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Xu P, Xu J, Guo Q, Xu Z, Ji W, Yu H, Cai J, Zhao L, Zhao J, Liu J, Chen X, Shen X. A recessive LRR-RLK gene causes hybrid breakdown in cotton. Theor Appl Genet 2023; 136:189. [PMID: 37582982 DOI: 10.1007/s00122-023-04427-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 07/24/2023] [Indexed: 08/17/2023]
Abstract
KEY MESSAGE An LRR-RLK gene causing interspecific hybrid breakdown between Gossypium. anomalum and G. hirsutum was identified by deploying a map-based cloning strategy. The self-destructing symptoms of hybrid incompatibility in most cases are attributed to autoimmunity. The cloning of genes responsible for hybrid incompatibility in cotton is helpful to clarify the mechanisms underlying hybrid incompatibility and can break the barriers in distant hybridization. In this study, a temperature-dependent lethality was identified in CSSL11-9 (chromosome segment substitution line) with Gossypium anomalum chromosome segment on chromosome A11. Transcriptome analysis showed the differentially expressed genes related to autoimmune responses were highly enriched, suggesting that expression of CSSL11-9 plant lethal gene activated autoimmunity in the absence of any pathogen or external stimulus, inducing programmed cell death (PCD) and causing a lethal phenotype. The lethal phenotype was controlled by a pair of recessive genes and then fine mapped between JAAS3191-JAAS3050 interval, which covered 63.87 kb in G. hirsutum genome and 98.66 kb in G. anomalum. We demonstrated that an LRR-RLK gene designated as hybrid breakdown 1 (GoanoHBD1) was the causal gene underlying this locus for interspecific hybrid incompatibility between G. anomalum and G. hirsutum. Silencing this LRR-RLK gene could restore CSSL11-9 plants from a lethal to a normal phenotype. Our findings provide new insights into reproductive isolation and may benefit cotton breeding.
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Affiliation(s)
- Peng Xu
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture and Rural Affairs, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Jianwen Xu
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture and Rural Affairs, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Qi Guo
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture and Rural Affairs, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Zhenzhen Xu
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture and Rural Affairs, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Wei Ji
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture and Rural Affairs, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Huan Yu
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture and Rural Affairs, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Jihong Cai
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture and Rural Affairs, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Liang Zhao
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture and Rural Affairs, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Jun Zhao
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture and Rural Affairs, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Jianguang Liu
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture and Rural Affairs, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Xianglong Chen
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture and Rural Affairs, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Xinlian Shen
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture and Rural Affairs, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
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Wang Y, Xia J, Huang L, Lin Q, Cai Q, Xie H, He W, Wei Y, Xie H, Tang W, Wu W, Zhang J. Transcriptome Analyses Indicate Significant Association of Increased Non-Additive and Allele-Specific Gene Expression with Hybrid Weakness in Rice ( Oryza sativa L.). Life (Basel) 2022; 12:life12081278. [PMID: 36013457 PMCID: PMC9410013 DOI: 10.3390/life12081278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 08/09/2022] [Accepted: 08/16/2022] [Indexed: 11/30/2022]
Abstract
The heterosis in hybrid rice is highly affected by the environment and hybrid weakness occurs frequently depending on the genotypes of the hybrid and its parents. Hybrid weakness was also observed in our field experiments on nine rice hybrids produced by 3 × 3 incomplete diallel crosses. Among the nine hybrids, five displayed mid-parent heterosis (MPH) for grain yield per plant, while four showed mid-parent hybrid weakness (MPHW). A sequencing analysis of transcriptomes in panicles at the seed-filling stage revealed a significant association between enhanced non-additive gene expression (NAE) and allele-specific gene expression (ASE) with hybrid weakness. High proportions of ASE genes, with most being of mono-allele expression, were detected in the four MPHW hybrids, ranging from 22.65% to 45.97%; whereas only 4.80% to 5.69% of ASE genes were found in the five MPH hybrids. Moreover, an independence test indicated that the enhancements of NAE and ASE in the MPHW hybrids were significantly correlated. Based on the results of our study, we speculated that an unfavorable environment might cause hybrid weakness by enhancing ASE and NAE at the transcriptome level.
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Affiliation(s)
- Yingheng Wang
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350019, China
- National Rice Engineering Research Center of China, Fuzhou 350003, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fuzhou 350003, China
- Incubator of National Key Laboratory of Fujian Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Science and Technology of China, Fuzhou 350003, China
- Base of South China, State Key Laboratory of Hybrid Rice, Fuzhou 350003, China
- Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Rural Affairs of China, Fuzhou 350003, China
- Fuzhou Branch, National Rice Improvement Center of China, Fuzhou 350003, China
- Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou 350003, China
- Fujian Key Laboratory of Rice Molecular Breeding, Fujian Academy of Agricultural Sciences, Fuzhou 350003, China
| | - Jing Xia
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Likun Huang
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Qiang Lin
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350019, China
- National Rice Engineering Research Center of China, Fuzhou 350003, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fuzhou 350003, China
- Incubator of National Key Laboratory of Fujian Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Science and Technology of China, Fuzhou 350003, China
- Base of South China, State Key Laboratory of Hybrid Rice, Fuzhou 350003, China
- Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Rural Affairs of China, Fuzhou 350003, China
- Fuzhou Branch, National Rice Improvement Center of China, Fuzhou 350003, China
- Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou 350003, China
- Fujian Key Laboratory of Rice Molecular Breeding, Fujian Academy of Agricultural Sciences, Fuzhou 350003, China
| | - Qiuhua Cai
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350019, China
- National Rice Engineering Research Center of China, Fuzhou 350003, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fuzhou 350003, China
- Incubator of National Key Laboratory of Fujian Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Science and Technology of China, Fuzhou 350003, China
- Base of South China, State Key Laboratory of Hybrid Rice, Fuzhou 350003, China
- Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Rural Affairs of China, Fuzhou 350003, China
- Fuzhou Branch, National Rice Improvement Center of China, Fuzhou 350003, China
- Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou 350003, China
- Fujian Key Laboratory of Rice Molecular Breeding, Fujian Academy of Agricultural Sciences, Fuzhou 350003, China
| | - Hongguang Xie
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350019, China
- National Rice Engineering Research Center of China, Fuzhou 350003, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fuzhou 350003, China
- Incubator of National Key Laboratory of Fujian Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Science and Technology of China, Fuzhou 350003, China
- Base of South China, State Key Laboratory of Hybrid Rice, Fuzhou 350003, China
- Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Rural Affairs of China, Fuzhou 350003, China
- Fuzhou Branch, National Rice Improvement Center of China, Fuzhou 350003, China
- Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou 350003, China
- Fujian Key Laboratory of Rice Molecular Breeding, Fujian Academy of Agricultural Sciences, Fuzhou 350003, China
| | - Wei He
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350019, China
- National Rice Engineering Research Center of China, Fuzhou 350003, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fuzhou 350003, China
- Incubator of National Key Laboratory of Fujian Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Science and Technology of China, Fuzhou 350003, China
- Base of South China, State Key Laboratory of Hybrid Rice, Fuzhou 350003, China
- Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Rural Affairs of China, Fuzhou 350003, China
- Fuzhou Branch, National Rice Improvement Center of China, Fuzhou 350003, China
- Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou 350003, China
- Fujian Key Laboratory of Rice Molecular Breeding, Fujian Academy of Agricultural Sciences, Fuzhou 350003, China
| | - Yidong Wei
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350019, China
- National Rice Engineering Research Center of China, Fuzhou 350003, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fuzhou 350003, China
- Incubator of National Key Laboratory of Fujian Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Science and Technology of China, Fuzhou 350003, China
- Base of South China, State Key Laboratory of Hybrid Rice, Fuzhou 350003, China
- Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Rural Affairs of China, Fuzhou 350003, China
- Fuzhou Branch, National Rice Improvement Center of China, Fuzhou 350003, China
- Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou 350003, China
- Fujian Key Laboratory of Rice Molecular Breeding, Fujian Academy of Agricultural Sciences, Fuzhou 350003, China
| | - Huaan Xie
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350019, China
- National Rice Engineering Research Center of China, Fuzhou 350003, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fuzhou 350003, China
- Incubator of National Key Laboratory of Fujian Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Science and Technology of China, Fuzhou 350003, China
- Base of South China, State Key Laboratory of Hybrid Rice, Fuzhou 350003, China
- Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Rural Affairs of China, Fuzhou 350003, China
- Fuzhou Branch, National Rice Improvement Center of China, Fuzhou 350003, China
- Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou 350003, China
- Fujian Key Laboratory of Rice Molecular Breeding, Fujian Academy of Agricultural Sciences, Fuzhou 350003, China
| | - Weiqi Tang
- Marine and Agricultural Biotechnology Laboratory, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou 350108, China
- Correspondence: (W.T.); (W.W.); (J.Z.)
| | - Weiren Wu
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (W.T.); (W.W.); (J.Z.)
| | - Jianfu Zhang
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350019, China
- National Rice Engineering Research Center of China, Fuzhou 350003, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fuzhou 350003, China
- Incubator of National Key Laboratory of Fujian Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Science and Technology of China, Fuzhou 350003, China
- Base of South China, State Key Laboratory of Hybrid Rice, Fuzhou 350003, China
- Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Rural Affairs of China, Fuzhou 350003, China
- Fuzhou Branch, National Rice Improvement Center of China, Fuzhou 350003, China
- Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou 350003, China
- Fujian Key Laboratory of Rice Molecular Breeding, Fujian Academy of Agricultural Sciences, Fuzhou 350003, China
- Correspondence: (W.T.); (W.W.); (J.Z.)
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Than Kutay Soe, Kunieda M, Sunohara H, Inukai Y, Reyes VP, Nishiuchi S, Doi K. A Novel Combination of Genes Causing Temperature-Sensitive Hybrid Weakness in Rice. Front Plant Sci 2022; 13:908000. [PMID: 35837460 PMCID: PMC9274174 DOI: 10.3389/fpls.2022.908000] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 05/26/2022] [Indexed: 09/29/2023]
Abstract
Reproductive isolation is an obstacle for plant breeding when a distant cross is demanded. It can be divided into two main types based on different growth stages: prezygotic isolation and postzygotic isolation. The hybrid weakness, which is a type of postzygotic isolation, can become a problem in crop breeding. In order to overcome reproductive isolation, it is necessary to elucidate its mechanism. In this study, genetic analysis for low temperature-dependent hybrid weakness was conducted in a rice F2 population derived from Taichung 65 (T65, Japonica) and Lijiangxintuanheigu (LTH, Japonica). The weak and severe weak plants in F2 showed shorter culm length, late heading, reduced panicle number, decreased grain numbers per panicle, and impaired root development in the field. Our result also showed that hybrid weakness was affected by temperature. It was observed that 24°C enhanced hybrid weakness, whereas 34°C showed recovery from hybrid weakness. In terms of the morphology of embryos, no difference was observed. Therefore, hybrid weakness affects postembryonic development and is independent of embryogenesis. The genotypes of 126 F2 plants were determined through genotyping-by-sequencing and a linkage map consisting of 862 single nucleotide polymorphism markers was obtained. Two major quantitative trait loci (QTLs) were detected on chromosomes 1 [hybrid weakness j 1 (hwj1)] and 11 [hybrid weakness j 2 (hwj2)]. Further genotyping indicated that the hybrid weakness was due to an incompatible interaction between the T65 allele of hwj1 and the LTH allele of hwj2. A large F2 populations consisting of 5,722 plants were used for fine mapping of hwj1 and hwj2. The two loci, hwj1 and hwj2, were mapped in regions of 65-kb on chromosome 1 and 145-kb on chromosome 11, respectively. For hwj1, the 65-kb region contained 11 predicted genes, while in the hwj2 region, 22 predicted genes were identified, two of which are disease resistance-related genes. The identified genes along these regions serve as preliminary information on the molecular networks associated with hybrid weakness in rice.
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Affiliation(s)
- Than Kutay Soe
- Laboratory of Information Sciences in Agricultural Lands, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
- Department of Botany, University of Yangon, Yangon, Myanmar
| | - Mai Kunieda
- Laboratory of Information Sciences in Agricultural Lands, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Hidehiko Sunohara
- Laboratory of Information Sciences in Agricultural Lands, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
- Environmental Control Center Co., Ltd., Hachioji, Japan
| | - Yoshiaki Inukai
- International Center for Research and Education in Agriculture, Nagoya University, Nagoya, Japan
| | - Vincent Pamugas Reyes
- Laboratory of Information Sciences in Agricultural Lands, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Shunsaku Nishiuchi
- Laboratory of Information Sciences in Agricultural Lands, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Kazuyuki Doi
- Laboratory of Information Sciences in Agricultural Lands, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
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Hu P, Wen Y, Wang Y, Wu H, Wang J, Wu K, Chai B, Zhu L, Zhang G, Gao Z, Ren D, Zhu L, Guo L, Zeng D, Xu J, Yan S, Qian Q, Rao Y, Hu J. Identification and Characterization of Short Crown Root 8, a Temperature-Sensitive Mutant Associated with Crown Root Development in Rice. Int J Mol Sci 2021; 22:9868. [PMID: 34576034 DOI: 10.3390/ijms22189868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 09/04/2021] [Accepted: 09/08/2021] [Indexed: 11/17/2022] Open
Abstract
Crown roots are essential for plants to obtain water and nutrients, perceive environmental changes, and synthesize plant hormones. In this study, we identified and characterized short crown root 8 (scr8), which exhibited a defective phenotype of crown root and vegetative development. Temperature treatment showed that scr8 was sensitive to temperature and that the mutant phenotypes were rescued when grown under low temperature condition (20 °C). Histological and EdU staining analysis showed that the crown root formation was hampered and that the root meristem activity was decreased in scr8. With map-based cloning strategy, the SCR8 gene was fine-mapped to an interval of 126.4 kb on chromosome 8. Sequencing analysis revealed that the sequence variations were only found in LOC_Os08g14850, which encodes a CC-NBS-LRR protein. Expression and inoculation test analysis showed that the expression level of LOC_Os08g14850 was significantly decreased under low temperature (20 °C) and that the resistance to Xanthomonas oryzae pv. Oryzae (Xoo) was enhanced in scr8. These results indicated that LOC_Os08g14850 may be the candidate of SCR8 and that its mutation activated the plant defense response, resulting in a crown root growth defect.
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