-spraying with GB effectively alleviated the negative effects of LL stress in pepper seedlings.
Collapse
Affiliation(s)
- Nenghui Li
- College of Horticulture, Gansu Agricultural University, Yingmen Village, Anning District, Lanzhou 730070, China
| | - Kaiguo Pu
- College of Horticulture, Gansu Agricultural University, Yingmen Village, Anning District, Lanzhou 730070, China
| | - Dongxia Ding
- College of Horticulture, Gansu Agricultural University, Yingmen Village, Anning District, Lanzhou 730070, China
| | - Yan Yang
- College of Horticulture, Gansu Agricultural University, Yingmen Village, Anning District, Lanzhou 730070, China
| | - Tianhang Niu
- College of Horticulture, Gansu Agricultural University, Yingmen Village, Anning District, Lanzhou 730070, China
| | - Jing Li
- College of Horticulture, Gansu Agricultural University, Yingmen Village, Anning District, Lanzhou 730070, China
| | - Jianming Xie
- College of Horticulture, Gansu Agricultural University, Yingmen Village, Anning District, Lanzhou 730070, China
| |
Collapse
|
16
|
Yang L, Lei L, Wang J, Zheng H, Xin W, Liu H, Zou D. qCTB7 positively regulates cold tolerance at booting stage in rice. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:135. [PMID: 37222778 DOI: 10.1007/s00122-023-04388-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 05/12/2023] [Indexed: 05/25/2023]
Abstract
KEY MESSAGE LOC_Os07g07690 on qCTB7 is associated with cold tolerance at the booting stage in rice, and analysis of transgenic plants demonstrated that qCTB7 influenced cold tolerance by altering the morphology and cytoarchitecture of anthers and pollen. Cold tolerance at the booting stage (CTB) in rice can significantly affect yield in high-latitude regions. Although several CTB genes have been isolated, their ability to induce cold tolerance is insufficient to ensure adequate rice yields in cold regions at high latitudes. Here, we identified the PHD-finger domain-containing protein gene qCTB7 using QTL-seq and linkage analysis through systematic measurement of CTB differences and the spike fertility of the Longjing31 and Longdao3 cultivars, resulting in the derivation of 1570 F2 progeny under cold stress. We then characterized the function of qCTB7 in rice. It was found that overexpression of qCTB7 promoted CTB and the same yield as Longdao3 under normal growing conditions while the phenotype of qctb7 knockout showed anther and pollen failure under cold stress. When subjected to cold stress, the germination of qctb7 pollen on the stigma was reduced, resulting in lower spike fertility. These findings indicate that qCTB7 regulates the appearance, morphology, and cytoarchitecture of the anthers and pollen. Three SNPs in the promoter region and coding region of qCTB7 were identified as recognition signals for CTB in rice and could assist breeding efforts to improve cold tolerance for rice production in high latitudes.
Collapse
Affiliation(s)
- Luomiao Yang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Lei Lei
- Institute of Crop Cultivation and Cultivation, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Jingguo Wang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Hongliang Zheng
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Wei Xin
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Hualong Liu
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China.
| | - Detang Zou
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China.
| |
Collapse
|
17
|
Huang P, Ding Z, Duan M, Xiong Y, Li X, Yuan X, Huang J. OsLUX Confers Rice Cold Tolerance as a Positive Regulatory Factor. Int J Mol Sci 2023; 24:ijms24076727. [PMID: 37047700 PMCID: PMC10094877 DOI: 10.3390/ijms24076727] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 03/26/2023] [Accepted: 03/28/2023] [Indexed: 04/07/2023] Open
Abstract
During the early seedling stage, rice (Oryza sativa L.) must overcome low-temperature stress. While a few cold-tolerance genes have been characterized, further excavation of cold-resistance genes is still needed. In this study, we identified a cold-induced transcription factor—LUX ARRHYTHMO (LUX)—in rice. OsLUX was found to be specifically expressed in leaf blades and upregulated by both cold stress and circadian rhythm. The full-length OsLUX showed autoactivation activity, and the OsLUX protein localized throughout the entire onion cell. Overexpressing OsLUX resulted in increased cold tolerance and reduced ion leakage under cold-stress conditions during the seedling stage. In contrast, the knockout of OsLUX decreased seedling cold tolerance and showed higher ion leakage compared to the wild type. Furthermore, overexpressing OsLUX upregulated the expression levels of oxidative stress-responsive genes, which improved reactive oxygen species (ROS) scavenging ability and enhanced tolerance to chilling stress. Promoter analysis showed that the OsLUX promoter contains two dehydration-responsive element binding (DREB) motifs at positions −510/−505 (GTCGGa) and −162/−170 (cCACCGccc), which indicated that OsDREB1s and OsDREB2s probably regulate OsLUX expression by binding to the motif to respond to cold stress. Thus, OsLUX may act as a downstream gene of the DREB pathway. These results demonstrate that OsLUX serves as a positive regulatory factor of cold stress and that overexpressing OsLUX could be used in rice breeding programs to enhance abiotic stress tolerance.
Collapse
Affiliation(s)
- Peng Huang
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Zhengquan Ding
- Jiaxing Academy of Agricultural Sciences, Jiaxing 314016, China
| | - Min Duan
- Taizhou Academy Agricultural of Sciences, Taizhou 317000, China
| | - Yi Xiong
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Xinxin Li
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Xi Yuan
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Ji Huang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| |
Collapse
|
18
|
Niu Y, Fan S, Cheng B, Li H, Wu J, Zhao H, Huang Z, Yan F, Qi B, Zhang L, Zhang G. Comparative transcriptomics and co-expression networks reveal cultivar-specific molecular signatures associated with reproductive-stage cold stress in rice. PLANT CELL REPORTS 2023; 42:707-722. [PMID: 36723676 DOI: 10.1007/s00299-023-02984-0] [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: 11/23/2022] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
The resistance of Huaidao5 results from the high constitutive expression of tolerance genes, while that of Huaidao9 is due to the cold-induced resistance in flag leaves and panicles. The regulation mechanism of rice seedlings' cold tolerance is relatively clear, and knowledge of its underlying mechanisms at the reproductive stage is limited. We performed differential expression and co-expression network analyses to transcriptomes from panicle and flag leaf tissues of a cold-tolerant cultivar (Huaidao5), and a sensitive cultivar (Huaidao9), under reproductive-stage cold stress. The results revealed that the expression levels of genes in stress-related pathways such as MAPK signaling pathway, diterpenoid biosynthesis, glutathione metabolism, plant-pathogen interaction and plant hormone signal transduction were constitutively highly expressed in Huaidao5, especially in panicles. Moreover, the Hudaidao5's panicle sample-specific (under cold) module contained some genes related to rice yield, such as GW5L, GGC2, SG1 and CTPS1. However, the resistance of Huaidao9 was derived from the induced resistance to cold in flag leaves and panicles. In the flag leaves, the responses included a series of stress response and signal transduction, while in the panicles nitrogen metabolism was severely affected, especially 66 endosperm-specific genes. Through integrating differential expression with co-expression networks, we predicted 161 candidate genes (79 cold-responsive genes common to both cultivars and 82 cold-tolerance genes associated with differences in cold tolerance between cultivars) potentially affecting cold response/tolerance, among which 85 (52.80%) were known to be cold-related genes. Moreover, 52 (65.82%) cold-responsive genes (e.g., TIFY11C, LSK1 and LPA) could be confirmed by previous transcriptome studies and 72 (87.80%) cold-tolerance genes (e.g., APX5, OsFbox17 and OsSTA109) were located within QTLs associated with cold tolerance. This study provides an efficient strategy for further discovery of mechanisms of cold tolerance in rice.
Collapse
Affiliation(s)
- Yuan Niu
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an, 223003, China
| | - Song Fan
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an, 223003, China
| | - Baoshan Cheng
- Huaiyin Institute of Agricultural Science in Xuhuai Region of Jiangsu Province, Huai'an, 223001, China.
| | - Henan Li
- Shanghai Bioelectronica Limited Liability Company, Shanghai, 200131, China
| | - Jiang Wu
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an, 223003, China
| | - Hongliang Zhao
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an, 223003, China
| | - Zhiwei Huang
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an, 223003, China
| | - Feiyu Yan
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an, 223003, China
| | - Bo Qi
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an, 223003, China
| | - Linqing Zhang
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an, 223003, China
| | - Guoliang Zhang
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an, 223003, China.
- State Key Laboratory of Soil and Agricultural Sustainable Development, Nanjing, 210008, China.
- Jiangsu Key Laboratory of Attapulgite Clay Resource Utilization, Huai'an, 223003, China.
| |
Collapse
|
19
|
Shi J, An G, Weber APM, Zhang D. Prospects for rice in 2050. PLANT, CELL & ENVIRONMENT 2023; 46:1037-1045. [PMID: 36805595 DOI: 10.1111/pce.14565] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
A key to achieve the goals put forward in the UN's 2030 Agenda for Sustainable Development, it will need transformative change to our agrifood systems. We must mount to the global challenge to achieve food security in a sustainable manner in the context of climate change, population growth, urbanization, and depletion of natural resources. Rice is one of the major staple cereal crops that has contributed, is contributing, and will still contribute to the global food security. To date, rice yield has held pace with increasing demands, due to advances in both fundamental and biological studies, as well as genomic and molecular breeding practices. However, future rice production depends largely on the planting of resilient cultivars that can acclimate and adapt to changing environmental conditions. This Special Issue highlight with reviews and original research articles the exciting and growing field of rice-environment interactions that could benefit future rice breeding. We also outline open questions and propose future directions of 2050 rice research, calling for more attentions to develop environment-resilient rice especially hybrid rice, upland rice and perennial rice.
Collapse
Affiliation(s)
- Jianxin Shi
- Department of Genetic and Developmental Science, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Shanghai, China
| | - Gynheung An
- Department of Genetic Engineering, Crop Biotech Institute and Graduate School of Biotechnology, Kyung Hee University, Yongin, South Korea
| | - Andreas P M Weber
- Department of Plant Biochemistry, Institute of Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich Heine University, Düsseldorf, Germany
| | - Dabing Zhang
- Department of Genetic and Developmental Science, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Shanghai, China
- Department of Agricultural Science, School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, Australia
| |
Collapse
|
20
|
Huang L, Yu J, Liu Q, Yu K, Zhang Q, Fan M, Jiang F, Han J, Wei H, Jian W, Zhao Z. Study on tillering stage cold tolerant response in overwintering cultivated rice via comparative transcriptomic. Food Energy Secur 2023. [DOI: 10.1002/fes3.450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2023] Open
Affiliation(s)
- Lunxiao Huang
- College of Life Sciences, Chongqing Engineering Research Center of Specialty Crop Resources Chongqing Normal University Chongqing China
| | - Jie Yu
- College of Life Sciences, Chongqing Engineering Research Center of Specialty Crop Resources Chongqing Normal University Chongqing China
| | - Qian Liu
- College of Life Sciences, Chongqing Engineering Research Center of Specialty Crop Resources Chongqing Normal University Chongqing China
| | - Kunchi Yu
- College of Life Sciences, Chongqing Engineering Research Center of Specialty Crop Resources Chongqing Normal University Chongqing China
| | - Qiuyu Zhang
- College of Life Sciences, Chongqing Engineering Research Center of Specialty Crop Resources Chongqing Normal University Chongqing China
| | - Mao Fan
- College of Life Sciences, Chongqing Engineering Research Center of Specialty Crop Resources Chongqing Normal University Chongqing China
| | - Fei Jiang
- College of Life Sciences, Chongqing Engineering Research Center of Specialty Crop Resources Chongqing Normal University Chongqing China
| | - Jiajia Han
- College of Life Sciences, Chongqing Engineering Research Center of Specialty Crop Resources Chongqing Normal University Chongqing China
| | - Hongyu Wei
- College of Life Sciences, Chongqing Engineering Research Center of Specialty Crop Resources Chongqing Normal University Chongqing China
| | - Wei Jian
- College of Life Sciences, Chongqing Engineering Research Center of Specialty Crop Resources Chongqing Normal University Chongqing China
| | - Zhengwu Zhao
- College of Life Sciences, Chongqing Engineering Research Center of Specialty Crop Resources Chongqing Normal University Chongqing China
| |
Collapse
|
21
|
Yao D, Wang J, Peng W, Zhang B, Wen X, Wan X, Wang X, Li X, Ma J, Liu X, Fan Y, Sun G. Transcriptomic profiling of wheat stem during meiosis in response to freezing stress. FRONTIERS IN PLANT SCIENCE 2023; 13:1099677. [PMID: 36714719 PMCID: PMC9878610 DOI: 10.3389/fpls.2022.1099677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 12/19/2022] [Indexed: 06/18/2023]
Abstract
Low temperature injury in spring has seriously destabilized the production and grain quality of common wheat. However, the molecular mechanisms underlying spring frost tolerance remain elusive. In this study, we investigated the response of a frost-tolerant wheat variety Zhongmai8444 to freezing stress at the meiotic stage. Transcriptome profiles over a time course were subsequently generated by high-throughput sequencing. Our results revealed that the prolonged freezing temperature led to the significant reductions in plant height and seed setting rate. Cell wall thickening in the vascular tissue was also observed in the stems. RNA-seq analyses demonstrated the identification of 1010 up-regulated and 230 down-regulated genes shared by all time points of freezing treatment. Enrichment analysis revealed that gene activity related to hormone signal transduction and cell wall biosynthesis was significantly modulated under freezing. In addition, among the identified differentially expressed genes, 111 transcription factors belonging to multiple gene families exhibited dynamic expression pattern. This study provided valuable gene resources beneficial for the breeding of wheat varieties with improved spring frost tolerance.
Collapse
Affiliation(s)
- Danyu Yao
- National Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Juan Wang
- National Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wentao Peng
- National Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Agricultural Science and Engineering, Liaocheng University, Liaocheng, Shandong, China
| | - Bowen Zhang
- National Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Agronomy, Jilin Agricultural University, Changchun, Jilin, China
| | - Xiaolan Wen
- National Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Landscape and Ecological Engineering, Hebei University of Engineering, Handan, Hebei, China
| | - Xiaoneng Wan
- National Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiuyuan Wang
- National Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Agricultural Science and Engineering, Liaocheng University, Liaocheng, Shandong, China
| | - Xinchun Li
- National Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jian Ma
- College of Agronomy, Jilin Agricultural University, Changchun, Jilin, China
| | - Xiaofen Liu
- College of Landscape and Ecological Engineering, Hebei University of Engineering, Handan, Hebei, China
| | - Yinglun Fan
- College of Agricultural Science and Engineering, Liaocheng University, Liaocheng, Shandong, China
| | - Guozhong Sun
- National Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| |
Collapse
|
22
|
Feng J, Li Z, Luo W, Liang G, Xu Y, Chong K. COG2 negatively regulates chilling tolerance through cell wall components altered in rice. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:19. [PMID: 36680595 DOI: 10.1007/s00122-023-04261-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 10/10/2022] [Indexed: 06/17/2023]
Abstract
Chilling-tolerant QTL gene COG2 encoded an extensin and repressed chilling tolerance by affecting the compositions of cell wall. Rice as a major crop is susceptible to chilling stress. Chilling tolerance is a complex trait controlled by multiple quantitative trait loci (QTLs). Here, we identify a QTL gene, COG2, that negatively regulates cold tolerance at seedling stage in rice. COG2 overexpression transgenic plants are sensitive to cold, whereas knockout transgenic lines enhance chilling tolerance. Natural variation analysis shows that Hap1 is a specific haplotype in japonica/Geng rice and correlates with chilling tolerance. The SNP1 in COG2 promoter is a specific divergency and leads to the difference in the expression level of COG2 between japonica/Geng and indica/Xian cultivars. COG2 encodes a cell wall-localized extensin and affects the compositions of cell wall, including pectin and cellulose, to defense the chilling stress. The results extend the understanding of the adaptation to the environment and provide an editing target for molecular design breeding of cold tolerance in rice.
Collapse
Affiliation(s)
- Jinglei Feng
- The Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhitao Li
- The Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Wei Luo
- The Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Guohua Liang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Centre for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Yunyuan Xu
- The Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100093, China
| | - Kang Chong
- The Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- University of the Chinese Academy of Sciences, Beijing, 100049, China.
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100093, China.
| |
Collapse
|
23
|
Li J, Khatab AA, Hu L, Zhao L, Yang J, Wang L, Xie G. Genome-Wide Association Mapping Identifies New Candidate Genes for Cold Stress and Chilling Acclimation at Seedling Stage in Rice ( Oryza sativa L.). Int J Mol Sci 2022; 23:ijms232113208. [PMID: 36361995 PMCID: PMC9655271 DOI: 10.3390/ijms232113208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/24/2022] [Accepted: 10/27/2022] [Indexed: 11/16/2022] Open
Abstract
Rice (Oryza sativa L.) is a chilling-sensitive staple food crop, and thus, low temperature significantly affects rice growth and yield. Many studies have focused on the cold shock of rice although chilling acclimation is more likely to happen in the field. In this paper, a genome-wide association study (GWAS) was used to identify the genes that participated in cold stress and chilling accumulation. A total of 235 significantly associated single-nucleotide polymorphisms (SNPs) were identified. Among them, we detected 120 and 88 SNPs for the relative shoot fresh weight under cold stress and chilling acclimation, respectively. Furthermore, 11 and 12 quantitative trait loci (QTLs) were identified for cold stress and chilling acclimation, respectively, by integrating the co-localized SNPs. Interestingly, we identified 10 and 15 candidate genes in 11 and 12 QTLs involved in cold stress and chilling acclimation, respectively, and two new candidate genes (LOC_Os01g62410, LOC_Os12g24490) were obviously up-regulated under chilling acclimation. Furthermore, OsMYB3R-2 (LOC_Os01g62410) that encodes a R1R2R3 MYB gene was associated with cold tolerance, while a new C3HC4-type zinc finger protein-encoding gene LOC_Os12g24490 was found to function as a putative E3 ubiquitin-protein ligase in rice. Moreover, haplotype, distribution, and Wright’s fixation index (FST) of both genes showed that haplotype 3 of LOC_Os12g24490 is more stable in chilling acclimation, and the SNP (A > T) showed a difference in latitudinal distribution. FST analysis of SNPs in OsMYB3R-2 (LOC_Os01g62410) and LOC_Os12g24490 indicated that several SNPs were under selection in rice indica and japonica subspecies. This study provided new candidate genes in genetic improvement of chilling acclimation response in rice.
Collapse
Affiliation(s)
- Jianguo Li
- State Key Laboratory for Conservation & Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ahmed Adel Khatab
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Lihua Hu
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China
- College of Life Science & Technology, Guangxi University, Nanning 530004, China
| | - Liyan Zhao
- State Key Laboratory for Conservation & Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiangyi Yang
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China
- College of Life Science & Technology, Guangxi University, Nanning 530004, China
| | - Lingqiang Wang
- State Key Laboratory for Conservation & Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China
- Correspondence:
| | - Guosheng Xie
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China
| |
Collapse
|
24
|
Zhang M, Zhao R, Huang K, Huang S, Wang H, Wei Z, Li Z, Bian M, Jiang W, Wu T, Du X. The OsWRKY63-OsWRKY76-OsDREB1B module regulates chilling tolerance in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:383-398. [PMID: 35996876 DOI: 10.1111/tpj.15950] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 08/05/2022] [Accepted: 08/18/2022] [Indexed: 06/15/2023]
Abstract
Rice (Oryza sativa) is sensitive to low temperatures, which affects the yield and quality of rice. Therefore, uncovering the molecular mechanisms behind chilling tolerance is a critical task for improving cold tolerance in rice cultivars. Here, we report that OsWRKY63, a WRKY transcription factor with an unknown function, negatively regulates chilling tolerance in rice. OsWRKY63-overexpressing rice lines are more sensitive to cold stress. Conversely, OsWRKY63-knockout mutants generated using a CRISPR/Cas9 genome editing approach exhibited increased chilling tolerance. OsWRKY63 was expressed in all rice tissues, and OsWRKY63 expression was induced under cold stress, dehydration stress, high salinity stress, and ABA treatment. OsWRKY63 localized in the nucleus plays a role as a transcription repressor and downregulates many cold stress-related genes and reactive oxygen species scavenging-related genes. Molecular, biochemical, and genetic assays showed that OsWRKY76 is a direct target gene of OsWRKY63 and that its expression is suppressed by OsWRKY63. OsWRKY76-knockout lines had dramatically decreased cold tolerance, and the cold-induced expression of five OsDREB1 genes was repressed. OsWRKY76 interacted with OsbHLH148, transactivating the expression of OsDREB1B to enhance chilling tolerance in rice. Thus, our study suggests that OsWRKY63 negatively regulates chilling tolerance through the OsWRKY63-OsWRKY76-OsDREB1B transcriptional regulatory cascade in rice.
Collapse
Affiliation(s)
- Mingxing Zhang
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Ranran Zhao
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Kai Huang
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Shuangzhan Huang
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Haitao Wang
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Zhiqi Wei
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Zhao Li
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Mingdi Bian
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Wenzhu Jiang
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Tao Wu
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Xinglin Du
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| |
Collapse
|
25
|
Combination of Genomics, Transcriptomics Identifies Candidate Loci Related to Cold Tolerance in Dongxiang Wild Rice. PLANTS 2022; 11:plants11182329. [PMID: 36145730 PMCID: PMC9506393 DOI: 10.3390/plants11182329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/22/2022] [Accepted: 09/02/2022] [Indexed: 11/17/2022]
Abstract
Rice, a cold-sensitive crop, is a staple food for more than 50% of the world’s population. Low temperature severely compromises the growth of rice and challenges China’s food safety. Dongxiang wild rice (DXWR) is the most northerly common wild rice in China and has strong cold tolerance, but the genetic basis of its cold tolerance is still unclear. Here, we report quantitative trait loci (QTLs) analysis for seedling cold tolerance (SCT) using a high-density single nucleotide polymorphism linkage map in the backcross recombinant inbred lines that were derived from a cross of DXWR, and an indica cultivar, GZX49. A total of 10 putative QTLs were identified for SCT under 4 °C cold treatment, each explaining 2.0–6.8% of the phenotypic variation in this population. Furthermore, transcriptome sequencing of DXWR seedlings before and after cold treatment was performed, and 898 and 3413 differentially expressed genes (DEGs) relative to 0 h in cold-tolerant for 4 h and 12 h were identified, respectively. Gene ontology and Kyoto encyclopedia of genes and genomes (KEGG) analysis were performed on these DEGs. Using transcriptome data and genetic linkage analysis, combined with qRT-PCR, sequence comparison, and bioinformatics, LOC_Os08g04840 was putatively identified as a candidate gene for the major effect locus qSCT8. These findings provided insights into the genetic basis of SCT for the improvement of cold stress potential in rice breeding programs.
Collapse
|
26
|
Chilling Tolerance in Maize: Insights into Advances—Toward Physio-Biochemical Responses’ and QTL/Genes’ Identification. PLANTS 2022; 11:plants11162082. [PMID: 36015386 PMCID: PMC9415788 DOI: 10.3390/plants11162082] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/06/2022] [Accepted: 08/07/2022] [Indexed: 12/04/2022]
Abstract
Maize, a major staple cereal crop in global food supply, is a thermophilic and short-day C4 plant sensitive to low-temperature stress. A low temperature is among the most severe agro-meteorological hazards in maize-growing areas. This review covers the latest research and progress in the field of chilling tolerance in maize in the last 40 years. It mainly focuses on how low-temperature stress affects the maize membrane and antioxidant systems, photosynthetic physiology, osmoregulatory substances and hormone levels. In addition, the research progress in identifying cold-tolerance QTLs (quantitative trait loci) and genes to genetically improve maize chilling toleranceis comprehensively discussed. Based on previous research, this reviewprovides anoutlook on potential future research directions and offers a reference for researchers in the maize cold-tolerance-related field.
Collapse
|