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Sivabharathi RC, Rajagopalan VR, Suresh R, Sudha M, Karthikeyan G, Jayakanthan M, Raveendran M. Haplotype-based breeding: A new insight in crop improvement. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 346:112129. [PMID: 38763472 DOI: 10.1016/j.plantsci.2024.112129] [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: 03/15/2024] [Revised: 05/09/2024] [Accepted: 05/15/2024] [Indexed: 05/21/2024]
Abstract
Haplotype-based breeding (HBB) is one of the cutting-edge technologies in the realm of crop improvement due to the increasing availability of Single Nucleotide Polymorphisms identified by Next Generation Sequencing technologies. The complexity of the data can be decreased with fewer statistical tests and a lower probability of spurious associations by combining thousands of SNPs into a few hundred haplotype blocks. The presence of strong genomic regions in breeding lines of most crop species facilitates the use of haplotypes to improve the efficiency of genomic and marker-assisted selection. Haplotype-based breeding as a Genomic Assisted Breeding (GAB) approach harnesses the genome sequence data to pinpoint the allelic variation used to hasten the breeding cycle and circumvent the challenges associated with linkage drag. This review article demonstrates ways to identify candidate genes, superior haplotype identification, haplo-pheno analysis, and haplotype-based marker-assisted selection. The crop improvement strategies that utilize superior haplotypes will hasten the breeding progress to safeguard global food security.
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Affiliation(s)
- R C Sivabharathi
- Department of Genetics and Plant breeding, CPBG, Tamil Nadu Agricultural University, Coimbatore 641003, India
| | - Veera Ranjani Rajagopalan
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, 641003, India
| | - R Suresh
- Department of Rice, CPBG, Tamil Nadu Agricultural University, Coimbatore 641003, India
| | - M Sudha
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, 641003, India.
| | - G Karthikeyan
- Department of Plant Pathology, CPPS, Tamil Nadu Agricultural University, Coimbatore 641003, India
| | - M Jayakanthan
- Department of Plant Molecular Biology and Bioinformatics, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India
| | - M Raveendran
- Directorate of research, Tamil Nadu Agricultural University, Coimbatore 641003, India.
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2
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Liu Y, Yu R, Shen L, Sun M, Peng Y, Zeng Q, Shen K, Yu X, Wu H, Ye B, Wang Z, Sun Z, Liu D, Sun X, Zhang Z, Dong J, Dong J, Han D, He Z, Hao Y, Wu J, Guo Z. Genomic insights into the modifications of spike morphology traits during wheat breeding. PLANT, CELL & ENVIRONMENT 2024. [PMID: 39205629 DOI: 10.1111/pce.15117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 08/13/2024] [Accepted: 08/14/2024] [Indexed: 09/04/2024]
Abstract
Over the past century, environmental changes have significantly impacted wheat spike morphology, crucial for adaptation and grain yield. However, the changes in wheat spike modifications during this period remain largely unknown. This study examines 16 spike morphology traits in 830 accessions released from 1900 to 2020. It finds that spike weight, grain number per spike (GN), and thousand kernel weight have significantly increased, while spike length has no significant change. The increase in fertile spikelets is due to fewer degenerated spikelets, resulting in a higher GN. Genome-wide association studies identified 49,994 significant SNPs, grouped into 293 genomic regions. The accumulation of favorable alleles in these genomic regions indicates the genetic basis for modification in spike morphology traits. Genetic network analysis of these genomic regions reveals the genetic basis for phenotypic correlations among spike morphology traits. The haplotypes of the identified genomic regions display obvious geographical differentiation in global accessions and environmental adaptation over the past 120 years. In summary, we reveal the genetic basis of adaptive evolution and the interactions of spike morphology, offering valuable resources for the genetic improvement of spike morphology to enhance environmental adaptation.
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Affiliation(s)
- Yangyang Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Rui Yu
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, Northwest A&F University, Yangling, Shaanxi, China
| | - Liping Shen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
| | - Mengjing Sun
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Yanchun Peng
- Key Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Qingdong Zeng
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi, China
| | - Kuocheng Shen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xuchang Yu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - He Wu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Botao Ye
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ziying Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhiweng Sun
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Danning Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaohui Sun
- Yantai Academy of Agricultural Sciences, Yantai, China
| | - Zhiliang Zhang
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Jiayu Dong
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Jing Dong
- Key Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Dejun Han
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi, China
| | - Zhonghu He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- International Maize and Wheat Improvement Center (CIMMYT) China Office, c/o CAAS, Beijing, China
| | - Yuanfeng Hao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Jianhui Wu
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, Northwest A&F University, Yangling, Shaanxi, China
| | - Zifeng Guo
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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3
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Yang W, Yang Z, Yang L, Li Z, Zhang Z, Wei T, Huang R, Li G. Genomic and transcriptomic analyses of the elite rice variety Huizhan provide insight into disease resistance and heat tolerance. Genomics 2024; 116:110915. [PMID: 39134161 DOI: 10.1016/j.ygeno.2024.110915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 08/09/2024] [Accepted: 08/09/2024] [Indexed: 08/16/2024]
Abstract
The indica rice variety Huizhan shows elite traits of disease resistance and heat tolerance. However, the underlying genetic basis of these traits is not fully understood due to limited genomic resources. Here, we used Nanopore long-read and next-generation sequencing technologies to generate a chromosome-scale genome assembly of Huizhan. Comparative genomics analysis uncovered a large chromosomal inversion and expanded gene families that are associated with plant growth, development and stress responses. Functional rice blast resistance genes, including Pi2, Pib and Ptr, and bacterial blight resistance gene Xa27, contribute to disease resistance of Huizhan. Furthermore, integrated genomics and transcriptomics analyses showed that OsHIRP1, OsbZIP60, the SOD gene family, and various transcription factors are involved in heat tolerance of Huizhan. The high-quality genome assembly and comparative genomics results presented in this study facilitate the use of Huizhan as an elite parental line in developing rice varieties adapted to disease pressure and climate challenges.
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Affiliation(s)
- Wei Yang
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Laboratory of Plant Pathology, The Center of Crop Nanobiotechnology, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhou Yang
- National Engineering Research Center of Rice (Nanchang), Key Laboratory of Germplasm innovation and Breeding of Double-cropping Rice (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Lei Yang
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Laboratory of Plant Pathology, The Center of Crop Nanobiotechnology, Huazhong Agricultural University, Wuhan 430070, China
| | - Zheng Li
- National Engineering Research Center of Rice (Nanchang), Key Laboratory of Germplasm innovation and Breeding of Double-cropping Rice (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China; National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Laboratory of Plant Pathology, The Center of Crop Nanobiotechnology, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhaowu Zhang
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen 518083, China; BGI Research, Wuhan 430074, China
| | - Tong Wei
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen 518083, China; BGI Research, Wuhan 430074, China
| | - Renliang Huang
- National Engineering Research Center of Rice (Nanchang), Key Laboratory of Germplasm innovation and Breeding of Double-cropping Rice (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China.
| | - Guotian Li
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Laboratory of Plant Pathology, The Center of Crop Nanobiotechnology, Huazhong Agricultural University, Wuhan 430070, China.
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Long Y, Wang C, Liu C, Li H, Pu A, Dong Z, Wei X, Wan X. Molecular mechanisms controlling grain size and weight and their biotechnological breeding applications in maize and other cereal crops. J Adv Res 2024; 62:27-46. [PMID: 37739122 PMCID: PMC11331183 DOI: 10.1016/j.jare.2023.09.016] [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: 06/17/2023] [Revised: 09/03/2023] [Accepted: 09/18/2023] [Indexed: 09/24/2023] Open
Abstract
BACKGROUND Cereal crops are a primary energy source for humans. Grain size and weight affect both evolutionary fitness and grain yield of cereals. Although studies on gene mining and molecular mechanisms controlling grain size and weight are constantly emerging in cereal crops, only a few systematic reviews on the underlying molecular mechanisms and their breeding applications are available so far. AIM OF REVIEW This review provides a general state-of-the-art overview of molecular mechanisms and targeted strategies for improving grain size and weight of cereals as well as insights for future yield-improving biotechnology-assisted breeding. KEY SCIENTIFIC CONCEPTS OF REVIEW In this review, the evolution of research on grain size and weight over the last 20 years is traced based on a bibliometric analysis of 1158 publications and the main signaling pathways and transcriptional factors involved are summarized. In addition, the roles of post-transcriptional regulation and photosynthetic product accumulation affecting grain size and weight in maize and rice are outlined. State-of-the-art strategies for discovering novel genes related to grain size and weight in maize and other cereal crops as well as advanced breeding biotechnology strategies being used for improving yield including marker-assisted selection, genomic selection, transgenic breeding, and genome editing are also discussed.
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Affiliation(s)
- Yan Long
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100083, China; Industry Research Institute of Biotechnology Breeding, Yili Normal University, Yining 835000, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Cheng Wang
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100083, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Chang Liu
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100083, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Huangai Li
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100083, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Aqing Pu
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100083, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Zhenying Dong
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100083, China; Industry Research Institute of Biotechnology Breeding, Yili Normal University, Yining 835000, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Xun Wei
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100083, China; Industry Research Institute of Biotechnology Breeding, Yili Normal University, Yining 835000, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Xiangyuan Wan
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100083, China; Industry Research Institute of Biotechnology Breeding, Yili Normal University, Yining 835000, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China.
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Wu L, Xie Z, Li D, Chen Y, Xia C, Kong X, Liu X, Zhang L. TaMYB72 directly activates the expression of TaFT to promote heading and enhance grain yield traits in wheat (Triticum aestivum L.). JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:1266-1269. [PMID: 38888244 DOI: 10.1111/jipb.13716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 05/21/2024] [Indexed: 06/20/2024]
Abstract
Heading date, grain number per spike, and grain weight are crucial traits affecting yield and adaptability in wheat. The transcription factor TaMYB72 is an important regulator of wheat grain yield and its knock-out mutants can be used as germplasm resources for wheat improvement.
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Affiliation(s)
- Lifen Wu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, the Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Sub-Center for National Maize Improvement Center, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China
| | - Zhencheng Xie
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, the Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Danping Li
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, the Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yaoyu Chen
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, the Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chuan Xia
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, the Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiuying Kong
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, the Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xu Liu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, the Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Sub-Center for National Maize Improvement Center, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China
| | - Lichao Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, the Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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6
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Gao J, Gao L, Chen W, Huang J, Qing D, Pan Y, Ma C, Wu H, Zhou W, Li J, Yang X, Dai G, Deng G. Genetic Effects of Grain Quality Enhancement in Indica Hybrid Rice: Insights for Molecular Design Breeding. RICE (NEW YORK, N.Y.) 2024; 17:39. [PMID: 38874692 PMCID: PMC11178727 DOI: 10.1186/s12284-024-00719-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Accepted: 06/04/2024] [Indexed: 06/15/2024]
Abstract
Improving rice quality remains a crucial breeding objective, second only to enhancing yield, yet progress in quality improvement lags behind yield. The high temperature and ripening conditions in Southern China often result in poor rice quality, impacting hybrid rice production and utilization. Therefore, to address this challenge, analyzing the molecular basis of high-quality traits is essential for molecular design breeding of high-quality hybrid rice varieties. In this study, we investigated the molecular basis of grain shape, amylose content, gel consistency, gelatinization temperature, and aroma, which influence rice quality. We discovered that quality related alleles gs3, GW7TFA, gw8, chalk5, Wxb, ALKTT, and fgr can enhance rice quality when applied in breeding programs. Polymerization of gs3, GW7TFA, gw8, and chalk5 genes improves rice appearance quality. The gs3 and GW7TFA allele polymerization increasing the grain's length-width ratio, adding the aggregation of gw8 allele can further reducing grain width. The chalk5 gene regulates low chalkiness, but low correlation to chalkiness was exhibited with grain widths below 2.0 mm, with minimal differences between Chalk5 and chalk5 alleles. Enhancing rice cooking and eating quality is achieved through Wxb and ALKTT gene polymerization, while introducing the fgr(E7) gene significantly improved rice aroma. Using molecular marker-assisted technology, we aggregated these genes to develop a batch of indica hybrid rice parents with improved rice quality are obtained. Cross-combining these enhanced parents can generate new, high-quality hybrid rice varieties suitable for cultivation in Southern China. Therefore, our findings contribute to a molecular breeding model for grain quality improvement in high-quality indica hybrid rice. This study, along with others, highlights the potential of molecular design breeding for enhancing complex traits, particularly rice grain quality.
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Affiliation(s)
- Ju Gao
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, 530007, China
| | - Lijun Gao
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, 530007, China
| | - Weiwei Chen
- Rice Research Institute, Guangxi Key Laboratory of Rice Genetics and Breeding, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, 530007, China
| | - Juan Huang
- Rice Research Institute, Guangxi Key Laboratory of Rice Genetics and Breeding, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, 530007, China
| | - Dongjin Qing
- Rice Research Institute, Guangxi Key Laboratory of Rice Genetics and Breeding, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, 530007, China
| | - Yinghua Pan
- Rice Research Institute, Guangxi Key Laboratory of Rice Genetics and Breeding, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, 530007, China
| | - Chonglie Ma
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, 530007, China
| | - Hao Wu
- Rice Research Institute, Guangxi Key Laboratory of Rice Genetics and Breeding, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, 530007, China
| | - Weiyong Zhou
- Rice Research Institute, Guangxi Key Laboratory of Rice Genetics and Breeding, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, 530007, China
| | - Jingcheng Li
- Rice Research Institute, Guangxi Key Laboratory of Rice Genetics and Breeding, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, 530007, China
| | - Xinghai Yang
- Rice Research Institute, Guangxi Key Laboratory of Rice Genetics and Breeding, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, 530007, China
| | - Gaoxing Dai
- Rice Research Institute, Guangxi Key Laboratory of Rice Genetics and Breeding, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, 530007, China.
| | - Guofu Deng
- Rice Research Institute, Guangxi Key Laboratory of Rice Genetics and Breeding, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, 530007, China.
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7
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Wei M, Yan Q, Huang D, Ma Z, Chen S, Yin X, Liu C, Qin Y, Zhou X, Wu Z, Lu Y, Yan L, Qin G, Zhang Y. Integration of molecular breeding and multi-resistance screening for developing a promising restorer line Guihui5501 with heavy grain, good grain quality, and endurance to biotic and abiotic stresses. FRONTIERS IN PLANT SCIENCE 2024; 15:1390603. [PMID: 38911983 PMCID: PMC11190317 DOI: 10.3389/fpls.2024.1390603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 05/20/2024] [Indexed: 06/25/2024]
Abstract
Rice, a critical staple on a global scale, faces escalating challenges in yield preservation due to the rising prevalence of abiotic and biotic stressors, exacerbated by frequent climatic fluctuations in recent years. Moreover, the scorching climate prevalent in the rice-growing regions of South China poses obstacles to the cultivation of good-quality, heavy-grain varieties. Addressing this dilemma requires the development of resilient varieties capable of withstanding multiple stress factors. To achieve this objective, our study employed the broad-spectrum blast-resistant line Digu, the brown planthopper (BPH)-resistant line ASD7, and the heavy-grain backbone restorer lines Fuhui838 (FH838) and Shuhui527 (SH527) as parental materials for hybridization and multiple crossings. The incorporation of molecular markers facilitated the rapid pyramiding of six target genes (Pi5, Pita, Pid2, Pid3, Bph2, and Wxb ). Through a comprehensive evaluation encompassing blast resistance, BPH resistance, cold tolerance, grain appearance, and quality, alongside agronomic trait selection, a promising restorer line, Guihui5501 (GH5501), was successfully developed. It demonstrated broad-spectrum resistance to blast, exhibiting a resistance frequency of 77.33% against 75 artificially inoculated isolates, moderate resistance to BPH (3.78 grade), strong cold tolerance during the seedling stage (1.80 grade), and characteristics of heavy grains (1,000-grain weight reaching 35.64 g) with good grain quality. The primary rice quality parameters for GH5501, with the exception of alkali spreading value, either met or exceeded the second-grade national standard for premium edible rice varieties, signifying a significant advancement in the production of good-quality heavy-grain varieties in the southern rice-growing regions. Utilizing GH5501, a hybrid combination named Nayou5501, characterized by high yield, good quality, and resistance to multiple stresses, was bred and received approval as a rice variety in Guangxi in 2021. Furthermore, genomic analysis with gene chips revealed that GH5501 possessed an additional 20 exceptional alleles, such as NRT1.1B for efficient nitrogen utilization, SKC1 for salt tolerance, and STV11 for resistance to rice stripe virus. Consequently, the restorer line GH5501 could serve as a valuable resource for the subsequent breeding of high-yielding, good-quality, and stress-tolerant hybrid rice varieties.
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Affiliation(s)
- Minyi Wei
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding/State Key Laboratory for Conservation and Utillzation of Subtropical Agro-bioresources, Nanning, China
| | - Qun Yan
- Plant Protection Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Dahui Huang
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding/State Key Laboratory for Conservation and Utillzation of Subtropical Agro-bioresources, Nanning, China
| | - Zengfeng Ma
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding/State Key Laboratory for Conservation and Utillzation of Subtropical Agro-bioresources, Nanning, China
| | - Shen Chen
- Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou, China
| | | | - Chi Liu
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding/State Key Laboratory for Conservation and Utillzation of Subtropical Agro-bioresources, Nanning, China
| | - Yuanyuan Qin
- Agricultural Science and Technology Information Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Xiaolong Zhou
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding/State Key Laboratory for Conservation and Utillzation of Subtropical Agro-bioresources, Nanning, China
| | - Zishuai Wu
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding/State Key Laboratory for Conservation and Utillzation of Subtropical Agro-bioresources, Nanning, China
| | - Yingping Lu
- Liuzhou Branch, Guangxi Academy of Agricultural Sciences, Liuzhou Research Center of Agricultural Sciences, Liuzhou, China
| | - Liuhui Yan
- Liuzhou Branch, Guangxi Academy of Agricultural Sciences, Liuzhou Research Center of Agricultural Sciences, Liuzhou, China
| | - Gang Qin
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding/State Key Laboratory for Conservation and Utillzation of Subtropical Agro-bioresources, Nanning, China
| | - Yuexiong Zhang
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding/State Key Laboratory for Conservation and Utillzation of Subtropical Agro-bioresources, Nanning, China
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8
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Gao R, Zong Y, Zhang S, Guo G, Zhang W, Chen Z, Lu R, Liu C, Wang Y, Li Y. Efficient isolated microspore culture protocol for callus induction and plantlet regeneration in japonica rice (Oryza sativa L.). PLANT METHODS 2024; 20:76. [PMID: 38790046 PMCID: PMC11127448 DOI: 10.1186/s13007-024-01189-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 04/18/2024] [Indexed: 05/26/2024]
Abstract
BACKGROUND Isolated microspore culture is a useful biotechnological technique applied in modern plant breeding programs as it can produce doubled haploid (DH) plants and accelerate the development of new varieties. Furthermore, as a single-cell culture technique, the isolated microspore culture provides an excellent platform for studying microspore embryogenesis. However, the reports on isolated microspore culture are rather limited in rice due to the low callus induction rate, poor regeneration capability, and high genotypic dependency. The present study developed an effective isolated microspore culture protocol for high-frequency androgenesis in four japonica rice genotypes. Several factors affecting the isolated microspore culture were studied to evaluate their effects on callus induction and plantlet regeneration. RESULTS Low-temperature pre-treatment at 4 ℃ for 10-15 days could effectively promote microspore embryogenesis in japonica rice. A simple and efficient method was proposed for identifying the microspore developmental stage. The anthers in yellow-green florets located on the second type of primary branch on the rice panicle were found to be the optimal stage for isolated microspore culture. The most effective induction media for callus induction were IM2 and IM3, depending on the genotype. The optimal concentration of 2, 4-D in the medium for callus induction was 1 mg/L. Callus induction was negatively affected by a high concentration of KT over 1.5 mg/L. The differentiation medium suitable for japonica rice microspore callus comprised 1/2 MS, 2 mg/L 6-BA, 0.5 mg/L NAA, 30 g/L sucrose, and 6 g/L agar. The regeneration frequency of the four genotypes ranged from 61-211 green plantlets per 100 mg calli, with Chongxiangjing showing the highest regeneration frequency. CONCLUSIONS This study presented an efficient protocol for improved callus induction and green plantlet regeneration in japonica rice via isolated microspore culture, which could provide valuable support for rice breeding and genetic research.
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Affiliation(s)
- Runhong Gao
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
| | - Yingjie Zong
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
| | - Shuwei Zhang
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
| | - Guimei Guo
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
| | - Wenqi Zhang
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
| | - Zhiwei Chen
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
| | - Ruiju Lu
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
| | - Chenghong Liu
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
| | - Yifei Wang
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China.
| | - Yingbo Li
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China.
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9
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Gao M, Hao Z, Ning Y, He Z. Revisiting growth-defence trade-offs and breeding strategies in crops. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1198-1205. [PMID: 38410834 PMCID: PMC11022801 DOI: 10.1111/pbi.14258] [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: 09/11/2023] [Revised: 11/02/2023] [Accepted: 11/20/2023] [Indexed: 02/28/2024]
Abstract
Plants have evolved a multi-layered immune system to fight off pathogens. However, immune activation is costly and is often associated with growth and development penalty. In crops, yield is the main breeding target and is usually affected by high disease resistance. Therefore, proper balance between growth and defence is critical for achieving efficient crop improvement. This review highlights recent advances in attempts designed to alleviate the trade-offs between growth and disease resistance in crops mediated by resistance (R) genes, susceptibility (S) genes and pleiotropic genes. We also provide an update on strategies for optimizing the growth-defence trade-offs to breed future crops with desirable disease resistance and high yield.
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Affiliation(s)
- Mingjun Gao
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science and Institute of Eco‐Chongming, School of Life SciencesFudan UniversityShanghaiChina
| | - Zeyun Hao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
| | - Yuese Ning
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
| | - Zuhua He
- CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghaiChina
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10
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Li J, Zhao Y, Wu Z, Wang X. Editorial: Crop improvement by omics and bioinformatics. FRONTIERS IN PLANT SCIENCE 2024; 15:1391334. [PMID: 38633453 PMCID: PMC11022161 DOI: 10.3389/fpls.2024.1391334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Accepted: 03/21/2024] [Indexed: 04/19/2024]
Affiliation(s)
- Jun Li
- Hainan Institute of Zhejiang University, Sanya, Hainan, China
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yan Zhao
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, Shandong, China
| | - Zhichao Wu
- National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Xueqiang Wang
- Hainan Institute of Zhejiang University, Sanya, Hainan, China
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
- Yazhouwan National Laboratory, Sanya, Hainan, China
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11
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Zhang H, Liu M, Yin K, Liu H, Liu J, Yan Z. A novel OsHB5-OsAPL-OsMADS27/OsWRKY102 regulatory module regulates grain size in rice. JOURNAL OF PLANT PHYSIOLOGY 2024; 295:154210. [PMID: 38460401 DOI: 10.1016/j.jplph.2024.154210] [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: 01/15/2024] [Revised: 02/17/2024] [Accepted: 02/29/2024] [Indexed: 03/11/2024]
Abstract
Grain size, a crucial trait that determines rice yield and quality, is typically regulated by multiple genes. Although numerous genes controlling grain size have been identified, the precise and dynamic regulatory network governing grain size is still not fully understood. In this study, we unveiled a novel regulatory module composed of OsHB5, OsAPL and OsMADS27/OsWRKY102, which plays a crucial role in modulating grain size in rice. As a positive regulator of grain size, OsAPL has been found to interact with OsHB5 both in vitro and in vivo. Through chromatin immunoprecipitation-sequencing, we successfully mapped two potential targets of OsAPL, namely OsMADS27, a positive regulator in grain size and OsWRKY102, a negative regulator in lignification that is also associated with grain size control. Further evidence from EMSA and chromatin immunoprecipitation-quantitative PCR experiments has shown that OsAPL acts as an upstream transcription factor that directly binds to the promoters of OsMADS27 and OsWRKY102. Moreover, EMSA and dual-luciferase reporter assays have indicated that the interaction between OsAPL and OsHB5 enhances the repressive effect of OsAPL on OsMADS27 and OsWRKY102. Collectively, our findings discovered a novel regulatory module, OsHB5-OsAPL-OsMADS27/OsWRKY102, which plays a significant role in controlling grain size in rice. These discoveries provide potential targets for breeding high-yield and high-quality rice varieties.
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Affiliation(s)
- Han Zhang
- Key Laboratory for Bio-resources and Eco-environment & State Key Lab of Hydraulics & Mountain River Engineering, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Meng Liu
- Key Laboratory for Bio-resources and Eco-environment & State Key Lab of Hydraulics & Mountain River Engineering, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Kangqun Yin
- Key Laboratory for Bio-resources and Eco-environment & State Key Lab of Hydraulics & Mountain River Engineering, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Huanhuan Liu
- Key Laboratory for Bio-resources and Eco-environment & State Key Lab of Hydraulics & Mountain River Engineering, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, China; National Demonstration Center for Experimental Biology Education (Sichuan University), Chengdu, 610064, China
| | - Jianquan Liu
- Key Laboratory for Bio-resources and Eco-environment & State Key Lab of Hydraulics & Mountain River Engineering, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, China; State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems and College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Zhen Yan
- Key Laboratory for Bio-resources and Eco-environment & State Key Lab of Hydraulics & Mountain River Engineering, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, China; National Demonstration Center for Experimental Biology Education (Sichuan University), Chengdu, 610064, China.
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12
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Zhong D, Chi Y, Ding J, Zhao N, Zeng L, Liu P, Huang Z, Zhou L. Decoupling of nitrogen allocation and energy partitioning in rice after flowering. Ecol Evol 2024; 14:e11297. [PMID: 38623520 PMCID: PMC11017445 DOI: 10.1002/ece3.11297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 03/28/2024] [Accepted: 04/04/2024] [Indexed: 04/17/2024] Open
Abstract
Estimation of energy partitioning at leaf scale, such as fluorescence yield (ΦF) and photochemical yield (ΦP), is crucial to tracking vegetation gross primary productivity (GPP) at global scale. Nitrogen is an important participant in the process of light capture, electron transfer, and carboxylation in vegetation photosynthesis. However, the quantitative relationship between leaf nitrogen allocation and leaf energy partitioning remains unexplored. Here, a field experiment was established to explore growth stage variations in energy partitioning and nitrogen allocation at leaf scale using active fluorescence detection and photosynthetic gas exchange method in rice in the subtropical region of China. We observed a strongly positive correlation between the investment proportion of leaf nitrogen in photosynthetic system and ΦF during the vegetative growth stage. There were significant differences in leaf energy partitioning, leaf nitrogen allocation, and the relationship between ΦF and ΦP before and after flowering. Furthermore, flowering weakened the correlation between the investment proportion of leaf nitrogen in photosynthetic system and ΦF. These findings highlight the crucial role of phenological factors in exploring seasonal photosynthetic dynamics and carbon fixation of ecosystems.
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Affiliation(s)
- Duwei Zhong
- College of Geography and Environmental SciencesZhejiang Normal UniversityJinhuaChina
| | - Yonggang Chi
- College of Geography and Environmental SciencesZhejiang Normal UniversityJinhuaChina
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources ResearchChinese Academy of SciencesBeijingChina
| | - Jianxi Ding
- College of Geography and Environmental SciencesZhejiang Normal UniversityJinhuaChina
| | - Ning Zhao
- College of Geography and Environmental SciencesZhejiang Normal UniversityJinhuaChina
| | - Linhui Zeng
- College of Geography and Environmental SciencesZhejiang Normal UniversityJinhuaChina
| | - Pai Liu
- College of Geography and Environmental SciencesZhejiang Normal UniversityJinhuaChina
| | - Zhi Huang
- College of Geography and Environmental SciencesZhejiang Normal UniversityJinhuaChina
| | - Lei Zhou
- College of Geography and Environmental SciencesZhejiang Normal UniversityJinhuaChina
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources ResearchChinese Academy of SciencesBeijingChina
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13
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Dong J, Ma Y, Hu H, Wang J, Yang W, Fu H, Zhang L, Chen J, Zhou L, Li W, Nie S, Liu Z, Zhao J, Liu B, Yang T, Zhang S. The Function of SD1 on Shoot Length and its Pyramiding Effect on Shoot Length and Plant Height in Rice (Oryza sativa L.). RICE (NEW YORK, N.Y.) 2024; 17:21. [PMID: 38526756 DOI: 10.1186/s12284-024-00699-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 03/08/2024] [Indexed: 03/27/2024]
Abstract
Strong seedling vigor is imperative to achieve stable seedling establishment and enhance the competitiveness against weeds in rice direct seeding. Shoot length (SL) is one of the important traits associated with seedling vigor in rice, but few genes for SL have been cloned so far. In the previous study, we identified two tightly linked and stably expressed QTLs for SL, qSL-1f and qSL-1d by genome-wide association study, and cloned the causal gene (LOC_Os01g68500) underlying qSL-1f. In the present study, we identify LOC_Os01g66100 (i.e. the semidwarf gene SD1), a well-known gene controlling plant height (PH) at the adult-plant stage, as the causal gene underlying qSL-1d through gene-based haplotype analysis and knockout transgenic verification. By measuring the phenotypes (SL and PH) of various haplotypes of the two genes and their knockout lines, we found SD1 and LOC_ Os01g68500 controlled both SL and PH, and worked in the same direction, which provided the directly genetic evidence for a positive correlation between SL and PH combined with the analysis of SL and PH in the diverse natural population. Moreover, the knockout transgenic experiments suggested that SD1 had a greater effect on PH compared with LOC_ Os01g68500, but no significant difference in the effect on SL. Further investigation of the pyramiding effects of SD1 and LOC_Os01g68500 based on their haplotype combinations suggested that SD1 may play a dominant role in controlling SL and PH when the two genes coexist. In this study, the effect of SD1 on SL at the seedling stage is validated. In total, two causal genes, SD1 and LOC_ Os01g68500, for SL are cloned in our studies, which controlled both SL and PH, and the suitable haplotypes of SD1 and LOC_ Os01g68500 are beneficial to achieve the desired SL and PH in different rice breeding objectives. These results provide a new clue to develop rice varieties for direct seeding and provide new genetic resources for molecular breeding of rice with suitable PH and strong seedling vigor.
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Affiliation(s)
- Jingfang Dong
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High -Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, Guangdong, China
| | - Yamei Ma
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High -Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, Guangdong, China
| | - Haifei Hu
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High -Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, Guangdong, China
| | - Jian Wang
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High -Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, Guangdong, China
| | - Wu Yang
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High -Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, Guangdong, China
| | - Hua Fu
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High -Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, Guangdong, China
| | - Longting Zhang
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High -Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, Guangdong, China
- College of Agriculture, South China Agricultural University, 510642, Guangzhou, China
| | - Jiansong Chen
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High -Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, Guangdong, China
| | - Lian Zhou
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High -Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, Guangdong, China
| | - Wenhui Li
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High -Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, Guangdong, China
| | - Shuai Nie
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High -Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, Guangdong, China
| | - Ziqiang Liu
- College of Agriculture, South China Agricultural University, 510642, Guangzhou, China
| | - Junliang Zhao
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High -Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, Guangdong, China
| | - Bin Liu
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High -Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, Guangdong, China
| | - Tifeng Yang
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High -Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, Guangdong, China.
| | - Shaohong Zhang
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High -Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, Guangdong, China.
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14
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Yin M, Tong X, Yang J, Cheng Y, Zhou P, Li G, Wang Y, Ying J. Dissecting the Genetic Basis of Yield Traits and Validation of a Novel Quantitative Trait Locus for Grain Width and Weight in Rice. PLANTS (BASEL, SWITZERLAND) 2024; 13:770. [PMID: 38592774 PMCID: PMC10975080 DOI: 10.3390/plants13060770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 02/29/2024] [Accepted: 03/06/2024] [Indexed: 04/11/2024]
Abstract
Grain yield in rice is a complex trait and it is controlled by a number of quantitative trait loci (QTL). To dissect the genetic basis of rice yield, QTL analysis for nine yield traits was performed using an F2 population containing 190 plants, which was developed from a cross between Youyidao (YYD) and Sanfenhe (SFH), and each plant in the population evaluated with respect to nine yield traits. In this study, the correlations among the nine yield traits were analyzed. The grain yield per plant positively correlated with six yield traits, except for grain length and grain width, and showed the highest correlation coefficient of 0.98 with the number of filled grains per plant. A genetic map containing 133 DNA markers was constructed and it spanned 1831.7 cM throughout 12 chromosomes. A total of 36 QTLs for the yield traits were detected on nine chromosomes, except for the remaining chromosomes 5, 8, and 9. The phenotypic variation was explained by a single QTL that ranged from 6.19% to 36.01%. Furthermore, a major QTL for grain width and weight, qGW2-1, was confirmed to be newly identified and was narrowed down to a relatively smaller interval of about ~2.94-Mb. Collectively, we detected a total of 36 QTLs for yield traits and a major QTL, qGW2-1, was confirmed to control grain weight and width, which laid the foundation for further map-based cloning and molecular design breeding in rice.
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Affiliation(s)
| | | | | | | | | | | | | | - Jiezheng Ying
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China; (M.Y.); (J.Y.); (Y.C.); (P.Z.); (G.L.); (Y.W.)
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15
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Lim I, Park YJ, Ha J. Evolutionary and synteny analysis of HIS1, BADH2, GBSS1, and GBSS2 in rice: insights for effective introgression breeding strategies. Sci Rep 2024; 14:5226. [PMID: 38433262 PMCID: PMC10909864 DOI: 10.1038/s41598-024-55581-w] [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: 01/16/2024] [Accepted: 02/26/2024] [Indexed: 03/05/2024] Open
Abstract
The key genes BADH2, GBSS1, GBSS2, and HIS1 regulate the fragrance, starch synthesis, and herbicide resistance in rice. Although the molecular functions of four genes have been investigated in the Oryza sativa species, little is known regarding their evolutionary history in the Oryza genus. Here, we studied the evolution of four focal genes in 10 Oryza species using phylogenetic and syntenic approaches. The HIS1 family underwent several times of tandem duplication events in the Oryza species, resulting in copy number variation ranging from 2 to 7. At most one copy of BADH2, GBSS1, and GBSS2 orthologs were identified in each Oryza species, and gene loss events of BADH2 and GBSS2 were identified in three Oryza species. Gene transfer analysis proposed that the functional roles of GBSS1 and GBSS2 were developed in the Asian and African regions, respectively, and most allelic variations of BADH2 in japonica rice emerged after the divergence between the Asian and African rice groups. These results provide clues to determine the origin and evolution of the key genes in rice breeding as well as valuable information for molecular breeders and scientists to develop efficient strategies to simultaneously improve grain quality and yield potential in rice.
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Affiliation(s)
- Insu Lim
- Department of Plant Science, Gangneung-Wonju National University, Gangneung, South Korea
| | - Yong-Jin Park
- Department of Plant Sciences, Kongju National University, Yesan, 340-702, Korea
| | - Jungmin Ha
- Department of Plant Science, Gangneung-Wonju National University, Gangneung, South Korea.
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16
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Wang C, Chang J, Tian L, Sun Y, Wang E, Yao Z, Ye L, Zhang H, Pang Y, Tian C. A Synthetic Microbiome Based on Dominant Microbes in Wild Rice Rhizosphere to Promote Sulfur Utilization. RICE (NEW YORK, N.Y.) 2024; 17:18. [PMID: 38429614 PMCID: PMC10907558 DOI: 10.1186/s12284-024-00695-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 02/14/2024] [Indexed: 03/03/2024]
Abstract
Sulfur (S) is one of the main components of important biomolecules, which has been paid more attention in the anaerobic environment of rice cultivation. In this study, 12 accessions of rice materials, belonging to two Asian rice domestication systems and one African rice domestication system, were used by shotgun metagenomics sequencing to compare the structure and function involved in S cycle of rhizosphere microbiome between wild and cultivated rice. The sulfur cycle functional genes abundances were significantly different between wild and cultivated rice rhizosphere in the processes of sulfate reduction and other sulfur compounds conversion, implicating that wild rice had a stronger mutually-beneficial relationship with rhizosphere microbiome, enhancing sulfur utilization. To assess the effects of sulfate reduction synthetic microbiomes, Comamonadaceae and Rhodospirillaceae, two families containing the genes of two key steps in the dissimilatory sulfate reduction, aprA and dsrA respectively, were isolated from wild rice rhizosphere. Compared with the control group, the dissimilatory sulfate reduction in cultivated rice rhizosphere was significantly improved in the inoculated with different proportions groups. It confirmed that the synthetic microbiome can promote the S-cycling in rice, and suggested that may be feasible to construct the synthetic microbiome step by step based on functional genes to achieve the target functional pathway. In summary, this study reveals the response of rice rhizosphere microbial community structure and function to domestication, and provides a new idea for the construction of synthetic microbiome.
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Affiliation(s)
- Changji Wang
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jingjing Chang
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
| | - Lei Tian
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
| | - Yu Sun
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
| | - Enze Wang
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zongmu Yao
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Libo Ye
- College of Life Science, Jilin Agricultural University, Jilin, Changchun, China
| | - Hengfei Zhang
- College of Life Science, Jilin Agricultural University, Jilin, Changchun, China
| | - Yingnan Pang
- College of Life Science, Jilin Agricultural University, Jilin, Changchun, China
| | - Chunjie Tian
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China.
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China.
- College of Resources and Environment, Jilin Agricultural University, Changchun, Jilin, China.
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17
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Yang L, Chen H, Zhu S, Zhao S, Huang S, Cheng D, Xu H, Zhang Z. Pectin-Coated Iron-Based Metal-Organic Framework Nanoparticles for Enhanced Foliar Adhesion and Targeted Delivery of Fungicides. ACS NANO 2024; 18:6533-6549. [PMID: 38355215 DOI: 10.1021/acsnano.3c12352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
Conventional agrochemicals are underutilized due to their large particle sizes, poor foliar retention rates, and difficult translocation in plants, and the development of functional nanodelivery carriers with high adhesion to the plant body surface and efficient uptake and translocation in plants remains challenging. In this study, a nanodelivery system based on a pectin-encapsulated iron-based MOF (TF@Fe-MOF-PT NPs) was constructed to enhance the utilization of thifluzamide (TF) in rice plants by taking advantage of the pectin affinity for plant cell walls. The prepared TF@Fe-MOF-PT NPs exhibited an average particle size of 126.55 nm, a loading capacity of 27.41%, and excellent dual-stimulus responses to reactive oxygen species and pectinase. Foliar washing experiments showed that the TF@Fe-MOF-PT NPs were efficiently adhered to the surfaces of rice leaves and stems. Confocal laser scanning microscopy showed that fluorescently labeled TF@Fe-MOF-PT NPs were bidirectionally delivered through vascular bundles in rice plants. The in vitro bactericidal activity of the TF@Fe-MOF-PT NPs showed better inhibitory activity than that of a TF suspension (TF SC), with an EC50 of 0.021 mg/L. A greenhouse test showed that the TF@Fe-MOF-PT NPs were more effective than TF SC at 7 and 14 d, with control effects of 85.88 and 78.59%, respectively. It also reduced the inhibition of seed stem length and root length by TF SC and promoted seedling growth. These results demonstrated that TF@Fe-MOF-PT NPs can be used as a pesticide nanodelivery system for efficient delivery and intelligent release in plants and applied for sustainable control of pests and diseases.
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Affiliation(s)
- Liupeng Yang
- National Key Laboratory of Green Pesticide, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Biological Pesticide Engineering Technology Research Center, South China Agricultural University, Guangzhou, 510642, China
| | - Huiya Chen
- National Key Laboratory of Green Pesticide, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Biological Pesticide Engineering Technology Research Center, South China Agricultural University, Guangzhou, 510642, China
| | - Shiqi Zhu
- National Key Laboratory of Green Pesticide, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Biological Pesticide Engineering Technology Research Center, South China Agricultural University, Guangzhou, 510642, China
| | - Shiji Zhao
- National Key Laboratory of Green Pesticide, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Biological Pesticide Engineering Technology Research Center, South China Agricultural University, Guangzhou, 510642, China
| | - Suqing Huang
- Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Dongmei Cheng
- Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Hanhong Xu
- National Key Laboratory of Green Pesticide, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Biological Pesticide Engineering Technology Research Center, South China Agricultural University, Guangzhou, 510642, China
| | - Zhixiang Zhang
- National Key Laboratory of Green Pesticide, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Biological Pesticide Engineering Technology Research Center, South China Agricultural University, Guangzhou, 510642, China
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18
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Lei Y, Zhang Y, Xu L, Ma W, Zhou Z, Li J, Quan P, Faruquee M, Yang D, Zhang F, Zhou Y, Quan G, Zhao X, Wang W, Liu B, Li Z, Xu J, Zheng T. Pedigree genome data of an early-matured Geng/japonica glutinous rice mega variety Longgeng 57. Sci Data 2024; 11:230. [PMID: 38388638 PMCID: PMC10884013 DOI: 10.1038/s41597-024-03057-x] [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: 10/23/2023] [Accepted: 02/08/2024] [Indexed: 02/24/2024] Open
Abstract
By using PacBio HiFi technology, we produced over 700 Gb of long-read sequencing (LRS) raw data; and by using Illumina paired-end whole-genome shotgun (WGS) sequencing technology, we generated more than 70 Gb of short-read sequencing (SRS) data. With LRS data, we assembled one genome and then generate a set of annotation data for an early-matured Geng/japonica glutinous rice mega variety genome, Longgeng 57 (LG57), which carries multiple elite traits including good grain quality and wide adaptability. Together with the SRS data from three parents of LG57, pedigree genome variations were called for three representative types of genes. These data sets can be used for deep variation mining, aid in the discovery of new insights into genome structure, function, and evolution, and help to provide essential support to biological research in general.
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Affiliation(s)
- Yuanbao Lei
- Jiamusi Rice Research Institute of Heilongjiang Academy of Agricultural Sciences, Jiamusi, 154026, China
- Institute of Crop Sciences/State Key Laboratory of Crop Gene Resources and Breeding/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Yunjiang Zhang
- Jiamusi Rice Research Institute of Heilongjiang Academy of Agricultural Sciences, Jiamusi, 154026, China
| | - Linyun Xu
- Institute of Crop Sciences/State Key Laboratory of Crop Gene Resources and Breeding/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wendong Ma
- Jiamusi Rice Research Institute of Heilongjiang Academy of Agricultural Sciences, Jiamusi, 154026, China
| | - Ziqi Zhou
- Institute of Crop Sciences/State Key Laboratory of Crop Gene Resources and Breeding/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jie Li
- Heilongjiang Lianjiangkou Seed Co., Ltd, Jiamusi, 154024, China
| | - Pengyu Quan
- Heilongjiang Lianjiangkou Seed Co., Ltd, Jiamusi, 154024, China
| | - Muhiuddin Faruquee
- International Rice Research Institute, Bangladesh Office, Dhaka, 1213, Bangladesh
| | - Dechen Yang
- Institute of Crop Sciences/State Key Laboratory of Crop Gene Resources and Breeding/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, 572024, China
| | - Fan Zhang
- Institute of Crop Sciences/State Key Laboratory of Crop Gene Resources and Breeding/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yongli Zhou
- Institute of Crop Sciences/State Key Laboratory of Crop Gene Resources and Breeding/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Guangjun Quan
- Heilongjiang Lianjiangkou Seed Co., Ltd, Jiamusi, 154024, China
| | - Xiuqin Zhao
- Institute of Crop Sciences/State Key Laboratory of Crop Gene Resources and Breeding/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wensheng Wang
- Institute of Crop Sciences/State Key Laboratory of Crop Gene Resources and Breeding/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, 572024, China
| | - Bailong Liu
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Zhikang Li
- Institute of Crop Sciences/State Key Laboratory of Crop Gene Resources and Breeding/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jianlong Xu
- Institute of Crop Sciences/State Key Laboratory of Crop Gene Resources and Breeding/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
- National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, 572024, China.
- Hainan Yazhou Bay Seed Lab, Sanya, 572024, China.
| | - Tianqing Zheng
- Institute of Crop Sciences/State Key Laboratory of Crop Gene Resources and Breeding/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
- National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, 572024, China.
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19
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Ashraf H, Ghouri F, Baloch FS, Nadeem MA, Fu X, Shahid MQ. Hybrid Rice Production: A Worldwide Review of Floral Traits and Breeding Technology, with Special Emphasis on China. PLANTS (BASEL, SWITZERLAND) 2024; 13:578. [PMID: 38475425 DOI: 10.3390/plants13050578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 01/26/2024] [Accepted: 02/08/2024] [Indexed: 03/14/2024]
Abstract
Rice is an important diet source for the majority of the world's population, and meeting the growing need for rice requires significant improvements at the production level. Hybrid rice production has been a significant breakthrough in this regard, and the floral traits play a major role in the development of hybrid rice. In grass species, rice has structural units called florets and spikelets and contains different floret organs such as lemma, palea, style length, anther, and stigma exsertion. These floral organs are crucial in enhancing rice production and uplifting rice cultivation at a broader level. Recent advances in breeding techniques also provide knowledge about different floral organs and how they can be improved by using biotechnological techniques for better production of rice. The rice flower holds immense significance and is the primary focal point for researchers working on rice molecular biology. Furthermore, the unique genetics of rice play a significant role in maintaining its floral structure. However, to improve rice varieties further, we need to identify the genomic regions through mapping of QTLs (quantitative trait loci) or by using GWAS (genome-wide association studies) and their validation should be performed by developing user-friendly molecular markers, such as Kompetitive allele-specific PCR (KASP). This review outlines the role of different floral traits and the benefits of using modern biotechnological approaches to improve hybrid rice production. It focuses on how floral traits are interrelated and their possible contribution to hybrid rice production to satisfy future rice demand. We discuss the significance of different floral traits, techniques, and breeding approaches in hybrid rice production. We provide a historical perspective of hybrid rice production and its current status and outline the challenges and opportunities in this field.
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Affiliation(s)
- Humera Ashraf
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Fozia Ghouri
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Faheem Shehzad Baloch
- Department of Biotechnology, Faculty of Science, Mersin University, Mersin 33100, Türkiye
| | - Muhammad Azhar Nadeem
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas 58140, Türkiye
| | - Xuelin Fu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
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20
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Yang T, Song L, Hu J, Qiao L, Yu Q, Wang Z, Chen X, Lu GD. Magnaporthe oryzae effector AvrPik-D targets a transcription factor WG7 to suppress rice immunity. RICE (NEW YORK, N.Y.) 2024; 17:14. [PMID: 38351214 PMCID: PMC10864242 DOI: 10.1186/s12284-024-00693-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 02/06/2024] [Indexed: 02/16/2024]
Abstract
Rice blast, caused by the fungal pathogen Magnaporthe oryzae, is one of the most devastating diseases for rice crops, significantly affecting crop yield and quality. During the infection process, M. oryzae secretes effector proteins that help in hijacking the host's immune responses to establish infection. However, little is known about the interaction between the effector protein AvrPik-D and the host protein Pikh, and how AvrPik-D increases disease severity to promote infection. In this study, we show that the M. oryzae effector AvrPik-D interacts with the zinc finger-type transcription factor WG7 in the nucleus and promotes its transcriptional activity. Genetic removal (knockout) of the gene WG7 in transgenic rice enhances resistance to M. oryzae and also results in an increased burst of reactive oxygen species after treatments with chitin. In addition, the hormone level of SA and JA, is increased and decreased respectively in WG7 KO plants, indicating that WG7 may negatively mediate resistance through salicylic acid pathway. Conversely, WG7 overexpression lines reduce resistance to M. oryzae. However, WG7 is not required for the Pikh-mediated resistance against rice blast. In conclusion, our results revealed that the M. oryzae effector AvrPik-D targets and promotes transcriptional activity of WG7 to suppress rice innate immunity to facilitate infection.
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Affiliation(s)
- Tao Yang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 35002, China
| | - Linlin Song
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 35002, China
| | - Jinxian Hu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 35002, China
| | - Luao Qiao
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 35002, China
| | - Qing Yu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 35002, China
| | - Zonghua Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 35002, China
- Fujian Universities Engineering Research Center of Marine Biology and Drugs, Fuzhou Institute of Oceanography, College of Geography and Oceanography, Minjiang University, Fuzhou, 350108, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Minjiang University, Fuzhou, 350108, China
| | - Xiaofeng Chen
- Fujian Universities Engineering Research Center of Marine Biology and Drugs, Fuzhou Institute of Oceanography, College of Geography and Oceanography, Minjiang University, Fuzhou, 350108, China.
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Minjiang University, Fuzhou, 350108, China.
| | - Guo-Dong Lu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 35002, China.
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21
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Yang W, Chen S, Hao Q, Zhu H, Tan Q, Lin S, Chen G, Li Z, Bu S, Liu Z, Liu G, Wang S, Zhang G. Pyramiding of Low Chalkiness QTLs Is an Effective Way to Reduce Rice Chalkiness. RICE (NEW YORK, N.Y.) 2024; 17:4. [PMID: 38185771 PMCID: PMC10772014 DOI: 10.1186/s12284-023-00680-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 12/26/2023] [Indexed: 01/09/2024]
Abstract
Rice chalkiness is a key limiting factor of high-quality rice. The breeding of low chalkiness varieties has always been a challenging task due to the complexity of chalkiness and its susceptibility to environmental factors. In previous studies, we identified six QTLs for the percentage of grain chalkiness (PGC), named qPGC5, qPGC6, qPGC8.1, qPGC8.2, qPGC9 and qPGC11, using single-segment substitution lines (SSSLs) with genetic background of Huajingxian 74 (HJX74). In this study, we utilized the six low chalkiness QTLs to develop 17 pyramiding lines with 2-4 QTLs. The results showed that the PGC decreased with the increase of QTLs in the pyramiding lines. The pyramiding lines with 4 QTLs significantly reduced the chalkiness of rice and reached the best quality level. Among the six QTLs, qPGC5 and qPGC6 showed greater additive effects and were classified as Group A, while the other four QTLs showed smaller additive effects and were classified as Group B. In pyramiding lines, although the presence of epistasis, additivity remained the main component of QTL effects. qPGC5 and qPGC6 showed stronger ability to reduce rice chalkiness, particularly in the environment of high temperature (HT) in the first cropping season (FCS). Our research demonstrates that by pyramiding low chalkiness QTLs, it is feasible to develop the high-quality rice varieties with low chalkiness at the best quality level even in the HT environment of FCS.
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Affiliation(s)
- Weifeng Yang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Songliang Chen
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Qingwen Hao
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Haitao Zhu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Quanya Tan
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Shaojun Lin
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Guodong Chen
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Zhan Li
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Suhong Bu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Zupei Liu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Guifu Liu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Shaokui Wang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China.
| | - Guiquan Zhang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China.
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22
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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.
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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.
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23
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Liu J, Liu J, He M, Zhang C, Liu Y, Li X, Wang Z, Jin X, Sui J, Zhou W, Bu Q, Tian X. OsMAPK6 positively regulates rice cold tolerance at seedling stage via phosphorylating and stabilizing OsICE1 and OsIPA1. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 137:10. [PMID: 38103049 DOI: 10.1007/s00122-023-04506-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 11/15/2023] [Indexed: 12/17/2023]
Abstract
Rice is a chilling-sensitive plant, and extremely low temperatures seriously decrease rice production. Several genes involved in chilling stress have been reported in rice; however, the chilling signaling in rice remains largely unknown. Here, we investigated the chilling tolerance phenotype of overexpression of constitutive active OsMAPK6 (CAMAPK6-OE) and OsMAPK6 mutant dsg1, and demonstrated that OsMAPK6 positively regulated rice chilling tolerance. It was shown that, under cold stress, the survival rate of dsg1 was significantly lower than that of WT, whereas CAMAPK6-OE display higher survival rate than WT. Physiological assays indicate that ion leakage and dead cell in dsg1 was much more severe than those in WT and CAMAPK6-OE. Consistently, expression of chilling responsive genes in dsg1, including OsCBFs and OsTPP1, was significantly lower than that of in WT and CAMAPK6-OE. Biochemical analyses revealed that chilling stress promotes phosphorylation of OsMAPK6. Besides, we found that OsMAPK6 interacts with and phosphorylates two key regulators in rice cold signaling, OsIPA1 and OsICE1, and then enhance their protein stability. Overall, our results revealed a cold-induced OsMAPK6-OsICE1/OsIPA1 signaling cascade by which OsMAPK6 was involved in rice chilling tolerance, which provides novel insights to understand rice cold response at seedling stage.
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Affiliation(s)
- Jiali Liu
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, 150040, China
| | - Jiaxin Liu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
| | - Mingliang He
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chuanzhong Zhang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
| | - Yingxiang Liu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiufeng Li
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
| | - Zhenyu Wang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
| | - Xin Jin
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jingjing Sui
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, 150040, China
| | - Wenyan Zhou
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, 150040, China
| | - Qingyun Bu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China.
| | - Xiaojie Tian
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China.
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24
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Lu T, Yin W, Zhang Y, Zhu C, Zhong Q, Li S, Wang N, Chen Z, Ye H, Fang Y, Mu D, Wang Y, Rao Y. WLP3 Encodes the Ribosomal Protein L18 and Regulates Chloroplast Development in Rice. RICE (NEW YORK, N.Y.) 2023; 16:59. [PMID: 38091105 PMCID: PMC10719208 DOI: 10.1186/s12284-023-00674-9] [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: 11/13/2023] [Accepted: 12/01/2023] [Indexed: 12/17/2023]
Abstract
Plastid ribosomal proteins play a crucial role in the growth and development of plants, mainly in the gene expression and translation of key genes in chloroplasts. While some information is known about the regulatory processes of plastid ribosomal proteins in various plant species, there is limited knowledge about the underlying mechanisms in rice. In this study, ethyl methanesulfonate (EMS) mutagenesis was used to generate a new mutant called wlp3 (white leaf and panicle3), characterized by white or albino leaves and panicles, which exhibited this phenotype from the second leaf stage until tillering. Furthermore, after a certain period, the newly emerging leaves developed the same phenotype as the rice variety ZH11, while the albino leaves of wlp3 showed an incomplete chloroplast structure and significantly low chlorophyll content. A transition mutation (T to C) at position 380 was identified in the coding region of the LOC_Os03g61260 gene, resulting in the substitution of isoleucine by threonine during translation. WLP3 encodes the ribosomal L18 subunit, which is localized in the chloroplast. Complementation experiments confirmed that LOC_Os03g61260 was responsible for the albino phenotype in rice. WLP3 has high expression in the coleoptile, leaves at the three-leaf stage, and panicles at the heading stage. Compared to the wild-type (WT), wlp3 exhibited reduced chlorophyll synthesis and significantly decreased expression levels of genes associated with plastid development. Yeast two-hybrid (Y2H) analysis revealed that WLP3 interacts with other ribosomal subunits, to influence chloroplast development. These results contribute to a better understanding of the underlying molecular mechanisms of chloroplast development and plastid gene translation.
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Affiliation(s)
- Tao Lu
- College of Life Sciences, Zhejiang Normal University, Jinhua, 321000, Zhejiang, China
| | - Wenjin Yin
- College of Life Sciences, Zhejiang Normal University, Jinhua, 321000, Zhejiang, China
| | - Yinuo Zhang
- College of Life Sciences, Zhejiang Normal University, Jinhua, 321000, Zhejiang, China
| | - Chaoyu Zhu
- College of Life Sciences, Zhejiang Normal University, Jinhua, 321000, Zhejiang, China
| | - Qianqian Zhong
- College of Life Sciences, Zhejiang Normal University, Jinhua, 321000, Zhejiang, China
| | - Sanfeng Li
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 310006, China
| | - Nuo Wang
- College of Life Sciences, Anqing Normal University, Anqing, 246133, Anhui, China
| | - Zhengai Chen
- College of Life Sciences, Zhejiang Normal University, Jinhua, 321000, Zhejiang, China
| | - Hanfei Ye
- College of Life Sciences, Zhejiang Normal University, Jinhua, 321000, Zhejiang, China
| | - Yuan Fang
- College of Life Sciences, Zhejiang Normal University, Jinhua, 321000, Zhejiang, China
| | - Dan Mu
- College of Life Sciences, Anqing Normal University, Anqing, 246133, Anhui, China.
| | - Yuexing Wang
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 310006, China.
| | - Yuchun Rao
- College of Life Sciences, Zhejiang Normal University, Jinhua, 321000, Zhejiang, China.
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25
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Zhu H, Lai R, Chen W, Lu C, Chachar Z, Lu S, Lin H, Fan L, Hu Y, An Y, Li X, Zhang X, Qi Y. Genetic dissection of maize (Zea maysL.) trace element traits using genome-wide association studies. BMC PLANT BIOLOGY 2023; 23:631. [PMID: 38062375 PMCID: PMC10704835 DOI: 10.1186/s12870-023-04643-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023]
Abstract
Maize (Zea mays L.) is an important food and feed crop worldwide and serves as a a vital source of biological trace elements, which are important breeding targets. In this study, 170 maize materials were used to detect QTNs related to the content of Mn, Fe and Mo in maize grains through two GWAS models, namely MLM_Q + K and MLM_PCA + K. The results identified 87 (Mn), 205 (Fe), and 310 (Mo) QTNs using both methods in the three environments. Considering comprehensive factors such as co-location across multiple environments, strict significance threshold, and phenotypic value in multiple environments, 8 QTNs related to Mn, 10 QTNs related to Fe, and 26 QTNs related to Mo were used to identify 44 superior alleles. Consequently, three cross combinations with higher Mn element, two combinations with higher Fe element, six combinations with higher Mo element, and two combinations with multiple element (Mn/Fe/Mo) were predicted to yield offspring with higher numbers of superior alleles, thereby increasing the likelihood of enriching the corresponding elements. Additionally, the candidate genes identified 100 kb downstream and upstream the QTNs featured function and pathways related to maize elemental transport and accumulation. These results are expected to facilitate the screening and development of high-quality maize varieties enriched with trace elements, establish an important theoretical foundation for molecular marker assisted breeding and contribute to a better understanding of the regulatory network governing trace elements in maize.
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Affiliation(s)
- Hang Zhu
- Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, Guangdong, China
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, Guangdong, China
- College of Agriculture, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Ruiqiang Lai
- Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, Guangdong, China
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, Guangdong, China
| | - Weiwei Chen
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, Guangdong, China
- Heyuan Provincial Academy of Sciences Research Institute, Guangdong Academy of Sciences, GDAS, Heyuan, 517001, Guangdong, China
| | - Chuanli Lu
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, Guangdong, China
- Heyuan Provincial Academy of Sciences Research Institute, Guangdong Academy of Sciences, GDAS, Heyuan, 517001, Guangdong, China
| | - Zaid Chachar
- Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, Guangdong, China
| | - Siqi Lu
- Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, Guangdong, China
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, Guangdong, China
| | - Huanzhang Lin
- Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, Guangdong, China
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, Guangdong, China
| | - Lina Fan
- Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, Guangdong, China
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, Guangdong, China
| | - Yuanqiang Hu
- Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, Guangdong, China
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, Guangdong, China
| | - Yuxing An
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, Guangdong, China
- Heyuan Provincial Academy of Sciences Research Institute, Guangdong Academy of Sciences, GDAS, Heyuan, 517001, Guangdong, China
| | - Xuhui Li
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, Guangdong, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, Guangdong, China.
- Heyuan Provincial Academy of Sciences Research Institute, Guangdong Academy of Sciences, GDAS, Heyuan, 517001, Guangdong, China.
| | - Xiangbo Zhang
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, Guangdong, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, Guangdong, China.
- Heyuan Provincial Academy of Sciences Research Institute, Guangdong Academy of Sciences, GDAS, Heyuan, 517001, Guangdong, China.
| | - Yongwen Qi
- Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, Guangdong, China.
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, Guangdong, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, Guangdong, China.
- College of Agriculture, Yangtze University, Jingzhou, 434025, Hubei, China.
- Heyuan Provincial Academy of Sciences Research Institute, Guangdong Academy of Sciences, GDAS, Heyuan, 517001, Guangdong, China.
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Chen DG, Guo J, Chen K, Ye CJ, Liu J, Chen YD, Zhou XQ, Liu CG. Pyramiding Breeding of Low-Glutelin-Content Indica Rice with Good Quality and Resistance. PLANTS (BASEL, SWITZERLAND) 2023; 12:3763. [PMID: 37960119 PMCID: PMC10647759 DOI: 10.3390/plants12213763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/18/2023] [Accepted: 10/19/2023] [Indexed: 11/15/2023]
Abstract
Low-glutelin-content rice, a type of functional rice with glutelin levels below 4%, is an essential dietary supplement for chronic kidney disease (CKD) patients. Developing low-glutelin-content rice varieties is crucial to catering to the growing CKD population. In this study, we aimed to create a new low-glutelin indica rice variety with excellent agronomic traits. To achieve this, we employed a combination of molecular-marker-assisted selection and traditional breeding techniques. The cultivars W3660, Wushansimiao (WSSM), and Nantaixiangzhan (NTXZ) were crossbred, incorporating the Lgc-1, Pi-2, Xa23, and fgr alleles into a single line. The result of this breeding effort was "Yishenxiangsimiao", a new indica rice variety that inherits the desirable characteristics of its parent lines. Yishenxiangsimiao (YSXSM) possesses not only a low glutelin content but also dual resistance to blast and bacterial blight (BB). It exhibits high-quality grains with a fragrant aroma. This new low-glutelin indica cultivar not only ensures a stable food supply for CKD patients but also serves as a healthy dietary option for the general public. We also performed RNA-seq of these rice varieties to investigate their internal gene expression differences. The YSXSM exhibited a higher biotic-resistance gene expression in comparison to NTXZ. In summary, we successfully developed a novel low-glutelin indica rice variety, "Yishenxiangsimiao", with superior agronomic traits. This rice variety addresses the dietary needs of CKD patients and offers a nutritious choice for all consumers.
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Affiliation(s)
- Da-Gang Chen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (D.-G.C.); (J.G.); (K.C.); (C.-J.Y.); (J.L.); (Y.-D.C.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Guangzhou 510640, China
- Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| | - Jie Guo
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (D.-G.C.); (J.G.); (K.C.); (C.-J.Y.); (J.L.); (Y.-D.C.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Guangzhou 510640, China
- Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| | - Ke Chen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (D.-G.C.); (J.G.); (K.C.); (C.-J.Y.); (J.L.); (Y.-D.C.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Guangzhou 510640, China
- Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| | - Chan-Juan Ye
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (D.-G.C.); (J.G.); (K.C.); (C.-J.Y.); (J.L.); (Y.-D.C.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Guangzhou 510640, China
- Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| | - Juan Liu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (D.-G.C.); (J.G.); (K.C.); (C.-J.Y.); (J.L.); (Y.-D.C.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Guangzhou 510640, China
- Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| | - You-Ding Chen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (D.-G.C.); (J.G.); (K.C.); (C.-J.Y.); (J.L.); (Y.-D.C.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Guangzhou 510640, China
- Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| | - Xin-Qiao Zhou
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (D.-G.C.); (J.G.); (K.C.); (C.-J.Y.); (J.L.); (Y.-D.C.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Guangzhou 510640, China
- Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| | - Chuan-Guang Liu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (D.-G.C.); (J.G.); (K.C.); (C.-J.Y.); (J.L.); (Y.-D.C.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Guangzhou 510640, China
- Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
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27
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Yang X, Pan Y, Xia X, Qing D, Chen W, Nong B, Zhang Z, Zhou W, Li J, Li D, Dai G, Deng G. Molecular basis of genetic improvement for key rice quality traits in Southern China. Genomics 2023; 115:110745. [PMID: 37977332 DOI: 10.1016/j.ygeno.2023.110745] [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: 07/11/2023] [Revised: 11/06/2023] [Accepted: 11/12/2023] [Indexed: 11/19/2023]
Abstract
Grain qualities including milling quality, appearance quality, eating and cooking quality, and nutritional quality are important indicators in rice breeding. Significant achievements in genetic improvement of rice quality have been made. In this study, we analyzed the variation patterns of 16 traits in 1570 rice varieties and found significant improvements in appearance quality and eating and cooking quality, particularly in hybrid rice. Through genome-wide association study and allelic functional nucleotide polymorphisms analysis of quality trait genes, we found that ALK, FGR1, FLO7, GL7/GW7, GLW7, GS2, GS3, ONAC129, OsGRF8, POW1, WCR1, and Wx were associated with the genetic improvement of rice quality traits in Southern China. Allelic functional nucleotide polymorphisms analysis of 13 important rice quality genes, including fragrance gene fgr, were performed using the polymerase chain reaction amplification refractory mutation system technology. The results showed that Gui516, Gui569, Gui721, Ryousi, Rsimiao, Rbasi, and Yuehui9802 possessed multiple superior alleles. This study elucidates the phenotypic changes and molecular basis of key quality traits of varieties in Southern China. The findings will provide guidance for genetic improvement of rice quality and the development of new varieties.
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Affiliation(s)
- Xinghai Yang
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi 530007, China
| | - Yinghua Pan
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi 530007, China
| | - Xiuzhong Xia
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi 530007, China
| | - Dongjin Qing
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi 530007, China
| | - Weiwei Chen
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi 530007, China
| | - Baoxuan Nong
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi 530007, China
| | - Zongqiong Zhang
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi 530007, China
| | - Weiyong Zhou
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi 530007, China
| | - Jingcheng Li
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi 530007, China
| | - Danting Li
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi 530007, China.
| | - Gaoxing Dai
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi 530007, China.
| | - Guofu Deng
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi 530007, China.
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28
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Gu Z, Gong J, Zhu Z, Li Z, Feng Q, Wang C, Zhao Y, Zhan Q, Zhou C, Wang A, Huang T, Zhang L, Tian Q, Fan D, Lu Y, Zhao Q, Huang X, Yang S, Han B. Structure and function of rice hybrid genomes reveal genetic basis and optimal performance of heterosis. Nat Genet 2023; 55:1745-1756. [PMID: 37679493 PMCID: PMC10562254 DOI: 10.1038/s41588-023-01495-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 08/02/2023] [Indexed: 09/09/2023]
Abstract
Exploitation of crop heterosis is crucial for increasing global agriculture production. However, the quantitative genomic analysis of heterosis was lacking, and there is currently no effective prediction tool to optimize cross-combinations. Here 2,839 rice hybrid cultivars and 9,839 segregation individuals were resequenced and phenotyped. Our findings demonstrated that indica-indica hybrid-improving breeding was a process that broadened genetic resources, pyramided breeding-favorable alleles through combinatorial selection and collaboratively improved both parents by eliminating the inferior alleles at negative dominant loci. Furthermore, we revealed that widespread genetic complementarity contributed to indica-japonica intersubspecific heterosis in yield traits, with dominance effect loci making a greater contribution to phenotypic variance than overdominance effect loci. On the basis of the comprehensive dataset, a genomic model applicable to diverse rice varieties was developed and optimized to predict the performance of hybrid combinations. Our data offer a valuable resource for advancing the understanding and facilitating the utilization of heterosis in rice.
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Affiliation(s)
- Zhoulin Gu
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Junyi Gong
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Zhou Zhu
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhen Li
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Qi Feng
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Changsheng Wang
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Yan Zhao
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Qilin Zhan
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Congcong Zhou
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Ahong Wang
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Tao Huang
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Lei Zhang
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Qilin Tian
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Danlin Fan
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Yiqi Lu
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Qiang Zhao
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Xuehui Huang
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Shihua Yang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China.
| | - Bin Han
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.
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29
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Wang X, Han L, Li J, Shang X, Liu Q, Li L, Zhang H. Next-generation bulked segregant analysis for Breeding 4.0. Cell Rep 2023; 42:113039. [PMID: 37651230 DOI: 10.1016/j.celrep.2023.113039] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 07/11/2023] [Accepted: 08/10/2023] [Indexed: 09/02/2023] Open
Abstract
Functional cloning and manipulation of genes controlling various agronomic traits are important for boosting crop production. Although bulked segregant analysis (BSA) is an efficient method for functional cloning, its low throughput cannot satisfy the current need for crop breeding and food security. Here, we review the rationale and development of conventional BSA and discuss its strengths and drawbacks. We then propose next-generation BSA (NG-BSA) integrating multiple cutting-edge technologies, including high-throughput phenotyping, biological big data, and the use of machine learning. NG-BSA increases the resolution of genetic mapping and throughput for cloning quantitative trait genes (QTGs) and optimizes candidate gene selection while providing a means to elucidate the interaction network of QTGs. The ability of NG-BSA to efficiently batch-clone QTGs makes it an important tool for dissecting molecular mechanisms underlying various traits, as well as for the improvement of Breeding 4.0 strategy, especially in targeted improvement and population improvement of crops.
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Affiliation(s)
- Xi Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Linqian Han
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Juan Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Xiaoyang Shang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Qian Liu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Lin Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China.
| | - Hongwei Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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30
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Wang Y, Li X, Ishikawa R, Luo X. Editorial: Mining and utilization of favorable gene resources in rice. FRONTIERS IN PLANT SCIENCE 2023; 14:1289069. [PMID: 37794934 PMCID: PMC10546390 DOI: 10.3389/fpls.2023.1289069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 09/13/2023] [Indexed: 10/06/2023]
Affiliation(s)
- Ying Wang
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology (Ministry of Education), School of Life Sciences, Fudan University, Shanghai, China
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Department of Ecology and Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Xueyong Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ryuji Ishikawa
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori, Japan
| | - Xiaojin Luo
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology (Ministry of Education), School of Life Sciences, Fudan University, Shanghai, China
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31
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Zhu X, Chen L, Zhang Z, Li J, Zhang H, Li Z, Pan Y, Wang X. Genetic-based dissection of resistance to bacterial leaf streak in rice by GWAS. BMC PLANT BIOLOGY 2023; 23:396. [PMID: 37596557 PMCID: PMC10436437 DOI: 10.1186/s12870-023-04412-7] [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: 06/28/2023] [Accepted: 08/14/2023] [Indexed: 08/20/2023]
Abstract
BACKGROUND Rice is the second-largest food crop in the world and vulnerable to bacterial leaf streak disease. A thorough comprehension of the genetic foundation of agronomic traits was essential for effective implementation of molecular marker-assisted selection. RESULTS Our study aimed to evaluate the vulnerability of rice to bacterial leaf streak disease (BLS) induced by the gram-negative bacterium Xanthomonas oryzae pv. oryzicola (Xoc). In order to accomplish this, we first analyzed the population structure of 747 accessions and subsequently assessed their phenotypes 20 days after inoculation with a strain of Xoc, GX01. We conducted genome-wide association studies (GWAS) on a population of 747 rice accessions, consisting of both indica and japonica subpopulations, utilizing phenotypic data on resistance to bacterial leaf streak (RBLS) and sequence data. We identified a total of 20 QTLs associated with RBLS in our analysis. Through the integration of linkage mapping, sequence analysis, haplotype analysis, and transcriptome analysis, we were able to identify five potential candidate genes (OsRBLS1-OsRBLS5) that possess the potential to regulate RBLS in rice. In order to gain a more comprehensive understanding of the genetic mechanism behind resistance to bacterial leaf streak, we conducted tests on these genes in both the indica and japonica subpopulations, ultimately identifying superior haplotypes that suggest the potential utilization of these genes in breeding disease-resistant rice varieties. CONCLUSIONS The findings of our study broaden our comprehension of the genetic mechanisms underlying RBLS in rice and offer significant insights that can be applied towards genetic improvement and breeding of disease-resistant rice in rapidly evolving environmental conditions.
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Affiliation(s)
- Xiaoyang Zhu
- State Key Laboratory of Agrobiotechnology / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Lei Chen
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, 572025, People's Republic of China
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Zhanying Zhang
- State Key Laboratory of Agrobiotechnology / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Jinjie Li
- State Key Laboratory of Agrobiotechnology / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Hongliang Zhang
- State Key Laboratory of Agrobiotechnology / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zichao Li
- State Key Laboratory of Agrobiotechnology / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Yinghua Pan
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, 572025, People's Republic of China.
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China.
| | - Xueqiang Wang
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, 572025, People's Republic of China.
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China.
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Zhang M, Mukhamed B, Yang Q, Luo Y, Tian L, Yuan Y, Huang Y, Feng B. Biochar and Nitrogen Fertilizer Change the Quality of Waxy and Non-Waxy Broomcorn Millet ( Panicum miliaceum L.) Starch. Foods 2023; 12:3009. [PMID: 37628008 PMCID: PMC10453922 DOI: 10.3390/foods12163009] [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: 07/17/2023] [Revised: 08/02/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
The overuse of nitrogen fertilizers has led to environmental pollution, which has prompted the widespread adoption of biochar as a soil conditioner in agricultural production. To date, there has been a lack of research on the effects of biochar and its combination with nitrogen fertilizer on the quality of broomcorn millet (Panicum miliaceum L.) starch. Thus, this study examined the physicochemical characteristics of starch in two types of broomcorn millet (waxy and non-waxy) under four different conditions, including a control group (N0), nitrogen fertilizer treatment alone (N150), biochar treatment alone (N0+B), and a combination of biochar and nitrogen fertilizer treatments (N150+B). The results showed that, in comparison to the control, all the treatments, particularly N150+B, decreased the content of amylose and gelatinization temperature and enhanced the starch transparency gel consistency and swelling power. In addition, biochar can improve the water solubility of starch and the gelatinization enthalpy. Importantly, the combination of biochar and nitrogen fertilizer increased the proportion of A-granules, final viscosity, starch content, and the average degree of amylopectin in polymerization. Thus, this research indicates that the combinations of biochar and nitrogen fertilizer result in the most significant improvement in the quality of starch produced from broomcorn millet.
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Affiliation(s)
| | | | | | | | | | | | | | - Baili Feng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China (Y.Y.)
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Zhong Q, Jia Q, Yin W, Wang Y, Rao Y, Mao Y. Advances in cloning functional genes for rice yield traits and molecular design breeding in China. FRONTIERS IN PLANT SCIENCE 2023; 14:1206165. [PMID: 37404533 PMCID: PMC10317195 DOI: 10.3389/fpls.2023.1206165] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 05/31/2023] [Indexed: 07/06/2023]
Abstract
Rice, a major food crop in China, contributes significantly to international food stability. Advances in rice genome sequencing, bioinformatics, and transgenic techniques have catalyzed Chinese researchers' discovery of novel genes that control rice yield. These breakthroughs in research also encompass the analysis of genetic regulatory networks and the establishment of a new framework for molecular design breeding, leading to numerous transformative findings in this field. In this review, some breakthroughs in rice yield traits and a series of achievements in molecular design breeding in China in recent years are presented; the identification and cloning of functional genes related to yield traits and the development of molecular markers of rice functional genes are summarized, with the intention of playing a reference role in the following molecular design breeding work and how to further improve rice yield.
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Affiliation(s)
- Qianqian Zhong
- College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Qiwei Jia
- College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Wenjing Yin
- College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Yuexing Wang
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, China
| | - Yuchun Rao
- College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Yijian Mao
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, China
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Huili Y, Ruoxi L, Zhimei P, Hezifan Z, Shuangnan H, Hanyao G, Binghan W, Weiping W, Yijun Y, Hongliang Z, Tonghui Q, Wenxiu X, Mi M, Zhenyan H. A phytoexclusion strategy for reducing contamination risk of rice based on low-Cd natural variations pyramid of root transporters. JOURNAL OF HAZARDOUS MATERIALS 2023; 458:131865. [PMID: 37339575 DOI: 10.1016/j.jhazmat.2023.131865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/02/2023] [Accepted: 06/13/2023] [Indexed: 06/22/2023]
Abstract
Cadmium pollution in rice is a threat to human health. Phytoexclusion is an effective strategy to reduce the Cd accumulation. Soil-to-root is the first step of Cd entering rice and plays a crucial role in Cd accumulation, so targeting root transporters could be an effective approach for phytoexclusion. This study utilized single-gene & multi-gene joint haplotype analysis to reveal the law of natural variations. The result showed that natural variations of rice root transporters assembled regularly following a certain pattern, rather than randomly. A total of 3 dominant nature variation combinations with 2 high-Cd combinations and 1 low-Cd combination were identified. In addition, indica-japonica differentiation was observed, with indica germplasms harboring high-Cd combinations while japonica germplasms harboring. In Chinese rice landraces, most of the collected indica landraces contained high-Cd combinations, indicating a high Cd contamination risk in indica landraces in terms of both phenotype and genotype. To address this issue, multiple superior low-Cd natural variations were pyramided to create two new low-Cd germplasms. In both pond and farmland trials, the ameliorated rice grain Cd did not exceed safety standards. This research provided a framework for future phytoexclusion, thus to reduce Cd-contamination risk in soil-rice system.
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Affiliation(s)
- Yan Huili
- Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China
| | - Liu Ruoxi
- Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peng Zhimei
- Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhang Hezifan
- Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hao Shuangnan
- Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guo Hanyao
- Hebei Normal University, Shijiazhuang 050024, China
| | - Wang Binghan
- Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wang Weiping
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha 410125, China
| | - Yu Yijun
- Zhejiang Station for Management of Arable Land Quality and Fertilizer, Hangzhou 310020, China
| | - Zhang Hongliang
- Sanya Institute of China Agricultural University, Sanya 572024, China
| | - Qian Tonghui
- Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China
| | - Xu Wenxiu
- Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China
| | - Ma Mi
- Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China
| | - He Zhenyan
- Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China.
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Li X, Dong J, Zhu W, Zhao J, Zhou L. Progress in the study of functional genes related to direct seeding of rice. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:46. [PMID: 37309311 PMCID: PMC10248684 DOI: 10.1007/s11032-023-01388-y] [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: 09/22/2022] [Accepted: 04/20/2023] [Indexed: 06/14/2023]
Abstract
Rice is a major food crop in the world. Owing to the shortage of rural labor and the development of agricultural mechanization, direct seeding has become the main method of rice cultivation. At present, the main problems faced by direct seeding of rice are low whole seedling rate, serious weeds, and easy lodging of rice in the middle and late stages of growth. Along with the rapid development of functional genomics, the functions of a large number of genes have been confirmed, including seed vigor, low-temperature tolerance germination, low oxygen tolerance growth, early seedling vigor, early root vigor, resistance to lodging, and other functional genes related to the direct seeding of rice. A review of the related functional genes has not yet been reported. In this study, the genes related to direct seeding of rice are summarized to comprehensively understand the genetic basis and mechanism of action in direct seeding of rice and to lay the foundation for further basic theoretical research and breeding application research in direct seeding of rice.
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Affiliation(s)
- Xuezhong Li
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225 Guangdong China
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory, Guangzhou, 510640 China
| | - Jingfang Dong
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory, Guangzhou, 510640 China
| | - Wen Zhu
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225 Guangdong China
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory, Guangzhou, 510640 China
| | - Junliang Zhao
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory, Guangzhou, 510640 China
| | - Lingyan Zhou
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225 Guangdong China
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36
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Liu Y, Jiang F, Zhang Y, Xu C, Fu L, Lin B. Phosphate-modified cellulose/chitosan with high drug loading for effective prevention of rice leaffolder (Cnaphalocrocis medinalis) outbreaks in fields. Int J Biol Macromol 2023:125145. [PMID: 37268070 DOI: 10.1016/j.ijbiomac.2023.125145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/25/2023] [Accepted: 05/27/2023] [Indexed: 06/04/2023]
Abstract
The continuous infestation of pests has seriously affected rice growth, yield and quality. How to reduce the use of pesticides and effectively control insect pests is a bottleneck problem. Herein, based on hydrogen bonding and electrostatic interactions, we posed a novel strategy to construct emamectin benzoate (EB) pesticide loading system using self-assembled phosphate-modified cellulose microspheres (CMP) and chitosan (CS). CMP provides more binding sites for EB loading and CS coating further enhances the carrier loading capacity up to 50.75 %, which jointly imparted pesticide photostability and pH-responsiveness. The retention capacity of EB-CMP@CS in rice growth soil reached 101.56-fold that of commercial EB, which effectively improved the absorption of pesticides during rice development. During the pest outbreak, EB-CMP@CS achieved effective pest control by increasing the pesticide content in rice stems and leaves, the control efficiency of the rice leaffolder (Cnaphalocrocis medinalis) reached 14-fold that of commercial EB, and could maintain the effective pest control effect during the booting stage of rice. Finally, EB-CMP@CS-treated paddy fields had improved yields and were free of pesticide residues in the rice grain. Therefore, EB-CMP@CS achieves effective control of rice leaffolder in paddy fields and has potential application value in green agricultural production.
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Affiliation(s)
- Yan Liu
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, PR China
| | - Fengqiong Jiang
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, PR China
| | - Yuwei Zhang
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, PR China
| | - Chuanhui Xu
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, PR China
| | - Lihua Fu
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, PR China
| | - Baofeng Lin
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, PR China.
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37
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Xie YN, Qi QQ, Li WH, Li YL, Zhang Y, Wang HM, Zhang YF, Ye ZH, Guo DP, Qian Q, Zhang ZF, Yan N. Domestication, breeding, omics research, and important genes of Zizania latifolia and Zizania palustris. FRONTIERS IN PLANT SCIENCE 2023; 14:1183739. [PMID: 37324716 PMCID: PMC10266587 DOI: 10.3389/fpls.2023.1183739] [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: 03/10/2023] [Accepted: 05/17/2023] [Indexed: 06/17/2023]
Abstract
Wild rice (Zizania spp.), an aquatic grass belonging to the subfamily Gramineae, has a high economic value. Zizania provides food (such as grains and vegetables), a habitat for wild animals, and paper-making pulps, possesses certain medicinal values, and helps control water eutrophication. Zizania is an ideal resource for expanding and enriching a rice breeding gene bank to naturally preserve valuable characteristics lost during domestication. With the Z. latifolia and Z. palustris genomes completely sequenced, fundamental achievements have been made toward understanding the origin and domestication, as well as the genetic basis of important agronomic traits of this genus, substantially accelerating the domestication of this wild plant. The present review summarizes the research results on the edible history, economic value, domestication, breeding, omics research, and important genes of Z. latifolia and Z. palustris over the past decades. These findings broaden the collective understanding of Zizania domestication and breeding, furthering human domestication, improvement, and long-term sustainability of wild plant cultivation.
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Affiliation(s)
- Yan-Ning Xie
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Qian-Qian Qi
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Wan-Hong Li
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Ya-Li Li
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Yu Zhang
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Hui-Mei Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Ya-Fen Zhang
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Zi-Hong Ye
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - De-Ping Guo
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Zhong-Feng Zhang
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Ning Yan
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
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Zhang Y, Yang Y, Zhang L, Zhang J, Zhou Z, Yang J, Hu Y, Gao X, Chen R, Huang Z, Xu Z, Li L. Antifungal mechanisms of the antagonistic bacterium Bacillus mojavensis UTF-33 and its potential as a new biopesticide. Front Microbiol 2023; 14:1201624. [PMID: 37293221 PMCID: PMC10246745 DOI: 10.3389/fmicb.2023.1201624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 05/09/2023] [Indexed: 06/10/2023] Open
Abstract
Biological control has gradually become the dominant means of controlling fungal disease over recent years. In this study, an endophytic strain of UTF-33 was isolated from acid mold (Rumex acetosa L.) leaves. Based on 16S rDNA gene sequence comparison, and biochemical and physiological characteristics, this strain was formally identified as Bacillus mojavensis. Bacillus mojavensis UTF-33 was sensitive to most of the antibiotics tested except neomycin. Moreover, the filtrate fermentation solution of Bacillus mojavensis UTF-33 had a significant inhibitory effect on the growth of rice blast and was used in field evaluation tests, which reduced the infestation of rice blast effectively. Rice treated with filtrate fermentation broth exhibited multiple defense mechanisms in response, including the enhanced expression of disease process-related genes and transcription factor genes, and significantly upregulated the gene expression of titin, salicylic acid pathway-related genes, and H2O2 accumulation, in plants; this may directly or indirectly act as an antagonist to pathogenic infestation. Further analysis revealed that the n-butanol crude extract of Bacillus mojavensis UTF-33 could retard or even inhibit conidial germination and prevent the formation of adherent cells both in vitro and in vivo. In addition, the amplification of functional genes for biocontrol using specific primers showed that Bacillus mojavensis UTF-33 expresses genes that can direct the synthesis of bioA, bmyB, fenB, ituD, srfAA and other substances; this information can help us to determine the extraction direction and purification method for inhibitory substances at a later stage. In conclusion, this is the first study to identify Bacillus mojavensis as a potential agent for the control of rice diseases; this strain, and its bioactive substances, have the potential to be developed as biopesticides.
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Affiliation(s)
- Yifan Zhang
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu, Sichuan, China
| | - Yanmei Yang
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu, Sichuan, China
| | - Luyi Zhang
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu, Sichuan, China
| | - Jia Zhang
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu, Sichuan, China
| | - Zhanmei Zhou
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu, Sichuan, China
| | - Jinchang Yang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yu Hu
- College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xiaoling Gao
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu, Sichuan, China
| | - Rongjun Chen
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu, Sichuan, China
| | - Zhengjian Huang
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu, Sichuan, China
| | - Zhengjun Xu
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu, Sichuan, China
| | - Lihua Li
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu, Sichuan, China
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Usman B, Derakhshani B, Jung KH. Recent Molecular Aspects and Integrated Omics Strategies for Understanding the Abiotic Stress Tolerance of Rice. PLANTS (BASEL, SWITZERLAND) 2023; 12:2019. [PMID: 37653936 PMCID: PMC10221523 DOI: 10.3390/plants12102019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/11/2023] [Accepted: 05/17/2023] [Indexed: 09/02/2023]
Abstract
Rice is an important staple food crop for over half of the world's population. However, abiotic stresses seriously threaten rice yield improvement and sustainable production. Breeding and planting rice varieties with high environmental stress tolerance are the most cost-effective, safe, healthy, and environmentally friendly strategies. In-depth research on the molecular mechanism of rice plants in response to different stresses can provide an important theoretical basis for breeding rice varieties with higher stress resistance. This review presents the molecular mechanisms and the effects of various abiotic stresses on rice growth and development and explains the signal perception mode and transduction pathways. Meanwhile, the regulatory mechanisms of critical transcription factors in regulating gene expression and important downstream factors in coordinating stress tolerance are outlined. Finally, the utilization of omics approaches to retrieve hub genes and an outlook on future research are prospected, focusing on the regulatory mechanisms of multi-signaling network modules and sustainable rice production.
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Affiliation(s)
- Babar Usman
- Graduate School of Green Green-Bio Science and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea; (B.U.)
| | - Behnam Derakhshani
- Graduate School of Green Green-Bio Science and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea; (B.U.)
| | - Ki-Hong Jung
- Graduate School of Green Green-Bio Science and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea; (B.U.)
- Research Center for Plant Plasticity, Kyung Hee University, Yongin 17104, Republic of Korea
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40
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Hu S, Ren H, Song Y, Liu F, Qian L, Zuo F, Meng L. Analysis of volatile compounds by GCMS reveals their rice cultivars. Sci Rep 2023; 13:7973. [PMID: 37198224 DOI: 10.1038/s41598-023-34797-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 05/08/2023] [Indexed: 05/19/2023] Open
Abstract
Due to the similarity in the grain and difference in the market value among many rice varieties, deliberate mislabeling and adulteration has become a serious problem. To check the authenticity, we aimed to discriminate rice varieties based on their volatile organic compounds (VOCs) composition by headspace solid phase microextraction (HS-SPME) coupled with gas chromatography mass spectrometry (GC-MS). The VOC profiles of Wuyoudao 4 from nine sites in Wuchang were compared to 11 rice cultivar from other regions. Multivariate analysis and unsupervised clustering showed an unambiguous distinction between Wuchang rice and non-Wuchang rice. Partial least squares discriminant analysis (PLS-DA) demonstrated a goodness of fit of 0.90 and a goodness of prediction of 0.85. The discriminating ability of volatile compounds is also supported by Random forest analysis. Our data revealed eight biomarkers including 2-acetyl-1-pyrroline (2-AP) that can be used for variation identification. Taken together, the current method can readily distinguish Wuchang rice from other varieties which it holds great potential in checking the authenticity of rice.
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Affiliation(s)
- Shengying Hu
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin, 150500, China
- Key Laboratory of Molecular Biology of Heilongjiang Province, College of Life Science, Heilongjiang University, Harbin, 150080, China
- Shandong Yanggu Huetai Chemical Co., Ltd., Shandong, 252300, China
| | - Hongbo Ren
- Quality and Safety Institute of Agricultural Products, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Yong Song
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin, 150500, China
- Key Laboratory of Molecular Biology of Heilongjiang Province, College of Life Science, Heilongjiang University, Harbin, 150080, China
| | - Feng Liu
- Quality and Safety Institute of Agricultural Products, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Lili Qian
- College of Food Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, 163319, China
| | - Feng Zuo
- College of Food Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, 163319, China
| | - Li Meng
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin, 150500, China.
- Key Laboratory of Molecular Biology of Heilongjiang Province, College of Life Science, Heilongjiang University, Harbin, 150080, China.
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Ashfaq M, Rasheed A, Zhu R, Ali M, Javed MA, Anwar A, Tabassum J, Shaheen S, Wu X. Genome-Wide Association Mapping for Yield and Yield-Related Traits in Rice ( Oryza Sativa L.) Using SNPs Markers. Genes (Basel) 2023; 14:genes14051089. [PMID: 37239449 DOI: 10.3390/genes14051089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 05/10/2023] [Accepted: 05/12/2023] [Indexed: 05/28/2023] Open
Abstract
Rice (Oryza sativa L.) is a staple food for more than 50% of the world's population. Rice cultivar improvement is critical in order to feed the world's growing population. Improving yield is one of the main aims of rice breeders. However, yield is a complex quantitative trait controlled by many genes. The presence of genetic diversity is the key factor to improve the yield hence, the presence of diversity in any germplasm is important for yield improvement. In the current study, the rice germplasm was collected from Pakistan and the United States of America and a panel of 100 diverse genotypes was utilized to identify important yield and yield-related traits. For this, a genome-wide association study (GWAS) was performed to identify the genetic loci related to yield. The GWAS on the diverse germplasm will lead to the identification of new genes which can be utilized in the breeding program for improvement of yield. For this reason, firstly, the germplasm was phenotypically evaluated in two growing seasons for yield and yield-related traits. The analysis of variance results showed significant differences among traits which showed the presence of diversity in the current germplasm. Secondly, the germplasm was also genotypically evaluated using 10K SNP. Genetic structure analysis showed the presence of four groups which showed that enough genetic diversity was present in the rice germplasm to be used for association mapping analysis. The results of GWAS identified 201 significant marker trait associations (MTAs. 16 MTAs were identified for plant height, 49 for days to flowering, three for days to maturity, four for tillers per plant, four for panicle length, eight for grains per panicle, 20 unfilled grains per panicle, 81 for seed setting %, four for thousand-grain weight, five for yield per plot and seven for yield per hectare. Apart from this, some pleiotropic loci were also identified. The results showed that panicle length (PL) and thousand-grain weight (TGW) were controlled by a pleiotropic locus OsGRb23906 on chromosome 1 at 10,116,371 cM. The loci OsGRb25803 and OsGRb15974 on chromosomes 4 and 8 at the position of 14,321,111 cM and 6,205,816 cM respectively, showed pleiotropic effects for seed setting % (SS) and unfilled grain per panicle (UG/P). A locus OsGRb09180 on chromosome 4 at 19,850,601 cM was significantly linked with SS and yield/ha. Furthermore, gene annotation was performed, and results indicated that the 190 candidate genes or QTLs that closely linked with studied traits. These candidate genes and novel significant markers could be useful in marker-assisted gene selection and QTL pyramiding to improve rice yield and the selection of potential parents, recombinants and MTAs which could be used in rice breeding programs to develop high-yielding rice varieties for sustainable food security.
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Affiliation(s)
- Muhammad Ashfaq
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore 54590, Pakistan
| | - Abdul Rasheed
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore 54590, Pakistan
| | - Renshan Zhu
- Department of Genetics, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Muhammad Ali
- Department of Entomology, Faculty of Agricultural Sciences, University of the Punjab, Lahore 54590, Pakistan
| | - Muhammad Arshad Javed
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore 54590, Pakistan
| | - Alia Anwar
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore 54590, Pakistan
| | - Javaria Tabassum
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore 54590, Pakistan
| | - Shabnum Shaheen
- Department of Botany, Lahore College for Women University, Lahore 54590, Pakistan
| | - Xianting Wu
- Department of Genetics, College of Life Sciences, Wuhan University, Wuhan 430072, China
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Zhao L, Liu H, Peng K, Huang X. Cold-upregulated glycosyltransferase gene 1 (OsCUGT1) plays important roles in rice height and spikelet fertility. JOURNAL OF PLANT RESEARCH 2023; 136:383-396. [PMID: 36952116 DOI: 10.1007/s10265-023-01455-7] [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: 01/24/2023] [Accepted: 03/17/2023] [Indexed: 06/18/2023]
Abstract
Glycosyltransferases (GTs) regulate many physiological processes and stress responses in plants. However, little is known about the function of GT in rice development. In this study, molecular analyses revealed that the expression of a rice GT gene (Cold-Upregulated Glycosyltransferase Gene 1, CUGT1) is developmentally controlled and stress-induced. OsCUGT1 was knocked out by using the clustered regularly interspaced short palindromic repeats (CRISPR) system to obtain the mutant oscugt1, which showed a severe dwarf and sterility phenotype. Further cytological analyses indicated that the dwarfism seen in the oscugt1 mutant might be caused by fewer and smaller cells. Histological pollen analysis suggests that the spikelet sterility in oscugt1 mutants may be caused by abnormal microsporogenesis. Moreover, multiple transgenic plants with knockdown of OsCUGT1 expression through RNA interference were obtained, which also showed obvious defects in plant height and fertility. RNA sequencing revealed that multiple biological processes associated with phenylpropanoid biosynthesis, cytokinin metabolism and pollen development are affected in the oscugt1 mutant. Overall, these results suggest that rice OsCUGT1 plays an essential role in rice development.
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Affiliation(s)
- Lanxin Zhao
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, 550025, China
| | - Hui Liu
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, 550025, China
| | - Kangli Peng
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, 550025, China
| | - Xiaozhen Huang
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, 550025, China.
- College of Tea Sciences, Guizhou University, Guiyang, 550025, China.
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43
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Lv Y, Zhang X, Hu Y, Liu S, Yin Y, Wang X. BOS1 is a basic helix-loop-helix transcription factor involved in regulating panicle development in rice. FRONTIERS IN PLANT SCIENCE 2023; 14:1162828. [PMID: 37180398 PMCID: PMC10169713 DOI: 10.3389/fpls.2023.1162828] [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: 02/10/2023] [Accepted: 04/03/2023] [Indexed: 05/16/2023]
Abstract
Panicle development is crucial to increase the grain yield of rice (Oryza sativa). The molecular mechanisms of the control of panicle development in rice remain unclear. In this study, we identified a mutant with abnormal panicles, termed branch one seed 1-1 (bos1-1). The bos1-1 mutant showed pleiotropic defects in panicle development, such as the abortion of lateral spikelets and the decreased number of primary panicle branches and secondary panicle branches. A combined map-based cloning and MutMap approach was used to clone BOS1 gene. The bos1-1 mutation was located in chromosome 1. A T-to-A mutation in BOS1 was identified, which changed the codon from TAC to AAC, resulting in the amino acid change from tyrosine to asparagine. BOS1 gene encoded a grass-specific basic helix-loop-helix transcription factor, which is a novel allele of the previously cloned LAX PANICLE 1 (LAX1) gene. Spatial and temporal expression profile analyses showed that BOS1 was expressed in young panicles and was induced by phytohormones. BOS1 protein was mainly localized in the nucleus. The expression of panicle development-related genes, such as OsPIN2, OsPIN3, APO1, and FZP, was changed by bos1-1 mutation, suggesting that the genes may be the direct or indirect targets of BOS1 to regulate panicle development. The analysis of BOS1 genomic variation, haplotype, and haplotype network showed that BOS1 gene had several genomic variations and haplotypes. These results laid the foundation for us to further dissect the functions of BOS1.
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Affiliation(s)
| | | | | | | | | | - Xiaoxue Wang
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
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Cao S, Wang Y, Gao Y, Xu R, Ma J, Xu Z, Shang-Guan K, Zhang B, Zhou Y. The RLCK-VND6 module coordinates secondary cell wall formation and adaptive growth in rice. MOLECULAR PLANT 2023:S1674-2052(23)00104-1. [PMID: 37050877 DOI: 10.1016/j.molp.2023.04.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 03/05/2023] [Accepted: 04/08/2023] [Indexed: 05/27/2023]
Abstract
The orderly deposition of secondary cell wall (SCW) in plants is implicated in various biological programs and is precisely controlled. Although many positive and negative regulators of SCW have been documented, the molecular mechanisms underlying SCW formation coordinated with distinct cellular physiological processes during plant adaptive growth remain largely unclear. Here, we report the identification of Cellulose Synthase co-expressed Kinase1 (CSK1), which encodes a receptor-like cytoplasmic kinase, as a negative regulator of SCW formation and its signaling cascade in rice. Transcriptome deep sequencing of developing internodes and genome-wide co-expression assays revealed that CSK1 is co-expressed with cellulose synthase genes and is responsive to various stress stimuli. The increased SCW thickness and vigorous vessel transport in csk1 indicate that CSK1 functions as a negative regulator of SCW biosynthesis. Through observation of green fluorescent protein-tagged CSK1 in rice protoplasts and stable transgenic plants, we found that CSK1 is localized in the nucleus and cytoplasm adjacent to the plasma membrane. Biochemical and molecular assays demonstrated that CSK1 phosphorylates VASCULAR-RELATED NAC-DOMAIN 6 (VND6), a master SCW-associated transcription factor, in the nucleus, which reduces the transcription of a suite of SCW-related genes, thereby attenuating SCW accumulation. Consistently, genetic analyses show that CSK1 functions upstream of VND6 in regulating SCW formation. Interestingly, our physiological analyses revealed that CSK1 and VND6 are involved in abscisic acid-mediated regulation of cell growth and SCW deposition. Taken together, these results indicate that the CSK1-VND6 module is an important component of the SCW biosynthesis machinery, which coordinates SCW accumulation and adaptive growth in rice. Our study not only identifies a new regulator of SCW biosynthesis but also reveals a fine-tuned mechanism for precise control of SCW deposition, offering tools for rationally tailoring agronomic traits.
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Affiliation(s)
- Shaoxue Cao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Yan Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yihong Gao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rui Xu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianing Ma
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zuopeng Xu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of the Ministry of Education for Plant Functional Genomics, College of Agriculture, Yangzhou University, Yangzhou, 225009, China
| | - Keke Shang-Guan
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Baocai Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Yihua Zhou
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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45
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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.
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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
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46
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Agata A, Ashikari M, Sato Y, Kitano H, Hobo T. Designing rice panicle architecture via developmental regulatory genes. BREEDING SCIENCE 2023; 73:86-94. [PMID: 37168816 PMCID: PMC10165343 DOI: 10.1270/jsbbs.22075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 12/03/2022] [Indexed: 05/13/2023]
Abstract
Rice panicle architecture displays remarkable diversity in branch number, branch length, and grain arrangement; however, much remains unknown about how such diversity in patterns is generated. Although several genes related to panicle branch number and panicle length have been identified, how panicle branch number and panicle length are coordinately regulated is unclear. Here, we show that panicle length and panicle branch number are independently regulated by the genes Prl5/OsGA20ox4, Pbl6/APO1, and Gn1a/OsCKX2. We produced near-isogenic lines (NILs) in the Koshihikari genetic background harboring the elite alleles for Prl5, regulating panicle rachis length; Pbl6, regulating primary branch length; and Gn1a, regulating panicle branching in various combinations. A pyramiding line carrying Prl5, Pbl6, and Gn1a showed increased panicle length and branching without any trade-off relationship between branch length or number. We successfully produced various arrangement patterns of grains by changing the combination of alleles at these three loci. Improvement of panicle architecture raised yield without associated negative effects on yield-related traits except for panicle number. Three-dimensional (3D) analyses by X-ray computed tomography (CT) of panicles revealed that differences in panicle architecture affect grain filling. Importantly, we determined that Prl5 improves grain filling without affecting grain number.
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Affiliation(s)
- Ayumi Agata
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan
- National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Motoyuki Ashikari
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Yutaka Sato
- National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Hidemi Kitano
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Tokunori Hobo
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan
- Corresponding author (e-mail: )
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47
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Gupta A, Hua L, Zhang Z, Yang B, Li W. CRISPR-induced miRNA156-recognition element mutations in TaSPL13 improve multiple agronomic traits in wheat. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:536-548. [PMID: 36403232 PMCID: PMC9946137 DOI: 10.1111/pbi.13969] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/01/2022] [Accepted: 11/09/2022] [Indexed: 05/19/2023]
Abstract
Increase in grain yield is always a major objective of wheat genetic improvement. The SQUAMOSA promoter-binding protein-like (SPL) genes, coding for a small family of diverse plant-specific transcription factors, represent important targets for improving grain yield and other major agronomic traits in rice. The function of the SPL genes in wheat remains to be investigated in this respect. In this study, we identified 56 wheat orthologues of rice SPL genes belonging to 19 homoeologous groups. Like in rice, nine orthologous TaSPL genes harbour the microRNA156 recognition elements (MRE) in their last exons except for TaSPL13, which harbour the MRE in its 3'-untranslated region (3'UTR). We modified the MRE of TaSPL13 using CRISPR-Cas9 and generated 12 mutations in the three homoeologous genes. As expected, the MRE mutations led to an approximately two-fold increase in the TaSPL13 mutant transcripts. The phenotypic evaluation showed that the MRE mutations in TaSPL13 resulted in a decrease in flowering time, tiller number, and plant height, and a concomitantly increase in grain size and number. The results show that the TaSPL13 mutants exhibit a combination of different phenotypes observed in Arabidopsis AtSPL3/4/5 mutants and rice OsSPL13/14/16 mutants and hold great potential in improving wheat yield by simultaneously increasing grain size and number and by refining plant architecture. The novel TaSPL13 mutations generated can be utilized in wheat breeding programmes to improve these agronomic traits.
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Affiliation(s)
- Ajay Gupta
- Department of Biology and MicrobiologySouth Dakota State UniversityBrookingsSouth DakotaUSA
- Present address:
Division of Plant Science and TechnologyUniversity of MissouriColumbiaMissouriUSA
| | - Lei Hua
- Department of Biology and MicrobiologySouth Dakota State UniversityBrookingsSouth DakotaUSA
- Present address:
Institute of Advanced Agricultural Science, Peking UniversityWeifangShandongChina
| | - Zhengzhi Zhang
- Division of Plant Science and TechnologyUniversity of MissouriColumbiaMissouriUSA
| | - Bing Yang
- Division of Plant Science and TechnologyUniversity of MissouriColumbiaMissouriUSA
- Donald Danforth Plant Science CenterSt. LouisMissouriUSA
| | - Wanlong Li
- Department of Biology and MicrobiologySouth Dakota State UniversityBrookingsSouth DakotaUSA
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48
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Zhao S, Zhang C, Wang L, Luo M, Zhang P, Wang Y, Malik WA, Wang Y, Chen P, Qiu X, Wang C, Lu H, Xiang Y, Liu Y, Ruan J, Qian Q, Zhi H, Chang Y. A prolific and robust whole-genome genotyping method using PCR amplification via primer-template mismatched annealing. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:633-645. [PMID: 36269601 DOI: 10.1111/jipb.13395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 10/21/2022] [Indexed: 06/16/2023]
Abstract
Whole-genome genotyping methods are important for breeding. However, it has been challenging to develop a robust method for simultaneous foreground and background genotyping that can easily be adapted to different genes and species. In our study, we accidently discovered that in adapter ligation-mediated PCR, the amplification by primer-template mismatched annealing (PTMA) along the genome could generate thousands of stable PCR products. Based on this observation, we consequently developed a novel method for simultaneous foreground and background integrated genotyping by sequencing (FBI-seq) using one specific primer, in which foreground genotyping is performed by primer-template perfect annealing (PTPA), while background genotyping employs PTMA. Unlike DNA arrays, multiple PCR, or genome target enrichments, FBI-seq requires little preliminary work for primer design and synthesis, and it is easily adaptable to different foreground genes and species. FBI-seq therefore provides a prolific, robust, and accurate method for simultaneous foreground and background genotyping to facilitate breeding in the post-genomics era.
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Affiliation(s)
- Sheng Zhao
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, China
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Cuicui Zhang
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Liqun Wang
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Minxuan Luo
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, China
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Peng Zhang
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Yue Wang
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Waqar Afzal Malik
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Yue Wang
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Peng Chen
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Xianjin Qiu
- College of Agriculture, Yangtze University, Jingzhou, 434023, China
| | - Chongrong Wang
- Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Hong Lu
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Yong Xiang
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Yuwen Liu
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Jue Ruan
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Qian Qian
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Haijian Zhi
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yuxiao Chang
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
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49
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Wang X, Li X, Luo X, Tang S, Wu T, Wang Z, Peng Z, Xia Q, Yu C, Xiao Y. Identification, Fine Mapping and Application of Quantitative Trait Loci for Grain Shape Using Single-Segment Substitution Lines in Rice ( Oryza sativa L.). PLANTS (BASEL, SWITZERLAND) 2023; 12:892. [PMID: 36840239 PMCID: PMC9966618 DOI: 10.3390/plants12040892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 02/11/2023] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
Quantitative trait loci (QTLs) and HQTL (heterosis QTLs) for grain shape are two major genetic factors of grain yield and quality in rice (Oryza sativa L.). Although many QTLs for grain shape have been reported, only a few are applied in production. In this study, 54 QTLs for grain shape were detected on 10 chromosomes using 33 SSSLs (single-segment substitution lines) and methods of statistical genetics. Among these, 23 exhibited significant positive additive genetic effects, including some novel QTLs, among which qTGW4-(1,2), qTGW10-2, and qTGW10-3 were three QTLs newly found in this study and should be paid more attention. Moreover, 26 HQTLs for grain shape were probed. Eighteen of these exhibited significant positive dominant genetic effects. Thirty-three QTLs for grain shape were further mapped using linkage analysis. Most of the QTLs for grain shape produced pleiotropic effects, which simultaneously controlled multiple appearance traits of grain shape. Linkage mapping of the F2 population derived from sub-single-segment substitution lines further narrowed the interval harbouring qTGW10-3 to 75.124 kb between PSM169 and RM25753. The candidate gene was identified and could be applied to breeding applications by molecular marker-assisted selection. These identified QTLs for grain shape will offer additional insights for improving grain yield and quality in rice breeding.
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Affiliation(s)
- Xiaoling Wang
- National Engineering Research Center of Rice (Nanchang), Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Institute of Tropical Bioscience and Biotechnology & San Ya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Xia Li
- National Engineering Research Center of Rice (Nanchang), Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Xin Luo
- National Engineering Research Center of Rice (Nanchang), Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Shusheng Tang
- National Engineering Research Center of Rice (Nanchang), Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Ting Wu
- National Engineering Research Center of Rice (Nanchang), Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Zhiquan Wang
- National Engineering Research Center of Rice (Nanchang), Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Zhiqin Peng
- National Engineering Research Center of Rice (Nanchang), Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Qiyu Xia
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Institute of Tropical Bioscience and Biotechnology & San Ya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Chuanyuan Yu
- National Engineering Research Center of Rice (Nanchang), Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Yulong Xiao
- National Engineering Research Center of Rice (Nanchang), Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
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Molecular bases of rice grain size and quality for optimized productivity. Sci Bull (Beijing) 2023; 68:314-350. [PMID: 36710151 DOI: 10.1016/j.scib.2023.01.026] [Citation(s) in RCA: 50] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/30/2022] [Accepted: 01/16/2023] [Indexed: 01/19/2023]
Abstract
The accomplishment of further optimization of crop productivity in grain yield and quality is a great challenge. Grain size is one of the crucial determinants of rice yield and quality; all of these traits are typical quantitative traits controlled by multiple genes. Research advances have revealed several molecular and developmental pathways that govern these traits of agronomical importance. This review provides a comprehensive summary of these pathways, including those mediated by G-protein, the ubiquitin-proteasome system, mitogen-activated protein kinase, phytohormone, transcriptional regulators, and storage product biosynthesis and accumulation. We also generalize the excellent precedents for rice variety improvement of grain size and quality, which utilize newly developed gene editing and conventional gene pyramiding capabilities. In addition, we discuss the rational and accurate breeding strategies, with the aim of better applying molecular design to breed high-yield and superior-quality varieties.
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