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Zhou T, Chang F, Li X, Yang W, Huang X, Yan J, Wu Q, Wen F, Pei J, Ma Y, Xu B. Role of auxin and gibberellin under low light in enhancing saffron corm starch degradation during sprouting. Int J Biol Macromol 2024; 279:135234. [PMID: 39218189 DOI: 10.1016/j.ijbiomac.2024.135234] [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: 06/03/2024] [Revised: 08/27/2024] [Accepted: 08/29/2024] [Indexed: 09/04/2024]
Abstract
The mechanisms by which low light accelerates starch macromolecules degradation by auxin and gibberellin (GA) in geophytes during sprouting remain largely unknown. This study investigated these mechanisms in saffron, grown under low light (50 μmol m-2 s-1) and optimal light (200 μmol m-2 s-1) during the sprouting phase. Low light reduced starch concentration in corms by 34.0 % and increased significantly sucrose levels in corms, leaves, and leaf sheaths by 19.2 %, 9.8 %, and 134.5 %, respectively. This was associated with a 33.3 % increase in GA3 level and enhanced auxin signaling. Leaves synthesized IAA under low light, which was transported to the corms to promote GA synthesis, facilitating starch degradation through a 228.7 % increase in amylase activity. Exogenous applications of GA and IAA, as well as the use of their synthesis or transport inhibitors, confirmed the synergistic role of these phytohormones in starch metabolism. The unigenes associated with GA biosynthesis and auxin signaling were upregulated under low light, highlighting the IAA-GA module role in starch degradation. Moreover, increased respiration rate and invertase activity, crucial for ATP biosynthesis and the tricarboxylic acid cycle, were consistent with the upregulation of related unigenes, suggesting that auxin signaling accelerates starch degradation by promoting energy metabolism. Upregulated of auxin signaling (CsSAUR32) and starch metabolism (CsSnRK1) genes under low light suggests that auxin directly regulate starch degradation in saffron corms. This study elucidates that low light modulates auxin and GA interactions to accelerate starch degradation in saffron corms during sprouting, offering insights for optimizing agricultural practices under suboptimal light conditions.
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Affiliation(s)
- Tao Zhou
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, Sichuan, China; College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, Sichuan, China
| | - Fei Chang
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, Sichuan, China; College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, Sichuan, China
| | - Xin Li
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, Sichuan, China; College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, Sichuan, China
| | - Weijing Yang
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, Sichuan, China; College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, Sichuan, China
| | - Xulong Huang
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, Sichuan, China; College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, Sichuan, China
| | - Jie Yan
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, Sichuan, China; College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, Sichuan, China
| | - Qinghua Wu
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, Sichuan, China; College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, Sichuan, China
| | - Feiyan Wen
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, Sichuan, China; College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, Sichuan, China
| | - Jin Pei
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, Sichuan, China; College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, Sichuan, China.
| | - Yuntong Ma
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, Sichuan, China; College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, Sichuan, China.
| | - Binjie Xu
- Innovative institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, Sichuan, China.
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Zhang G, Hua D, Wang Y, Xu J, He Y, Liu Y, Tang A, Liu H, Sun J. Combined physicochemical and transcriptomic analyses reveal the effect of the OsGA20ox1 gene on the starch properties of germinated brown rice. Int J Biol Macromol 2024; 278:134849. [PMID: 39159794 DOI: 10.1016/j.ijbiomac.2024.134849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 05/27/2024] [Accepted: 08/16/2024] [Indexed: 08/21/2024]
Abstract
Genes play a pivotal role in regulating the germination of cereal grains; however, there is limited research on the impact of germination genes on the physicochemical properties of germinated cereal starch. We investigated the effects of the OsGA20ox1 gene on the multiscale structural features and adhesion behavior of germinated brown rice starch. Compared to the knockout lines group, the wild type exhibited a decrease in double-helix content (62.74 %), relative crystallinity (47.39 %), and short-range molecular ordering (2.47 %), accompanied by enhanced erosion on the surface of starch granules. The damage to glycosidic bonds at the double-helix level and the heightened structural amorphization (90.95 %) led to reduced entanglement and interaction among starch molecules, ultimately resulting in reduced characteristic viscosity. Further transcriptomic analysis revealed that OsGA20ox1 could regulate the expression of starch-related enzyme genes in the starch metabolism pathway during germination of brown rice. This study contributes to understanding the role of germination genes in promoting the physicochemical properties of starch in germinated grains, thereby opening up new avenues for the improvement of plant-based starch, and paving the way for further research in this field.
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Affiliation(s)
- Guangchen Zhang
- College of Food Science and Technology, Bohai University, Jinzhou, Liaoning, China
| | - Dong Hua
- College of Food Science and Technology, Bohai University, Jinzhou, Liaoning, China
| | - Yiqiao Wang
- Collaborative Innovation Center for Genetic Improvement and High Quality and Efficiency Production of Northeast Japonica Rice in China, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Jiaxin Xu
- College of Food Science and Technology, Bohai University, Jinzhou, Liaoning, China
| | - Yutang He
- College of Food Science and Technology, Bohai University, Jinzhou, Liaoning, China
| | - Youhong Liu
- Institute of Crop Cultivation and Tillage, Heilongjiang Academy of Agricultural Sciences, Northeast Branch of National Center of Technology Innovation for Saline-Alkali Tolerant Rice, Harbin, China
| | - Ao Tang
- Institute of Crop Cultivation and Tillage, Heilongjiang Academy of Agricultural Sciences, Northeast Branch of National Center of Technology Innovation for Saline-Alkali Tolerant Rice, Harbin, China
| | - He Liu
- College of Food Science and Technology, Bohai University, Jinzhou, Liaoning, China.
| | - Jian Sun
- Collaborative Innovation Center for Genetic Improvement and High Quality and Efficiency Production of Northeast Japonica Rice in China, Shenyang Agricultural University, Shenyang, Liaoning, China.
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3
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Zhao Z, Xie Y, Tian M, Liu J, Chen C, Zhou J, Guo T, Xiao W. Enhancing Coleoptile Length of Rice Seeds under Submergence through NAL11 Knockout. PLANTS (BASEL, SWITZERLAND) 2024; 13:2593. [PMID: 39339568 PMCID: PMC11434697 DOI: 10.3390/plants13182593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2024] [Revised: 09/08/2024] [Accepted: 09/15/2024] [Indexed: 09/30/2024]
Abstract
Submergence stress challenges direct seeding in rice cultivation. In this study, we identified a heat shock protein, NAL11, with a DnaJ domain, which can regulate the length of rice coleoptiles under flooded conditions. Through bioinformatics analyses, we identified cis-regulatory elements in its promoter, making it responsive to abiotic stresses, such as hypoxia or anoxia. Expression of NAL11 was higher in the basal regions of shoots and coleoptiles during flooding. NAL11 knockout triggered the rapid accumulation of abscisic acid (ABA) and reduction of Gibberellin (GA), stimulating rice coleoptile elongation and contributes to flooding stress management. In addition, NAL11 mutants were found to be more sensitive to ABA treatments. Such knockout lines exhibited enhanced cell elongation for coleoptile extension. Quantitative RT-PCR analysis revealed that NAL11 mediated the gluconeogenic pathway, essential for the energy needed in cell expansion. Furthermore, NAL11 mutants reduced the accumulation of reactive oxygen species (ROS) and malondialdehyde under submerged stress, attributed to an improved antioxidant enzyme system compared to the wild-type. In conclusion, our findings underscore the pivotal role of NAL11 knockout in enhancing the tolerance of rice to submergence stress by elucidating its mechanisms. This insight offers a new strategy for improving resilience against flooding in rice cultivation.
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Affiliation(s)
- Zhe Zhao
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Yuelan Xie
- Yangjiang Institute of Agricultural Sciences, Yangjiang 529500, China
| | - Mengqing Tian
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Jinzhao Liu
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Chun Chen
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Jiyong Zhou
- Guangdong Agricultural Technology Extension Center, Guangzhou 510520, China
| | - Tao Guo
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Wuming Xiao
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China
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4
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Yan Z, Deng R, Tang H, Zhu S. Genetic Diversity and Divergence between Southern Japonica and Northern Japonica Rice Varieties in China. Genes (Basel) 2024; 15:1182. [PMID: 39336773 PMCID: PMC11431492 DOI: 10.3390/genes15091182] [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: 08/20/2024] [Revised: 08/29/2024] [Accepted: 09/03/2024] [Indexed: 09/30/2024] Open
Abstract
Given the notable ecological and breeding disparities between southern and northern rice regions, delving into the genetic diversity and divergence between southern and northern japonica rice contributes to enhancing the genetic pool for japonica rice breeding. In this study, we analyzed 90 southern and 51 northern japonica rice varieties, focusing on nucleotide diversity (Pi), agronomic trait variations, population structure, genetic divergence, and a neutral test. For genetic diversity, the results demonstrated higher Pi in northern japonica rice varieties (NJRVs) on Chr2, Chr5, Chr6, Chr8, and Chr10, whereas in southern japonica rice varieties (SJRVs) on Chr7 and Chr9. In addition, SJRVs exhibited higher grain width and thickness, whereas NJRVs featured a higher grain aspect ratio, filled grain number, and grain number per panicle. Regarding genetic divergence, geographic differentiation existed between NJRVs and SJRVs, with Chr5 exhibiting numerous higher genetic differentiation windows, including cloned grain shape-controlling genes RGA1 and SFD5, stemming from intensified selection pressure on SJRVs. In summary, SJRVs and NJRVs exhibited diversity differences and genetic differentiation. Hence, it was suggested to conduct genetic introgression between NJRVs and SJRVs to broaden the genetic basis of the local japonica rice germplasm. By exploiting their heterotic advantage, new japonica rice cultivars with superior comprehensive traits could be developed.
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Affiliation(s)
- Zhiqiang Yan
- Guizhou Provincial Academy of Agricultural Sciences, Guiyang 550000, China
| | - Ruyue Deng
- Guizhou Provincial Academy of Agricultural Sciences, Guiyang 550000, China
| | - Huihui Tang
- Guizhou Provincial Academy of Agricultural Sciences, Guiyang 550000, China
| | - Susong Zhu
- Guizhou Provincial Academy of Agricultural Sciences, Guiyang 550000, China
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5
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Yin W, Yang H, Feng P, Qi P, Li B, Li Y, Huang Q, Peng Y, Wang N, Hu Y. Rapid function analysis of OsiWAK1 using a Dual-Luciferase assay in rice. Sci Rep 2024; 14:19412. [PMID: 39169077 PMCID: PMC11339413 DOI: 10.1038/s41598-024-69955-7] [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: 03/26/2024] [Accepted: 08/12/2024] [Indexed: 08/23/2024] Open
Abstract
In the past decade, the exploration of genetic resources in rice has significantly enhanced the efficacy of rice breeding. However, the exploration of genetic resources is hindered by the identification of candidate genes. To expedite the identification of candidate genes, this study examined tapetum programmed cell death-related genes OsiWAK1, OsPDT1, EAT1, TDR, and TIP2 to assess the efficacy of the Dual-Luciferase (Dual-LUC) assay in rapidly determining gene relationships. The study found that, in the Dual-LUC assay, OsiWAK1 and its various recombinant proteins exhibit comparable activation abilities on the EAT1 promoter, potentially indicating a false positive. However, the Dual-LUC assay can reveal that OsiWAK1 impacts both the function of its upstream regulatory factor OsPDT1 and the TDR/TIP2 transcription complex. By rapidly studying the relationship between diverse candidate genes and regulatory genes in a well-known trait via the Dual-LUC assay, this study provides a novel approach to expedite the determination of candidate genes such as genome-wide association study.
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Affiliation(s)
- Wuzhong Yin
- College of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010, China
| | - Hongxia Yang
- Key Laboratory of Application and Safety Control of Genetically Modified Crops, College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
| | - Ping Feng
- Key Laboratory of Application and Safety Control of Genetically Modified Crops, College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
| | - Pan Qi
- College of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010, China
| | - Biluo Li
- College of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010, China
| | - Yuanyuan Li
- College of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010, China
| | - Qingxiong Huang
- College of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010, China
| | - Youlin Peng
- College of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010, China
| | - Nan Wang
- Key Laboratory of Application and Safety Control of Genetically Modified Crops, College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China.
| | - Yungao Hu
- College of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010, China.
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6
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Gong M, Kong M, Huo Q, He J, He J, Yan Z, Lu C, Jiang Y, Song J, Han W, Lv G. Ultrasonic treatment can improve maize seed germination and abiotic stress resistance. BMC PLANT BIOLOGY 2024; 24:758. [PMID: 39112960 PMCID: PMC11308701 DOI: 10.1186/s12870-024-05474-x] [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: 05/15/2024] [Accepted: 07/31/2024] [Indexed: 08/10/2024]
Abstract
Constant-frequency ultrasonic treatment helped to improve seed germination. However, variable-frequency ultrasonic treatment on maize seed germination were rarely reported. In this study, maize seeds were exposed to 20-40 kHz ultrasonic for 40 s. The germination percentage and radicle length of maize seeds increased by 10.4% and 230.5%. Ultrasonic treatment also significantly increased the acid protease, α-amylase, and β-amylase contents by 96.4%, 73.8%, and 49.1%, respectively. Transcriptome analysis showed that 11,475 differentially expressed genes (DEGs) were found in the ultrasonic treatment and control groups, including 5,695 upregulated and 5,780 downregulated. Metabolic pathways and transcription factors (TFs) were significantly enriched among DEGs after ultrasonic treatment. This included metabolism and genetic information processing, that is, ribosome, proteasome, and pyruvate metabolism, sesquiterpenoid, triterpenoid, and phenylpropanoid biosynthesis, and oxidative phosphorylation, as well as transcription factors in the NAC, MYB, bHLH, WRKY, AP2, bZIP, and ARF families. Variable-frequency ultrasonic treatment increased auxin, gibberellin, and salicylic acid by 5.5%, 37.3%, and 28.9%, respectively. Abscisic acid significantly decreased by 33.2%. The related DEGs were upregulated and downregulated to varying degrees. Seed germination under the abiotic stress conditions of salt stress (NaCl solution), drought (PEG solution), and waterlogging (water-saturated sand bed) under ultrasonic treatment were promoted, radicle length was significantly increased by 30.2%, 30.5%, and 27.3%, respectively; and germination percentage by 14.8%, 20.1%, and 21.6%, respectively. These findings provide new insight into the mechanisms through ultrasonic to promote maize seed germination.
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Affiliation(s)
- Min Gong
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Zhongguancun South Street No. 12, Haidian District, Beijing, 100081, China
| | - Meng Kong
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Zhongguancun South Street No. 12, Haidian District, Beijing, 100081, China
| | - Qiuyan Huo
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Zhongguancun South Street No. 12, Haidian District, Beijing, 100081, China
| | - Jiuxing He
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Zhongguancun South Street No. 12, Haidian District, Beijing, 100081, China
| | - Juan He
- National Agro-tech Extension and Service Center, Beijing, 100125, China
| | - Zhuosheng Yan
- Guangzhou Jindao Agricultural Technology Co., Ltd, Guangzhou, 510940, China
| | - Chun Lu
- Guangzhou Jindao Agricultural Technology Co., Ltd, Guangzhou, 510940, China
| | - Yawen Jiang
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Zhongguancun South Street No. 12, Haidian District, Beijing, 100081, China
| | - Jiqing Song
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Zhongguancun South Street No. 12, Haidian District, Beijing, 100081, China
| | - Wei Han
- Shandong Agri-tech Extension Center, Jiefang Road No. 15, Lixia District, Jinan, 250013, China.
| | - Guohua Lv
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Zhongguancun South Street No. 12, Haidian District, Beijing, 100081, China.
- Institute of Dongying Shengli Salt Alkali Agriculture Industrialization and Technology Research, Dongying, 257000, China.
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He Y, Zhao J, Wang Z. Rice seed germination priming by salicylic acid and the emerging role of phytohormones in anaerobic germination. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:1537-1539. [PMID: 38923381 DOI: 10.1111/jipb.13728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024]
Abstract
This Commentary examines a recent study that identified peroxisomal cinnamate: CoA ligases as key enzymes for salicylic acid biosynthesis, which promotes submerged germination by releasing the inhibition of rice germination by indole-acetic acid. This study thus provides important information for developing rice varieties suitable for direct seeding.
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Affiliation(s)
- Yongqi He
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Jia Zhao
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Zhoufei Wang
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China
- Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, 510642, China
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
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Sugimura Y, Oikawa K, Sugihara Y, Utsushi H, Kanzaki E, Ito K, Ogasawara Y, Fujioka T, Takagi H, Shimizu M, Shimono H, Terauchi R, Abe A. Impact of rice GENERAL REGULATORY FACTOR14h (GF14h) on low-temperature seed germination and its application to breeding. PLoS Genet 2024; 20:e1011369. [PMID: 39110723 PMCID: PMC11343456 DOI: 10.1371/journal.pgen.1011369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 08/23/2024] [Accepted: 07/12/2024] [Indexed: 08/25/2024] Open
Abstract
Direct seeding is employed to circumvent the labor-intensive process of rice (Oryza sativa) transplantation, but this approach requires varieties with vigorous low-temperature germination (LTG) when sown in cold climates. To investigate the genetic basis of LTG, we identified the quantitative trait locus (QTL) qLTG11 from rice variety Arroz da Terra, which shows rapid seed germination at lower temperatures, using QTL-seq. We delineated the candidate region to a 52-kb interval containing GENERAL REGULATORY FACTOR14h (GF14h) gene, which is expressed during seed germination. The Arroz da Terra GF14h allele encodes functional GF14h, whereas Japanese rice variety Hitomebore harbors a 4-bp deletion in the coding region. Knocking out functional GF14h in a near-isogenic line (NIL) carrying the Arroz da Terra allele decreased LTG, whereas overexpressing functional GF14h in Hitomebore increased LTG, indicating that GF14h is the causal gene behind qLTG11. Analysis of numerous Japanese rice accessions revealed that the functional GF14h allele was lost from popular varieties during modern breeding. We generated a NIL in the Hitomebore background carrying a 172-kb genomic fragment from Arroz da Terra including GF14h. The NIL showed superior LTG compared to Hitomebore, with otherwise comparable agronomic traits. The functional GF14h allele from Arroz da Terra represents a valuable resource for direct seeding in cold regions.
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Affiliation(s)
| | - Kaori Oikawa
- Iwate Biotechnology Research Center, Kitakami, Iwate, Japan
| | - Yu Sugihara
- Crop Evolution Laboratory, Kyoto University, Muko, Kyoto, Japan
| | - Hiroe Utsushi
- Iwate Biotechnology Research Center, Kitakami, Iwate, Japan
| | - Eiko Kanzaki
- Iwate Biotechnology Research Center, Kitakami, Iwate, Japan
| | - Kazue Ito
- Iwate Biotechnology Research Center, Kitakami, Iwate, Japan
| | | | | | - Hiroki Takagi
- Iwate Biotechnology Research Center, Kitakami, Iwate, Japan
| | - Motoki Shimizu
- Iwate Biotechnology Research Center, Kitakami, Iwate, Japan
| | - Hiroyuki Shimono
- Faculty of Agriculture, Iwate University, Morioka, Iwate, Japan
- Agri-Innovation Center, Iwate University, Morioka, Iwate, Japan
| | - Ryohei Terauchi
- Iwate Biotechnology Research Center, Kitakami, Iwate, Japan
- Crop Evolution Laboratory, Kyoto University, Muko, Kyoto, Japan
| | - Akira Abe
- Iwate Biotechnology Research Center, Kitakami, Iwate, Japan
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9
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Hu Y, Ma M, Zhao W, Niu P, Li R, Luo J. Identification of hub genes involved in gibberellin-regulated elongation of coleoptiles of rice seeds germinating under submerged conditions. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:3862-3876. [PMID: 38571323 DOI: 10.1093/jxb/erae144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 04/03/2024] [Indexed: 04/05/2024]
Abstract
Rapid elongation of coleoptiles from rice seeds to reach the water surface enables plants to survive submergence stress and therefore plays a crucial role in allowing direct seeding in rice cultivation. Gibberellin (GA) positively influences growth in rice, but the molecular mechanisms underlying its regulation of coleoptile elongation under submerged conditions remain unclear. In this study, we performed a weighted gene co-expression network analysis to conduct a preliminarily examination of the mechanisms. Four key modules were identified with high correlations to the GA regulation of submergence tolerance. The genes within these modules were mainly involved in the Golgi apparatus and carbohydrate metabolic pathways, suggesting their involvement in enhancing submergence tolerance. Further analysis of natural variation revealed that the specific hub genes Os03g0337900, Os03g0355600, and Os07g0638400 exhibited strong correlations with subspecies divergence of the coleoptile elongation phenotype. Consistent with this analysis, mutation of Os07g0638400 resulted in a lower germination potential and a stronger inhibition of coleoptile elongation under submerged conditions. The hub genes identified in this study provide new insights into the molecular mechanisms underlying GA-dependent tolerance to submergence stress in rice, and a potential basis for future modification of rice germplasm to allow for direct seeding.
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Affiliation(s)
- Yunfei Hu
- College of Life Science and Technology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning 530004, China
| | - Mingqing Ma
- College of Life Science and Technology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning 530004, China
| | - Wenlong Zhao
- College of Life Science and Technology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning 530004, China
| | - Pengwei Niu
- College of Life Science and Technology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning 530004, China
| | - Rongbai Li
- College of Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning 530004, China
| | - Jijing Luo
- College of Life Science and Technology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning 530004, China
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10
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Wang Y, Jin G, Song S, Jin Y, Wang X, Yang S, Shen X, Gan Y, Wang Y, Li R, Liu JX, Hu J, Pan R. A peroxisomal cinnamate:CoA ligase-dependent phytohormone metabolic cascade in submerged rice germination. Dev Cell 2024; 59:1363-1378.e4. [PMID: 38579719 DOI: 10.1016/j.devcel.2024.03.023] [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: 11/23/2023] [Revised: 01/30/2024] [Accepted: 03/11/2024] [Indexed: 04/07/2024]
Abstract
The mechanism underlying the ability of rice to germinate underwater is a largely enigmatic but key research question highly relevant to rice cultivation. Moreover, although rice is known to accumulate salicylic acid (SA), SA biosynthesis is poorly defined, and its role in underwater germination is unknown. It is also unclear whether peroxisomes, organelles essential to oilseed germination and rice SA accumulation, play a role in rice germination. Here, we show that submerged imbibition of rice seeds induces SA accumulation to promote germination in submergence. Two submergence-induced peroxisomal Oryza sativa cinnamate:CoA ligases (OsCNLs) are required for this SA accumulation. SA exerts this germination-promoting function by inducing indole-acetic acid (IAA) catabolism through the IAA-amino acid conjugating enzyme GH3. The metabolic cascade we identified may potentially be adopted in agriculture to improve the underwater germination of submergence-intolerant rice varieties. SA pretreatment is also a promising strategy to improve submerged rice germination in the field.
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Affiliation(s)
- Yukang Wang
- State Key Laboratory of Rice Biology and Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, Zhejiang, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, Zhejiang, China
| | - Gaochen Jin
- State Key Laboratory of Rice Biology and Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Shuyan Song
- State Key Laboratory of Rice Biology and Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, Zhejiang, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, Zhejiang, China
| | - Yijun Jin
- State Key Laboratory of Rice Biology and Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Xiaowen Wang
- State Key Laboratory of Rice Biology and Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Shuaiqi Yang
- State Key Laboratory of Rice Biology and Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Xingxing Shen
- State Key Laboratory of Rice Biology and Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Yinbo Gan
- State Key Laboratory of Rice Biology and Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Yuexing Wang
- China National Rice Research Institute, Hangzhou 310006, China
| | - Ran Li
- State Key Laboratory of Rice Biology and Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Jian-Xiang Liu
- State Key Laboratory of Plant Environmental Resilience, College of Life Sciences, Zhejiang University, Hangzhou 310027, China
| | - Jianping Hu
- Michigan State University-Department of Energy Plant Research Laboratory and Plant Biology Department, Michigan State University, East Lansing, MI 48824, USA
| | - Ronghui Pan
- State Key Laboratory of Rice Biology and Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, Zhejiang, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, Zhejiang, China.
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11
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Wang J, Han M, Huang Y, Zhao J, Liu C, Ma Y. Flooding Tolerance of Rice: Regulatory Pathways and Adaptive Mechanisms. PLANTS (BASEL, SWITZERLAND) 2024; 13:1178. [PMID: 38732393 PMCID: PMC11085783 DOI: 10.3390/plants13091178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/20/2024] [Accepted: 04/21/2024] [Indexed: 05/13/2024]
Abstract
Rice is a major food crop for more than half of the world's population, while its production is seriously threatened by flooding, a common environmental stress worldwide. Flooding leads to oxygen deficiency, which is a major problem for submerged plants. Over the past three decades, significant progress has been made in understanding rice adaptation and molecular regulatory mechanisms in response to flooding. At the seed germination and seedling establishment stages, the CIPK15-SnRK1A-MYBS1 signaling cascade plays a central role in determining rice submergence tolerance. However, from seedlings to mature plants for harvesting, SUB1A- and SK1/SK2-regulated pathways represent two principal and opposite regulatory mechanisms in rice. In addition, phytohormones, especially gibberellins, induce adaptive responses to flooding throughout the rice growth period. This review summarizes the significant adaptive traits observed in flooded rice varieties and updates the molecular genetics and mechanisms of submergence tolerance in rice.
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Affiliation(s)
- Jing Wang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China; (J.W.); (Y.H.)
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (M.H.); (J.Z.); (C.L.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| | - Mingzhen Han
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (M.H.); (J.Z.); (C.L.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Yongxiang Huang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China; (J.W.); (Y.H.)
| | - Junliang Zhao
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (M.H.); (J.Z.); (C.L.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| | - Chuanguang Liu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (M.H.); (J.Z.); (C.L.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| | - Yamei Ma
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (M.H.); (J.Z.); (C.L.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
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12
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Chen K, Yang H, Wu D, Peng Y, Lian L, Bai L, Wang L. Weed biology and management in the multi-omics era: Progress and perspectives. PLANT COMMUNICATIONS 2024; 5:100816. [PMID: 38219012 PMCID: PMC11009161 DOI: 10.1016/j.xplc.2024.100816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 11/20/2023] [Accepted: 01/08/2024] [Indexed: 01/15/2024]
Abstract
Weeds pose a significant threat to crop production, resulting in substantial yield reduction. In addition, they possess robust weedy traits that enable them to survive in extreme environments and evade human control. In recent years, the application of multi-omics biotechnologies has helped to reveal the molecular mechanisms underlying these weedy traits. In this review, we systematically describe diverse applications of multi-omics platforms for characterizing key aspects of weed biology, including the origins of weed species, weed classification, and the underlying genetic and molecular bases of important weedy traits such as crop-weed interactions, adaptability to different environments, photoperiodic flowering responses, and herbicide resistance. In addition, we discuss limitations to the application of multi-omics techniques in weed science, particularly compared with their extensive use in model plants and crops. In this regard, we provide a forward-looking perspective on the future application of multi-omics technologies to weed science research. These powerful tools hold great promise for comprehensively and efficiently unraveling the intricate molecular genetic mechanisms that underlie weedy traits. The resulting advances will facilitate the development of sustainable and highly effective weed management strategies, promoting greener practices in agriculture.
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Affiliation(s)
- Ke Chen
- Key Laboratory of Indica Rice Genetics and Breeding in the Middle and Lower Reaches of Yangtze River Valley, Ministry of Agriculture and Rural Affairs, Hunan Rice Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China; State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha 410125, China; Longping Branch, College of Biology, Hunan University, Changsha 410125, China; Hunan Weed Science Key Laboratory, Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Haona Yang
- State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha 410125, China; Hunan Weed Science Key Laboratory, Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Di Wu
- State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Yajun Peng
- State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha 410125, China; Hunan Weed Science Key Laboratory, Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Lei Lian
- Qingdao Kingagroot Compounds Co. Ltd, Qingdao 266000, China
| | - Lianyang Bai
- Key Laboratory of Indica Rice Genetics and Breeding in the Middle and Lower Reaches of Yangtze River Valley, Ministry of Agriculture and Rural Affairs, Hunan Rice Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China; State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha 410125, China; Longping Branch, College of Biology, Hunan University, Changsha 410125, China; Huangpu Research Institute of Longping Agricultural Science and Technology, Guangzhou 510715, China; Hunan Weed Science Key Laboratory, Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China.
| | - Lifeng Wang
- Key Laboratory of Indica Rice Genetics and Breeding in the Middle and Lower Reaches of Yangtze River Valley, Ministry of Agriculture and Rural Affairs, Hunan Rice Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China; State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha 410125, China; Longping Branch, College of Biology, Hunan University, Changsha 410125, China; Huangpu Research Institute of Longping Agricultural Science and Technology, Guangzhou 510715, China; Hunan Weed Science Key Laboratory, Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China.
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13
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Yuan H, Zheng Z, Bao Y, Zhao X, Lv J, Tang C, Wang N, Liang Z, Li H, Xiang J, Qian Y, Shi Y. Identification and Regulation of Hypoxia-Tolerant and Germination-Related Genes in Rice. Int J Mol Sci 2024; 25:2177. [PMID: 38396854 PMCID: PMC10889564 DOI: 10.3390/ijms25042177] [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: 12/18/2023] [Revised: 01/25/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
In direct seeding, hypoxia is a major stress faced by rice plants. Therefore, dissecting the response mechanism of rice to hypoxia stress and the molecular regulatory network is critical to the development of hypoxia-tolerant rice varieties and direct seeding of rice. This review summarizes the morphological, physiological, and ecological changes in rice under hypoxia stress, the discovery of hypoxia-tolerant and germination-related genes/QTLs, and the latest research on candidate genes, and explores the linkage of hypoxia tolerance genes and their distribution in indica and japonica rice through population variance analysis and haplotype network analysis. Among the candidate genes, OsMAP1 is a typical gene located on the MAPK cascade reaction for indica-japonica divergence; MHZ6 is involved in both the MAPK signaling and phytohormone transduction pathway. MHZ6 has three major haplotypes and one rare haplotype, with Hap3 being dominated by indica rice varieties, and promotes internode elongation in deep-water rice by activating the SD1 gene. OsAmy3D and Adh1 have similar indica-japonica varietal differentiation, and are mainly present in indica varieties. There are three high-frequency haplotypes of OsTPP7, namely Hap1 (n = 1109), Hap2 (n = 1349), and Hap3 (n = 217); Hap2 is more frequent in japonica, and the genetic background of OsTPP7 was derived from the japonica rice subpopulation. Further artificial selection, natural domestication, and other means to identify more resistance mechanisms of this gene may facilitate future research to breed superior rice cultivars. Finally, this study discusses the application of rice hypoxia-tolerant germplasm in future breeding research.
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Affiliation(s)
- Hongyan Yuan
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (H.Y.); (Z.Z.); (Y.B.); (X.Z.); (J.L.); (C.T.); (N.W.); (Z.L.); (H.L.); (J.X.); (Y.Q.)
| | - Zhenzhen Zheng
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (H.Y.); (Z.Z.); (Y.B.); (X.Z.); (J.L.); (C.T.); (N.W.); (Z.L.); (H.L.); (J.X.); (Y.Q.)
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yaling Bao
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (H.Y.); (Z.Z.); (Y.B.); (X.Z.); (J.L.); (C.T.); (N.W.); (Z.L.); (H.L.); (J.X.); (Y.Q.)
| | - Xueyu Zhao
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (H.Y.); (Z.Z.); (Y.B.); (X.Z.); (J.L.); (C.T.); (N.W.); (Z.L.); (H.L.); (J.X.); (Y.Q.)
| | - Jiaqi Lv
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (H.Y.); (Z.Z.); (Y.B.); (X.Z.); (J.L.); (C.T.); (N.W.); (Z.L.); (H.L.); (J.X.); (Y.Q.)
| | - Chenghang Tang
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (H.Y.); (Z.Z.); (Y.B.); (X.Z.); (J.L.); (C.T.); (N.W.); (Z.L.); (H.L.); (J.X.); (Y.Q.)
| | - Nansheng Wang
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (H.Y.); (Z.Z.); (Y.B.); (X.Z.); (J.L.); (C.T.); (N.W.); (Z.L.); (H.L.); (J.X.); (Y.Q.)
| | - Zhaojie Liang
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (H.Y.); (Z.Z.); (Y.B.); (X.Z.); (J.L.); (C.T.); (N.W.); (Z.L.); (H.L.); (J.X.); (Y.Q.)
| | - Hua Li
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (H.Y.); (Z.Z.); (Y.B.); (X.Z.); (J.L.); (C.T.); (N.W.); (Z.L.); (H.L.); (J.X.); (Y.Q.)
| | - Jun Xiang
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (H.Y.); (Z.Z.); (Y.B.); (X.Z.); (J.L.); (C.T.); (N.W.); (Z.L.); (H.L.); (J.X.); (Y.Q.)
| | - Yingzhi Qian
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (H.Y.); (Z.Z.); (Y.B.); (X.Z.); (J.L.); (C.T.); (N.W.); (Z.L.); (H.L.); (J.X.); (Y.Q.)
| | - Yingyao Shi
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (H.Y.); (Z.Z.); (Y.B.); (X.Z.); (J.L.); (C.T.); (N.W.); (Z.L.); (H.L.); (J.X.); (Y.Q.)
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14
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Guo N, Tang S, Wang Y, Chen W, An R, Ren Z, Hu S, Tang S, Wei X, Shao G, Jiao G, Xie L, Wang L, Chen Y, Zhao F, Sheng Z, Hu P. A mediator of OsbZIP46 deactivation and degradation negatively regulates seed dormancy in rice. Nat Commun 2024; 15:1134. [PMID: 38326370 PMCID: PMC10850359 DOI: 10.1038/s41467-024-45402-z] [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: 11/27/2022] [Accepted: 01/22/2024] [Indexed: 02/09/2024] Open
Abstract
Preharvest sprouting (PHS) is a deleterious phenotype that occurs frequently in rice-growing regions where the temperature and precipitation are high. It negatively affects yield, quality, and downstream grain processing. Seed dormancy is a trait related to PHS. Longer seed dormancy is preferred for rice production as it can prevent PHS. Here, we map QTLs associated with rice seed dormancy and clone Seed Dormancy 3.1 (SDR3.1) underlying one major QTL. SDR3.1 encodes a mediator of OsbZIP46 deactivation and degradation (MODD). We show that SDR3.1 negatively regulates seed dormancy by inhibiting the transcriptional activity of ABIs. In addition, we reveal two critical amino acids of SDR3.1 that are critical for the differences in seed dormancy between the Xian/indica and Geng/japonica cultivars. Further, SDR3.1 has been artificially selected during rice domestication. We propose a two-line model for the process of rice seed dormancy domestication from wild rice to modern cultivars. We believe the candidate gene and germplasm studied in this study would be beneficial for the genetic improvement of rice seed dormancy.
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Affiliation(s)
- Naihui Guo
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
- Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, P. R. China
| | - Shengjia Tang
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Yakun Wang
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
- National Nanfan Research Academy (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572024, P. R. China
| | - Wei Chen
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Ruihu An
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Zongliang Ren
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Shikai Hu
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Shaoqing Tang
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Xiangjin Wei
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Gaoneng Shao
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Guiai Jiao
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Lihong Xie
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Ling Wang
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Ying Chen
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Fengli Zhao
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Zhonghua Sheng
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China.
- Jiangxi Early-season Rice Research Center, Pingxiang, Jiangxi Province, 337000, P. R. China.
| | - Peisong Hu
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China.
- Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, P. R. China.
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15
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Jiang W, He J, Babla M, Wu T, Tong T, Riaz A, Zeng F, Qin Y, Chen G, Deng F, Chen ZH. Molecular evolution and interaction of 14-3-3 proteins with H+-ATPases in plant abiotic stresses. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:689-707. [PMID: 37864845 DOI: 10.1093/jxb/erad414] [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: 05/18/2023] [Accepted: 10/20/2023] [Indexed: 10/23/2023]
Abstract
Environmental stresses severely affect plant growth and crop productivity. Regulated by 14-3-3 proteins (14-3-3s), H+-ATPases (AHAs) are important proton pumps that can induce diverse secondary transport via channels and co-transporters for the abiotic stress response of plants. Many studies demonstrated the roles of 14-3-3s and AHAs in coordinating the processes of plant growth, phytohormone signaling, and stress responses. However, the molecular evolution of 14-3-3s and AHAs has not been summarized in parallel with evolutionary insights across multiple plant species. Here, we comprehensively review the roles of 14-3-3s and AHAs in cell signaling to enhance plant responses to diverse environmental stresses. We analyzed the molecular evolution of key proteins and functional domains that are associated with 14-3-3s and AHAs in plant growth and hormone signaling. The results revealed evolution, duplication, contraction, and expansion of 14-3-3s and AHAs in green plants. We also discussed the stress-specific expression of those 14-3-3and AHA genes in a eudicotyledon (Arabidopsis thaliana), a monocotyledon (Hordeum vulgare), and a moss (Physcomitrium patens) under abiotic stresses. We propose that 14-3-3s and AHAs respond to abiotic stresses through many important targets and signaling components of phytohormones, which could be promising to improve plant tolerance to single or multiple environmental stresses.
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Affiliation(s)
- Wei Jiang
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River, College of Agriculture, Yangtze University, Jingzhou, 434025, China
- School of Science, Western Sydney University, Penrith, NSW 2751, Australia
| | - Jing He
- School of Science, Western Sydney University, Penrith, NSW 2751, Australia
| | - Mohammad Babla
- School of Science, Western Sydney University, Penrith, NSW 2751, Australia
| | - Ting Wu
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW 2751, Australia
| | - Tao Tong
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River, College of Agriculture, Yangtze University, Jingzhou, 434025, China
| | - Adeel Riaz
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River, College of Agriculture, Yangtze University, Jingzhou, 434025, China
| | - Fanrong Zeng
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River, College of Agriculture, Yangtze University, Jingzhou, 434025, China
| | - Yuan Qin
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River, College of Agriculture, Yangtze University, Jingzhou, 434025, China
| | - Guang Chen
- Central Laboratory, Zhejiang Academy of Agricultural Science, Hangzhou 310021, China
| | - Fenglin Deng
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River, College of Agriculture, Yangtze University, Jingzhou, 434025, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Zhong-Hua Chen
- School of Science, Western Sydney University, Penrith, NSW 2751, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW 2751, Australia
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16
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Khalil MI, Hassan MM, Samanta SC, Chowdhury AK, Hassan MZ, Ahmed NU, Somaddar U, Ghosal S, Robin AHK, Nath UK, Mostofa MG, Burritt DJ, Ha CV, Gupta A, Tran LSP, Saha G. Unraveling the genetic enigma of rice submergence tolerance: Shedding light on the role of ethylene response factor-encoding gene SUB1A-1. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 206:108224. [PMID: 38091930 DOI: 10.1016/j.plaphy.2023.108224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 11/07/2023] [Accepted: 11/21/2023] [Indexed: 02/15/2024]
Abstract
The world's low-lying rice (Oryza sativa) cultivation areas are under threat of submergence or flash flooding due to global warming. Rice plants manifest a variety of physiological and morphological changes to cope with submergence and hypoxia, including lowering carbohydrate consumption, inhibiting shoot elongation, and forming a thicker leaf gas film during submergence. Functional studies have revealed that submergence tolerance in rice is mainly determined by an ethylene response factor (ERF) transcription factor-encoding gene, namely SUBMERGENCE 1A-1 (SUB1A-1) located in the SUB1 quantitative trait locus. The SUB1A-1-dependent submergence tolerance is manifested through hormonal signaling involving ethylene, gibberellic acid, brassinosteroid, auxin and jasmonic acid. Considerable progress has been made toward the introduction of SUB1A-1 into rice varieties through a conventional marker-assisted backcrossing approach. Here, we review the recent advances in the physiological, biochemical and molecular dynamics of rice submergence tolerance mediated by the 'quiescence strategy'. Thus, the present review aims to provide researchers with insights into the genetics of rice submergence tolerance and future perspectives for designing submergence-resilient plants for sustainable agriculture under the uncertainties of climate change.
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Affiliation(s)
- Md Ibrahim Khalil
- Department of Agronomy, Patuakhali Science and Technology University, Dumki, Patuakhali, 8602, Bangladesh; Department of Genetics and Plant Breeding, Patuakhali Science and Technology University, Dumki, Patuakhali, 8602, Bangladesh.
| | - Md Mahmudul Hassan
- Department of Genetics and Plant Breeding, Patuakhali Science and Technology University, Dumki, Patuakhali, 8602, Bangladesh.
| | - Swadesh Chandra Samanta
- Department of Agronomy, Patuakhali Science and Technology University, Dumki, Patuakhali, 8602, Bangladesh.
| | - Abul Kashem Chowdhury
- Department of Genetics and Plant Breeding, Patuakhali Science and Technology University, Dumki, Patuakhali, 8602, Bangladesh.
| | - Md Zahid Hassan
- Department of Agronomy, Patuakhali Science and Technology University, Dumki, Patuakhali, 8602, Bangladesh.
| | - Nasar Uddin Ahmed
- Department of Genetics and Plant Breeding, Patuakhali Science and Technology University, Dumki, Patuakhali, 8602, Bangladesh.
| | - Uzzal Somaddar
- Department of Agronomy, Patuakhali Science and Technology University, Dumki, Patuakhali, 8602, Bangladesh.
| | - Sharmistha Ghosal
- Plant Breeding Division, Bangladesh Rice Research Institute, Gazipur, 1701, Bangladesh.
| | - Arif Hasan Khan Robin
- Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh.
| | - Ujjal Kumar Nath
- Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh.
| | - Mohammad Golam Mostofa
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA.
| | - David J Burritt
- Department of Botany, University of Otago, Dunedin, 9054, New Zealand.
| | - Chien Van Ha
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA.
| | - Aarti Gupta
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA.
| | - Lam-Son Phan Tran
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA.
| | - Gopal Saha
- Department of Agronomy, Patuakhali Science and Technology University, Dumki, Patuakhali, 8602, Bangladesh.
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Lu K, Guo Z, Di S, Lu Y, Muhammad IAR, Rong C, Ding Y, Li W, Ding C. OsMFT1 Inhibits Seed Germination by Modulating Abscisic Acid Signaling and Gibberellin Biosynthesis under Salt Stress in Rice. PLANT & CELL PHYSIOLOGY 2023; 64:674-685. [PMID: 37022148 DOI: 10.1093/pcp/pcad029] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 03/20/2023] [Accepted: 04/05/2023] [Indexed: 06/16/2023]
Abstract
Seed dormancy and germination are regulated by endogenous gene expression as well as hormonal and environmental conditions, such as salinity, which greatly inhibits seed germination. MOTHER OF FT AND TFL1 (MFT), which encodes a phosphatidylethanolamine-binding protein, is a key regulator of seed germination in Arabidopsis thaliana. There are two orthologous genes of AtMFT in rice (Oryza sativa), namely, OsMFT1 and OsMFT2. However, the functions of these two genes in regulating rice seed germination under salt stress remain unknown. In this study, we found that seeds of loss-of-function osmft1 mutants germinated faster than wild-type (WT) seeds under salt stress, but this was not the case for loss-of-function osmft2 mutants. Overexpression of OsMFT1 (OsMFT1OE) or OsMFT2 increased the sensitivity to salt stress during seed germination. Transcriptome comparisons of osmft1 vs WT in the absence and presence of salt stress yielded several differentially expressed genes, which were associated with salt stress, plant hormone metabolism and signaling pathways, such as B-BOX ZINC FINGER 6, O. sativa bZIP PROTEIN 8 and GIBBERELLIN (GA) 20-oxidase 1. In addition, the sensitivity of OsMFT1OE seeds to GA and osmft1 seeds to abscisic acid (ABA) during seed germination increased under salt stress. Overall, our results indicate that ABA and GA metabolism and their signaling pathways are regulated by OsMFT1, modulating seed germination in rice under salt stress.
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Affiliation(s)
- Kunxun Lu
- College of Agriculture, Nanjing Agricultural University, No.1 Weigang, Nanjing 210095, China
| | - Ziyu Guo
- College of Agriculture, Nanjing Agricultural University, No.1 Weigang, Nanjing 210095, China
| | - Shiyu Di
- College of Agriculture, Nanjing Agricultural University, No.1 Weigang, Nanjing 210095, China
| | - Yuyang Lu
- College of Agriculture, Nanjing Agricultural University, No.1 Weigang, Nanjing 210095, China
| | | | - Chenyu Rong
- College of Agriculture, Nanjing Agricultural University, No.1 Weigang, Nanjing 210095, China
| | - Yanfeng Ding
- College of Agriculture, Nanjing Agricultural University, No.1 Weigang, Nanjing 210095, China
- Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, No.1 Weigang, Nanjing 210095, China
- Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry, Nanjing Agricultural University, No.1 Weigang, Nanjing 210095, China
| | - Weiqiang Li
- Jilin Da'an Agro-ecosystem National Observation Research Station, Changchun Jingyuetan Remote Sensing Experiment Station, Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, No.4888 Shengbei Street, Changchun 130102, China
| | - Chengqiang Ding
- College of Agriculture, Nanjing Agricultural University, No.1 Weigang, Nanjing 210095, China
- Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, No.1 Weigang, Nanjing 210095, China
- Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry, Nanjing Agricultural University, No.1 Weigang, Nanjing 210095, China
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18
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Li X, Dong J, Zhu W, Zhao J, Zhou L. Progress in the study of functional genes related to direct seeding of rice. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:46. [PMID: 37309311 PMCID: PMC10248684 DOI: 10.1007/s11032-023-01388-y] [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: 09/22/2022] [Accepted: 04/20/2023] [Indexed: 06/14/2023]
Abstract
Rice is a major food crop in the world. Owing to the shortage of rural labor and the development of agricultural mechanization, direct seeding has become the main method of rice cultivation. At present, the main problems faced by direct seeding of rice are low whole seedling rate, serious weeds, and easy lodging of rice in the middle and late stages of growth. Along with the rapid development of functional genomics, the functions of a large number of genes have been confirmed, including seed vigor, low-temperature tolerance germination, low oxygen tolerance growth, early seedling vigor, early root vigor, resistance to lodging, and other functional genes related to the direct seeding of rice. A review of the related functional genes has not yet been reported. In this study, the genes related to direct seeding of rice are summarized to comprehensively understand the genetic basis and mechanism of action in direct seeding of rice and to lay the foundation for further basic theoretical research and breeding application research in direct seeding of rice.
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Affiliation(s)
- Xuezhong Li
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225 Guangdong China
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory, Guangzhou, 510640 China
| | - Jingfang Dong
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory, Guangzhou, 510640 China
| | - Wen Zhu
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225 Guangdong China
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory, Guangzhou, 510640 China
| | - Junliang Zhao
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory, Guangzhou, 510640 China
| | - Lingyan Zhou
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225 Guangdong China
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19
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Gajardo HA, Gómez-Espinoza O, Boscariol Ferreira P, Carrer H, Bravo LA. The Potential of CRISPR/Cas Technology to Enhance Crop Performance on Adverse Soil Conditions. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091892. [PMID: 37176948 PMCID: PMC10181257 DOI: 10.3390/plants12091892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/22/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023]
Abstract
Worldwide food security is under threat in the actual scenery of global climate change because the major staple food crops are not adapted to hostile climatic and soil conditions. Significant efforts have been performed to maintain the actual yield of crops, using traditional breeding and innovative molecular techniques to assist them. However, additional strategies are necessary to achieve the future food demand. Clustered regularly interspaced short palindromic repeat/CRISPR-associated protein (CRISPR/Cas) technology, as well as its variants, have emerged as alternatives to transgenic plant breeding. This novelty has helped to accelerate the necessary modifications in major crops to confront the impact of abiotic stress on agriculture systems. This review summarizes the current advances in CRISPR/Cas applications in crops to deal with the main hostile soil conditions, such as drought, flooding and waterlogging, salinity, heavy metals, and nutrient deficiencies. In addition, the potential of extremophytes as a reservoir of new molecular mechanisms for abiotic stress tolerance, as well as their orthologue identification and edition in crops, is shown. Moreover, the future challenges and prospects related to CRISPR/Cas technology issues, legal regulations, and customer acceptance will be discussed.
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Affiliation(s)
- Humberto A Gajardo
- Laboratorio de Fisiología y Biología Molecular Vegetal, Instituto de Agroindustria, Departamento de Ciencias Agronómicas y Recursos Naturales, Facultad de Ciencias Agropecuarias y Medioambiente & Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 1145, Chile
| | - Olman Gómez-Espinoza
- Laboratorio de Fisiología y Biología Molecular Vegetal, Instituto de Agroindustria, Departamento de Ciencias Agronómicas y Recursos Naturales, Facultad de Ciencias Agropecuarias y Medioambiente & Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 1145, Chile
- Centro de Investigación en Biotecnología, Escuela de Biología, Instituto Tecnológico de Costa Rica, Cartago 30101, Costa Rica
| | - Pedro Boscariol Ferreira
- Department of Biological Sciences, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Piracicaba 13418-900, Brazil
| | - Helaine Carrer
- Department of Biological Sciences, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Piracicaba 13418-900, Brazil
| | - León A Bravo
- Laboratorio de Fisiología y Biología Molecular Vegetal, Instituto de Agroindustria, Departamento de Ciencias Agronómicas y Recursos Naturales, Facultad de Ciencias Agropecuarias y Medioambiente & Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 1145, Chile
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20
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He Y, Sun S, Zhao J, Huang Z, Peng L, Huang C, Tang Z, Huang Q, Wang Z. UDP-glucosyltransferase OsUGT75A promotes submergence tolerance during rice seed germination. Nat Commun 2023; 14:2296. [PMID: 37085517 PMCID: PMC10121563 DOI: 10.1038/s41467-023-38085-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 04/14/2023] [Indexed: 04/23/2023] Open
Abstract
Submergence stress represents a major obstacle limiting the application of direct seeding in rice cultivation. Under flooding conditions, coleoptile elongation can function as an escape strategy that contributes to submergence tolerance during seed germination in rice; however, the underlying molecular bases have yet to be fully determined. Herein, we report that natural variation of rice coleoptile length subjected to submergence is determined by the glucosyltransferase encoding gene OsUGT75A. OsUGT75A regulates coleoptile length via decreasing free abscisic acid (ABA) and jasmonic acid (JA) levels by promoting glycosylation of these two phytohormones under submergence. Moreover, we find that OsUGT75A accelerates coleoptile length through mediating the interactions between JASMONATE ZIMDOMAIN (OsJAZ) and ABSCISIC ACID-INSENSITIVE (OsABI) proteins. Last, we reveal the origin of the haplotype that contributes to coleoptile length in response to submergence and transferring this haplotype to indica rice can enhance coleoptile length in submergence conditions. Thus, we propose that OsUGT75A is a useful target in breeding of rice varieties suitable for direct seeding cultivation.
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Affiliation(s)
- Yongqi He
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, 510642, Guangzhou, China
| | - Shan Sun
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, 510642, Guangzhou, China
| | - Jia Zhao
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, 510642, Guangzhou, China
| | - Zhibo Huang
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, 510642, Guangzhou, China
| | - Liling Peng
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, 510642, Guangzhou, China
| | - Chengwei Huang
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, 510642, Guangzhou, China
| | - Zhengbin Tang
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, 510642, Guangzhou, China
| | - Qianqian Huang
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, 510642, Guangzhou, China
| | - Zhoufei Wang
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, 510642, Guangzhou, China.
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21
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Dalle Carbonare L, Jiménez JDLC, Lichtenauer S, van Veen H. Plant responses to limited aeration: Advances and future challenges. PLANT DIRECT 2023; 7:e488. [PMID: 36993903 PMCID: PMC10040318 DOI: 10.1002/pld3.488] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 06/19/2023]
Abstract
Limited aeration that is caused by tissue geometry, diffusion barriers, high elevation, or a flooding event poses major challenges to plants and is often, but not exclusively, associated with low oxygen. These processes span a broad interest in the research community ranging from whole plant and crop responses, post-harvest physiology, plant morphology and anatomy, fermentative metabolism, plant developmental processes, oxygen sensing by ERF-VIIs, gene expression profiles, the gaseous hormone ethylene, and O2 dynamics at cellular resolution. The International Society for Plant Anaerobiosis (ISPA) gathers researchers from all over the world contributing to understand the causes, responses, and consequences of limited aeration in plants. During the 14th ISPA meeting, major research progress was related to the evolution of O2 sensing mechanisms and the intricate network that balances low O2 signaling. Here, the work moved beyond flooding stress and emphasized novel underexplored roles of low O2 and limited aeration in altitude adaptation, fruit development and storage, and the vegetative development of growth apices. Regarding tolerance towards flooding, the meeting stressed the relevance and regulation of developmental plasticity, aerenchyma, and barrier formation to improve internal aeration. Additional newly explored flood tolerance traits concerned resource balance, senescence, and the exploration of natural genetic variation for novel tolerance loci. In this report, we summarize and synthesize the major progress and future challenges for low O2 and aeration research presented at the conference.
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Affiliation(s)
| | | | - Sophie Lichtenauer
- Institute of Plant Biology and BiotechnologyUniversity of MünsterMünsterGermany
| | - Hans van Veen
- Plant Stress Resilience, Institute of Environmental BiologyUtrecht UniversityUtrechtThe Netherlands
- Groningen Institute for Evolutionary Life SciencesUniversity of GroningenGroningenThe Netherlands
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22
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Wang W, Huang R, Wu G, Sun J, Zhu Y, Wang H. Transcriptomic and QTL Analysis of Seed Germination Vigor under Low Temperature in Weedy Rice WR04-6. PLANTS (BASEL, SWITZERLAND) 2023; 12:871. [PMID: 36840221 PMCID: PMC9961040 DOI: 10.3390/plants12040871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/10/2023] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
Low temperature is one of the major factors affecting rice germination, and low temperature germination (LTG) is an important agronomic trait. Although significant progress has been made in the study of rice LTG, the molecular mechanism of LTG remains poorly understood. To explore more rice LTG gene resources, we first demonstrated that weedy rice WR04-6 (Oryza sativa f. spontanea) had significantly higher LTG ability at 10 °C than the cultivated rice Qishanzhan (QSZ Oryza sativa L. ssp. indica). RNA-seq was used to investigate the gene expression of WR04-6 and QSZ at 10 °C for 10, 12 and 14 days after imbibition (DAI) of seed germination. The results of Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment revealed that the differentially expressed genes (DEGs) between WR04-6 and QSZ were mainly concentrated on the response to starch catabolic processes and the response to abscisic acid (ABA). This is consistent with the results of α-amylase activity, ABA and gibberellins (GA) treatment. A recombinant inbred line (RIL) population derived from a cross between WR04-6 and QSZ and its high-density SNP genetic map were used to detect quantitative trait loci (QTL) for LTG rates. The results showed that two new QTLs were located on chromosome 3 and chromosome 12. Combined with the mapped QTLs and RNA-seq DEGs, sixteen candidate genes potentially associated with LTG were identified. Validation of the expression of the candidates by qRT-PCR were consistent with the RNA-seq data. These results will enable us to understand the genetic basis of LTG in weedy rice and provide new genetic resources for the generation of rice germplasm with improved LTG.
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Affiliation(s)
- Wenjia Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Ruizhi Huang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Gengwei Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jian Sun
- Rice Research Institute, Shenyang Agricultural University, Shenyang 110866, China
| | - Ying Zhu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Hua Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
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23
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Liang W, Du H, Pang B, Cheng J, He B, Hu F, Lv Y, Zhang Y. High-density genetic mapping identified QTLs for anaerobic germination tolerance in rice. FRONTIERS IN PLANT SCIENCE 2022; 13:1076600. [PMID: 36618635 PMCID: PMC9822775 DOI: 10.3389/fpls.2022.1076600] [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: 10/21/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
The tolerance of rice anaerobic germination (AG) is the main limiting factor for direct seeding application, yet the genetics mechanism is still in its infancy. In the study, recombinant inbred lines population of TD70 Japonica cultivar and Kasalath Indica cultivar, was employed to construct a high-density genetic map by whole genome re-sequencing. As a result, a genetic map containing 12,328 bin-markers was constructed and a total of 50 QTLs were then detected for CL(coleoptile length), CD (coleoptile diameter), CSA (coleoptile surface area) and CV (coleoptile volume) related traits in the two stages of anaerobic treatment using complete interval mapping method (inclusive composite interval mapping, ICIM). Among the four traits associated with coleoptile, coleoptile volume had the largest number of QTLs (17), followed by coleoptile diameter (16), and coleoptile length had 5 QTLs. These QTLs could explain phenotypic contribution rates ranging from 0.34% to 11.17% and LOD values ranging from 2.52 to 11.57. Combined with transcriptome analysis, 31 candidate genes were identified. Furthermore, 12 stable QTLs were used to detect the aggregation effect analysis. Besides, It was found that individuals with more aggregation synergistic alleles had higher phenotypic values in different environments. Totally, high-density genetic map, QTL mapping and aggregation effect analysis of different loci related to the anaerobic germination of rice seeds were conducted to lay a foundation for the fine mapping of related genes in subsequent assisted breeding.
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Affiliation(s)
- Wenhua Liang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Hongyang Du
- Excellence and Innovation Center, Jiangsu Academy of Agricultural, Sciences, Nanjing, China
- Key Laboratory of Rice Genetic Breeding of Anhui Province, Rice Research Institute, Anhui Academy of Agricultural Science, Hefei, China
| | - Bingwen Pang
- Excellence and Innovation Center, Jiangsu Academy of Agricultural, Sciences, Nanjing, China
| | - Junjie Cheng
- Excellence and Innovation Center, Jiangsu Academy of Agricultural, Sciences, Nanjing, China
| | - Bing He
- Excellence and Innovation Center, Jiangsu Academy of Agricultural, Sciences, Nanjing, China
| | - Fengqin Hu
- Excellence and Innovation Center, Jiangsu Academy of Agricultural, Sciences, Nanjing, China
| | - Yuanda Lv
- Excellence and Innovation Center, Jiangsu Academy of Agricultural, Sciences, Nanjing, China
| | - Yadong Zhang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
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24
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Li Z, Gui R, Yu X, Liang C, Cui J, Zhao X, Zhang X, Yu P, Chen W, Sun J. Genetic basis of the early heading of high-latitude weedy rice. FRONTIERS IN PLANT SCIENCE 2022; 13:1059197. [PMID: 36544870 PMCID: PMC9760980 DOI: 10.3389/fpls.2022.1059197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 11/11/2022] [Indexed: 06/17/2023]
Abstract
Japonica rice (Oryza sativa L.) is an important staple food in high-latitude regions and is widely distributed in northern China, Japan, Korea, and Europe. However, the genetic diversity of japonica rice is relatively narrow and poorly adapted. Weedy rice (Oryza sativa f. spontanea) is a semi-domesticated rice. Its headings are earlier than the accompanied japonica rice, making it a potential new genetic resource, which can make up for the defects of wild rice that are difficult to be directly applied to japonica rice improvement caused by reproductive isolation. In this study, we applied a natural population consisting of weedy rice, japonica landrace, and japonica cultivar to conduct a genome-wide association study (GWAS) of the heading date and found four loci that could explain the natural variation of the heading date in this population. At the same time, we developed recombinant inbred lines (RILs) crossed by the early-heading weedy rice WR04-6 and its accompanied japonica cultivar ShenNong 265 (SN265) to carry out a QTL mapping analysis of the heading date and mapped four quantitative trait locus (QTLs) and three epistatic effect gene pairs. The major locus on chromosome 6 overlapped with the GWAS result. Further analysis found that two genes, Hd1 and OsCCT22, on chromosome 6 (Locus 2 and Locus 3) may be the key points of the early-heading character of weedy rice. As minor effect genes, Dth7 and Hd16 also have genetic contributions to the early heading of weedy rice. In the process of developing the RIL population, we introduced fragments of Locus 2 and Locus 3 from the weedy rice into super-high-yielding japonica rice, which successfully promoted its heading date by at least 10 days and expanded the rice suitable cultivation area northward by about 400 km. This study successfully revealed the genetic basis of the early heading of weedy rice and provided a new idea for the genetic improvement of cultivated rice by weedy rice.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Wenfu Chen
- *Correspondence: Wenfu Chen, ; Jian Sun,
| | - Jian Sun
- *Correspondence: Wenfu Chen, ; Jian Sun,
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25
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Two bHLH transcription factors affect sprouting by regulating the level of ABA. Nat Genet 2022; 54:1772-1773. [PMID: 36471072 DOI: 10.1038/s41588-022-01238-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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26
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Zhang G, Xu J, Wang Y, Sun X, Huang S, Huang L, Liu Y, Liu H, Sun J. Combined transcriptome and metabolome analyses reveal the mechanisms of ultrasonication improvement of brown rice germination. ULTRASONICS SONOCHEMISTRY 2022; 91:106239. [PMID: 36435087 PMCID: PMC9694063 DOI: 10.1016/j.ultsonch.2022.106239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/12/2022] [Accepted: 11/22/2022] [Indexed: 06/16/2023]
Abstract
This study investigated the effects of ultrasonication treatment on the germination rate of brown rice. Brown rice grains were subjected to ultrasound (40 kHz/30 min) and then incubated for 36 h at 37 °C to germinate the seeds. Ultrasonic treatment increased the germination rate of brown rice by up to ∼28 % at 30 h. Transcriptomic and metabolomic analyses were performed to explore the mechanisms underlying the effect of ultrasonic treatment on the brown rice germination rate. Comparing the treated and control check samples, 867 differentially expressed genes (DEGs) were identified, including 638 upregulated and 229 downregulated), as well as 498 differentially accumulated metabolites (DAMs), including 422 up accumulated and 76 down accumulated. Multi-omics analysis revealed that the germination rate of brown rice was promoted by increased concentrations of low-molecular metabolites (carbohydrates and carbohydrate conjugates, fatty acids, amino acids, peptides, and analogues), and transcription factors (ARR-B, NAC, bHLH and AP2/EREBP families) as well as increased carbon metabolism. These findings provide new insights into the mechanisms of action of ultrasound in improving the brown rice germination rate and candidate DEGs and DAMs responsible for germination have been identified.
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Affiliation(s)
- Guangchen Zhang
- College of Food Science and Technology, Bohai University, Jinzhou, Liaoning, China
| | - Jiaxin Xu
- College of Food Science and Technology, Bohai University, Jinzhou, Liaoning, China
| | - Yiqiao Wang
- Rice Research Institute, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Xue Sun
- College of Food Science and Technology, Bohai University, Jinzhou, Liaoning, China
| | - Shaosong Huang
- Rice Research Institute, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Lihua Huang
- College of Food Science and Technology, Bohai University, Jinzhou, Liaoning, China
| | - Youhong Liu
- Institute of Crop Cultivation and Tillage, Heilongjiang Academy of Agricultural Sciences/Northeast Branch of National Center of Technology Innovation for Saline-Alkali Tolerant Rice, Harbin, China
| | - He Liu
- College of Food Science and Technology, Bohai University, Jinzhou, Liaoning, China.
| | - Jian Sun
- Rice Research Institute, Shenyang Agricultural University, Shenyang, Liaoning, China; Collaborative Innovation Center for Genetic Improvement and High Quality and Efficiency Production of Northeast Japonica Rice in China, Shenyang Agricultural University, Shenyang, Liaoning, China.
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