101
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Cheng YC, Li G, Yin M, Adegoke TV, Wang YF, Tong XH, Zhang J, Ying JZ. Verification and dissection of one quantitative trait locus for grain size and weight on chromosome 1 in rice. Sci Rep 2021; 11:18252. [PMID: 34521909 PMCID: PMC8440748 DOI: 10.1038/s41598-021-97622-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 08/23/2021] [Indexed: 11/09/2022] Open
Abstract
Grain size and weight are the key traits determining rice quality and yield and are mainly controlled by quantitative trait loci (QTL). In this study, one minor QTL that was previously mapped in the marker interval of JD1009-JD1019 using the Huanghuazhan/Jizi1560 (HHZ/JZ1560) recombinant inbred line (RIL) population, qTGW1-2, was validated to regulate grain size and weight across four rice-growing seasons using twenty-one near isogenic line (NIL)-F2 populations. The twenty-one populations were in two types of genetic background that were derived from the same parents HHZ and JZ1560. Twelve F9, F10 or F11 NIL-F2 populations with the sequential residual heterozygous regions covering JD1009-RM6840 were developed from one residual heterozygote (RH) in the HHZ/JZ1560 RIL population, and the remaining nine BC3F3, BC3F4 or BC3F5 NIL-F2 populations with the sequential residual heterozygous regions covering JD1009-RM6840 were constructed through consecutive backcrosses to the recurrent parent HHZ followed with marker assistant selection in each generation. Based on the QTL analysis of these genetic populations, qTGW1-2 was successfully confirmed to control grain length, width and weight and further dissected into two QTLs, qTGW1-2a and qTGW1-2b, which were respectively narrowed down to the marker intervals of JD1139-JD1127 (~ 978.2-kb) and JD1121-JD1102 (~ 54.8-kb). Furthermore, the two types of NIL-F2 populations were proved to be able to decrease the genetic background noise and increase the detection power of minor QTL. These results provided an important basis for further map-based cloning and molecular design breeding with the two QTLs in rice.
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Affiliation(s)
- Yi-Chen Cheng
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Guan Li
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Man Yin
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Tosin Victor Adegoke
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Yi-Feng Wang
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Xiao-Hong Tong
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Jian Zhang
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China.
| | - Jie-Zheng Ying
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China. .,State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Zhejiang Province, China.
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102
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Hao J, Wang D, Wu Y, Huang K, Duan P, Li N, Xu R, Zeng D, Dong G, Zhang B, Zhang L, Inzé D, Qian Q, Li Y. The GW2-WG1-OsbZIP47 pathway controls grain size and weight in rice. MOLECULAR PLANT 2021; 14:1266-1280. [PMID: 33930509 DOI: 10.1016/j.molp.2021.04.011] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 03/05/2021] [Accepted: 04/25/2021] [Indexed: 06/12/2023]
Abstract
Regulation of seed size is a key strategy for improving crop yield and is also a basic biological question. However, the molecular mechanisms by which plants determine their seed size remain elusive. Here, we report that the GW2-WG1-OsbZIP47 regulatory module controls grain width and weight in rice. WG1, which encodes a glutaredoxin protein, promotes grain growth by increasing cell proliferation. Interestingly, WG1 interacts with the transcription factor OsbZIP47 and represses its transcriptional activity by associating with the transcriptional co-repressor ASP1, indicating that WG1 may act as an adaptor protein to recruit the transcriptional co-repressor. In contrary, OsbZIP47 restricts grain growth by decreasing cell proliferation. Further studies reveal that the E3 ubiquitin ligase GW2 ubiquitinates WG1 and targets it for degradation. Genetic analyses confirm that GW2, WG1, and OsbZIP47 function in a common pathway to control grain growth. Taken together, our findings reveal a genetic and molecular framework for the control of grain size and weight by the GW2-WG1-OsbZIP47 regulatory module, providing new targets for improving seed size and weight in crops.
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Affiliation(s)
- Jianqin Hao
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Dekai Wang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Yingbao Wu
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Ke Huang
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Penggen Duan
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Na Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Ran Xu
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Dali Zeng
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Guojun Dong
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Baolan Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Limin Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Dirk Inzé
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Yunhai Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100039, China.
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103
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Chen K, Łyskowski A, Jaremko Ł, Jaremko M. Genetic and Molecular Factors Determining Grain Weight in Rice. FRONTIERS IN PLANT SCIENCE 2021; 12:605799. [PMID: 34322138 PMCID: PMC8313227 DOI: 10.3389/fpls.2021.605799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 06/22/2021] [Indexed: 05/06/2023]
Abstract
Grain weight is one of the major factors determining single plant yield production of rice and other cereal crops. Research has begun to reveal the regulatory mechanisms underlying grain weight as well as grain size, highlighting the importance of this research for plant molecular biology. The developmental trait of grain weight is affected by multiple molecular and genetic aspects that lead to dynamic changes in cell division, expansion and differentiation. Additionally, several important biological pathways contribute to grain weight, such as ubiquitination, phytohormones, G-proteins, photosynthesis, epigenetic modifications and microRNAs. Our review integrates early and more recent findings, and provides future perspectives for how a more complete understanding of grain weight can optimize strategies for improving yield production. It is surprising that the acquired wealth of knowledge has not revealed more insights into the underlying molecular mechanisms. To accelerating molecular breeding of rice and other cereals is becoming an emergent and critical task for agronomists. Lastly, we highlighted the importance of leveraging gene editing technologies as well as structural studies for future rice breeding applications.
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Affiliation(s)
- Ke Chen
- Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
| | - Andrzej Łyskowski
- Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Faculty of Chemistry, Rzeszow University of Technology, Rzeszow, Poland
| | - Łukasz Jaremko
- Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Mariusz Jaremko
- Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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104
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Groppi A, Liu S, Cornille A, Decroocq S, Bui QT, Tricon D, Cruaud C, Arribat S, Belser C, Marande W, Salse J, Huneau C, Rodde N, Rhalloussi W, Cauet S, Istace B, Denis E, Carrère S, Audergon JM, Roch G, Lambert P, Zhebentyayeva T, Liu WS, Bouchez O, Lopez-Roques C, Serre RF, Debuchy R, Tran J, Wincker P, Chen X, Pétriacq P, Barre A, Nikolski M, Aury JM, Abbott AG, Giraud T, Decroocq V. Population genomics of apricots unravels domestication history and adaptive events. Nat Commun 2021; 12:3956. [PMID: 34172741 PMCID: PMC8233370 DOI: 10.1038/s41467-021-24283-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 06/08/2021] [Indexed: 01/27/2023] Open
Abstract
Among crop fruit trees, the apricot (Prunus armeniaca) provides an excellent model to study divergence and adaptation processes. Here, we obtain nearly 600 Armeniaca apricot genomes and four high-quality assemblies anchored on genetic maps. Chinese and European apricots form two differentiated gene pools with high genetic diversity, resulting from independent domestication events from distinct wild Central Asian populations, and with subsequent gene flow. A relatively low proportion of the genome is affected by selection. Different genomic regions show footprints of selection in European and Chinese cultivated apricots, despite convergent phenotypic traits, with predicted functions in both groups involved in the perennial life cycle, fruit quality and disease resistance. Selection footprints appear more abundant in European apricots, with a hotspot on chromosome 4, while admixture is more pervasive in Chinese cultivated apricots. Our study provides clues to the biology of selected traits and targets for fruit tree research and breeding.
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Affiliation(s)
- Alexis Groppi
- Univ. Bordeaux, Centre de Bioinformatique de Bordeaux (CBiB), Bordeaux, 33076, France
- Univ. Bordeaux, CNRS, IBGC, UMR 5095, Bordeaux, 33077, France
| | - Shuo Liu
- Univ. Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, 71 Av. E. Bourlaux, Villenave d'Ornon, 33140, France
- Liaoning Institute of Pomology, Tiedong Street, Xiongyue, Bayuquan District, Yingkou City, 115009, Liaoning, China
| | - Amandine Cornille
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, UMR GQE-Le Moulon, Gif-sur-Yvette, 91190, France
| | - Stéphane Decroocq
- Univ. Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, 71 Av. E. Bourlaux, Villenave d'Ornon, 33140, France
| | - Quynh Trang Bui
- Univ. Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, 71 Av. E. Bourlaux, Villenave d'Ornon, 33140, France
| | - David Tricon
- Univ. Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, 71 Av. E. Bourlaux, Villenave d'Ornon, 33140, France
| | - Corinne Cruaud
- Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, 2 Rue Gaston Crémieux, Evry, 91057, France
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux, Evry, 91057, France
| | - Sandrine Arribat
- French Plant Genomic Resource Center, INRAE-CNRGV, Castanet Tolosan, France
| | - Caroline Belser
- Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, 2 Rue Gaston Crémieux, Evry, 91057, France
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux, Evry, 91057, France
| | - William Marande
- French Plant Genomic Resource Center, INRAE-CNRGV, Castanet Tolosan, France
| | - Jérôme Salse
- INRAE/UBP UMR 1095 GDEC Genetique, Diversite et Ecophysiologie des Cereales, Laboratory PaleoEVO Paleogenomics & Evolution, 5 Chemin de Beaulieu, Clermont Ferrand, 63100, France
| | - Cécile Huneau
- INRAE/UBP UMR 1095 GDEC Genetique, Diversite et Ecophysiologie des Cereales, Laboratory PaleoEVO Paleogenomics & Evolution, 5 Chemin de Beaulieu, Clermont Ferrand, 63100, France
| | - Nathalie Rodde
- French Plant Genomic Resource Center, INRAE-CNRGV, Castanet Tolosan, France
| | - Wassim Rhalloussi
- French Plant Genomic Resource Center, INRAE-CNRGV, Castanet Tolosan, France
| | - Stéphane Cauet
- French Plant Genomic Resource Center, INRAE-CNRGV, Castanet Tolosan, France
| | - Benjamin Istace
- Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, 2 Rue Gaston Crémieux, Evry, 91057, France
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux, Evry, 91057, France
| | - Erwan Denis
- Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, 2 Rue Gaston Crémieux, Evry, 91057, France
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux, Evry, 91057, France
| | - Sébastien Carrère
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Jean-Marc Audergon
- INRAE UR1052 GAFL, Domaine Saint Maurice, CS60094, Montfavet, 84143, France
| | - Guillaume Roch
- INRAE UR1052 GAFL, Domaine Saint Maurice, CS60094, Montfavet, 84143, France
- CEP INNOVATION, 23 Rue Jean Baldassini, Lyon, 69364, Cedex 07, France
| | - Patrick Lambert
- INRAE UR1052 GAFL, Domaine Saint Maurice, CS60094, Montfavet, 84143, France
| | - Tetyana Zhebentyayeva
- The Schatz Center for Tree Molecular Genetics, Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, 16802, PA, USA
| | - Wei-Sheng Liu
- Liaoning Institute of Pomology, Tiedong Street, Xiongyue, Bayuquan District, Yingkou City, 115009, Liaoning, China
| | - Olivier Bouchez
- INRAE, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, 31326, France
| | | | - Rémy-Félix Serre
- INRAE, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, 31326, France
| | - Robert Debuchy
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, 91198, France
| | - Joseph Tran
- EGFV, Bordeaux Sciences Agro, INRAE, Univ. Bordeaux, ISVV, Villenave d'Ornon, 33882, France
| | - Patrick Wincker
- Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, 2 Rue Gaston Crémieux, Evry, 91057, France
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux, Evry, 91057, France
| | - Xilong Chen
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, UMR GQE-Le Moulon, Gif-sur-Yvette, 91190, France
| | - Pierre Pétriacq
- Univ. Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, 71 Av. E. Bourlaux, Villenave d'Ornon, 33140, France
| | - Aurélien Barre
- Univ. Bordeaux, Centre de Bioinformatique de Bordeaux (CBiB), Bordeaux, 33076, France
| | - Macha Nikolski
- Univ. Bordeaux, Centre de Bioinformatique de Bordeaux (CBiB), Bordeaux, 33076, France
- Univ. Bordeaux, CNRS, IBGC, UMR 5095, Bordeaux, 33077, France
| | - Jean-Marc Aury
- Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, 2 Rue Gaston Crémieux, Evry, 91057, France
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux, Evry, 91057, France
| | - Albert Glenn Abbott
- Forest Health Research and Education Center, University of Kentucky, Lexington, KY, USA
| | - Tatiana Giraud
- Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay AgroParisTech, Orsay, 91400, France.
| | - Véronique Decroocq
- Univ. Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, 71 Av. E. Bourlaux, Villenave d'Ornon, 33140, France.
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105
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Feng Y, Yuan X, Wang Y, Yang Y, Zhang M, Yu H, Xu Q, Wang S, Niu X, Wei X. Validation of a QTL for Grain Size and Weight Using an Introgression Line from a Cross between Oryza sativa and Oryza minuta. RICE (NEW YORK, N.Y.) 2021; 14:43. [PMID: 34014427 PMCID: PMC8137761 DOI: 10.1186/s12284-021-00472-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 03/10/2021] [Indexed: 05/28/2023]
Abstract
BACKGROUND Grain size and weight are important target traits determining grain yield and quality in rice. Wild rice species possess substantial elite genes that can be served as an important resource for genetic improvement of rice. In this study, we identify and validate a novel QTL on chromosome 7 affecting the grain size and weight using introgression lines from cross of Oryza sativa and Oryza minuta. RESULTS An introgression line 'IL188' has been achieved from a wild species Oryza minuta (2n = 48, BBCC, W303) into O. sativa japonica Nipponbare. The F2 and F2:3 populations derived from a cross between IL188 and Nipponbare were used to map QTLs for five grain size traits, including grain length (GL), grain width (GW), grain length to width ratio (LWR), grain thickness (GT) and thousand grain weight (TGW). A total of 12 QTLs for the five grain traits were identified on chromosomes 1, 2, 3, 6, 7, and 8. The QTL-qGL7 controlling GL on chromosome 7 was detected stably in the F2 and F2:3 populations, and explained 15.09-16.30% of the phenotypic variance. To validate the effect of qGL7, eight residual heterozygous line (RHL) populations were developed through selfing four F2:3 and four F2:4 plants with different heterozygous segments for the target region. By further developing SSR and Indel markers in the target interval, qGL7 was delimited to a ~ 261 kb region between Indel marker Y7-12 and SSR marker Y7-38, which also showed significant effects on grain width and thousand grain weight. Comparing with the reference genome of Nipponbare, stop or frameshift mutations in the exon of the three putative genes LOC_Os07g36830, LOC_Os07g36900 and LOC_Os07g36910 encoding F-box domain-containing proteins may be the candidate genes for qGL7. Scanning electron microscopy analysis of the glume's epidermal cells showed that the cell length and width of NIL-qGL7IL188 was higher than NIL-qGL7Nip, indicating that qGL7 increases grain size and weight by regulating cell expansion. CONCLUSIONS In this study, we detected 12 QTLs regulating grain size and weight using an introgression line from a cross between Oryza sativa and Oryza minuta. Of these loci, we confirmed and delimited the qGL7 to a ~ 261 kb region. Three putative genes, LOC_Os07g36830, LOC_Os07g36900 and LOC_Os07g36910 encoding F-box domain-containing proteins may be the candidate genes for qGL7. These results provide a basis for map-based cloning of the qGL7 gene and useful information for marker assisted selection in rice grain quality improvement.
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Affiliation(s)
- Yue Feng
- Chinese National Center for Rice Improvement and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
| | - Xiaoping Yuan
- Chinese National Center for Rice Improvement and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Yiping Wang
- Chinese National Center for Rice Improvement and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Yaolong Yang
- Chinese National Center for Rice Improvement and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Mengchen Zhang
- Chinese National Center for Rice Improvement and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Hanyong Yu
- Chinese National Center for Rice Improvement and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Qun Xu
- Chinese National Center for Rice Improvement and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Shan Wang
- Chinese National Center for Rice Improvement and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Xiaojun Niu
- Chinese National Center for Rice Improvement and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Xinghua Wei
- Chinese National Center for Rice Improvement and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
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106
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Mapping QTLs for yield component traits using overwintering cultivated rice. J Genet 2021. [DOI: 10.1007/s12041-021-01279-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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107
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Selvaraj R, Singh AK, Singh VK, Abbai R, Habde SV, Singh UM, Kumar A. Superior haplotypes towards development of low glycemic index rice with preferred grain and cooking quality. Sci Rep 2021; 11:10082. [PMID: 33980871 PMCID: PMC8115083 DOI: 10.1038/s41598-021-87964-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 03/19/2021] [Indexed: 02/03/2023] Open
Abstract
Increasing trends in the occurrence of diabetes underline the need to develop low glycemic index (GI) rice with preferred grain quality. In the current study, a diverse set of 3 K sub-panel of rice consisting of 150 accessions was evaluated for resistant starch and predicted glycemic index, including nine other quality traits under transplanted situation. Significant variations were noticed among the accessions for the traits evaluated. Trait associations had shown that amylose content possess significant positive and negative association with resistant starch and predicted glycemic index. Genome-wide association studies with 500 K SNPs based on MLM model resulted in a total of 41 marker-trait associations (MTAs), which were further confirmed and validated with mrMLM multi-locus model. We have also determined the allelic effect of identified MTAs for 11 targeted traits and found favorable SNPs for 8 traits. A total of 11 genes were selected for haplo-pheno analysis to identify the superior haplotypes for the target traits where haplotypes ranges from 2 (Os10g0469000-GC) to 15 (Os06g18720-AC). Superior haplotypes for RS and PGI, the candidate gene Os06g11100 (H4-3.28% for high RS) and Os08g12590 (H13-62.52 as intermediate PGI). The identified superior donors possessing superior haplotype combinations may be utilized in Haplotype-based breeding to developing next-generation tailor-made high quality healthier rice varieties suiting consumer preference and market demand.
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Affiliation(s)
- Ramchander Selvaraj
- IRRI South Asia Hub (IRRI-SAH), ICRISAT Campus, Patancheru, Hyderabad, India
| | - Arun Kumar Singh
- IRRI South Asia Hub (IRRI-SAH), ICRISAT Campus, Patancheru, Hyderabad, India
| | - Vikas Kumar Singh
- IRRI South Asia Hub (IRRI-SAH), ICRISAT Campus, Patancheru, Hyderabad, India
| | - Ragavendran Abbai
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Sonali Vijay Habde
- South-Asia Regional Centre (SARC), International Rice Research Institute (IRRI), Varanasi, India
| | - Uma Maheshwar Singh
- South-Asia Regional Centre (SARC), International Rice Research Institute (IRRI), Varanasi, India
| | - Arvind Kumar
- IRRI South Asia Hub (IRRI-SAH), ICRISAT Campus, Patancheru, Hyderabad, India.
- South-Asia Regional Centre (SARC), International Rice Research Institute (IRRI), Varanasi, India.
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108
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Wang J, Wu X, Yue W, Zhao C, Yang J, Zhou M. Identification of QTL for barley grain size. PeerJ 2021; 9:e11287. [PMID: 33986999 PMCID: PMC8088763 DOI: 10.7717/peerj.11287] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 03/25/2021] [Indexed: 01/22/2023] Open
Abstract
Background Barley grain size is one of the key factors determining storage capacity during grain filling. Large, well-filled grains also have a high malt extract potential. Grain size is a complex quantitative trait and can be easily affected by environmental factors thus the identification of genes controlling the trait and the use of molecular markers linked to the genes in breeding program is the most effective way of improving grain size. Methods Grain sizes of 188 doubled-haploid (DH) lines derived from the cross of a Japanese malting barley variety (Naso Nijo) and a Chinese feed barley variety (TX9425) were obtained from three different sites in two consecutive years. The average data were used for identifying QTL for grain size. Results A total of four significant QTL were identified for grain length (GL) and three for grain width (GW). The two major GL QTL are located at similar positions to the QTL for malt extract on 2H and uzu gene on 3H, respectively. However, the GL QTL on 2H is more likely a different one from the malt extract QTL as most of the candidate genes are located outside the fine mapped QTL region for malt extract. The GL QTL on 3H is closely linked with uzu gene but not due to a pleiotropic effect of uzu. The three QTL for grain width on 1H, 2H and 5H, respectively, were located at same position to those for GL.
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Affiliation(s)
- Junmei Wang
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xiaojian Wu
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Wenhao Yue
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Chenchen Zhao
- Tasmanian Institute of Agriculture, University of Tasmania, Prospect, TAS, Australia
| | - Jianming Yang
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Meixue Zhou
- Tasmanian Institute of Agriculture, University of Tasmania, Prospect, TAS, Australia
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109
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Liang P, Wang H, Zhang Q, Zhou K, Li M, Li R, Xiang S, Zhang T, Ling Y, Yang Z, He G, Zhao F. Identification and Pyramiding of QTLs for Rice Grain Size Based on Short-Wide Grain CSSL-Z563 and Fine-Mapping of qGL3-2. RICE (NEW YORK, N.Y.) 2021; 14:35. [PMID: 33847838 PMCID: PMC8044274 DOI: 10.1186/s12284-021-00477-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 03/26/2021] [Indexed: 05/25/2023]
Abstract
BACKGROUND Chromosome segment substitution lines (CSSLs) can be used to dissect complex traits, from which single-segment substitution lines (SSSLs) containing a target quantitative trait loci (QTL) can be developed, and they are thus important for functional analysis and molecular breeding. RESULTS A rice line with short wide grains, CSSL-Z563, was isolated from advanced-generation backcross population (BC3F6) derived from 'Xihui 18' (the recipient parent) and 'Huhan 3' (the donor parent). Z563 carried seven segments from 'Huhan 3', distributed on chromosomes 3, 7, and 8, with average substitution length of 5.52 Mb. Eleven QTLs for grain size were identified using secondary F2 population of 'Xihui 18'/Z563. The QTLs qGL3-1, qGL3-2, and qGL7 control grain length in Z563 and have additive effects to reduce grain length; qGW3-1 and qGW3-2 control grain width in Z563 and have additive effects to increase grain width. Four SSSLs, three double-segment substitution lines (D1-D3), and two triple-segment substitution lines (T1 and T2) were developed containing the target QTLs. The genetic stability of eight QTLs, including qGL3-2, qGL3-1, and qGL7, was verified by the SSSLs. D1 (containing qGL3-2 and qGL3-1), D2 (qGL3-1 and qGL7), and T1 (qGL3-2, qGL3-1, and qGL7) had positive epistatic effects on grain length, and their grain length was shorter than that of the corresponding SSSLs. The QTL qGL3-2 was fine-mapped to a 696 Kb region of chromosome 3 containing five candidate genes that differed between 'Xihui 18' and Z563. These results are important for functional research on qGL3-2 and molecular breeding of hybrid rice cultivars. CONCLUSIONS The short and wide grain of Z563 was mainly controlled by qGL3-1, qGL3-2, qGL7, qGW3-1 and qGW3-2. The major QTL qGL3-2 was fine-mapped to a 696 Kb region of chromosome 3 containing five candidate genes. Different QTLs pyramiding displayed various phenotypes. In essence, the performance after pyramiding of genes depended on the comparison between the algebraic sum of the additive and epistatic effects of QTLs in the pyramidal line and the additive effect value of the single QTL. The results lay good foundation in the functional analysis of qGL3-2 and molecular design breeding of novel hybrid rice cultivars.
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Affiliation(s)
- Peixuan Liang
- Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Hui Wang
- Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Qiuli Zhang
- Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Kai Zhou
- Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Miaomiao Li
- Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Ruxiang Li
- Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Siqian Xiang
- Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Ting Zhang
- Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Yinghua Ling
- Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Zhenglin Yang
- Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Guanghua He
- Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Fangming Zhao
- Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China.
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Usman B, Zhao N, Nawaz G, Qin B, Liu F, Liu Y, Li R. CRISPR/Cas9 Guided Mutagenesis of Grain Size 3 Confers Increased Rice ( Oryza sativa L.) Grain Length by Regulating Cysteine Proteinase Inhibitor and Ubiquitin-Related Proteins. Int J Mol Sci 2021; 22:ijms22063225. [PMID: 33810044 PMCID: PMC8004693 DOI: 10.3390/ijms22063225] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/19/2021] [Accepted: 03/20/2021] [Indexed: 12/21/2022] Open
Abstract
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated protein (Cas9)-mediated genome editing has become an important way for molecular breeding in crop plants. To promote rice breeding, we edited the Grain Size 3 (GS3) gene for obtaining valuable and stable long-grain rice mutants. Furthermore, isobaric tags for the relative and absolute quantitation (iTRAQ)-based proteomic method were applied to determine the proteome-wide changes in the GS3 mutants compared with wild type (WT). Two target sites were designed to construct the vector, and the Agrobacterium-mediated method was used for rice transformation. Specific mutations were successfully introduced, and the grain length (GL) and 1000-grain weight (GWT) of the mutants were increased by 31.39% and 27.15%, respectively, compared with WT. The iTRAQ-based proteomic analysis revealed that a total of 31 proteins were differentially expressed in the GS3 mutants, including 20 up-regulated and 11 down-regulated proteins. Results showed that differentially expressed proteins (DEPs) were mainly related to cysteine synthase, cysteine proteinase inhibitor, vacuolar protein sorting-associated, ubiquitin, and DNA ligase. Furthermore, functional analysis revealed that DEPs were mostly enriched in cellular process, metabolic process, binding, transmembrane, structural, and catalytic activities. Pathway enrichment analysis revealed that DEPs were mainly involved in lipid metabolism and oxylipin biosynthesis. The protein-to-protein interaction (PPI) network found that proteins related to DNA damage-binding, ubiquitin-40S ribosomal, and cysteine proteinase inhibitor showed a higher degree of interaction. The homozygous mutant lines featured by stable inheritance and long-grain phenotype were obtained using the CRISPR/Cas9 system. This study provides a convenient and effective way of improving grain yield, which could significantly accelerate the breeding process of long-grain japonica parents and promote the development of high-yielding rice.
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Affiliation(s)
- Babar Usman
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (B.U.); (N.Z.); (G.N.); (B.Q.); (F.L.)
| | - Neng Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (B.U.); (N.Z.); (G.N.); (B.Q.); (F.L.)
| | - Gul Nawaz
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (B.U.); (N.Z.); (G.N.); (B.Q.); (F.L.)
| | - Baoxiang Qin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (B.U.); (N.Z.); (G.N.); (B.Q.); (F.L.)
| | - Fang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (B.U.); (N.Z.); (G.N.); (B.Q.); (F.L.)
| | - Yaoguang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agricultural Bioresources, South China Agricultural University, Guangzhou 510642, China
- Correspondence: (Y.L.); (R.L.); Tel.: +86-20-8528-1908 (Y.L.); +86-136-0009-4135 (R.L.)
| | - Rongbai Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (B.U.); (N.Z.); (G.N.); (B.Q.); (F.L.)
- Correspondence: (Y.L.); (R.L.); Tel.: +86-20-8528-1908 (Y.L.); +86-136-0009-4135 (R.L.)
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Zhu X, Zhang S, Chen Y, Mou C, Huang Y, Liu X, Ji J, Yu J, Hao Q, Yang C, Cai M, Nguyen T, Song W, Wang P, Dong H, Liu S, Jiang L, Wan J. Decreased grain size1, a C3HC4-type RING protein, influences grain size in rice (Oryza sativa L.). PLANT MOLECULAR BIOLOGY 2021; 105:405-417. [PMID: 33387175 DOI: 10.1007/s11103-020-01096-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 11/08/2020] [Indexed: 05/16/2023]
Abstract
We reported that DGS1 plays a positive role in regulating grain size in rice and was regulated by OsBZR1. Grain size is an important agronomic trait that contributes to grain yield. However, the underlying molecular mechanisms that determine final grain size are still largely unknown. We isolated a rice mutant showing reduced grain size in a 60Co-irradiated variety Nanjing 35 population. We named the mutant decreased grain size1 (dgs1). Map-based cloning and subsequent transgenic CRISPR and complementation assays indicated that a mutation had occurred in LOC_Os03g49900 and that the DGS1 allele regulated grain size. DGS1 encodes a protein with a 7-transmembrane domain and C3HC4 type RING domain. It was widely expressed, especially in young tissues. DGS1 is a membrane-located protein. OsBZR1 (BRASSINAZOLE-RESISTANT1), a core transcription activator of BR signaling, also plays a positive role in grain size. We provided preliminary evidence that OsBZR1 can bind to the DGS1 promoter to activate expression of DGS1.
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Affiliation(s)
- Xingjie Zhu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shengzhong Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yaping Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Changlin Mou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yunshuai Huang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xi Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jingli Ji
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiangfeng Yu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qixian Hao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chunyan Yang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Mengying Cai
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Thanhliem Nguyen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
- Department of Biology and Agricultural Engineering, Quynhon University, Quynhon, Binhdinh, 590000, Vietnam
| | - Weihan Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ping Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hui Dong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shijia Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ling Jiang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Jianmin Wan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China.
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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112
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Cai G, Wang G, Kim SC, Li J, Zhou Y, Wang X. Increased expression of fatty acid and ABC transporters enhances seed oil production in camelina. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:49. [PMID: 33640013 PMCID: PMC7913393 DOI: 10.1186/s13068-021-01899-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 02/09/2021] [Indexed: 05/04/2023]
Abstract
BACKGROUND Lipid transporters play an essential role in lipid delivery and distribution, but their influence on seed oil production in oilseed crops is not well studied. RESULTS Here, we examined the effect of two lipid transporters, FAX1 (fatty acid export1) and ABCA9 (ATP-binding cassette transporter subfamily A9) on oil production and lipid metabolism in the oilseed plant Camelina sativa. Overexpression (OE) of FAX1 and ABCA9 increased seed weight and size, with FAX1-OEs and ABCA9-OEs increasing seed length and width, respectively, whereas FAX1/ABCA9-OEs increasing both. FAX1-OE and ABCA9-OE displayed additive effects on seed oil content and seed yield. Also, OE of FAX1 and ABCA9 affected membrane lipid composition in developing pods, especially on phosphatidylcholine, phosphatidylethanolamine, and phosphatidylglycerol. The expression of some genes involved in seed oil synthesis, such as DGAT2, PDAT1, and LEC1, was increased in developing seeds of FAX1- and/or ABCA9-OEs. CONCLUSION These results indicate that increased expression of FAX1 and ABCA9 can potentially be applied to improving camelina oil production.
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Affiliation(s)
- Guangqin Cai
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062 Hubei China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 Hubei China
- Department of Biology, University of Missouri, St. Louis, MO 63121 USA
- Donald Danforth Plant Science Center, St. Louis, MO 63132 USA
| | - Geliang Wang
- Department of Biology, University of Missouri, St. Louis, MO 63121 USA
- Donald Danforth Plant Science Center, St. Louis, MO 63132 USA
| | - Sang-Chul Kim
- Department of Biology, University of Missouri, St. Louis, MO 63121 USA
- Donald Danforth Plant Science Center, St. Louis, MO 63132 USA
| | - Jianwu Li
- Department of Biology, University of Missouri, St. Louis, MO 63121 USA
- Donald Danforth Plant Science Center, St. Louis, MO 63132 USA
| | - Yongming Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Xuemin Wang
- Department of Biology, University of Missouri, St. Louis, MO 63121 USA
- Donald Danforth Plant Science Center, St. Louis, MO 63132 USA
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113
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Sahu G, Panda BB, Dash SK, Chandra T, Shaw BP. Cell cycle events and expression of cell cycle regulators are determining factors in differential grain filling in rice spikelets based on their spatial location on compact panicles. FUNCTIONAL PLANT BIOLOGY : FPB 2021; 48:268-285. [PMID: 33120000 DOI: 10.1071/fp20196] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 09/23/2020] [Indexed: 06/11/2023]
Abstract
Rice being a staple crop for human, its production is required to be increased significantly, particularly keeping in view the expected world's population of 9.6 billion by the year 2050. In this context, although the rice breeding programs have been successful in increasing the number of spikelets per panicle, the basal spikelets remain poorly filled, undermining the yield potential. The present study also found the grain filling to bear negative correlation with the panicle grain density. The poorly filled basal spikelets of the compact-panicle cultivars showed a lower endosperm cell division rate and ploidy status of the endosperm nuclei coupled with no significant greater expression of CYCB;1 and CYCH;1 compared with the apical spikelets, unlike that observed in the lax-panicle cultivars, which might have prevented them from overcoming apical dominance. Significantly greater expression of CYCB2;2 in the basal spikelets than in the apical spikelets might also have prevented the former to enter into endoreduplication. Furthermore, expression studies of KRPs in the caryopses revealed that a higher expression of KRP;1 and KRP;4 in the basal spikelets than in the apical spikelets of the compact-panicle cultivars could also be detrimental to grain filling in the former, as KRPs form complex primarily with CDKA-CYCD that promotes S-phase activity and G1/S transition, and thus inhibits endosperm cell division. The study indicates that targeted manipulation of expression of CYCB1;1, CYCB2;2, CYCH1;1, KRP;1 and KRP4 in the basal spikelets of the compact-panicle cultivars may significantly improve their yield performance.
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Affiliation(s)
- Gyanasri Sahu
- Abiotic Stress and Agro-Biotechnology Laboratory, Institute of Life Sciences, Nalco Square, Bhubaneswar 751023, Odisha, India
| | - Binay B Panda
- Abiotic Stress and Agro-Biotechnology Laboratory, Institute of Life Sciences, Nalco Square, Bhubaneswar 751023, Odisha, India
| | - Sushanta K Dash
- Crop Improvement Division, ICAR-National Rice Research Institute (Formerly Central Rice Research Institute), Cuttack, Odisha, India
| | - Tilak Chandra
- Abiotic Stress and Agro-Biotechnology Laboratory, Institute of Life Sciences, Nalco Square, Bhubaneswar 751023, Odisha, India
| | - Birendra P Shaw
- Abiotic Stress and Agro-Biotechnology Laboratory, Institute of Life Sciences, Nalco Square, Bhubaneswar 751023, Odisha, India; and Corresponding author.
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114
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Verma A, Prakash G, Ranjan R, Tyagi AK, Agarwal P. Silencing of an Ubiquitin Ligase Increases Grain Width and Weight in indica Rice. Front Genet 2021; 11:600378. [PMID: 33510769 PMCID: PMC7835794 DOI: 10.3389/fgene.2020.600378] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 11/27/2020] [Indexed: 11/18/2022] Open
Abstract
Many quantitative trait loci (QTLs) have been identified by molecular genetic studies which control grain size by regulating grain width, length, and/or thickness. Grain width 2 (GW2) is one such QTL that codes for a RING-type E3 ubiquitin ligase and increases grain size by regulating grain width through ubiquitin-mediated degradation of unknown substrates. A natural variation (single-nucleotide polymorphism at the 346th position) in the functional domain-coding region of OsGW2 in japonica rice genotypes has been shown to cause an increase in grain width/weight in rice. However, this variation is absent in indica rice genotypes. In this study, we report that reduced expression of OsGW2 can alter grain size, even though natural sequence variation is not responsible for increased grain size in indica rice genotypes. OsGW2 shows high expression in seed development stages and the protein localizes to the nucleus and cytoplasm. Downregulation of OsGW2 by RNAi technology results in wider and heavier grains. Microscopic observation of grain morphology suggests that OsGW2 determines grain size by influencing both cell expansion and cell proliferation in spikelet hull. Using transcriptome analysis, upregulated genes related to grain size regulation have been identified among 1,426 differentially expressed genes in an OsGW2_RNAi transgenic line. These results reveal that OsGW2 is a negative regulator of grain size in indica rice and affects both cell number and cell size in spikelet hull.
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Affiliation(s)
- Ankit Verma
- National Institute of Plant Genome Research, New Delhi, India
| | - Geeta Prakash
- National Institute of Plant Genome Research, New Delhi, India.,Department of Botany, Gargi College, University of Delhi, New Delhi, India
| | - Rajeev Ranjan
- National Institute of Plant Genome Research, New Delhi, India.,Department of Plant Molecular Biology, University of Delhi, New Delhi, India
| | - Akhilesh K Tyagi
- National Institute of Plant Genome Research, New Delhi, India.,Department of Plant Molecular Biology, University of Delhi, New Delhi, India
| | - Pinky Agarwal
- National Institute of Plant Genome Research, New Delhi, India
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115
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Pan YH, Gao LJ, Liang YT, Zhao Y, Liang HF, Chen WW, Yang XH, Qing DJ, Gao J, Wu H, Huang J, Zhou WY, Huang CC, Dai GX, Deng GF. OrMKK3 Influences Morphology and Grain Size in Rice. JOURNAL OF PLANT BIOLOGY = SINGMUL HAKHOE CHI 2021; 66:269-282. [PMID: 33424241 PMCID: PMC7780602 DOI: 10.1007/s12374-020-09290-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 11/15/2020] [Accepted: 11/18/2020] [Indexed: 05/28/2023]
Abstract
Although morphology and grain size are important to rice growth and yield, the identity of abundant natural allelic variations that determine agronomically important differences in crops is unknown. Here, we characterized the function of mitogen-activated protein kinase 3 from Oryza officinalis Wall. ex Watt encoded by OrMKK3. Different alternative splicing variants occurred in OrMKK3. Green fluorescent protein (GFP)-OrMKK3 fusion proteins localized to the cell membrane and nuclei of rice protoplasts. Overexpression of OrMKK3 influenced the expression levels of the grain size-related genes SMG1, GW8, GL3, GW2, and DEP3. Phylogenetic analysis showed that OrMKK3 is well conserved in plants while showing large amounts of variation between indica, japonica, and wild rice. In addition, OrMKK3 slightly influenced brassinosteroid (BR) responses and the expression levels of BR-related genes. Our findings thus identify a new gene, OrMKK3, influencing morphology and grain size and that represents a possible link between mitogen-activated protein kinase and BR response pathways in grain growth. Supplementary Information The online version contains supplementary material available at 10.1007/s12374-020-09290-2.
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Affiliation(s)
- Ying Hua Pan
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, 530007 China
| | - Li Jun Gao
- Guangxi Academy of Agricultural Sciences/Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Nanning, 530007 China
| | - Yun Tao Liang
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, 530007 China
| | - Yan Zhao
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, 271018 Shandong China
| | - Hai Fu Liang
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, 530007 China
| | - Wei Wei Chen
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, 530007 China
| | - Xing Hai Yang
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, 530007 China
| | - Dong Jin Qing
- Guangxi Academy of Agricultural Sciences/Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Nanning, 530007 China
| | - Ju Gao
- Guangxi Academy of Agricultural Sciences/Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Nanning, 530007 China
| | - Hao Wu
- Guangxi Academy of Agricultural Sciences/Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Nanning, 530007 China
| | - Juan Huang
- Guangxi Academy of Agricultural Sciences/Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Nanning, 530007 China
| | - Wei Yong Zhou
- Guangxi Academy of Agricultural Sciences/Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Nanning, 530007 China
| | - Cheng Cui Huang
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, 530007 China
| | - Gao Xing Dai
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, 530007 China
| | - Guo Fu Deng
- Guangxi Academy of Agricultural Sciences/Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Nanning, 530007 China
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116
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Zhao J, He Y, Huang S, Wang Z. Advances in the Identification of Quantitative Trait Loci and Genes Involved in Seed Vigor in Rice. FRONTIERS IN PLANT SCIENCE 2021; 12:659307. [PMID: 34335643 PMCID: PMC8316977 DOI: 10.3389/fpls.2021.659307] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/22/2021] [Indexed: 05/08/2023]
Abstract
Seed vigor is a complex trait, including the seed germination, seedling emergence, and growth, as well as seed storability and stress tolerance, which is important for direct seeding in rice. Seed vigor is established during seed development, and its level is decreased during seed storage. Seed vigor is influenced by genetic and environmental factors during seed development, storage, and germination stages. A lot of factors, such as nutrient reserves, seed dying, seed dormancy, seed deterioration, stress conditions, and seed treatments, will influence seed vigor during seed development to germination stages. This review highlights the current advances on the identification of quantitative trait loci (QTLs) and regulatory genes involved in seed vigor at seed development, storage, and germination stages in rice. These identified QTLs and regulatory genes will contribute to the improvement of seed vigor by breeding, biotechnological, and treatment approaches.
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Pan Y, Chen L, Zhao Y, Guo H, Li J, Rashid MAR, Lu C, Zhou W, Yang X, Liang Y, Wu H, Qing D, Gao L, Dai G, Li D, Deng G. Natural Variation in OsMKK3 Contributes to Grain Size and Chalkiness in Rice. FRONTIERS IN PLANT SCIENCE 2021; 12:784037. [PMID: 34899812 PMCID: PMC8655879 DOI: 10.3389/fpls.2021.784037] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 11/03/2021] [Indexed: 05/17/2023]
Abstract
Rice (Oryza sativa L.) is an important staple food crop for more than half of the world's population. Enhancing the grain quality and yield of rice to meet growing demand remains a major challenge. Here, we show that OsMKK3 encode a MAP kinase kinase that controls grain size and chalkiness by affecting cell proliferation in spikelet hulls. We showed that OsSPL16, GS5, and GIF1 have a substantial effect on the OsMKK3-regulated grain size pathway. OsMKK3 has experienced strong directional selection in indica and japonica. Wild rice accessions contained four OsMKK3 haplotypes, suggesting that the OsMKK3 haplotypes present in cultivated rice likely originated from different wild rice accessions during rice domestication. OsMKK3-Hap1, gs3, and gw8 were polymerized to enhance the grain length. Polymerization of beneficial alleles, such as OsMKK3-Hap1, gs3, gw8, fgr, alk, chalk5, and wx, also improved the quality of hybrid rice. Overall, the results indicated that beneficial OsMKK3 alleles could be used for genomic-assisted breeding for rice cultivar improvement and be polymerized with other beneficial alleles.
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Affiliation(s)
- Yinghua Pan
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Lei Chen
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Yan Zhao
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, China
| | - Haifeng Guo
- Beijing Key Laboratory of Crop Genetic Improvement, State Key Laboratory of Agrobiotechnology, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Jingcheng Li
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | | | - Chunju Lu
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Weiyong Zhou
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Xingka Yang
- Guangxi Lvhai Seed Co., Ltd., Nanning, China
| | - Yuntao Liang
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Hao Wu
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Dongjing Qing
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Lijun Gao
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Guangxi Academy of Agricultural Sciences, Nanning, China
- *Correspondence: Lijun Gao,
| | - Gaoxing Dai
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
- Gaoxing Dai,
| | - Danting Li
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
- Danting Li,
| | - Guofu Deng
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Guangxi Academy of Agricultural Sciences, Nanning, China
- Guofu Deng,
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Ayaad M, Han Z, Zheng K, Hu G, Abo-Yousef M, Sobeih SES, Xing Y. Bin-based genome-wide association studies reveal superior alleles for improvement of appearance quality using a 4-way MAGIC population in rice. J Adv Res 2020; 28:183-194. [PMID: 33364055 PMCID: PMC7753235 DOI: 10.1016/j.jare.2020.08.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 07/19/2020] [Accepted: 08/02/2020] [Indexed: 12/18/2022] Open
Abstract
4-way Multiparental population covered the limitations of the biparental structure. The combination of SNP and bin-GWAS showed a powerful tool for QTL mapping. qPGWC8.2 harbored a novel predicted gene for rice chalkiness quality.
Introduction The multiparental population provides us the chance to identify superior alleles controlling a trait for genetic improvement. Genome wide association studies at bin level (bin-GWAS) are expected to be more power in QTL mapping than GWAS at SNP level (SNP-GWAS). Objectives This study is to estimate genetic effects of QTL conferring grain appearance quality in rice by SNP-GWAS and bin-GWAS, compare their power in QTL mapping and identify the superior alleles of all detected QTL from 4 parents for genetic improvement. Methods A 4-way MAGIC population and its four founders were cultivated in two environments to dissect the genetic basis of rice grain appearance quality. Both SNP-GWAS and bin-GWAS were conducted for QTL mapping. Multiple comparison among 4 parental bin/alleles was used to identify the superior alleles. Results A total of 16 and 20 QTL associated with grain appearance quality were identified by SNP- and bin-GWAS, respectively. A minor chalkiness QTL qPGWC8.2/qDEC8 was assigned to a 30-kb genomic region, in which OsMH_08T0121900 is the potential candidate gene because its encoded protein, glucan endo-1,3-beta-glucosidase precursor is involved in the starch and sucrose metabolism pathway. The superior parental alleles for GS3, GL3.1, GW5, GW7, and Chalk5 and two QTLs were almost carried by the high-quality parents Cypress and Yuejingsimiao (YJSM), while the poor-quality parent Guichao-2 (GC2) always carried the inferior alleles. The top five recombinant inbred lines with the highest quality of grain shape and chalkiness traits all carried gene combinations of superior alleles. Conclusions Both SNP- and bin-GWAS methods are encouraged for joint QTL mapping with MAGIC population. qPGWC8.2/qDEC8 is a novel candidate gene strongly associated with chalkiness. The superior alleles of GS3, GW5, GL3.1, GW7, Chalk5 and qPGWC8.2 were identified, and the pyramiding of these superior alleles is helpful to improve rice appearance quality.
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Affiliation(s)
- Mohammed Ayaad
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan 430070, China.,Plant Research Department, Nuclear Research Center, Atomic Energy Authority, Abo-Zaabal 13759, Egypt
| | - Zhongmin Han
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan 430070, China
| | - Kou Zheng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan 430070, China
| | - Gang Hu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan 430070, China
| | - Mahmoud Abo-Yousef
- Rice Research and Training Center, Agriculture Research Center, Sakha 33717, Egypt
| | - Sobeih El S Sobeih
- Plant Research Department, Nuclear Research Center, Atomic Energy Authority, Abo-Zaabal 13759, Egypt
| | - Yongzhong Xing
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan 430070, China
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Usman B, Nawaz G, Zhao N, Liao S, Qin B, Liu F, Liu Y, Li R. Programmed Editing of Rice ( Oryza sativa L.) OsSPL16 Gene Using CRISPR/Cas9 Improves Grain Yield by Modulating the Expression of Pyruvate Enzymes and Cell Cycle Proteins. Int J Mol Sci 2020; 22:E249. [PMID: 33383688 PMCID: PMC7795130 DOI: 10.3390/ijms22010249] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/21/2020] [Accepted: 12/25/2020] [Indexed: 12/17/2022] Open
Abstract
Rice (Oryza sativa L.) is one of the major crops in the world and significant increase in grain yield is constant demand for breeders to meet the needs of a rapidly growing population. The size of grains is one of major components determining rice yield and a vital trait for domestication and breeding. To increase the grain size in rice, OsSPL16/qGW8 was mutagenized through CRISPR/Cas9, and proteomic analysis was performed to reveal variations triggered by mutations. More specifically, mutants were generated with two separate guide RNAs targeting recognition sites on opposite strands and genomic insertions and deletions were characterized. Mutations followed Mendelian inheritance and homozygous and heterozygous mutants lacking any T-DNA and off-target effects were screened. The mutant lines showed a significant increase in grain yield without any change in other agronomic traits in T0, T1, and T2 generations. Proteomic screening found a total of 44 differentially expressed proteins (DEPs), out of which 33 and 11 were up and downregulated, respectively. Most of the DEPs related to pyruvate kinase, pyruvate dehydrogenase, and cell division and proliferation were upregulated in the mutant plants. Pathway analysis revealed that DEPs were enriched in the biosynthesis of secondary metabolites, pyruvate metabolism, glycolysis/gluconeogenesis, carbon metabolism, ubiquinone and other terpenoid-quinone biosynthesis, and citrate cycle. Gene Ontology (GO) analysis presented that most of the DEPs were involved in the pyruvate metabolic process and pyruvate dehydrogenase complex. Proteins related to pyruvate dehydrogenase E1 component subunit alpha-1 displayed higher interaction in the protein-protein interaction (PPI) network. Thus, the overall results revealed that CRISPR/Cas9-guided OsSPL16 mutations have the potential to boost the grain yield of rice. Additionally, global proteome analysis has broad applications for discovering molecular components and dynamic regulation underlying the targeted gene mutations.
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Affiliation(s)
- Babar Usman
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (B.U.); (G.N.); (N.Z.); (S.L.); (B.Q.); (F.L.)
| | - Gul Nawaz
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (B.U.); (G.N.); (N.Z.); (S.L.); (B.Q.); (F.L.)
| | - Neng Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (B.U.); (G.N.); (N.Z.); (S.L.); (B.Q.); (F.L.)
| | - Shanyue Liao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (B.U.); (G.N.); (N.Z.); (S.L.); (B.Q.); (F.L.)
| | - Baoxiang Qin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (B.U.); (G.N.); (N.Z.); (S.L.); (B.Q.); (F.L.)
| | - Fang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (B.U.); (G.N.); (N.Z.); (S.L.); (B.Q.); (F.L.)
| | - Yaoguang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agricultural Bioresources, South China Agricultural University, Guangzhou 510642, China
| | - Rongbai Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (B.U.); (G.N.); (N.Z.); (S.L.); (B.Q.); (F.L.)
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Chang S, Chen Y, Jia S, Li Y, Liu K, Lin Z, Wang H, Chu Z, Liu J, Xi C, Zhao H, Han S, Wang Y. Auxin apical dominance governed by the OsAsp1-OsTIF1 complex determines distinctive rice caryopses development on different branches. PLoS Genet 2020; 16:e1009157. [PMID: 33108367 PMCID: PMC7647119 DOI: 10.1371/journal.pgen.1009157] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 11/06/2020] [Accepted: 09/26/2020] [Indexed: 01/25/2023] Open
Abstract
In rice (Oryza sativa), caryopses located on proximal secondary branches (CSBs) have smaller grain size and poorer grain filling than those located on apical primary branches (CPBs), greatly limiting grain yield. However, the molecular mechanism responsible for developmental differences between CPBs and CSBs remains elusive. In this transcriptome-wide expression study, we identified the gene Aspartic Protease 1 (OsAsp1), which reaches an earlier and higher transcriptional peak in CPBs than in CSBs after pollination. Disruption of OsAsp1 expression in the heterozygous T-DNA line asp1-1+/–eliminated developmental differences between CPBs and CSBs. OsAsp1 negatively regulated the transcriptional inhibitor of auxin biosynthesis, OsTAA1 transcriptional inhibition factor 1 (OsTIF1), to preserve indole-3-acetic acid (IAA) apical dominance in CPBs and CSBs. IAA also facilitated OsTIF1 translocation from the endoplasmic reticulum (ER) to the nucleus by releasing the interaction of OsTIF1 with OsAsp1 to regulate caryopses IAA levels via a feedback loop. IAA promoted transcription of OsAsp1 through MADS29 to maintain an OsAsp1 differential between CPBs and CSBs during pollination. Together, these findings provide a mechanistic explanation for the distributed auxin differential between CPBs and CSBs to regulate distinct caryopses development in different rice branches and potential targets for engineering yield improvement in crops. Rice is a major food crop and an important model plant. Compared with caryopses on apical primary branches (CPBs) of rice, those located on proximal secondary branches (CSBs) display smaller grains and poor grain filling, which greatly limit rice yield potential fulfilment, especially among ‘super’ rice cultivars. In this study, we demonstrated that high indole-3-acetic (IAA) levels upregulated Aspartic Protease 1 (OsAsp1) transcription via MADS29 post-pollination to produce higher OsAsp1 levels in CPBs than in CSBs. OsAsp1 then interacted with OsTAA1 transcriptional inhibition factor 1 (OsTIF1) in the endoplasmic reticulum (ER) to dispel OsTIF1 transcriptional inhibition of OsTAA1, causing IAA content to peak in CPBs at 5 days after fertilisation (DAF). IAA facilitated OsTIF1 translocation from the ER to the nucleus by reducing its interaction with OsAsp1 as feedback regulation of IAA levels in caryopses. Thus, differential auxin levels between CPBs and CSBs are determined by the OsAsp1-OsTIF1 complex, and are essential for the distinct development of CPBs and CSBs, providing potential targets for engineering yield improvement in crops.
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Affiliation(s)
- Shu Chang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, China
| | - Yixing Chen
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, China
| | - Shenghua Jia
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, China
| | - Yihao Li
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, China
| | - Kun Liu
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, China
| | - Zhouhua Lin
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, China
| | - Hanmeng Wang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, China
| | - Zhilin Chu
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, China
| | - Jin Liu
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, China
| | - Chao Xi
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, China
| | - Heping Zhao
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, China
| | - Shengcheng Han
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, China
- Academy of Plateau Science and Sustainability of the People's Government of Qinghai Province & Beijing Normal University, Qinghai Normal University, Qinghai, China
- * E-mail: (SH); (YW)
| | - Yingdian Wang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, China
- Academy of Plateau Science and Sustainability of the People's Government of Qinghai Province & Beijing Normal University, Qinghai Normal University, Qinghai, China
- * E-mail: (SH); (YW)
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Zou G, Zhai G, Yan S, Li S, Zhou L, Ding Y, Liu H, Zhang Z, Zou J, Zhang L, Chen J, Xin Z, Tao Y. Sorghum qTGW1a encodes a G-protein subunit and acts as a negative regulator of grain size. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5389-5401. [PMID: 32497208 DOI: 10.1093/jxb/eraa277] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 05/28/2020] [Indexed: 06/11/2023]
Abstract
Grain size is a major determinant of grain yield in sorghum and other cereals. Over 100 quantitative trait loci (QTLs) of grain size have been identified in sorghum. However, no gene underlying any grain size QTL has been cloned. Here, we describe the fine mapping and cloning of one grain size QTL. From an F8 recombinant inbred line population derived from a cross between inbred lines 654 and LTR108, we identified 44 grain size QTLs. One QTL, qTGW1a, was detected consistently on the long arm of chromosome 1 in the span of 4 years. Using the extreme recombinants from an F2:3 fine-mapping population, qTGW1a was delimited within a ~33 kb region containing three predicted genes. One of them, SORBI_3001G341700, predicted to encode a G-protein γ subunit and homologous to GS3 in rice, is likely to be the causative gene for qTGW1a. qTGW1a appears to act as a negative regulator of grain size in sorghum. The functional allele of the putatively causative gene of qTGW1a from inbred line 654 decreased grain size, plant height, and grain yield in transgenic rice. Identification of the gene underlying qTGW1a advances our understanding of the regulatory mechanisms of grain size in sorghum and provides a target to manipulate grain size through genome editing.
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Affiliation(s)
- Guihua Zou
- Institute of Crop and Nuclear Technology Utilization, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Guowei Zhai
- Institute of Crop and Nuclear Technology Utilization, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Song Yan
- Rice National Engineering Laboratory, Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, China
| | - Sujuan Li
- Institute of Crop and Nuclear Technology Utilization, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Lengbo Zhou
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Yanqing Ding
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Heqin Liu
- Institute of Crop and Nuclear Technology Utilization, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zhipeng Zhang
- Chinese National Sorghum Improvement Center, Liaoning Academy of Agricultural Sciences, Shenyang, China
| | - Jianqiu Zou
- Chinese National Sorghum Improvement Center, Liaoning Academy of Agricultural Sciences, Shenyang, China
| | - Liyi Zhang
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Junping Chen
- Plant Stress & Germplasm Development Unit, Cropping Systems Research Laboratory, USDA-ARS, Lubbock, TX, USA
| | - Zhanguo Xin
- Plant Stress & Germplasm Development Unit, Cropping Systems Research Laboratory, USDA-ARS, Lubbock, TX, USA
| | - Yuezhi Tao
- Institute of Crop and Nuclear Technology Utilization, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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Zhang L, Ma B, Bian Z, Li X, Zhang C, Liu J, Li Q, Liu Q, He Z. Grain Size Selection Using Novel Functional Markers Targeting 14 Genes in Rice. RICE (NEW YORK, N.Y.) 2020; 13:63. [PMID: 32902771 PMCID: PMC7481322 DOI: 10.1186/s12284-020-00427-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 09/02/2020] [Indexed: 05/19/2023]
Abstract
BACKGROUND Grain size is an extremely important aspect of rice breeding, affecting both grain yield and quality traits. It is controlled by multiple genes and tracking these genes in breeding schemes should expedite selection of lines with superior grain yield and quality, thus it is essential to develop robust, efficient markers. RESULT In this study, 14 genes related to grain size (GW2, GS2, qLGY3, GS3, GL3.1, TGW3, GS5, GW5, GS6, TGW6, GW6a, GLW7, GL7 and GW8) were selected for functional marker development. Twenty-one PCR-gel-based markers were developed to genotype the candidate functional nucleotide polymorphisms (FNPs) of these genes, and all markers can effectively recognize the corresponding allele types. To test the allele effects of different FNPs, a global collection of rice cultivars including 257 accessions from the Rice Diversity Panel 1 was used for allele mining, and four grain-size-related traits were investigated at two planting locations. Three FNPs for GW2, GS2 and GL3.1 were genotyped as rare alleles only found in cultivars with notably large grains, and the allele contributions of the remaining FNPs were clarified in both the indica and japonica subspecies. Significant trait contributions were found for most of the FNPs, especially GS3, GW5 and GL7. Of note, GW5 could function as a key regulator to coordinate the performance of other grain size genes. The allele effects of several FNPs were also tested by QTL analysis using an F2 population, and GW5 was further identified as the major locus with the largest contribution to grain width and length to width ratio. CONCLUSIONS The functional markers are robust for genotyping different cultivars and may facilitate the rational design of grain size to achieve a balance between grain yield and quality in future rice breeding efforts.
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Affiliation(s)
- Lin Zhang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding /Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009 China
| | - Bin Ma
- School of Life Science and Technology, Shanghai Tech University, Shanghai, 201210 China
| | - Zhong Bian
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding /Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009 China
| | - Xiaoyuan Li
- School of Life Science and Technology, Shanghai Tech University, Shanghai, 201210 China
| | - Changquan Zhang
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009 China
| | - Jiyun Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, 200032 China
| | - Qun Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, 200032 China
| | - Qiaoquan Liu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding /Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009 China
| | - Zuhua He
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009 China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, 200032 China
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Lo S, Cheng M, Hsing YC, Chen Y, Lee K, Hong Y, Hsiao Y, Hsiao A, Chen P, Wong L, Chen N, Reuzeau C, Ho TD, Yu S. Rice Big Grain 1 promotes cell division to enhance organ development, stress tolerance and grain yield. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:1969-1983. [PMID: 32034845 PMCID: PMC7415788 DOI: 10.1111/pbi.13357] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 01/07/2020] [Accepted: 01/19/2020] [Indexed: 05/18/2023]
Abstract
Grain/seed yield and plant stress tolerance are two major traits that determine the yield potential of many crops. In cereals, grain size is one of the key factors affecting grain yield. Here, we identify and characterize a newly discovered gene Rice Big Grain 1 (RBG1) that regulates grain and organ development, as well as abiotic stress tolerance. Ectopic expression of RBG1 leads to significant increases in the size of not only grains but also other major organs such as roots, shoots and panicles. Increased grain size is primarily due to elevated cell numbers rather than cell enlargement. RBG1 is preferentially expressed in meristematic and proliferating tissues. Ectopic expression of RBG1 promotes cell division, and RBG1 co-localizes with microtubules known to be involved in cell division, which may account for the increase in organ size. Ectopic expression of RBG1 also increases auxin accumulation and sensitivity, which facilitates root development, particularly crown roots. Moreover, overexpression of RBG1 up-regulated a large number of heat-shock proteins, leading to enhanced tolerance to heat, osmotic and salt stresses, as well as rapid recovery from water-deficit stress. Ectopic expression of RBG1 regulated by a specific constitutive promoter, GOS2, enhanced harvest index and grain yield in rice. Taken together, we have discovered that RBG1 regulates two distinct and important traits in rice, namely grain yield and stress tolerance, via its effects on cell division, auxin and stress protein induction.
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Affiliation(s)
- Shuen‐Fang Lo
- Institute of Molecular BiologyAcademia SinicaNankangTaipeiTaiwan, ROC
- Biotechnology CenterNational Chung Hsing UniversityTaichungTaiwan, ROC
| | - Ming‐Lung Cheng
- Institute of Molecular BiologyAcademia SinicaNankangTaipeiTaiwan, ROC
- Department of Life SciencesNational Cheng Kung UniversityTainanTaiwan, ROC
| | | | - Yi‐Shih Chen
- Institute of Molecular BiologyAcademia SinicaNankangTaipeiTaiwan, ROC
| | - Kuo‐Wei Lee
- Institute of Molecular BiologyAcademia SinicaNankangTaipeiTaiwan, ROC
| | - Ya‐Fang Hong
- Institute of Plant and Microbial BiologyAcademia SinicaNankangTaipeiTaiwan, ROC
| | - Yu Hsiao
- Institute of Molecular BiologyAcademia SinicaNankangTaipeiTaiwan, ROC
| | - An‐Shan Hsiao
- Institute of Plant and Microbial BiologyAcademia SinicaNankangTaipeiTaiwan, ROC
| | - Pei‐Jing Chen
- Institute of Molecular BiologyAcademia SinicaNankangTaipeiTaiwan, ROC
- Biotechnology CenterNational Chung Hsing UniversityTaichungTaiwan, ROC
| | - Lai‐In Wong
- Institute of Molecular BiologyAcademia SinicaNankangTaipeiTaiwan, ROC
- Biotechnology CenterNational Chung Hsing UniversityTaichungTaiwan, ROC
| | - Nan‐Chen Chen
- Institute of Molecular BiologyAcademia SinicaNankangTaipeiTaiwan, ROC
- Institute of Plant and Microbial BiologyAcademia SinicaNankangTaipeiTaiwan, ROC
| | | | - Tuan‐Hua David Ho
- Biotechnology CenterNational Chung Hsing UniversityTaichungTaiwan, ROC
- Department of Life SciencesNational Cheng Kung UniversityTainanTaiwan, ROC
- Institute of Plant and Microbial BiologyAcademia SinicaNankangTaipeiTaiwan, ROC
- Department of Life SciencesNational Chung Hsing UniversityTaichungTaiwan, ROC
| | - Su‐May Yu
- Institute of Molecular BiologyAcademia SinicaNankangTaipeiTaiwan, ROC
- Biotechnology CenterNational Chung Hsing UniversityTaichungTaiwan, ROC
- Department of Life SciencesNational Cheng Kung UniversityTainanTaiwan, ROC
- Department of Life SciencesNational Chung Hsing UniversityTaichungTaiwan, ROC
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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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125
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Shi CL, Dong NQ, Guo T, Ye WW, Shan JX, Lin HX. A quantitative trait locus GW6 controls rice grain size and yield through the gibberellin pathway. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:1174-1188. [PMID: 32365409 DOI: 10.1111/tpj.14793] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 04/14/2020] [Accepted: 04/22/2020] [Indexed: 05/18/2023]
Abstract
Grain size is one of the essential components determining rice yield and is a target for both domestication and artificial breeding. Gibberellins (GAs) are diterpenoid phytohormones that influence diverse aspects of plant growth and development. Several quantitative trait loci (QTLs) have been identified that control grain size through phytohormone regulation. However, little is known about the role of GAs in the control of grain size. Here we report the cloning and characterization of a QTL, GW6 (GRAIN WIDTH 6), which encodes a GA-regulated GAST family protein and positively regulates grain width and weight. GW6 is highly expressed in the young panicle and increases grain width by promoting cell expansion in the spikelet hull. Knockout of GW6 exhibits reduced grain size and weight, whereas overexpression of GW6 results in increased grain size and weight. GW6 is induced by GA and its knockout downregulates the expression of GA biosynthesis genes and decreases GA content in the young panicle. We found that a natural variation in the cis element CAAT-box in the promoter of GW6 is associated with its expression level and grain width and weight. Furthermore, introduction of GW6 to Oryza indica variety HJX74 can lead to a 10.44% increase in rice grain yield, indicating that GW6 has great potential to improve grain yield in rice.
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Affiliation(s)
- Chuan-Lin Shi
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics and Development, Shanghai Institute of Plant Physiology and Ecology, Chinese Academic of Sciences, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Nai-Qian Dong
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics and Development, Shanghai Institute of Plant Physiology and Ecology, Chinese Academic of Sciences, Shanghai, 200032, China
| | - Tao Guo
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics and Development, Shanghai Institute of Plant Physiology and Ecology, Chinese Academic of Sciences, Shanghai, 200032, China
| | - Wang-Wei Ye
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics and Development, Shanghai Institute of Plant Physiology and Ecology, Chinese Academic of Sciences, Shanghai, 200032, China
| | - Jun-Xiang Shan
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics and Development, Shanghai Institute of Plant Physiology and Ecology, Chinese Academic of Sciences, Shanghai, 200032, China
| | - Hong-Xuan Lin
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics and Development, Shanghai Institute of Plant Physiology and Ecology, Chinese Academic of Sciences, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
- School of Life Science and Technology, Shanghai Tech University, Shanghai, 201210, China
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126
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Wang GJ, Wang Y, Ying JZ, Song XJ. Identification of qLG2, qLG8, and qWG2 as novel quantitative trait loci for grain shape and the allelic analysis in cultivated rice. PLANTA 2020; 252:18. [PMID: 32671480 DOI: 10.1007/s00425-020-03420-3] [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: 03/19/2020] [Accepted: 07/08/2020] [Indexed: 06/11/2023]
Abstract
Three novel QTLs for grain shape were genetically fine mapped, with two of which to a 250-kb target interval on rice chromosome 2 that contains fourteen candidate genes. Grain shape (grain length, width, and thickness) determines crop yield and grain quality. However, the trait is regulated by numerous naturally occurring quantitative trait loci (QTLs) and the underlying mechanism remains largely unknown. Here, we report the genetic mapping of three new QTLs, qLG2, qWG2, and qLG8 that each exerts a semi-dominant effect on grain shape in cultivated rice. These QTLs were validated using populations derived from the corresponding chromosome segment substitution lines (CSSLs), and were further delimited to small genomic intervals in progeny testing experiments. Especially, qLG2/qWG2 was placed into an about 250-kb genomic candidate region, and 14 predicted ORFs localized within the interval. We also evaluated the individual and pyramiding genetic effect(s) of these QTL(s) using the corresponding nearly isogenic lines, and found that they have additive effects on the traits. Collectively, these findings provided useful information as a tool to improve grain shape in crop breeding programs and established foundations for future QTL cloning.
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Affiliation(s)
- Gao-Jie Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, The Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ying Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, The Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jie-Zheng Ying
- National Key Laboratory of Rice Biology and Chinese Center of Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Xian-Jun Song
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, The Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, China.
- The Innovative Academy of Seed Design, The Chinese Academy of Sciences, Beijing, China.
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127
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Ruan B, Shang L, Zhang B, Hu J, Wang Y, Lin H, Zhang A, Liu C, Peng Y, Zhu L, Ren D, Shen L, Dong G, Zhang G, Zeng D, Guo L, Qian Q, Gao Z. Natural variation in the promoter of TGW2 determines grain width and weight in rice. THE NEW PHYTOLOGIST 2020; 227:629-640. [PMID: 32167575 DOI: 10.1111/nph.16540] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 03/03/2020] [Indexed: 05/10/2023]
Abstract
Understanding the genetic basis of natural variation in grain size among diverse rice varieties can help breeders develop high-yielding rice cultivars. Here, we report the discovery of qTGW2, a new semidominant quantitative trait locus for grain width and weight. The corresponding gene, TGW2, encodes CELL NUMBER REGULATOR 1 (OsCNR1) localized to the plasma membrane. A single nucleotide polymorphism (SNP) variation 1818 bp upstream of TGW2 is responsible for its different expression, leading to alteration in grain width and weight by influencing cell proliferation and expansion in glumes. TGW2 interacts with KRP1, a regulator of cell cycle in plants, to negatively regulate grain width and weight. Genetic diversity analysis of TGW2 in 141 rice accessions revealed it as a breeding target in a selective sweep region. Our findings provide new insights into the genetic mechanism underlying grain morphology and grain weight, and uncover a promising gene for improving rice yield.
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Affiliation(s)
- Banpu Ruan
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China
| | - Lianguang Shang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Bin Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Jiang Hu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China
| | - Yuexing Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China
| | - Hai Lin
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Anpeng Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China
| | - Chaolei Liu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China
| | - Youlin Peng
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China
| | - Li Zhu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China
| | - Deyong Ren
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China
| | - Lan Shen
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China
| | - Guojun Dong
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China
| | - Guangheng Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China
| | - Dali Zeng
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China
| | - Longbiao Guo
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Zhenyu Gao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China
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128
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Zhou SR, Xue HW. The rice PLATZ protein SHORT GRAIN6 determines grain size by regulating spikelet hull cell division. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:847-864. [PMID: 31207036 DOI: 10.1111/jipb.12851] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 06/13/2019] [Indexed: 05/12/2023]
Abstract
Grain size is a major determinant of cereal grain yields; however, the relevant regulatory mechanisms controlling this trait have not been fully elucidated. The rice (Oryza sativa) mutant short grain6 (sg6) was identified based on its reduced grain length and weight. Here, we functionally characterized the role of SG6 in determining grain size through the regulation of spikelet hull cell division. SG6 encodes a previously uncharacterized plant AT-rich sequence and zinc-binding (PLATZ) protein that is ubiquitously localized throughout the cell and is preferentially expressed in the early developing panicles but not in the endosperm. The overexpression of SG6 resulted in significantly larger and heavier grains, as well as increased plant heights, which is consistent with its elevated spikelet hull cell division rate. Yeast two-hybrid analyses revealed that SG6 interacts with the core cell cycle machinery DP protein and several other putative cell division regulators, consistent with our transcriptomic analysis, which showed that SG6 activates the expression of many DNA replication and cell-cycle-related genes. These results confirm the crucial role of SG6 in determining grain size by regulating spikelet hull cell division and provide clues for understanding the functions of PLATZ family proteins and the network regulating cereal grain size.
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Affiliation(s)
- Shi-Rong Zhou
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, the Chinese Academy of Sciences, Shanghai, 200032, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hong-Wei Xue
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, the Chinese Academy of Sciences, Shanghai, 200032, China
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
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129
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UDP-glucosyltransferase regulates grain size and abiotic stress tolerance associated with metabolic flux redirection in rice. Nat Commun 2020; 11:2629. [PMID: 32457405 PMCID: PMC7250897 DOI: 10.1038/s41467-020-16403-5] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 05/01/2020] [Indexed: 12/22/2022] Open
Abstract
Grain size is an important component trait of grain yield, which is frequently threatened by abiotic stress. However, little is known about how grain yield and abiotic stress tolerance are regulated. Here, we characterize GSA1, a quantitative trait locus (QTL) regulating grain size and abiotic stress tolerance associated with metabolic flux redirection. GSA1 encodes a UDP-glucosyltransferase, which exhibits glucosyltransferase activity toward flavonoids and monolignols. GSA1 regulates grain size by modulating cell proliferation and expansion, which are regulated by flavonoid-mediated auxin levels and related gene expression. GSA1 is required for the redirection of metabolic flux from lignin biosynthesis to flavonoid biosynthesis under abiotic stress and the accumulation of flavonoid glycosides, which protect rice against abiotic stress. GSA1 overexpression results in larger grains and enhanced abiotic stress tolerance. Our findings provide insights into the regulation of grain size and abiotic stress tolerance associated with metabolic flux redirection and a potential means to improve crops. Increasing grain yield needs to be put in the context of environmental stress. Here, the authors reveal that a UDP-glucosyltransferase is associated with regulation of rice grain size, abiotic stress tolerance, flavonoid-mediated auxin signaling, and redirection of carbon flux to flavonoid glycosides synthesis.
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130
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Xu Q, Yu H, Xia S, Cui Y, Yu X, Liu H, Zeng D, Hu J, Zhang Q, Gao Z, Zhang G, Zhu L, Shen L, Guo L, Rao Y, Qian Q, Ren D. The C2H2 zinc-finger protein LACKING RUDIMENTARY GLUME 1 regulates spikelet development in rice. Sci Bull (Beijing) 2020; 65:753-764. [PMID: 36659109 DOI: 10.1016/j.scib.2020.01.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 12/23/2019] [Accepted: 01/06/2020] [Indexed: 01/21/2023]
Abstract
Rice (Oryza sativa) spikelets are a unique inflorescence structure and their development directly determines grain size and yield. Although many genes related to spikelet development have been reported, the molecular mechanisms underlying this process have not been fully elucidated. In this study, we identified a new recessive rice mutant, lacking rudimentary glume 1 (lrg1). The lrg1 spikelets only formed one rudimentary glume, which, along with the sterile lemmas, was homeotically transformed into lemma-like organs and acquired lemma identity. The transition from the spikelet to the floral meristem was delayed in the lrg1 mutant, resulting in the formation of an ectopic lemma-like organ between the sterile lemma and the terminal floret. In addition, we found that the abnormal lrg1 grain phenotype resulted from the alteration of cell numbers and the hull size. LRG1 encodes a ZOS4-06-C2H2 zinc-finger protein with the typical EAR motifs, and is expressed in all organs and tissues. LRG1 localizes to the nucleus and can interact with the TOPLESS-RELATED PROTEINs (TPRs) to repress the expressions of their downstream target genes. Taken together, our results reveal that LRG1 plays an important role in the regulation of spikelet organ identity and grain size.
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Affiliation(s)
- Qiankun Xu
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Haiping Yu
- 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
| | - Yuanjiang Cui
- 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
| | - He Liu
- 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
| | - Jiang Hu
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Qiang Zhang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Zhenyu Gao
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Guangheng Zhang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Li Zhu
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Lan Shen
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Longbiao Guo
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Yuchun Rao
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, 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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131
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Guo T, Chen K, Dong NQ, Ye WW, Shan JX, Lin HX. Tillering and small grain 1 dominates the tryptophan aminotransferase family required for local auxin biosynthesis in rice. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:581-600. [PMID: 31081210 DOI: 10.1111/jipb.12820] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 04/26/2019] [Indexed: 05/23/2023]
Abstract
Auxin is a crucial phytohormone, controlling multiple aspects of plant growth and responses to the changing environment. However, the role of local auxin biosynthesis in specific developmental programs remains unknown in crops. This study characterized the rice tillering and small grain 1 (tsg1) mutant, which has more tillers but a smaller panicle and grain size resulting from a reduction in endogenous auxin. TSG1 encodes a tryptophan aminotransferase that is allelic to the FISH BONE (FIB) gene. The tsg1 mutant showed hypersensitivity to indole-3-acetic acid and the competitive inhibitor of aminotransferase, L-kynurenine. TSG1 knockout resulted in an increased tiller number but reduction in grain number and size, and decrease in height. Meanwhile, deletion of the TSG1 homologs OsTAR1, OsTARL1, and OsTARL2 caused no obvious changes, although the phenotype of the TSG1/OsTAR1 double mutant was intensified and infertile, suggesting gene redundancy in the rice tryptophan aminotransferase family. Interestingly, TSG1 and OsTAR1, but not OsTARL1 and OsTARL2, displayed marked aminotransferase activity. Meanwhile, subcellular localization was identified as the endoplasmic reticulum, while phylogenetic analysis revealed functional divergence of TSG1 and OsTAR1 from OsTARL1 and OsTARL2. These findings suggest that TSG1 dominates the tryptophan aminotransferase family, playing a prominent role in local auxin biosynthesis in rice.
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Affiliation(s)
- Tao Guo
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Ke Chen
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Nai-Qian Dong
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Wang-Wei Ye
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Jun-Xiang Shan
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Hong-Xuan Lin
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
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132
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Gouda G, Gupta MK, Donde R, Mohapatra T, Vadde R, Behera L. Marker-assisted selection for grain number and yield-related traits of rice ( Oryza sativa L.). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:885-898. [PMID: 32377039 PMCID: PMC7196572 DOI: 10.1007/s12298-020-00773-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 02/11/2020] [Accepted: 02/13/2020] [Indexed: 05/11/2023]
Abstract
Continuous rise in the human population has resulted in an upsurge in food demand, which in turn demand grain yield enhancement of cereal crops, including rice. Rice yield is estimated via the number of tillers, grain number per panicles, and the number of spikes present per panicle. Marker-assisted selection (MAS) serve as one of the best ways to introduce QTLs/gene associated with yield in the rice plant. MAS has also been employed effectively in dissecting several other complex agricultural traits, for instance, drought, cold tolerance, salinity, etc. in rice plants. Thus, in this review, authors attempted to collect information about various genes/QTLs associated with high yield, including grain number, in rice and how different scheme of MAS can be employed to introduce them in rice (Oryza sativa L.) plant, which in turn will enhance rice yield. Information obtained to date suggest that, numerous QTLs, e.g., Gn1a, Dep1, associated with grain number and yield-related traits, have been identified either via mapping or cloning approaches. These QTLs have been successfully introduced into rice plants using various schemes of MAS for grain yield enhancement in rice. However, sometimes, MAS does not perform well in breeding, which might be due to lack of resources, skilled labors, reliable markers, and high costs associated with MAS. Thus, by overcoming these problems, we can enhance the application of MAS in plant breeding, which, in turn, may help us in increasing yield, which subsequently may help in bridging the gap between demand and supply of food for the continuously growing population.
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Affiliation(s)
- Gayatri Gouda
- ICAR-National Rice Research Institute, Cuttack, Odisha 753 006 India
| | - Manoj Kumar Gupta
- Department of Biotechnology and Bioinformatics, Yogi Vemana University, Kadapa, Andhra Pradesh 516 005 India
| | - Ravindra Donde
- ICAR-National Rice Research Institute, Cuttack, Odisha 753 006 India
| | - Trilochan Mohapatra
- Secretary (DARE) and Director General (ICAR), Government of India, New Delhi, India
| | - Ramakrishna Vadde
- Department of Biotechnology and Bioinformatics, Yogi Vemana University, Kadapa, Andhra Pradesh 516 005 India
| | - Lambodar Behera
- ICAR-National Rice Research Institute, Cuttack, Odisha 753 006 India
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133
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Huang Y, Bai X, Cheng N, Xiao J, Li X, Xing Y. Wide Grain 7 increases grain width by enhancing H3K4me3 enrichment in the OsMADS1 promoter in rice (Oryza sativa L.). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 102:517-528. [PMID: 31830332 DOI: 10.1111/tpj.14646] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 11/29/2019] [Indexed: 05/22/2023]
Abstract
Grain size is a major determinant of grain weight, a key component of grain yield of rice. Here, we identified the grain size gene WIDE GRAIN 7 (WG7) from a T-DNA insertion mutant. The grain size of WG7 knockout mutants and WG7 overexpression lines indicated that WG7 is a positive regulator of grain size. WG7 encodes a cysteine-tryptophan (CW) domain-containing transcriptional activator. EMSAs and ChIP-qPCR assay confirmed that WG7 directly bound to the promoter of OsMADS1, a grain size gene, and thereby significantly activated its expression. Point mutations showed that the cis-element CATTTC motif in the promoter was the binding site of WG7. Compared with the wild-type, deletion mutants of the cis-element motif exhibited lower expression of OsMADS1 and produced narrower grains, implicating the requirement of this motif for WG7 function. ChIP-qPCR assays showed that WG7 enhanced histone H3K4me3 enrichment in the promoter of OsMADS1. WG7 underwent directional selection due to the poor fertility of the non-functional mutant. These findings demonstrated that WG7 upregulated OsMADS1 expression by directly binding to its promoter, enhanced histone H3K4me3 enrichment in the promoter and ultimately increased grain width. This study will enrich the knowledge concerning the regulatory network of grain size formation in rice.
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Affiliation(s)
- Yong Huang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xufeng Bai
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Niannian Cheng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jinghua Xiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xianghua Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yongzhong Xing
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, 434100, China
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Ponce K, Zhang Y, Guo L, Leng Y, Ye G. Genome-Wide Association Study of Grain Size Traits in Indica Rice Multiparent Advanced Generation Intercross (MAGIC) Population. FRONTIERS IN PLANT SCIENCE 2020; 11:395. [PMID: 32391027 PMCID: PMC7193545 DOI: 10.3389/fpls.2020.00395] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 03/19/2020] [Indexed: 05/15/2023]
Abstract
Rice grain size plays a crucial role in determining grain quality and yield. In this study, two multiparent advanced generation intercross (MAGIC) populations, DC1 and BIM, were evaluated for grain size across three environments and genotyped with 55K array-based SNP detection and genotype-by-sequencing (GBS), respectively, to identify QTLs and SNPs associated with grain length, grain width, grain length-width ratio, grain thickness, and thousand grain weight. A total of 18 QTLs were identified for the five grain size-related traits and explained 6.43-63.35% of the total phenotypic variance. Twelve of these QTLs colocalized with the cloned genes, GS3, GW5/qSW5, GW7/GL7/SLG7, and GW8/OsSPL16, of which the first two genes showed the strongest effect for grain length and grain width, respectively. Four potential new genes were also identified from the QTLs, which exhibited both genetic background independency and environment stability and could be validated in future studies. Moreover, the significant SNP markers identified are valuable for direct utilization in marker-assisted breeding to improve rice grain size.
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Affiliation(s)
- Kimberly Ponce
- CAAS-IRRI Joint Laboratory for Genomics-assisted Germplasm Enhancement, Agricultural Genomics Institute in Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- State Key Laboratory for Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Ya Zhang
- CAAS-IRRI Joint Laboratory for Genomics-assisted Germplasm Enhancement, Agricultural Genomics Institute in Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- State Key Laboratory for Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Longbiao Guo
- State Key Laboratory for Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Yujia Leng
- CAAS-IRRI Joint Laboratory for Genomics-assisted Germplasm Enhancement, Agricultural Genomics Institute in Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Guoyou Ye
- CAAS-IRRI Joint Laboratory for Genomics-assisted Germplasm Enhancement, Agricultural Genomics Institute in Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Strategic Innovation Platform, International Rice Research Institute, Metro Manila, Philippines
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OsINV3 and Its Homolog, OsINV2, Control Grain Size in Rice. Int J Mol Sci 2020; 21:ijms21062199. [PMID: 32209971 PMCID: PMC7139340 DOI: 10.3390/ijms21062199] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 03/16/2020] [Accepted: 03/21/2020] [Indexed: 01/31/2023] Open
Abstract
Vacuolar invertase is involved in sugar metabolism and plays a crucial role in plant growth and development, thus regulating seed size. However, information linking vacuolar invertase and seed size in rice is limited. Here we characterized a small grain mutant sg2 (grain size on chromosome 2) that showed a reduced in grain size and 1000-grain weight compared to the wild type. Map-based cloning and genetic complementation showed that OsINV3 is responsible for the observed phenotype. Loss-of-function of OsINV3 resulted in grains of smaller size when compared to the wild type, while overexpression showed increased grain size. We also obtained a T-DNA insertion mutant of OsINV2, which is a homolog of OsINV3 and generated double knockout (KO) mutants of OsINV2 and OsINV3 using CRISPR/Cas9. Genetic data showed that OsINV2, that has no effect on grain size by itself, reduces grain length and width in the absence of OsINV3. Altered sugar content with increased sucrose and decreased hexose levels, as well as changes vacuolar invertase activities and starch constitution in INV3KO, INV2KO, INV3KOINV2KO mutants indicate that OsINV2 and OsINV3 affect sucrose metabolism in sink organs. In summary, we identified OsINV3 as a positive regulator of grain size in rice, and while OsINV2 has no function on grain size by itself. In the absence of OsINV3, it is possible to detect a role of OsINV2 in the regulation of grain size. Both OsINV3 and OsINV2 are involved in sucrose metabolism, and thus regulate grain size. Our findings increase our understanding of the role of OsINV3 and its homolog, OsINV2, in grain size development and also suggest a potential strategy to improve grain yield in rice.
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Zhang H, Zhu YJ, Zhu AD, Fan YY, Huang TX, Zhang JF, Xie HA, Zhuang JY. Fine-mapping of qTGW2, a quantitative trait locus for grain weight in rice ( Oryza sativa L.). PeerJ 2020; 8:e8679. [PMID: 32181056 PMCID: PMC7060756 DOI: 10.7717/peerj.8679] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 02/03/2020] [Indexed: 11/25/2022] Open
Abstract
Background Grain weight is a grain yield component, which is an integrated index of grain length, width and thickness. They are controlled by a large number of quantitative trait loci (QTLs). Besides major QTLs, minor QTLs play an essential role. In our previous studies, QTL analysis for grain length and width was performed using a recombinant inbred line population derived from rice cross TQ/IRBB lines. Two major QTLs were detected, which were located in proximity to GS3 and GW5 that have been cloned. In the present study, QTLs for grain weight and shape were identified using rice populations that were homozygous at GS3 and GW5. Method Nine populations derived from the indica rice cross TQ/IRBB52 were used. An F10:11population named W1, consisting of 250 families and covering 16 segregating regions, was developed from one residual heterozygote (RH) in the F7generation of Teqing/IRBB52. Three near isogenic line (NIL)-F2 populations, ZH1, ZH2 and ZH3 that comprised 205, 239 and 234 plants, respectively, were derived from three RHs in F10:11. They segregated the target QTL region in an isogenic background. Two NIL populations, HY2 and HY3, were respectively produced from homozygous progeny of the ZH2 and ZH3 populations. Three other NIL-F2 populations, Z1, Z2 and Z3, were established using three RHs having smaller heterozygous segments. QTL analysis for 1000-grain weight (TGW), grain length (GL), grain width (GW), and length/width ratio (LWR) was conducted using QTL IciMapping and SAS procedure with GLM model. Result A total of 27 QTLs distributed on 12 chromosomes were identified. One QTL cluster, qTGW2/qGL2/qGW2 located in the terminal region of chromosome 2, were selected for further analysis. Two linked QTLs were separated in region Tw31911−RM266. qGL2 was located in Tw31911−Tw32437 and mainly controlled GL and GW. The effects were larger on GL than on GW and the allelic directions were opposite. qTGW2 was located in Tw35293−RM266 and affected TGW, GL and GW with the same allelic direction. Finally, qTGW2 was delimited within a 103-kb region flanked by Tw35293 and Tw35395. Conclusion qTGW2 with significant effects on TGW, GL and GW was validated and fine-mapped using NIL and NIL-F2 populations. These results provide a basis for map-based cloning of qTGW2 and utilization of qTGW2 in the breeding of high-yielding rice varieties.
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Affiliation(s)
- Hui Zhang
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China.,State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, China.,Rice Research Institute and Fuzhou Branch of the National Center for Rice Improvement, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Yu-Jun Zhu
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, China
| | - An-Dong Zhu
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, China
| | - Ye-Yang Fan
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, China
| | - Ting-Xu Huang
- Rice Research Institute and Fuzhou Branch of the National Center for Rice Improvement, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Jian-Fu Zhang
- Rice Research Institute and Fuzhou Branch of the National Center for Rice Improvement, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Hua-An Xie
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China.,Rice Research Institute and Fuzhou Branch of the National Center for Rice Improvement, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Jie-Yun Zhuang
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, China
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Genome-Wide Identification of lncRNAs During Rice Seed Development. Genes (Basel) 2020; 11:genes11030243. [PMID: 32110990 PMCID: PMC7140839 DOI: 10.3390/genes11030243] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 02/16/2020] [Accepted: 02/21/2020] [Indexed: 12/16/2022] Open
Abstract
Rice seed is a pivotal reproductive organ that directly determines yield and quality. Long non-coding RNAs (lncRNAs) have been recognized as key regulators in plant development, but the roles of lncRNAs in rice seed development remain unclear. In this study, we performed a paired-end RNA sequencing in samples of rice pistils and seeds at three and seven days after pollination (DAP) respectively. A total of 540 lncRNAs were obtained, among which 482 lncRNAs had significantly different expression patterns during seed development. Results from semi-qPCR conducted on 15 randomly selected differentially expressed lncRNAs suggested high reliability of the transcriptomic data. RNA interference of TCONS_00023703, which is predominantly transcribed in developing seeds, significantly reduced grain length and thousand-grain weight. These results expanded the dataset of lncRNA in rice and enhanced our understanding of the biological functions of lncRNAs in rice seed development.
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Yu F, Wan W, Lv MJ, Zhang JL, Meng LS. Molecular Mechanism Underlying the Effect of the Intraspecific Alternation of Seed Size on Plant Drought Tolerance. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:703-711. [PMID: 31904950 DOI: 10.1021/acs.jafc.9b06491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
In crop plants, the yield loss caused by drought exceeds the losses resulting from other adverse environment stresses. In numerous plant species, seedling establishment is positively correlated with the initial seed size under drought stress conditions. In intra- and interspecies, plants with large seeds can withstand water deficiency stresses, whereas those with small seeds are efficient colonizers as a result of their ability to produce more seeds. Therefore, larger initial seeds confer more drought resistance on germinating seedlings. Although this phenomenon has been observed by evolutionary biologists and ecologists, the correlation of initial seed size with the drought resistance of seedlings/plants is not well-reviewed and characterized. Furthermore, the related molecular mechanisms are unknown. Understanding these mechanisms will benefit future breeding or design strategies to increase crop yields. In the present review, we focus on recent research to analyze the genetic factors of plants/crops involved in the regulation of seed size and drought tolerance and their corresponding signal transduction pathways. Several signaling pathways that determine plant drought tolerance through influencing the initial seed size are identified. Such pathways include those that are involved in mitogen-activated protein kinase, abscisic acid, brassinosteroids, and several transcription factors and sugar signaling pathways.
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Affiliation(s)
- Fei Yu
- Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province , Jiangsu Normal University , Xuzhou , Jiangsu 221116 , People's Republic of China
| | - Wen Wan
- Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province , Jiangsu Normal University , Xuzhou , Jiangsu 221116 , People's Republic of China
| | - Meng-Jiao Lv
- Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province , Jiangsu Normal University , Xuzhou , Jiangsu 221116 , People's Republic of China
| | - Jin-Lin Zhang
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology , Lanzhou University , Lanzhou , Gansu 730020 , People's Republic of China
| | - Lai-Sheng Meng
- Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province , Jiangsu Normal University , Xuzhou , Jiangsu 221116 , People's Republic of China
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Wu L, Cui Y, Xu Z, Xu Q. Identification of Multiple Grain Shape-Related Loci in Rice Using Bulked Segregant Analysis With High-Throughput Sequencing. FRONTIERS IN PLANT SCIENCE 2020; 11:303. [PMID: 32308659 PMCID: PMC7145986 DOI: 10.3389/fpls.2020.00303] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 03/03/2020] [Indexed: 05/17/2023]
Abstract
Grain shape (GS) is an important agronomic trait that can improve rice breeding for optimal appearance quality, and it varies highly between indica and japonica subspecies. In this study, we conducted a genome sequencing of a series of recombination inbred lines (RILs) derived from a cross between japonica variety Shennong265 (SN265) and indica variety R99, and we successfully detected seven loci associated with GS. Subsequent analysis showed that a major quantitative trait locus (QTL) corresponded to the qSW5/GW5. To identify a main-effect locus, we conducted bulked segregant analysis (BSA) in two F2 populations. A 0.8-Mb region on chromosome 9 was identified as the candidate region of GS. There are 101 predicted genes in this region, and eight single nucleotide polymorphisms/insertions and deletions (SNPs/INDELs) caused frameshift. We found that a 637-bp stretch in exon 5 of the DENSE AND ERECT PANICLE 1 (DEP1) locus in SN265 was replaced by a 12-bp sequence. The two types of CRISPR/Cas9 gene-edited plants confirmed that DEP1 affected GS, and both Gγ and Cys-rich domains participated in this regulatory mechanism. These findings improve our understanding of the underlying mechanism of GS in rice and provide an effective and rapid strategy for the identification of main-effect loci of target traits.
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Du H, Zhang H, Wei L, Li C, Duan Y, Wang H. A high-density genetic map constructed using specific length amplified fragment (SLAF) sequencing and QTL mapping of seed-related traits in sesame (Sesamum indicum L.). BMC PLANT BIOLOGY 2019; 19:588. [PMID: 31881840 PMCID: PMC6935206 DOI: 10.1186/s12870-019-2172-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 11/28/2019] [Indexed: 05/20/2023]
Abstract
BACKGROUND Sesame (Sesamum indicum L., 2n = 2x = 26) is an important oilseed crop with high oil content but small seed size. To reveal the genetic loci of the quantitative seed-related traits, we constructed a high-density single nucleotide polymorphism (SNP) linkage map of an F2 population by using specific length amplified fragment (SLAF) technique and determined the quantitative trait loci (QTLs) of seed-related traits for sesame based on the phenotypes of F3 progeny. RESULTS The genetic map comprised 2159 SNP markers distributed on 13 linkage groups (LGs) and was 2128.51 cM in length, with an average distance of 0.99 cM between adjacent markers. QTL mapping revealed 19 major-effect QTLs with the phenotypic effect (R2) more than 10%, i.e., eight QTLs for seed coat color, nine QTLs for seed size, and two QTLs for 1000-seed weight (TSW), using composite interval mapping method. Particularly, LG04 and LG11 contained collocated QTL regions for the seed coat color and seed size traits, respectively, based on their close or identical locations. In total, 155 candidate genes for seed coat color, 22 for seed size traits, and 54 for TSW were screened and analyzed. CONCLUSIONS This report presents the first QTL mapping of seed-related traits in sesame using an F2 population. The results reveal the location of specific markers associated with seed-related traits in sesame and provide the basis for further seed quality traits research.
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Affiliation(s)
- Hua Du
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002 People’s Republic of China
| | - Haiyang Zhang
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002 People’s Republic of China
| | - Libin Wei
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002 People’s Republic of China
| | - Chun Li
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002 People’s Republic of China
| | - Yinghui Duan
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002 People’s Republic of China
| | - Huili Wang
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002 People’s Republic of China
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Yang J, Zhou Y, Zhang Y, Hu W, Wu Q, Chen Y, Wang X, Guo G, Liu Z, Cao T, Zhao H. Cloning, characterization of TaGS3 and identification of allelic variation associated with kernel traits in wheat (Triticum aestivum L.). BMC Genet 2019; 20:98. [PMID: 31852431 PMCID: PMC6921503 DOI: 10.1186/s12863-019-0800-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 12/12/2019] [Indexed: 11/19/2022] Open
Abstract
Background Grain weight is an important yield component. Selection of advanced lines with heavy grains show high grain sink potentials and strong sink activity, which is an increasingly important objective in wheat breeding programs. Rice OsGS3 has been identified as a major quantitative trait locus for both grain weight and grain size. However, allelic variation of GS3 has not been characterized previously in hexaploid wheat. Results We cloned 2445, 2393, and 2409 bp sequences of the homologs TaGS3-4A, TaGS3-7A, and TaGS3-7D in wheat ‘Changzhi 6406’, a cultivar that shows high grain weight. The TaGS3 genes each contained five exons and four introns, and encoded a deduced protein of 170, 169, and 169 amino acids, respectively. Phylogenetic analysis of plant GS3 protein sequences revealed GS3 to be a monocotyledon-specific gene and the GS3 proteins were resolved into three classes. The length of the atypical Gγ domain and the cysteine-rich region was conserved within each class and not conserved between classes. A single-nucleotide polymorphism in the fifth exon (at position 1907) of TaGS3-7A leads to an amino acid change (ALA/THR) and showed different frequencies in two pools of Chinese wheat accessions representing extremes in grain weight. Association analysis indicated that the TaGS3-7A-A allele was associated with higher grain weight in the natural population. The TaGS3-7A-A allele was favoured in global modern wheat cultivars but the allelic frequency varied among different wheat-production regions of China, which indicated that this allele is of potential utility to improve wheat grain weight in certain wheat-production areas of China. Conclusions The novel molecular information on wheat GS3 homologs and the KASP functional marker designed in this study may be useful in marker-assisted breeding for genetic improvement of wheat.
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Affiliation(s)
- Jian Yang
- National Laboratory of Wheat Engineering, Key Laboratory of Wheat Biology and Genetic Breeding in Central Huang-Huai Region, Ministry of Agriculture, Institute of Wheat, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China
| | - Yanjie Zhou
- National Laboratory of Wheat Engineering, Key Laboratory of Wheat Biology and Genetic Breeding in Central Huang-Huai Region, Ministry of Agriculture, Institute of Wheat, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China
| | - Yu'e Zhang
- National Laboratory of Wheat Engineering, Key Laboratory of Wheat Biology and Genetic Breeding in Central Huang-Huai Region, Ministry of Agriculture, Institute of Wheat, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China
| | - Weiguo Hu
- National Laboratory of Wheat Engineering, Key Laboratory of Wheat Biology and Genetic Breeding in Central Huang-Huai Region, Ministry of Agriculture, Institute of Wheat, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China
| | - Qiuhong Wu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yongxing Chen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xicheng Wang
- National Laboratory of Wheat Engineering, Key Laboratory of Wheat Biology and Genetic Breeding in Central Huang-Huai Region, Ministry of Agriculture, Institute of Wheat, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China
| | - Guanghao Guo
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhiyong Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Tingjie Cao
- National Laboratory of Wheat Engineering, Key Laboratory of Wheat Biology and Genetic Breeding in Central Huang-Huai Region, Ministry of Agriculture, Institute of Wheat, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China.
| | - Hong Zhao
- National Laboratory of Wheat Engineering, Key Laboratory of Wheat Biology and Genetic Breeding in Central Huang-Huai Region, Ministry of Agriculture, Institute of Wheat, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China
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Tian P, Liu J, Mou C, Shi C, Zhang H, Zhao Z, Lin Q, Wang J, Wang J, Zhang X, Guo X, Cheng Z, Zhu S, Ren Y, Lei C, Wang H, Wan J. GW5-Like, a homolog of GW5, negatively regulates grain width, weight and salt resistance in rice. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:1171-1185. [PMID: 30450718 DOI: 10.1111/jipb.12745] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 11/09/2018] [Indexed: 05/23/2023]
Abstract
Grain size is an important determinant of yield potential in crops. We previously demonstrated that natural mutations in the regulatory sequences of qSW5/GW5 confer grain width diversity in rice. However, the biological function of a GW5 homolog, named GW5-Like (GW5L), remains unknown. In this study, we report on GW5L knockout mutants in Kitaake, a japonica cultivar (cv.) considered to have a weak gw5 variant allele that confers shorter and wider grains. GW5L is evenly expressed in various tissues, and its protein product is localized to the plasma membrane. Biochemical assays verified that GW5L functions in a similar fashion to GW5. It positively regulates brassinosteroid (BR) signaling through repression of the phosphorylation activity of GSK2. Genetic data show that GW5L overexpression in either Kitaake or a GW5 knockout line, Kasaorf3 (indica cv. Kasalath background), causes more slender, longer grains relative to the wild-type. We also show that GW5L could confer salt stress resistance through an association with calmodulin protein OsCaM1-1. These findings identify GW5L as a negative regulator of both grain size and salt stress tolerance, and provide a potential target for breeders to improve grain yield and salt stress resistance in rice.
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Affiliation(s)
- Peng Tian
- Institute of Crop Sciences, the Chinese Academy of Agriculture Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081, China
| | - Jiafan Liu
- Institute of Crop Sciences, the Chinese Academy of Agriculture Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081, China
| | - Changling Mou
- Key Laboratory of Crop Genetics and Germplasm Enhancement/Jiangsu Provincial Center of Plant Gene Engineering, Nanjing Agricultural University, Nanjing, 210095, China
| | - Cuilan Shi
- Institute of Crop Sciences, the Chinese Academy of Agriculture Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081, China
| | - Huan Zhang
- Key Laboratory of Crop Genetics and Germplasm Enhancement/Jiangsu Provincial Center of Plant Gene Engineering, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhichao Zhao
- Institute of Crop Sciences, the Chinese Academy of Agriculture Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081, China
| | - Qibing Lin
- Institute of Crop Sciences, the Chinese Academy of Agriculture Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081, China
| | - Jie Wang
- Institute of Crop Sciences, the Chinese Academy of Agriculture Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081, China
| | - Jiulin Wang
- Institute of Crop Sciences, the Chinese Academy of Agriculture Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081, China
| | - Xin Zhang
- Institute of Crop Sciences, the Chinese Academy of Agriculture Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081, China
| | - Xiuping Guo
- Institute of Crop Sciences, the Chinese Academy of Agriculture Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081, China
| | - Zhijun Cheng
- Institute of Crop Sciences, the Chinese Academy of Agriculture Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081, China
| | - Shanshan Zhu
- Institute of Crop Sciences, the Chinese Academy of Agriculture Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081, China
| | - Yulong Ren
- Institute of Crop Sciences, the Chinese Academy of Agriculture Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081, China
| | - Cailin Lei
- Institute of Crop Sciences, the Chinese Academy of Agriculture Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081, China
| | - Haiyang Wang
- Institute of Crop Sciences, the Chinese Academy of Agriculture Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081, China
| | - Jianmin Wan
- Institute of Crop Sciences, the Chinese Academy of Agriculture Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081, China
- Key Laboratory of Crop Genetics and Germplasm Enhancement/Jiangsu Provincial Center of Plant Gene Engineering, Nanjing Agricultural University, Nanjing, 210095, China
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Fan C, Wang G, Wang Y, Zhang R, Wang Y, Feng S, Luo K, Peng L. Sucrose Synthase Enhances Hull Size and Grain Weight by Regulating Cell Division and Starch Accumulation in Transgenic Rice. Int J Mol Sci 2019; 20:ijms20204971. [PMID: 31600873 PMCID: PMC6829484 DOI: 10.3390/ijms20204971] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 10/07/2019] [Accepted: 10/08/2019] [Indexed: 12/20/2022] Open
Abstract
Grain size and weight are two important determinants of grain yield in rice. Although overexpression of sucrose synthase (SUS) genes has led to several improvements on cellulose and starch-based traits in transgenic crops, little is reported about SUS enhancement of hull size and grain weight in rice. In this study, we selected transgenic rice plants that overexpressed OsSUS1-6 genes driven with the maize Ubi promoter. Compared to the controls (wild type and empty vector line), all independent OsSUS homozygous transgenic lines exhibited considerably increased grain yield and grain weights. Using the representative OsSUS3 overexpressed transgenic plants, four independent homozygous lines showed much raised cell numbers for larger hull sizes, consistent with their enhanced primary cell wall cellulose biosynthesis and postponed secondary wall synthesis. Accordingly, the OsSUS3 transgenic lines contained much larger endosperm volume and higher starch levels than those of the controls in the mature grains, leading to increased brown grain weights by 15–19%. Hence, the results have demonstrated that OsSUS overexpression could significantly improve hull size and grain weight by dynamically regulating cell division and starch accumulation in the transgenic rice.
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Affiliation(s)
- Chunfen Fan
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Institute of Resources Botany, School of Life Sciences, Southwest University, Chongqing 400715, China.
- Biomass & Bioenergy Research Centre, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Guangya Wang
- Biomass & Bioenergy Research Centre, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Youmei Wang
- Biomass & Bioenergy Research Centre, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Ran Zhang
- Biomass & Bioenergy Research Centre, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Yanting Wang
- Biomass & Bioenergy Research Centre, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Shengqiu Feng
- Biomass & Bioenergy Research Centre, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Keming Luo
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Institute of Resources Botany, School of Life Sciences, Southwest University, Chongqing 400715, China.
| | - Liangcai Peng
- Biomass & Bioenergy Research Centre, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China.
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144
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Teng X, Zhong M, Zhu X, Wang C, Ren Y, Wang Y, Zhang H, Jiang L, Wang D, Hao Y, Wu M, Zhu J, Zhang X, Guo X, Wang Y, Wan J. FLOURY ENDOSPERM16 encoding a NAD-dependent cytosolic malate dehydrogenase plays an important role in starch synthesis and seed development in rice. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:1914-1927. [PMID: 30860317 PMCID: PMC6737025 DOI: 10.1111/pbi.13108] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 03/07/2019] [Indexed: 05/18/2023]
Abstract
Starch is the most important form of energy storage in cereal crops. Many key enzymes involved in starch biosynthesis have been identified. However, the molecular mechanisms underlying the regulation of starch biosynthesis are largely unknown. In this study, we isolated a novel floury endosperm rice (Oryza sativa) mutant flo16 with defective starch grain (SG) formation. The amylose content and amylopectin structure were both altered in the flo16 mutant. Map-based cloning and complementation tests demonstrated that FLO16 encodes a NAD-dependent cytosolic malate dehydrogenase (CMDH). The ATP contents were decreased in the mutant, resulting in significant reductions in the activity of starch synthesis-related enzymes. Our results indicated that FLO16 plays a critical role in redox homeostasis that is important for compound SG formation and subsequent starch biosynthesis in rice endosperm. Overexpression of FLO16 significantly improved grain weight, suggesting a possible application of FLO16 in rice breeding. These findings provide a novel insight into the regulation of starch synthesis and seed development in rice.
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Affiliation(s)
- Xuan Teng
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjingChina
| | - Mingsheng Zhong
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjingChina
| | - Xiaopin Zhu
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjingChina
| | - Chunming Wang
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjingChina
| | - Yulong Ren
- National Key Facility for Crop Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
| | - Yunlong Wang
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjingChina
| | - Huan Zhang
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjingChina
| | - Ling Jiang
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjingChina
| | - Di Wang
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjingChina
| | - Yuanyuan Hao
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjingChina
| | - Mingming Wu
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjingChina
| | - Jianping Zhu
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjingChina
| | - Xin Zhang
- National Key Facility for Crop Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
| | - Xiuping Guo
- National Key Facility for Crop Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
| | - Yihua Wang
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjingChina
| | - Jianmin Wan
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjingChina
- National Key Facility for Crop Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
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145
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Chen K, Guo T, Li XM, Yang YB, Dong NQ, Shi CL, Ye WW, Shan JX, Lin HX. NAL8 encodes a prohibitin that contributes to leaf and spikelet development by regulating mitochondria and chloroplasts stability in rice. BMC PLANT BIOLOGY 2019; 19:395. [PMID: 31510917 PMCID: PMC6737680 DOI: 10.1186/s12870-019-2007-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 08/30/2019] [Indexed: 05/24/2023]
Abstract
BACKGROUND Leaf morphology and spikelet number are two important traits associated with grain yield. To understand how genes coordinating with sink and sources of cereal crops is important for grain yield improvement guidance. Although many researches focus on leaf morphology or grain number in rice, the regulating molecular mechanisms are still unclear. RESULTS In this study, we identified a prohibitin complex 2α subunit, NAL8, that contributes to multiple developmental process and is required for normal leaf width and spikelet number at the reproductive stage in rice. These results were consistent with the ubiquitous expression pattern of NAL8 gene. We used genetic complementation, CRISPR/Cas9 gene editing system, RNAi gene silenced system and overexpressing system to generate transgenic plants for confirming the fuctions of NAL8. Mutation of NAL8 causes a reduction in the number of plastoglobules and shrunken thylakoids in chloroplasts, resulting in reduced cell division. In addition, the auxin levels in nal8 mutants are higher than in TQ, while the cytokinin levels are lower than in TQ. Moreover, RNA-sequencing and proteomics analysis shows that NAL8 is involved in multiple hormone signaling pathways as well as photosynthesis in chloroplasts and respiration in mitochondria. CONCLUSIONS Our findings provide new insights into the way that NAL8 functions as a molecular chaperone in regulating plant leaf morphology and spikelet number through its effects on mitochondria and chloroplasts associated with cell division.
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Affiliation(s)
- Ke Chen
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Tao Guo
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai, 200032, China
| | - Xin-Min Li
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai, 200032, China
| | - Yi-Bing Yang
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Nai-Qian Dong
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai, 200032, China
| | - Chuan-Lin Shi
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Wang-Wei Ye
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai, 200032, China
| | - Jun-Xiang Shan
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai, 200032, China
| | - Hong-Xuan Lin
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai, 200032, China.
- University of the Chinese Academy of Sciences, Beijing, 100049, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
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146
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Hao D, Xue L, Zhang Z, Cheng Y, Chen G, Zhou G, Li P, Yang Z, Xu C. Combined linkage and association mapping reveal candidate loci for kernel size and weight in maize. BREEDING SCIENCE 2019; 69:420-428. [PMID: 31598074 PMCID: PMC6776153 DOI: 10.1270/jsbbs.18185] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 04/10/2019] [Indexed: 05/25/2023]
Abstract
Yield improvement is a top priority for maize breeding. Kernel size and weight are important determinants of maize grain yield. In this study, a recombinant inbred line (RIL) population and an association panel were used to identify quantitative trait loci (QTLs) for four maize kernel-related traits: kernel length, width, thickness and 100-kernel weight. Twenty-seven QTLs were identified for kernel-related traits across three environments and the best linear unbiased predictions (BLUPs) of each trait by linkage analysis, and four QTLs were stably detected in more than two environments. Additionally, 29 single nucleotide polymorphisms (SNPs) were identified as significantly associated with the four kernel-related traits and BLUPs by genome-wide association study, and two loci could be stably detected in both environments. In total, four QTLs/SNPs were co-associated with various traits in both populations. Using combined-linkage analysis and association mapping, PZE-101066560 on chromosome 1, associated with kernel width and with 100-kernel weight in the association panel, was co-localized within the QTL interval of qKW1-3 for kernel width in the RILs. Two annotated genes in the candidate region were considered as potential candidate genes. The QTLs and candidate genes identified here will facilitate molecular breeding for grain yield improvement in maize.
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Affiliation(s)
- Derong Hao
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University,
Yangzhou 225009,
China
- Nantong Key Laboratory for Exploitation of Crop Genetic Resources and Molecular Breeding, Jiangsu Yanjiang Institute of Agricultural Sciences,
Nantong 226541,
China
| | - Lin Xue
- Nantong Key Laboratory for Exploitation of Crop Genetic Resources and Molecular Breeding, Jiangsu Yanjiang Institute of Agricultural Sciences,
Nantong 226541,
China
- Jiangsu Collaborative Innovation Center for Modern Crop Production,
Nanjing 210095,
China
| | - Zhenliang Zhang
- Nantong Key Laboratory for Exploitation of Crop Genetic Resources and Molecular Breeding, Jiangsu Yanjiang Institute of Agricultural Sciences,
Nantong 226541,
China
| | - Yujing Cheng
- Nantong Key Laboratory for Exploitation of Crop Genetic Resources and Molecular Breeding, Jiangsu Yanjiang Institute of Agricultural Sciences,
Nantong 226541,
China
| | - Guoqing Chen
- Nantong Key Laboratory for Exploitation of Crop Genetic Resources and Molecular Breeding, Jiangsu Yanjiang Institute of Agricultural Sciences,
Nantong 226541,
China
- Jiangsu Collaborative Innovation Center for Modern Crop Production,
Nanjing 210095,
China
| | - Guangfei Zhou
- Nantong Key Laboratory for Exploitation of Crop Genetic Resources and Molecular Breeding, Jiangsu Yanjiang Institute of Agricultural Sciences,
Nantong 226541,
China
| | - Pengcheng Li
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University,
Yangzhou 225009,
China
| | - Zefeng Yang
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University,
Yangzhou 225009,
China
| | - Chenwu Xu
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University,
Yangzhou 225009,
China
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147
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Chen K, Guo T, Li XM, Zhang YM, Yang YB, Ye WW, Dong NQ, Shi CL, Kan Y, Xiang YH, Zhang H, Li YC, Gao JP, Huang X, Zhao Q, Han B, Shan JX, Lin HX. Translational Regulation of Plant Response to High Temperature by a Dual-Function tRNA His Guanylyltransferase in Rice. MOLECULAR PLANT 2019; 12:1123-1142. [PMID: 31075443 DOI: 10.1016/j.molp.2019.04.012] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 04/11/2019] [Accepted: 04/29/2019] [Indexed: 05/23/2023]
Abstract
As sessile organisms, plants have evolved numerous strategies to acclimate to changes in environmental temperature. However, the molecular basis of this acclimation remains largely unclear. In this study we identified a tRNAHis guanylyltransferase, AET1, which contributes to the modification of pre-tRNAHis and is required for normal growth under high-temperature conditions in rice. Interestingly, AET1 possibly interacts with both RACK1A and eIF3h in the endoplasmic reticulum. Notably, AET1 can directly bind to OsARF mRNAs including the uORFs of OsARF19 and OsARF23, indicating that AET1 is associated with translation regulation. Furthermore, polysome profiling assays suggest that the translational status remains unaffected in the aet1 mutant, but that the translational efficiency of OsARF19 and OsARF23 is reduced; moreover, OsARF23 protein levels are obviously decreased in the aet1 mutant under high temperature, implying that AET1 regulates auxin signaling in response to high temperature. Our findings provide new insights into the molecular mechanisms whereby AET1 regulates the environmental temperature response in rice by playing a dual role in tRNA modification and translational control.
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Affiliation(s)
- Ke Chen
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai 200032, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Tao Guo
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai 200032, China
| | - Xin-Min Li
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai 200032, China
| | - Yi-Min Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai 200032, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yi-Bing Yang
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai 200032, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Wang-Wei Ye
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai 200032, China
| | - Nai-Qian Dong
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai 200032, China
| | - Chuan-Lin Shi
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai 200032, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Kan
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai 200032, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - You-Huang Xiang
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai 200032, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Hai Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai 200032, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Ya-Chao Li
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai 200032, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Ji-Ping Gao
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai 200032, China
| | - Xuehui Huang
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Qiang Zhao
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Bin Han
- University of the Chinese Academy of Sciences, Beijing 100049, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Jun-Xiang Shan
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai 200032, China.
| | - Hong-Xuan Lin
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai 200032, China; University of the Chinese Academy of Sciences, Beijing 100049, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
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148
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Wang A, Hou Q, Si L, Huang X, Luo J, Lu D, Zhu J, Shangguan Y, Miao J, Xie Y, Wang Y, Zhao Q, Feng Q, Zhou C, Li Y, Fan D, Lu Y, Tian Q, Wang Z, Han B. The PLATZ Transcription Factor GL6 Affects Grain Length and Number in Rice. PLANT PHYSIOLOGY 2019; 180:2077-2090. [PMID: 31138620 PMCID: PMC6670106 DOI: 10.1104/pp.18.01574] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 05/09/2019] [Indexed: 05/18/2023]
Abstract
Grain size is one of the key determinants of grain yield. Although a number of genes that control grain size in rice (Oryza sativa) have been identified, the overall regulatory networks behind this process remain poorly understood. Here, we report the map-based cloning and functional characterization of the quantitative trait locus GL6, which encodes a plant-specific plant AT-rich sequence- and zinc-binding transcription factor that regulates rice grain length and spikelet number. GL6 positively controls grain length by promoting cell proliferation in young panicles and grains. The null gl6 mutant possesses short grains, whereas overexpression of GL6 results in large grains and decreased grain number per panicle. We demonstrate that GL6 participates in RNA polymerase III transcription machinery by interacting with RNA polymerase III subunit C53 and transcription factor class C1 to regulate the expression of genes involved in rice grain development. Our findings reveal a further player involved in the regulation of rice grain size that may be exploited in future rice breeding.
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Affiliation(s)
- Ahong Wang
- National Center for Gene Research, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 2000233, China
| | - Qingqing Hou
- National Center for Gene Research, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 2000233, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lizhen Si
- National Center for Gene Research, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 2000233, China
| | - Xuehui Huang
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Jianghong Luo
- National Center for Gene Research, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 2000233, China
| | - Danfeng Lu
- National Center for Gene Research, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 2000233, China
| | - Jingjie Zhu
- National Center for Gene Research, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 2000233, China
| | - Yingying Shangguan
- National Center for Gene Research, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 2000233, China
| | - Jiashun Miao
- National Center for Gene Research, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 2000233, China
| | - Yifan Xie
- National Center for Gene Research, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 2000233, China
| | - Yongchun Wang
- National Center for Gene Research, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 2000233, China
| | - Qiang Zhao
- National Center for Gene Research, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 2000233, China
| | - Qi Feng
- National Center for Gene Research, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 2000233, China
| | - Congcong Zhou
- National Center for Gene Research, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 2000233, China
| | - Yan Li
- National Center for Gene Research, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 2000233, China
| | - Danlin Fan
- National Center for Gene Research, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 2000233, China
| | - Yiqi Lu
- National Center for Gene Research, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 2000233, China
| | - Qilin Tian
- National Center for Gene Research, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 2000233, China
| | - Zixuan Wang
- National Center for Gene Research, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 2000233, China
| | - Bin Han
- National Center for Gene Research, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 2000233, China
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149
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Lin Z, Yan J, Su J, Liu H, Hu C, Li G, Wang F, Lin Y. Novel OsGRAS19 mutant, D26, positively regulates grain shape in rice (Oryza sativa). FUNCTIONAL PLANT BIOLOGY : FPB 2019; 46:857-868. [PMID: 31146805 DOI: 10.1071/fp18266] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 05/10/2019] [Indexed: 05/23/2023]
Abstract
Grain size is an important factor in rice yield. Several genes related to grain size have been reported, but most of them are determined by quantitative trail loci (QTL) traits. Gene D26 is a novel site mutation of OsGRAS19 and involved in the brassinosteroid (BR) signalling pathway. However, whether D26 is involved in the process of rice reproductive development remains unclear. Here, gene cloning and functional analysis revealed that D26 has an obvious regulatory effect on grain size. Overexpression or CRISP/Cas9 mutant of D26 also showed that grain size was positively influenced. Cellular analyses show that D26 modulates grain size by promoting cell division and regulating the cell number in the upper epidermis of the glume. The overexpression results further suggest that the level of D26 expression positively impacts grain length and leaf angles and that the expression of several known grain size genes is involved in the regulation. Based on our results, D26, as a transcription factor, effectively improves rice grain shape.
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Affiliation(s)
- Zhimin Lin
- Department of Bioengineering and Biotechnology, School of Chemical Engineering, Huaqiao University, Xiamen 361021, China; and Fujian Academy of Agricultural Sciences Biotechnology Institute, Key Laboratory of Genetic Engineering for Agriculture, Fuzhou 350003, China
| | - Jingwan Yan
- Fujian Academy of Agricultural Sciences Biotechnology Institute, Key Laboratory of Genetic Engineering for Agriculture, Fuzhou 350003, China
| | - Jun Su
- Fujian Academy of Agricultural Sciences Biotechnology Institute, Key Laboratory of Genetic Engineering for Agriculture, Fuzhou 350003, China
| | - Huaqing Liu
- Fujian Academy of Agricultural Sciences Biotechnology Institute, Key Laboratory of Genetic Engineering for Agriculture, Fuzhou 350003, China
| | - Changquan Hu
- Fujian Academy of Agricultural Sciences Biotechnology Institute, Key Laboratory of Genetic Engineering for Agriculture, Fuzhou 350003, China
| | - Gang Li
- Fujian Academy of Agricultural Sciences Biotechnology Institute, Key Laboratory of Genetic Engineering for Agriculture, Fuzhou 350003, China
| | - Feng Wang
- Fujian Academy of Agricultural Sciences Biotechnology Institute, Key Laboratory of Genetic Engineering for Agriculture, Fuzhou 350003, China; and Corresponding authors. Emails: ;
| | - Yi Lin
- Department of Bioengineering and Biotechnology, School of Chemical Engineering, Huaqiao University, Xiamen 361021, China; and Corresponding authors. Emails: ;
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The Rho-family GTPase OsRac1 controls rice grain size and yield by regulating cell division. Proc Natl Acad Sci U S A 2019; 116:16121-16126. [PMID: 31320586 DOI: 10.1073/pnas.1902321116] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Grain size is a key factor for determining grain yield in crops and is a target trait for both domestication and breeding, yet the mechanisms underlying the regulation of grain size are largely unclear. Here we show that the grain size and yield of rice (Oryza sativa) is positively regulated by ROP GTPase (Rho-like GTPase from plants), a versatile molecular switch modulating plant growth, development, and responses to the environment. Overexpression of rice OsRac1ROP not only increases cell numbers, resulting in a larger spikelet hull, but also accelerates grain filling rate, causing greater grain width and weight. As a result, OsRac1 overexpression improves grain yield in O. sativa by nearly 16%. In contrast, down-regulation or deletion of OsRac1 causes the opposite effects. RNA-seq and cell cycle analyses suggest that OsRac1 promotes cell division. Interestingly, OsRac1 interacts with and regulates the phosphorylation level of OsMAPK6, which is known to regulate cell division and grain size in rice. Thus, our findings suggest OsRac1 modulates rice grain size and yield by influencing cell division. This study provides insights into the molecular mechanisms underlying the control of rice grain size and suggests that OsRac1 could serve as a potential target gene for breeding high-yield crops.
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