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Han Y, Hu Q, Gong N, Yan H, Khan NU, Du Y, Sun H, Zhao Q, Peng W, Li Z, Zhang Z, Li J. Natural variation in MORE GRAINS 1 regulates grain number and grain weight in rice. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:1440-1458. [PMID: 38780111 DOI: 10.1111/jipb.13674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 04/14/2024] [Indexed: 05/25/2024]
Abstract
Grain yield is determined mainly by grain number and grain weight. In this study, we identified and characterized MORE GRAINS1 (MOG1), a gene associated with grain number and grain weight in rice (Oryza sativa L.), through map-based cloning. Overexpression of MOG1 increased grain yield by 18.6%-22.3% under field conditions. We determined that MOG1, a bHLH transcription factor, interacts with OsbHLH107 and directly activates the expression of LONELY GUY (LOG), which encodes a cytokinin-activating enzyme and the cell expansion gene EXPANSIN-LIKE1 (EXPLA1), positively regulating grain number per panicle and grain weight. Natural variations in the promoter and coding regions of MOG1 between Hap-LNW and Hap-HNW alleles resulted in changes in MOG1 expression level and transcriptional activation, leading to functional differences. Haplotype analysis revealed that Hap-HNW, which results in a greater number and heavier grains, has undergone strong selection but has been poorly utilized in modern lowland rice breeding. In summary, the MOG1-OsbHLH107 complex activates LOG and EXPLA1 expression to promote cell expansion and division of young panicles through the cytokinin pathway, thereby increasing grain number and grain weight. These findings suggest that Hap-HNW could be used in strategies to breed high-yielding temperate japonica lowland rice.
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Affiliation(s)
- Yingchun Han
- Henan Key Laboratory of Rice Molecular Breeding and High Efficiency Production, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Qianfeng Hu
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Nuo Gong
- Henan Key Laboratory of Rice Molecular Breeding and High Efficiency Production, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Huimin Yan
- Henan Key Laboratory of Rice Molecular Breeding and High Efficiency Production, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Najeeb Ullah Khan
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yanxiu Du
- Henan Key Laboratory of Rice Molecular Breeding and High Efficiency Production, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Hongzheng Sun
- Henan Key Laboratory of Rice Molecular Breeding and High Efficiency Production, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Quanzhi Zhao
- Henan Key Laboratory of Rice Molecular Breeding and High Efficiency Production, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
- Rice Industrial Technology Research Institute, Guizhou University, Guiyang, 550025, China
| | - Wanxi Peng
- School of Forestry, Henan Agricultural University, Zhengzhou, 450046, China
| | - Zichao Li
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Zhanying Zhang
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Junzhou Li
- Henan Key Laboratory of Rice Molecular Breeding and High Efficiency Production, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
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Kartseva T, Aleksandrov V, Alqudah AM, Arif MAR, Kocheva K, Doneva D, Prokopova K, Börner A, Misheva S. GWAS in a Collection of Bulgarian Old and Modern Bread Wheat Accessions Uncovers Novel Genomic Loci for Grain Protein Content and Thousand Kernel Weight. PLANTS (BASEL, SWITZERLAND) 2024; 13:1084. [PMID: 38674493 PMCID: PMC11054703 DOI: 10.3390/plants13081084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 04/03/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024]
Abstract
Genetic enhancement of grain production and quality is a priority in wheat breeding projects. In this study, we assessed two key agronomic traits-grain protein content (GPC) and thousand kernel weight (TKW)-across 179 Bulgarian contemporary and historic varieties and landraces across three growing seasons. Significant phenotypic variation existed for both traits among genotypes and seasons, and no discernible difference was evident between the old and modern accessions. To understand the genetic basis of the traits, we conducted a genome-wide association study with MLM using phenotypic data from the crop seasons, best linear unbiased estimators, and genotypic data from the 25K Infinium iSelect array. As a result, we detected 16 quantitative trait nucleotides (QTNs) associated with GPC and 15 associated with TKW, all of which passed the false discovery rate threshold. Seven loci favorably influenced GPC, resulting in an increase of 1.4% to 8.1%, while four loci had a positive impact on TKW with increases ranging from 1.9% to 8.4%. While some loci confirmed previously published associations, four QTNs linked to GPC on chromosomes 2A, 7A, and 7B, as well as two QTNs related to TKW on chromosomes 1B and 6A, may represent novel associations. Annotations for proteins involved in the senescence-associated nutrient remobilization and in the following buildup of resources required for seed germination have been found for selected putative candidate genes. These include genes coding for storage proteins, cysteine proteases, cellulose-synthase, alpha-amylase, transcriptional regulators, and F-box and RWP-RK family proteins. Our findings highlight promising genomic regions for targeted breeding programs aimed at improving grain yield and protein content.
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Affiliation(s)
- Tania Kartseva
- Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Block 21, 1113 Sofia, Bulgaria; (T.K.); (V.A.)
| | - Vladimir Aleksandrov
- Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Block 21, 1113 Sofia, Bulgaria; (T.K.); (V.A.)
| | - Ahmad M. Alqudah
- Biological Science Program, Department of Biological and Environmental Sciences, College of Art and Science, Qatar University, Doha P.O. Box 2713, Qatar;
| | - Mian Abdur Rehman Arif
- Nuclear Institute for Agriculture and Biology College, Pakistan Institute of Engineering and Applied Sciences (NIAB-C, PIEAS), Jhang Road, Faisalabad 38000, Pakistan;
| | - Konstantina Kocheva
- Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Block 21, 1113 Sofia, Bulgaria; (T.K.); (V.A.)
| | - Dilyana Doneva
- Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Block 21, 1113 Sofia, Bulgaria; (T.K.); (V.A.)
| | - Katelina Prokopova
- Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Block 21, 1113 Sofia, Bulgaria; (T.K.); (V.A.)
| | - Andreas Börner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK Gatersleben), OT Gatersleben, Corrensstraße 3, 06466 Seeland, Germany;
| | - Svetlana Misheva
- Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Block 21, 1113 Sofia, Bulgaria; (T.K.); (V.A.)
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Salami M, Heidari B, Alizadeh B, Batley J, Wang J, Tan XL, Dadkhodaie A, Richards C. Dissection of quantitative trait nucleotides and candidate genes associated with agronomic and yield-related traits under drought stress in rapeseed varieties: integration of genome-wide association study and transcriptomic analysis. FRONTIERS IN PLANT SCIENCE 2024; 15:1342359. [PMID: 38567131 PMCID: PMC10985355 DOI: 10.3389/fpls.2024.1342359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 02/26/2024] [Indexed: 04/04/2024]
Abstract
Introduction An important strategy to combat yield loss challenge is the development of varieties with increased tolerance to drought to maintain production. Improvement of crop yield under drought stress is critical to global food security. Methods In this study, we performed multiomics analysis in a collection of 119 diverse rapeseed (Brassica napus L.) varieties to dissect the genetic control of agronomic traits in two watering regimes [well-watered (WW) and drought stress (DS)] for 3 years. In the DS treatment, irrigation continued till the 50% pod development stage, whereas in the WW condition, it was performed throughout the whole growing season. Results The results of the genome-wide association study (GWAS) using 52,157 single-nucleotide polymorphisms (SNPs) revealed 1,281 SNPs associated with traits. Six stable SNPs showed sequence variation for flowering time between the two irrigation conditions across years. Three novel SNPs on chromosome C04 for plant weight were located within drought tolerance-related gene ABCG16, and their pleiotropically effects on seed weight per plant and seed yield were characterized. We identified the C02 peak as a novel signal for flowering time, harboring 52.77% of the associated SNPs. The 288-kbps LD decay distance analysis revealed 2,232 candidate genes (CGs) associated with traits. The CGs BIG1-D, CAND1, DRG3, PUP10, and PUP21 were involved in phytohormone signaling and pollen development with significant effects on seed number, seed weight, and grain yield in drought conditions. By integrating GWAS and RNA-seq, 215 promising CGs were associated with developmental process, reproductive processes, cell wall organization, and response to stress. GWAS and differentially expressed genes (DEGs) of leaf and seed in the yield contrasting accessions identified BIG1-D, CAND1, and DRG3 genes for yield variation. Discussion The results of our study provide insights into the genetic control of drought tolerance and the improvement of marker-assisted selection (MAS) for breeding high-yield and drought-tolerant varieties.
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Affiliation(s)
- Maryam Salami
- Department of Plant Production and Genetics, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Bahram Heidari
- Department of Plant Production and Genetics, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Bahram Alizadeh
- Oil Crops Research Department, Seed and Plant Improvement Institute, Agricultural Research Education and Extension, Organization, (AREEO), Karaj, Iran
| | - Jacqueline Batley
- School of Biological Sciences, University of Western Australia, Perth, WA, Australia
| | - Jin Wang
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Xiao-Li Tan
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Ali Dadkhodaie
- Department of Plant Production and Genetics, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Christopher Richards
- United States Department of Agriculture (USDA), Agricultural Research Service (ARS), National Laboratory for Genetic Resources Preservation, Fort Collins, CO, United States
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Wang Y, Lv Y, Yu H, Hu P, Wen Y, Wang J, Tan Y, Wu H, Zhu L, Wu K, Chai B, Liu J, Zeng D, Zhang G, Zhu L, Gao Z, Dong G, Ren D, Shen L, Zhang Q, Li Q, Guo L, Xiong G, Qian Q, Hu J. GR5 acts in the G protein pathway to regulate grain size in rice. PLANT COMMUNICATIONS 2024; 5:100673. [PMID: 37596786 PMCID: PMC10811372 DOI: 10.1016/j.xplc.2023.100673] [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: 02/24/2023] [Revised: 08/09/2023] [Accepted: 08/14/2023] [Indexed: 08/20/2023]
Abstract
Grain size is an important determinant of grain yield in rice. Although dozens of grain size genes have been reported, the molecular mechanisms that control grain size remain to be fully clarified. Here, we report the cloning and characterization of GR5 (GRAIN ROUND 5), which is allelic to SMOS1/SHB/RLA1/NGR5 and encodes an AP2 transcription factor. GR5 acts as a transcriptional activator and determines grain size by influencing cell proliferation and expansion. We demonstrated that GR5 physically interacts with five Gγ subunit proteins (RGG1, RGG2, DEP1, GS3, and GGC2) and acts downstream of the G protein complex. Four downstream target genes of GR5 in grain development (DEP2, DEP3, DRW1, and CyCD5;2) were revealed and their core T/CGCAC motif identified by yeast one-hybrid, EMSA, and ChIP-PCR experiments. Our results revealed that GR5 interacts with Gγ subunits and cooperatively determines grain size by regulating the expression of downstream target genes. These findings provide new insight into the genetic regulatory network of the G protein signaling pathway in the control of grain size and provide a potential target for high-yield rice breeding.
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Affiliation(s)
- Yueying Wang
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Yang Lv
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Haiping Yu
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Peng Hu
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Yi Wen
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Junge Wang
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Yiqing Tan
- Nanjing Agricultural University, Nan Jing 210000, Jiangsu, China
| | - Hao Wu
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Lixin Zhu
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Kaixiong Wu
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Bingze Chai
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Jialong Liu
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Dali Zeng
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Guangheng Zhang
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Li Zhu
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Zhenyu Gao
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Guojun Dong
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Deyong Ren
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Lan Shen
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Qiang Zhang
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Qing Li
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Longbiao Guo
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Guosheng Xiong
- Nanjing Agricultural University, Nan Jing 210000, Jiangsu, China.
| | - Qian Qian
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China; Hainan Yazhou Bay Seed Laboratory, Sanya 572024, Hainan, China; National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China.
| | - Jiang Hu
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China; Hainan Yazhou Bay Seed Laboratory, Sanya 572024, Hainan, China; National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China.
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5
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Bai F, Ma H, Cai Y, Shahid MQ, Zheng Y, Lang C, Chen Z, Wu J, Liu X, Wang L. Natural allelic variation in GRAIN SIZE AND WEIGHT 3 of wild rice regulates the grain size and weight. PLANT PHYSIOLOGY 2023; 193:502-518. [PMID: 37249047 PMCID: PMC10469372 DOI: 10.1093/plphys/kiad320] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 04/18/2023] [Accepted: 05/02/2023] [Indexed: 05/31/2023]
Abstract
Grain size is important for yield in rice (Oryza sativa L.). Although many genes involved in grain size have been isolated, few can be used in breeding due to their interactions and phenotypic effects. Here, we describe natural variation in the granule-type quantitative trait locus GRAIN SIZE AND WEIGHT 3 (GSW3) located on chromosome 3 in wild rice (Oryza rufipogon Griff.) that encodes a GTPase-regulated protein and negatively regulates grain length, grain width, and 1,000-grain weight. The insertion of a 232-bp fragment of the genomic sequence in the wild rice, a natural allelic variant gene (GSW3), increased the expression levels and reduced the grain length and width and 1,000-grain weight. Knockout of GSW3 in the wild rice inbred line Huaye 3 increased the grain length and width and 1,000-grain weight. Introducing GSW3Huaye3 into cultivated rice line KJ01 and overexpressing GSW3Huaye3 in Huaye 3 resulted in reduced grain length and width and 1,000-grain weight, and grain size and 1,000-grain weight changes were closely related to GSW3 expression levels. GSW3 regulated the grain length and width simultaneously by promoting grain glume cell division and longitudinal and transverse cell growth. GSW3 was also involved in regulating the gibberellic acid signaling pathway and negatively regulated plant growth. Furthermore, a critical SNP in the GSW3 coding region was obviously correlated with grain size variation in a core collection of cultivated rice. This SNP resulted in an amino acid substitution from Gln to Arg at position 161 in GSW3, which reduced the grain size. Our study shows that GSW3 negatively regulates the grain shape, which could explain different grain shapes in modern cultivars and wild rice. GSW3 may also be used for breeding rice varieties with improved grain shapes and higher yield.
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Affiliation(s)
- Feng Bai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- College of Agriculture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Huijin Ma
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- College of Agriculture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Yichang Cai
- College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- College of Agriculture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Yuebin Zheng
- College of Agriculture, South China Agricultural University, Guangzhou 510642, China
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Chuan Lang
- College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Zhixiong Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- College of Agriculture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Jinwen Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- College of Agriculture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Xiangdong Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- College of Agriculture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Lan Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- College of Agriculture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
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Developing Genetic Engineering Techniques for Control of Seed Size and Yield. Int J Mol Sci 2022; 23:ijms232113256. [PMID: 36362043 PMCID: PMC9655546 DOI: 10.3390/ijms232113256] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/15/2022] [Accepted: 10/15/2022] [Indexed: 11/06/2022] Open
Abstract
Many signaling pathways regulate seed size through the development of endosperm and maternal tissues, which ultimately results in a range of variations in seed size or weight. Seed size can be determined through the development of zygotic tissues (endosperm and embryo) and maternal ovules. In addition, in some species such as rice, seed size is largely determined by husk growth. Transcription regulator factors are responsible for enhancing cell growth in the maternal ovule, resulting in seed growth. Phytohormones induce significant effects on entire features of growth and development of plants and also regulate seed size. Moreover, the vegetative parts are the major source of nutrients, including the majority of carbon and nitrogen-containing molecules for the reproductive part to control seed size. There is a need to increase the size of seeds without affecting the number of seeds in plants through conventional breeding programs to improve grain yield. In the past decades, many important genetic factors affecting seed size and yield have been identified and studied. These important factors constitute dynamic regulatory networks governing the seed size in response to environmental stimuli. In this review, we summarized recent advances regarding the molecular factors regulating seed size in Arabidopsis and other crops, followed by discussions on strategies to comprehend crops' genetic and molecular aspects in balancing seed size and yield.
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7
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Ye Y, Wang S, Ren Y, Yang H, Guo J, Jiang H, Zhu X, Li W, Tao L, Zhan Y, Wu Y, Fu X, Wu K, Liu B. Low grain weight, a new allele of BRITTLE CULM12, affects grain size through regulating GW7 expression in rice. FRONTIERS IN PLANT SCIENCE 2022; 13:997624. [PMID: 36176686 PMCID: PMC9513473 DOI: 10.3389/fpls.2022.997624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 08/16/2022] [Indexed: 06/16/2023]
Abstract
Grain weight is a major determinant in rice yield, which is tightly associated with grain size. However, the underlying molecular mechanisms that control this trait remain unclear. Here, we report a rice (Oryza sativa) mutant, low grain weight (lgw), which shows that reduced grain length is caused by decreased cell elongation and proliferation. Map-based cloning revealed that all mutant phenotypes resulted from a nine-base pair (bp) deletion in LGW, which encodes the kinesin-like protein BRITTLE CULM12 (BC12). Protein sequence alignment analysis revealed that the mutation site was located at the nuclear localization signal (NLS) of LGW/BC12, resulting in the lgw protein not being located in the nucleus. LGW is preferentially expressed in both culms and roots, as well as in the early developing panicles. Overexpression of LGW increased the grain length, indicating that LGW is a positive regulator for regulating grain length. In addition, LGW/BC12 is directly bound to the promoter of GW7 and activates its expression. Elevating the GW7 expression levels in lgw plants rescued the small grain size phenotype. We conclude that LGW regulates grain development by directly binding to the GW7 promoter and activating its expression. Our findings revealed that LGW plays an important role in regulating grain size, and manipulation of this gene provides a new strategy for regulating grain weight in rice.
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Affiliation(s)
- Yafeng Ye
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
- Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Shuoxun Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yan Ren
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
- Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Huijie Yang
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
- Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Junyao Guo
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
- Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Hongrui Jiang
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
- Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Xiaotong Zhu
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
- Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Wenhao Li
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
- Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Liangzhi Tao
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
- Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Yue Zhan
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
- Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Yuejin Wu
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
- Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Xiangdong Fu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Kun Wu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Binmei Liu
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
- Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
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Varshney V, Majee M. Emerging roles of the ubiquitin-proteasome pathway in enhancing crop yield by optimizing seed agronomic traits. PLANT CELL REPORTS 2022; 41:1805-1826. [PMID: 35678849 DOI: 10.1007/s00299-022-02884-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
Ubiquitin-proteasome pathway has the potential to modulate crop productivity by influencing agronomic traits. Being sessile, the plant often uses the ubiquitin-proteasome pathway to maintain the stability of different regulatory proteins to survive in an ever-changing environment. The ubiquitin system influences plant reproduction, growth, development, responses to the environment, and processes that control critical agronomic traits. E3 ligases are the major players in this pathway, and they are responsible for recognizing and tagging the targets/substrates. Plants have a variety of E3 ubiquitin ligases, whose functions have been studied extensively, ranging from plant growth to defense strategies. Here we summarize three agronomic traits influenced by ubiquitination: seed size and weight, seed germination, and accessory plant agronomic traits particularly panicle architecture, tillering in rice, and tassels branch number in maize. This review article highlights some recent progress on how the ubiquitin system influences the stability/modification of proteins that determine seed agronomic properties like size, weight, germination and filling, and ultimately agricultural productivity and quality. Further research into the molecular basis of the aforementioned processes might lead to the identification of genes that could be modified or selected for crop development. Likewise, we also propose advances and future perspectives in this regard.
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Affiliation(s)
- Vishal Varshney
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Manoj Majee
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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9
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Zhao Y, Shi Y, Jiang G, Wu Y, Ma M, Zhang X, Liang X, Zhou JM. Rice extra-large G proteins play pivotal roles in controlling disease resistance and yield-related traits. THE NEW PHYTOLOGIST 2022; 234:607-617. [PMID: 35090194 DOI: 10.1111/nph.17997] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 01/12/2022] [Indexed: 06/14/2023]
Abstract
To better explore the potential of rice extra-large G (XLG) proteins in future breeding, we characterised the function of OsXLG1, OsXLG2 and OsXLG3 in disease resistance. Loss-of-function Osxlg2 and Osxlg3 mutants showed reduced resistance to the fungal pathogen Magnaporthe oryzae, whereas Osxlg1 mutants were specifically compromised in resistance to the bacterial pathogen Xanthomonas oryzae pv oryzae. Consistent with their effects on rice blast resistance, mutations in OsXLG2 and OsXLG3 caused greater defects than did mutations in OsXLG1 for chitin-induced defence responses. All three OsXLGs interacted with components of a surface immune receptor complex composed of OsCERK1, OsRLCK176 and OsRLCK185. Further characterisation of yield-related traits showed that the Osxlg3 mutants displayed reduced plant height, panicle length and 1000grain weight, whereas Osxlg1 mutants exhibited increased plant height, panicle length and 1000-grain weight. Together the study shows the differential contributions of the three OsXLG proteins to disease resistance to fungal and bacterial pathogens, their yield-related traits and provides insights for future improvement of rice production.
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Affiliation(s)
- Yan Zhao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yiyun Shi
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Guanghuai Jiang
- Center for Molecular Agrobiology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yufeng Wu
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Miaomiao Ma
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaojuan Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiangxiu Liang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Jian-Min Zhou
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
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10
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Tiwari R, Bisht NC. The multifaceted roles of heterotrimeric G-proteins: lessons from models and crops. PLANTA 2022; 255:88. [PMID: 35304667 DOI: 10.1007/s00425-022-03868-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 03/04/2022] [Indexed: 06/14/2023]
Abstract
The review summarizes our advanced understanding of the heterotrimeric G-protein research from model plants and their emerging roles in modulating various plant architecture and agronomical traits in crop species. Heterotrimeric G-proteins (hereafter G-proteins), consisting of G-alpha (Gα), G-beta (Gβ) and G-gamma (Gγ) subunits, are key signal transducers conserved across different forms of life. The discovery of plant lineage-specific G-protein components (extra-large G-proteins and type-C Gγ subunits), inherent polyploidy in angiosperms, and unique modes of G-protein cycle regulation in plants pointed out to a few fundamental differences of plant G-protein signaling from its animal counterpart. Over the last 2 decades, extensive studies in the model plant Arabidopsis thaliana have confirmed the involvement of G-proteins in a wide range of plant growth and development, and stress adaptation processes. The G-protein research in crop species, however, is still in its infancy, and a handful of studies suggest important roles of G-proteins in regulating plant architectural and key agronomical traits including plant's response to abiotic and biotic factors. We propose that the advancement made in plant G-proteins research will facilitate the development of novel approaches to manage plant yield and fitness in changing environments.
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Affiliation(s)
- Ruchi Tiwari
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Naveen C Bisht
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India.
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11
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Li P, Chen YH, Lu J, Zhang CQ, Liu QQ, Li QF. Genes and Their Molecular Functions Determining Seed Structure, Components, and Quality of Rice. RICE (NEW YORK, N.Y.) 2022; 15:18. [PMID: 35303197 PMCID: PMC8933604 DOI: 10.1186/s12284-022-00562-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 03/01/2022] [Indexed: 05/14/2023]
Abstract
With the improvement of people's living standards and rice trade worldwide, the demand for high-quality rice is increasing. Therefore, breeding high quality rice is critical to meet the market demand. However, progress in improving rice grain quality lags far behind that of rice yield. This might be because of the complexity of rice grain quality research, and the lack of consensus definition and evaluation standards for high quality rice. In general, the main components of rice grain quality are milling quality (MQ), appearance quality (AQ), eating and cooking quality (ECQ), and nutritional quality (NQ). Importantly, all these quality traits are determined directly or indirectly by the structure and composition of the rice seeds. Structurally, rice seeds mainly comprise the spikelet hull, seed coat, aleurone layer, embryo, and endosperm. Among them, the size of spikelet hull is the key determinant of rice grain size, which usually affects rice AQ, MQ, and ECQ. The endosperm, mainly composed of starch and protein, is the major edible part of the rice seed. Therefore, the content, constitution, and physicochemical properties of starch and protein are crucial for multiple rice grain quality traits. Moreover, the other substances, such as lipids, minerals, vitamins, and phytochemicals, included in different parts of the rice seed, also contribute significantly to rice grain quality, especially the NQ. Rice seed growth and development are precisely controlled by many genes; therefore, cloning and dissecting these quality-related genes will enhance our knowledge of rice grain quality and will assist with the breeding of high quality rice. This review focuses on summarizing the recent progress on cloning key genes and their functions in regulating rice seed structure and composition, and their corresponding contributions to rice grain quality. This information will facilitate and advance future high quality rice breeding programs.
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Affiliation(s)
- Pei Li
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology/State Key Laboratory of Hybrid Rice, College of Agriculture, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Yu-Hao Chen
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology/State Key Laboratory of Hybrid Rice, College of Agriculture, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Jun Lu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology/State Key Laboratory of Hybrid Rice, College of Agriculture, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Chang-Quan Zhang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology/State Key Laboratory of Hybrid Rice, College of Agriculture, Yangzhou University, Yangzhou, 225009, Jiangsu, China
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Qiao-Quan Liu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology/State Key Laboratory of Hybrid Rice, College of Agriculture, Yangzhou University, Yangzhou, 225009, Jiangsu, China.
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, Jiangsu, China.
| | - Qian-Feng Li
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology/State Key Laboratory of Hybrid Rice, College of Agriculture, Yangzhou University, Yangzhou, 225009, Jiangsu, China.
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, Jiangsu, China.
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12
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Liang W, Hu F, Qi W, Zhao C, Chen T, Wang C, Lv Y, Zhang Y. Comprehensive Transcriptome Analysis of GS3 Near-Isogenic Lines During Panicle Development in Rice (Oryza sativa L.). Front Genet 2022; 13:857143. [PMID: 35299956 PMCID: PMC8921255 DOI: 10.3389/fgene.2022.857143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 02/15/2022] [Indexed: 11/13/2022] Open
Abstract
Panicle architecture is an important agronomic trait in rice that affects rice yields and quality. The GRAIN SIZE 3 (GS3) locus has been identified as a major quantitative trait locus (QTL) affecting grain length and weight. The current understanding of the function of the GS3 gene, especially concerning the regulatory mechanism of panicle development, is still in its infancy. In this study, we generated GS3 near-isogenic lines (NILs) by successive crossing and backcrossing of TD70 (large grain) with Kasalath (small grain), using Kasalath as the recurrent parent. To identify potential transcription dynamic changes in rice panicle formation and grain shape, we deeply analyzed transcriptional profiles for the NILs (NIL-GS3 and NIL-gs3) at three different panicle developmental stages (S, M, and L). A total of 887, 1,768, and 1,478 differentially expressed genes (DEGs) were identified at stages S, M, and L, respectively. We also found 542 differential expressed long non-coding RNAs (lncRNAs). Co-expression analysis further revealed significant clusters associated with different development periods in NIL-gs3 lines. Gene Ontology and KEGG enrichment analysis revealed G-protein signaling and hormones pathway were successively activated at the M and L stages of NIL-gs3, which indicated activation of the G-protein signaling pathway might trigger the down-streaming hormone signaling transduction. we found that other hormones such ABA, Auxin, CK were significantly enriched in the L stage in the NIL-gs3. We highlighted the synergistic interplay of G-protein and multiple hormones signaling pathways and their essential roles in regulating rice panicle formation and the grain shape. Our study provides an invaluable resource for further molecular mechanistic studies that affect rice grain size and provide new insight for directed selection by marker-assisted backcross breeding.
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Affiliation(s)
- Wenhua Liang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- Jiangsu High Quality Rice R&D Center, Nanjing Branch of China National Center for Rice Improvement, Nanjing, China
| | - Fengqin Hu
- Excellence and Innovation Center, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Weicong Qi
- Excellence and Innovation Center, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Chunfang Zhao
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- Jiangsu High Quality Rice R&D Center, Nanjing Branch of China National Center for Rice Improvement, Nanjing, China
| | - Tao Chen
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- Jiangsu High Quality Rice R&D Center, Nanjing Branch of China National Center for Rice Improvement, Nanjing, China
| | - Cailin Wang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- Jiangsu High Quality Rice R&D Center, Nanjing Branch of China National Center for Rice Improvement, Nanjing, China
| | - Yuanda Lv
- Excellence and Innovation Center, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- *Correspondence: Yuanda Lv, ; Yadong Zhang,
| | - Yadong Zhang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- Jiangsu High Quality Rice R&D Center, Nanjing Branch of China National Center for Rice Improvement, Nanjing, China
- Key Laboratory of Jiangsu Province for Agrobiology, Nanjing, China
- *Correspondence: Yuanda Lv, ; Yadong Zhang,
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13
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Gao X, Zhang J, Li J, Wang Y, Zhang R, Du H, Yin J, Cai G, Wang R, Zhang B, Zhao Z, Zhang H, Huang J. The phosphoproteomic and interactomic landscape of qGL3/OsPPKL1-mediated brassinosteroid signaling in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:1048-1063. [PMID: 34839552 DOI: 10.1111/tpj.15613] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 11/17/2021] [Accepted: 11/25/2021] [Indexed: 06/13/2023]
Abstract
Oryza sativa L. (rice) is one of the most important crops in the world, and grain size is a major component determining rice yield. Recent studies have identified a number of grain size regulators, which are involved in phytohormone signaling, G protein signaling, the mitogen-activated protein kinase signaling pathway, the ubiquitin-proteasome pathway or transcriptional regulation. In a previous study, we cloned qGL3/OsPPKL1 encoding a rice protein phosphatase that negatively modulates brassinosteroid (BR) signaling and grain length. Here, to further explore the qGL3-mediated BR signaling network, we performed phosphoproteomic screenings using two pairs of rice materials: the indica rice cultivar 9311 and its near-isogenic line NILqgl3 and the japonica rice cultivar Dongjin and its qGL3 knockout mutant m-qgl3. Together with qGL3-interacting proteins, we constructed the qGL3-mediated network, which reveals the relationships between BR signaling and other critical signaling pathways. Transgenic plants of these network components showed BR-related alterations in plant architecture. From this network, we validated a qGL3-interacting protein, O. sativa VERNALIZATION INSENSITIVE 3-LIKE 1 (OsVIL1), and demonstrated that qGL3 dephosphorylates OsVIL1 to modulate BR signaling. The qGL3-dependent network uncovered in this study increases our understanding of BR signaling and provides a profound foundation for addressing how BR modulates plant architecture in rice.
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Affiliation(s)
- Xiuying Gao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Provincial Engineering Research Center of Seed Industry Science and Technology, Nanjing, 210095, China
| | - Jiaqi Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Provincial Engineering Research Center of Seed Industry Science and Technology, Nanjing, 210095, China
| | - Jianbo Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Provincial Engineering Research Center of Seed Industry Science and Technology, Nanjing, 210095, China
| | - Yuji Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Provincial Engineering Research Center of Seed Industry Science and Technology, Nanjing, 210095, China
| | - Rong Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Provincial Engineering Research Center of Seed Industry Science and Technology, Nanjing, 210095, China
| | - Huaying Du
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Provincial Engineering Research Center of Seed Industry Science and Technology, Nanjing, 210095, China
| | - Jing Yin
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Provincial Engineering Research Center of Seed Industry Science and Technology, Nanjing, 210095, China
| | - Guang Cai
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Provincial Engineering Research Center of Seed Industry Science and Technology, Nanjing, 210095, China
| | - Ruqin Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Provincial Engineering Research Center of Seed Industry Science and Technology, Nanjing, 210095, China
| | - Baoyi Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Provincial Engineering Research Center of Seed Industry Science and Technology, Nanjing, 210095, China
| | - Zhuang Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Provincial Engineering Research Center of Seed Industry Science and Technology, Nanjing, 210095, China
| | - Hongsheng Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Provincial Engineering Research Center of Seed Industry Science and Technology, Nanjing, 210095, China
| | - Ji Huang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Provincial Engineering Research Center of Seed Industry Science and Technology, Nanjing, 210095, China
- Jiangsu Key Laboratory for Information Agriculture, Nanjing, 210095, China
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14
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Liu L, Zhou Y, Mao F, Gu Y, Tang Z, Xin Y, Liu F, Tang T, Gao H, Zhao X. Fine-Tuning of the Grain Size by Alternative Splicing of GS3 in Rice. RICE (NEW YORK, N.Y.) 2022; 15:4. [PMID: 35015162 PMCID: PMC8752655 DOI: 10.1186/s12284-022-00549-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 12/29/2021] [Indexed: 06/14/2023]
Abstract
Grain size is subtly regulated by multiple signaling pathways in rice. Alternative splicing is a general mechanism that regulates gene expression at the post-transcriptional level. However, to our knowledge, the molecular mechanism underlying grain size regulation by alternative splicing is largely unknown. GS3, the first identified QTL for grain size in rice, is regulated at the transcriptional and post-translational level. In this study, we identified that GS3 is subject to alternative splicing. GS3.1 and GS3.2, two dominant isoforms, accounts for about 50% and 40% of total transcripts, respectively. GS3.1 encodes the full-length protein, while GS3.2 generated a truncated proteins only containing OSR domain due to a 14 bp intronic sequence retention. Genetic analysis revealed that GS3.1 overexpressors decreased grain size, but GS3.2 showed no significant effect on grain size. Furthermore, we demonstrated that GS3.2 disrupts GS3.1 signaling by competitive occupation of RGB1. Therefore, we draw a conclusion that the alternative splicing of GS3 decreases the amount of GS3.1 and GS3.2 disrupts the GS3.1 signaling to inhibit the negative effects of GS3.1 to fine-tune grain size. Moreover, the mechanism is conserved in cereals rather than in Cruciferae, which is associated with its effects on grain size. The results provide a novel, conserved and important mechanism underlying grain size regulation at the post-transcriptional level in cereals.
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Affiliation(s)
- Lei Liu
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Huaiyin Normal University, Huai'an, 223300, China.
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huai'an, 223300, China.
| | - Ying Zhou
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Huaiyin Normal University, Huai'an, 223300, China
| | - Feng Mao
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Huaiyin Normal University, Huai'an, 223300, China
| | - Yujuan Gu
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Huaiyin Normal University, Huai'an, 223300, China
- College of Marine Resources and Environment, Hebei Normal University of Science and Technology, Qinhuangdao, 066600, China
| | - Ziwei Tang
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Huaiyin Normal University, Huai'an, 223300, China
| | - Yi Xin
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Huaiyin Normal University, Huai'an, 223300, China
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huai'an, 223300, China
| | - Fuxia Liu
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Huaiyin Normal University, Huai'an, 223300, China
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huai'an, 223300, China
| | - Tang Tang
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Huaiyin Normal University, Huai'an, 223300, China
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huai'an, 223300, China
| | - Hui Gao
- College of Marine Resources and Environment, Hebei Normal University of Science and Technology, Qinhuangdao, 066600, China
| | - Xiangxiang Zhao
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Huaiyin Normal University, Huai'an, 223300, China.
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huai'an, 223300, China.
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15
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Yang W, Wu K, Wang B, Liu H, Guo S, Guo X, Luo W, Sun S, Ouyang Y, Fu X, Chong K, Zhang Q, Xu Y. The RING E3 ligase CLG1 targets GS3 for degradation via the endosome pathway to determine grain size in rice. MOLECULAR PLANT 2021; 14:1699-1713. [PMID: 34216830 DOI: 10.1016/j.molp.2021.06.027] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 06/26/2021] [Accepted: 06/27/2021] [Indexed: 05/02/2023]
Abstract
G-protein signaling and ubiquitin-dependent degradation are both involved in grain development in rice, but how these pathways are coordinated in regulating this process is unknown. Here, we show that Chang Li Geng 1 (CLG1), which encodes an E3 ligase, regulates grain size by targeting the Gγ protein GS3, a negative regulator of grain length, for degradation. Overexpression of CLG1 led to increased grain length, while overexpression of mutated CLG1 with changes in three conserved amino acids decreased grain length. We found that CLG1 physically interacts with and ubiquitinats GS3which is subsequently degraded through the endosome degradation pathway, leading to increased grain size. Furthermore, we identified a critical SNP in the exon 3 of CLG1 that is significantly associated with grain size variation in a core collection of cultivated rice. This SNP results in an amino acid substitution from Arg to Ser at position 163 of CLG1 that enhances the E3 ligase activity of CLG1 and thus increases rice grain size. Both the expression level of CLG1 and the SNP CLG1163S may be useful variations for manipulating grain size in rice.
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Affiliation(s)
- Wensi Yang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kun Wu
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Bo Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huanhuan Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Siyi Guo
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoyu Guo
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Luo
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Shengyuan Sun
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Yidan Ouyang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiangdong Fu
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Kang Chong
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China; Innovation Academy for Seed Design, CAS, Beijing 100101, China
| | - Qifa Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China.
| | - Yunyuan Xu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; Innovation Academy for Seed Design, CAS, Beijing 100101, China.
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Qiao J, Jiang H, Lin Y, Shang L, Wang M, Li D, Fu X, Geisler M, Qi Y, Gao Z, Qian Q. A novel miR167a-OsARF6-OsAUX3 module regulates grain length and weight in rice. MOLECULAR PLANT 2021; 14:1683-1698. [PMID: 34186219 DOI: 10.1016/j.molp.2021.06.023] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 05/26/2021] [Accepted: 06/25/2021] [Indexed: 05/02/2023]
Abstract
Grain size is one of the most important factors that control rice yield, as it is associated with grain weight (GW). To date, dozens of rice genes that regulate grain size have been isolated; however, the regulatory mechanism underlying GW control is not fully understood. Here, the quantitative trait locus qGL5 for grain length (GL) and GW was identified in recombinant inbred lines of 9311 and Nipponbare (NPB) and fine mapped to a candidate gene, OsAUX3. Sequence variations between 9311 and NPB in the OsAUX3 promoter and loss of function of OsAUX3 led to higher GL and GW. RNA sequencing, gene expression quantification, dual-luciferase reporter assays, chromatin immunoprecipitation-quantitative PCR, and yeast one-hybrid assays demonstrated that OsARF6 is an upstream transcription factor regulating the expression of OsAUX3. OsARF6 binds directly to the auxin response elements of the OsAUX3 promoter, covering a single-nucleotide polymorphism site between 9311 and NPB/Dongjin/Hwayoung, and thereby controls GL by altering longitudinal expansion and auxin distribution/content in glume cells. Furthermore, we showed that miR167a positively regulate GL and GW by directing OsARF6 mRNA silencing. Taken together, our study reveals that a novel miR167a-OsARF6-OsAUX3 module regulates GL and GW in rice, providing a potential target for the improvement of rice yield.
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Affiliation(s)
- Jiyue Qiao
- Key Laboratory of Herbage & Endemic Crop Biology of Ministry of Education, Inner Mongolia Key Laboratory of Herbage & Endemic Crop Biotechnology, School of Life Sciences, Inner Mongolia University, Hohhot 010000, China; State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Hongzhen Jiang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Yuqing Lin
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Lianguang Shang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Mei Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Dongming Li
- Key Laboratory of Herbage & Endemic Crop Biology of Ministry of Education, Inner Mongolia Key Laboratory of Herbage & Endemic Crop Biotechnology, School of Life Sciences, Inner Mongolia University, Hohhot 010000, China
| | - Xiangdong Fu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, University of Chinese Academy of Sciences, 100049, China
| | - Markus Geisler
- Department of Biology, University of Fribourg, Rue Albert-Gockel 3, CH-1700 Fribourg, Switzerland
| | - Yanhua Qi
- Key Laboratory of Herbage & Endemic Crop Biology of Ministry of Education, Inner Mongolia Key Laboratory of Herbage & Endemic Crop Biotechnology, School of Life Sciences, Inner Mongolia University, Hohhot 010000, China; State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Zhenyu Gao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China.
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China; Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China.
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Pathak RR, Mandal VK, Jangam AP, Sharma N, Madan B, Jaiswal DK, Raghuram N. Heterotrimeric G-protein α subunit (RGA1) regulates tiller development, yield, cell wall, nitrogen response and biotic stress in rice. Sci Rep 2021; 11:2323. [PMID: 33504880 PMCID: PMC7840666 DOI: 10.1038/s41598-021-81824-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 01/12/2021] [Indexed: 01/27/2023] Open
Abstract
G-proteins are implicated in plant productivity, but their genome-wide roles in regulating agronomically important traits remain uncharacterized. Transcriptomic analyses of rice G-protein alpha subunit mutant (rga1) revealed 2270 differentially expressed genes (DEGs) including those involved in C/N and lipid metabolism, cell wall, hormones and stress. Many DEGs were associated with root, leaf, culm, inflorescence, panicle, grain yield and heading date. The mutant performed better in total weight of filled grains, ratio of filled to unfilled grains and tillers per plant. Protein–protein interaction (PPI) network analysis using experimentally validated interactors revealed many RGA1-responsive genes involved in tiller development. qPCR validated the differential expression of genes involved in strigolactone-mediated tiller formation and grain development. Further, the mutant growth and biomass were unaffected by submergence indicating its role in submergence response. Transcription factor network analysis revealed the importance of RGA1 in nitrogen signaling with DEGs such as Nin-like, WRKY, NAC, bHLH families, nitrite reductase, glutamine synthetase, OsCIPK23 and urea transporter. Sub-clustering of DEGs-associated PPI network revealed that RGA1 regulates metabolism, stress and gene regulation among others. Predicted rice G-protein networks mapped DEGs and revealed potential effectors. Thus, this study expands the roles of RGA1 to agronomically important traits and reveals their underlying processes.
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Affiliation(s)
- Ravi Ramesh Pathak
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sector 16C, Dwarka, New Delhi, 110078, India
| | - Vikas Kumar Mandal
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sector 16C, Dwarka, New Delhi, 110078, India
| | - Annie Prasanna Jangam
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sector 16C, Dwarka, New Delhi, 110078, India
| | - Narendra Sharma
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sector 16C, Dwarka, New Delhi, 110078, India
| | - Bhumika Madan
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sector 16C, Dwarka, New Delhi, 110078, India
| | - Dinesh Kumar Jaiswal
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sector 16C, Dwarka, New Delhi, 110078, India.
| | - Nandula Raghuram
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sector 16C, Dwarka, New Delhi, 110078, India.
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18
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Liu C, Ye X, Zou L, Xiang D, Wu Q, Wan Y, Wu X, Zhao G. Genome-wide identification of genes involved in heterotrimeric G-protein signaling in Tartary buckwheat (Fagopyrum tataricum) and their potential roles in regulating fruit development. Int J Biol Macromol 2021; 171:435-447. [PMID: 33434548 DOI: 10.1016/j.ijbiomac.2021.01.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/08/2020] [Accepted: 01/04/2021] [Indexed: 11/18/2022]
Abstract
Tartary buckwheat (Fagopyrum tataricum Gaertn.) is an economical crop with excellent edible, nutritional, and medicinal values. However, the production of Tartary buckwheat is very low and it is urgent to breed high-yield varieties for satisfying the increasing market demand. Heterotrimeric G-protein signaling involves in the regulation of agronomical traits and fruit development in several plant species. In this study, fifteen genes involved in G-protein signaling were characterized in Tartary buckwheat and their potential roles in fruit development were revealed by expression analysis. The exon-intron organization and conserved motif of Tartary buckwheat G-protein signaling genes were similar to those in other dicot plants. All these genes were ubiquitously and differently expressed in five tissues. The expression patterns of Tartary buckwheat G-protein signaling genes in fruit suggested they may play important roles in the fruit at early development stage, which was supported by meta-analysis of G-protein signaling genes' expression in the fruits from different species. Furthermore, we found the expression of G-protein signaling genes in fruit showed high correlation with 178 transcription factors, which indicated a transcriptional regulatory loop moderating G-protein signaling genes' expression during fruit development. This paper provides new insights into the physiological functions of G-protein signaling in fruit.
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Affiliation(s)
- Changying Liu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, PR China
| | - Xueling Ye
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, PR China
| | - Liang Zou
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, PR China
| | - Dabing Xiang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, PR China
| | - Qi Wu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, PR China
| | - Yan Wan
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, PR China
| | - Xiaoyong Wu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, PR China.
| | - Gang Zhao
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, PR China.
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Ge Q, Tang Y, Luo W, Zhang J, Chong K, Xu Y. A Cyclophilin OsCYP20-2 Interacts with OsSYF2 to Regulate Grain Length by Pre-mRNA Splicing. RICE (NEW YORK, N.Y.) 2020; 13:64. [PMID: 32910367 PMCID: PMC7483694 DOI: 10.1186/s12284-020-00425-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 08/31/2020] [Indexed: 05/04/2023]
Abstract
BACKGROUND Grain size is one of the key agronomic traits that impact grain yield. Several regulatory pathways had been reported to participate in grain size determination via cell expansion or proliferation in rice. However, little is known about cyclophilin and spliceosome participation in grain shape regulation. RESULTS Here, we identified OsCYP20-2, a cyclophilin that influences spliceosome assembly to determine grain length. oscyp20-2 t1, a knock out mutant of OsCYP20-2 caused by T-DNA insertion, produced shorter grains with deficient cell elongation. Through yeast two-hybrid screening and pull-down assays, OsSYF2, a pre-mRNA splicing factor, was identified as an interacting protein of OsCYP20-2. The phenotypes of transgenic lines indicated that OsSYF2 positively regulates grain length via its influence on cell expansion. Transcriptomic analysis showed that OsSYF2 controls the expression and pre-mRNA alternative splicing of genes involved in sugar metabolism. In addition, these two genes have similar effects on panicle architecture. CONCLUSIONS Taken together, OsSYF2, an interacting protein of OsCYP20-2, controls grain length and panicle architecture by regulating the alternative splicing of pre-mRNA involved in cell elongation and sugar metabolism.
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Affiliation(s)
- Qiang Ge
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Present Address: College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Yongyan Tang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Wei Luo
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Jingyu Zhang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Kang Chong
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- Innovation Academy for Seed Design, CAS, Beijing, 100101, China
| | - Yunyuan Xu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- Innovation Academy for Seed Design, CAS, Beijing, 100101, 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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21
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Affiliation(s)
- John Harada
- Department of Plant Biology, University of California, Davis, CA, 95616, USA
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