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Anjum N, Maiti MK. OsNAC121 regulates root development, tillering, panicle morphology, and grain filling in rice plant. PLANT MOLECULAR BIOLOGY 2024; 114:82. [PMID: 38954114 DOI: 10.1007/s11103-024-01476-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 06/11/2024] [Indexed: 07/04/2024]
Abstract
Transcription factors in coordination with phytohormones form an intricate regulatory network modulating vital cellular mechanisms like development, growth and senescence in plants. In this study, we have functionally characterized the transcription factor OsNAC121 by developing gene silencing and overexpressing transgenic rice plants, followed by detailed analyses of the plant architecture. Transgenic lines exhibited remodelling in crown root development, lateral root structure and density, tiller height and number, panicle and grain morphologies, underpinning the imbalanced auxin: cytokinin ratio due to perturbed auxin transportation. Application of cytokinin, auxin and abscisic acid increased OsNAC121 gene expression nearly 17-, 6- and 91-folds, respectively. qRT-PCR results showed differential expressions of auxin and cytokinin pathway genes, implying their altered levels. A 47-fold higher expression level of OsNAC121 during milky stage in untransformed rice, compared to 14-day old shoot tissue, suggests its crucial role in grain filling; as evidenced by a large number of undeveloped grains produced by the gene silenced lines. Crippled gravitropic response by the transgenic plants indicates their impaired auxin transport. Bioinformatics revealed that OsNAC121 interacts with co-repressor (TOPLESS) proteins and forms a part of the inhibitor complex OsIAA10, an essential core component of auxin signalling pathway. Therefore, OsNAC121 emerges as an important regulator of various aspects of plant architecture through modulation of crosstalk between auxin and cytokinin, altering their concentration gradient in the meristematic zones, and consequently modifying different plant organogenesis processes.
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Affiliation(s)
- Nazma Anjum
- Department of Bioscience and Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India
| | - Mrinal K Maiti
- Department of Bioscience and Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India.
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Zhang H, Zhang J, Xu P, Li M, Li Y. Insertion of a miniature inverted-repeat transposable element into the promoter of OsTCP4 results in more tillers and a lower grain size in rice. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1421-1436. [PMID: 37988625 DOI: 10.1093/jxb/erad467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 11/21/2023] [Indexed: 11/23/2023]
Abstract
A class I PCF type protein, TCP4, was identified as a transcription factor associated with both grain size and tillering through a DNA pull-down-MS assay combined with a genome-wide association study. This transcription factor was found to have a significant role in the variations among the 533 rice accessions, dividing them into two main subspecies. A Tourist-like miniature inverted-repeat transposable element (MITE) was discovered in the promoter of TCP4 in japonica/geng accessions (TCP4M+), which was found to suppress the expression of TCP4 at the transcriptional level. The MITE-deleted haplotype (TCP4M-) was mainly found in indica/xian accessions. ChIP-qPCR and EMSA demonstrated the binding of TCP4 to promoters of grain reservoir genes such as SSIIa and Amy3D in vivo and in vitro, respectively. The introduction of the genomic sequence of TCP4M+ into different TCP4M- cultivars was found to affect the expression of TCP4 in the transgenic rice, resulting in decreased expression of its downstream target gene SSIIa, increased tiller number, and decreased seed length. This study revealed that a Tourist-like MITE contributes to subspecies divergence by regulating the expression of TCP4 in response to environmental pressure, thus influencing source-sink balance by regulating starch biosynthesis in rice.
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Affiliation(s)
- Hui Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China
| | - Juncheng Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China
| | - Pengkun Xu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China
| | - Ming Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430026, China
| | - Yibo Li
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China
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Zhu M, Jiang S, Huang J, Li Z, Xu S, Liu S, He Y, Zhang Z. Biochemical and Transcriptome Analyses Reveal a Stronger Capacity for Photosynthate Accumulation in Low-Tillering Rice Varieties. Int J Mol Sci 2024; 25:1648. [PMID: 38338929 PMCID: PMC10855222 DOI: 10.3390/ijms25031648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/23/2024] [Accepted: 01/27/2024] [Indexed: 02/12/2024] Open
Abstract
Moderate control of rice tillering and the development of rice varieties with large panicles are important topics for future high-yield rice breeding. Herein, we found that low-tillering rice varieties stopped tillering earlier and had a larger leaf area of the sixth leaf. Notably, at 28 days after sowing, the rice seedlings of the low-tillering group had an average single-culm above-ground biomass of 0.84 g, significantly higher than that of the multi-tillering group by 56.26%, and their NSC (non-structural carbohydrate) and starch contents in sheaths were increased by 43.34% and 97.75%, respectively. These results indicated that the low-tillering group of rice varieties had a stronger ability to store photosynthetic products in the form of starch in their sheaths, which was thus more beneficial for their large panicle development. The results of carbon and nitrogen metabolism analyses showed that the low-tillering group had a relatively strong carbon metabolism activity, which was more favorable for the accumulation of photosynthesis products and the following development of large panicles, while the multi-tillering group showed relatively strong nitrogen metabolism activity, which was more beneficial for the development and formation of new organs, such as tillers. Accordingly, in the low-tillering rice varieties, the up-regulated genes were enriched in the pathways mainly related to the synthesis of carbohydrates, while the down-regulated genes were mainly enriched in the nitrogen metabolism pathways. This study provides new insights into the mechanism of rice tillering regulation and promotes the development of new varieties with ideal plant types.
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Affiliation(s)
- Mingqiang Zhu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China; (M.Z.); (S.J.); (J.H.); (Z.L.); (S.X.); (S.L.)
| | - Shan Jiang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China; (M.Z.); (S.J.); (J.H.); (Z.L.); (S.X.); (S.L.)
| | - Jinqiu Huang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China; (M.Z.); (S.J.); (J.H.); (Z.L.); (S.X.); (S.L.)
| | - Zhihui Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China; (M.Z.); (S.J.); (J.H.); (Z.L.); (S.X.); (S.L.)
| | - Shuang Xu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China; (M.Z.); (S.J.); (J.H.); (Z.L.); (S.X.); (S.L.)
| | - Shaojia Liu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China; (M.Z.); (S.J.); (J.H.); (Z.L.); (S.X.); (S.L.)
| | - Yonggang He
- Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan 430070, China
| | - Zhihong Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China; (M.Z.); (S.J.); (J.H.); (Z.L.); (S.X.); (S.L.)
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Feng G, Xu X, Liu W, Hao F, Yang Z, Nie G, Huang L, Peng Y, Bushman S, He W, Zhang X. Transcriptome Profiling Provides Insights into the Early Development of Tiller Buds in High- and Low-Tillering Orchardgrass Genotypes. Int J Mol Sci 2023; 24:16370. [PMID: 38003564 PMCID: PMC10671593 DOI: 10.3390/ijms242216370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/03/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
Orchardgrass (Dactylis glomerata L.) is among the most economically important perennial cool-season grasses, and is considered an excellent hay, pasture, and silage crop in temperate regions worldwide. Tillering is a vital feature that dominates orchardgrass regeneration and biomass yield. However, transcriptional dynamics underlying early-stage bud development in high- and low-tillering orchardgrass genotypes are unclear. Thus, this study assessed the photosynthetic parameters, the partially essential intermediate biomolecular substances, and the transcriptome to elaborate the early-stage profiles of tiller development. Photosynthetic efficiency and morphological development significantly differed between high- (AKZ-NRGR667) and low-tillering genotypes (D20170203) at the early stage after tiller formation. The 206.41 Gb of high-quality reads revealed stage-specific differentially expressed genes (DEGs), demonstrating that signal transduction and energy-related metabolism pathways, especially photosynthetic-related processes, influence tiller induction and development. Moreover, weighted correlation network analysis (WGCNA) and functional enrichment identified distinctively co-expressed gene clusters and four main regulatory pathways, including chlorophyll, lutein, nitrogen, and gibberellic acid (GA) metabolism pathways. Therefore, photosynthesis, carbohydrate synthesis, nitrogen efficient utilization, and phytohormone signaling pathways are closely and intrinsically linked at the transcriptional level. These findings enhance our understanding of tillering in orchardgrass and perennial grasses, providing a new breeding strategy for improving forage biomass yield.
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Affiliation(s)
- Guangyan Feng
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaoheng Xu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Wen Liu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Feigxiang Hao
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhongfu Yang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Gang Nie
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Linkai Huang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yan Peng
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Shaun Bushman
- Forage and Range Research Laboratory, United States Department of Agriculture, 695 North 1100 East, Logan, UT 84322-6300, USA
| | - Wei He
- Grassland Research Institute, Chongqing Academy of Animal Science, Chongqing 402460, China
| | - Xinquan Zhang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
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Yadav B, Majhi A, Phagna K, Meena MK, Ram H. Negative regulators of grain yield and mineral contents in rice: potential targets for CRISPR-Cas9-mediated genome editing. Funct Integr Genomics 2023; 23:317. [PMID: 37837547 DOI: 10.1007/s10142-023-01244-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/27/2023] [Accepted: 09/29/2023] [Indexed: 10/16/2023]
Abstract
Rice is a major global staple food crop, and improving its grain yield and nutritional quality has been a major thrust research area since last decades. Yield and nutritional quality are complex traits which are controlled by multiple signaling pathways. Sincere efforts during past decades of research have identified several key genetic and molecular regulators that governed these complex traits. The advent of clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9)-mediated gene knockout approaches has accelerated the development of improved varieties; however, finding out target gene with negative regulatory function in particular trait without giving any pleiotropic effect remains a challenge. Here, we have reviewed past and recent literature and identified important negative regulators of grain yield and mineral contents which could be potential targets for CRISPR-Cas9-mediated gene knockout. Additionally, we have also compiled a list of microRNAs (miRNAs), which target positive regulators of grain yield, plant stress tolerance, and grain mineral contents. Knocking out these miRNAs could help to increase expression of such positive regulators and thus improve the plant trait. The knowledge presented in this review would help to further accelerate the CRISPR-Cas9-mediated trait improvement in rice.
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Affiliation(s)
- Banita Yadav
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Ashis Majhi
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Kanika Phagna
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Mukesh Kumar Meena
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India.
| | - Hasthi Ram
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India.
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Yoon DK, Choi I, Won YJ, Shin Y, Cheon KS, Oh H, Lee C, Lee S, Cho MH, Jun S, Kim Y, Kim SL, Baek J, Jeong H, Lyu JI, Lee GS, Kim KH, Ji H. QTL Mapping of Tiller Number in Korean Japonica Rice Varieties. Genes (Basel) 2023; 14:1593. [PMID: 37628644 PMCID: PMC10454613 DOI: 10.3390/genes14081593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 07/25/2023] [Accepted: 08/02/2023] [Indexed: 08/27/2023] Open
Abstract
Tiller number is an important trait associated with yield in rice. Tiller number in Korean japonica rice was analyzed under greenhouse conditions in 160 recombinant inbred lines (RILs) derived from a cross between the temperate japonica varieties Odae and Unbong40 to identify quantitative trait loci (QTLs). A genetic map comprising 239 kompetitive allele-specific PCR (KASP) and 57 cleaved amplified polymorphic sequence markers was constructed. qTN3, a major QTL for tiller number, was identified at 132.4 cm on chromosome 3. This QTL was also detected under field conditions in a backcross population; thus, qTN3 was stable across generations and environments. qTN3 co-located with QTLs associated with panicle number per plant and culm diameter, indicating it had pleiotropic effects. The qTN3 regions of Odae and Unbong40 differed in a known functional variant (4 bp TGTG insertion/deletion) in the 5' UTR of OsTB1, a gene underlying variation in tiller number and culm strength. Investigation of variation in genotype and tiller number revealed that varieties with the insertion genotype had lower tiller numbers than those with the reference genotype. A high-resolution melting marker was developed to enable efficient marker-assisted selection. The QTL qTN3 will therefore be useful in breeding programs developing japonica varieties with optimal tiller numbers for increased yield.
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Affiliation(s)
- Dong-Kyung Yoon
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea; (D.-K.Y.); (H.O.); (S.L.); (M.H.C.); (S.J.); (Y.K.); (S.L.K.); (J.B.); (H.J.); (J.I.L.); (G.-S.L.); (K.-H.K.)
| | - Inchan Choi
- Department of Agricultural Engineering, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54875, Republic of Korea;
| | - Yong Jae Won
- Cheorwon Branch, National Institute of Crop Science, Rural Development Administration (RDA), Cheorwon 24010, Republic of Korea;
| | - Yunji Shin
- Genecell Biotech Inc., Wanju 55322, Republic of Korea;
| | - Kyeong-Seong Cheon
- Department of Forest Bioresources, National Institute of Forest Science, Suwon 16631, Republic of Korea;
| | - Hyoja Oh
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea; (D.-K.Y.); (H.O.); (S.L.); (M.H.C.); (S.J.); (Y.K.); (S.L.K.); (J.B.); (H.J.); (J.I.L.); (G.-S.L.); (K.-H.K.)
| | - Chaewon Lee
- Department of Central Area Crop Science, National Institute of Crop Science, Rural Development Administration (RDA), Suwon 16429, Republic of Korea;
| | - Seoyeon Lee
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea; (D.-K.Y.); (H.O.); (S.L.); (M.H.C.); (S.J.); (Y.K.); (S.L.K.); (J.B.); (H.J.); (J.I.L.); (G.-S.L.); (K.-H.K.)
| | - Mi Hyun Cho
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea; (D.-K.Y.); (H.O.); (S.L.); (M.H.C.); (S.J.); (Y.K.); (S.L.K.); (J.B.); (H.J.); (J.I.L.); (G.-S.L.); (K.-H.K.)
| | - Soojin Jun
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea; (D.-K.Y.); (H.O.); (S.L.); (M.H.C.); (S.J.); (Y.K.); (S.L.K.); (J.B.); (H.J.); (J.I.L.); (G.-S.L.); (K.-H.K.)
| | - Yeongtae Kim
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea; (D.-K.Y.); (H.O.); (S.L.); (M.H.C.); (S.J.); (Y.K.); (S.L.K.); (J.B.); (H.J.); (J.I.L.); (G.-S.L.); (K.-H.K.)
| | - Song Lim Kim
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea; (D.-K.Y.); (H.O.); (S.L.); (M.H.C.); (S.J.); (Y.K.); (S.L.K.); (J.B.); (H.J.); (J.I.L.); (G.-S.L.); (K.-H.K.)
| | - Jeongho Baek
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea; (D.-K.Y.); (H.O.); (S.L.); (M.H.C.); (S.J.); (Y.K.); (S.L.K.); (J.B.); (H.J.); (J.I.L.); (G.-S.L.); (K.-H.K.)
| | - HwangWeon Jeong
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea; (D.-K.Y.); (H.O.); (S.L.); (M.H.C.); (S.J.); (Y.K.); (S.L.K.); (J.B.); (H.J.); (J.I.L.); (G.-S.L.); (K.-H.K.)
| | - Jae Il Lyu
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea; (D.-K.Y.); (H.O.); (S.L.); (M.H.C.); (S.J.); (Y.K.); (S.L.K.); (J.B.); (H.J.); (J.I.L.); (G.-S.L.); (K.-H.K.)
| | - Gang-Seob Lee
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea; (D.-K.Y.); (H.O.); (S.L.); (M.H.C.); (S.J.); (Y.K.); (S.L.K.); (J.B.); (H.J.); (J.I.L.); (G.-S.L.); (K.-H.K.)
| | - Kyung-Hwan Kim
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea; (D.-K.Y.); (H.O.); (S.L.); (M.H.C.); (S.J.); (Y.K.); (S.L.K.); (J.B.); (H.J.); (J.I.L.); (G.-S.L.); (K.-H.K.)
| | - Hyeonso Ji
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea; (D.-K.Y.); (H.O.); (S.L.); (M.H.C.); (S.J.); (Y.K.); (S.L.K.); (J.B.); (H.J.); (J.I.L.); (G.-S.L.); (K.-H.K.)
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Li Z, Hu Y, Ma X, Da L, She J, Liu Y, Yi X, Cao Y, Xu W, Jiao Y, Su Z. WheatCENet: A Database for Comparative Co-expression Networks Analysis of Allohexaploid Wheat and Its Progenitors. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:324-336. [PMID: 35660007 PMCID: PMC10626052 DOI: 10.1016/j.gpb.2022.04.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 03/16/2022] [Accepted: 05/08/2022] [Indexed: 06/15/2023]
Abstract
Genetic and epigenetic changes after polyploidization events could result in variable gene expression and modified regulatory networks. Here, using large-scale transcriptome data, we constructed co-expression networks for diploid, tetraploid, and hexaploid wheat species, and built a platform for comparing co-expression networks of allohexaploid wheat and its progenitors, named WheatCENet. WheatCENet is a platform for searching and comparing specific functional co-expression networks, as well as identifying the related functions of the genes clustered therein. Functional annotations like pathways, gene families, protein-protein interactions, microRNAs (miRNAs), and several lines of epigenome data are integrated into this platform, and Gene Ontology (GO) annotation, gene set enrichment analysis (GSEA), motif identification, and other useful tools are also included. Using WheatCENet, we found that the network of WHEAT ABERRANT PANICLE ORGANIZATION 1 (WAPO1) has more co-expressed genes related to spike development in hexaploid wheat than its progenitors. We also found a novel motif of CCWWWWWWGG (CArG) specifically in the promoter region of WAPO-A1, suggesting that neofunctionalization of the WAPO-A1 gene affects spikelet development in hexaploid wheat. WheatCENet is useful for investigating co-expression networks and conducting other analyses, and thus facilitates comparative and functional genomic studies in wheat. WheatCENet is freely available at http://bioinformatics.cpolar.cn/WheatCENet and http://bioinformatics.cau.edu.cn/WheatCENet.
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Affiliation(s)
- Zhongqiu Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yiheng Hu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuelian Ma
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Lingling Da
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Jiajie She
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yue Liu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xin Yi
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yaxin Cao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Wenying Xu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yuannian Jiao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Zhen Su
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
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Sloan JM, Mujab AAM, Mashitah J, Zulkarami B, Wilson MJ, Toh LS, Nur Zahirah AJ, Afiq K, Asyraf AT, Zhu XG, Yaapar N, Fleming AJ. Elevated CO 2 Priming as a Sustainable Approach to Increasing Rice Tiller Number and Yield Potential. RICE (NEW YORK, N.Y.) 2023; 16:16. [PMID: 36947269 PMCID: PMC10033790 DOI: 10.1186/s12284-023-00629-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 03/05/2023] [Indexed: 06/18/2023]
Abstract
Tillering and yield are linked in rice, with significant efforts being invested to understand the genetic basis of this phenomenon. However, in addition to genetic factors, tillering is also influenced by the environment. Exploiting experiments in which seedlings were first grown in elevated CO2 (eCO2) before transfer and further growth under ambient CO2 (aCO2) levels, we found that even moderate exposure times to eCO2 were sufficient to induce tillering in seedlings, which was maintained in plants grown to maturity plants in controlled environment chambers. We then explored whether brief exposure to eCO2 (eCO2 priming) could be implemented to regulate tiller number and yield in the field. We designed a cost-effective growth system, using yeast to increase the CO2 level for the first 24 days of growth, and grew these seedlings to maturity in semi-field conditions in Malaysia. The increased growth caused by eCO2 priming translated into larger mature plants with increased tillering, panicle number, and improved grain filling and 1000 grain weight. In order to make the process more appealing to conventional rice farmers, we then developed a system in which fungal mycelium was used to generate the eCO2 via respiration of sugars derived by growing the fungus on lignocellulosic waste. Not only does this provide a sustainable source of CO2, it also has the added financial benefit to farmers of generating economically valuable oyster mushrooms as an end-product of mycelium growth. Our experiments show that the system is capable of generating sufficient CO2 to induce increased tillering in rice seedlings, leading eventually to 18% more tillers and panicles in mature paddy-grown crop. We discuss the potential of eCO2 priming as a rapidly implementable, broadly applicable and sustainable system to increase tillering, and thus yield potential in rice.
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Affiliation(s)
- Jennifer M Sloan
- School of Biosciences, Plants, Photosynthesis and Soil, The University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Azzami Adam Muhamad Mujab
- Commercialization and Business Centre, Malaysian Agricultural Research and Development Institute, MARDI Parit, 32800, Parit, Perak, Malaysia
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, UPM, 43400, Serdang, Selangor, Malaysia
| | - Jusoh Mashitah
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, UPM, 43400, Serdang, Selangor, Malaysia
| | - Berahim Zulkarami
- Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, UPM, 43400, Serdang, Selangor, Malaysia
| | - Matthew J Wilson
- School of Biosciences, Plants, Photosynthesis and Soil, The University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Liang Su Toh
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, UPM, 43400, Serdang, Selangor, Malaysia
| | - A Jalil Nur Zahirah
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, UPM, 43400, Serdang, Selangor, Malaysia
| | - Kamaruzali Afiq
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, UPM, 43400, Serdang, Selangor, Malaysia
| | - Ahmad Tajuddin Asyraf
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, UPM, 43400, Serdang, Selangor, Malaysia
| | - Xin-Guang Zhu
- Center of Excellence for Molecular Plant Science, Institute of Plant Physiology and Ecology, CAS, Shanghai, 200032, China
| | - Nazmin Yaapar
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, UPM, 43400, Serdang, Selangor, Malaysia.
| | - Andrew J Fleming
- School of Biosciences, Plants, Photosynthesis and Soil, The University of Sheffield, Western Bank, Sheffield, S10 2TN, UK.
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9
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Fang D, Zhang W, Ye Z, Hu F, Cheng X, Cao J. The plant specific SHORT INTERNODES/STYLISH (SHI/STY) proteins: Structure and functions. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 194:685-695. [PMID: 36565613 DOI: 10.1016/j.plaphy.2022.12.018] [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: 05/24/2022] [Revised: 12/02/2022] [Accepted: 12/18/2022] [Indexed: 06/17/2023]
Abstract
Plant specific SHORT INTERNODES/STYLISH (SHI/STY) protein is a transcription factor involved in the formation and development of early lateral organs in plants. However, research on the SHI/STY protein family is not focused enough. In this article, we review recent studies on SHI/STY genes and explore the evolution and structure of SHI/STY. The biological functions of SHI/STYs are discussed in detail in this review, and the application of each biological function to modern agriculture is discussed. All SHI/STY proteins contain typical conserved RING-like zinc finger domain and IGGH domain. SHI/STYs are involved in the formation and development of lateral root, stem extension, leaf morphogenesis, and root nodule development. They are also involved in the regulation of pistil and stamen development and flowering time. At the same time, the regulation of some GA, JA, and auxin signals also involves these family proteins. For each aspect, unanswered or poorly understood questions were identified to help define future research areas. This review will provide a basis for further functional study of this gene family.
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Affiliation(s)
- Da Fang
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Weimeng Zhang
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Ziyi Ye
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Fei Hu
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Xiuzhu Cheng
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Jun Cao
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China.
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10
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Zhao X, Liu DK, Wang QQ, Ke S, Li Y, Zhang D, Zheng Q, Zhang C, Liu ZJ, Lan S. Genome-wide identification and expression analysis of the GRAS gene family in Dendrobium chrysotoxum. FRONTIERS IN PLANT SCIENCE 2022; 13:1058287. [PMID: 36518517 PMCID: PMC9742484 DOI: 10.3389/fpls.2022.1058287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/11/2022] [Indexed: 06/17/2023]
Abstract
The GRAS gene family encodes transcription factors that participate in plant growth and development phases. They are crucial in regulating light signal transduction, plant hormone (e.g. gibberellin) signaling, meristem growth, root radial development, response to abiotic stress, etc. However, little is known about the features and functions of GRAS genes in Orchidaceae, the largest and most diverse angiosperm lineage. In this study, genome-wide analysis of the GRAS gene family was conducted in Dendrobium chrysotoxum (Epidendroideae, Orchidaceae) to investigate its physicochemical properties, phylogenetic relationships, gene structure, and expression patterns under abiotic stress in orchids. Forty-six DchGRAS genes were identified from the D. chrysotoxum genome and divided into ten subfamilies according to their phylogenetic relationships. Sequence analysis showed that most DchGRAS proteins contained conserved VHIID and SAW domains. Gene structure analysis showed that intronless genes accounted for approximately 70% of the DchGRAS genes, the gene structures of the same subfamily were the same, and the conserved motifs were also similar. The Ka/Ks ratios of 12 pairs of DchGRAS genes were all less than 1, indicating that DchGRAS genes underwent negative selection. The results of cis-acting element analysis showed that the 46 DchGRAS genes contained a large number of hormone-regulated and light-responsive elements as well as environmental stress-related elements. In addition, the real-time reverse transcription quantitative PCR (RT-qPCR) experimental results showed significant differences in the expression levels of 12 genes under high temperature, drought and salt treatment, among which two members of the LISCL subfamily (DchGRAS13 and DchGRAS15) were most sensitive to stress. Taken together, this paper provides insights into the regulatory roles of the GRAS gene family in orchids.
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Affiliation(s)
- Xuewei Zhao
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ding-Kun Liu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qian-Qian Wang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shijie Ke
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuanyuan Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Diyang Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qinyao Zheng
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Cuili Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhong-Jian Liu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Siren Lan
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
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11
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Lu Y, Chuan M, Wang H, Chen R, Tao T, Zhou Y, Xu Y, Li P, Yao Y, Xu C, Yang Z. Genetic and molecular factors in determining grain number per panicle of rice. FRONTIERS IN PLANT SCIENCE 2022; 13:964246. [PMID: 35991390 PMCID: PMC9386260 DOI: 10.3389/fpls.2022.964246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 07/15/2022] [Indexed: 06/15/2023]
Abstract
It was suggested that the most effective way to improve rice grain yield is to increase the grain number per panicle (GN) through the breeding practice in recent decades. GN is a representative quantitative trait affected by multiple genetic and environmental factors. Understanding the mechanisms controlling GN has become an important research field in rice biotechnology and breeding. The regulation of rice GN is coordinately controlled by panicle architecture and branch differentiation, and many GN-associated genes showed pleiotropic effect in regulating tillering, grain size, flowering time, and other domestication-related traits. It is also revealed that GN determination is closely related to vascular development and the metabolism of some phytohormones. In this review, we summarize the recent findings in rice GN determination and discuss the genetic and molecular mechanisms of GN regulators.
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Affiliation(s)
- Yue Lu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Mingli Chuan
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Hanyao Wang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Rujia Chen
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Tianyun Tao
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Yong Zhou
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
| | - Yang Xu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Pengcheng Li
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Youli Yao
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Chenwu Xu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
| | - Zefeng Yang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
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12
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Identification of quantitative trait loci for tillering, root, and shoot biomass at the maximum tillering stage in rice. Sci Rep 2022; 12:13304. [PMID: 35922462 PMCID: PMC9349274 DOI: 10.1038/s41598-022-17109-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 07/20/2022] [Indexed: 11/14/2022] Open
Abstract
Tillering and plant biomass are key determinants of rice crop productivity. Tillering at the vegetative stage is associated with weed competition, nutrient uptake, and methane emissions. However, little information is available on quantitative trait loci (QTLs) associated with tiller number (qTN), root biomass (qRB), and shoot biomass (qSB) at the active tillering stage which occurs approximately 6 weeks after planting. Here, we mapped tiller and biomass QTLs with ~ 250 recombinant inbred lines derived from a ‘Francis’ by ‘Rondo’ cross using data collected at the maximum tillering stage from two years of greenhouse study, and further compared these QTLs with those mapped at the harvest stage from a field study. Across these three studies, we discovered six qTNs, two qRBs, and three qSBs. Multiple linear regression further indicated that qTN1-2, qTN3-3, qTN4-1, qRB3-1, and qRB5-1 were significant at the maximum tillering stage while qTN3-2 was detected only at the harvest stage. Moreover, qTN3-1 was consistently significant across different developmental stages and growing environments. The genes identified from the peak target qTN regions included a carotenoid metabolism enzyme, a MYB transcription factor, a CBS domain-containing protein, a SAC3/GANP family protein, a TIFY motif containing protein, and an ABC transporter protein. Two genes in the qRB peak target regions included an expressed protein and a WRKY gene. This knowledge of the QTLs, associated markers, candidate genes, and germplasm resources with high TN, RB and SB is of value to rice cultivar improvement programs.
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13
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Li D, Zhang F, Pinson SRM, Edwards JD, Jackson AK, Xia X, Eizenga GC. Assessment of Rice Sheath Blight Resistance Including Associations with Plant Architecture, as Revealed by Genome-Wide Association Studies. RICE (NEW YORK, N.Y.) 2022; 15:31. [PMID: 35716230 PMCID: PMC9206596 DOI: 10.1186/s12284-022-00574-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 05/13/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Sheath blight (ShB) disease caused by Rhizoctonia solani Kühn, is one of the most economically damaging rice (Oryza sativa L.) diseases worldwide. There are no known major resistance genes, leaving only partial resistance from small-effect QTL to deploy for cultivar improvement. Many ShB-QTL are associated with plant architectural traits detrimental to yield, including tall plants, late maturity, or open canopy from few or procumbent tillers, which confound detection of physiological resistance. RESULTS To identify QTL for ShB resistance, 417 accessions from the Rice Diversity Panel 1 (RDP1), developed for association mapping studies, were evaluated for ShB resistance, plant height and days to heading in inoculated field plots in Arkansas, USA (AR) and Nanning, China (NC). Inoculated greenhouse-grown plants were used to evaluate ShB using a seedling-stage method to eliminate effects from height or maturity, and tiller (TN) and panicle number (PN) per plant. Potted plants were used to evaluate the RDP1 for TN and PN. Genome-wide association (GWA) mapping with over 3.4 million SNPs identified 21 targeted SNP markers associated with ShB which tagged 18 ShB-QTL not associated with undesirable plant architecture traits. Ten SNPs were associated with ShB among accessions of the Indica subspecies, ten among Japonica subspecies accessions, and one among all RDP1 accessions. Across the 18 ShB QTL, only qShB4-1 was not previously reported in biparental mapping studies and qShB9 was not reported in the GWA ShB studies. All 14 PN QTL overlapped with TN QTL, with 15 total TN QTL identified. Allele effects at the five TN QTL co-located with ShB QTL indicated that increased TN does not inevitably increase disease development; in fact, for four ShB QTL that overlapped TN QTL, the alleles increasing resistance were associated with increased TN and PN, suggesting a desirable coupling of alleles at linked genes. CONCLUSIONS Nineteen accessions identified as containing the most SNP alleles associated with ShB resistance for each subpopulation were resistant in both AR and NC field trials. Rice breeders can utilize these accessions and SNPs to develop cultivars with enhanced ShB resistance along with increased TN and PN for improved yield potential.
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Affiliation(s)
- Danting Li
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Fantao Zhang
- College of Life Sciences, Jiangxi Normal University, Nanchang, Jiangxi, China
| | - Shannon R M Pinson
- USDA Dale Bumpers National Rice Research Center, 2890 Highway 130 East, Stuttgart, AR, 72160, USA.
| | - Jeremy D Edwards
- USDA Dale Bumpers National Rice Research Center, 2890 Highway 130 East, Stuttgart, AR, 72160, USA
| | - Aaron K Jackson
- USDA Dale Bumpers National Rice Research Center, 2890 Highway 130 East, Stuttgart, AR, 72160, USA
| | - Xiuzhong Xia
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Georgia C Eizenga
- USDA Dale Bumpers National Rice Research Center, 2890 Highway 130 East, Stuttgart, AR, 72160, USA.
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14
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Waseem M, Nkurikiyimfura O, Niyitanga S, Jakada BH, Shaheen I, Aslam MM. GRAS transcription factors emerging regulator in plants growth, development, and multiple stresses. Mol Biol Rep 2022; 49:9673-9685. [PMID: 35713799 DOI: 10.1007/s11033-022-07425-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 02/23/2022] [Accepted: 03/24/2022] [Indexed: 10/18/2022]
Abstract
GRAS transcription factors play multifunctional roles in plant growth, development, and resistance to various biotic and abiotic stresses. The structural and functional features of GRAS TFs have been unveiled in the last two decades. A typical GRAS protein contained a C-terminal GRAS domain with a highly variable N-terminal region. Studies on these TFs increase in numbers and are reported to be involved in various important developmental processes such as flowering, root formation, and stress responses. The GRAS TFs and hormone signaling crosstalk can be implicated in plant development and to stress responses. There are relatively few reports about GRAS TFs roles in plants, and no related reviews have been published. In this review, we summarized the features of GRAS TFs, their targets, and the roles these GRAS TFs playing in plant development and multiple stresses.
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Affiliation(s)
- Muhammad Waseem
- Department of Botany, University of Narowal, Narowal, Punjab, Pakistan. .,College of Life Science, Hainan University, Hainan, P.R. China.
| | - Oswald Nkurikiyimfura
- Key Lab for Bio-Pesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, 350002, Fuzhou, Fujian, China
| | - Sylvain Niyitanga
- Department of Plant Pathology, Fujian Agriculture and Forestry University, 350002, Fuzhou, China
| | - Bello Hassan Jakada
- College of Life Science, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, 350002, Fuzhou, Fujian, China
| | - Iffat Shaheen
- Faculty of Agriculture Science and Technology, Bahauddin Zakariya University, Multan, Pakistan
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15
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Identification of C-T novel polymorphism in 3rd exon of OsSPL14 gene governing seed sequence in rice. PLoS One 2022; 17:e0264478. [PMID: 35286332 PMCID: PMC8920263 DOI: 10.1371/journal.pone.0264478] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 02/10/2022] [Indexed: 12/13/2022] Open
Abstract
Recently food shortage has become the major flagging scenario around the globe. To resolve this challenge, there is dire need to significantly increase crop productivity per unit area. In the present study, 24 genotypes of rice were grown in pots to assess their tillering number, number of primary and secondary branches per panicle, number of grains per panicle, number of grains per plant, and grain yield, respectively. In addition, the potential function of miR156 was analyzed, regulating seed sequence in rice. Furthermore, OsSPL14 gene for miR156 was sequenced to identify additional mutations within studied region. The results demonstrated Bas-370 and L-77 showed highest and lowest tillers, respectively. Bas-370, Rachna basmati, Bas-2000, and Kashmir Basmati showed high panicle branches whereas, L-77, L-46, Dilrosh, L-48, and L-20 displayed lowest panicle branches. Bas-370 and four other studied accessions contained C allele whereas, L-77 and 18 other investigated accessions had heterozygous (C and T) alleles in their promoter region. C-T allelic mutation was found in 3rd exon of the OsSPL14 gene. The sequence analysis of 12 accessions revealed a novel mutation (C-T) present ~2bp upstream and substitution of C-A allele. However, no significant correlation for novel mutation was found for tillering and panicle branches in studied rice accessions. Taken together present results suggested novel insight into the binding of miR156 to detected mutation found in 3rd exon of the OsSPL14 gene. Nevertheless, L-77, L-46, Dilrosh, L-48, and L-20 could be used as potential breeding resource for improving panicle architecture contributing yield improvement of rice crop.
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16
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Khan Y, Xiong Z, Zhang H, Liu S, Yaseen T, Hui T. Expression and roles of GRAS gene family in plant growth, signal transduction, biotic and abiotic stress resistance and symbiosis formation-a review. PLANT BIOLOGY (STUTTGART, GERMANY) 2022; 24:404-416. [PMID: 34854195 DOI: 10.1111/plb.13364] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 10/15/2021] [Indexed: 06/13/2023]
Abstract
The GRAS (derived from GAI, RGA and SCR) gene family consists of plant-specific genes, works as a transcriptional regulator and plays a key part in the regulation of plant growth and development. The past decade has witnessed significant progress in understanding and advances on GRAS transcription factors in various plants. A notable concern is to what extent the mechanisms found in plants, particularly crops, are shared by other species, and what other characteristics are dependent on GRAS transcription factor (TFS)-mediated gene expression. GRAS are involved in many processes that are intimately linked to plant growth regulation. However, GRAS also perform additional roles against environmental stresses, allowing plants to function more efficiently. GRAS increase plant growth and development by improving several physiological processes, such as phytohormone, biosynthetic and signalling pathways. Furthermore, the GRAS gene family plays an important role in response to abiotic stresses, e.g. photooxidative stress. Moreover, evidence shows the involvement of GRAS in arbuscule development during plant-mycorrhiza associations. In this review, the diverse roles of GRAS in plant systems are highlighted that could be useful in enhancing crop productivity through genetic modification, especially of crops. This is the first review to report the role and function of the GRAS gene family in plant systems. Furthermore, a large number of studies are reviewed, and several limitations and research gaps identified that must be addressed in future studies.
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Affiliation(s)
- Y Khan
- Key Laboratory of Plant Nutrition and Agri-environment in Northwest China, Ministry of Agriculture, College of Natural Resource and Environment, Northwest A&F University, Yangling, Shaanxi, China
| | - Z Xiong
- Key Laboratory of Plant Nutrition and Agri-environment in Northwest China, Ministry of Agriculture, College of Natural Resource and Environment, Northwest A&F University, Yangling, Shaanxi, China
| | - H Zhang
- Key Laboratory of Plant Nutrition and Agri-environment in Northwest China, Ministry of Agriculture, College of Natural Resource and Environment, Northwest A&F University, Yangling, Shaanxi, China
| | - S Liu
- Key Laboratory of Plant Nutrition and Agri-environment in Northwest China, Ministry of Agriculture, College of Natural Resource and Environment, Northwest A&F University, Yangling, Shaanxi, China
| | - T Yaseen
- Department of Botany, Bacha Khan University, Charsadda, Khyber Pakhtunkhwa, Pakistan
| | - T Hui
- Key Laboratory of Plant Nutrition and Agri-environment in Northwest China, Ministry of Agriculture, College of Natural Resource and Environment, Northwest A&F University, Yangling, Shaanxi, China
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17
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Bai Y, Zhao X, Yao X, Yao Y, An L, Li X, Wang Y, Gao X, Jia Y, Guan L, Li M, Wu K, Wang Z. Genome wide association study of plant height and tiller number in hulless barley. PLoS One 2021; 16:e0260723. [PMID: 34855842 PMCID: PMC8639095 DOI: 10.1371/journal.pone.0260723] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 11/15/2021] [Indexed: 11/18/2022] Open
Abstract
Hulless barley (Hordeum vulgare L. var. nudum), also called naked barley, is a unique variety of cultivated barley. The genome-wide specific length amplified fragment sequencing (SLAF-seq) method is a rapid deep sequencing technology that is used for the selection and identification of genetic loci or markers. In this study, we collected 300 hulless barley accessions and used the SLAF-seq method to identify candidate genes involved in plant height (PH) and tiller number (TN). We obtained a total of 1407 M paired-end reads, and 228,227 SLAF tags were developed. After filtering using an integrity threshold of >0.8 and a minor allele frequency of >0.05, 14,504,892 single-nucleotide polymorphisms (SNP) loci were screened out. The remaining SNPs were used for the construction of a neighbour-joining phylogenetic tree, and the three subcluster members showed no obvious differentiation among regional varieties. We used a genome wide association study approach to identify 1006 and 113 SNPs associated with TN and PH, respectively. Based on best linear unbiased predictors (BLUP), 41 and 29 SNPs associated with TN and PH, respectively. Thus, several of genes, including Hd3a and CKX5, may be useful candidates for the future genetic breeding of hulless barley. Taken together, our results provide insight into the molecular mechanisms controlling barley architecture, which is important for breeding and yield.
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Affiliation(s)
- Yixiong Bai
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
- Qinghai University, Qinghai Academy of Agricultural and Forestry Sciences, Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, Qinghai Province, China
| | - Xiaohong Zhao
- Qinghai University, Qinghai Academy of Agricultural and Forestry Sciences, Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, Qinghai Province, China
- Good Agricultural Practices Research Center of Traditional, Chongqing Institute of Medicinal Plant Cultivation, Chongqing, China
| | - Xiaohua Yao
- Qinghai University, Qinghai Academy of Agricultural and Forestry Sciences, Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, Qinghai Province, China
| | - Youhua Yao
- Qinghai University, Qinghai Academy of Agricultural and Forestry Sciences, Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, Qinghai Province, China
| | - Likun An
- Qinghai University, Qinghai Academy of Agricultural and Forestry Sciences, Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, Qinghai Province, China
| | - Xin Li
- Qinghai University, Qinghai Academy of Agricultural and Forestry Sciences, Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, Qinghai Province, China
| | - Yong Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Xin Gao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Yatao Jia
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Lulu Guan
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Man Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Kunlun Wu
- Qinghai University, Qinghai Academy of Agricultural and Forestry Sciences, Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, Qinghai Province, China
- * E-mail: (KW); (ZW)
| | - Zhonghua Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
- * E-mail: (KW); (ZW)
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18
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Guo M, Long Y, Xu L, Zhang W, Liu T, Zhang C, Hou X, Li Y. CELL CYCLE SEITCH 52 regulates tillering by interacting with LATERAL SUPPRESSOR in non-heading Chinese cabbage. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 309:110934. [PMID: 34134841 DOI: 10.1016/j.plantsci.2021.110934] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 04/28/2021] [Accepted: 05/01/2021] [Indexed: 06/12/2023]
Abstract
With the discovery of essential genes regulating tillering, such as MONOCULM 1 (MOC1) in rice and LATERAL SUPPRESSOR (LAS in Arabidopsis, LS in tomato), research on tillering mechanisms has made great progress; however, the study of tillering in non-heading Chinese cabbage (NHCC) is rare. Here, we report that BcLAS, as a member of the GRAS family, plays an important role in the tillering of NHCC during its vegetative growth. BcLAS was almost not expressed in other examed parts except leaf axils throughout life. When the expression of BcLAS was silenced utilizing virus-induced gene silencing (VIGS) technology, we found that the tiller number of 'Maertou' decreased sharply. In 'Suzhouqing', overexpression of BcLAS significantly promoted tillering. BcCCS52, the orthologue to CELL CYCLE SEITCH 52 (CCS52), interacts with BcLAS. Downregulation of the expression of BcCCS52 promoted tillering of 'Suzhouqing'; therefore, we conclude that BcCCS52 plays a negative role in tillering regulation. Our findings reveal the tillering regulation mechanism of NHCCs at the vegetative stage and report an orthologue of CCS52 regulating tillering in NHCC.
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Affiliation(s)
- Mingliang Guo
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of the P.R. China, China; Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education of the P.R. China, Nanjing, 210095, China
| | - Yan Long
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of the P.R. China, China; Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education of the P.R. China, Nanjing, 210095, China
| | - Lanlan Xu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of the P.R. China, China; Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education of the P.R. China, Nanjing, 210095, China
| | - Wei Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of the P.R. China, China; Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education of the P.R. China, Nanjing, 210095, China
| | - Tongkun Liu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of the P.R. China, China; Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education of the P.R. China, Nanjing, 210095, China
| | - Changwei Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of the P.R. China, China; Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education of the P.R. China, Nanjing, 210095, China
| | - Xilin Hou
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of the P.R. China, China; Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education of the P.R. China, Nanjing, 210095, China
| | - Ying Li
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of the P.R. China, China; Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education of the P.R. China, Nanjing, 210095, China.
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19
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Genome-Wide Identification of GRAS Gene Family and Their Responses to Abiotic Stress in Medicago sativa. Int J Mol Sci 2021; 22:ijms22147729. [PMID: 34299352 PMCID: PMC8304046 DOI: 10.3390/ijms22147729] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/15/2021] [Accepted: 07/16/2021] [Indexed: 02/02/2023] Open
Abstract
Alfalfa (Medicago sativa) is a high-quality legume forage crop worldwide, and alfalfa production is often threatened by abiotic environmental stresses. GRAS proteins are important transcription factors that play a vital role in plant development, as well as in response to environmental stress. In this study, the availability of alfalfa genome "Zhongmu No.1" allowed us to identify 51 GRAS family members, i.e., MsGRAS. MsGRAS proteins could be classified into nine subgroups with distinct conserved domains, and tandem and segmental duplications were observed as an expansion strategy of this gene family. In RNA-Seq analysis, 14 MsGRAS genes were not expressed in the leaf or root, 6 GRAS genes in 3 differentially expressed gene clusters were involved in the salinity stress response in the leaf. Moreover, qRT-PCR results confirmed that MsGRAS51 expression was induced under drought stress and hormone treatments (ABA, GA and IAA) but down-regulated in salinity stress. Collectively, our genome-wide characterization, evolutionary, and expression analysis suggested that the MsGRAS proteins might play crucial roles in response to abiotic stresses and hormonal cues in alfalfa. For the breeding of alfalfa, it provided important information on stress resistance and functional studies on MsGRAS and hormone signaling.
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20
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Yan Y, Wei M, Li Y, Tao H, Wu H, Chen Z, Li C, Xu JH. MiR529a controls plant height, tiller number, panicle architecture and grain size by regulating SPL target genes in rice (Oryza sativa L.). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 302:110728. [PMID: 33288029 DOI: 10.1016/j.plantsci.2020.110728] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 10/18/2020] [Accepted: 10/21/2020] [Indexed: 05/02/2023]
Abstract
Rice is one of the most important food crops in the world. Breeding high-yield, multi-resistant and high-quality varieties has always been the goal of rice breeding. Rice tiller, panicle architecture and grain size are the constituent factors of yield, which are regulated by both genetic and environmental factors, including miRNAs, transcription factors, and downstream target genes. Previous studies have shown that SPL (SQUAMOSA PROMOTER BINDING-LIKE) transcription factors can control rice tiller, panicle architecture and grain size, which were regulated by miR156, miR529 and miR535. In this study, we obtained miR529a target mimicry (miR529a-MIMIC) transgenic plants to investigate plant phenotypes, physiological and molecular characteristics together with miR529a overexpression (miR529a-OE) and wild type (WT) to explore the function of miR529a and its SPL target genes in rice. We found that OsSPL2, OsSPL17 and OsSPL18 at seedling stage were regulated by miR529a, but there had complicated mechanism to control plant height. OsSPL2, OsSPL16, OsSPL17 and SPL18 at tillering stage were regulated by miR529a to control plant height and tiller number. And panicle architecture and grain size were controlled by miR529a through altering the expression of all five target genes OsSPL2, OsSPL7, OsSPL14, OsSPL16, OsSPL17 and OsSPL18. Our study suggested that miR529a might control rice growth and development by regulating different SPL target genes at different stages, which could provide a new method to improve rice yield by regulating miR529a and its SPL target genes.
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Affiliation(s)
- Yan Yan
- Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058, China
| | - Mingxiao Wei
- Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058, China
| | - Yu Li
- Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058, China
| | - Hua Tao
- Henan Agricultural Radio and Television School, Zhengzhou, 450008, China
| | - Haoyu Wu
- Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058, China
| | - Zhufeng Chen
- Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058, China
| | - Can Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030, China.
| | - Jian-Hong Xu
- Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058, China.
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21
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Zhou H, Yang W, Ma S, Luan X, Zhu H, Wang A, Huang C, Rong B, Dong S, Meng L, Wang S, Zhang G, Liu G. Unconditional and conditional analysis of epistasis between tillering QTLs based on single segment substitution lines in rice. Sci Rep 2020; 10:15912. [PMID: 32985566 PMCID: PMC7523009 DOI: 10.1038/s41598-020-73047-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 09/07/2020] [Indexed: 11/08/2022] Open
Abstract
Epistasis plays an important role in manipulating rice tiller number, but epistatic mechanism still remains a challenge. Here we showed the process of epistatic analysis between tillering QTLs. A half diallel mating scheme was conducted based on 6 single segment substitution lines and 9 dual segment pyramiding lines to allow the analysis of 4 epistatic components. Additive-additive, additive-dominance, dominance-additive, and dominance-dominance epistatic effects were estimated at 9 stages of development via unconditional QTL analysis simultaneously. Unconditional QTL effect (QTL cumulative effect before a certain stage) was then divided into several conditional QTL components (QTL net effect in a certain time interval). The results indicated that epistatic interaction was prevalent, all QTL pairs harboring epistasis and one QTL always interacting with other QTLs in various component ways. Epistatic effects were dynamic, occurring mostly within 14d and 21-35d after transplant and exhibited mainly negative effects. The genetic and developmental mechanism on several tillering QTLs was further realized and perhaps was useful for molecular pyramiding breeding and heterosis utilization for improving plant architecture.
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Affiliation(s)
- Huaqian Zhou
- Guangdong Key Lab of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Weifeng Yang
- Guangdong Key Lab of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Shuaipeng Ma
- Guangdong Key Lab of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, People's Republic of China
- Guangzhou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Guangzhou, 510642, People's Republic of China
| | - Xin Luan
- Guangdong Key Lab of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Haitao Zhu
- Guangdong Key Lab of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Aimin Wang
- Zhuhai Modern Agriculture Development Center, Zhuhai, 519000, People's Republic of China
| | - Congling Huang
- Zhuhai Modern Agriculture Development Center, Zhuhai, 519000, People's Republic of China
| | - Biao Rong
- Zhuhai Modern Agriculture Development Center, Zhuhai, 519000, People's Republic of China
| | - Shangzhi Dong
- Zhuhai Modern Agriculture Development Center, Zhuhai, 519000, People's Republic of China
| | - Lijun Meng
- Agricultural Genomics Institute in Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 440307, People's Republic of China.
| | - Shaokui Wang
- Guangdong Key Lab of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, People's Republic of China.
| | - Guiquan Zhang
- Guangdong Key Lab of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, People's Republic of China.
| | - Guifu Liu
- Guangdong Key Lab of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, People's Republic of China.
- Zhuhai Modern Agriculture Development Center, Zhuhai, 519000, People's Republic of China.
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22
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Park SI, Kim JJ, Shin SY, Kim YS, Yoon HS. ASR Enhances Environmental Stress Tolerance and Improves Grain Yield by Modulating Stomatal Closure in Rice. FRONTIERS IN PLANT SCIENCE 2020; 10:1752. [PMID: 32117337 PMCID: PMC7033646 DOI: 10.3389/fpls.2019.01752] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 12/13/2019] [Indexed: 05/24/2023]
Abstract
Abscisic acid-, stress-, and ripening-induced (ASR) genes are involved in responding to abiotic stresses, but their precise roles in enhancing grain yield under stress conditions remain to be determined. We cloned a rice (Oryza sativa) ASR gene, OsASR1, and characterized its function in rice plants. OsASR1 expression was induced by abscisic acid (ABA), salt, and drought treatments. Transgenic rice plants overexpressing OsASR1 displayed improved water regulation under salt and drought stresses, which was associated with osmolyte accumulation, improved modulation of stomatal closure, and reduced transpiration rates. OsASR1-overexpressing plants were hypersensitive to exogenous ABA and accumulated higher endogenous ABA levels under salt and drought stresses, indicating that OsASR1 is a positive regulator of the ABA signaling pathway. The growth of OsASR1-overexpressing plants was superior to that of wild-type (WT) plants under paddy field conditions when irrigation was withheld, likely due to improved modulation of stomatal closure via modified ABA signaling. The transgenic plants had higher grain yields than WT plants for four consecutive generations. We conclude that OsASR1 has a crucial role in ABA-mediated regulation of stomatal closure to conserve water under salt- and drought-stress conditions, and OsASR1 overexpression can enhance salinity and drought tolerance, resulting in improved crop yields.
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Affiliation(s)
- Seong-Im Park
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, South Korea
- School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu, South Korea
| | - Jin-Ju Kim
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, South Korea
- School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu, South Korea
| | - Sun-Young Shin
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, South Korea
| | - Young-Saeng Kim
- Research Institute for Dok-do and Ulleung-do, Kyungpook National University, Daegu, South Korea
| | - Ho-Sung Yoon
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, South Korea
- School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu, South Korea
- Advanced Bio-Resource Research Center, Kyungpook National University, Daegu, South Korea
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23
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Nutan KK, Rathore RS, Tripathi AK, Mishra M, Pareek A, Singla-Pareek SL. Integrating the dynamics of yield traits in rice in response to environmental changes. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:490-506. [PMID: 31410470 DOI: 10.1093/jxb/erz364] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 07/29/2019] [Indexed: 05/23/2023]
Abstract
Reductions in crop yields as a consequence of global climate change threaten worldwide food security. It is therefore imperative to develop high-yielding crop plants that show sustainable production under stress conditions. In order to achieve this aim through breeding or genetic engineering, it is crucial to have a complete and comprehensive understanding of the molecular basis of plant architecture and the regulation of its sub-components that contribute to yield under stress. Rice is one of the most widely consumed crops and is adversely affected by abiotic stresses such as drought and salinity. Using it as a model system, in this review we present a summary of our current knowledge of the physiological and molecular mechanisms that determine yield traits in rice under optimal growth conditions and under conditions of environmental stress. Based on physiological functioning, we also consider the best possible combination of genes that may improve grain yield under optimal as well as environmentally stressed conditions. The principles that we present here for rice will also be useful for similar studies in other grain crops.
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Affiliation(s)
- Kamlesh Kant Nutan
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - Ray Singh Rathore
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - Amit Kumar Tripathi
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - Manjari Mishra
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Sneh Lata Singla-Pareek
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
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24
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Hua W, Tan C, Xie J, Zhu J, Shang Y, Yang J, Zhang XQ, Wu X, Wang J, Li C. Alternative splicing of a barley gene results in an excess-tillering and semi-dwarf mutant. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:163-177. [PMID: 31690990 DOI: 10.1007/s00122-019-03448-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 09/24/2019] [Indexed: 06/10/2023]
Abstract
An excess-tillering semi-dwarf gene Hvhtd was identified from an EMS-induced mutant in barley and alternative splicing results in excess-tillering semi-dwarf traits. Tillering and plant height are important traits determining plant architecture and grain production in cereal crops. This study identified an excess-tillering semi-dwarf mutant (htd) from an EMS-treated barley population. Genetic analysis of the F1, F2, and F2:3 populations showed that a single recessive gene controlled the excess-tillering semi-dwarf in htd. Using BSR-Seq and gene mapping, the Hvhtd gene was delimited within a 1.8 Mb interval on chromosome 2HL. Alignment of the RNA-Seq data with the functional genes in the interval identified a gene HORVU2Hr1G098820 with alternative splicing between exon2 and exon3 in the mutant, due to a G to A single-nucleotide substitution at the exon and intron junction. An independent mutant with a similar phenotype confirmed the result, with alternative splicing between exon3 and exon4. In both cases, the alternative splicing resulted in a non-functional protein. And the gene HORVU2Hr1G098820 encodes a trypsin family protein and may be involved in the IAA signaling pathway and differs from the mechanism of Green Revolution genes in the gibberellic acid metabolic pathway.
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Affiliation(s)
- Wei Hua
- Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
- Western Barley Genetics Alliance, Murdoch University, Murdoch, WA, 6150, Australia
| | - Cong Tan
- Western Barley Genetics Alliance, Murdoch University, Murdoch, WA, 6150, Australia
| | - Jingzhong Xie
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jinghuan Zhu
- Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Yi Shang
- Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Jianming Yang
- Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Xiao-Qi Zhang
- Western Barley Genetics Alliance, Murdoch University, Murdoch, WA, 6150, Australia
| | - Xiaojian Wu
- Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Junmei Wang
- Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
| | - Chengdao Li
- Western Barley Genetics Alliance, Murdoch University, Murdoch, WA, 6150, Australia.
- Department of Primary Industry and Regional Development, 3 Baron-Hay Court, South Perth, WA, 6151, Australia.
- Hubei Collaborative Innovation Centre for Grain Industry, Yangtze University, Jingzhou, 434025, Hubei, China.
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25
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Tanaka W, Hirano HY. Antagonistic action of TILLERS ABSENT1 and FLORAL ORGAN NUMBER2 regulates stem cell maintenance during axillary meristem development in rice. THE NEW PHYTOLOGIST 2020; 225:974-984. [PMID: 31486529 DOI: 10.1111/nph.16163] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 08/26/2019] [Indexed: 06/10/2023]
Abstract
Shoot branches are formed from the axillary meristem and their formation is a key process in plant development. Although our understanding of the mechanisms underlying stem cell maintenance in the shoot apical meristem (SAM) is progressing, our knowledge of these mechanisms during the process of axillary meristem development is insufficient. To elucidate the genetic mechanisms underlying axillary meristem development in rice (Oryza sativa), we undertook a molecular genetic analysis focusing on TILLERS ABSENT1 (TAB1) and FLORAL ORGAN NUMBER2 (FON2), respective orthologs of the WUSCHEL and CLAVATA3 genes involved in SAM maintenance in Arabidopsis (Arabidopsis thaliana). We revealed that stem cells were established at an early stage of axillary meristem development in the wild-type, but were not maintained in tab1. By contrast, the stem cell region and TAB1 expression domain were expanded in fon2, and FON2 overexpression inhibited axillary meristem formation. These results indicate that TAB1 is required to maintain stem cells during axillary meristem development, whereas FON2 negatively regulates stem cell fate by restricting TAB1 expression. Thus, the genetic pathway regulating SAM maintenance in Arabidopsis seems to have been recruited to play a specific role within a narrow developmental window - namely, axillary meristem establishment - in rice.
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Affiliation(s)
- Wakana Tanaka
- Department of Biological Sciences, School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8654, Japan
| | - Hiro-Yuki Hirano
- Department of Biological Sciences, School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8654, Japan
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26
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Zhang X, Zhou J, Huang N, Mo L, Lv M, Gao Y, Chen C, Yin S, Ju J, Dong G, Zhou Y, Yang Z, Li A, Wang Y, Huang J, Yao Y. Transcriptomic and Co-Expression Network Profiling of Shoot Apical Meristem Reveal Contrasting Response to Nitrogen Rate between Indica and Japonica Rice Subspecies. Int J Mol Sci 2019; 20:E5922. [PMID: 31775351 PMCID: PMC6928681 DOI: 10.3390/ijms20235922] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 11/22/2019] [Accepted: 11/23/2019] [Indexed: 12/17/2022] Open
Abstract
Reducing nitrogen (N) input is a key measure to achieve a sustainable rice production in China, especially in Jiangsu Province. Tiller is the basis for achieving panicle number that plays as a major factor in the yield determination. In actual production, excessive N is often applied in order to produce enough tillers in the early stages. Understanding how N regulates tillering in rice plants is critical to generate an integrative management to reduce N use and reaching tiller number target. Aiming at this objective, we utilized RNA sequencing and weighted gene co-expression network analysis (WGCNA) to compare the transcriptomes surrounding the shoot apical meristem of indica (Yangdao6, YD6) and japonica (Nipponbare, NPB) rice subspecies. Our results showed that N rate influenced tiller number in a different pattern between the two varieties, with NPB being more sensitive to N enrichment, and YD6 being more tolerant to high N rate. Tiller number was positively related to N content in leaf, culm and root tissue, but negatively related to the soluble carbohydrate content, regardless of variety. Transcriptomic comparisons revealed that for YD6 when N rate enrichment from low (LN) to medium (MN), it caused 115 DEGs (LN vs. MN), from MN to high level (HN) triggered 162 DEGs (MN vs. HN), but direct comparison of low with high N rate showed a 511 DEGs (LN vs. HN). These numbers of DEG in NPB were 87 (LN vs. MN), 40 (MN vs. HN), and 148 (LN vs. HN). These differences indicate that continual N enrichment led to a bumpy change at the transcription level. For the reported sixty-five genes which affect tillering, thirty-six showed decent expression in SAM at tiller starting phase, among them only nineteen being significantly influenced by N level, and two genes showed significant interaction between N rate and variety. Gene ontology analysis revealed that the majority of the common DEGs are involved in general stress responses, stimulus responses, and hormonal signaling process. WGCNA network identified twenty-two co-expressing gene modules and ten candidate hubgenes for each module. Several genes associated with tillering and N rate fall on the related modules. These indicate that there are more genes participating in tillering regulation in response to N enrichment.
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Affiliation(s)
- Xiaoxiang Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China; (X.Z.); (J.Z.); (L.M.); (M.L.); (Y.G.); (S.Y.); (G.D.); (Y.Z.); (Z.Y.); (Y.W.)
- Lixiahe Agricultural Research Institute of Jiangsu Province, Yangzhou 225007, China; (N.H.); (A.L.)
| | - Juan Zhou
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China; (X.Z.); (J.Z.); (L.M.); (M.L.); (Y.G.); (S.Y.); (G.D.); (Y.Z.); (Z.Y.); (Y.W.)
| | - Niansheng Huang
- Lixiahe Agricultural Research Institute of Jiangsu Province, Yangzhou 225007, China; (N.H.); (A.L.)
| | - Lanjing Mo
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China; (X.Z.); (J.Z.); (L.M.); (M.L.); (Y.G.); (S.Y.); (G.D.); (Y.Z.); (Z.Y.); (Y.W.)
| | - Minjia Lv
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China; (X.Z.); (J.Z.); (L.M.); (M.L.); (Y.G.); (S.Y.); (G.D.); (Y.Z.); (Z.Y.); (Y.W.)
| | - Yingbo Gao
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China; (X.Z.); (J.Z.); (L.M.); (M.L.); (Y.G.); (S.Y.); (G.D.); (Y.Z.); (Z.Y.); (Y.W.)
| | - Chen Chen
- Zhenjiang Agricultural Research Institute of Jiangsu Province, Jurong 212400, China;
| | - Shuangyi Yin
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China; (X.Z.); (J.Z.); (L.M.); (M.L.); (Y.G.); (S.Y.); (G.D.); (Y.Z.); (Z.Y.); (Y.W.)
| | - Jing Ju
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou 225000, China;
| | - Guichun Dong
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China; (X.Z.); (J.Z.); (L.M.); (M.L.); (Y.G.); (S.Y.); (G.D.); (Y.Z.); (Z.Y.); (Y.W.)
| | - Yong Zhou
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China; (X.Z.); (J.Z.); (L.M.); (M.L.); (Y.G.); (S.Y.); (G.D.); (Y.Z.); (Z.Y.); (Y.W.)
| | - Zefeng Yang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China; (X.Z.); (J.Z.); (L.M.); (M.L.); (Y.G.); (S.Y.); (G.D.); (Y.Z.); (Z.Y.); (Y.W.)
| | - Aihong Li
- Lixiahe Agricultural Research Institute of Jiangsu Province, Yangzhou 225007, China; (N.H.); (A.L.)
| | - Yulong Wang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China; (X.Z.); (J.Z.); (L.M.); (M.L.); (Y.G.); (S.Y.); (G.D.); (Y.Z.); (Z.Y.); (Y.W.)
| | - Jianye Huang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China; (X.Z.); (J.Z.); (L.M.); (M.L.); (Y.G.); (S.Y.); (G.D.); (Y.Z.); (Z.Y.); (Y.W.)
| | - Youli Yao
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China; (X.Z.); (J.Z.); (L.M.); (M.L.); (Y.G.); (S.Y.); (G.D.); (Y.Z.); (Z.Y.); (Y.W.)
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Mutation of ONAC096 Enhances Grain Yield by Increasing Panicle Number and Delaying Leaf Senescence during Grain Filling in Rice. Int J Mol Sci 2019; 20:ijms20205241. [PMID: 31652646 PMCID: PMC6829889 DOI: 10.3390/ijms20205241] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 10/21/2019] [Accepted: 10/21/2019] [Indexed: 01/20/2023] Open
Abstract
Exploring genetic methods to improve yield in grain crops such as rice (Oryza sativa) is essential to help meet the needs of the increasing population. Here, we report that rice ONAC096 affects grain yield by regulating leaf senescence and panicle number. ONAC096 expression increased rapidly in rice leaves upon the initiation of aging- and dark-induced senescence. Two independent T-DNA insertion mutants (onac096-1 and onac096-2) with downregulated ONAC096 expression retained their green leaf color during natural senescence in the field, thus extending their photosynthetic capacity. Reverse-transcription quantitative PCR analysis showed that ONAC096 upregulated genes controlling chlorophyll degradation and leaf senescence. Repressed OsCKX2 (encoding cytokinin oxidase/dehydrogenase) expression in the onac096 mutants led to a 15% increase in panicle number without affecting grain weight or fertility. ONAC096 mediates abscisic acid (ABA)-induced leaf senescence by upregulating the ABA signaling genes ABA INSENSITIVE5 and ENHANCED EM LEVEL. The onac096 mutants showed a 16% increase in grain yield, highlighting the potential for using this gene to increase grain production.
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28
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Li J, Jiao Z, He R, Sun Y, Xu Q, Zhang J, Jiang Y, Li Q, Niu J. Gene Expression Profiles and microRNA Regulation Networks in Tiller Primordia, Stem Tips, and Young Spikes of Wheat Guomai 301. Genes (Basel) 2019; 10:genes10090686. [PMID: 31500166 PMCID: PMC6770858 DOI: 10.3390/genes10090686] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 08/07/2019] [Accepted: 08/22/2019] [Indexed: 01/26/2023] Open
Abstract
Tillering and spike differentiation are two key events for wheat (Triticum aestivum L.). A study on the transcriptomes and microRNA group profiles of wheat at the two key developmental stages will bring insight into the molecular regulation mechanisms. Guomai 301 is a representative excellent new high yield wheat cultivar in the Henan province in China. The transcriptomes and microRNA (miRNA) groups of tiller primordia (TPs), stem tips (STs), and young spikes (YSs) in Guomai 301 were compared to each other. A total of 1741 tillering specifically expressed and 281 early spikes differentiating specifically expressed differentially expressed genes (DEGs) were identified. Six major expression profile clusters of tissue-specific DEGs for the three tissues were classified by gene co-expression analysis using K-means cluster. The ribosome (ko03010), photosynthesis-antenna proteins (ko00196), and plant hormone signal transduction (ko04075) were the main metabolic pathways in TPs, STs, and YSs, respectively. Similarly, 67 TP specifically expressed and 19 YS specifically expressed differentially expressed miRNAs were identified, 65 of them were novel. The roles of 3 well known miRNAs, tae-miR156, tae-miR164, and tae-miR167a, in post-transcriptional regulation were similar to that of other researches. There were 651 significant negative miRNA-mRNA interaction pairs in TPs and YSs, involving 63 differentially expressed miRNAs (fold change > 4) and 416 differentially expressed mRNAs. Among them 12 key known miRNAs and 16 novel miRNAs were further analyzed, and miRNA-mRNA regulatory networks during tillering and early spike differentiating were established.
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Affiliation(s)
- Junchang Li
- National Centre of Engineering and Technological Research for Wheat / Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, China
| | - Zhixin Jiao
- National Centre of Engineering and Technological Research for Wheat / Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, China
| | - Ruishi He
- National Centre of Engineering and Technological Research for Wheat / Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, China
| | - Yulong Sun
- National Centre of Engineering and Technological Research for Wheat / Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, China
| | - Qiaoqiao Xu
- National Centre of Engineering and Technological Research for Wheat / Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, China
| | - Jing Zhang
- National Centre of Engineering and Technological Research for Wheat / Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, China
| | - Yumei Jiang
- National Centre of Engineering and Technological Research for Wheat / Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, China
| | - Qiaoyun Li
- National Centre of Engineering and Technological Research for Wheat / Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, China
| | - Jishan Niu
- National Centre of Engineering and Technological Research for Wheat / Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, China.
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Fujino K, Hirayama Y, Kaji R. Marker-assisted selection in rice breeding programs in Hokkaido. BREEDING SCIENCE 2019; 69:383-392. [PMID: 31598070 PMCID: PMC6776137 DOI: 10.1270/jsbbs.19062] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 06/06/2019] [Indexed: 05/27/2023]
Abstract
Rice breeding programs in Hokkaido over the past 100 years have dramatically increased productivity and improved the eating quality of rice. Commercial varieties with high yield and good eating quality, such as Kirara 397, Hoshinoyume, and Nanatsuboshi, have been continuously registered since 1990. Furthermore, varieties with better eating quality using Wx1-1, which reduces amylose content to improve the taste of sticky rice, such as Oborozuki and Yumepirika, were registered in 2006 and 2008, respectively. However, to the best of our knowledge the genomic changes associated with these improvements have not been determined. Better understanding of the relationships between DNA sequences and agricultural traits could facilitate rice breeding programs in Hokkaido. Marker-assisted selection (MAS), which can select the plants with chromosomal regions tagged with DNA markers for desirable traits, is an advanced technology to manage genetic improvements. Here, we summarize the current states of MAS in rice breeding programs in Hokkaido before huge data sets of genome sequences using next-generation sequencing technology come into practical use in rice breeding programs.
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Affiliation(s)
- Kenji Fujino
- Hokkaido Agricultural Research Center, National Agricultural Research Organization,
Sapporo, Hokkaido 062-8555,
Japan
| | - Yuji Hirayama
- Kamikawa Agricultural Experiment Station, Local Independent Administrative Agency Hokkaido Research Organization,
Pippu, Hokkaido 078-0397,
Japan
| | - Ryota Kaji
- Hokkaido Agricultural Research Center, National Agricultural Research Organization,
Sapporo, Hokkaido 062-8555,
Japan
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30
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Mahender A, Ali J, Prahalada GD, Sevilla MAL, Balachiranjeevi CH, Md J, Maqsood U, Li Z. Genetic dissection of developmental responses of agro-morphological traits under different doses of nutrient fertilizers using high-density SNP markers. PLoS One 2019; 14:e0220066. [PMID: 31335882 PMCID: PMC6650078 DOI: 10.1371/journal.pone.0220066] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Accepted: 07/07/2019] [Indexed: 11/19/2022] Open
Abstract
The production and productivity of rice (Oryza sativa L.) are primarily influenced by the application of the critical nutrients nitrogen (N), phosphorus (P), and potassium (K). However, excessive application of these fertilizers is detrimental to the environment and increases the cost of production. Hence, there is a need to develop varieties that simultaneously increase yields under both optimal and suboptimal rates of fertilizer application by maximizing nutrient use efficiency (NuUE). To unravel the hidden genetic variation and understand the molecular and physiological mechanisms of NuUE, three different mapping populations (MPs; BC1F5) derived from three donors (Haoannong, Cheng-Hui 448, and Zhong 413) and recipient Weed Tolerant Rice 1 were developed. A total of three favorable agronomic traits (FATs) were considered as the measure of NuUE. Analysis of variance and descriptive statistics indicated the existence of genetic variation for NuUE and quantitative inheritance of FATs. The genotypic data from single-nucleotide polymorphism (SNP) markers from Tunable Genotyping-By-Sequencing (tGBS) and phenotypic values were used for locating the genomic regions conferring NuUE. A total of 19 quantitative trait loci (QTLs) were detected, out of which 11 QTLs were putative on eight chromosomes, which individually explained 17.02% to 34.85% of the phenotypic variation. Notably, qLC-II_1 and qLC-II_11 detected at zero fertilizer application showed higher performance for LC under zero percentage of NPK fertilizer. The remarkable findings of the present study are that the detected QTLs were associated in building tolerance to low/no nutrient application and six candidate genes on chromosomes 2 and 5 within these putative QTLs were found associated with low nutrient tolerance and related to several physiological and metabolic pathways involved in abiotic stress tolerance. The identified superior introgressed lines (ILs) and trait-associated genetic regions can be effectively used in marker-assisted selection (MAS) for NuUE breeding programs.
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Affiliation(s)
- Anumalla Mahender
- Rice Breeding Platform, International Rice Research Institute, Los Baños, Manila, Philippines
| | - Jauhar Ali
- Rice Breeding Platform, International Rice Research Institute, Los Baños, Manila, Philippines
- * E-mail:
| | - G. D. Prahalada
- Strategic Innovation Platform, International Rice Research Institute, Los Baños, Manila, Philippines
| | - Ma. Anna Lynn Sevilla
- Rice Breeding Platform, International Rice Research Institute, Los Baños, Manila, Philippines
| | - C. H. Balachiranjeevi
- Rice Breeding Platform, International Rice Research Institute, Los Baños, Manila, Philippines
| | - Jamaloddin Md
- Rice Breeding Platform, International Rice Research Institute, Los Baños, Manila, Philippines
| | - Umer Maqsood
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Pakistan
| | - Zhikang Li
- Chinese Academy of Agricultural Sciences, Haidian District, P.R. China
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31
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Genomic Bayesian Confirmatory Factor Analysis and Bayesian Network To Characterize a Wide Spectrum of Rice Phenotypes. G3-GENES GENOMES GENETICS 2019; 9:1975-1986. [PMID: 30992319 PMCID: PMC6553530 DOI: 10.1534/g3.119.400154] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
With the advent of high-throughput phenotyping platforms, plant breeders have a means to assess many traits for large breeding populations. However, understanding the genetic interdependencies among high-dimensional traits in a statistically robust manner remains a major challenge. Since multiple phenotypes likely share mutual relationships, elucidating the interdependencies among economically important traits can better inform breeding decisions and accelerate the genetic improvement of plants. The objective of this study was to leverage confirmatory factor analysis and graphical modeling to elucidate the genetic interdependencies among a diverse agronomic traits in rice. We used a Bayesian network to depict conditional dependencies among phenotypes, which can not be obtained by standard multi-trait analysis. We utilized Bayesian confirmatory factor analysis which hypothesized that 48 observed phenotypes resulted from six latent variables including grain morphology, morphology, flowering time, physiology, yield, and morphological salt response. This was followed by studying the genetics of each latent variable, which is also known as factor, using single nucleotide polymorphisms. Bayesian network structures involving the genomic component of six latent variables were established by fitting four algorithms (i.e., Hill Climbing, Tabu, Max-Min Hill Climbing, and General 2-Phase Restricted Maximization algorithms). Physiological components influenced the flowering time and grain morphology, and morphology and grain morphology influenced yield. In summary, we show the Bayesian network coupled with factor analysis can provide an effective approach to understand the interdependence patterns among phenotypes and to predict the potential influence of external interventions or selection related to target traits in the interrelated complex traits systems.
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32
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Huang W, Nie H, Feng F, Wang J, Lu K, Fang Z. Altered expression of OsNPF7.1 and OsNPF7.4 differentially regulates tillering and grain yield in rice. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 283:23-31. [PMID: 31128693 DOI: 10.1016/j.plantsci.2019.01.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 01/11/2019] [Accepted: 01/16/2019] [Indexed: 05/24/2023]
Abstract
The rice nitrate and di/tripeptide transporter (NPF) gene family plays an indispensable role in nitrogen transport and plant growth. In this study, 18 alternatively spliced OsNPF genes with 36 different forms of mRNAs were identified, and two of these, namely OsNPF7.1 and OsNPF7.4, showed opposite expression patterns in axillary buds under different nitrogen concentrations. Our results indicate that the expression levels of OsNPF7.1 and OsNPF7.4 determine the axillary bud outgrowth, especially for the second bud, and subsequently influence the tiller number in rice. The overexpression of either of the variants of OsNPF7.1 or the knockout of OsNPF7.4 increased the seedling biomass as well as the tiller number, filled grain number, and grain yield in rice. However, the RNAi-mediated silencing of OsNPF7.1 or the overexpression of either of the variants of OsNPF7.4 had an opposite effect. The overexpression of OsNPF7.1 or OsNPF7.4 could improve the uptake of nitrate, but the OsNPF7.4-overexpressing plants had lower biomass. It is possible that excessive nitrate in the OsNPF7.4-overexpressing plants led to the accumulation of amino acids in the leaf sheath, which inhibited seedling biomass. In addition, the reduced reutilization of nitrate in the seedlings also limited the plant biomass. However, the moderate increase in nitrate and amino acid concentrations in the OsNPF7.1-overexpressing plants could promote seedling biomass and enhance grain yield. In conclusion, our data suggest that different members in the NPF family have different roles in rice, and this study suggests an alternative way to modify rice architecture and enhance grain yield by regulating the expression of OsNPF7.1 and OsNPF7.4.
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Affiliation(s)
- Weiting Huang
- Hubei Engineering Research Center of Viral Vector, Wuhan University of Bioengineering, Wuhan 430415, China
| | - Haipeng Nie
- Hubei Engineering Research Center of Viral Vector, Wuhan University of Bioengineering, Wuhan 430415, China; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Fei Feng
- Hubei Engineering Research Center of Viral Vector, Wuhan University of Bioengineering, Wuhan 430415, China; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jie Wang
- Hubei Engineering Research Center of Viral Vector, Wuhan University of Bioengineering, Wuhan 430415, China
| | - Kai Lu
- Hubei Engineering Research Center of Viral Vector, Wuhan University of Bioengineering, Wuhan 430415, China
| | - Zhongming Fang
- Hubei Engineering Research Center of Viral Vector, Wuhan University of Bioengineering, Wuhan 430415, China; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
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33
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Ustyantsev KV, Goncharov NP. Homology of Genes Controlling Architectonics of Vegetative and Generative Organs in Barley and Rice and Their Application for Wheat Biodiversity Expansion and Breeding. RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419050156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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34
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Fujino K, Obara M, Ikegaya T. Establishment of adaptability to the northern-limit of rice production. Mol Genet Genomics 2019; 294:729-737. [PMID: 30874890 DOI: 10.1007/s00438-019-01542-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 02/23/2019] [Indexed: 10/27/2022]
Abstract
The domestication of cultivated crops from their wild relatives narrowed down their genetic diversity in a bottleneck effect. Subsequently, the cultivation areas of crops have expanded all over the world into various environmental conditions from the original area along with human migration after domestication. Here, we demonstrated the genetic changes in the adaptation of rice to Hokkaido (41°2-45°3N latitude), Japan, from the tropics of their origin in Asian cultivated rice, Oryza sativa L. Although cultivated rice originated from the tropics, Hokkaido is one of the northern-limits of rice cultivation worldwide. Population genomics focusing on the local populations showed the varieties had genetically distinct classes with limited genetic diversity. In addition, some varieties in the class carried unique genotypes for flowering time, exhibiting extremely early flowering time. Certain mutations in unique genotypes can split off the varieties that are able to grow in Hokkaido. Furthermore, the changes in the genotype for flowering time during rice cultivation in Hokkaido demonstrated novel combinations of genes for flowering time owing to the intensive artificial selection on natural variation and rice breeding programs to achieve stable rice production in Hokkaido.
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Affiliation(s)
- Kenji Fujino
- Hokkaido Agricultural Research Center, National Agricultural Research Organization, Sapporo, 062-8555, Japan.
| | - Mari Obara
- Hokkaido Agricultural Research Center, National Agricultural Research Organization, Sapporo, 062-8555, Japan
| | - Tomohito Ikegaya
- Hokkaido Agricultural Research Center, National Agricultural Research Organization, Sapporo, 062-8555, Japan
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35
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Barbier FF, Dun EA, Kerr SC, Chabikwa TG, Beveridge CA. An Update on the Signals Controlling Shoot Branching. TRENDS IN PLANT SCIENCE 2019; 24:220-236. [PMID: 30797425 DOI: 10.1016/j.tplants.2018.12.001] [Citation(s) in RCA: 154] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 12/11/2018] [Accepted: 12/20/2018] [Indexed: 05/21/2023]
Abstract
Many new questions on the regulation of shoot branching have been raised in recent years, prompting a review and reassessment of the role of each signal involved. Sugars and their signaling networks have been attributed a major role in the early events of axillary bud outgrowth, whereas cytokinin appears to play a critical role in the modulation of this process in response to the environment. Perception of the recently discovered hormone strigolactone is now quite well understood, while the downstream targets remain largely unknown. Recent literature has highlighted that auxin export from a bud is important for its subsequent growth.
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Affiliation(s)
- Francois F Barbier
- The University of Queensland, School of Biological Sciences, St. Lucia, QLD 4072, Australia
| | - Elizabeth A Dun
- The University of Queensland, School of Biological Sciences, St. Lucia, QLD 4072, Australia; These authors contributed equally to this publication
| | - Stephanie C Kerr
- The University of Queensland, School of Biological Sciences, St. Lucia, QLD 4072, Australia; These authors contributed equally to this publication
| | - Tinashe G Chabikwa
- The University of Queensland, School of Biological Sciences, St. Lucia, QLD 4072, Australia
| | - Christine A Beveridge
- The University of Queensland, School of Biological Sciences, St. Lucia, QLD 4072, Australia.
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36
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Wu D, Guo Z, Ye J, Feng H, Liu J, Chen G, Zheng J, Yan D, Yang X, Xiong X, Liu Q, Niu Z, Gay AP, Doonan JH, Xiong L, Yang W. Combining high-throughput micro-CT-RGB phenotyping and genome-wide association study to dissect the genetic architecture of tiller growth in rice. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:545-561. [PMID: 30380099 PMCID: PMC6322582 DOI: 10.1093/jxb/ery373] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 07/24/2018] [Indexed: 05/20/2023]
Abstract
Manual phenotyping of rice tillers is time consuming and labor intensive, and lags behind the rapid development of rice functional genomics. Thus, automated, non-destructive methods of phenotyping rice tiller traits at a high spatial resolution and high throughput for large-scale assessment of rice accessions are urgently needed. In this study, we developed a high-throughput micro-CT-RGB imaging system to non-destructively extract 739 traits from 234 rice accessions at nine time points. We could explain 30% of the grain yield variance from two tiller traits assessed in the early growth stages. A total of 402 significantly associated loci were identified by genome-wide association study, and dynamic and static genetic components were found across the nine time points. A major locus associated with tiller angle was detected at time point 9, which contained a major gene, TAC1. Significant variants associated with tiller angle were enriched in the 3'-untranslated region of TAC1. Three haplotypes for the gene were found, and rice accessions containing haplotype H3 displayed much smaller tiller angles. Further, we found two loci containing associations with both vigor-related traits identified by high-throughput micro-CT-RGB imaging and yield. The superior alleles would be beneficial for breeding for high yield and dense planting.
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Affiliation(s)
- Di Wu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, and College of Engineering, Huazhong Agricultural University, Wuhan, China
| | - Zilong Guo
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, and College of Engineering, Huazhong Agricultural University, Wuhan, China
| | - Junli Ye
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, and College of Engineering, Huazhong Agricultural University, Wuhan, China
| | - Hui Feng
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, and College of Engineering, Huazhong Agricultural University, Wuhan, China
| | - Jianxiao Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, and College of Engineering, Huazhong Agricultural University, Wuhan, China
| | - Guoxing Chen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, and College of Engineering, Huazhong Agricultural University, Wuhan, China
| | - Jingshan Zheng
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, and College of Engineering, Huazhong Agricultural University, Wuhan, China
| | - Dongmei Yan
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, and Key Laboratory of Ministry of Education for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoquan Yang
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, and Key Laboratory of Ministry of Education for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan, China
| | - Xiong Xiong
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, and Key Laboratory of Ministry of Education for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan, China
| | - Qian Liu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, and Key Laboratory of Ministry of Education for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan, China
| | - Zhiyou Niu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, and College of Engineering, Huazhong Agricultural University, Wuhan, China
| | - Alan P Gay
- The National Plant Phenomics Centre, Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - John H Doonan
- The National Plant Phenomics Centre, Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Lizhong Xiong
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, and College of Engineering, Huazhong Agricultural University, Wuhan, China
| | - Wanneng Yang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, and College of Engineering, Huazhong Agricultural University, Wuhan, China
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37
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Identification and Characterization of a Novel Strigolactone-Insensitive Mutant, Dwarfism with High Tillering Ability 34 (dhta-34) in Rice (Oryza sativa L.). Biochem Genet 2019; 57:403-420. [PMID: 30600409 DOI: 10.1007/s10528-018-9896-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 12/04/2018] [Indexed: 10/27/2022]
Abstract
Rice tillering ability and plant height are two of the important traits determining the grain yield. A novel rice (Oryza sativa L.) mutant dhta-34 from an Indica cultivar Zhenong 34 treated by ethyl methy1 sulfonate (EMS) was investigated in this study. The dhta-34 mutant significantly revealed thrifty tillers with reduced plant height, smaller panicles and lighter grains. It also exhibited late-maturing (19.80 days later than the wild type) and withered leaf tip during the mature stage. The length of each internode was reduced compared to the wild type, belonging to the dn type (each internode of the plant stem decreased in the same ratio). The longitudinal section of dhta-34 internodes showed that the length of cells was reduced leading to the dwarfism of the mutant. The F2 population derived from a cross between dhta-34 and an Japonica cultivar Zhenongda 104 were used for gene mapping by using the map-based cloning strategy. The gene DHTA-34 was fine mapped in 183.8kb region flanked by markers 3R-7 and 3R-10. The cloning and sequencing of the target region from the mutant revealed that there was a substitution of G to A in the second exon of LOC_Os03g10620, which resulted in an amino acid substitution arginine to histidine. DHTA-34 encoded a protein of the α/β-fold hydrolase superfamily, which could suppress the tillering ability of rice. DHTA-34 was a strong loss-of-function allele of the Arabidopsis thaliana D14 gene, which was involved in part of strigolactones (SLs) perception and signaling. Moreover, the relative expression of DHTA-34 gene in leaf was higher than that in bud, internode, root or sheath. This study revealed that DHTA-34 played an important role in inhabiting tiller development in rice and further identifying the function of D14.
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Peng D, Tan X, Zhang L, Yuan D, Lin J, Liu X, Jiang Y, Zhou B. Increasing branch and seed yield through heterologous expression of the novel rice S-acyl transferase gene OsPAT15 in Brassica napus L. BREEDING SCIENCE 2018; 68:326-335. [PMID: 30100799 PMCID: PMC6081303 DOI: 10.1270/jsbbs.17126] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 02/18/2018] [Indexed: 06/08/2023]
Abstract
Branching is a predominant element in the plant architecture of Brassica napus L. and represents an important determinant of seed yield. OsPAT15 (OsDHHC1), a novel DHHC-type zinc finger protein gene, was reported to regulate rice plant architecture by altering the tillering. However, whether heterologous overexpression of the OsPAT15 gene from the monocot rice into the dicot B. napus L. would have the same effect on branching or seed yield is unknown. In this study, the DHHC-type zinc finger protein gene OsPAT15 was determined to have sulfur acyl transferase activity in the akr1Δ yeast mutant in a complementation experiment. Heterologously expressing OsPAT15 transgenic B. napus L. plants were obtained using the Agrobacterium-mediated floral-dip transformation method. As anticipated, OsPAT15 transgenic plants exhibited branching and seed yield. Compared with non-transgenic plants, OsPAT15 transgenic plants had increased primary branches (1.58-1.76-fold) and siliques (1.86-1.89-fold), resulting in a significant increase in seed yield (around 2.39-2.51-fold). Therefore, overexpression of the sulfur acyl transferase gene OsPAT15 in B. napus L. could be used to increase seed yield and produce excellent varieties.
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Affiliation(s)
- Dan Peng
- Faculty of Life Science and Technology, Central South University of Forestry and Technology,
410004, Changsha,
China
- Forestry Biotechnology Hunan Key Laboratories,
410004, Changsha,
China
| | - Xiaofeng Tan
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology,
410004, Changsha,
China
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Tree, Central South University of Forestry and Technology,
410004, Changsha,
China
- Collaborative Innovation Central of Cultivation and Utilization for Non-Wood Forest Tree Central South University of Forestry and Technology,
410004, Changsha,
China
| | - Lin Zhang
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology,
410004, Changsha,
China
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Tree, Central South University of Forestry and Technology,
410004, Changsha,
China
- Collaborative Innovation Central of Cultivation and Utilization for Non-Wood Forest Tree Central South University of Forestry and Technology,
410004, Changsha,
China
| | - Deyi Yuan
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology,
410004, Changsha,
China
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Tree, Central South University of Forestry and Technology,
410004, Changsha,
China
- Collaborative Innovation Central of Cultivation and Utilization for Non-Wood Forest Tree Central South University of Forestry and Technology,
410004, Changsha,
China
| | - Jianzhong Lin
- Key Laboratory of Plant Function Genomic for Development and Regulation, Hunan University,
410082, Changsha,
China
| | - Xuanming Liu
- Key Laboratory of Plant Function Genomic for Development and Regulation, Hunan University,
410082, Changsha,
China
| | - Yueqiao Jiang
- Faculty of Life Science and Technology, Central South University of Forestry and Technology,
410004, Changsha,
China
| | - Bo Zhou
- Faculty of Life Science and Technology, Central South University of Forestry and Technology,
410004, Changsha,
China
- Key Laboratory of Plant Function Genomic for Development and Regulation, Hunan University,
410082, Changsha,
China
- Forestry Biotechnology Hunan Key Laboratories,
410004, Changsha,
China
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Liu B, Sun Y, Xue J, Jia X, Li R. Genome-wide characterization and expression analysis of GRAS gene family in pepper ( Capsicum annuum L.). PeerJ 2018; 6:e4796. [PMID: 29868257 PMCID: PMC5983004 DOI: 10.7717/peerj.4796] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 04/29/2018] [Indexed: 12/14/2022] Open
Abstract
Plant-specific GRAS transcription factors regulate various biological processes in plant growth, development and stress responses. However, this important gene family was not fully characterized in pepper (Capsicum annuum L.), an economically important vegetable crop. Here, a total of 50 CaGRAS members were identified in pepper genome and renamed by their respective chromosomal distribution. Genomic organization revealed that most CaGRAS genes (84%) have no intron. Phylogenetic analysis divided pepper CaGRAS members into 10 subfamilies, with each having distinct conserved domains and functions. For the expansion of the GRAS genes in pepper, segmental duplication contributed more than tandem duplication did. Gene expression analysis in various tissues demonstrated that most of CaGRAS genes exhibited a tissue- and development stage-specific expression pattern, uncovering their potential functions in pepper growth and development. Moreover, 21 CaGRAS genes were differentially expressed under cold, drought, salt and gibberellin acid (GA) treatments, indicating that they may implicated in plant response to abiotic stress. Notably, GA responsive cis-elements were detected in the promoter regions of the majority of CaGRAS genes, suggesting that CaGRAS may involve in signal cross-talking. The first comprehensive analysis of GRAS gene family in pepper genome by this study provide insights into understanding the GRAS-mediated regulation network, benefiting the genetic improvements in pepper and some other relative plants.
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Affiliation(s)
- Baoling Liu
- Institute of Molecular Agriculture and Bioenergy, Shanxi Agricultural University, Jinzhong City, China
| | - Yan Sun
- Institute of Molecular Agriculture and Bioenergy, Shanxi Agricultural University, Jinzhong City, China
| | - Jinai Xue
- Institute of Molecular Agriculture and Bioenergy, Shanxi Agricultural University, Jinzhong City, China
| | - Xiaoyun Jia
- Institute of Molecular Agriculture and Bioenergy, Shanxi Agricultural University, Jinzhong City, China
| | - Runzhi Li
- Institute of Molecular Agriculture and Bioenergy, Shanxi Agricultural University, Jinzhong City, China
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Wang J, Lu K, Nie H, Zeng Q, Wu B, Qian J, Fang Z. Rice nitrate transporter OsNPF7.2 positively regulates tiller number and grain yield. RICE (NEW YORK, N.Y.) 2018; 11:12. [PMID: 29484500 PMCID: PMC5826914 DOI: 10.1186/s12284-018-0205-6] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 02/21/2018] [Indexed: 05/18/2023]
Abstract
BACKGROUND Rice tiller number is one of the most important factors that determine grain yield, while nitrogen is essential for the crop growth and development, especially for tiller formation. Genes involved in nitrogen use efficiency processes have been identified in the previous studies, however, only a small number of these genes have been found to improve grain yield by promoting tillering. RESULTS We constructed over-expression (OX) lines and RNA-interference (Ri) lines, and selected a mutant of OsNPF7.2, a low-affinity nitrate transporter. Our analyses showed that rice tiller number and grain yield were significantly increased in OX lines, whereas Ri lines and mutant osnpf7.2 had fewer tiller number and lower grain yield. Under different nitrate concentrations, tiller buds grew faster in OX lines than in WT, but they grew slower in Ri lines and mutant osnpf7.2. These results indicated that altered expression of OsNPF7.2 plays a significant role in the control of tiller bud growth and regulation of tillering. Elevated expression of OsNPF7.2 also improved root length, root number, fresh weight, and dry weight. However, reduced expression of OsNPF7.2 had the opposite result on these characters. OsNPF7.2 OX lines showed more significantly enhanced influx of nitrate and had a higher nitrate concentration than WT. The levels of gene transcripts related to cytokinin pathway and cell cycle in tiller bud, and cytokinins concentration in tiller basal portion were higher in OX lines than that in WT, suggesting that altered expression of OsNPF7.2 controlled tiller bud growth and root development by regulating cytokinins content and cell cycle in plant cells. Altered expression of OsNPF7.2 also was responsible for the change in expression of the genes involved in strigolactone pathway, such as D27, D17, D10, Os900, Os1400, D14, D3, and OsFC1. CONCLUSION Our results suggested that OsNPF7.2 is a positive regulator of nitrate influx and concentration, and that it also regulates cell division in tiller bud and alters expression of genes involved in cytokinin and strigolactone pathways, resulting in the control over rice tiller number. Since elevated expression of OsNPF7.2 is capable of improving rice grain yield, this gene might be applied to high-yield rice breeding.
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Affiliation(s)
- Jie Wang
- Center of Applied Biotechnology, Wuhan Institute of Bioengineering, Wuhan, 430415, China
| | - Kai Lu
- Center of Applied Biotechnology, Wuhan Institute of Bioengineering, Wuhan, 430415, China
| | - Haipeng Nie
- Center of Applied Biotechnology, Wuhan Institute of Bioengineering, Wuhan, 430415, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qisen Zeng
- Center of Applied Biotechnology, Wuhan Institute of Bioengineering, Wuhan, 430415, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Bowen Wu
- Center of Applied Biotechnology, Wuhan Institute of Bioengineering, Wuhan, 430415, China
| | - Junjie Qian
- Center of Applied Biotechnology, Wuhan Institute of Bioengineering, Wuhan, 430415, China
| | - Zhongming Fang
- Center of Applied Biotechnology, Wuhan Institute of Bioengineering, Wuhan, 430415, China.
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
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Huang W, Bai G, Wang J, Zhu W, Zeng Q, Lu K, Sun S, Fang Z. Two Splicing Variants of OsNPF7.7 Regulate Shoot Branching and Nitrogen Utilization Efficiency in Rice. FRONTIERS IN PLANT SCIENCE 2018; 9:300. [PMID: 29568307 PMCID: PMC5852072 DOI: 10.3389/fpls.2018.00300] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Accepted: 02/21/2018] [Indexed: 05/20/2023]
Abstract
Rice includes 93 nitrate and peptide transporters family (NPF) members that facilitate the soil uptake and internal reallocation of nitrogen for growth and development. This study demonstrated that OsNPF7.7 had two splicing variants, and altered expression of each variant could regulate shoot branching and nitrogen utilization efficiency (NUtE) in rice. The expression of both variants was down-regulated in the buds by increased nitrogen level in the Japonica rice variety ZH11. The expression level of long-variant OsNPF7.7-1 was higher in panicles at reproductive stage, however, the expression level of short-variant OsNPF7.7-2 was higher in buds and leaves at vegetative stage compared to each other in ZH11. OsNPF7.7-1 was localized in the plasma membrane, whereas OsNPF7.7-2 was localized in the vacuole membrane. Furthermore, the results indicated that the expression level of each variant for OsNPF7.7 determined axillary bud outgrowth, and then influenced the rice tiller number. Overexpression of OsNPF7.7-1 could promote nitrate influx and concentration in root, whereas overexpression of OsNPF7.7-2 could improve ammonium influx and concentration in root. RNAi and osnpf7.7 lines of OsNPF7.7 showed an increased amount of amino acids in leaf sheaths, but a decreased amount in leaf blades, which affected nitrogen allocation and plant growth. The elevated expression of each variant for OsNPF7.7 in ZH11 enhanced NUtE using certain fertilization regimes under paddy field conditions. Moreover, overexpression of each variant for OsNPF7.7 in KY131 increased significantly the filled grain number per plant. Thus, increased each variant of OsNPF7.7 has the potential to improve grain yield and NUtE in rice.
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Affiliation(s)
- Weiting Huang
- Center of Applied Biotechnology, Wuhan Institute of Bioengineering, Wuhan, China
| | - Genxiang Bai
- Center of Applied Biotechnology, Wuhan Institute of Bioengineering, Wuhan, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Jie Wang
- Center of Applied Biotechnology, Wuhan Institute of Bioengineering, Wuhan, China
| | - Wei Zhu
- Center of Applied Biotechnology, Wuhan Institute of Bioengineering, Wuhan, China
| | - Qisen Zeng
- Center of Applied Biotechnology, Wuhan Institute of Bioengineering, Wuhan, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Kai Lu
- Center of Applied Biotechnology, Wuhan Institute of Bioengineering, Wuhan, China
| | - Shiyong Sun
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Zhongming Fang
- Center of Applied Biotechnology, Wuhan Institute of Bioengineering, Wuhan, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- *Correspondence: Zhongming Fang, ;
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Lantzouni O, Klermund C, Schwechheimer C. Largely additive effects of gibberellin and strigolactone on gene expression in Arabidopsis thaliana seedlings. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 92:924-938. [PMID: 28977719 DOI: 10.1111/tpj.13729] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 09/01/2017] [Accepted: 09/27/2017] [Indexed: 05/22/2023]
Abstract
The phytohormones gibberellin (GA) and strigolactone (SL) are involved in essential processes in plant development. Both GA and SL signal transduction mechanisms employ α/β-hydrolase-derived receptors that confer E3 ubiquitin ligase-mediated protein degradation processes. This suggests a common evolutionary origin of these pathways and possibly a molecular interaction between them. One such indication stems from rice, where the DELLA protein of the GA pathway was reported to interact with the SL receptor. Here, we examine the physiological interaction between both pathways through the analysis of GA (ga1) and SL biosynthesis (max1 and max3) mutants. In ga1 max double mutants, we find indications only for additive interactions when examining several phenotypic readouts. We further identify short-term transcriptional responses to GA and the synthetic SL rac-GR24 through next-generation sequencing of poly-adenylated RNAs (RNA-seq) in ga1 max1. Remarkably, both hormones lead to predominantly additive transcriptional changes of a largely overlapping set of genes. The expression of only a few genes was altered in a synergistic manner but, interestingly, these include the genes encoding the GA catabolic enzyme GA2 OXIDASE2 (GA2ox2) as well as the SL pathway regulators BRANCHED1 (BRC1) and SUPPRESSOR OF max2 1-LIKE8 (SMXL8). We conclude that GA and rac-GR24 signaling in Arabidopsis seedlings converge at the level of transcription of a common gene-set.
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Affiliation(s)
- Ourania Lantzouni
- Plant Systems Biology, Technische Universität München, Emil-Ramann-Straße 8, 85354, Freising, Germany
| | - Carina Klermund
- Plant Systems Biology, Technische Universität München, Emil-Ramann-Straße 8, 85354, Freising, Germany
| | - Claus Schwechheimer
- Plant Systems Biology, Technische Universität München, Emil-Ramann-Straße 8, 85354, Freising, Germany
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Yue E, Li C, Li Y, Liu Z, Xu JH. MiR529a modulates panicle architecture through regulating SQUAMOSA PROMOTER BINDING-LIKE genes in rice (Oryza sativa). PLANT MOLECULAR BIOLOGY 2017; 94:469-480. [PMID: 28551765 DOI: 10.1007/s11103-017-0618-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 05/09/2017] [Indexed: 05/21/2023]
Abstract
MiR529a affects rice panicle architecture by targeting OsSPL2,OsSPL14 and OsSPL17 genes that could regulate their downstream panicle related genes. The panicle architecture determines the grain yield and quality of rice, which could be regulated by many transcriptional factors. The SQUAMOSA PROMOTER BINDING-LIKE (SPL) transcription factors are involved in the regulation of panicle development, which are targeted by miR156 and miR529. The expression profile demonstrated that miR529a is preferentially expressed in the early panicle of rice and it might regulate panicle development in rice. However, the regulation mechanism of miR529-SPL is still not clear. In this study, we predicted five miR529a putative target genes, OsSPL2, OsSPL14, OsSPL16, OsSPL17 and OsSPL18, while only the expression of OsSPL2, OsSPL14, and OsSPL17 was regulated by miR529a in the rice panicle. Overexpression of miR529a dramatically affected panicle architecture, which was regulated by OsSPL2, OsSPL14, and OsSPL17. Furthermore, the 117, 35, and 25 pathway genes associated with OsSPL2, OsSPL14 and OsSPL17, respectively, were predicted, and they shared 20 putative pathway genes. Our results revealed that miR529a could play a vital role in the regulation of panicle architecture through regulating OsSPL2, OsSPL14, OsSPL17 and the complex networks formed by their pathway and downstream genes. These findings will provide new genetic resources for reshaping ideal plant architecture and breeding high yield rice varieties.
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Affiliation(s)
- Erkui Yue
- Zhejiang Key Laboratory of Crop Germplasm, Institute of Crop Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China
| | - Chao Li
- Zhejiang Key Laboratory of Crop Germplasm, Institute of Crop Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China
| | - Yu Li
- Zhejiang Key Laboratory of Crop Germplasm, Institute of Crop Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China
| | - Zhen Liu
- Zhejiang Key Laboratory of Crop Germplasm, Institute of Crop Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China
| | - Jian-Hong Xu
- Zhejiang Key Laboratory of Crop Germplasm, Institute of Crop Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China.
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Lu G, Casaretto JA, Ying S, Mahmood K, Liu F, Bi YM, Rothstein SJ. Overexpression of OsGATA12 regulates chlorophyll content, delays plant senescence and improves rice yield under high density planting. PLANT MOLECULAR BIOLOGY 2017; 94:215-227. [PMID: 28342018 DOI: 10.1007/s11103-017-0604-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 03/15/2017] [Indexed: 05/19/2023]
Abstract
Agronomic traits controlling the formation, architecture and physiology of source and sink organs are main determinants of rice productivity. Semi-dwarf rice varieties with low tiller formation but high seed production per panicle and dark green and thick leaves with prolonged source activity are among the desirable traits to further increase the yield potential of rice. Here, we report the functional characterization of a zinc finger transcription factor, OsGATA12, whose overexpression causes increased leaf greenness, reduction of leaf and tiller number, and affects yield parameters. Reduced tillering allowed testing the transgenic plants under high density which resulted in significantly increased yield per area and higher harvest index compared to wild-type. We show that delayed senescence of transgenic plants and the corresponding longer stay-green phenotype is mainly due to increased chlorophyll and chloroplast number. Further, our work postulates that the increased greenness observed in the transgenic plants is due to more chlorophyll synthesis but most significantly to decreased chlorophyll degradation, which is supported by the reduced expression of genes involved in the chlorophyll degradation pathway. In particular we show evidence for the down-regulation of the STAY GREEN RICE gene and in vivo repression of its promoter by OsGATA12, which suggests a transcriptional repression function for a GATA transcription factor for prolonging the onset of senescence in cereals.
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Affiliation(s)
- Guangwen Lu
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road E., Guelph, ON, N1G 2W1, Canada
| | - José A Casaretto
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road E., Guelph, ON, N1G 2W1, Canada.
| | - Shan Ying
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road E., Guelph, ON, N1G 2W1, Canada
| | - Kashif Mahmood
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road E., Guelph, ON, N1G 2W1, Canada
| | - Fang Liu
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road E., Guelph, ON, N1G 2W1, Canada
| | - Yong-Mei Bi
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road E., Guelph, ON, N1G 2W1, Canada
| | - Steven J Rothstein
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road E., Guelph, ON, N1G 2W1, Canada
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Zhou B, Lin JZ, Peng D, Yang YZ, Guo M, Tang DY, Tan X, Liu XM. Plant architecture and grain yield are regulated by the novel DHHC-type zinc finger protein genes in rice (Oryza sativa L.). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 254:12-21. [PMID: 27964781 DOI: 10.1016/j.plantsci.2016.08.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 08/08/2016] [Accepted: 08/29/2016] [Indexed: 06/06/2023]
Abstract
In many plants, architecture and grain yield are affected by both the environment and genetics. In rice, the tiller is a vital factor impacting plant architecture and regulated by many genes. In this study, we cloned a novel DHHC-type zinc finger protein gene Os02g0819100 and its alternative splice variant OsDHHC1 from the cDNA of rice (Oryza sativa L.), which regulate plant architecture by altering the tiller in rice. The tillers increased by about 40% when this type of DHHC-type zinc finger protein gene was over-expressed in Zhong Hua 11 (ZH11) rice plants. Moreover, the grain yield of transgenic rice increased approximately by 10% compared with wild-type ZH11. These findings provide an important genetic engineering approach for increasing rice yields.
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Affiliation(s)
- Bo Zhou
- College of Bioscience and Biotechnology of Central South University of Forestry and Technology, Changsha 410018, Hunan, China; Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, 410018 Changsha, China
| | - Jian Zhong Lin
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Changsha 410082, Hunan, China; College of Biology, Hunan University, Changsha 410082, Hunan, China; Bioenergy and Biomaterial Research Center, College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, Hunan, China
| | - Dan Peng
- College of Bioscience and Biotechnology of Central South University of Forestry and Technology, Changsha 410018, Hunan, China; Academy of Seed Industry of Hunan Yahua, Changsha 410013, Hunan, China; Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, 410018 Changsha, China
| | - Yuan Zhu Yang
- Academy of Seed Industry of Hunan Yahua, Changsha 410013, Hunan, China
| | - Ming Guo
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Changsha 410082, Hunan, China; College of Biology, Hunan University, Changsha 410082, Hunan, China; Bioenergy and Biomaterial Research Center, College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, Hunan, China
| | - Dong Ying Tang
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Changsha 410082, Hunan, China; College of Biology, Hunan University, Changsha 410082, Hunan, China; Bioenergy and Biomaterial Research Center, College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, Hunan, China
| | - Xiaofeng Tan
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, 410018 Changsha, China
| | - Xuan Ming Liu
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Changsha 410082, Hunan, China; College of Biology, Hunan University, Changsha 410082, Hunan, China; Bioenergy and Biomaterial Research Center, College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, Hunan, China.
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Lu H, Dai Z, Li L, Wang J, Miao X, Shi Z. OsRAMOSA2 Shapes Panicle Architecture through Regulating Pedicel Length. FRONTIERS IN PLANT SCIENCE 2017; 8:1538. [PMID: 28955349 PMCID: PMC5601049 DOI: 10.3389/fpls.2017.01538] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 08/22/2017] [Indexed: 05/05/2023]
Abstract
The panicle architecture of rice is an important characteristic that influences reproductive success and yield. It is largely determined by the number and length of the primary and secondary branches. The number of panicle branches is defined by the inflorescence meristem state between determinacy and indeterminacy; for example, the maize ramosa2 (ra2) mutant has more branches in its tassel through loss of spikelet determinacy. Some genes and factors influencing the number of primary and secondary branches have been studied, but little is known about the molecular mechanism underlying pedicel development, which also influences panicle architecture. We report here that rice OsRAMOSA2 (OsRA2) gene modifies panicle architecture through regulating pedicel length. Ectopic expression of OsRA2 resulted in a shortened pedicel while inhibition of OsRA2 through RNA interference produced elongated pedicel. In addition, OsRA2 influenced seed morphology. The OsRA2 protein localized to the nucleus and showed transcriptional activation in yeast; in accordance with its function in pedicel development, OsRA2 mRNA was enriched in the anlagen of axillary meristems, such as primary and secondary branch meristems and the spikelet meristems of young panicles. This indicates a conserved role of OsRA2 for shaping the initial steps of inflorescence architecture. Genetic analysis revealed that OsRA2 may control panicle architecture using the same pathway as that of the axillary meristem gene LAX1 (LAX PANICLE1). Moreover, OsRA2 acted downstream of RCN2 in regulating pedicel and branch lengths, but upstream of RCN2 for control of the number of secondary branches, indicating that branch number and length development in the panicle were respectively regulated using parallel pathway. Functional conservation between OsRA2 and AtLOB, and the conservation and diversification of RA2 in maize and rice are also discussed.
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Affiliation(s)
- Huan Lu
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of SciencesShanghai, China
- University of Chinese Academy of SciencesShanghai, China
| | - Zhengyan Dai
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of SciencesShanghai, China
| | - Ling Li
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of SciencesShanghai, China
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of SciencesShanghai, China
- Ministry of Agriculture Key Laboratory of Urban Agriculture (South), Plant Biotechnology Research Center, School of Agriculture and Biology, Shanghai Jiao Tong UniversityShanghai, China
| | - Jiang Wang
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of SciencesShanghai, China
| | - Xuexia Miao
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of SciencesShanghai, China
| | - Zhenying Shi
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of SciencesShanghai, China
- *Correspondence: Zhenying Shi,
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Wang H, Cheng H, Wang W, Liu J, Hao M, Mei D, Zhou R, Fu L, Hu Q. Identification of BnaYUCCA6 as a candidate gene for branch angle in Brassica napus by QTL-seq. Sci Rep 2016; 6:38493. [PMID: 27922076 PMCID: PMC5138835 DOI: 10.1038/srep38493] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 11/11/2016] [Indexed: 11/12/2022] Open
Abstract
Oilseed rape (Brassica napus L.) is one of the most important oil crops in China as well as worldwide. Branch angle as a plant architecture component trait plays an important role for high density planting and yield performance. In this study, bulked segregant analysis (BSA) combined with next generation sequencing technology was used to fine map QTL for branch angle. A major QTL, designated as branch angle 1 (ba1) was identified on A06 and further validated by Indel marker-based classical QTL mapping in an F2 population. Eighty-two genes were identified in the ba1 region. Among these genes, BnaA0639380D is a homolog of AtYUCCA6. Sequence comparison of BnaA0639380D from small- and big-branch angle oilseed rape lines identified six SNPs and four amino acid variation in the promoter and coding region, respectively. The expression level of BnaA0639380D is significantly higher in the small branch angle line Purler than in the big branch angle line Huyou19, suggesting that the genomic mutations may result in reduced activity of BnaA0639380D in Huyou19. Phytohormone determination showed that the IAA content in Purler was also obviously increased. Taken together, our results suggested BnaA0639380D is a possible candidate gene for branch angle in oilseed rape.
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Affiliation(s)
- Hui Wang
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong 2nd Road, Wuhan 430062, P.R. China
| | - Hongtao Cheng
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong 2nd Road, Wuhan 430062, P.R. China
| | - Wenxiang Wang
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong 2nd Road, Wuhan 430062, P.R. China
| | - Jia Liu
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong 2nd Road, Wuhan 430062, P.R. China
| | - Mengyu Hao
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong 2nd Road, Wuhan 430062, P.R. China
| | - Desheng Mei
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong 2nd Road, Wuhan 430062, P.R. China
| | - Rijin Zhou
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong 2nd Road, Wuhan 430062, P.R. China
| | - Li Fu
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong 2nd Road, Wuhan 430062, P.R. China
| | - Qiong Hu
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong 2nd Road, Wuhan 430062, P.R. China
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MicroRNA393 is involved in nitrogen-promoted rice tillering through regulation of auxin signal transduction in axillary buds. Sci Rep 2016; 6:32158. [PMID: 27574184 PMCID: PMC5004122 DOI: 10.1038/srep32158] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 08/03/2016] [Indexed: 02/08/2023] Open
Abstract
Rice tillering has an important influence on grain yield, and is promoted by nitrogen (N) fertilizer. Several genes controlling rice tillering, which are regulated by poor N supply, have been identified. However, the molecular mechanism associated with the regulation of tillering based on N supply is poorly understood. Here, we report that rice microRNA393 (OsmiR393) is involved in N-mediated tillering by decreasing auxin signal sensitivity in axillary buds. Expression analysis showed that N fertilizer causes up-regulation of OsmiR393, but down-regulation of two target genes (OsAFB2 and OsTB1). In situ expression analysis showed that OsmiR393 is highly expressed in the lateral axillary meristem. OsmiR393 overexpression mimicked N-mediated tillering in wild type Zhonghua 11 (ZH11). Mutation of OsMIR393 in ZH11 repressed N-promoted tillering, which simulated the effects of limited N, and this could not be restored by supplying N fertilizer. Western blot analysis showed that OsIAA6 was accumulated in both OsmiR393-overexpressing lines and N-treated wild type rice, but was reduced in the OsMIR393 mutant. Therefore, we deduced that N-induced OsmiR393 accumulation reduces the expression of OsTIR1 and OsAFB2, which alleviates sensitivity to auxin in the axillary buds and stabilizes OsIAA6, thereby promoting rice tillering.
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Rebolledo MC, Peña AL, Duitama J, Cruz DF, Dingkuhn M, Grenier C, Tohme J. Combining Image Analysis, Genome Wide Association Studies and Different Field Trials to Reveal Stable Genetic Regions Related to Panicle Architecture and the Number of Spikelets per Panicle in Rice. FRONTIERS IN PLANT SCIENCE 2016; 7:1384. [PMID: 27703460 PMCID: PMC5029283 DOI: 10.3389/fpls.2016.01384] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Accepted: 08/30/2016] [Indexed: 05/19/2023]
Abstract
Number of spikelets per panicle (NSP) is a key trait to increase yield potential in rice (O. sativa). The architecture of the rice inflorescence which is mainly determined by the length and number of primary (PBL and PBN) and secondary (SBL and SBN) branches can influence NSP. Although several genes controlling panicle architecture and NSP in rice have been identified, there is little evidence of (i) the genetic control of panicle architecture and NSP in different environments and (ii) the presence of stable genetic associations with panicle architecture across environments. This study combines image phenotyping of 225 accessions belonging to a genetic diversity array of indica rice grown under irrigated field condition in two different environments and Genome Wide Association Studies (GWAS) based on the genotyping of the diversity panel, providing 83,374 SNPs. Accessions sown under direct seeding in one environement had reduced Panicle Length (PL), NSP, PBN, PBL, SBN, and SBL compared to those established under transplanting in the second environment. Across environments, NSP was significantly and positively correlated with PBN, SBN and PBL. However, the length of branches (PBL and SBL) was not significantly correlated with variables related to number of branches (PBN and SBN), suggesting independent genetic control. Twenty- three GWAS sites were detected with P ≤ 1.0E-04 and 27 GWAS sites with p ≤ 5.9E-04. We found 17 GWAS sites related to NSP, 10 for PBN and 11 for SBN, 7 for PBL and 11 for SBL. This study revealed new regions related to NSP, but only three associations were related to both branching number (PBN and SBN) and NSP. Two GWAS sites associated with SBL and SBN were stable across contrasting environments and were not related to genes previously reported. The new regions reported in this study can help improving NSP in rice for both direct seeded and transplanted conditions. The integrated approach of high-throughput phenotyping, multi-environment field trials and GWAS has the potential to dissect complex traits, such as NSP, into less complex traits and to match single nucleotide polymorphisms with relevant function under different environments, offering a potential use for molecular breeding.
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Affiliation(s)
- Maria C. Rebolledo
- Agrobiodiversity, International Center for Tropical AgriculturePalmira, Colombia
- *Correspondence: Maria C. Rebolledo
| | - Alexandra L. Peña
- Agrobiodiversity, International Center for Tropical AgriculturePalmira, Colombia
| | - Jorge Duitama
- Agrobiodiversity, International Center for Tropical AgriculturePalmira, Colombia
| | - Daniel F. Cruz
- Agrobiodiversity, International Center for Tropical AgriculturePalmira, Colombia
| | - Michael Dingkuhn
- Agrobiodiversity, International Center for Tropical AgriculturePalmira, Colombia
- Agricultural Research for Development - CIRAD, Unités Mixtes de Recherche - Amélioration Génétique et Adaptation des PlantesMontpellier, France
| | - Cecile Grenier
- Agrobiodiversity, International Center for Tropical AgriculturePalmira, Colombia
- Agricultural Research for Development - CIRAD, Unités Mixtes de Recherche - Amélioration Génétique et Adaptation des PlantesMontpellier, France
| | - Joe Tohme
- Agrobiodiversity, International Center for Tropical AgriculturePalmira, Colombia
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Lu G, Coneva V, Casaretto JA, Ying S, Mahmood K, Liu F, Nambara E, Bi YM, Rothstein SJ. OsPIN5b modulates rice (Oryza sativa) plant architecture and yield by changing auxin homeostasis, transport and distribution. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 83:913-925. [PMID: 26213119 DOI: 10.1111/tpj.12939] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 07/01/2015] [Accepted: 07/08/2015] [Indexed: 05/21/2023]
Abstract
Plant architecture attributes such as tillering, plant height and panicle size are important agronomic traits that determine rice (Oryza sativa) productivity. Here, we report that altered auxin content, transport and distribution affect these traits, and hence rice yield. Overexpression of the auxin efflux carrier-like gene OsPIN5b causes pleiotropic effects, mainly reducing plant height, leaf and tiller number, shoot and root biomass, seed-setting rate, panicle length and yield parameters. Conversely, reduced expression of OsPIN5b results in higher tiller number, more vigorous root system, longer panicles and increased yield. We show that OsPIN5b is an endoplasmic reticulum (ER) -localized protein that participates in auxin homeostasis, transport and distribution in vivo. This work describes an example of an auxin-related gene where modulating its expression can simultaneously improve plant architecture and yield potential in rice, and reveals an important effect of hormonal signaling on these traits.
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Affiliation(s)
- Guangwen Lu
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Viktoriya Coneva
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - José A Casaretto
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Shan Ying
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Kashif Mahmood
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Fang Liu
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Eiji Nambara
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Yong-Mei Bi
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Steven J Rothstein
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
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