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Daryani P, Amirbakhtiar N, Soorni J, Loni F, Darzi Ramandi H, Shobbar ZS. Uncovering the Genomic Regions Associated with Yield Maintenance in Rice Under Drought Stress Using an Integrated Meta-Analysis Approach. RICE (NEW YORK, N.Y.) 2024; 17:7. [PMID: 38227151 DOI: 10.1186/s12284-024-00684-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 01/03/2024] [Indexed: 01/17/2024]
Abstract
The complex trait of yield is controlled by several quantitative trait loci (QTLs). Given the global water deficit issue, the development of rice varieties suitable for non-flooded cultivation holds significant importance in breeding programs. The powerful approach of Meta-QTL (MQTL) analysis can be used for the genetic dissection of complicated quantitative traits. In the current study, a comprehensive MQTL analysis was conducted to identify consistent QTL regions associated with drought tolerance and yield-related traits under water deficit conditions in rice. In total, 1087 QTLs from 134 rice populations, published between 2000 to 2021, were utilized in the analysis. Distinct MQTL analysis of the relevant traits resulted in the identification of 213 stable MQTLs. The confidence interval (CI) for the detected MQTLs was between 0.12 and 19.7 cM. The average CI of the identified MQTLs (4.68 cM) was 2.74 times narrower compared to the average CI of the initial QTLs. Interestingly, 63 MQTLs coincided with SNP peak positions detected by genome-wide association studies for yield and drought tolerance-associated traits under water deficit conditions in rice. Considering the genes located both in the QTL-overview peaks and the SNP peak positions, 19 novel candidate genes were introduced, which are associated with drought response index, plant height, panicle number, biomass, and grain yield. Moreover, an inclusive MQTL analysis was performed on all the traits to obtain "Breeding MQTLs". This analysis resulted in the identification of 96 MQTLs with a CI ranging from 0.01 to 9.0 cM. The mean CI of the obtained MQTLs (2.33 cM) was 4.66 times less than the mean CI of the original QTLs. Thirteen MQTLs fulfilling the criteria of having more than 10 initial QTLs, CI < 1 cM, and an average phenotypic variance explained greater than 10%, were designated as "Breeding MQTLs". These findings hold promise for assisting breeders in enhancing rice yield under drought stress conditions.
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Affiliation(s)
- Parisa Daryani
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Nazanin Amirbakhtiar
- National Plant Gene Bank of Iran, Seed and Plant Improvement Institute (SPII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Jahad Soorni
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Fatemeh Loni
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Hadi Darzi Ramandi
- Department of Plant Production and Genetics, Faculty of Agriculture, Bu-Ali Sina University, Hamedan, Iran.
| | - Zahra-Sadat Shobbar
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran.
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Qiao L, Wu Q, Yuan L, Huang X, Yang Y, Li Q, Shahzad N, Li H, Li W. SMALL PLANT AND ORGAN 1 ( SPO1) Encoding a Cellulose Synthase-like Protein D4 (OsCSLD4) Is an Important Regulator for Plant Architecture and Organ Size in Rice. Int J Mol Sci 2023; 24:16974. [PMID: 38069299 PMCID: PMC10707047 DOI: 10.3390/ijms242316974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 11/27/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
Plant architecture and organ size are considered as important traits in crop breeding and germplasm improvement. Although several factors affecting plant architecture and organ size have been identified in rice, the genetic and regulatory mechanisms remain to be elucidated. Here, we identified and characterized the small plant and organ 1 (spo1) mutant in rice (Oryza sativa), which exhibits narrow and rolled leaf, reductions in plant height, root length, and grain width, and other morphological defects. Map-based cloning revealed that SPO1 is allelic with OsCSLD4, a gene encoding the cellulose synthase-like protein D4, and is highly expressed in the roots at the seedling and tillering stages. Microscopic observation revealed the spo1 mutant had reduced number and width in leaf veins, smaller size of leaf bulliform cells, reduced cell length and cell area in the culm, and decreased width of epidermal cells in the outer glume of the grain. These results indicate the role of SPO1 in modulating cell division and cell expansion, which modulates plant architecture and organ size. It is showed that the contents of endogenous hormones including auxin, abscisic acid, gibberellin, and zeatin tested in the spo1 mutant were significantly altered, compared to the wild type. Furthermore, the transcriptome analysis revealed that the differentially expressed genes (DEGs) are significantly enriched in the pathways associated with plant hormone signal transduction, cell cycle progression, and cell wall formation. These results indicated that the loss of SPO1/OsCSLD4 function disrupted cell wall cellulose synthase and hormones homeostasis and signaling, thus leading to smaller plant and organ size in spo1. Taken together, we suggest the functional role of SPO1/OsCSLD4 in the control of rice plant and organ size by modulating cell division and expansion, likely through the effects of multiple hormonal pathways on cell wall formation.
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Affiliation(s)
- Lei Qiao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, China (X.H.); (Y.Y.); (Q.L.); (N.S.)
- College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Qilong Wu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, China (X.H.); (Y.Y.); (Q.L.); (N.S.)
| | - Liuzhen Yuan
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, China (X.H.); (Y.Y.); (Q.L.); (N.S.)
| | - Xudong Huang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, China (X.H.); (Y.Y.); (Q.L.); (N.S.)
| | - Yutao Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, China (X.H.); (Y.Y.); (Q.L.); (N.S.)
| | - Qinying Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, China (X.H.); (Y.Y.); (Q.L.); (N.S.)
| | - Nida Shahzad
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, China (X.H.); (Y.Y.); (Q.L.); (N.S.)
| | - Haifeng Li
- College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Wenqiang Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, China (X.H.); (Y.Y.); (Q.L.); (N.S.)
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3
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Wen Y, Wu K, Chai B, Fang Y, Hu P, Tan Y, Wang Y, Wu H, Wang J, Zhu L, Zhang G, Gao Z, Ren D, Zeng D, Shen L, Dong G, Zhang Q, Li Q, Qian Q, Hu J. NLG1, encoding a mitochondrial membrane protein, controls leaf and grain development in rice. BMC PLANT BIOLOGY 2023; 23:418. [PMID: 37689677 PMCID: PMC10492415 DOI: 10.1186/s12870-023-04417-2] [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: 02/21/2023] [Accepted: 08/22/2023] [Indexed: 09/11/2023]
Abstract
BACKGROUND Mitochondrion is the key respiratory organ and participate in multiple anabolism and catabolism pathways in eukaryote. However, the underlying mechanism of how mitochondrial membrane proteins regulate leaf and grain development remains to be further elucidated. RESULTS Here, a mitochondria-defective mutant narrow leaf and slender grain 1 (nlg1) was identified from an EMS-treated mutant population, which exhibits narrow leaves and slender grains. Moreover, nlg1 also presents abnormal mitochondria structure and was sensitive to the inhibitors of mitochondrial electron transport chain. Map-based cloning and transgenic functional confirmation revealed that NLG1 encodes a mitochondrial import inner membrane translocase containing a subunit Tim21. GUS staining assay and RT-qPCR suggested that NLG1 was mainly expressed in leaves and panicles. The expression level of respiratory function and auxin response related genes were significantly down-regulated in nlg1, which may be responsible for the declination of ATP production and auxin content. CONCLUSIONS These results suggested that NLG1 plays an important role in the regulation of leaf and grain size development by maintaining mitochondrial homeostasis. Our finding provides a novel insight into the effects of mitochondria development on leaf and grain morphogenesis in rice.
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Affiliation(s)
- Yi Wen
- Rice Research Institute of Shenyang Agricultural University/Key Laboratory of Northern Japonica Rice Genetics and Breeding, Ministry of Education and Liaoning Province, Shenyang, 110866, China
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 310006, China
| | - Kaixiong Wu
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 310006, China
| | - Bingze Chai
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 310006, China
| | - Yunxia Fang
- College of Life and Environmental Sciences, Hangzhou Normal University, 16 Xiasha Road, Hangzhou, 310036, China
| | - Peng Hu
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 310006, China
| | - Yiqing Tan
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 310006, China
| | - Yueying Wang
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 310006, China
| | - Hao Wu
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 310006, China
| | - Junge Wang
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 310006, China
| | - Li Zhu
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 310006, China
| | - Guangheng Zhang
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 310006, China
| | - Zhenyu Gao
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 310006, China
| | - Deyong Ren
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 310006, China
| | - Dali Zeng
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 310006, China
| | - Lan Shen
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 310006, China
| | - Guojun Dong
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 310006, China
| | - Qiang Zhang
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 310006, China
| | - Qing Li
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 310006, China
| | - Qian Qian
- Rice Research Institute of Shenyang Agricultural University/Key Laboratory of Northern Japonica Rice Genetics and Breeding, Ministry of Education and Liaoning Province, Shenyang, 110866, China.
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 310006, China.
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, 572024, China.
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572024, China.
| | - Jiang Hu
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 310006, China.
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4
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Guo D, Chen L, Liu S, Jiang W, Ye Q, Wu Z, Wang X, Hu X, Zhang Z, He H, Hu L. Curling Leaf 1, Encoding a MYB-Domain Protein, Regulates Leaf Morphology and Affects Plant Yield in Rice. PLANTS (BASEL, SWITZERLAND) 2023; 12:3127. [PMID: 37687373 PMCID: PMC10490398 DOI: 10.3390/plants12173127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 08/26/2023] [Accepted: 08/27/2023] [Indexed: 09/10/2023]
Abstract
The leaf is the main site of photosynthesis and is an important component in shaping the ideal rice plant architecture. Research on leaf morphology and development will lay the foundation for high-yield rice breeding. In this study, we isolated and identified a novel curling leaf mutant, designated curling leaf 1 (cl1). The cl1 mutant exhibited an inward curling phenotype because of the defective development of sclerenchymatous cells on the abaxial side. Meanwhile, the cl1 mutant showed significant reductions in grain yield and thousand-grain weight due to abnormal leaf development. Through map-based cloning, we identified the CL1 gene, which encodes a MYB transcription factor that is highly expressed in leaves. Subcellular localization studies confirmed its typical nuclear localization. Transcriptome analysis revealed a significant differential expression of the genes involved in photosynthesis, leaf morphology, yield formation, and hormone metabolism in the cl1 mutant. Yeast two-hybrid assays demonstrated that CL1 interacts with alpha-tubulin protein SRS5 and AP2/ERF protein MFS. These findings provide theoretical foundations for further elucidating the mechanisms of CL1 in regulating leaf morphology and offer genetic resources for practical applications in high-yield rice breeding.
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Affiliation(s)
- Dandan Guo
- College of Agriculture, Jiangxi Agricultural University, Nanchang 330045, China; (D.G.); (W.J.); (Q.Y.); (Z.W.); (X.W.); (X.H.); (Z.Z.)
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang 330045, China; (L.C.); (S.L.)
| | - Lianghai Chen
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang 330045, China; (L.C.); (S.L.)
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China
| | - Shiqiang Liu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang 330045, China; (L.C.); (S.L.)
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China
| | - Wenxiang Jiang
- College of Agriculture, Jiangxi Agricultural University, Nanchang 330045, China; (D.G.); (W.J.); (Q.Y.); (Z.W.); (X.W.); (X.H.); (Z.Z.)
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang 330045, China; (L.C.); (S.L.)
| | - Qing Ye
- College of Agriculture, Jiangxi Agricultural University, Nanchang 330045, China; (D.G.); (W.J.); (Q.Y.); (Z.W.); (X.W.); (X.H.); (Z.Z.)
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang 330045, China; (L.C.); (S.L.)
| | - Zheng Wu
- College of Agriculture, Jiangxi Agricultural University, Nanchang 330045, China; (D.G.); (W.J.); (Q.Y.); (Z.W.); (X.W.); (X.H.); (Z.Z.)
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang 330045, China; (L.C.); (S.L.)
| | - Xiaoqing Wang
- College of Agriculture, Jiangxi Agricultural University, Nanchang 330045, China; (D.G.); (W.J.); (Q.Y.); (Z.W.); (X.W.); (X.H.); (Z.Z.)
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang 330045, China; (L.C.); (S.L.)
| | - Xiafei Hu
- College of Agriculture, Jiangxi Agricultural University, Nanchang 330045, China; (D.G.); (W.J.); (Q.Y.); (Z.W.); (X.W.); (X.H.); (Z.Z.)
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang 330045, China; (L.C.); (S.L.)
| | - Zelin Zhang
- College of Agriculture, Jiangxi Agricultural University, Nanchang 330045, China; (D.G.); (W.J.); (Q.Y.); (Z.W.); (X.W.); (X.H.); (Z.Z.)
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang 330045, China; (L.C.); (S.L.)
| | - Haohua He
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang 330045, China; (L.C.); (S.L.)
| | - Lifang Hu
- College of Agriculture, Jiangxi Agricultural University, Nanchang 330045, China; (D.G.); (W.J.); (Q.Y.); (Z.W.); (X.W.); (X.H.); (Z.Z.)
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5
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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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6
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Hemalatha P, Abda EM, Shah S, Venkatesa Prabhu S, Jayakumar M, Karmegam N, Kim W, Govarthanan M. Multi-faceted CRISPR-Cas9 strategy to reduce plant based food loss and waste for sustainable bio-economy - A review. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 332:117382. [PMID: 36753844 DOI: 10.1016/j.jenvman.2023.117382] [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: 12/09/2022] [Revised: 01/14/2023] [Accepted: 01/25/2023] [Indexed: 06/18/2023]
Abstract
Currently, international development requires innovative solutions to address imminent challenges like climate change, unsustainable food system, food waste, energy crisis, and environmental degradation. All the same, addressing these concerns with conventional technologies is time-consuming, causes harmful environmental impacts, and is not cost-effective. Thus, biotechnological tools become imperative for enhancing food and energy resilience through eco-friendly bio-based products by valorisation of plant and food waste to meet the goals of circular bioeconomy in conjunction with Sustainable Developmental Goals (SDGs). Genome editing can be accomplished using a revolutionary DNA modification tool, CRISPR-Cas9, through its uncomplicated guided mechanism, with great efficiency in various organisms targeting different traits. This review's main objective is to examine how the CRISPR-Cas system, which has positive features, could improve the bioeconomy by reducing food loss and waste with all-inclusive food supply chain both at on-farm and off-farm level; utilising food loss and waste by genome edited microorganisms through food valorisation; efficient microbial conversion of low-cost substrates as biofuel; valorisation of agro-industrial wastes; mitigating greenhouse gas emissions through forestry plantation crops; and protecting the ecosystem and environment. Finally, the ethical implications and regulatory issues that are related to CRISPR-Cas edited products in the international markets have also been taken into consideration.
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Affiliation(s)
- Palanivel Hemalatha
- Department of Biotechnology, Center of Excellence for Biotechnology and Bioprocess, College of Biological and Chemical Engineering, Addis Ababa Science and Technology University, PO Box 16417, Addis Ababa, Ethiopia
| | - Ebrahim M Abda
- Department of Biotechnology, Center of Excellence for Biotechnology and Bioprocess, College of Biological and Chemical Engineering, Addis Ababa Science and Technology University, PO Box 16417, Addis Ababa, Ethiopia
| | - Shipra Shah
- Department of Forestry, College of Agriculture, Fisheries and Forestry, Fiji National University, Kings Road, Koronivia, P. O. Box 1544, Nausori, Republic of Fiji
| | - S Venkatesa Prabhu
- Department of Chemical Engineering, Center of Excellence for Biotechnology and Bioprocess, College of Biological and Chemical Engineering, Addis Ababa Science and Technology University, PO Box 16417, Addis Ababa, Ethiopia
| | - M Jayakumar
- Department of Chemical Engineering, Haramaya Institute of Technology, Haramaya University, P.O. Box 138, Dire Dawa, Ethiopia.
| | - N Karmegam
- PG and Research Department of Botany, Government Arts College (Autonomous), Salem, 636 007, Tamil Nadu, India
| | - Woong Kim
- Department of Environmental Engineering, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - M Govarthanan
- Department of Environmental Engineering, Kyungpook National University, Daegu, 41566, Republic of Korea; Department of Biomaterials, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences, Chennai, 600 077, India.
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7
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Tan W, Miao J, Xu B, Zhou C, Wang Y, Gu X, Liang S, Wang B, Chen C, Zhu J, Zuo S, Yang Z, Gong Z, You A, Wu S, Liang G, Zhou Y. Rapid production of novel beneficial alleles for improving rice appearance quality by targeting a regulatory element of SLG7. PLANT BIOTECHNOLOGY JOURNAL 2023. [PMID: 36965149 DOI: 10.1111/pbi.14041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 02/27/2023] [Accepted: 03/02/2023] [Indexed: 06/18/2023]
Affiliation(s)
- Wenchen Tan
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, China
| | - Jun Miao
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Bo Xu
- Institute of Lianyungang Agricultural Science of Xuhuai Area, Lianyungang, China
| | - Chuting Zhou
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, China
| | - Yirui Wang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, China
| | - Xueqi Gu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, China
| | - Shuainan Liang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, China
| | - Baoxiang Wang
- Institute of Lianyungang Agricultural Science of Xuhuai Area, Lianyungang, China
| | - Chen Chen
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, China
| | - Jinyan Zhu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, China
| | - Shimin Zuo
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, China
| | - Zefeng Yang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, China
| | - Zhiyun Gong
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, China
| | - Aiqing You
- Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Shujun Wu
- Key Laboratory of Germplasm Innovation and Genetic Improvement of Grain and Oil Crops, Ministry of Agriculture and Rural Affairs, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Guohua Liang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Yong Zhou
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
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8
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Jing Y, Wenbo C, Zhifeng H, Yan X, XinFang Z, Mi W, RuHui W, Wenqiang S, Jun Z, QianNan D, Guanghua H, Yunfeng L, Ting Z. DEGENERATED LEMMA ( DEL) regulates lemma development and affects rice grain yield. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:335-347. [PMID: 37033767 PMCID: PMC10073388 DOI: 10.1007/s12298-023-01297-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 03/12/2023] [Accepted: 03/13/2023] [Indexed: 06/19/2023]
Abstract
In grass, the lemma is a unique floral organ structure that directly determines grain size and yield. Despite a great deal of research on grain enlargement caused by changes in glume cells, the importance of normal development of the glume for normal grain development has been poorly studied. In this study, we investigated a rice spikelet mutant, degenerated lemma (del), which developed florets with a slightly degenerated or rod-like lemma. More importantly, del also showed a significant reduction in grain length and width, seed setting rate, and 1000-grain weight, which led to a reduction in yield. The results indicate that the mutation of the DEL gene further affects rice grain yield. Map-based cloning shows a single-nucleotide substitution from T to A within Os01g0527600/DEL/OsRDR6, causing an amino acid mutation of Leu-34 to His-34 in the del mutant. Compared with the wild type, the expression of DEL in del was significantly reduced, which might be caused by single base substitution. In addition, the expression level of tasiR-ARF in del was lower than that of the wild type. RT-qPCR results show that the expression of some floral organ identity genes was changed, which indicates that the DEL gene regulates lemma development by modulating the expression of these genes. The present results suggest that the normal expression of DEL is necessary for the formation of lemma and the normal development of grain morphology and therefore has an important effect on the yield. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-023-01297-6.
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Affiliation(s)
- You Jing
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715 China
| | - Chen Wenbo
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715 China
| | - He Zhifeng
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715 China
| | - Xiang Yan
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715 China
| | - Zhang XinFang
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715 China
| | - Wei Mi
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715 China
| | - Wu RuHui
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715 China
| | - Shen Wenqiang
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715 China
| | - Zhang Jun
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715 China
| | - Duan QianNan
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715 China
| | - He Guanghua
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715 China
| | - Li Yunfeng
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715 China
| | - Zhang Ting
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715 China
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9
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Bibliometric Analysis of Functional Crops and Nutritional Quality: Identification of Gene Resources to Improve Crop Nutritional Quality through Gene Editing Technology. Nutrients 2023; 15:nu15020373. [PMID: 36678244 PMCID: PMC9865409 DOI: 10.3390/nu15020373] [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: 12/01/2022] [Revised: 12/25/2022] [Accepted: 01/07/2023] [Indexed: 01/15/2023] Open
Abstract
Food security and hidden hunger are two worldwide serious and complex challenges nowadays. As one of the newly emerged technologies, gene editing technology and its application to crop improvement offers the possibility to relieve the pressure of food security and nutrient needs. In this paper, we analyzed the research status of quality improvement based on gene editing using four major crops, including rice, soybean, maize, and wheat, through a bibliometric analysis. The research hotspots now focus on the regulatory network of related traits, quite different from the technical improvements to gene editing in the early stage, while the trends in deregulation in gene-edited crops have accelerated related research. Then, we mined quality-related genes that can be edited to develop functional crops, including 16 genes related to starch, 15 to lipids, 14 to proteins, and 15 to other functional components. These findings will provide useful reference information and gene resources for the improvement of functional crops and nutritional quality based on gene editing technology.
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10
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Liu C, Ma T, Yuan D, Zhou Y, Long Y, Li Z, Dong Z, Duan M, Yu D, Jing Y, Bai X, Wang Y, Hou Q, Liu S, Zhang J, Chen S, Li D, Liu X, Li Z, Wang W, Li J, Wei X, Ma B, Wan X. The OsEIL1-OsERF115-target gene regulatory module controls grain size and weight in rice. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1470-1486. [PMID: 35403801 PMCID: PMC9342608 DOI: 10.1111/pbi.13825] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 04/03/2022] [Accepted: 04/07/2022] [Indexed: 06/14/2023]
Abstract
Grain size is one of the essential determinants of rice yield. Our previous studies revealed that ethylene plays an important role in grain-size control; however, the precise mechanism remains to be determined. Here, we report that the ethylene response factor OsERF115 functions as a key downstream regulator for ethylene-mediated grain development. OsERF115 encodes an AP2/ERF-type transcriptional factor that is specifically expressed in young spikelets and developing caryopses. Overexpression of OsERF115 significantly increases grain length, width, thickness and weight by promoting longitudinal elongation and transverse division of spikelet hull cells, as well as enhancing grain-filling activity, whereas its knockout mutations lead to the opposite effects, suggesting that OsERF115 positively regulates grain size and weight. OsERF115 transcription is strongly induced by ethylene, and OsEIL1 directly binds to the promoter to activate its expression. OsERF115 acts as a transcriptional repressor to directly or indirectly modulate a set of grain-size genes during spikelet growth and endosperm development. Importantly, haplotype analysis reveals that the SNP variations in the EIN3-binding sites of OsERF115 promoter are significantly associated with the OsERF115 expression levels and grain weight, suggesting that natural variations in the OsERF115 promoter contribute to grain-size diversity. In addition, the OsERF115 orthologues are identified only in grass species, implying a conserved and unique role in the grain development of cereal crops. Our results provide insights into the molecular mechanism of ethylene-mediated grain-size control and a potential strategy based on the OsEIL1-OsERF115-target gene regulatory module for genetic improvement of rice yield.
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Affiliation(s)
- Chang Liu
- Shunde Graduate SchoolResearch Center of Biology and AgricultureZhongzhi International Institute of Agricultural BiosciencesUniversity of Science and Technology BeijingBeijingChina
- Beijing Engineering Laboratory of Main Crop Bio‐Tech BreedingBeijing International Science and Technology Cooperation Base of Bio‐Tech BreedingBeijing Solidwill Sci‐Tech Co. Ltd.BeijingChina
| | - Tian Ma
- Guangdong Laboratory for Lingnan Modern AgricultureCollege of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Dingyang Yuan
- State Key Laboratory of Hybrid RiceHunan Hybrid Rice Research CentreChangshaChina
- College of AgronomyHunan Agricultural UniversityChangshaChina
| | - Yang Zhou
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Yan Long
- Shunde Graduate SchoolResearch Center of Biology and AgricultureZhongzhi International Institute of Agricultural BiosciencesUniversity of Science and Technology BeijingBeijingChina
- Beijing Engineering Laboratory of Main Crop Bio‐Tech BreedingBeijing International Science and Technology Cooperation Base of Bio‐Tech BreedingBeijing Solidwill Sci‐Tech Co. Ltd.BeijingChina
| | - Ziwen Li
- Shunde Graduate SchoolResearch Center of Biology and AgricultureZhongzhi International Institute of Agricultural BiosciencesUniversity of Science and Technology BeijingBeijingChina
- Beijing Engineering Laboratory of Main Crop Bio‐Tech BreedingBeijing International Science and Technology Cooperation Base of Bio‐Tech BreedingBeijing Solidwill Sci‐Tech Co. Ltd.BeijingChina
| | - Zhenying Dong
- Shunde Graduate SchoolResearch Center of Biology and AgricultureZhongzhi International Institute of Agricultural BiosciencesUniversity of Science and Technology BeijingBeijingChina
- Beijing Engineering Laboratory of Main Crop Bio‐Tech BreedingBeijing International Science and Technology Cooperation Base of Bio‐Tech BreedingBeijing Solidwill Sci‐Tech Co. Ltd.BeijingChina
| | - Meijuan Duan
- College of AgronomyHunan Agricultural UniversityChangshaChina
| | - Dong Yu
- College of AgronomyHunan Agricultural UniversityChangshaChina
| | - Yizhi Jing
- Shunde Graduate SchoolResearch Center of Biology and AgricultureZhongzhi International Institute of Agricultural BiosciencesUniversity of Science and Technology BeijingBeijingChina
| | - Xiaoyue Bai
- Shunde Graduate SchoolResearch Center of Biology and AgricultureZhongzhi International Institute of Agricultural BiosciencesUniversity of Science and Technology BeijingBeijingChina
| | - Yanbo Wang
- Shunde Graduate SchoolResearch Center of Biology and AgricultureZhongzhi International Institute of Agricultural BiosciencesUniversity of Science and Technology BeijingBeijingChina
| | - Quancan Hou
- Shunde Graduate SchoolResearch Center of Biology and AgricultureZhongzhi International Institute of Agricultural BiosciencesUniversity of Science and Technology BeijingBeijingChina
- Beijing Engineering Laboratory of Main Crop Bio‐Tech BreedingBeijing International Science and Technology Cooperation Base of Bio‐Tech BreedingBeijing Solidwill Sci‐Tech Co. Ltd.BeijingChina
| | - Shuangshuang Liu
- Shunde Graduate SchoolResearch Center of Biology and AgricultureZhongzhi International Institute of Agricultural BiosciencesUniversity of Science and Technology BeijingBeijingChina
- Beijing Engineering Laboratory of Main Crop Bio‐Tech BreedingBeijing International Science and Technology Cooperation Base of Bio‐Tech BreedingBeijing Solidwill Sci‐Tech Co. Ltd.BeijingChina
| | - Jin‐Song Zhang
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Shou‐Yi Chen
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Dayong Li
- National Engineering Research Center for VegetablesBeijing Vegetable Research CenterBeijing Academy of Agriculture and Forestry ScienceBeijingChina
| | - Xue Liu
- National Engineering Research Center for VegetablesBeijing Vegetable Research CenterBeijing Academy of Agriculture and Forestry ScienceBeijingChina
| | - Zhikang Li
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Wensheng Wang
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Jinping Li
- Beijing Engineering Laboratory of Main Crop Bio‐Tech BreedingBeijing International Science and Technology Cooperation Base of Bio‐Tech BreedingBeijing Solidwill Sci‐Tech Co. Ltd.BeijingChina
| | - Xun Wei
- Shunde Graduate SchoolResearch Center of Biology and AgricultureZhongzhi International Institute of Agricultural BiosciencesUniversity of Science and Technology BeijingBeijingChina
- Beijing Engineering Laboratory of Main Crop Bio‐Tech BreedingBeijing International Science and Technology Cooperation Base of Bio‐Tech BreedingBeijing Solidwill Sci‐Tech Co. Ltd.BeijingChina
| | - Biao Ma
- Guangdong Laboratory for Lingnan Modern AgricultureCollege of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Xiangyuan Wan
- Shunde Graduate SchoolResearch Center of Biology and AgricultureZhongzhi International Institute of Agricultural BiosciencesUniversity of Science and Technology BeijingBeijingChina
- Beijing Engineering Laboratory of Main Crop Bio‐Tech BreedingBeijing International Science and Technology Cooperation Base of Bio‐Tech BreedingBeijing Solidwill Sci‐Tech Co. Ltd.BeijingChina
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11
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Genome-Wide Identification of R2R3-MYB Transcription Factor and Expression Analysis under Abiotic Stress in Rice. PLANTS 2022; 11:plants11151928. [PMID: 35893632 PMCID: PMC9330779 DOI: 10.3390/plants11151928] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/22/2022] [Accepted: 07/23/2022] [Indexed: 11/22/2022]
Abstract
The myeloblastosis (MYB) family comprises a large group of transcription factors (TFs) that has a variety of functions. Among them, the R2R3-MYB type of proteins are the largest group in plants, which are involved in controlling various biological processes such as plant growth and development, physiological metabolism, defense, and responses to abiotic and biotic stresses. In this study, bioinformatics was adopted to conduct genome-wide identification of the R2R3-MYB TFs in rice. We identified 190 MYB TFs (99 R2R3-MYBs), which are unevenly distributed on the 12 chromosomes of rice. Based on the phylogenetic clustering and protein sequence characteristics, OsMYBs were classified into five subgroups, and 59.6% of the Os2R_MYB genes contained two introns. Analysis of cis-acting elements in the 2000 bp upstream region of Os2R_MYB genes showed that all Os2R_MYB genes contained plant hormones-related or stress-responsive elements since 91.9%, 79.8%, 79.8%, and 58.6% of Os2R_MYB genes contain ABRE, TGACG, CGTCA, and MBS motifs, respectively. Protein–protein network analysis showed that the Os2R_MYBs were involved in metabolic process, biosynthetic process, and tissue development. In addition, some genes showed a tissue-specific or developmental-stage-specific expression pattern. Moreover, the transcription levels of 20 Os2R_MYB genes under polyethylene glycol (PEG) and cadmium chloride (CdCl2) stress inducers were dissected by qRT-PCR. The results indicated genes with an altered expression upon PEG or CdCl2 stress induction. These results potentially supply a basis for further research on the role that Os2R_MYB genes play in plant development and stress responses.
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12
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Zhang J, Ma H, Liu Y. Analysis on characteristics of female gametophyte and functional identification of genes related to inflorescences development of Kentucky bluegrass. PROTOPLASMA 2022; 259:1061-1079. [PMID: 34743240 DOI: 10.1007/s00709-021-01720-3] [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: 09/25/2021] [Accepted: 10/21/2021] [Indexed: 06/13/2023]
Abstract
The inflorescence is composed of spikes, and the spike is the carrier of grass seed formation and development, so the development status of inflorescence implies grass seed yield and quality. So far, the systematic analysis of inflorescence development of Kentucky bluegrass has not been reported. The development process of the female gametophyte of wild germplasm materials of Kentucky bluegrass in Gannan, Gansu Province of China (KB-GN), was observed. Based on this, the key developmental stages of inflorescence in KB-GN were divided into premeiosis (GPreM), meiosis (GM), postmeiosis (GPostM), and anthesis (GA), and four stages of inflorescence were selected to analyze the transcriptome expression profile. We found that its sexual reproduction formed a polygonum-type embryo sac. Transcriptome analysis showed that 4256, 1125, 1699, and 3127 genes were highly expressed in GPreM, GM, GPostM, and GA, respectively. And a large number of transcription factors (TFs) such as MADS-box, MYB and NAC, AP2, C2H2, FAR1, B3, bHLH, WRKY, and TCP were highly expressed throughout the inflorescence development stages. KEGG enrichment and MapMan analysis showed that genes involved in plant hormone metabolism were also highly expressed at the entire stages of inflorescence development. However, a few TFs belong to stage-specific genes, such as TRAF proteins with unknown function in plants was screened firstly, which was specifically and highly expressed in the GPreM, indicating that TRAF may regulate the preparatory events of meiosis or be essential for the development of megaspore mother cell (MMC). The expression patterns of 15 MADS-box genes were analyzed by qRT-PCR, and the expression results were consistent with that of the transcriptome. The study on the inflorescence development of KB-GN will be great significant works and contribution to illustrate the basic mechanism of grass seeds formation and development.
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Affiliation(s)
- Jinqing Zhang
- College of Pratacultural Science, Gansu Agricultural University, Key Laboratory of Grassland Ecosystem, Ministry of Education, Pratacultural Engineering Laboratory of Gansu Province, Sino-U.S. Center for Grazingland Ecosystem Sustainability, Lanzhou, Gansu, 730070, China
| | - Huiling Ma
- College of Pratacultural Science, Gansu Agricultural University, Key Laboratory of Grassland Ecosystem, Ministry of Education, Pratacultural Engineering Laboratory of Gansu Province, Sino-U.S. Center for Grazingland Ecosystem Sustainability, Lanzhou, Gansu, 730070, China.
| | - Yan Liu
- College of Pratacultural Science, Gansu Agricultural University, Key Laboratory of Grassland Ecosystem, Ministry of Education, Pratacultural Engineering Laboratory of Gansu Province, Sino-U.S. Center for Grazingland Ecosystem Sustainability, Lanzhou, Gansu, 730070, China
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13
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Si F, Yang C, Yan B, Yan W, Tang S, Yan Y, Cao X, Song X. Control of OsARF3a by OsKANADI1 contributes to lemma development in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:1717-1730. [PMID: 35403315 DOI: 10.1111/tpj.15766] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 04/02/2022] [Accepted: 04/05/2022] [Indexed: 06/14/2023]
Abstract
In rice (Oryza sativa), the lemma and palea protect the internal organs of the floret,provide nutrients for seed development, and determine grain size. We previously revealed that a trans-acting small interfering RNA targeting AUXIN RESPONSE FACTORS (tasiR-ARF) regulates lemma polarity establishment via post-transcriptional repression of AUXIN RESPONSE FACTORS (ARFs) in rice. TasiR-ARF formation requires RNA-DEPENDENT RNA POLYMERASE 6 (RDR6). However, the underlying molecular mechanism of the tasiR-ARF-ARF regulon in lemma development remains unclear. Here, by genetic screening for suppressors of the thermosensitive mutant osrdr6-1, we identified three suppressors, huifu 1 (hf1), hf9, and hf17. Mapping-by-sequencing revealed that HF1 encodes a MYB transcription factor belonging to the KANADI1 family. The hf1 mutation partially rescued the osrdr6-1 lemma defect but not the defect in tasiR-ARF levels. DNA affinity purification sequencing analysis identified 17 725 OsKANADI1-associated sites, most of which contain the SPBP-box binding motif (RGAATAWW) and are located in the promoter, protein-coding, intron, and intergenic regions. Moreover, we found that OsKANADI1 could directly bind to the intron of OsARF3a in vitro and in vivo and promote OsARF3a expression at the transcriptional level. In addition, hf9 and hf17 are intragenic suppressors containing mutations in OsRDR6 that partially rescue tasiR-ARF levels by restoring OsRDR6 protein levels. Collectively, our results demonstrate that OsKANADI1 and tasiR-ARFs synergistically maintain the proper expression of OsARF3a and thus contribute to rice lemma development.
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Affiliation(s)
- Fuyan Si
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chao Yang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Bin Yan
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wei Yan
- Southern University of Science and Technology, Shenzhen, 518055, China
| | - Shanjie Tang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Yan Yan
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
- CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xianwei Song
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- Innovative Academy of Seed Design (INASEED), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
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14
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Xie W, Liu W, Yu X, Zeng D, Ren D. Fine Mapping of Rice Specific MR1, a Gene Determines Palea Identity. FRONTIERS IN PLANT SCIENCE 2022; 13:864099. [PMID: 35685009 PMCID: PMC9171376 DOI: 10.3389/fpls.2022.864099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 02/17/2022] [Indexed: 06/15/2023]
Abstract
The hull (palea and lemma) is the specific organ of grass florets. Although many genes related to the hull development have been cloned, the genetic mechanisms behind the development are still unclear, and the evolutionary relationship has different explanations and heated arguments between the palea and lemma. In this study, we found a specific mr1 mutant with a reduced palea, showing an enlarged mrp and degraded bop. Phenotype observations and molecular evidences showed that the bop was converted to the mrp-like organ. Our findings first reveal that the bop and mrp are homologous structures, and the palea and lemma are the same whorl floral organs. MR1 may prevent the transformation of the bop into mrp by regulating the expressions of hull identity genes. Meantime, the mr1 mutant showed altered grain size and grain quality, with defective physical and chemical contents. MR1 was controlled by a single recessive gene and was finally located on chromosome 1, with a physical distance of 70 kb. More work will be needed for confirming the target gene of MR1, which would contribute to our understanding of grain formation and the origin between the lemma, bop, and mrp.
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15
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Guo M, Zhang W, Mohammadi MA, He Z, She Z, Yan M, Shi C, Lin L, Wang A, Liu J, Tian D, Zhao H, Qin Y. OsDDM1b Controls Grain Size by Influencing Cell Cycling and Regulating Homeostasis and Signaling of Brassinosteroid in Rice. FRONTIERS IN PLANT SCIENCE 2022; 13:873993. [PMID: 35463416 PMCID: PMC9024357 DOI: 10.3389/fpls.2022.873993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
Snf2 family proteins are the crucial subunits of chromatin-remodeling complexes (CRCs), which contributes to the biological processes of transcription, replication, and DNA repair using ATP as energy. Some CRC subunits have been confirmed to be the critical regulators in various aspects of plant growth and development and in epigenetic mechanisms such as histone modification, DNA methylation, and histone variants. However, the functions of Snf2 family genes in rice were poorly investigated. In this study, the relative expression profile of 40 members of Snf2 family in rice was studied at certain developmental stages of seed. Our results revealed that OsCHR741/OsDDM1b (Decrease in DNA methylation 1) was accumulated highly in the early developmental stage of seeds. We further analyzed the OsDDM1b T-DNA insertion loss-of-function of mutant, which exhibited dwarfism, smaller organ size, and shorter and wider grain size than the wild type (Hwayoung, HY), yet no difference in 1,000-grain weight. Consistent with the grain size, the outer parenchyma cell layers of lemma in osddm1b developed more cells with decreased size. OsDDM1b encoded a nucleus, membrane-localized protein and was distributed predominately in young spikelets and seeds, asserting its role in grain size. Meanwhile, the osddm1b was less sensitive to brassinosteroids (BRs) while the endogenous BR levels increased. We detected changes in the expression levels of the BR signaling pathway and feedback-inhibited genes with and without exogenous BR application, and the alterations of expression were also observed in grain size-related genes in the osddm1b. Altogether, our results suggest that OsDDM1b plays a crucial role in grain size via influencing cell proliferation and regulating BR signaling and homeostasis.
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Affiliation(s)
- Mingliang Guo
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wenchao Zhang
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mohammad Aqa Mohammadi
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, China
| | - Zhimei He
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zeyuan She
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, China
| | - Maokai Yan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, China
| | - Chao Shi
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lingwei Lin
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Aqiong Wang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jindian Liu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Dagang Tian
- Biotechnology Research Institute, Fujian Provincial Key Laboratory of Genetic Engineering for Agriculture, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Heming Zhao
- Center for Crop Biotechnology, College of Agriculture, Anhui Science and Technology University, Fengyang, China
| | - Yuan Qin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, China
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
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16
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She Z, Huang X, Aslam M, Wang L, Yan M, Qin R, Chen Y, Qin Y, Niu X. Expression characterization and cross-species complementation uncover the functional conservation of YABBY genes for leaf abaxial polarity and carpel polarity establishment in Saccharum spontaneum. BMC PLANT BIOLOGY 2022; 22:124. [PMID: 35300591 PMCID: PMC8932074 DOI: 10.1186/s12870-022-03501-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Cell polarity establishment and maintenance is indispensable for plant growth and development. In plants, the YABBY transcription factor family has a distinct role in leaf asymmetric polarity establishment and lateral organ initiation. However, for the important sugar crop Saccharum, little information on YABBY genes is available. RESULTS In this study, a total of 20 sequences for 7 SsYABBY genes were identified in the sugarcane genome, designated as SsYABBY1-7 based on their chromosome locations, and characterized by phylogenetic analysis. We provided a high-resolution map of SsYABBYs' global expression dynamics during vegetative and reproductive organ morphogenesis and revealed that SsYABBY3/4/5 are predominately expressed at the seedling stage of stem and leaf basal zone; SsYABBY2/5/7 are highly expressed in ovules. Besides, cross-species overexpression and/or complementation verified the conserved function of SsYABBY2 in establishing leaf adaxial-abaxial polarity and ovules development. We found that the SsYABBY2 could successfully rescue the leaves curling, carpel dehiscence, and ovule abortion defects in Arabidopsis crc mutant. CONCLUSIONS Collectively, our study demonstrates that SsYABBY genes retained a conserved function in establishing and preserving leaf adaxial-abaxial polarity and lateral organ development during evolution.
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Affiliation(s)
- Zeyuan She
- Guangxi Key Laboratory of Sugarcane Biology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Xiaoyi Huang
- College of Life Science, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Mohammad Aslam
- Guangxi Key Laboratory of Sugarcane Biology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Lulu Wang
- Guangxi Key Laboratory of Sugarcane Biology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Maokai Yan
- Guangxi Key Laboratory of Sugarcane Biology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Rongjuan Qin
- Fishery Multiplication Management Station of Lijiang River Water Supply Hub Project, Guilin, 541001, China
| | - Yingzhi Chen
- Guangxi Key Laboratory of Sugarcane Biology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Yuan Qin
- Guangxi Key Laboratory of Sugarcane Biology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, China.
- College of Life Science, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Xiaoping Niu
- Guangxi Key Laboratory of Sugarcane Biology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, China.
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Hu H, Ren D, Hu J, Jiang H, Chen P, Zeng D, Qian Q, Guo L. WHITE AND LESION-MIMIC LEAF1, encoding a lumazine synthase, affects reactive oxygen species balance and chloroplast development in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:1690-1703. [PMID: 34628678 DOI: 10.1111/tpj.15537] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 09/26/2021] [Accepted: 09/29/2021] [Indexed: 06/13/2023]
Abstract
The riboflavin derivatives flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) are essential cofactors for enzymes in multiple cellular processes. Characterizing mutants with impaired riboflavin metabolism can help clarify the role of riboflavin in plant development. Here, we characterized a rice (Oryza sativa) white and lesion-mimic (wll1) mutant, which displays a lesion-mimic phenotype with white leaves, chlorophyll loss, chloroplast defects, excess reactive oxygen species (ROS) accumulation, decreased photosystem protein levels, changes in expression of chloroplast development and photosynthesis genes, and cell death. Map-based cloning and complementation test revealed that WLL1 encodes lumazine synthase, which participates in riboflavin biosynthesis. Indeed, the wll1 mutant showed riboflavin deficiency, and application of FAD rescued the wll1 phenotype. In addition, transcriptome analysis showed that cytokinin metabolism was significantly affected in wll1 mutant, which had increased cytokinin and δ-aminolevulinic acid contents. Furthermore, WLL1 and riboflavin synthase (RS) formed a complex, and the rs mutant had a similar phenotype to the wll1 mutant. Taken together, our findings revealed that WLL1 and RS play pivotal roles in riboflavin biosynthesis, which is necessary for ROS balance and chloroplast development in rice.
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Affiliation(s)
- Haitao Hu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, China
| | - Deyong Ren
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Jiang Hu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Hongzhen Jiang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Ping Chen
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Dali Zeng
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Longbiao Guo
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
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18
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Liu B, Zhang D, Sun M, Li M, Ma X, Jia S, Mao P. PSII Activity Was Inhibited at Flowering Stage with Developing Black Bracts of Oat. Int J Mol Sci 2021; 22:ijms22105258. [PMID: 34067635 PMCID: PMC8156022 DOI: 10.3390/ijms22105258] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/10/2021] [Accepted: 05/12/2021] [Indexed: 11/16/2022] Open
Abstract
The color of bracts generally turns yellow or black from green during cereal grain development. However, the impact of these phenotypic changes on photosynthetic physiology during black bract formation remains unclear. Two oat cultivars (Avena sativa L.), ‘Triple Crown’ and ‘Qinghai 444’, with yellow and black bracts, respectively, were found to both have green bracts at the heading stage, but started to turn black at the flowering stage and become blackened at the milk stage for ‘Qinghai 444’. Their photosynthetic characteristics were analyzed and compared, and the key genes, proteins and regulatory pathways affecting photosynthetic physiology were determined in ‘Triple Crown’ and ‘Qinghai 444’ bracts. The results show that the actual PSII photochemical efficiency and PSII electron transfer rate of ‘Qinghai 444’ bracts had no significant changes at the heading and milk stages but decreased significantly (p < 0.05) at the flowering stage compared with ‘Triple Crown’. The chlorophyll content decreased, the LHCII involved in the assembly of supercomplexes in the thylakoid membrane was inhibited, and the expression of Lhcb1 and Lhcb5 was downregulated at the flowering stage. During this critical stage, the expression of Bh4 and C4H was upregulated, and the biosynthetic pathway of p-coumaric acid using tyrosine and phenylalanine as precursors was also enhanced. Moreover, the key upregulated genes (CHS, CHI and F3H) of anthocyanin biosynthesis might complement the impaired PSII activity until recovered at the milk stage. These findings provide a new insight into how photosynthesis alters during the process of oat bract color transition to black.
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Affiliation(s)
- Bei Liu
- Forage Seed Laboratory, College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China; (B.L.); (D.Z.); (M.S.); (M.L.); (X.M.); (S.J.)
- Key Laboratory of Pratacultural Science, Beijing Municipality, Yuanmingyuan West Road, Haidian District, Beijing 100193, China
| | - Di Zhang
- Forage Seed Laboratory, College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China; (B.L.); (D.Z.); (M.S.); (M.L.); (X.M.); (S.J.)
- Key Laboratory of Pratacultural Science, Beijing Municipality, Yuanmingyuan West Road, Haidian District, Beijing 100193, China
| | - Ming Sun
- Forage Seed Laboratory, College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China; (B.L.); (D.Z.); (M.S.); (M.L.); (X.M.); (S.J.)
- Key Laboratory of Pratacultural Science, Beijing Municipality, Yuanmingyuan West Road, Haidian District, Beijing 100193, China
| | - Manli Li
- Forage Seed Laboratory, College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China; (B.L.); (D.Z.); (M.S.); (M.L.); (X.M.); (S.J.)
- Key Laboratory of Pratacultural Science, Beijing Municipality, Yuanmingyuan West Road, Haidian District, Beijing 100193, China
| | - Xiqing Ma
- Forage Seed Laboratory, College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China; (B.L.); (D.Z.); (M.S.); (M.L.); (X.M.); (S.J.)
- Key Laboratory of Pratacultural Science, Beijing Municipality, Yuanmingyuan West Road, Haidian District, Beijing 100193, China
| | - Shangang Jia
- Forage Seed Laboratory, College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China; (B.L.); (D.Z.); (M.S.); (M.L.); (X.M.); (S.J.)
- Key Laboratory of Pratacultural Science, Beijing Municipality, Yuanmingyuan West Road, Haidian District, Beijing 100193, China
| | - Peisheng Mao
- Forage Seed Laboratory, College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China; (B.L.); (D.Z.); (M.S.); (M.L.); (X.M.); (S.J.)
- Key Laboratory of Pratacultural Science, Beijing Municipality, Yuanmingyuan West Road, Haidian District, Beijing 100193, China
- Correspondence: ; Tel.: +86-010-6273-3311
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19
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Cui Y, Peng Y, Zhang Q, Xia S, Ruan B, Xu Q, Yu X, Zhou T, Liu H, Zeng D, Zhang G, Gao Z, Hu J, Zhu L, Shen L, Guo L, Qian Q, Ren D. Disruption of EARLY LESION LEAF 1, encoding a cytochrome P450 monooxygenase, induces ROS accumulation and cell death in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:942-956. [PMID: 33190327 DOI: 10.1111/tpj.15079] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 10/23/2020] [Accepted: 10/28/2020] [Indexed: 05/18/2023]
Abstract
Lesion-mimic mutants (LMMs) provide a valuable tool to reveal the molecular mechanisms determining programmed cell death (PCD) in plants. Despite intensive research, the mechanisms behind PCD and the formation of lesions in various LMMs still remain to be elucidated. Here, we identified a rice (Oryza sativa) LMM, early lesion leaf 1 (ell1), cloned the causal gene by map-based cloning, and verified this by complementation. ELL1 encodes a cytochrome P450 monooxygenase, and the ELL1 protein was located in the endoplasmic reticulum. The ell1 mutant exhibited decreased chlorophyll contents, serious chloroplast degradation, upregulated expression of chloroplast degradation-related genes, and attenuated photosynthetic protein activity, indicating that ELL1 is involved in chloroplast development. RNA sequencing analysis showed that genes related to oxygen binding were differentially expressed in ell1 and wild-type plants; histochemistry and paraffin sectioning results indicated that hydrogen peroxide (H2 O2 ) and callose accumulated in the ell1 leaves, and the cell structure around the lesions was severely damaged, which indicated that reactive oxygen species (ROS) accumulated and cell death occurred in the mutant. TUNEL staining and comet experiments revealed that severe DNA degradation and abnormal PCD occurred in the ell1 mutants, which implied that excessive ROS accumulation may induce DNA damage and ROS-mediated cell death in the mutant. Additionally, lesion initiation in the ell1 mutant was light dependent and temperature sensitive. Our findings revealed that ELL1 affects chloroplast development or function, and that loss of ELL1 function induces ROS accumulation and lesion formation in rice.
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Affiliation(s)
- Yuanjiang Cui
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Youlin Peng
- Rice Research Institute, Southwest University of Science and Technology, Mianyang, 621010, P. R. China
| | - Qiang Zhang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Saisai Xia
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Banpu Ruan
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Qiankun Xu
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Xiaoqi Yu
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Tingting Zhou
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - He Liu
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Dali Zeng
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Guangheng Zhang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Zhenyu Gao
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Jiang Hu
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Li Zhu
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Lan Shen
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Longbiao Guo
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Qian Qian
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Deyong Ren
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, P. R. China
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20
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Tiwari M, Trivedi P, Pandey A. Emerging tools and paradigm shift of gene editing in cereals, fruits, and horticultural crops for enhancing nutritional value and food security. Food Energy Secur 2020. [DOI: 10.1002/fes3.258] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Affiliation(s)
- Manish Tiwari
- National Institute of Plant Genome Research New Delhi India
| | - Prabodh Trivedi
- CSIR‐Central Institute of Medicinal and Aromatic Plants Lucknow India
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21
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Xu Q, Yu X, Cui Y, Xia S, Zeng D, Qian Q, Ren D. LRG1 maintains sterile lemma identity by regulating OsMADS6 expression in rice. SCIENCE CHINA-LIFE SCIENCES 2020; 64:1190-1192. [PMID: 33141301 DOI: 10.1007/s11427-020-1816-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 09/08/2020] [Indexed: 11/29/2022]
Affiliation(s)
- Qiankun Xu
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Xiaoqi Yu
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Yuanjiang Cui
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Saisai Xia
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Dali Zeng
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Qian Qian
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
| | - Deyong Ren
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
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22
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Fu C, Chen H, Gao H, Lu Y, Han C, Han Y. Two papaya
MYB
proteins function in fruit ripening by regulating some genes involved in cell‐wall degradation and carotenoid biosynthesis. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2020; 100:4442-4448. [PMID: 32388883 DOI: 10.1002/jsfa.10484] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 04/27/2020] [Accepted: 05/09/2020] [Indexed: 05/02/2023]
Affiliation(s)
- Changchun Fu
- College of Biology and Environmental EngineeringZhejiang Shuren University Hangzhou China
| | - Hangjun Chen
- Key Laboratory of Post‐Harvest Handling of Fruits, Ministry of Agriculture and Rural Affairs; Key Laboratory of Fruits and Vegetables Postharvest and Processing Technology Research of Zhejiang Province; Key Laboratory of China Light IndustryFood Science Institute, Zhejiang Academy of Agricultural Sciences Hangzhou China
| | - Haiyan Gao
- Key Laboratory of Post‐Harvest Handling of Fruits, Ministry of Agriculture and Rural Affairs; Key Laboratory of Fruits and Vegetables Postharvest and Processing Technology Research of Zhejiang Province; Key Laboratory of China Light IndustryFood Science Institute, Zhejiang Academy of Agricultural Sciences Hangzhou China
| | - Yin Lu
- College of Biology and Environmental EngineeringZhejiang Shuren University Hangzhou China
| | - Chao Han
- College of Biology and Environmental EngineeringZhejiang Shuren University Hangzhou China
| | - Yanchao Han
- Key Laboratory of Post‐Harvest Handling of Fruits, Ministry of Agriculture and Rural Affairs; Key Laboratory of Fruits and Vegetables Postharvest and Processing Technology Research of Zhejiang Province; Key Laboratory of China Light IndustryFood Science Institute, Zhejiang Academy of Agricultural Sciences Hangzhou China
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23
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Li Q, Lu L, Liu H, Bai X, Zhou X, Wu B, Yuan M, Yang L, Xing Y. A minor QTL, SG3, encoding an R2R3-MYB protein, negatively controls grain length in rice. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:2387-2399. [PMID: 32472264 DOI: 10.1007/s00122-020-03606-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 05/12/2020] [Indexed: 05/28/2023]
Abstract
SG3, an R2R3 MYB protein coding gene that tightly linked to a major QTLGS3, negatively regulates grain length while dependent on the status ofGS3in rice. It is often very difficult to isolate a minor QTL that is closely linked to a major QTL in rice. In this study, we focused on the isolation of a minor grain length QTL, small grain 3 (SG3), which is closely linked to the major QTL grain size 3 (GS3). The genetic effect of SG3 on grain length was dependent on GS3 status. Its genetic effect was larger in the presence of nonfunctional sg3 than functional SG3. A large number of near-isogenic F2 plants in which GS3 was fixed with nonfunctional alleles were developed to clone SG3. A gene encoding an R2R3 MYB domain transcriptional regulator was identified as the candidate gene for SG3. SG3 overexpression and knockdown plants showed shortened and elongated grains, respectively, which demonstrated that SG3 acts as a negative regulator of grain length. SG3 was preferentially expressed in panicles after flowering, and SG3 acted as a transcription activator. Comparative sequencing analysis identified a 12-bp insertion in the third exon of NYZ that led to a frameshift and resulted in a premature stop codon. The insertion/deletion was associated with grain length in the presence of functional GS3 in the indica subspecies. SG3 and GS3 were frequently in coupling phase in indica rice, making them good targets for the breeding of cultivars with short or long grains. The isolation of the SG3 MYB gene provides new gene resource and contributes to the regulatory network of grain length in rice.
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Affiliation(s)
- Qiuping Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan, 430070, China
| | - Li Lu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan, 430070, China
| | - Haiyang Liu
- College of Agriculture, Yangtze University, Jingzhou, 434000, China
| | - Xufeng Bai
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan, 430070, China
| | - Xin Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan, 430070, China
| | - Bi Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan, 430070, China
| | - Mengqi Yuan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan, 430070, China
| | - Lin Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan, 430070, China
| | - Yongzhong Xing
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan, 430070, China.
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24
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Crop reproductive meristems in the genomic era: a brief overview. Biochem Soc Trans 2020; 48:853-865. [PMID: 32573650 DOI: 10.1042/bst20190441] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 05/15/2020] [Accepted: 05/27/2020] [Indexed: 11/17/2022]
Abstract
Modulation of traits beneficial for cultivation and yield is one of the main goals of crop improvement. One of the targets for enhancing productivity is changing the architecture of inflorescences since in many species it determines fruit and seed yield. Inflorescence shape and organization is genetically established during the early stages of reproductive development and depends on the number, arrangement, activities, and duration of meristems during the reproductive phase of the plant life cycle. Despite the variety of inflorescence architectures observable in nature, many key aspects of inflorescence development are conserved among different species. For instance, the genetic network in charge of specifying the identity of the different reproductive meristems, which can be indeterminate or determinate, seems to be similar among distantly related species. The availability of a large number of published transcriptomic datasets for plants with different inflorescence architectures, allowed us to identify transcription factor gene families that are differentially expressed in determinate and indeterminate reproductive meristems. The data that we review here for Arabidopsis, rice, barley, wheat, and maize, particularly deepens our knowledge of their involvement in meristem identity specification.
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25
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Liu N, Cheng F. Association mapping for yield traits in Paeonia rockii based on SSR markers within transcription factors of comparative transcriptome. BMC PLANT BIOLOGY 2020; 20:245. [PMID: 32487017 PMCID: PMC7265254 DOI: 10.1186/s12870-020-02449-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 05/18/2020] [Indexed: 05/30/2023]
Abstract
BACKGROUND Allelic variation underlying the quantitative traits in plants is caused by the extremely complex regulation process. Tree peony originated in China is a peculiar ornamental, medicinal and oil woody plant. Paeonia rockii, one of tree peony species, is a precious emerging woody oil crop. However, in this valuable plant, the study of functional loci associated with yield traits has rarely been identified. Therefore, to explore the genetic architecture of 24 yield quantitative traits, the association mapping was first reported in 420 unrelated cultivated P. rockii individuals based on the next-generation sequencing (NGS) and single-molecule long-read sequencing (SMLRS). RESULTS The developed 58 pairs of polymorphic expressed sequence tag-simple sequence repeat (EST-SSR) markers from 959 candidate transcription factors (TFs) associated with yield were used for genotyping the 420 P. rockii accessions. We observed a high level of genetic diversity (polymorphic information content, PIC = 0.514) and low linkage disequilibrium (LD) between EST-SSRs. Moreover, four subpopulations in the association population were revealed by STRUCTURE analyses. Further, single-marker association analysis identified 141 significant associations, involving 17 quantitative traits and 41 EST-SSRs. These loci were mainly from AP2, TCP, MYB, HSF, bHLH, GATA, and B3 gene families and showed a small proportion of the phenotypic variance (3.79 to 37.45%). CONCLUSIONS Our results summarize a valuable collection of functional loci associated with yield traits in P. rockii, and provide a precious resource that reveals allelic variation underlying quantitative traits in Paeonia and other woody oil crops.
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Affiliation(s)
- Na Liu
- Peony International Institute, Beijing Advanced Innovation Center of Tree Breeding by Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Fangyun Cheng
- Peony International Institute, Beijing Advanced Innovation Center of Tree Breeding by Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China.
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26
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ABNORMAL FLOWER AND GRAIN 1 encodes OsMADS6 and determines palea identity and affects rice grain yield and quality. SCIENCE CHINA-LIFE SCIENCES 2020; 63:228-238. [PMID: 31919631 DOI: 10.1007/s11427-019-1593-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 11/28/2019] [Indexed: 12/21/2022]
Abstract
The palea and lemma are floral organ structures unique to grasses; these structures form the hull and directly affect grain size and quality. However, the molecular mechanisms controlling the development of the hull are not well understood. In this study, we characterized the rice (Oryza sativa) abnormal flower and grain1 (afg1) mutant, a new allele of OsMADS6. Similar to previously characterized osmads6 alleles, in the afg1 floret, the palea lost its marginal region and acquired the lemma identity. However, in contrast to other osmads6 alleles, the afg1 mutant showed altered grain size and grain quality, with decreased total starch and amylose contents, and increased protein and soluble sugar contents. The analysis of transcriptional activity suggested that AFG1 is a transcriptional activator and may affect grain size by regulating the expression levels of several genes related to cell expansion and proliferation in the afg1 mutant. These results revealed that AFG1 plays an important role in determining palea identity and affecting grain yield and quality in rice.
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