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Shen L, Zhang LH, Xia X, Yang SX, Yang X. Cytochrome P450 SmCYP78A7a positively functions in eggplant response to salt stress via forming a positive feedback loop with SmWRKY11. Int J Biol Macromol 2024; 269:132139. [PMID: 38719008 DOI: 10.1016/j.ijbiomac.2024.132139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 04/25/2024] [Accepted: 05/05/2024] [Indexed: 05/12/2024]
Abstract
Accumulating salinity in soil critically affected growth, development, and yield in plant. However, the mechanisms of plant against salt stress largely remain unknown. Herein, we identified a gene named SmCYP78A7a, which encoded a cytochrome P450 monooxygenase and belonged to the CYP78A sub-family, and its transcript level was significantly up-regulated by salt stress and down-regulated by dehydration stress. SmCYP78A7a located in the endoplasmic reticulum. Silencing of SmCYP78A7a enhanced susceptibility of eggplant to salt stress, and significantly down-regulated the transcript levels of salt stress defense related genes SmGSTU10 and SmWRKY11 as well as increased hydrogen peroxide (H2O2) content and decreased catalase (CAT), peroxidase (POD), and ascorbate peroxidase (APX) enzyme activities. In addition, SmCYP78A7a transient expression enhanced eggplant tolerance to salt stress. By chromatin immunoprecipitation PCR (ChIP-PCR), luciferase reporter assay, and electrophoretic mobility shift assay (EMSA), SmWRKY11 activated SmCYP78A7a expression by directly binding to the W-box 6-8 (W-box 6, W-box 7, and W-box 8) within SmCYP78A7a promoter to confer eggplant tolerance to salt stress. In summary, our finds reveal that SmCYP78A7a positively functions in eggplant response to salt stress via forming a positive feedback loop with SmWRKY11, and provide a new insight into regulatory mechanisms of eggplant to salt stress.
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Affiliation(s)
- Lei Shen
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China.
| | - Long-Hao Zhang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| | - Xin Xia
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| | - Shi-Xin Yang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| | - Xu Yang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China.
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2
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Cao Y, Han Z, Zhang Z, He L, Huang C, Chen J, Dai F, Xuan L, Yan S, Si Z, Hu Y, Zhang T. UDP-glucosyltransferase 71C4 controls the flux of phenylpropanoid metabolism to shape cotton seed development. PLANT COMMUNICATIONS 2024:100938. [PMID: 38689494 DOI: 10.1016/j.xplc.2024.100938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 04/24/2024] [Accepted: 04/29/2024] [Indexed: 05/02/2024]
Abstract
Seeds play a crucial role in plant reproduction, making it essential to identify genes that affect seed development. In this study, we focused on UDP-glucosyltransferase 71C4 (UGT71C4) in cotton, a member of the glycosyltransferase family that shapes seed width and length, thereby influencing seed index and seed cotton yield. Overexpression of UGT71C4 results in seed enlargement owing to its glycosyltransferase activity on flavonoids, which redirects metabolic flux from lignin to flavonoid metabolism. This shift promotes cell proliferation in the ovule via accumulation of flavonoid glycosides, significantly enhancing seed cotton yield and increasing the seed index from 10.66 g to 11.91 g. By contrast, knockout of UGT71C4 leads to smaller seeds through activation of the lignin metabolism pathway and redirection of metabolic flux back to lignin synthesis. This redirection leads to increased ectopic lignin deposition in the ovule, inhibiting ovule growth and development, and alters yield components, increasing the lint percentage from 41.42% to 43.40% and reducing the seed index from 10.66 g to 8.60 g. Our research sheds new light on seed size development and reveals potential pathways for enhancing seed yield.
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Affiliation(s)
- Yiwen Cao
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China; Hainan Institute, Zhejiang University, Sanya, China
| | - Zegang Han
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | | | - Lu He
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Chujun Huang
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Jinwen Chen
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Fan Dai
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Lisha Xuan
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Sunyi Yan
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Zhanfeng Si
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yan Hu
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China; Hainan Institute, Zhejiang University, Sanya, China
| | - Tianzhen Zhang
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China; Hainan Institute, Zhejiang University, Sanya, China.
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3
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Yan Y, Zhu X, Qi H, Zhang H, He J. Regulatory mechanism and molecular genetic dissection of rice ( Oryza sativa L.) grain size. Heliyon 2024; 10:e27139. [PMID: 38486732 PMCID: PMC10938125 DOI: 10.1016/j.heliyon.2024.e27139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 02/18/2024] [Accepted: 02/25/2024] [Indexed: 03/17/2024] Open
Abstract
With the sharp increase of the global population, adequate food supply is a great challenge. Grain size is an essential determinant of rice yield and quality. It is a typical quantitative trait controlled by multiple genes. In this paper, we summarized the quantitative trait loci (QTL) that have been molecularly characterized and provided a comprehensive summary of the regulation mechanism and genetic pathways of rice grain size. These pathways include the ubiquitin-proteasome system, G-protein, mitogen-activated protein kinase, phytohormone, transcriptional factors, abiotic stress. In addition, we discuss the possible application of advanced molecular biology methods and reasonable breeding strategies, and prospective on the development of high-yielding and high-quality rice varieties using molecular biology techniques.
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Affiliation(s)
- Yuntao Yan
- College of Agronomy, Hunan Agricultural University, Changsha 420128, China
| | - Xiaoya Zhu
- College of Agronomy, Hunan Agricultural University, Changsha 420128, China
| | - Hui Qi
- College of Agronomy, Hunan Agricultural University, Changsha 420128, China
- Hunan Institute of Nuclear Agricultural Science and Space Breeding, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Haiqing Zhang
- College of Agronomy, Hunan Agricultural University, Changsha 420128, China
| | - Jiwai He
- College of Agronomy, Hunan Agricultural University, Changsha 420128, China
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4
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Doll NM, Nowack MK. Endosperm cell death: roles and regulation in angiosperms. JOURNAL OF EXPERIMENTAL BOTANY 2024:erae052. [PMID: 38364847 DOI: 10.1093/jxb/erae052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Indexed: 02/18/2024]
Abstract
Double fertilization in angiosperms results in the formation of a second zygote, the fertilized endosperm. Unlike its embryo sibling, the endosperm is a transient structure that eventually undergoes developmentally controlled programmed cell death (PCD) at specific time points of seed development or germination. The nature of endosperm PCD exhibits a considerable diversity, both across different angiosperm taxa and within distinct endosperm tissues. In endosperm-less species, PCD might cause central cell degeneration as a mechanism preventing the formation of a fertilized endosperm. In most other angiosperms, embryo growth necessitates the elimination of surrounding endosperm cells. Nevertheless, complete elimination of the endosperm is rare, and in most cases, specific endosperm tissues persist. In mature seeds, these persisting cells may be dead, such as the starchy endosperm in cereals, or remain alive to die only during germination, like the cereal aleurone or the endosperm of castor beans. In this review, we explore the current knowledge surrounding the cellular, molecular, and genetic aspects of endosperm PCD, and the influence environmental stresses have on PCD processes. Overall, this review provides an exhaustive overview of endosperm PCD processes in angiosperms, shedding light on its diverse mechanisms and its significance in seed development and seedling establishment.
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Affiliation(s)
- Nicolas M Doll
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center of Plant Systems Biology, Ghent 9052, Belgium
| | - Moritz K Nowack
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center of Plant Systems Biology, Ghent 9052, Belgium
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Tan J, Shen M, Chai N, Liu Q, Liu YG, Zhu Q. Genome editing for plant synthetic metabolic engineering and developmental regulation. JOURNAL OF PLANT PHYSIOLOGY 2023; 291:154141. [PMID: 38016350 DOI: 10.1016/j.jplph.2023.154141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/31/2023] [Accepted: 11/17/2023] [Indexed: 11/30/2023]
Abstract
Plant metabolism and development are a reflection of the orderly expression of genetic information intertwined with the environment interactions. Genome editing is the cornerstone for scientists to modify endogenous genes or introduce exogenous functional genes and metabolic pathways, holding immense potential applications in molecular breeding and biosynthesis. Over the course of nearly a decade of development, genome editing has advanced significantly beyond the simple cutting of double-stranded DNA, now enabling precise base and fragment replacements, regulation of gene expression and translation, as well as epigenetic modifications. However, the utilization of genome editing in plant synthetic metabolic engineering and developmental regulation remains exploratory. Here, we provide an introduction and a comprehensive overview of the editing attributes associated with various CRISPR/Cas tools, along with diverse strategies for the meticulous control of plant metabolic pathways and developments. Furthermore, we discuss the limitations of current approaches and future prospects for genome editing-driven plant breeding.
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Affiliation(s)
- Jiantao Tan
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Key Laboratory of Genetics and Breeding of High-Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, 510640, China.
| | - Mengyuan Shen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Key Laboratory of Genetics and Breeding of High-Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, 510640, China
| | - Nan Chai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Qi Liu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Key Laboratory of Genetics and Breeding of High-Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, 510640, China
| | - Yao-Guang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Qinlong Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
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Zhou C, Lin Q, Ren Y, Lan J, Miao R, Feng M, Wang X, Liu X, Zhang S, Pan T, Wang J, Luo S, Qian J, Luo W, Mou C, Nguyen T, Cheng Z, Zhang X, Lei C, Zhu S, Guo X, Wang J, Zhao Z, Liu S, Jiang L, Wan J. A CYP78As-small grain4-coat protein complex Ⅱ pathway promotes grain size in rice. THE PLANT CELL 2023; 35:4325-4346. [PMID: 37738653 PMCID: PMC10689148 DOI: 10.1093/plcell/koad239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 07/11/2023] [Accepted: 08/11/2023] [Indexed: 09/24/2023]
Abstract
CYP78A, a cytochrome P450 subfamily that includes rice (Oryza sativa L.) BIG GRAIN2 (BG2, CYP78A13) and Arabidopsis thaliana KLUH (KLU, CYP78A5), generate an unknown mobile growth signal (referred to as a CYP78A-derived signal) that increases grain (seed) size. However, the mechanism by which the CYP78A pathway increases grain size remains elusive. Here, we characterized a rice small grain mutant, small grain4 (smg4), with smaller grains than its wild type due to restricted cell expansion and cell proliferation in spikelet hulls. SMG4 encodes a multidrug and toxic compound extrusion (MATE) transporter. Loss of function of SMG4 causes smaller grains while overexpressing SMG4 results in larger grains. SMG4 is mainly localized to endoplasmic reticulum (ER) exit sites (ERESs) and partially localized to the ER and Golgi. Biochemically, SMG4 interacts with coat protein complex Ⅱ (COPⅡ) components (Sar1, Sec23, and Sec24) and CYP78As (BG2, GRAIN LENGTH 3.2 [GL3.2], and BG2-LIKE 1 [BG2L1]). Genetically, SMG4 acts, at least in part, in a common pathway with Sar1 and CYP78As to regulate grain size. In summary, our findings reveal a CYP78As-SMG4-COPⅡ regulatory pathway for grain size in rice, thus providing new insights into the molecular and genetic regulatory mechanism of grain size.
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Affiliation(s)
- Chunlei Zhou
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qibing Lin
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yulong Ren
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jie Lan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Rong Miao
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Miao Feng
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xin Wang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xi Liu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Shengzhong Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Tian Pan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiachang Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Sheng Luo
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jinsheng Qian
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wenfan Luo
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Changling Mou
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Thanhliem Nguyen
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhijun Cheng
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xin Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Cailin Lei
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shanshan Zhu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiuping Guo
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jie Wang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhichao Zhao
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shijia Liu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Ling Jiang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Jianmin Wan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Zhao Y, Yin T, Ran X, Liu W, Shen Y, Guo H, Peng Y, Zhang C, Ding Y, Tang S. Stimulus-responsive proteins involved in multi-process regulation of storage substance accumulation during rice grain filling under elevated temperature. BMC PLANT BIOLOGY 2023; 23:547. [PMID: 37936114 PMCID: PMC10631114 DOI: 10.1186/s12870-023-04563-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 10/26/2023] [Indexed: 11/09/2023]
Abstract
BACKGROUND The intensified global warming during grain filling deteriorated rice quality, in particular increasing the frequency of chalky grains which markedly impact market value. The formation of rice quality is a complex process influenced by multiple genes, proteins and physiological metabolic processes. Proteins responsive to stimulus can adjust the ability of plants to respond to unfavorable environments, which may be an important protein involved in the regulation of quality formation under elevated temperature. However, relatively few studies have hindered our further understanding of rice quality formation under elevated temperature. RESULTS We conducted the actual field elevated temperature experiment and performed proteomic analysis of rice grains at the early stage of grain filling. Starting with the response to stimulus in GO annotation, 22 key proteins responsive to stimulus were identified in the regulation of grain filling and response to elevated temperature. Among the proteins responsive to stimulus, during grain filling, an increased abundance of signal transduction and other stress response proteins, a decreased abundance of reactive oxygen species-related proteins, and an increased accumulation of storage substance metabolism proteins consistently contributed to grain filling. However, the abundance of probable indole-3-acetic acid-amido synthetase GH3.4, probable indole-3-acetic acid-amido synthetase GH3.8 and CBL-interacting protein kinase 9 belonged to signal transduction were inhibited under elevated temperature. In the reactive oxygen species-related protein, elevated temperature increased the accumulation of cationic peroxidase SPC4 and persulfide dioxygenase ETHE1 homolog to maintain normal physiological homeostasis. The increased abundance of alpha-amylase isozyme 3E and seed allergy protein RA5 was related to the storage substance metabolism, which regulated starch and protein accumulation under elevated temperature. CONCLUSION Auxin synthesis and calcium signal associated with signal transduction, other stress responses, protein transport and modification, and reactive oxygen species-related proteins may be key proteins responsive to stimulus in response to elevated temperature. Alpha-amylase isozyme 3E and seed allergy protein RA5 may be the key proteins to regulate grain storage substance accumulation and further influence quality under elevated temperature. This study enriched the regulatory factors involved in the response to elevated temperature and provided a new idea for a better understanding of grain response to temperature.
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Affiliation(s)
- Yufei Zhao
- College of Agronomy, Nanjing Agricultural University, 210095, Nanjing, People's Republic of China
| | - Tongyang Yin
- College of Agronomy, Nanjing Agricultural University, 210095, Nanjing, People's Republic of China
| | - Xuan Ran
- College of Agronomy, Nanjing Agricultural University, 210095, Nanjing, People's Republic of China
| | - Wenzhe Liu
- College of Agronomy, Nanjing Agricultural University, 210095, Nanjing, People's Republic of China
| | - Yingying Shen
- College of Agronomy, Nanjing Agricultural University, 210095, Nanjing, People's Republic of China
| | - Hao Guo
- College of Agronomy, Nanjing Agricultural University, 210095, Nanjing, People's Republic of China
| | - Yuxuan Peng
- College of Agronomy, Nanjing Agricultural University, 210095, Nanjing, People's Republic of China
| | - Chen Zhang
- College of Agronomy, Nanjing Agricultural University, 210095, Nanjing, People's Republic of China
| | - Yanfeng Ding
- College of Agronomy, Nanjing Agricultural University, 210095, Nanjing, People's Republic of China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, 210095, Nanjing, People's Republic of China
| | - She Tang
- College of Agronomy, Nanjing Agricultural University, 210095, Nanjing, People's Republic of China.
- Jiangsu Collaborative Innovation Center for Modern Crop Production, 210095, Nanjing, People's Republic of China.
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Liu Z, Sun H, Zhang Y, Du M, Xiang J, Li X, Chang Y, Sun J, Cheng X, Xiong M, Zhao Z, Liu E. Mining the candidate genes of rice panicle traits via a genome-wide association study. Front Genet 2023; 14:1239550. [PMID: 37732315 PMCID: PMC10507276 DOI: 10.3389/fgene.2023.1239550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 08/16/2023] [Indexed: 09/22/2023] Open
Abstract
Panicle traits are important for improving the panicle architecture and grain yield of rice. Therefore, we performed a genome-wide association study (GWAS) to analyze and determine the genetic determinants of five panicle traits. A total of 1.29 million single nucleotide polymorphism (SNP) loci were detected in 162 rice materials. We carried out a GWAS of panicle length (PL), total grain number per panicle (TGP), filled grain number per panicle (FGP), seed setting rate (SSR) and grain weight per panicle (GWP) in 2019, 2020 and 2021. Four quantitative trait loci (QTLs) for PL were detected on chromosomes 1, 6, and 9; one QTL for TGP, FGP, and GWP was detected on chromosome 4; two QTLs for FGP were detected on chromosomes 4 and 7; and one QTL for SSR was detected on chromosome 1. These QTLs were detected via a general linear model (GLM) and mixed linear model (MLM) in both years of the study period. In this study, the genomic best linear unbiased prediction (BLUP) method was used to verify the accuracy of the GWAS results. There are nine QTLs were both detected by the multi-environment GWAS method and the BLUP method. Moreover, further analysis revealed that three candidate genes, LOC_Os01g43700, LOC_Os09g25784, and LOC_Os04g47890, may be significantly related to panicle traits of rice. Haplotype analysis indicated that LOC_Os01g43700 and LOC_Os09g25784 are highly associated with PL and that LOC_Os04g47890 is highly associated with TGP, FGP, and GWP. Our results offer essential genetic information for the molecular improvement of panicle traits. The identified candidate genes and elite haplotypes could be used in marker-assisted selection to improve rice yield through pyramid breeding.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Erbao Liu
- College of Agronomy, Anhui Agricultural University, Hefei, China
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9
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Qing D, Chen W, Huang S, Li J, Pan Y, Zhou W, Liang Q, Yuan J, Gan D, Chen L, Chen L, Huang J, Zhou Y, Dai G, Deng G. Editing of rice (Oryza sativa L.) OsMKK3 gene using CRISPR/Cas9 decreases grain length by modulating the expression of photosystem components. Proteomics 2023; 23:e2200538. [PMID: 37376803 DOI: 10.1002/pmic.202200538] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 06/14/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023]
Abstract
Grain size is one of the most important agronomic traits for grain yield determination in rice. To better understand the proteins that are regulated by the grain size regulatory gene OsMKK3, this gene was knocked out using the CRISPR/Cas9 system, and tandem mass tag (TMT) labeling combined with liquid chromatograph-tandem mass spectrometry analysis was performed to study the regulation of proteins in the panicle. Quantitative proteomic screening revealed a total of 106 differentially expressed proteins (DEPs) via comparison of the OsMKK3 mutant line to the wild-type YexiangB, including 15 and 91 up-regulated and down-regulated DEPs, respectively. Pathway analysis revealed that DEPs were enriched in metabolic pathways, biosynthesis of secondary metabolites, phenylpropanoid biosynthesis, and photosynthesis. Strong interactions were detected among seven down-regulated proteins related to photosystem components in the protein-protein interaction network, and photosynthetic rate was decreased in mutant plants. The results of the liquid chromatography-parallel reaction monitoring/mass spectromery analysis and western blot analysis were consistent with the results of the proteomic analysis, and the results of the quantitative reverse transcription polymerase chain reaction analysis revealed that the expression levels of most candidate genes were consistent with protein levels. Overall, OsMKK3 controls grain size by regulating the protein content in cells. Our findings provide new candidate genes that will aid the study of grain size regulatory mechanisms associated with the mitogen-activated protein kinase (MAPK) signaling pathway.
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Affiliation(s)
- Dongjin Qing
- Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Nanning, China
| | - Weiwei Chen
- Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Nanning, China
| | - Suosheng Huang
- Guangxi Academy of Agricultural Sciences, Plant Protection Research Institute, Nanning, China
| | - Jingcheng Li
- Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Nanning, China
| | - Yinghua Pan
- Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Nanning, China
| | - Weiyong Zhou
- Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Nanning, China
| | - Qiongyue Liang
- Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Nanning, China
| | - Jinghua Yuan
- Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Nanning, China
| | - Dongmei Gan
- Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Nanning, China
| | - Li Chen
- Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Nanning, China
| | - Lei Chen
- Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Nanning, China
| | - Juan Huang
- Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Nanning, China
| | - Yan Zhou
- Key Laboratory of Chemistry and Engineering of Forest Products, School of Chemistry and Chemical Engineering, Guangxi Minzu University, Nanning, China
| | - Gaoxing Dai
- Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Nanning, China
| | - Guofu Deng
- Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Nanning, China
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10
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Wang N, Zhang W, Wang X, Zheng Z, Bai D, Li K, Zhao X, Xiang J, Liang Z, Qian Y, Wang W, Shi Y. Genome-Wide Association Study of Xian Rice Grain Shape and Weight in Different Environments. PLANTS (BASEL, SWITZERLAND) 2023; 12:2549. [PMID: 37447110 PMCID: PMC10347298 DOI: 10.3390/plants12132549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/29/2023] [Accepted: 07/03/2023] [Indexed: 07/15/2023]
Abstract
Drought is one of the key environmental factors affecting the growth and yield potential of rice. Grain shape, on the other hand, is an important factor determining the appearance, quality, and yield of rice grains. Here, we re-sequenced 275 Xian accessions and then conducted a genome-wide association study (GWAS) on six agronomic traits with the 404,411 single nucleotide polymorphisms (SNPs) derived by the best linear unbiased prediction (BLUP) for each trait. Under two years of drought stress (DS) and normal water (NW) treatments, a total of 16 QTLs associated with rice grain shape and grain weight were detected on chromosomes 1, 2, 3, 4, 5, 7, 8, 11, and 12. In addition, these QTLs were analyzed by haplotype analysis and functional annotation, and one clone (GSN1) and five new candidate genes were identified in the candidate interval. The findings provide important genetic information for the molecular improvement of grain shape and weight in rice.
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Affiliation(s)
- Nansheng Wang
- College of Agronomy, Anhui Agricultural University, Hefei 230000, China; (N.W.); (W.Z.); (X.W.); (Z.Z.); (D.B.); (K.L.); (X.Z.); (J.X.); (Z.L.); (Y.Q.)
| | - Wanyang Zhang
- College of Agronomy, Anhui Agricultural University, Hefei 230000, China; (N.W.); (W.Z.); (X.W.); (Z.Z.); (D.B.); (K.L.); (X.Z.); (J.X.); (Z.L.); (Y.Q.)
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xinchen Wang
- College of Agronomy, Anhui Agricultural University, Hefei 230000, China; (N.W.); (W.Z.); (X.W.); (Z.Z.); (D.B.); (K.L.); (X.Z.); (J.X.); (Z.L.); (Y.Q.)
| | - Zhenzhen Zheng
- College of Agronomy, Anhui Agricultural University, Hefei 230000, China; (N.W.); (W.Z.); (X.W.); (Z.Z.); (D.B.); (K.L.); (X.Z.); (J.X.); (Z.L.); (Y.Q.)
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Di Bai
- College of Agronomy, Anhui Agricultural University, Hefei 230000, China; (N.W.); (W.Z.); (X.W.); (Z.Z.); (D.B.); (K.L.); (X.Z.); (J.X.); (Z.L.); (Y.Q.)
| | - Keyang Li
- College of Agronomy, Anhui Agricultural University, Hefei 230000, China; (N.W.); (W.Z.); (X.W.); (Z.Z.); (D.B.); (K.L.); (X.Z.); (J.X.); (Z.L.); (Y.Q.)
| | - Xueyu Zhao
- College of Agronomy, Anhui Agricultural University, Hefei 230000, China; (N.W.); (W.Z.); (X.W.); (Z.Z.); (D.B.); (K.L.); (X.Z.); (J.X.); (Z.L.); (Y.Q.)
| | - Jun Xiang
- College of Agronomy, Anhui Agricultural University, Hefei 230000, China; (N.W.); (W.Z.); (X.W.); (Z.Z.); (D.B.); (K.L.); (X.Z.); (J.X.); (Z.L.); (Y.Q.)
| | - Zhaojie Liang
- College of Agronomy, Anhui Agricultural University, Hefei 230000, China; (N.W.); (W.Z.); (X.W.); (Z.Z.); (D.B.); (K.L.); (X.Z.); (J.X.); (Z.L.); (Y.Q.)
| | - Yingzhi Qian
- College of Agronomy, Anhui Agricultural University, Hefei 230000, China; (N.W.); (W.Z.); (X.W.); (Z.Z.); (D.B.); (K.L.); (X.Z.); (J.X.); (Z.L.); (Y.Q.)
| | - Wensheng Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yingyao Shi
- College of Agronomy, Anhui Agricultural University, Hefei 230000, China; (N.W.); (W.Z.); (X.W.); (Z.Z.); (D.B.); (K.L.); (X.Z.); (J.X.); (Z.L.); (Y.Q.)
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11
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Molecular bases of rice grain size and quality for optimized productivity. Sci Bull (Beijing) 2023; 68:314-350. [PMID: 36710151 DOI: 10.1016/j.scib.2023.01.026] [Citation(s) in RCA: 39] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/30/2022] [Accepted: 01/16/2023] [Indexed: 01/19/2023]
Abstract
The accomplishment of further optimization of crop productivity in grain yield and quality is a great challenge. Grain size is one of the crucial determinants of rice yield and quality; all of these traits are typical quantitative traits controlled by multiple genes. Research advances have revealed several molecular and developmental pathways that govern these traits of agronomical importance. This review provides a comprehensive summary of these pathways, including those mediated by G-protein, the ubiquitin-proteasome system, mitogen-activated protein kinase, phytohormone, transcriptional regulators, and storage product biosynthesis and accumulation. We also generalize the excellent precedents for rice variety improvement of grain size and quality, which utilize newly developed gene editing and conventional gene pyramiding capabilities. In addition, we discuss the rational and accurate breeding strategies, with the aim of better applying molecular design to breed high-yield and superior-quality varieties.
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12
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Chen P, Liu Q, Sun B, Lv S, Jiang L, Zhang J, Mao X, Yu H, Chen Y, Chen W, Fan Z, Pan D, Li C. Creation and gene expression analysis of a giant embryo rice mutant with high GABA content. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:3. [PMID: 37312870 PMCID: PMC10248637 DOI: 10.1007/s11032-022-01353-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 12/27/2022] [Indexed: 06/15/2023]
Abstract
Gamma-amino butyric acid (GABA) is a natural non-protein amino acid involved in stress, signal transmission, carbon and nitrogen balance, and other physiological processes in plants. In the human body, GABA has the effects of lowering blood pressure, anti-aging, and activating the liver and kidneys. However, there are few studies on the molecular regulation mechanism of genes in the metabolic pathways of GABA during grain development of giant embryo rice with high GABA content. In this study, three glant embryo (ge) mutants of different embryo sizes were obtained by CRISPR/Cas9 knockout, and it was found that GABA, protein, crude fat, and various mineral contents of the ge mutants were significantly increased. RNA-seq and qRT-PCR analysis showed that in the GABA shunt and polyamine degradation pathways, the expression levels of most of the genes encoding enzymes promoting GABA accumulation were significantly upregulated in the ge-1 mutant, whereas, the expression levels of most of the genes encoding enzymes involved GABA degradation were significantly downregulated in the ge-1 mutant. This is most likely responsible for the significant increase in GABA content of the ge mutant. These results help reveal the molecular regulatory network of GABA metabolism in giant embryo rice and provide a theoretical basis for the study of its development mechanisms, which is conducive to the rapid cultivation of GABA-rich rice varieties, promoting human nutrition, and ensuring health. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01353-1.
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Affiliation(s)
- Pingli Chen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory/Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640 China
| | - Qing Liu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory/Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640 China
| | - Bingrui Sun
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory/Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640 China
| | - Shuwei Lv
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory/Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640 China
| | - Liqun Jiang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory/Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640 China
| | - Jing Zhang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory/Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640 China
| | - Xingxue Mao
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory/Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640 China
| | - Hang Yu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory/Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640 China
| | - Yangyang Chen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory/Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640 China
| | - Wenfeng Chen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory/Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640 China
| | - Zhilan Fan
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory/Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640 China
| | - Dajian Pan
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory/Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640 China
| | - Chen Li
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory/Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640 China
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13
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Fang X, Wang Y, Cui J, Yue L, Jiang A, Liu J, Wu Y, He X, Li C, Zhang J, Ding M, Yi Z. Transcriptome and metabolome analyses reveal the key genes related to grain size of big grain mutant in Tartary Buckwheat ( Fagopyrum tartaricum). FRONTIERS IN PLANT SCIENCE 2022; 13:1079212. [PMID: 36618631 PMCID: PMC9815120 DOI: 10.3389/fpls.2022.1079212] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
Grain size with high heritability and stability is an important selection target during Tartary buckwheat breeding. However, the mechanisms that regulate Tartary buckwheat grain development are unknown. We generated transcriptome and metabolome sequencing from 10 and 15 days past anthesis (DPA) grains of big grain mutant (bg1) and WT, and identified 4108 differentially expressed genes (DEGs) including 93 significantly up-regulated differential genes and 85 significantly down-regulated genes in both stages, simultaneously. Meanwhile, we identified DEGs involved in ubiquitin-proteasome pathway, HAI-KU (IKU) pathway, mitogen-activated protein kinase (MAPK) signaling pathway, plant hormone (auxin, brassinosteroids and cytokinins) transduction pathway and five transcription factor families, including APETALA (AP2), GROWTH-REGULATING FACTORS (GRF), AUXIN RESPONSE FACTOR (ARF), WRKY and MYB. Weighted gene co-expression network analysis (WGCNA) was performed and obtained 9 core DEGs. Conjoint analyses of transcriptome and metabolome sequencing screened out 394 DEGs. Using a combined comprehensive analysis, we identified 24 potential candidate genes that encode E3 ubiquitin-protein ligase HIP1, EMBRYO-DEFECTIVE (EMB) protein, receptor-like protein kinase FERONIA (FER), kinesin-4 protein SRG1, and so on, which may be associated with the big-grain mutant bg1. Finally, a quantitative real-time Polymerase Chain Reaction (qRT-PCR) assay was conducted to validate the identified DEGs. Our results provide additional knowledge for identification and functions of causal candidate genes responsible for the variation in grain size and will be an invaluable resource for the genetic dissection of Tartary buckwheat high-yield molecular breeding.
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Affiliation(s)
- Xiaomei Fang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
| | - Yingqian Wang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Jingbin Cui
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Linqing Yue
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Aohua Jiang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Jiaqi Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Yichao Wu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Xingxing He
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Chunhua Li
- Baicheng Academy of Agricultural Sciences of Jilin Province, Baicheng, Jilin, China
| | - Jian Zhang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
| | - Mengqi Ding
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
| | - Zelin Yi
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
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14
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Pan L, Wang M, Yang Y, Chen C, Dai H, Zhang Z, Hua B, Miao M. Whole-genome resequencing identified QTLs, candidate genes and Kompetitive Allele-Specific PCR markers associated with the large fruit of Atlantic Giant ( Cucurbita maxima). FRONTIERS IN PLANT SCIENCE 2022; 13:942004. [PMID: 35937359 PMCID: PMC9354748 DOI: 10.3389/fpls.2022.942004] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/01/2022] [Indexed: 06/15/2023]
Abstract
Atlantic Giant (AG) pumpkin (Cucurbita maxima) produces the world's largest fruit. Elucidating the molecular mechanism of AG fruit formation is of scientific and practical importance. In this research, genome-wide resequencing of an F2 population produced by a cross between AG and its small-fruit ancestor Hubbard was used to identify quantitative trait loci (QTLs) and candidate genes. Transgressive segregation of fruit size-related traits was observed in the F2 population, suggesting that fruit size was a quantitative trait controlled by multiple genes. A genetic map with an average physical distance of 154 kb per marker was constructed, and 13 QTLs related to fruit size were identified using bin-map construction. RNA sequencing analysis revealed that pathways associated with assimilate accumulation into the fruit, including carbohydrate metabolism, were significantly enriched in differentially expressed genes. According to the predicted impact of mutation on the biological function of certain proteins, 13 genes were selected as candidate genes associated with fruit size, among which two phytohormone-related genes, CmaCh17G011340 (a flavin-containing monooxygenase) and CmaCh04G029660 (a leucine-rich repeat protein kinase) were chosen for further investigation. Finally, one insertion-deletion (inDel) and three single nucleotide polymorphisms (SNPs) were successfully transformed to Kompetitive Allele-Specific PCR (KASP) markers. The novel QTLs and candidate genes identified provide insights into the genetic mechanism of large fruit formation of AG, and the genetic map and tightly linked KASP markers developed in this study can be employed for marker-assisted breeding to alter fruit size of C. maxima.
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Affiliation(s)
- Liu Pan
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Min Wang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Yating Yang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Chen Chen
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Haibo Dai
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Zhiping Zhang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Bing Hua
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Minmin Miao
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, China
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15
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Chen Y, Liu Y, Zhang J, Torrance A, Watanabe N, Adamski NM, Uauy C. The Triticum ispahanicum elongated glume locus P2 maps to chromosome 6A and is associated with the ectopic expression of SVP-A1. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2313-2331. [PMID: 35583655 PMCID: PMC9271103 DOI: 10.1007/s00122-022-04114-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 04/21/2022] [Indexed: 05/26/2023]
Abstract
We propose the MADS-box transcription factor SVP-A1 as a promising candidate gene for the elongated glume locus P2, which maps to chromosome 6A instead of the previously proposed chromosome 7B. In rice and wheat, glume and floral organ length are positively correlated with grain size, making them an important target to increase grain size and potentially yield. The wheat subspecies Triticum ispahanicum is known to develop elongated glumes and floral organs as well as long grains. These multiple phenotypic effects are controlled by the P2 locus, which was previously mapped to wheat chromosome 7B. Using three mapping populations, we show that the long glume locus P2 does not map to chromosome 7B, but instead maps to a 1.68 Mbp interval on chromosome 6A. Within this interval, we identified SVP-A1, a MADS box transcription factor which is the direct ortholog of the maize gene underlying the 'pod corn' Tunicate locus and is a paralog to the T. polonicum elongated glume P1 gene. In T. ispahanicum, we identified a unique allele which has a 482-bp deletion in the SVP-A1 promoter and is associated with ectopic and higher expression of SVP-A1 in the elongated glumes and floral organs. We used near-isogenic lines (NILs) to show that P2 has a consistent positive effect on the length of glume, lemma, palea, spike and grain. Based on the mapping data, natural variation, biological function of SVP genes in cereals and expression analyses, we propose the MADS-box transcription factor SVP-A1 as a promising candidate for P2.
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Affiliation(s)
- Yi Chen
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Yinqi Liu
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
- King's College London, Guy's Campus, London, SE1 1UL, UK
| | - Junli Zhang
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Adam Torrance
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Nobuyoshi Watanabe
- The Little Nursery, 1152 Ina, Toride, Ibaraki, 302-0026, Japan
- College of Agriculture, Ibaraki University, 3-21-1 Chuo, Ami, Inashiki, Ibaraki, 300-0393, Japan
| | | | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
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16
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Sun L, Deng R, Liu J, Lai M, Wu J, Liu X, Shahid MQ. An overview of sucrose transporter (SUT) genes family in rice. Mol Biol Rep 2022; 49:5685-5695. [PMID: 35699859 DOI: 10.1007/s11033-022-07611-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 05/17/2022] [Indexed: 10/18/2022]
Abstract
INTRODUCTION Photosynthesis provides the energy basis for the life activities of plants by producing organic compounds, mainly sugar. As the main energy form of photosynthesis, sugar affects the growth and development of plants. During long-distance transportation, sucrose is the main form of transportation. The rate of sugar transport and the allocation of carbohydrates affect the biomass of crops and are closely related to the reproductive growth of crops. MAIN TEXT The transportation of sugar is divided into active transportation and passive transportation. So how does the sucrose transporters (SUT) genes, which are the main carriers of sucrose in active transportation, affect the performance of rice agronomic traits is still to be explored. In this article, we describe the structure of inflorescence and review the transport forms and metabolic processes of sucrose in rice, such as how CO2 is fixed, carbohydrate assimilation, and transport of organic matter. Sucrose transporters exhibited remarkable effects on the development of reproductive organs in rice. CONCLUSIONS Here, the effects of different factors, such as the effects of anthers morphology on starch enrichment of pollen, effects of biotic and abiotic factors on sucrose transporters, effects of changes in trace elements on sucrose transporters, were discussed. Moreover, the regulation of transcription or translation level provides ideas for future research on sucrose transporters.
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Affiliation(s)
- Lixia Sun
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China.,College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Ruilian Deng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China.,College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Jingwen Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China.,College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Mingyu Lai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China.,College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Jinwen Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China.,College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Xiangdong Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China.,College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China. .,Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China. .,Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China. .,College of Agriculture, South China Agricultural University, Guangzhou, 510642, China.
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17
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Xun Q, Mei M, Song Y, Rong C, Liu J, Zhong T, Ding Y, Ding C. SWI2/SNF2 chromatin remodeling ATPases SPLAYED and BRAHMA control embryo development in rice. PLANT CELL REPORTS 2022; 41:1389-1401. [PMID: 35348854 DOI: 10.1007/s00299-022-02864-z] [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: 01/24/2022] [Accepted: 03/14/2022] [Indexed: 05/23/2023]
Abstract
Chromatin remodeling ATPases OsSYD and OsBRM are involved in shoot establishment, and both affect OSH gene transcription. OsSYD protein interacts with RFL, but OsBRM does not. In plants, SPLAYED (SYD) and BRAHMA (BRM) encode chromatin remodeling ATPases that use the energy derived from ATP hydrolysis to restructure nucleosomes and render certain genomic regions available to transcription factors. However, the function of SYD and BRM on rice growth and development is unknown. Here, we constructed ossyd and osbrm mutants using CRISPR/Cas9 technology and analyzed the effects of mutations on rice embryo development. We discovered that the ossyd and osbrm mutants exhibited severe defects during embryonic development, whereas endosperm development was normal. These results indicated that the development of the embryo and endosperm is independent of each other. Consequently, the ossyd- and osbrm-null mutants did not germinate due to the abnormal embryos. Furthermore, we observed the embryos of ossyd- and osbrm-null mutants, and they indeed had distinct differentiation defects in shoot establishment, acquired during embryogenesis. To verify the function of OsSYD and OsBRM in embryogenesis, we measured the transcript levels of marker genes at different stages. Compared with wild type, the expression levels of multiple OSH genes were significantly reduced in the mutants, which was consistent with the defective shoot establishment phenotypes. The interaction between SYD and RICE FLORICAULA/LFY (RFL) was revealed using a yeast two-hybrid screening system, suggesting that the interaction between the LFY homolog and chromatin remodeling ATPases is ubiquitous in plants. Collectively, our findings provide the basis for elucidating the function of OsSYD and OsBRM during embryo development in rice.
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Affiliation(s)
- Qian Xun
- College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Min Mei
- College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Ye Song
- College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Chenyu Rong
- College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Jiajun Liu
- College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Tianhui Zhong
- College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Yanfeng Ding
- College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
- Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing, 210095, People's Republic of China
- Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry, Nanjing, 210095, People's Republic of China
| | - Chengqiang Ding
- College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
- Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing, 210095, People's Republic of China.
- Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry, Nanjing, 210095, People's Republic of China.
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Li Q, Feng Q, Snouffer A, Zhang B, Rodríguez GR, van der Knaap E. Increasing Fruit Weight by Editing a Cis-Regulatory Element in Tomato KLUH Promoter Using CRISPR/Cas9. FRONTIERS IN PLANT SCIENCE 2022; 13:879642. [PMID: 35481139 PMCID: PMC9037380 DOI: 10.3389/fpls.2022.879642] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 03/07/2022] [Indexed: 06/01/2023]
Abstract
CRISPR/Cas-mediated genome editing is a powerful approach to accelerate yield enhancement to feed growing populations. Most applications focus on "negative regulators" by targeting coding regions and promoters to create nulls or weak loss-of-function alleles. However, many agriculturally important traits are conferred by gain-of-function alleles. Therefore, creating gain-of-function alleles for "positive regulators" by CRISPR will be of great value for crop improvement. CYP78A family members are the positive regulators of organ weight and size in crops. In this study, we engineered allelic variation by editing tomato KLUH promoter around a single-nucleotide polymorphism (SNP) that is highly associated with fruit weight. The SNP was located in a conserved putative cis-regulatory element (CRE) as detected by the homology-based prediction and the Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq). Twenty-one mutant alleles with various insertion and deletion sizes were generated in the LA1589 background. Five mutant alleles (m2+4bp , m3+1bp , m5-1bp , m13-8bp , and m14-9bp ) showed a consistent increase in fruit weight and a significant decrease in the proportion of small fruits in all experimental evaluations. Notably, m2+4bp and m3+1bp homozygote significantly increase fruit weight by 10.7-15.7 and 8.7-16.3%, respectively. Further analysis of fruit weight based on fruit position on the inflorescence indicated that the five beneficial alleles increase the weight of all fruits along inflorescence. We also found that allele types and transcriptional changes of SlKLUH were poor predictors of the changes in fruit weight. This study not only provides a way of identifying conserved CRE but also highlights enormous potential for CRISPR/Cas-mediated cis-engineering of CYP78A members in yield improvement.
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Affiliation(s)
- Qiang Li
- College of Horticulture, Hebei Agricultural University, State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, Baoding, China
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
| | - Qian Feng
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
| | - Ashley Snouffer
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
| | - Biyao Zhang
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
| | - Gustavo Rubén Rodríguez
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR), Cátedra de Genética, Facultad de Ciencias Agrarias UNR, Santa Fe, Argentina
| | - Esther van der Knaap
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
- Department of Horticulture, University of Georgia, Athens, GA, United States
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19
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TaKLU Plays as a Time Regulator of Leaf Growth via Auxin Signaling. Int J Mol Sci 2022; 23:ijms23084219. [PMID: 35457033 PMCID: PMC9033062 DOI: 10.3390/ijms23084219] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/01/2022] [Accepted: 04/08/2022] [Indexed: 02/04/2023] Open
Abstract
The growth of leaves is subject to strict time regulation. Several genes influencing leaf growth have been identified, but little is known about how genes regulate the orderly initiation and growth of leaves. Here, we demonstrate that TaKLU/TaCYP78A5 contributes to a time regulation mechanism in leaves from initiation to expansion. TaKLU encodes the cytochrome P450 CYP78A5, and its homolog AtKLU has been described whose deletion is detrimental to organ growth. Our results show that TaKLU overexpression increases leaf size and biomass by altering the time of leaf initiation and expansion. TaKLU-overexpressing plants have larger leaves with more cells. Further dynamic observations indicate that enlarged wheat leaves have experienced a longer expansion time. Different from AtKLU inactivation increases leaf number and initiation rates, TaKLU overexpression only smooths the fluctuations of leaf initiation rates by adjusting the initiation time of local leaves, without affecting the overall leaf number and initiation rates. In addition, complementary analyses suggest TaKLU is functionally conserved with AtKLU in controlling the leaf initiation and size and may involve auxin accumulation. Our results provide a new insight into the time regulation mechanisms of leaf growth in wheat.
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20
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Chaitavon K, Sumriddetchkajorn S, Prasertsak A, Chanhorm S, Prempree P, Intaravanne Y. Mobile-device-based two-dimensional measurement for estimating the embryo and endosperm areas of brown rice. APPLIED OPTICS 2022; 61:E14-E20. [PMID: 35297869 DOI: 10.1364/ao.444854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 12/27/2021] [Indexed: 06/14/2023]
Abstract
The rice kernel inside a hull is composed of the embryo and endosperm. The embryo or germ of the rice seed will grow and become the shoot and the root parts of a seedling, while the endosperm is an important nutrient source for the embryo in the early stages. Hence, the health of seedlings depends particularly on the sizes of the embryo and endosperm. In this work, we propose and experimentally demonstrate how the embryo and endosperm areas of brown rice can simply be determined. Our key idea is based on the utilization of a smart mobile device equipped with our specifically designed lens module arranged in a simple cross-polarization imaging configuration for acquiring a rice grain image upon the illumination of a white light source and then spatially analyzing the sizes of embryo and endosperm areas. The prototype shows promising results in identifying the sizes of the embryo and endosperm within 2 s per seed with a measurement error of <9% compared with the use of off-the-shelf image editing software. In addition, the prototype is in a small package of 20×32.5×6.5cm3 with 4 kg weight, thus showing high potential to perform in the real scenario.
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21
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Wang W, Xiong H, Sun K, Zhang B, Sun MX. New insights into cell-cell communications during seed development in flowering plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:215-229. [PMID: 34473416 DOI: 10.1111/jipb.13170] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/01/2021] [Indexed: 06/13/2023]
Abstract
The evolution of seeds is a major reason why flowering plants are a dominant life form on Earth. The developing seed is composed of two fertilization products, the embryo and endosperm, which are surrounded by a maternally derived seed coat. Accumulating evidence indicates that efficient communication among all three seed components is required to ensure coordinated seed development. Cell communication within plant seeds has drawn much attention in recent years. In this study, we review current knowledge of cross-talk among the endosperm, embryo, and seed coat during seed development, and highlight recent advances in this field.
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Affiliation(s)
- Wei Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Hanxian Xiong
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Kaiting Sun
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Bo Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Meng-Xiang Sun
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
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22
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Yoon J, Cho L, Kim S, Tun W, Peng X, Pasriga R, Moon S, Hong W, Ji H, Jung K, Jeon J, An G. CTP synthase is essential for early endosperm development by regulating nuclei spacing. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:2177-2191. [PMID: 34058048 PMCID: PMC8541778 DOI: 10.1111/pbi.13644] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 05/04/2021] [Accepted: 05/22/2021] [Indexed: 06/12/2023]
Abstract
Cereal grain endosperms are an important source of human nutrition. Nuclear division in early endosperm development plays a major role in determining seed size; however, this development is not well understood. We identified the rice mutant endospermless 2 (enl2), which shows defects in the early stages of endosperm development. These phenotypes arise from mutations in OsCTPS1 that encodes a cytidine triphosphate synthase (CTPS). Both wild-type and mutant endosperms were normal at 8 h after pollination (HAP). In contrast, at 24 HAP, enl2 endosperm had approximately 10-16 clumped nuclei while wild-type nuclei had increased in number and migrated to the endosperm periphery. Staining of microtubules in endosperm at 24 HAP revealed that wild-type nuclei were evenly distributed by microtubules while the enl2-2 nuclei were tightly packed due to their reduction in microtubule association. In addition, OsCTPS1 interacts with tubulins; thus, these observations suggest that OsCTPS1 may be involved in microtubule formation. OsCTPS1 transiently formed macromolecular structures in the endosperm during early developmental stages, further supporting the idea that OsCTPS1 may function as a structural component during endosperm development. Finally, overexpression of OsCTPS1 increased seed weight by promoting endosperm nuclear division, suggesting that this trait could be used to increase grain yield.
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Affiliation(s)
- Jinmi Yoon
- Crop Biotech Institute and Graduate School of BiotechnologyKyung Hee UniversityYonginRepublic of Korea
- Department of Plant BioscienceCollege of Natural Resources and Life SciencePusan National UniversityMiryangRepublic of Korea
| | - Lae‐Hyeon Cho
- Crop Biotech Institute and Graduate School of BiotechnologyKyung Hee UniversityYonginRepublic of Korea
- Department of Plant BioscienceCollege of Natural Resources and Life SciencePusan National UniversityMiryangRepublic of Korea
| | - Sung‐Ryul Kim
- Gene Identification and Validation GroupGenetic Design and Validation UnitInternational Rice Research Institute (IRRI)Metro ManilaPhilippines
| | - Win Tun
- Crop Biotech Institute and Graduate School of BiotechnologyKyung Hee UniversityYonginRepublic of Korea
| | - Xin Peng
- Crop Biotech Institute and Graduate School of BiotechnologyKyung Hee UniversityYonginRepublic of Korea
- Institution of Genomics and BioinformaticsSouth China Agricultural UniversityGuangzhouChina
| | - Richa Pasriga
- Crop Biotech Institute and Graduate School of BiotechnologyKyung Hee UniversityYonginRepublic of Korea
| | - Sunok Moon
- Crop Biotech Institute and Graduate School of BiotechnologyKyung Hee UniversityYonginRepublic of Korea
| | - Woo‐Jong Hong
- Crop Biotech Institute and Graduate School of BiotechnologyKyung Hee UniversityYonginRepublic of Korea
| | - Hyeonso Ji
- National Institute of Agricultural Sciences, Rural Development AdministrationJeonjuRepublic of Korea
| | - Ki‐Hong Jung
- Crop Biotech Institute and Graduate School of BiotechnologyKyung Hee UniversityYonginRepublic of Korea
| | - Jong‐Seong Jeon
- Crop Biotech Institute and Graduate School of BiotechnologyKyung Hee UniversityYonginRepublic of Korea
| | - Gynheung An
- Crop Biotech Institute and Graduate School of BiotechnologyKyung Hee UniversityYonginRepublic of Korea
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Banerjee A, Singh A, Roychoudhury A. Fluoride toxicity variably affects overall physiology and grain development in three contrasting rice genotypes, representing a potential biohazard. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:40220-40232. [PMID: 32930987 DOI: 10.1007/s11356-020-10604-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 08/23/2020] [Indexed: 06/11/2023]
Abstract
Ingestion of fluoride through consumption of contaminated food grains has been regarded to be hazardous for consumer health. The current study indicated the possible occurrence of such biohazard due to fluoride bioaccumulation in rice grains and straw (cattle feed). The effects of fluoride toxicity at three stages of grain development in three rice genotypes, viz., IR-64, Gobindobhog (aromatic), and Khitish, were also studied. Irrigation with fluoride-infested water inhibited grain formation in IR-64 and reduced grain yield in Gobindobhog. Fluoride toxicity promoted seed sterility in IR-64 by triggering reactive oxygen species (ROS) production and cellular necrosis, suppressing genes like GIF1, DEP1, and SPL14 (positively controlling seed formation) and inducing GW2 (negatively mediating grain development). Gobindobhog showed intermediate fluoride sensitivity and accumulated high levels of proline, anthocyanins, flavonoids, and phenolics due to the induction of genes like P5CS, ANS, and PAL in developing grains. The agronomic attributes in Khitish were unaffected by fluoride stress due to regulated fluoride uptake and high expression of GIF1, DEP1, and SPL14 along with an increased synthesis of anthocyanins, flavonoids, and phenolics. Khitish also accumulated low ROS as a result of which lowest lipoxygenase expression (among selected cultivars) was observed in developing grains. Fluoride entry was accelerated in the straw of Khitish, possibly due to the absence of regulated uptake mechanism in dead seedlings. Furthermore, the ecological concerns regarding fluoride bioaccumulation and reduced grain yield at the varietal level were also established, based on statistical modelling.
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Affiliation(s)
- Aditya Banerjee
- Post Graduate Department of Biotechnology, St. Xavier's College (Autonomous), 30, Mother Teresa Sarani, Kolkata, West Bengal, 700016, India
| | - Ankur Singh
- Post Graduate Department of Biotechnology, St. Xavier's College (Autonomous), 30, Mother Teresa Sarani, Kolkata, West Bengal, 700016, India
| | - Aryadeep Roychoudhury
- Post Graduate Department of Biotechnology, St. Xavier's College (Autonomous), 30, Mother Teresa Sarani, Kolkata, West Bengal, 700016, India.
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24
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Cui D, Tang C, Lu H, Li J, Ma X, A X, Han B, Yang Y, Dong C, Zhang F, Dai L, Han L. Genetic differentiation and restricted gene flow in rice landraces from Yunnan, China: effects of isolation-by-distance and isolation-by-environment. RICE (NEW YORK, N.Y.) 2021; 14:54. [PMID: 34131824 PMCID: PMC8206287 DOI: 10.1186/s12284-021-00497-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 05/25/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Understanding and identifying the factors responsible for genetic differentiation is of fundamental importance for efficient utilization and conservation of traditional rice landraces. In this study, we examined the spatial genetic differentiation of 594 individuals sampled from 28 locations in Yunnan Province, China, covering a wide geographic distribution and diverse growing conditions. All 594 accessions were studied using ten unlinked target genes and 48 microsatellite loci, and the representative 108 accessions from the whole collection were sampled for resequencing. RESULTS The genetic diversity of rice landraces was quite different geographically and exhibited a geographical decline from south to north in Yunnan, China. Population structure revealed that the rice landraces could be clearly differentiated into japonica and indica groups, respectively. In each group, the rice accessions could be further differentiated corresponded to their geographic locations, including three subgroups from northern, southern and middle locations. We found more obvious internal geographic structure in the japonica group than in the indica group. In the japonica group, we found that genetic and phenotypic differentiation were strongly related to geographical distance, suggesting a pattern of isolation by distance (IBD); this relationship remained highly significant when we controlled for environmental effects, where the likelihood of gene flow is inversely proportional to the distance between locations. Moreover, the gene flow also followed patterns of isolation by environment (IBE) whereby gene flow rates are higher in similar environments. We detected 314 and 216 regions had been differentially selected between Jap-N and Jap-S, Ind-N and Ind-S, respectively, and thus referred to as selection signatures for different geographic subgroups. We also observed a number of significant and interesting associations between loci and environmental factors, which implies adaptation to local environment. CONCLUSIONS Our findings highlight the influence of geographical isolation and environmental heterogeneity on the pattern of the gene flow, and demonstrate that both geographical isolation and environment drives adaptive divergence play dominant roles in the genetic differentiation of the rice landraces in Yunnan, China as a result of limited dispersal.
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Affiliation(s)
- Di Cui
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun Nandajie, 100081 Beijing, China
| | - Cuifeng Tang
- Institute of Biotech and Germplasm Resources, Yunnan Academy of Agricultural Sciences, No. 9 Xueyunlu, 650205 Kunming, Yunnan, China
| | - Hongfeng Lu
- Novogene Bioinformatics Institute, 100083 Beijing, China
| | - Jinmei Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun Nandajie, 100081 Beijing, China
| | - Xiaoding Ma
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun Nandajie, 100081 Beijing, China
| | - Xinxiang A
- Institute of Biotech and Germplasm Resources, Yunnan Academy of Agricultural Sciences, No. 9 Xueyunlu, 650205 Kunming, Yunnan, China
| | - Bing Han
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun Nandajie, 100081 Beijing, China
| | - Yayun Yang
- Institute of Biotech and Germplasm Resources, Yunnan Academy of Agricultural Sciences, No. 9 Xueyunlu, 650205 Kunming, Yunnan, China
| | - Chao Dong
- Institute of Biotech and Germplasm Resources, Yunnan Academy of Agricultural Sciences, No. 9 Xueyunlu, 650205 Kunming, Yunnan, China
| | - Feifei Zhang
- Institute of Biotech and Germplasm Resources, Yunnan Academy of Agricultural Sciences, No. 9 Xueyunlu, 650205 Kunming, Yunnan, China
| | - Luyuan Dai
- Institute of Biotech and Germplasm Resources, Yunnan Academy of Agricultural Sciences, No. 9 Xueyunlu, 650205 Kunming, Yunnan, China
| | - Longzhi Han
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun Nandajie, 100081 Beijing, China
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25
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Jiang L, Yoshida T, Stiegert S, Jing Y, Alseekh S, Lenhard M, Pérez-Alfocea F, Fernie AR. Multi-omics approach reveals the contribution of KLU to leaf longevity and drought tolerance. PLANT PHYSIOLOGY 2021; 185:352-368. [PMID: 33721894 PMCID: PMC8133585 DOI: 10.1093/plphys/kiaa034] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 11/05/2020] [Indexed: 05/05/2023]
Abstract
KLU, encoded by a cytochrome P450 CYP78A family gene, generates an important-albeit unknown-mobile signal that is distinct from the classical phytohormones. Multiple lines of evidence suggest that KLU/KLU-dependent signaling functions in several vital developmental programs, including leaf initiation, leaf/floral organ growth, and megasporocyte cell fate. However, the interactions between KLU/KLU-dependent signaling and the other classical phytohormones, as well as how KLU influences plant physiological responses, remain poorly understood. Here, we applied in-depth, multi-omics analysis to monitor transcriptome and metabolome dynamics in klu-mutant and KLU-overexpressing Arabidopsis plants. By integrating transcriptome sequencing data and primary metabolite profiling alongside phytohormone measurements, our results showed that cytokinin signaling, with its well-established function in delaying leaf senescence, was activated in KLU-overexpressing plants. Consistently, KLU-overexpressing plants exhibited significantly delayed leaf senescence and increased leaf longevity, whereas the klu-mutant plants showed early leaf senescence. In addition, proline biosynthesis and catabolism were enhanced following KLU overexpression owing to increased expression of genes associated with proline metabolism. Furthermore, KLU-overexpressing plants showed enhanced drought-stress tolerance and reduced water loss. Collectively, our work illustrates a role for KLU in positively regulating leaf longevity and drought tolerance by synergistically activating cytokinin signaling and promoting proline metabolism. These data promote KLU as a potential ideal genetic target to improve plant fitness.
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Affiliation(s)
- Liang Jiang
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Wissenschaftspark Golm, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Takuya Yoshida
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Wissenschaftspark Golm, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Sofia Stiegert
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Wissenschaftspark Golm, Am Mühlenberg 1, 14476 Potsdam, Germany
- Department of Genetics, University of Potsdam, 14469 Potsdam, Germany
| | - Yue Jing
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Wissenschaftspark Golm, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Saleh Alseekh
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Wissenschaftspark Golm, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Michael Lenhard
- Department of Genetics, University of Potsdam, 14469 Potsdam, Germany
| | - Francisco Pérez-Alfocea
- Department of Plant Nutrition, CEBAS-CSIC, Campus Universitario de Espinardo, 30100 Murcia, Spain
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Wissenschaftspark Golm, Am Mühlenberg 1, 14476 Potsdam, Germany
- Department of Genetics, University of Potsdam, 14469 Potsdam, Germany
- Author for communication:
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26
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Li Q, Chakrabarti M, Taitano NK, Okazaki Y, Saito K, Al-Abdallat AM, van der Knaap E. Differential expression of SlKLUH controlling fruit and seed weight is associated with changes in lipid metabolism and photosynthesis-related genes. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:1225-1244. [PMID: 33159787 PMCID: PMC7904157 DOI: 10.1093/jxb/eraa518] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 11/02/2020] [Indexed: 05/21/2023]
Abstract
The sizes of plant organs such as fruit and seed are crucial yield components. Tomato KLUH underlies the locus fw3.2, an important regulator of fruit and seed weight. However, the mechanism by which the expression levels of KLUH affect organ size is poorly understood. We found that higher expression of SlKLUH increased cell proliferation in the pericarp within 5 d post-anthesis in tomato near-isogenic lines. Differential gene expression analyses showed that lower expression of SlKLUH was associated with increased expression of genes involved in lipid metabolism. Lipidomic analysis revealed that repression of SlKLUH mainly increased the contents of certain non-phosphorus glycerolipids and phospholipids and decreased the contents of four unknown lipids. Co-expression network analyses revealed that lipid metabolism was possibly associated with but not directly controlled by SlKLUH, and that this gene instead controls photosynthesis-related processes. In addition, many transcription factors putatively involved in the KLUH pathway were identified. Collectively, we show that SlKLUH regulates fruit and seed weight which is associated with altered lipid metabolism. The results expand our understanding of fruit and seed weight regulation and offer a valuable resource for functional studies of candidate genes putatively involved in regulation of organ size in tomato and other crops.
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Affiliation(s)
- Qiang Li
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | - Manohar Chakrabarti
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, USA
| | - Nathan K Taitano
- Institute for Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, USA
| | - Yozo Okazaki
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Graduate School of Bioresources, Mie University, Tsu, Japan
| | - Kazuki Saito
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | | | - Esther van der Knaap
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
- Institute for Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, USA
- Department of Horticulture, University of Georgia, Athens, GA, USA
- Correspondence:
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Hu Z, Xiong Q, Wang K, Zhang L, Yan Y, Cao L, Niu F, Zhu J, Hu J, Wu S. Identification of a New Giant Emrbryo Allele, and Integrated Transcriptomics and Metabolomics Analysis of Giant Embryo Development in Rice. FRONTIERS IN PLANT SCIENCE 2021; 12:697889. [PMID: 34434206 PMCID: PMC8381154 DOI: 10.3389/fpls.2021.697889] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 07/05/2021] [Indexed: 05/16/2023]
Abstract
Rice embryos are rich in high-quality protein, lipid, vitamins and minerals, representing the most important nutritional part of brown rice. However, the molecular mechanism of rice embryo development is poorly understood. In this study, two rice cultivars with contrasting embryo size (the giant embryo cultivar Dapeimi and the normal embryo cultivar 187R) were used to explore excellent genes controlling embryo size, and the developed near-isogenic lines (NILs) (NIL-D, which has the giant embryo phenotype, and its matching line, NIL-X) were used to explore transcript and metabolic properties in the earlier maturation stage of giant embryo development under natural conditions. The map-based cloning results demonstrated that Dapeimi is a novel allelic mutant of the rice GIANT EMBRYO (GE) gene, and the functional mutation site is a single cytosine deletion in the exon1. A total of 285 differentially accumulated metabolites (DAMs) and 677 differentially expressed genes (DEGs) were identified between NIL-D and NIL-X. The analysis of DAMs indicated that plants lacking GE mainly promoted energy metabolism, amino acid metabolism, and lipid metabolism pathways in the rice embryo. Pearson correlation coefficient showed that 300 pairs of gene-metabolites were highly correlated. Among them, OsZS_02G0528500 and OsZS_12G0013700 were considered to be key genes regulating L-Aspartic acid and L-Tryptophan content during rice giant embryo development, which are promising to be good candidate genes to improve rice nutrition. By analyzing rice embryo development through a combination of strategies, this research contributes to a greater understanding of the molecular mechanism of rice embryo development, and provides a theoretical foundation for breeding high-nutrition varieties.
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Affiliation(s)
- Zejun Hu
- Rice Research Center, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Shanghai Agricultural Products Preservation Processing Engineering Technology Research Center, Shanghai, China
| | - Qiangqiang Xiong
- Innovation Center of Rice Cultivation Technology in Yangtze Valley, Ministry of Agriculture, Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Kai Wang
- Rice Research Center, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Lixia Zhang
- Rice Research Center, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Shanghai Agricultural Products Preservation Processing Engineering Technology Research Center, Shanghai, China
| | - Ying Yan
- Rice Research Center, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Liming Cao
- Rice Research Center, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Shanghai Agricultural Products Preservation Processing Engineering Technology Research Center, Shanghai, China
| | - Fuan Niu
- Rice Research Center, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Jinyan Zhu
- Innovation Center of Rice Cultivation Technology in Yangtze Valley, Ministry of Agriculture, Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Jinlong Hu
- Innovation Center of Rice Cultivation Technology in Yangtze Valley, Ministry of Agriculture, Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Shujun Wu
- Rice Research Center, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Shanghai Agricultural Products Preservation Processing Engineering Technology Research Center, Shanghai, China
- *Correspondence: Shujun Wu,
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Wang X, Li L, Sun X, Xu J, Ouyang L, Bian J, Chen X, Li W, Peng X, Hu L, Cai Y, Zhou D, He X, Fu J, Fu H, He H, Zhu C. Fine Mapping of a Novel Major Quantitative Trait Locus, qPAA7, That Controls Panicle Apical Abortion in Rice. FRONTIERS IN PLANT SCIENCE 2021; 12:683329. [PMID: 34305980 PMCID: PMC8293750 DOI: 10.3389/fpls.2021.683329] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Accepted: 06/09/2021] [Indexed: 05/17/2023]
Abstract
The panicle apical abortion (PAA) causes severe yield losses in rice production, but details about its development and molecular basis remain elusive. Here, we detected PAA quantitative trait loci (QTLs) in three environments using a set of chromosome segment substitution lines (CSSLs) that was constructed with indica Changhui121 as the recurrent parent and japonica Koshihikari as the donor parent. First, we identified a novel major effector quantitative trait locus, qPAA7, and selected a severe PAA line, CSSL176, which had the highest PAA rate among CSSLs having Koshihikari segments at this locus. Next, an F2 population was constructed from a cross between CSS176 and CH121. Using F2 to make recombinantion analysis, qPAA7 was mapped to an 73.8-kb interval in chromosome 7. Among nine candidate genes within this interval, there isn't any known genes affecting PAA. According to the gene annotation, gene expression profile and alignment of genomic DNA, LOC_Os07g41220 and LOC_Os07g41280 were predicted as putative candidate genes of qPAA7. Our study provides a foundation for cloning and functional characterization of the target gene from this locus.
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Qi D, Wen Q, Meng Z, Yuan S, Guo H, Zhao H, Cui S. OsLFR is essential for early endosperm and embryo development by interacting with SWI/SNF complex members in Oryza sativa. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:901-916. [PMID: 32808364 DOI: 10.1111/tpj.14967] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 07/09/2020] [Accepted: 07/29/2020] [Indexed: 05/26/2023]
Abstract
Rice (Oryza sativa L.) endosperm provides the developing embryo with nutrients and provides human beings with a staple food. The embryo eventually develops into a new sporophyte generation. Despite their important roles, the molecular mechanisms underlying early-stage endosperm and embryo development remain elusive. Here, we established the fundamental functions of rice OsLFR, an ortholog of the Arabidopsis SWI/SNF chromatin-remodeling complex (CRC) component LFR. OsLFR was expressed primarily in the rice spikelets and seeds, and the OsLFR protein was localized to the nucleus. We conducted genetic, cellular and molecular analyses of loss-of-function mutants and transgenic rescue lines. OsLFR depletion resulted in homozygous lethality in the early seed stage through endosperm and embryo defects, which could be successfully recovered by the OsLFR genomic sequence. Cytological observations revealed that the oslfr endosperm had relatively fewer free nuclei, had abnormal and arrested cellularization, and demonstrated premature programed cell death: the embryo was reduced in size and failed to differentiate. Transcriptome profiling showed that many genes, involved in DNA replication, cell cycle, cell wall assembly and cell death, were differentially expressed in a knockout mutant of OsLFR (oslfr-1), which was consistent with the observed seed defects. Protein-protein interaction analysis showed that OsLFR physically interacts with several putative rice SWI/SNF CRC components. Our findings demonstrate that OsLFR, possibly as one component of the SWI/SNF CRC, is an essential regulator of rice seed development, and provide further insights into the regulatory mechanism of early-stage rice endosperm and embryo development.
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Affiliation(s)
- Dongmei Qi
- Hebei Key Laboratory of Molecular and Cellular Biology, Hebei Normal University, Hebei, 050024, China
- Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Normal University, Hebei, 050024, China
- Hebei Collaboration Innovation Center for Cell Signaling, Hebei Normal University, Hebei, 050024, China
- College of Life Science, Hebei Normal University, Hebei, 050024, China
| | - Qingqing Wen
- Hebei Key Laboratory of Molecular and Cellular Biology, Hebei Normal University, Hebei, 050024, China
- Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Normal University, Hebei, 050024, China
- Hebei Collaboration Innovation Center for Cell Signaling, Hebei Normal University, Hebei, 050024, China
- College of Life Science, Hebei Normal University, Hebei, 050024, China
| | - Ze Meng
- Hebei Key Laboratory of Molecular and Cellular Biology, Hebei Normal University, Hebei, 050024, China
- Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Normal University, Hebei, 050024, China
- Hebei Collaboration Innovation Center for Cell Signaling, Hebei Normal University, Hebei, 050024, China
- College of Life Science, Hebei Normal University, Hebei, 050024, China
| | - Shan Yuan
- Hebei Key Laboratory of Molecular and Cellular Biology, Hebei Normal University, Hebei, 050024, China
- Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Normal University, Hebei, 050024, China
- Hebei Collaboration Innovation Center for Cell Signaling, Hebei Normal University, Hebei, 050024, China
- College of Life Science, Hebei Normal University, Hebei, 050024, China
| | - Hong Guo
- Hebei Key Laboratory of Molecular and Cellular Biology, Hebei Normal University, Hebei, 050024, China
- Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Normal University, Hebei, 050024, China
- Hebei Collaboration Innovation Center for Cell Signaling, Hebei Normal University, Hebei, 050024, China
- College of Life Science, Hebei Normal University, Hebei, 050024, China
| | - Hongtao Zhao
- Hebei Key Laboratory of Molecular and Cellular Biology, Hebei Normal University, Hebei, 050024, China
- Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Normal University, Hebei, 050024, China
- Hebei Collaboration Innovation Center for Cell Signaling, Hebei Normal University, Hebei, 050024, China
- College of Life Science, Hebei Normal University, Hebei, 050024, China
| | - Sujuan Cui
- Hebei Key Laboratory of Molecular and Cellular Biology, Hebei Normal University, Hebei, 050024, China
- Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Normal University, Hebei, 050024, China
- Hebei Collaboration Innovation Center for Cell Signaling, Hebei Normal University, Hebei, 050024, China
- College of Life Science, Hebei Normal University, Hebei, 050024, China
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Maeda S, Yokotani N, Oda K, Mori M. Enhanced resistance to fungal and bacterial diseases in tomato and Arabidopsis expressing BSR2 from rice. PLANT CELL REPORTS 2020; 39:1493-1503. [PMID: 32772129 DOI: 10.1007/s00299-020-02578-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 08/01/2020] [Indexed: 06/11/2023]
Abstract
The overexpression of rice BSR2 would offer a simple and effective strategy to protect plants from multiple devastating diseases in tomato and Arabidopsis. Many devastating plant diseases are caused by pathogens possessing a wide host range. Fungal Botrytis cinerea and Rhizoctonia solani, as well as bacterial Pseudomonas syringae and Ralstonia pseudosolanacearum are four such pathogens that infect hundreds of plant species, including agronomically important crops, and cause serious diseases, leading to severe economic losses. However, reports of genes that can confer resistance to broad host-range pathogens via traditional breeding methods are currently limited. We previously reported that Arabidopsis plants overexpressing rice BROAD-SPECTRUM RESISTANCE2 (BSR2/CYP78A15) showed tolerance not only to bacterial P. syringae pv. tomato DC3000 but also to fungal Colletotrichum higginsianum and R. solani. Rice plants overexpressing BSR2 displayed tolerance to two R. solani anastomosis groups. In the present study, first, BSR2-overexpressing (OX) Arabidopsis plants were shown to be additionally tolerant to B. cinerea, R. solani, and R. pseudosolanacearum. Next, tomato 'Micro-Tom' was used as a model to determine whether such tolerance by BSR2 can be introduced into dicot crops to prevent infection from pathogens possessing wide host range. BSR2-OX tomato displayed broad-spectrum disease tolerance to fungal B. cinerea and R. solani, as well as to bacterial P. syringae and R. pseudosolanacearum. Additionally, undesirable traits such as morphological changes were not detected. Thus, BSR2 overexpression can offer a simple and effective strategy to protect crops from multiple destructive diseases.
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Affiliation(s)
- Satoru Maeda
- Institute of Agrobiological Sciences, NARO (NIAS), Tsukuba, Japan
| | - Naoki Yokotani
- Research Institute for Biological Sciences, Okayama Prefectural Technology Center for Agriculture, Forestry, and Fisheries, Okayama, Japan
- Kazusa DNA Research Institute, Chiba, Japan
| | - Kenji Oda
- Research Institute for Biological Sciences, Okayama Prefectural Technology Center for Agriculture, Forestry, and Fisheries, Okayama, Japan
| | - Masaki Mori
- Institute of Agrobiological Sciences, NARO (NIAS), Tsukuba, Japan.
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Mathew IE, Priyadarshini R, Mahto A, Jaiswal P, Parida SK, Agarwal P. SUPER STARCHY1/ONAC025 participates in rice grain filling. PLANT DIRECT 2020; 4:e00249. [PMID: 32995698 PMCID: PMC7507516 DOI: 10.1002/pld3.249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 06/10/2020] [Accepted: 07/10/2020] [Indexed: 05/04/2023]
Abstract
NAC transcription factors (TFs) are known for their role in development and stress. This article attempts to functionally validate the role of rice SS1/ ONAC025 (LOC_Os11g31330) during seed development. The gene is seed-specific and its promoter directs reporter expression in the developing endosperm and embryo in rice transgenic plants. Furthermore, rice transgenic plants ectopically expressing SS1/ ONAC025 have a plantlet lethal phenotype with hampered vegetative growth, but increased tillers and an altered shoot apical meristem structure. The vegetative cells of these plantlets are filled with distinct starch granules. RNAseq analysis of two independent plantlets reveals the differential expression of reproductive and photosynthetic genes. A comparison with seed development transcriptome indicates differential regulation of many seed-related genes by SS1/ ONAC025. Genes involved in starch biosynthesis, especially amylopectin and those encoding seed storage proteins, and regulating seed size are also differentially expressed. In conjunction, SS1/ ONAC025 shows highest expression in japonica rice. As a TF, SS1/ ONAC025 is a transcriptional repressor localized to endoplasmic reticulum and nucleus. The article shows that SS1/ ONAC025 is a seed-specific gene promoting grain filling in rice, and negatively affecting vegetative growth.
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Affiliation(s)
| | | | - Arunima Mahto
- National Institute of Plant Genome ResearchNew DelhiIndia
| | - Priya Jaiswal
- National Institute of Plant Genome ResearchNew DelhiIndia
| | | | - Pinky Agarwal
- National Institute of Plant Genome ResearchNew DelhiIndia
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Generation of High Yielding and Fragrant Rice ( Oryza sativa L.) Lines by CRISPR/Cas9 Targeted Mutagenesis of Three Homoeologs of Cytochrome P450 Gene Family and OsBADH2 and Transcriptome and Proteome Profiling of Revealed Changes Triggered by Mutations. PLANTS 2020; 9:plants9060788. [PMID: 32586052 PMCID: PMC7355857 DOI: 10.3390/plants9060788] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/19/2020] [Accepted: 06/19/2020] [Indexed: 12/12/2022]
Abstract
The significant increase in grain yield and quality are often antagonistic but a constant demand for breeders and consumers. Some genes related to cytochrome P450 family are known for rice organ growth but their role in controlling grain yield is still unknown. Here, we generated new rice mutants with high yield and improved aroma by simultaneously editing three cytochrome P450 homoeologs (Os03g0603100, Os03g0568400, and GL3.2) and OsBADH2 with the CRISPR/Cas9 system, and RNA-sequencing and proteomic analysis were performed to unveil the subsequent changes. High mutation efficiency was achieved in both target sites of each gene and the mutations were predominantly only deletions, while insertions were rare, and no mutations were detected in the five most likely off-target sites against each sgRNA. Mutants exhibited increased grain size, 2-acetyl-1-pyrroline (2AP) content, and grain cell numbers while there was no change in other agronomic traits. Transgene-DNA-free mutant lines appeared with a frequency of 44.44% and homozygous mutations were stably transmitted, and bi-allelic and heterozygous mutations followed Mendelian inheritance, while the inheritance of chimeric mutations was unpredictable. Deep RNA sequencing and proteomic results revealed the regulation of genes and proteins related to cytochrome P450 family, grain size and development, and cell cycle. The KEGG and hub-gene and protein network analysis showed that the gene and proteins related to ribosomal and photosynthesis pathways were mainly enriched, respectively. Our findings provide a broad and detailed basis to understand the role of CRISPR/Cas9 in rice yield and quality improvement.
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Xu A, Wei C. Comprehensive comparison and applications of different sections in investigating the microstructure and histochemistry of cereal kernels. PLANT METHODS 2020; 16:8. [PMID: 32021644 PMCID: PMC6995210 DOI: 10.1186/s13007-020-0558-x] [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: 10/17/2019] [Accepted: 01/22/2020] [Indexed: 05/19/2023]
Abstract
This review summarizes the main applications of different sections and some improved sectioning methods in investigating the microstructure and histochemistry of cereal kernels. Thick sections of developing kernels prepared by free-hand and sliding microtome-aided sectioning method can be employed to elucidate tissue anatomy and histochemistry. The thin sections of mature kernels prepared by ultramicrotome-aided sectioning method can exhibit the micromorphology of starch granules when stained with iodine solution. The paraffin sections of developing kernels can exhibit the tissue anatomy of kernel, the accumulation of storage substances, and the location of protein and gene transcripts with immunohistochemistry and in situ hybridization techniques. The semithin resin sections can clearly exhibit the morphology of cells, starch granules, and protein bodies in kernel, but the sections prepared with different resins have various advantages and disadvantages for research investigating the morphology and histochemistry of cereal kernels. The improved methods of free-hand sectioning and ultramicrotome-aided sectioning of mature kernels are suitable for investigating the morphology of starch granules in a large number of samples in a short time. The modified method for preparing resin sections of whole kernels can be employed to determine the morphology and distribution of cells, starch granules, and storage protein in mature, developing, germinated, and cooked kernels in situ. This review could help researchers choose appropriate sections for investigating the microstructure and histochemistry of cereal kernels according to their study objectives.
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Affiliation(s)
- Ahui Xu
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009 China
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009 China
| | - Cunxu Wei
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009 China
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009 China
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Chen M, Bergman CJ, Grimm CC, McClung AM. A rice mutant with a giant embryo has increased levels of lipophilic antioxidants, E vitamers, and γ‐oryzanol fraction. Cereal Chem 2019. [DOI: 10.1002/cche.10242] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Ming‐Hsuan Chen
- Dale Bumpers National Rice Research Center USDA, ARS Stuttgart AR USA
| | - Christine J. Bergman
- Food & Beverage and Event Management Department University of Nevada Las Vegas NV USA
| | - Casey C. Grimm
- Southern Regional Research Center USDA, ARS New Orleans LA USA
| | - Anna M. McClung
- Dale Bumpers National Rice Research Center USDA, ARS Stuttgart AR USA
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Abstract
The size of seeds affects not only evolutionary fitness but also grain yield of crops. Understanding the mechanisms controlling seed size has become an important research field in plant science. Seed size is determined by the integrated signals of maternal and zygotic tissues, which control the coordinated growth of the embryo, endosperm, and seed coat. Recent advances have identified several signaling pathways that control seed size through maternal tissues, including or involving the ubiquitin-proteasome pathway, G-protein signaling, mitogen-activated protein kinase (MAPK) signaling, phytohormone perception and homeostasis, and some transcriptional regulators. Meanwhile, growth of the zygotic tissues is regulated in part by the HAIKU (IKU) pathway and phytohormones. This review provides a general overview of current findings in seed size control and discusses the emerging molecular mechanisms and regulatory networks found to be involved.
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Affiliation(s)
- Na Li
- State Key Laboratory of Plant Cell and Chromosome Engineering and Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, 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 and Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China;
| | - Yunhai Li
- State Key Laboratory of Plant Cell and Chromosome Engineering and Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China;
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Lee G, Piao R, Lee Y, Kim B, Seo J, Lee D, Jang S, Jin Z, Lee C, Chin JH, Koh HJ. Identification and Characterization of LARGE EMBRYO, a New Gene Controlling Embryo Size in Rice (Oryza sativa L.). RICE (NEW YORK, N.Y.) 2019; 12:22. [PMID: 30972509 PMCID: PMC6458227 DOI: 10.1186/s12284-019-0277-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 03/11/2019] [Indexed: 05/03/2023]
Abstract
BACKGROUND Although embryo accounts for only 2-3% of the total weight of a rice grain, it is a good source of various nutrients for human health. Because enlarged embryo size causes increase of the amount of nutrients and bioactive compounds stored within rice grain, giant embryo mutants of rice (Oryza sativa L.) are excellent genetic resources for improving the nutritional value of rice grains. RESULTS Three giant embryo mutants, including large embryo (le), giant embryo (ge) and super-giant embryo (ges), with variable embryo size were used in this study. We investigated whether genes controlling embryo size in these mutants (le, ge and ges) were allelic to each other. Although ge and ges was allelic to GIANT EMBRY (GE), le was not allelic to ge and ges in allelism test. The GE gene carried a unique nucleotide substitution in each of the two mutants (ge and ges), resulting in non-synonymous mutations in exon 2 of GE in both mutants. However, the GE gene of the le mutant did not carry any mutation, suggesting that the enlarged embryo phenotype of le was governed by another gene. Using map-based cloning, we mapped the LE gene to the short arm of chromosome 3. The le mutant showed mild enlargement in embryo size, which resulted from an increase in the size of scutellar parenchyma cells. The LE encodes a C3HC4-type RING finger protein and was expressed to relatively high levels in seeds at a late developmental stage. Knockdown of LE expression using RNA interference increased the embryo size of rice grains, confirming the role of LE in determining the embryo size. CONCLUSION Overall, we identified a new gene controlling embryo size in rice. Phenotypic and molecular characterization results suggest that the le mutant will serve as a valuable resource for developing new rice cultivars with large embryos and nutrient-dense grains.
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Affiliation(s)
- Gileung Lee
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 South Korea
| | - Rihua Piao
- Rice Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, 136100 Jilin China
| | - Yunjoo Lee
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 South Korea
| | - Backki Kim
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 South Korea
| | - Jeonghwan Seo
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 South Korea
| | - Dongryung Lee
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 South Korea
| | - Su Jang
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 South Korea
| | - Zhuo Jin
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 South Korea
| | - Choonseok Lee
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 South Korea
| | - Joong Hyoun Chin
- Graduate School of Integrated Bioindustry, Sejong University, 209, Neungdong-ro, Gwangjin-gu, Seoul 05006 South Korea
| | - Hee-Jong Koh
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 South Korea
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Radkova M, Revalska M, Kertikova D, Iantcheva A. Zinc finger CCHC-type protein related with seed size in model legume species Medicago truncatula. BIOTECHNOL BIOTEC EQ 2019. [DOI: 10.1080/13102818.2019.1568914] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Affiliation(s)
- Mariana Radkova
- Functional Genetic Group, AgroBioInstitute, Agricultural Academy, Sofia, Bulgaria
| | - Miglena Revalska
- Functional Genetic Group, AgroBioInstitute, Agricultural Academy, Sofia, Bulgaria
| | - Daniela Kertikova
- Department of Breeding and Seed Production of Forage Crops, Institute of Forage Crops, Agricultural Academy, Pleven, Bulgaria
| | - Anelia Iantcheva
- Functional Genetic Group, AgroBioInstitute, Agricultural Academy, Sofia, Bulgaria
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The rice CYP78A gene BSR2 confers resistance to Rhizoctonia solani and affects seed size and growth in Arabidopsis and rice. Sci Rep 2019; 9:587. [PMID: 30679785 PMCID: PMC6345848 DOI: 10.1038/s41598-018-37365-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 11/28/2018] [Indexed: 11/08/2022] Open
Abstract
The fungal pathogen Rhizoctonia solani causes devastating diseases in hundreds of plant species. Among these, R. solani causes sheath blight, one of the three major diseases in rice. To date, few genes have been reported that confer resistance to R. solani. Here, rice-FOX Arabidopsis lines identified as having resistance to a bacterial pathogen, Pseudomonas syringae pv. tomato DC3000, and a fungal pathogen, Colletotrichum higginsianum were screened for disease resistance to R. solani. BROAD-SPECTRUM RESISTANCE2 (BSR2), a gene encoding an uncharacterized cytochrome P450 protein belonging to the CYP78A family, conferred resistance to R. solani in Arabidopsis. When overexpressed in rice, BSR2 also conferred resistance to two R. solani anastomosis groups. Both Arabidopsis and rice plants overexpressing BSR2 had slower growth and produced longer seeds than wild-type control plants. In contrast, BSR2-knockdown rice plants were more susceptible to R. solani and displayed faster growth and shorter seeds in comparison with the control. These results indicate that BSR2 is associated with disease resistance, growth rate and seed size in rice and suggest that its function is evolutionarily conserved in both monocot rice and dicot Arabidopsis.
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Li P, Chang T, Chang S, Ouyang X, Qu M, Song Q, Xiao L, Xia S, Deng Q, Zhu XG. Systems model-guided rice yield improvements based on genes controlling source, sink, and flow. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2018; 60:1154-1180. [PMID: 30415497 DOI: 10.1111/jipb.12738] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 11/07/2018] [Indexed: 06/09/2023]
Abstract
A large number of genes related to source, sink, and flow have been identified after decades of research in plant genetics. Unfortunately, these genes have not been effectively utilized in modern crop breeding. This perspective paper aims to examine the reasons behind such a phenomenon and propose a strategy to resolve this situation. Specifically, we first systematically survey the currently cloned genes related to source, sink, and flow; then we discuss three factors hindering effective application of these identified genes, which include the lack of effective methods to identify limiting or critical steps in a signaling network, the misplacement of emphasis on properties, at the leaf, instead of the whole canopy level, and the non-linear complex interaction between source, sink, and flow. Finally, we propose the development of systems models of source, sink and flow, together with a detailed simulation of interactions between them and their surrounding environments, to guide effective use of the identified elements in modern rice breeding. These systems models will contribute directly to the definition of crop ideotype and also identification of critical features and parameters that limit the yield potential in current cultivars.
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Affiliation(s)
- Pan Li
- State Key Laboratory of Hybrid Rice, Key Laboratory of Phytochromes, Hunan Agriculture University, Changsha 410125, China
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha 410125, China
| | - Tiangen Chang
- National Key Laboratory for Plant Molecular Genetics, CAS Center of Excellence of Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, CAS, Shanghai 200031, China
| | - Shuoqi Chang
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha 410125, China
| | - Xiang Ouyang
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha 410125, China
| | - Mingnan Qu
- National Key Laboratory for Plant Molecular Genetics, CAS Center of Excellence of Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, CAS, Shanghai 200031, China
| | - Qingfeng Song
- National Key Laboratory for Plant Molecular Genetics, CAS Center of Excellence of Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, CAS, Shanghai 200031, China
| | - Langtao Xiao
- State Key Laboratory of Hybrid Rice, Key Laboratory of Phytochromes, Hunan Agriculture University, Changsha 410125, China
| | - Shitou Xia
- State Key Laboratory of Hybrid Rice, Key Laboratory of Phytochromes, Hunan Agriculture University, Changsha 410125, China
| | - Qiyun Deng
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha 410125, China
| | - Xin-Guang Zhu
- National Key Laboratory for Plant Molecular Genetics, CAS Center of Excellence of Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, CAS, Shanghai 200031, China
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Cook F, Hughes N, Nibau C, Orman-Ligeza B, Schatlowski N, Uauy C, Trafford K. Barley lys3 mutants are unique amongst shrunken-endosperm mutants in having abnormally large embryos. J Cereal Sci 2018; 82:16-24. [PMID: 30245543 PMCID: PMC6142819 DOI: 10.1016/j.jcs.2018.04.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Accepted: 04/30/2018] [Indexed: 01/12/2023]
Abstract
Many shrunken endosperm mutants of barley (Hordeum vulgare L.) have been described and several of these are known to have lesions in starch biosynthesis genes. Here we confirm that one type of shrunken endosperm mutant, lys3 (so called because it was first identified as a high-lysine mutant) has an additional phenotype: as well as shrunken endosperm it also has enlarged embryos. The lys3 embryos have a dry weight that is 50-150% larger than normal. Observations of developing lys3 embryos suggest that they undergo a form of premature germination and the mature lys3 grains show reduced dormancy. In many respects, the phenotype of barley lys3 is similar to that of rice GIANT EMBRYO mutants (affected in the OsGE gene). However, the barley orthologue of OsGE is located on a different chromosome from Lys3. Together these results suggest that the gene underlying Lys3 is unlikely to encode a starch biosynthesis protein but rather a protein influencing grain development.
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Affiliation(s)
- Frederick Cook
- The John Innes Centre, Norwich Research Park, Colney Lane, Norwich, Norfolk NR4 7UH, UK
| | - Nathan Hughes
- The National Plant Phenomics Centre, Institute of Biological, Rural and Environmental Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth SY23 3EE, UK
| | - Candida Nibau
- The National Plant Phenomics Centre, Institute of Biological, Rural and Environmental Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth SY23 3EE, UK
| | - Beata Orman-Ligeza
- The National Institute of Agricultural Botany, Huntingdon Road, Cambridge, Cambridgeshire CB3 0LE, UK
| | - Nicole Schatlowski
- The National Institute of Agricultural Botany, Huntingdon Road, Cambridge, Cambridgeshire CB3 0LE, UK
| | - Cristobal Uauy
- The John Innes Centre, Norwich Research Park, Colney Lane, Norwich, Norfolk NR4 7UH, UK
| | - Kay Trafford
- The National Institute of Agricultural Botany, Huntingdon Road, Cambridge, Cambridgeshire CB3 0LE, UK
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Li N, Xu R, Duan P, Li Y. Control of grain size in rice. PLANT REPRODUCTION 2018; 31:237-251. [PMID: 29523952 DOI: 10.1007/s00497-018-0333-6] [Citation(s) in RCA: 128] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 02/28/2018] [Indexed: 05/18/2023]
Abstract
Summary of rice grain size. Rice is one of the most important crops in the world. Increasing rice yield has been an urgent need to support the rapid growth of global population. The size of grains is one of major components determining rice yield; thus, grain size has been an essential target during rice breeding. Understanding the genetic and molecular mechanisms of grain size control can provide new strategies for yield improvement in rice. In general, the final size of rice grains is coordinately controlled by cell proliferation and cell expansion in the spikelet hull, which sets the storage capacity of the grain and limits grain filling. Recent studies have identified several quantitative trait loci and a number of genes as key grain size regulators. These regulators are involved in G protein signaling, the mitogen-activated protein kinase signaling pathway, the ubiquitin-proteasome pathway, phytohormone signalings, or transcriptional regulation. In this review, we summarize current knowledge on grain size control in rice and discuss the genetic and molecular mechanisms of these grain size regulators.
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Affiliation(s)
- Na Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ran Xu
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Penggen Duan
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yunhai Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
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Gao M, Yin X, Yang W, Lam SM, Tong X, Liu J, Wang X, Li Q, Shui G, He Z. GDSL lipases modulate immunity through lipid homeostasis in rice. PLoS Pathog 2017; 13:e1006724. [PMID: 29131851 PMCID: PMC5703576 DOI: 10.1371/journal.ppat.1006724] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 11/27/2017] [Accepted: 10/31/2017] [Indexed: 12/04/2022] Open
Abstract
Lipids and lipid metabolites play important roles in plant-microbe interactions. Despite the extensive studies of lipases in lipid homeostasis and seed oil biosynthesis, the involvement of lipases in plant immunity remains largely unknown. In particular, GDSL esterases/lipases, characterized by the conserved GDSL motif, are a subfamily of lipolytic enzymes with broad substrate specificity. Here, we functionally identified two GDSL lipases, OsGLIP1 and OsGLIP2, in rice immune responses. Expression of OsGLIP1 and OsGLIP2 was suppressed by pathogen infection and salicylic acid (SA) treatment. OsGLIP1 was mainly expressed in leaf and leaf sheath, while OsGLIP2 showed high expression in elongating internodes. Biochemical assay demonstrated that OsGLIP1 and OsGLIP2 are functional lipases that could hydrolyze lipid substrates. Simultaneous down-regulation of OsGLIP1 and OsGLIP2 increased plant resistance to both bacterial and fungal pathogens, whereas disease resistance in OsGLIP1 and OsGLIP2 overexpression plants was significantly compromised, suggesting that both genes act as negative regulators of disease resistance. OsGLIP1 and OsGLIP2 proteins mainly localize to lipid droplets and the endoplasmic reticulum (ER) membrane. The proper cellular localization of OsGLIP proteins is indispensable for their functions in immunity. Comprehensive lipid profiling analysis indicated that the alteration of OsGLIP gene expression was associated with substantial changes of the levels of lipid species including monogalactosyldiacylglycerol (MGDG) and digalactosyldiacylglycerol (DGDG). We show that MGDG and DGDG feeding could attenuate disease resistance. Taken together, our study indicates that OsGLIP1 and OsGLIP2 negatively regulate rice defense by modulating lipid metabolism, thus providing new insights into the function of lipids in plant immunity. Lipases are a large family of enzymes conferring lipid metabolism. Lipids and their metabolites play diverse roles in plant growth as well as response to environmental stimuli. Accumulating evidence implicates lipids as signaling molecules mediating plant immunity. Therefore, lipases are presumed to be actively involved in plant defense responses. Based on gene expression profiling, we have identified two functional GDSL lipases, encoded by OsGLIP1 and OsGLIP2, whose expression was suppressed by pathogen infection in the model cereal rice. Both OsGLIP1 and OsGLIP2 proteins localize to lipid droplets and the endoplasmic reticulum (ER) membrane, and they likely coordinate lipid metabolism with differential but complementary expression patterns in tissues and developmental stages. Consequently, alteration of OsGLIP gene expression was associated with substantial changes of lipid abundance and plant disease resistance. Our work identifies and characterizes two lipases that function as negative regulators of plant immune responses, strengthening the understanding of lipid metabolism in plant-microbe interactions.
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Affiliation(s)
- Mingjun Gao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences/Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Xin Yin
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences/Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Weibing Yang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences/Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Sin Man Lam
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Xiaohong Tong
- China National Rice Research Institute, Hangzhou, China
| | - Jiyun Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences/Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Xin Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences/Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Qun Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences/Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Guanghou Shui
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Zuhua He
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences/Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, China
- * E-mail:
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Huang X, Peng X, Sun MX. OsGCD1 is essential for rice fertility and required for embryo dorsal-ventral pattern formation and endosperm development. THE NEW PHYTOLOGIST 2017; 215:1039-1058. [PMID: 28585692 DOI: 10.1111/nph.14625] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 04/25/2017] [Indexed: 05/20/2023]
Abstract
Rice fertility is critical for rice reproduction and is thus a focus of interest. Most studies have addressed male sterility and its relation to rice production. The mechanisms of regulation of embryogenesis and endosperm development are essential for rice reproduction, but remain largely unknown. Here, we report a functional analysis of the rice gene OsGCD1, which encodes a highly conserved homolog of Arabidopsis GCD1 (GAMETE CELLS DEFECTIVE1). OsGCD1 mutants were generated using the CRISPR/Cas9 system and subjected to functional analysis. The homozygote mutants cannot be obtained, whereas heterozygotes showed altered phenotypes. In the majority of aborted seeds, the endosperm nucleus divided a limited number of times. The free nuclei were distributed only at the micropylar end of embryo sacs, and their oriented positioning was blocked. In addition, aleurone differentiation was interrupted. The embryo developed slowly, and pattern formation, particularly the dorsal-ventral pattern and symmetry establishment, of embryos was disturbed. Thus, the embryos showed various morphological and structural dysplasias. Our findings reveal that OsGCD1 is essential for rice fertility and is required for dorsal-ventral pattern formation and endosperm free nucleus positioning, suggesting a critical role in sexual reproduction of both monocotyledon and dicotyledon plants.
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Affiliation(s)
- Xiaorong Huang
- College of Life Science, State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan, 430072, China
| | - Xiongbo Peng
- College of Life Science, State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan, 430072, China
| | - Meng-Xiang Sun
- College of Life Science, State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan, 430072, China
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Zhao GC, Xie MX, Wang YC, Li JY. Molecular Mechanisms Underlying γ-Aminobutyric Acid (GABA) Accumulation in Giant Embryo Rice Seeds. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:4883-4889. [PMID: 28587460 DOI: 10.1021/acs.jafc.7b00013] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
To uncover the molecular mechanisms underlying GABA accumulation in giant embryo rice seeds, we analyzed the expression levels of GABA metabolism genes and contents of GABA and GABA metabolic intermediates in developing grains and germinated brown rice of giant embryo rice 'Shangshida No. 5' and normal embryo rice 'Chao2-10' respectively. In developing grains, the higher GABA contents in 'Shangshida No. 5' were accompanied with upregulation of gene transcripts and intermediate contents in the polyamine pathway and downregulation of GABA catabolic gene transcripts, as compared with those in 'Chao2-10'. In germinated brown rice, the higher GABA contents in 'Shangshida No. 5' were parallel with upregulation of OsGAD and polyamine pathway gene transcripts and Glu and polyamine pathway intermediate contents and downregulation of GABA catabolic gene transcripts. These results are the first to indicate that polyamine pathway and GABA catabolic genes play a crucial role in GABA accumulation in giant embryo rice seeds.
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Affiliation(s)
- Guo-Chao Zhao
- Development Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University , Shanghai, 200234, People's Republic of China
| | - Mi-Xue Xie
- Development Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University , Shanghai, 200234, People's Republic of China
| | - Ying-Cun Wang
- Development Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University , Shanghai, 200234, People's Republic of China
| | - Jian-Yue Li
- Development Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University , Shanghai, 200234, People's Republic of China
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Du J, Wang S, He C, Zhou B, Ruan YL, Shou H. Identification of regulatory networks and hub genes controlling soybean seed set and size using RNA sequencing analysis. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:1955-1972. [PMID: 28087653 PMCID: PMC5429000 DOI: 10.1093/jxb/erw460] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 11/11/2016] [Indexed: 05/19/2023]
Abstract
To understand the gene expression networks controlling soybean seed set and size, transcriptome analyses were performed in three early seed developmental stages, using two genotypes with contrasting seed size. The two-dimensional data set provides a comprehensive and systems-level view on dynamic gene expression networks underpinning soybean seed set and subsequent development. Using pairwise comparisons and weighted gene coexpression network analyses, we identified modules of coexpressed genes and hub genes for each module. Of particular importance are the discoveries of specific modules for the large seed size variety and for seed developmental stages. A large number of candidate regulators for seed size, including those involved in hormonal signaling pathways and transcription factors, were transiently and specifically induced in the early developmental stages. The soybean homologs of a brassinosteroid signaling receptor kinase, a brassinosteroid-signaling kinase, were identified as hub genes operating in the seed coat network in the early seed maturation stage. Overexpression of a candidate seed size regulatory gene, GmCYP78A5, in transgenic soybean resulted in increased seed size and seed weight. Together, these analyses identified a large number of potential key regulators controlling soybean seed set, seed size, and, consequently, yield potential, thereby providing new insights into the molecular networks underlying soybean seed development.
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Affiliation(s)
- Juan Du
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, China
| | - Shoudong Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, China
| | - Cunman He
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, China
| | - Bin Zhou
- Institute of Crop Science, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Yong-Ling Ruan
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, Australia
| | - Huixia Shou
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, China
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Merino I, Abrahamsson M, Sterck L, Craven-Bartle B, Canovas F, von Arnold S. Transcript profiling for early stages during embryo development in Scots pine. BMC PLANT BIOLOGY 2016; 16:255. [PMID: 27863470 PMCID: PMC5116219 DOI: 10.1186/s12870-016-0939-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 10/28/2016] [Indexed: 05/22/2023]
Abstract
BACKGROUND Characterization of the expression and function of genes regulating embryo development in conifers is interesting from an evolutionary point of view. However, our knowledge about the regulation of embryo development in conifers is limited. During early embryo development in Pinus species the proembyo goes through a cleavage process, named cleavage polyembryony, giving rise to four embryos. One of these embryos develops to a dominant embryo, which will develop further into a mature, cotyledonary embryo, while the other embryos, the subordinate embryos, are degraded. The main goal of this study has been to identify processes that might be important for regulating the cleavage process and for the development of a dominant embryo. RESULTS RNA samples from embryos and megagametophytes at four early developmental stages during seed development in Pinus sylvestris were subjected to high-throughput sequencing. A total of 6.6 million raw reads was generated, resulting in 121,938 transcripts, out of which 36.106 contained ORFs. 18,638 transcripts were differentially expressed (DETs) in embryos and megagametophytes. GO enrichment analysis of transcripts up-regulated in embryos showed enrichment for different cellular processes, while those up-regulated in megagametophytes were enriched for accumulation of storage material and responses to stress. The highest number of DETs was detected during the initiation of the cleavage process. Transcripts related to embryogenic competence, cell wall modifications, cell division pattern, axis specification and response to hormones and stress were highly abundant and differentially expressed during early embryo development. The abundance of representative DETs was confirmed by qRT-PCR analyses. CONCLUSION Based on the processes identified in the GO enrichment analyses and the expression of the selected transcripts we suggest that (i) processes related to embryogenic competence and cell wall loosening are involved in activating the cleavage process; (ii) apical-basal polarization is strictly regulated in dominant embryos but not in the subordinate embryos; (iii) the transition from the morphogenic phase to the maturation phase is not completed in subordinate embryos. This is the first genome-wide transcript expression profiling of the earliest stages during embryo development in a Pinus species. Our results can serve as a framework for future studies to reveal the functions of identified genes.
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Affiliation(s)
- Irene Merino
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Box 7080, 750 07 Uppsala, Sweden
| | - Malin Abrahamsson
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Box 7080, 750 07 Uppsala, Sweden
| | - Lieven Sterck
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent, B-9000 Belgium
| | - Blanca Craven-Bartle
- Department of Molecular Biology and Biochemistry, School of Sciences, Campus de Teatinos, Universidad de Malaga, 29071 Malaga, Spain
| | - Francisco Canovas
- Department of Molecular Biology and Biochemistry, School of Sciences, Campus de Teatinos, Universidad de Malaga, 29071 Malaga, Spain
| | - Sara von Arnold
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Box 7080, 750 07 Uppsala, Sweden
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Srivastava R, Bajaj D, Sayal YK, Meher PK, Upadhyaya HD, Kumar R, Tripathi S, Bharadwaj C, Rao AR, Parida SK. Genome-wide development and deployment of informative intron-spanning and intron-length polymorphism markers for genomics-assisted breeding applications in chickpea. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 252:374-387. [PMID: 27717474 DOI: 10.1016/j.plantsci.2016.08.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 08/03/2016] [Accepted: 08/24/2016] [Indexed: 06/06/2023]
Abstract
The discovery and large-scale genotyping of informative gene-based markers is essential for rapid delineation of genes/QTLs governing stress tolerance and yield component traits in order to drive genetic enhancement in chickpea. A genome-wide 119169 and 110491 ISM (intron-spanning markers) from 23129 desi and 20386 kabuli protein-coding genes and 7454 in silico InDel (insertion-deletion) (1-45-bp)-based ILP (intron-length polymorphism) markers from 3283 genes were developed that were structurally and functionally annotated on eight chromosomes and unanchored scaffolds of chickpea. A much higher amplification efficiency (83%) and intra-specific polymorphic potential (86%) detected by these markers than that of other sequence-based genetic markers among desi and kabuli chickpea accessions was apparent even by a cost-effective agarose gel-based assay. The genome-wide physically mapped 1718 ILP markers assayed a wider level of functional genetic diversity (19-81%) and well-defined phylogenetics among domesticated chickpea accessions. The gene-derived 1424 ILP markers were anchored on a high-density (inter-marker distance: 0.65cM) desi intra-specific genetic linkage map/functional transcript map (ICC 4958×ICC 2263) of chickpea. This reference genetic map identified six major genomic regions harbouring six robust QTLs mapped on five chromosomes, which explained 11-23% seed weight trait variation (7.6-10.5 LOD) in chickpea. The integration of high-resolution QTL mapping with differential expression profiling detected six including one potential serine carboxypeptidase gene with ILP markers (linked tightly to the major seed weight QTLs) exhibiting seed-specific expression as well as pronounced up-regulation especially in seeds of high (ICC 4958) as compared to low (ICC 2263) seed weight mapping parental accessions. The marker information generated in the present study was made publicly accessible through a user-friendly web-resource, "Chickpea ISM-ILP Marker Database". The designing of multiple ISM and ILP markers (2-5 markers/gene) from an individual gene (transcription factor) with numerous aforementioned desirable genetic attributes can widen the user-preference to select suitable primer combination for simultaneous large-scale assaying of functional allelic variation, natural allelic diversity, molecular mapping and expression profiling of genes among chickpea accessions. This will essentially accelerate the identification of functionally relevant molecular tags regulating vital agronomic traits for genomics-assisted crop improvement by optimal resource expenses in chickpea.
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Affiliation(s)
- Rishi Srivastava
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Deepak Bajaj
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Yogesh K Sayal
- Centre for Agricultural Bioinformatics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Statistics Research Institute, New Delhi 110012, India
| | - Prabina K Meher
- Division of Statistical Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Statistics Research Institute, New Delhi 110012, India
| | - Hari D Upadhyaya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Telangana, India
| | - Rajendra Kumar
- U.P. Council of Agricultural Research, Gomati Nagar, Lucknow 226010, Uttar Pradesh, India
| | - Shailesh Tripathi
- Division of Genetics, Indian Agricultural Research Institute (IARI), New Delhi 110012, India
| | - Chellapilla Bharadwaj
- Division of Genetics, Indian Agricultural Research Institute (IARI), New Delhi 110012, India
| | - Atmakuri R Rao
- Centre for Agricultural Bioinformatics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Statistics Research Institute, New Delhi 110012, India
| | - Swarup K Parida
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India.
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Li N, Li Y. Signaling pathways of seed size control in plants. CURRENT OPINION IN PLANT BIOLOGY 2016; 33:23-32. [PMID: 27294659 DOI: 10.1016/j.pbi.2016.05.008] [Citation(s) in RCA: 238] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 05/23/2016] [Accepted: 05/31/2016] [Indexed: 05/18/2023]
Abstract
Seed size is one of the most important yield traits in plants. In angiosperms, a mature seed consists of the embryo, the endosperm and the seed coat, which develop from the zygote, the fertilized central cell and the maternal integuments, respectively. Seed size is therefore coordinately controlled by the growth of maternal and zygotic tissues. Several signaling pathways that determine seed size by influencing the endosperm and/or maternal tissue growth have been identified, including the IKU pathway, the ubiquitin-proteasome pathway, G-protein signaling, the mitogen-activated protein kinase signaling pathway, phytohormones and transcriptional regulatory factors. The functions of several seed size regulators are conserved in Arabidopsis and rice; therefore it is promising to convert basic research on seed size into practical applications in crops. In this review, we summarize recent research progress on seed size control, with particular emphasis on the genetic and molecular mechanisms of several newly identified regulators of seed size in Arabidopsis and rice.
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Affiliation(s)
- 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, Chinese Academy of Sciences, Beijing 100101, 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, Chinese Academy of Sciences, Beijing 100101, China.
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Sakata M, Seno M, Matsusaka H, Takahashi K, Nakamura Y, Yamagata Y, Angeles ER, Mochizuki T, Kumamaru T, Sato M, Enomoto A, Tashiro K, Kuhara S, Satoh H, Yoshimura A. Development and evaluation of rice giant embryo mutants for high oil content originated from a high-yielding cultivar 'Mizuhochikara'. BREEDING SCIENCE 2016; 66:425-33. [PMID: 27436953 PMCID: PMC4902460 DOI: 10.1270/jsbbs.15135] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 03/15/2016] [Indexed: 05/03/2023]
Abstract
Rice bran oil is a byproduct of the milling of rice (Oryza sativa L.). It offers various health benefits and has a beneficial fatty acid composition. To increase the amount of rice bran as a sink for triacylglycerol (TAG), we developed and characterized new breeding materials with giant embryos. To induce mutants, we treated fertilized egg cells of the high-yielding cultivar 'Mizuhochikara' with N-methyl-N-nitrosourea (MNU). By screening M2 seeds, we isolated four giant embryo mutant lines. Genetic analysis revealed that the causative loci in lines MGE12 and MGE13 were allelic to giant embryo (ge) on chromosome 7, and had base changes in the causal gene Os07g0603700. On the other hand, the causative loci in lines MGE8 and MGE14 were not allelic to ge, and both were newly mapped on chromosome 3. The TAG contents of all four mutant lines increased relative to their wild type, 'Mizuhochikara'. MGE13 was agronomically similar to 'Mizuhochikara' and would be useful for breeding for improved oil content.
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Affiliation(s)
- Mitsukazu Sakata
- Faculty of Agriculture, Kyushu University,
6-10-1, Hakozaki, Higashi-ku, Fukuoka 812-8581,
Japan
| | - Mari Seno
- Faculty of Agriculture, Kyushu University,
6-10-1, Hakozaki, Higashi-ku, Fukuoka 812-8581,
Japan
| | - Hiroaki Matsusaka
- Faculty of Agriculture, Kyushu University,
6-10-1, Hakozaki, Higashi-ku, Fukuoka 812-8581,
Japan
| | - Kiyomi Takahashi
- Faculty of Agriculture, Kyushu University,
6-10-1, Hakozaki, Higashi-ku, Fukuoka 812-8581,
Japan
| | - Yuki Nakamura
- Faculty of Agriculture, Kyushu University,
6-10-1, Hakozaki, Higashi-ku, Fukuoka 812-8581,
Japan
| | - Yoshiyuki Yamagata
- Faculty of Agriculture, Kyushu University,
6-10-1, Hakozaki, Higashi-ku, Fukuoka 812-8581,
Japan
| | - Enrique R. Angeles
- Institute of Tropical Agriculture, Kyushu University,
6-10-1, Hakozaki, Higashi-ku, Fukuoka 812-8581,
Japan
| | - Toshihiro Mochizuki
- Faculty of Agriculture, Kyushu University,
6-10-1, Hakozaki, Higashi-ku, Fukuoka 812-8581,
Japan
| | - Toshihiro Kumamaru
- Faculty of Agriculture, Kyushu University,
6-10-1, Hakozaki, Higashi-ku, Fukuoka 812-8581,
Japan
| | - Masao Sato
- Faculty of Agriculture, Kyushu University,
6-10-1, Hakozaki, Higashi-ku, Fukuoka 812-8581,
Japan
| | - Akiko Enomoto
- Faculty of Agriculture, Kyushu University,
6-10-1, Hakozaki, Higashi-ku, Fukuoka 812-8581,
Japan
| | - Kosuke Tashiro
- Faculty of Agriculture, Kyushu University,
6-10-1, Hakozaki, Higashi-ku, Fukuoka 812-8581,
Japan
| | - Satoru Kuhara
- Faculty of Agriculture, Kyushu University,
6-10-1, Hakozaki, Higashi-ku, Fukuoka 812-8581,
Japan
| | - Hikaru Satoh
- Faculty of Agriculture, Kyushu University,
6-10-1, Hakozaki, Higashi-ku, Fukuoka 812-8581,
Japan
| | - Atsushi Yoshimura
- Faculty of Agriculture, Kyushu University,
6-10-1, Hakozaki, Higashi-ku, Fukuoka 812-8581,
Japan
- Corresponding author (e-mail: )
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50
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Ju Y, Liu C, Lu W, Zhang Q, Sodmergen. Arabidopsis mitochondrial protein slow embryo development1 is essential for embryo development. Biochem Biophys Res Commun 2016; 474:371-376. [PMID: 27109472 DOI: 10.1016/j.bbrc.2016.04.114] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 04/20/2016] [Indexed: 10/21/2022]
Abstract
The plant seeds formation are crucial parts in reproductive process in seed plants as well as food source for humans. Proper embryo development ensure viable seed formation. Here, we showed an Arabidopsis T-DNA insertion mutant slow embryo development1 (sed1) which exhibited retarded embryogenesis, led to aborted seeds. Embryo without SED1 developed slower compared to normal one and could be recognized at early globular stage by its white appearance. In later development stage, storage accumulated poorly with less protein and lipid body production. In vitro culture did not rescue albino embryo. SED1 encoded a protein targeted to mitochondria. Transmission electron microscopic analysis revealed that mitochondria developed abnormally, and more strikingly plastid failed to construct grana in time in sed1/sed1 embryo. These data indicated that SED1 is indispensable for embryogenesis in Arabidopsis, and the mitochondria may be involved in the regulation of many aspects of seed development.
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Affiliation(s)
- Yan Ju
- Key Laboratory of Cell Proliferation and Differentiation (Ministry of Education), College of Life Sciences, Peking University, Beijing 100871, China
| | - Chunying Liu
- Key Laboratory of Cell Proliferation and Differentiation (Ministry of Education), College of Life Sciences, Peking University, Beijing 100871, China
| | - Wenwen Lu
- Key Laboratory of Cell Proliferation and Differentiation (Ministry of Education), College of Life Sciences, Peking University, Beijing 100871, China
| | - Quan Zhang
- Key Laboratory of Cell Proliferation and Differentiation (Ministry of Education), College of Life Sciences, Peking University, Beijing 100871, China
| | - Sodmergen
- Key Laboratory of Cell Proliferation and Differentiation (Ministry of Education), College of Life Sciences, Peking University, Beijing 100871, China.
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