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Lu Z, Huang W, Zhu L, Liang G, Huang Y, Wu J, Chen R, Li X, Liu X. Cytological Observation and RNA-Seq Analyses Reveal miR9564 and Its Target Associated with Pollen Sterility in Autotetraploid Rice. PLANTS (BASEL, SWITZERLAND) 2024; 13:1461. [PMID: 38891270 PMCID: PMC11175005 DOI: 10.3390/plants13111461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 05/18/2024] [Accepted: 05/22/2024] [Indexed: 06/21/2024]
Abstract
Understanding the regulation of autotetraploid sterility is essential for harnessing the strong advantages in genomic buffer capacity, biodiversity, and heterosis of autotetraploid rice. miRNAs play crucial roles in fertility regulation, yet information about their reproductive roles and target genes in tetraploid rice remains limited. Here, we used three tetraploid lines, H1 (fertile), HF (fertile), and LF (sterile), to investigate cytological features and identify factors associated with autotetraploid sterility. LF showed abnormal meiosis, resulting in low pollen fertility and viability, ultimately leading to scarce fertilization and a low-seed setting compared to H1 and HF. RNA-seq revealed 30 miRNA-candidate target pairs related to autotetraploid pollen sterility. These pairs showed opposite expression patterns, with differential expression between fertile lines (H1 and HF) and the sterile line (LF). qRT-PCR confirmed that miR9564, miR528, and miR27874 were highly expressed in the anthers of H1 and HF but not in LF, while opposite results were obtained in their targets (ARPS, M2T, and OsRPC53). Haplotype and expression pattern analyses revealed that ARPS was specifically expressed in lines with the same haplotype of MIR9564 (the precursor of miR9564) as LF. Furthermore, the Dual-GFP assay verified that miR9564 inhibited the fluorescence signal of ARPS-GFP. The over-expression of ARPS significantly decreased the seed setting rate (59.10%) and pollen fertility (50.44%) of neo-tetraploid rice, suggesting that ARPS plays important roles in autotetraploid pollen sterility. This study provides insights into the cytological characteristic and miRNA expression profiles of tetraploid lines with different fertility, shedding light on the role of miRNAs in polyploid rice.
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Affiliation(s)
- Zijun Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China; (Z.L.); (W.H.); (L.Z.); (G.L.); (Y.H.); (J.W.); (R.C.)
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Shaoguan University, Shaoguan 512005, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- Guangdong Base Bank for Lingnan Rice Germplasm Resources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Weicong Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China; (Z.L.); (W.H.); (L.Z.); (G.L.); (Y.H.); (J.W.); (R.C.)
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- Guangdong Base Bank for Lingnan Rice Germplasm Resources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Lianjun Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China; (Z.L.); (W.H.); (L.Z.); (G.L.); (Y.H.); (J.W.); (R.C.)
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- Guangdong Base Bank for Lingnan Rice Germplasm Resources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Guobin Liang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China; (Z.L.); (W.H.); (L.Z.); (G.L.); (Y.H.); (J.W.); (R.C.)
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- Guangdong Base Bank for Lingnan Rice Germplasm Resources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Yu Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China; (Z.L.); (W.H.); (L.Z.); (G.L.); (Y.H.); (J.W.); (R.C.)
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- Guangdong Base Bank for Lingnan Rice Germplasm Resources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Jinwen Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China; (Z.L.); (W.H.); (L.Z.); (G.L.); (Y.H.); (J.W.); (R.C.)
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- Guangdong Base Bank for Lingnan Rice Germplasm Resources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Rou Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China; (Z.L.); (W.H.); (L.Z.); (G.L.); (Y.H.); (J.W.); (R.C.)
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- Guangdong Base Bank for Lingnan Rice Germplasm Resources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Xiang Li
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Shaoguan University, Shaoguan 512005, China
| | - Xiangdong Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China; (Z.L.); (W.H.); (L.Z.); (G.L.); (Y.H.); (J.W.); (R.C.)
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- Guangdong Base Bank for Lingnan Rice Germplasm Resources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
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Shao M, Feng Y, Yang S, Feng T, Zeng F, Lu S, Ma Z, Chen B, Mao J. Molecular evolution of Phytocyanin gene and analysis of expression at different coloring periods in apple (Malus domestica). BMC PLANT BIOLOGY 2024; 24:374. [PMID: 38714922 PMCID: PMC11077699 DOI: 10.1186/s12870-024-05069-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 04/26/2024] [Indexed: 05/12/2024]
Abstract
BACKGROUND PC (phytocyanin) is a class of copper-containing electron transfer proteins closely related to plant photosynthesis, abiotic stress responses growth and development in plants, and regulation of the expression of some flavonoids and phenylpropanoids, etc., however, compared with other plants, the PC gene family has not been systematically characterized in apple. RESULTS A total of 59 MdPC gene members unevenly distributed across 12 chromosomes were identified at the genome-wide level. The proteins of the MdPC family were classified into four subfamilies based on differences in copper binding sites and glycosylation sites: Apple Early nodulin-like proteins (MdENODLs), Apple Uclacyanin-like proteins (MdUCLs), Apple Stellacyanin-like proteins (MdSCLs), and Apple Plantacyanin-like proteins (MdPLCLs). Some MdPC members with similar gene structures and conserved motifs belong to the same group or subfamily. The internal collinearity analysis revealed 14 collinearity gene pairs among members of the apple MdPC gene. Interspecific collinearity analysis showed that apple had 31 and 35 homologous gene pairs with strawberry and grape, respectively. Selection pressure analysis indicated that the MdPC gene was under purifying selection. Prediction of protein interactions showed that MdPC family members interacted strongly with the Nad3 protein. GO annotation results indicated that the MdPC gene also regulated the biosynthesis of phenylpropanoids. Chip data analysis showed that (MdSCL3, MdSCL7 and MdENODL27) were highly expressed in mature fruits and peels. Many cis-regulatory elements related to light response, phytohormones, abiotic stresses and flavonoid biosynthetic genes regulation were identified 2000 bp upstream of the promoter of the MdPC gene, and qRT-PCR results showed that gene members in Group IV (MdSCL1/3, MdENODL27) were up-regulated at all five stages of apple coloring, but the highest expression was observed at the DAF13 (day after fruit bag removal) stage. The gene members in Group II (MdUCL9, MdPLCL3) showed down-regulated or lower expression in the first four stages of apple coloring but up-regulated and highest expression in the DAF 21 stage. CONCLUSION Herein, one objective of these findings is to provide valuable information for understanding the structure, molecular evolution, and expression pattern of the MdPC gene, another major objective in this study was designed to lay the groundwork for further research on the molecular mechanism of PC gene regulation of apple fruit coloration.
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Affiliation(s)
- Miao Shao
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, PR China
| | - Yongqing Feng
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, PR China
| | - Shangwen Yang
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, PR China
| | - Tong Feng
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, PR China
| | - Fanwei Zeng
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, PR China
| | - Shixiong Lu
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, PR China
| | - Zonghuan Ma
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, PR China
| | - Baihong Chen
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, PR China
| | - Juan Mao
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, PR China.
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Shi D, Huang H, Zhang Y, Qian Z, Du J, Huang L, Yan X, Lin S. The roles of non-coding RNAs in male reproductive development and abiotic stress responses during this unique process in flowering plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 341:111995. [PMID: 38266717 DOI: 10.1016/j.plantsci.2024.111995] [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: 09/10/2023] [Revised: 01/16/2024] [Accepted: 01/19/2024] [Indexed: 01/26/2024]
Abstract
Successful male reproductive development is the guarantee for sexual reproduction of flowering plants. Male reproductive development is a complicated and multi-stage process that integrates physiological processes and adaptation and tolerance to a myriad of environmental stresses. This well-coordinated process is governed by genetic and epigenetic machineries. Non-coding RNAs (ncRNAs) play pleiotropic roles in the plant growth and development. The identification, characterization and functional analysis of ncRNAs and their target genes have opened a new avenue for comprehensively revealing the regulatory network of male reproductive development and its response to environmental stresses in plants. This review briefly addresses the types, origin, biogenesis and mechanisms of ncRNAs in plants, highlights important updates on the roles of ncRNAs in regulating male reproductive development and emphasizes the contribution of ncRNAs, especially miRNAs and lncRNAs, in responses to abiotic stresses during this unique process in flowering plants.
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Affiliation(s)
- Dexi Shi
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China
| | - Huiting Huang
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China
| | - Yuting Zhang
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China
| | - Zhihao Qian
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China
| | - Jiao Du
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China
| | - Li Huang
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Xiufeng Yan
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China; Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, Wenzhou University, Wenzhou 325035, China.
| | - Sue Lin
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China; Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, Wenzhou University, Wenzhou 325035, China.
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Cao W, Yang L, Zhuang M, Lv H, Wang Y, Zhang Y, Ji J. Plant non-coding RNAs: The new frontier for the regulation of plant development and adaptation to stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 208:108435. [PMID: 38402798 DOI: 10.1016/j.plaphy.2024.108435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 02/07/2024] [Accepted: 02/11/2024] [Indexed: 02/27/2024]
Abstract
Most plant transcriptomes constitute functional non-coding RNAs (ncRNAs) that lack the ability to encode proteins. In recent years, more research has demonstrated that ncRNAs play important regulatory roles in almost all plant biological processes by modulating gene expression. Thus, it is important to study the biogenesis and function of ncRNAs, particularly in plant growth and development and stress tolerance. In this review, we systematically explore the process of formation and regulatory mechanisms of ncRNAs, particularly those of microRNAs (miRNAs), small interfering RNAs (siRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs). Additionally, we provide a comprehensive overview of the recent advancements in ncRNAs research, including their regulation of plant growth and development (seed germination, root growth, leaf morphogenesis, floral development, and fruit and seed development) and responses to abiotic and biotic stress (drought, heat, cold, salinity, pathogens and insects). We also discuss research challenges and provide recommendations to advance the understanding of the roles of ncRNAs in agronomic applications.
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Affiliation(s)
- Wenxue Cao
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs/Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No. 12 ZhongGuanCun South St., Beijing 100081, China
| | - Limei Yang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs/Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No. 12 ZhongGuanCun South St., Beijing 100081, China
| | - Mu Zhuang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs/Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No. 12 ZhongGuanCun South St., Beijing 100081, China
| | - Honghao Lv
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs/Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No. 12 ZhongGuanCun South St., Beijing 100081, China
| | - Yong Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs/Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No. 12 ZhongGuanCun South St., Beijing 100081, China
| | - Yangyong Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs/Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No. 12 ZhongGuanCun South St., Beijing 100081, China.
| | - Jialei Ji
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs/Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No. 12 ZhongGuanCun South St., Beijing 100081, China.
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5
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Han X, Tang S, Ma X, Liu W, Yang R, Zhang S, Wang N, Song X, Fu C, Yang R, Cao X. Blocking miR528 function promotes tillering and regrowth in switchgrass. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:712-721. [PMID: 37929781 PMCID: PMC10893936 DOI: 10.1111/pbi.14218] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 09/28/2023] [Accepted: 10/17/2023] [Indexed: 11/07/2023]
Abstract
MiRNAs have been reported to be the key regulators involving a wide range of biological processes in diverse plant species, but their functions in switchgrass, an important biofuel and forage crop, are largely unknown. Here, we reported the novel function of miR528, which has expanded to four copies in switchgrass, in controlling biomass trait of tillering number and regrowth rate after mowing. Blocking miR528 activity by expressing short tandem target mimic (STTM) increased tiller number and regrowth rate after mowing. The quadruple pvmir528 mutant lines derived from genome editing also showed such improved traits. Degradome and RNA-seq analysis, combined with in situ hybridization assay revealed that up-regulation of two miR528 targets coding for Cu/Zn-SOD enzymes, might be responsible for the improved traits of tillering and regrowth in pvmir528 mutant. Additionally, natural variations in the miR528-SOD interaction exist in C3 and C4 monocot species, implying the distinct regulatory strength of the miR528-SOD module during monocot evolution. Overall, our data illuminated a novel role of miR528 in controlling biomass traits and provided a new target for genetic manipulation-mediated crop improvement.
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Affiliation(s)
- Xiangyan Han
- Department of Plant Biology and Ecology, Tianjin Key Laboratory of Protein Sciences, College of Life SciencesNankai UniversityTianjinChina
- Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Shanjie Tang
- Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
- College of Life SciencesUniversity of the Chinese Academy of SciencesBeijingChina
| | - Xuan Ma
- College of Life Sciences, Tianjin Key Laboratory of Animal and Plant ResistanceTianjin Normal UniversityTianjinChina
| | - Wenwen Liu
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdaoChina
- Shandong Energy InstituteQingdaoChina
- Qingdao New Energy Shandong LaboratoryQingdaoChina
| | - Ruijuan Yang
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdaoChina
- Shandong Energy InstituteQingdaoChina
- Qingdao New Energy Shandong LaboratoryQingdaoChina
| | - Shuaibin Zhang
- Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Ningning Wang
- Department of Plant Biology and Ecology, Tianjin Key Laboratory of Protein Sciences, College of Life SciencesNankai UniversityTianjinChina
| | - Xianwei Song
- Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Chunxiang Fu
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdaoChina
- Shandong Energy InstituteQingdaoChina
- Qingdao New Energy Shandong LaboratoryQingdaoChina
| | - Rongxin Yang
- Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life ScienceNanchang UniversityJiangxiChina
| | - Xiaofeng Cao
- Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
- College of Life SciencesUniversity of the Chinese Academy of SciencesBeijingChina
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Li Y, Zhang X, Ye J, Xu F, Zhang W, Liao Y, Yang X. The long noncoding RNAs lnc10 and lnc11 regulating flavonoid biosynthesis in Ginkgo biloba. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 339:111948. [PMID: 38097046 DOI: 10.1016/j.plantsci.2023.111948] [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: 09/01/2023] [Revised: 10/27/2023] [Accepted: 12/04/2023] [Indexed: 12/22/2023]
Abstract
Although long non-coding RNAs have been recognized to play important roles in plant, their possible functions and potential mechanism in Ginkgo biloba flavonoid biosynthesis are poorly understood. Flavonoids are important secondary metabolites and healthy components of Ginkgo biloba. They have been widely used in food, medicine, and natural health products. Most previous studies have focused on the molecular mechanisms of structural genes and transcription factors that regulate flavonoid biosynthesis. Few reports have examined the biological functions of flavonoid biosynthesis by long non-coding RNAs in G. biloba. Long noncoding RNAs associated with flavonoid biosynthesis in G. biloba have been identified through RNA sequencing, but the function of lncRNAs has not been reported. In this study, the expression levels of lnc10 and lnc11 were identified. Quantitative real-time polymerase chain reaction analysis revealed that lnc10 and lnc11 were expressed in all detected organs, and they showed significantly higher levels in immature and mature leaves than in other organs. In addition, to fully identify the function of lnc10 and lnc11 in flavonoid biosynthesis in G. biloba, lnc10 and lnc11 were cloned from G. biloba, and were transformed into Arabidopsis and overexpressed. Compared with the wild type, the flavonoid content was increased in transgenic plants. Moreover, the RNA-sequencing analysis of wild-type, lnc10-overexpression, and lnc11-overexpression plants screened out 2019 and 2552 differentially expressed genes, and the transcript levels of structural genes and transcription factors associated with flavonoid biosynthesis were higher in transgenic Arabidopsis than in the wild type, indicating that lnc10 and lnc11 activated flavonoid biosynthesis in the transgenic lines. Overall, these results suggest that lnc10 and lnc11 positively regulate flavonoid biosynthesis in G. biloba.
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Affiliation(s)
- Yuting Li
- College of Horticulture and Gardening, Yangtze University, Jingzhou 434025, Hubei, China
| | - Xiaoxi Zhang
- College of Horticulture and Gardening, Yangtze University, Jingzhou 434025, Hubei, China
| | - Jiabao Ye
- College of Horticulture and Gardening, Yangtze University, Jingzhou 434025, Hubei, China.
| | - Feng Xu
- College of Horticulture and Gardening, Yangtze University, Jingzhou 434025, Hubei, China.
| | - Weiwei Zhang
- College of Horticulture and Gardening, Yangtze University, Jingzhou 434025, Hubei, China
| | - Yongling Liao
- College of Horticulture and Gardening, Yangtze University, Jingzhou 434025, Hubei, China
| | - Xiaoyan Yang
- College of Horticulture and Gardening, Yangtze University, Jingzhou 434025, Hubei, China
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Zhang Z, Sun M, Xiong T, Ye F, Zhao Z. Development and genetic regulation of pollen intine in Arabidopsis and rice. Gene 2024; 893:147936. [PMID: 38381507 DOI: 10.1016/j.gene.2023.147936] [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: 06/09/2023] [Revised: 10/03/2023] [Accepted: 10/26/2023] [Indexed: 02/22/2024]
Abstract
Pollen intine serves as a protective layer situated between the pollen exine and the plasma membrane. It performs essential functions during pollen development, including maintaining the morphological structure of the pollen, preventing the loss of pollen contents, and facilitating pollen germination. The formation of the intine layer commences at the bicellular pollen stage. Pectin, cellulose, hemicellulose and structural proteins are the key constituents of the pollen intine. In Arabidopsis and rice, numerous regulatory factors associated with polysaccharide metabolism and material transport have been identified, which regulate intine development. In this review, we elucidate the developmental processes of the pollen wall and provide a concise summary of the research advancements in the development and genetic regulation of the pollen intine in Arabidopsis and rice. A comprehensive understanding of intine development and regulation is crucial for unraveling the genetic network underlying intine development in higher plants.
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Affiliation(s)
- Zaibao Zhang
- School of Life and Health Science, Huzhou College, Huzhou, Zhejiang, China.
| | - Mengke Sun
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China
| | - Tao Xiong
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China
| | - Fan Ye
- College of International Education, Xinyang Normal University, Xinyang, Henan, China
| | - Ziwei Zhao
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China
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Guo S, Zheng C, Wang Y, Xu Y, Wu J, Wang L, Liu X, Chen Z. OsmiRNA5488 Regulates the Development of Embryo Sacs and Targets OsARF25 in Rice ( Oryza sativa L.). Int J Mol Sci 2023; 24:16240. [PMID: 38003430 PMCID: PMC10671434 DOI: 10.3390/ijms242216240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 11/02/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
Small RNAs are a class of non-coding RNAs that typically range from 20 to 24 nucleotides in length. Among them, microRNAs (miRNAs) are particularly important regulators for plant development. The biological function of the conserved miRNAs has been studied extensively in plants, while that of the species-specific miRNAs has been studied in-depth. In this study, the regulatory role of a rice-specific OsmiRNA5488 (OsmiR5488) was characterized with the miR5488-overexpressed line (miR5488-OE) and miR5488-silenced line (STTM-5488). The seed-setting rate was notably reduced in miR5488-OE lines, but not in STTM-5488 lines. Cytological observation demonstrated the different types of abnormal mature embryo sacs, including the degeneration of embryo sacs and other variant types, in miR5488-OE lines. The percentage of the abnormal mature embryo sacs accounted for the reduced value of the seed-setting rate. Furthermore, OsARF25 was identified as a target of OsmiR5488 via RNA ligase-mediated 3'-amplifification of cDNA ends, dual luciferase assays, and transient expression assays. The primary root length was decreased with the increases in auxin concentrations in miR5488-OE lines compared to wild-type rice. Summarily, our results suggested that OsmiR5488 regulates the seed-setting rate and down-regulates the targeted gene OsARF25.
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Affiliation(s)
- Shengyuan Guo
- Department of Plant Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; (S.G.); (C.Z.); (Y.W.); (Y.X.); (J.W.); (L.W.)
| | - Chuanjiang Zheng
- Department of Plant Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; (S.G.); (C.Z.); (Y.W.); (Y.X.); (J.W.); (L.W.)
| | - Yan Wang
- Department of Plant Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; (S.G.); (C.Z.); (Y.W.); (Y.X.); (J.W.); (L.W.)
| | - Yangwen Xu
- Department of Plant Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; (S.G.); (C.Z.); (Y.W.); (Y.X.); (J.W.); (L.W.)
| | - Jinwen Wu
- Department of Plant Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; (S.G.); (C.Z.); (Y.W.); (Y.X.); (J.W.); (L.W.)
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Lan Wang
- Department of Plant Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; (S.G.); (C.Z.); (Y.W.); (Y.X.); (J.W.); (L.W.)
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Xiangdong Liu
- Department of Plant Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; (S.G.); (C.Z.); (Y.W.); (Y.X.); (J.W.); (L.W.)
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Zhixiong Chen
- Department of Plant Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; (S.G.); (C.Z.); (Y.W.); (Y.X.); (J.W.); (L.W.)
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China
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Liu M, Zhou Y, Sun J, Mao F, Yao Q, Li B, Wang Y, Gao Y, Dong X, Liao S, Wang P, Huang S. From the floret to the canopy: High temperature tolerance during flowering. PLANT COMMUNICATIONS 2023; 4:100629. [PMID: 37226443 PMCID: PMC10721465 DOI: 10.1016/j.xplc.2023.100629] [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: 02/20/2023] [Revised: 04/29/2023] [Accepted: 05/22/2023] [Indexed: 05/26/2023]
Abstract
Heat waves induced by climate warming have become common in food-producing regions worldwide, frequently coinciding with high temperature (HT)-sensitive stages of many crops and thus threatening global food security. Understanding the HT sensitivity of reproductive organs is currently of great interest for increasing seed set. The responses of seed set to HT involve multiple processes in both male and female reproductive organs, but we currently lack an integrated and systematic summary of these responses for the world's three leading food crops (rice, wheat, and maize). In the present work, we define the critical high temperature thresholds for seed set in rice (37.2°C ± 0.2°C), wheat (27.3°C ± 0.5°C), and maize (37.9°C ± 0.4°C) during flowering. We assess the HT sensitivity of these three cereals from the microspore stage to the lag period, including effects of HT on flowering dynamics, floret growth and development, pollination, and fertilization. Our review synthesizes existing knowledge about the effects of HT stress on spikelet opening, anther dehiscence, pollen shedding number, pollen viability, pistil and stigma function, pollen germination on the stigma, and pollen tube elongation. HT-induced spikelet closure and arrest of pollen tube elongation have a catastrophic effect on pollination and fertilization in maize. Rice benefits from pollination under HT stress owing to bottom anther dehiscence and cleistogamy. Cleistogamy and secondary spikelet opening increase the probability of pollination success in wheat under HT stress. However, cereal crops themselves also have protective measures under HT stress. Lower canopy/tissue temperatures compared with air temperatures indicate that cereal crops, especially rice, can partly protect themselves from heat damage. In maize, husk leaves reduce inner ear temperature by about 5°C compared with outer ear temperature, thereby protecting the later phases of pollen tube growth and fertilization processes. These findings have important implications for accurate modeling, optimized crop management, and breeding of new varieties to cope with HT stress in the most important staple crops.
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Affiliation(s)
- Mayang Liu
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Yuhan Zhou
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Jiaxin Sun
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Fen Mao
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Qian Yao
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Baole Li
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Yuanyuan Wang
- College of Agronomy, South China Agricultural University, Guangdong, China
| | - Yingbo Gao
- Shandong Academy of Agricultural Sciences, Jinan, China
| | - Xin Dong
- Chongqing Academy of Agricultural Sciences, Chongqing, China
| | - Shuhua Liao
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Pu Wang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Shoubing Huang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China.
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Li X, Huang X, Wen M, Yin W, Chen Y, Liu Y, Liu X. Cytological observation and RNA-seq analysis reveal novel miRNAs high expression associated with the pollen fertility of neo-tetraploid rice. BMC PLANT BIOLOGY 2023; 23:434. [PMID: 37723448 PMCID: PMC10506311 DOI: 10.1186/s12870-023-04453-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 09/11/2023] [Indexed: 09/20/2023]
Abstract
BACKGROUND Neo-tetraploid rice lines exhibit high fertility and strong heterosis and harbor novel specific alleles, which are useful germplasm for polyploid rice breeding. However, the mechanism of the fertility associated with miRNAs remains unknown. In this study, a neo-tetraploid rice line, termed Huaduo21 (H21), was used. Cytological observation and RNA-sequencing were employed to identify the fertility-related miRNAs in neo-tetraploid rice. RESULTS H21 showed high pollen fertility (88.08%), a lower percentage of the pollen mother cell (PMC) abnormalities, and lower abnormalities during double fertilization and embryogenesis compared with autotetraploid rice. A total of 166 non-additive miRNAs and 3108 non-additive genes were detected between H21 and its parents. GO and KEGG analysis of non-additive genes revealed significant enrichments in the DNA replication, Chromosome and associated proteins, and Replication and repair pathways. Comprehensive multi-omics analysis identified 32 pairs of miRNA/target that were associated with the fertility in H21. Of these, osa-miR408-3p and osa-miR528-5p displayed high expression patterns, targeted the phytocyanin genes, and were associated with high pollen fertility. Suppression of osa-miR528-5p in Huaduo1 resulted in a low seed set and a decrease in the number of grains. Moreover, transgenic analysis implied that osa-MIR397b-p3, osa-miR5492, and osa-MIR5495-p5 might participate in the fertility of H21. CONCLUSION Taken together, the regulation network of fertility-related miRNAs-targets pairs might contribute to the high seed setting in neo-tetraploid rice. These findings enhance our understanding of the regulatory mechanisms of pollen fertility associated with miRNAs in neo-tetraploid rice.
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Affiliation(s)
- Xiang Li
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Shaoguan University, Shaoguan, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China.
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China.
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China.
- College of Biology and Agriculture, Shaoguan University, Shaoguan, China.
| | - Xu Huang
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
| | - Minsi Wen
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
| | - Wei Yin
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
| | - Yuanmou Chen
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
| | - Yuanlong Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
| | - Xiangdong Liu
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China.
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China.
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China.
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11
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Xia H, Pu X, Zhu X, Yang X, Guo H, Diao H, Zhang Q, Wang Y, Sun X, Zhang H, Zhang Z, Zeng Y, Li Z. Genome-Wide Association Study Reveals the Genetic Basis of Total Flavonoid Content in Brown Rice. Genes (Basel) 2023; 14:1684. [PMID: 37761824 PMCID: PMC10531027 DOI: 10.3390/genes14091684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 08/21/2023] [Accepted: 08/22/2023] [Indexed: 09/29/2023] Open
Abstract
Flavonoids have anti-inflammatory, antioxidative, and anticarcinogenic effects. Breeding rice varieties rich in flavonoids can prevent chronic diseases such as cancer and cardio-cerebrovascular diseases. However, most of the genes reported are known to regulate flavonoid content in leaves or seedlings. To further elucidate the genetic basis of flavonoid content in rice grains and identify germplasm rich in flavonoids in grains, a set of rice core collections containing 633 accessions from 32 countries was used to determine total flavonoid content (TFC) in brown rice. We identified ten excellent germplasms with TFC exceeding 300 mg/100 g. Using a compressed mixed linear model, a total of 53 quantitative trait loci (QTLs) were detected through a genome-wide association study (GWAS). By combining linkage disequilibrium (LD) analysis, location of significant single nucleotide polymorphisms (SNPs), gene expression, and haplotype analysis, eight candidate genes were identified from two important QTLs (qTFC1-6 and qTFC9-7), among which LOC_Os01g59440 and LOC_Os09g24260 are the most likely candidate genes. We also analyzed the geographic distribution and breeding utilization of favorable haplotypes of the two genes. Our findings provide insights into the genetic basis of TFC in brown rice and could facilitate the breeding of flavonoid-rich varieties, which may be a prevention and adjuvant treatment for cancer and cardio-cerebrovascular diseases.
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Affiliation(s)
- Haijian Xia
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China; (H.X.)
| | - Xiaoying Pu
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences/Agricultural Biotechnology Key Laboratory of Yunnan Province, Kunming 650205, China; (X.P.)
| | - Xiaoyang Zhu
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China; (H.X.)
| | - Xiaomeng Yang
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences/Agricultural Biotechnology Key Laboratory of Yunnan Province, Kunming 650205, China; (X.P.)
| | - Haifeng Guo
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China; (H.X.)
| | - Henan Diao
- Heihe Branch of Heilongjiang Academy of Agricultural Sciences, Heihe 164300, China
| | - Quan Zhang
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China; (H.X.)
| | - Yulong Wang
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China; (H.X.)
| | - Xingming Sun
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China; (H.X.)
| | - Hongliang Zhang
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China; (H.X.)
| | - Zhanying Zhang
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China; (H.X.)
| | - Yawen Zeng
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences/Agricultural Biotechnology Key Laboratory of Yunnan Province, Kunming 650205, China; (X.P.)
| | - Zichao Li
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China; (H.X.)
- Sanya Institute, China Agricultural University, Sanya 572025, China
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12
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Robinson R, Sprott D, Couroux P, Routly E, Labbé N, Xing T, Robert LS. The triticale mature pollen and stigma proteomes - assembling the proteins for a productive encounter. J Proteomics 2023; 278:104867. [PMID: 36870675 DOI: 10.1016/j.jprot.2023.104867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/13/2023] [Accepted: 02/20/2023] [Indexed: 03/06/2023]
Abstract
Triticeae crops are major contributors to global food production and ensuring their capacity to reproduce and generate seeds is critical. However, despite their importance our knowledge of the proteins underlying Triticeae reproduction is severely lacking and this is not only true of pollen and stigma development, but also of their pivotal interaction. When the pollen grain and stigma are brought together they have each accumulated the proteins required for their intended meeting and accordingly studying their mature proteomes is bound to reveal proteins involved in their diverse and complex interactions. Using triticale as a Triticeae representative, gel-free shotgun proteomics was used to identify 11,533 and 2977 mature stigma and pollen proteins respectively. These datasets, by far the largest to date, provide unprecedented insights into the proteins participating in Triticeae pollen and stigma development and interactions. The study of the Triticeae stigma has been particularly neglected. To begin filling this knowledge gap, a developmental iTRAQ analysis was performed revealing 647 proteins displaying differential abundance as the stigma matures in preparation for pollination. An in-depth comparison to an equivalent Brassicaceae analysis divulged both conservation and diversification in the makeup and function of proteins involved in the pollen and stigma encounter. SIGNIFICANCE: Successful pollination brings together the mature pollen and stigma thus initiating an intricate series of molecular processes vital to crop reproduction. In the Triticeae crops (e.g. wheat, barley, rye, triticale) there persists a vast deficit in our knowledge of the proteins involved which needs to be addressed if we are to face the many upcoming challenges to crop production such as those associated with climate change. At maturity, both the pollen and stigma have acquired the protein complement necessary for their forthcoming encounter and investigating their proteomes will inevitably provide unprecedented insights into the proteins enabling their interactions. By combining the analysis of the most comprehensive Triticeae pollen and stigma global proteome datasets to date with developmental iTRAQ investigations, proteins implicated in the different phases of pollen-stigma interaction enabling pollen adhesion, recognition, hydration, germination and tube growth, as well as those underlying stigma development were revealed. Extensive comparisons between equivalent Triticeae and Brassiceae datasets highlighted both the conservation of biological processes in line with the shared goal of activating the pollen grain and promoting pollen tube invasion of the pistil to effect fertilization, as well as the significant distinctions in their proteomes consistent with the considerable differences in their biochemistry, physiology and morphology.
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Affiliation(s)
- Reneé Robinson
- Ottawa Research and Development Centre, 960 Carling Ave., Ottawa, Ontario K1A 0C6, Canada; Carleton University, Department of Biology, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada
| | - David Sprott
- Ottawa Research and Development Centre, 960 Carling Ave., Ottawa, Ontario K1A 0C6, Canada
| | - Philippe Couroux
- Ottawa Research and Development Centre, 960 Carling Ave., Ottawa, Ontario K1A 0C6, Canada
| | - Elizabeth Routly
- Ottawa Research and Development Centre, 960 Carling Ave., Ottawa, Ontario K1A 0C6, Canada
| | - Natalie Labbé
- Ottawa Research and Development Centre, 960 Carling Ave., Ottawa, Ontario K1A 0C6, Canada
| | - Tim Xing
- Carleton University, Department of Biology, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada
| | - Laurian S Robert
- Ottawa Research and Development Centre, 960 Carling Ave., Ottawa, Ontario K1A 0C6, Canada.
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13
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Mahto A, Yadav A, P V A, Parida SK, Tyagi AK, Agarwal P. Cytological, transcriptome and miRNome temporal landscapes decode enhancement of rice grain size. BMC Biol 2023; 21:91. [PMID: 37076907 PMCID: PMC10116700 DOI: 10.1186/s12915-023-01577-3] [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: 05/12/2022] [Accepted: 03/27/2023] [Indexed: 04/21/2023] Open
Abstract
BACKGROUND Rice grain size (GS) is an essential agronomic trait. Though several genes and miRNA modules influencing GS are known and seed development transcriptomes analyzed, a comprehensive compendium connecting all possible players is lacking. This study utilizes two contrasting GS indica rice genotypes (small-grained SN and large-grained LGR). Rice seed development involves five stages (S1-S5). Comparative transcriptome and miRNome atlases, substantiated with morphological and cytological studies, from S1-S5 stages and flag leaf have been analyzed to identify GS proponents. RESULTS Histology shows prolonged endosperm development and cell enlargement in LGR. Stand-alone and comparative RNAseq analyses manifest S3 (5-10 days after pollination) stage as crucial for GS enhancement, coherently with cell cycle, endoreduplication, and programmed cell death participating genes. Seed storage protein and carbohydrate accumulation, cytologically and by RNAseq, is shown to be delayed in LGR. Fourteen transcription factor families influence GS. Pathway genes for four phytohormones display opposite patterns of higher expression. A total of 186 genes generated from the transcriptome analyses are located within GS trait-related QTLs deciphered by a cross between SN and LGR. Fourteen miRNA families express specifically in SN or LGR seeds. Eight miRNA-target modules display contrasting expressions amongst SN and LGR, while 26 (SN) and 43 (LGR) modules are differentially expressed in all stages. CONCLUSIONS Integration of all analyses concludes in a "Domino effect" model for GS regulation highlighting chronology and fruition of each event. This study delineates the essence of GS regulation, providing scope for future exploits. The rice grain development database (RGDD) ( www.nipgr.ac.in/RGDD/index.php ; https://doi.org/10.5281/zenodo.7762870 ) has been developed for easy access of data generated in this paper.
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Affiliation(s)
- Arunima Mahto
- National Institute of Plant Genome Research, New Delhi, India
| | - Antima Yadav
- National Institute of Plant Genome Research, New Delhi, India
| | - Aswathi P V
- National Institute of Plant Genome Research, New Delhi, India
| | - Swarup K Parida
- National Institute of Plant Genome Research, New Delhi, India
| | - Akhilesh K Tyagi
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Pinky Agarwal
- National Institute of Plant Genome Research, New Delhi, India.
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14
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Qu A, Bai Y, Wang J, Zhao J, Zeng J, Liu Y, Chen X, Ke Q, Jiang P, Zhang X, Li X, Xu P, Zhou T. Integrated mRNA and miRNA expression analyses for Cryptocaryon irritans resistance in large yellow croaker (Larimichthys crocea). FISH & SHELLFISH IMMUNOLOGY 2023; 135:108650. [PMID: 36858330 DOI: 10.1016/j.fsi.2023.108650] [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: 09/27/2022] [Revised: 02/23/2023] [Accepted: 02/26/2023] [Indexed: 06/18/2023]
Abstract
Large yellow croaker (Larimichthys crocea) is one of the most important mariculture fish in China. However, cryptocaryonosis caused by Cryptocryon irritans infection has brought huge economic losses and threatened the healthy and sustainable development of L. crocea industry. Recently, a new C. irritans resistance strain of L. crocea (RS) has been bred using genomic selection technology in our laboratory work. However, the molecular mechanisms for C. irritans resistance of RS have not been fully understood. MicroRNAs (miRNAs) are endogenous small non-coding RNAs that are post-transcriptional regulators, and they play vital roles in immune process of bony fish. Identification of anti-C.irritans relevant miRNA signatures could, therefore, be of tremendous translational value. In the present study, integrated mRNA and miRNA expression analysis was used to explore C. irritans resistance mechanisms of the L. crocea. RS as well as a control strain (CS) of L. crocea, were artificially infected with C. irritans for 100 h, and their gill was collected at 0 h (pre-infection), 24 h (initial infection), and 72 h (peak infection) time points. The total RNA from gill tissues was extracted and used for transcriptome sequencing and small RNA sequencing. After sequencing, 23,172 known mRNAs and 289 known miRNAs were identified. The differential expression was analyzed in these mRNAs and mRNAs and the interactions of miRNA-mRNA pairs were constructed. KEGG pathway enrichment analyses showed that these putative target mRNAs of differentially expressed miRNAs (DEMs) were enriched in different immune-related pathways after C. irritans infection in RS and CS. Among them, necroptosis was the immune-related pathway that was only significantly enriched at two infection stages of RS group (RS-24 h/RS-0h and RS-72 h/RS-0h). Further investigation indicates that necroptosis may be activated by DEMs such as miR-133a-3p, miR-142a-3p and miR-135c, this promotes inflammation responses and pathogen elimination. These DEMs were selected as miRNAs that could potentially regulate the C. irritans resistance of L. crocea. Though these inferences need to be further verified, these findings will be helpful for the research of the molecular mechanism of C. irritans resistance of L. crocea and miRNA-assisted molecular breeding of aquatic animals.
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Affiliation(s)
- Ang Qu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Yulin Bai
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Jiaying Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Ji Zhao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Junjia Zeng
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Yue Liu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Xintong Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Qiaozhen Ke
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Pengxin Jiang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Xinyi Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Xin Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Peng Xu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China; State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, 352130, China; Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Tao Zhou
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China; State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, 352130, China; Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China.
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15
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Zhong J, Cui J, Liu J, Zhong C, Hu F, Dong J, Cheng J, Hu K. Fine-mapping and candidate gene analysis of the Mcgy1 locus responsible for gynoecy in bitter gourd (Momordica spp.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:81. [PMID: 36952023 DOI: 10.1007/s00122-023-04314-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 01/28/2023] [Indexed: 06/18/2023]
Abstract
The Mcgy1 locus responsible for gynoecy was fine-mapped into a 296.94-kb region, in which four single-nucleotide variations and six genes adjacent to them might be associate with sex differentiation in bitter gourd. Gynoecy plays an important role in high-efficiency hybrid seed production, and gynoecious plants are excellent materials for dissecting sex differentiation in Cucurbitaceae crop species, including bitter gourd. However, the gene responsible for gynoecy in bitter gourd is unknown. Here, we first identified a gynoecy locus designated Mcgy1 using the F2 population (n = 291) crossed from the gynoecious line S156G and the monoecious line K8-201 via bulked segregant analysis with whole-genome resequencing (BSA-seq) and molecular marker linkage analysis. Then, a large S156G × K8-201 F2 population (n = 5,656) was used for fine-mapping to delimit the Mcgy1 locus into a 296.94-kb physical region on pseudochromosome MC01, where included 33 annotated genes different from any homologous gynoecy genes previously reported in Cucurbitaceae species. Within this region, four underlying single-nucleotide variations (SNVs) that might cause gynoecy were identified by multiple genomic sequence variation analysis, and their six neighbouring genes were considered as potential candidate genes for Mcgy1. Of these, only MC01g1681 showed a significant differential expression at two-leaf developmental stage between S156G and its monoecious near-isogenic line S156 based on RNA sequencing (RNA-seq) and qRT-PCR analyses. In addition, transcriptome analysis revealed 21 key differentially expressed genes (DEGs) and possible regulatory pathways of the formation of gynoecy in bitter gourd. Our findings provide a new clue for researching on gynoecious plants in Cucurbitaceae species and a theoretical basis for breeding gynoecious bitter gourd lines by the use of molecular markers-assisted selection.
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Affiliation(s)
- Jian Zhong
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Guangdong Vegetables Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Junjie Cui
- Department of Horticulture, Foshan University, Foshan, 528225, China
| | - Jia Liu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Guangdong Vegetables Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Chunfeng Zhong
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Guangdong Vegetables Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Fang Hu
- Henry Fok School of Biology and Agricultural, Shaoguan University, Shaoguan, 512023, China
| | - Jichi Dong
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Guangdong Vegetables Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Jiaowen Cheng
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Guangdong Vegetables Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China.
| | - Kailin Hu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Guangdong Vegetables Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China.
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16
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Guo Y, Wang Y, Chen H, Du Q, Wang Z, Gong X, Sun Q, Li WX. Nitrogen supply affects ion homeostasis by modifying root Casparian strip formation through the miR528-LAC3 module in maize. PLANT COMMUNICATIONS 2023:100553. [PMID: 36681862 PMCID: PMC10363476 DOI: 10.1016/j.xplc.2023.100553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 12/02/2022] [Accepted: 01/18/2023] [Indexed: 06/17/2023]
Abstract
Although nitrogen (N) is known to affect mineral element homeostasis in plants, the molecular mechanisms of interactions between N and other nutrients remain largely unclear. We report here that N supply affects ion homeostasis in maize. Berberine hemisulfate staining and a propidium iodide penetration assay showed that N luxury significantly delayed Casparian strip (CS) formation in maize roots. We further demonstrated that N-mediated CS formation in maize was independent of RBOHF-activated H2O2 production. N luxury induced the expression of ZmmiR528 in whole roots and root tips. Knockdown and loss-of-function of ZmmiR528 promoted CS formation under both N-luxury and N-deficient conditions. Both ZmMIR528a and ZmMIR528b contribute to early CS formation under different N conditions. RNA-seq and real-time RT-PCR analysis demonstrated that ZmLAC3, but not ZmLAC5, responded to N treatments. Consistent with results obtained with ZmmiR528 TM transgenic maize and mir528a/b loss-of-function mutants, transgenic maize overexpressing ZmLAC3 displayed early CS formation under different N conditions. Under field conditions, K, Ca, Mn, Cu, Mg, and Zn concentrations were greater in the ear leaf of ZmLAC3-overexpressing transgenic maize than in the wild type. These results indicate that ZmmiR528 affects CS formation in maize by regulating the expression of ZmLAC3, and modification of CS formation has the potential to improve maize quality.
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Affiliation(s)
- Yu Guo
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yafei Wang
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Huan Chen
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qingguo Du
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhonghua Wang
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaoping Gong
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qing Sun
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Qingdao Agricultural University, Qingdao 266109, China
| | - Wen-Xue Li
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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Chen W, Dong T, Chen Y, Lin P, Wang C, Chen K, Tang Y, Wang M, Liu J, Yu H. Combined analysis of mRNA and miRNA reveals the banana potassium absorption regulatory network and validation of miRNA160a. PLANT MOLECULAR BIOLOGY 2022; 110:531-543. [PMID: 35962899 DOI: 10.1007/s11103-022-01304-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 07/21/2022] [Indexed: 06/15/2023]
Abstract
Potassium (K) has an important effect on the growth and development of plants. Banana contains higher K content than many other fruits, and its plant requires more K nutrient in soil. However, the soil in the banana-producing areas in China is generally deficient in K. Therefore, understanding the mechanism of banana K absorption may assist in providing effective strategy to solve this problem. This study used two banana varieties with contrasting K tolerance, 'Guijiao No. 1' (low-K tolerant), and 'Brazilian banana' (low-K sensitive)to investigate K absorption mechanisms in response to low-K stress through miRNA and mRNA sequencing analysis. Under low-K condition, 'Guijiao No.1' showed higher plant height, dry weight, tissue K content and ATPase activity. Analysis of transcription factors showed that they were mainly in the types or classes of MYB, AP-EREBP, bHLH, etc. The sequencing results showed that 'Guijiao No. 1' had 776 differentially expressed genes (DEGs) and 27 differentially expressed miRNAs (DEMs), and 'Brazilian banana' had 71 DEGs and 14 DEMs between normal and low K treatments. RT-qPCR results showed that all miRNAs and mRNAs showed similar expression patterns with RNA-Seq and transcriptome. miRNA regulatory network was constructed by integrated analysis of miRNA-mRNA data. miR160a was screened out as a key miRNA, and preliminary functional validation was performed. Arabidopsis overexpressing miR160a showed reduced tolerance to low K, and inhibited phenotypic traits such as shorter root length, and reduced K accumulation. The overexpressed miR160a had a targeting relationship with ARF10 and ARF16 in Arabidopsis. These results indicate that miR160a may regulate K absorption in bananas through the auxin pathway. This study provides a theoretical basis for further study on the molecular mechanism of banana response to low potassium stress.
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Affiliation(s)
- Wenliang Chen
- Institute of Horticulture Science and Engineering, Huaqiao University, Xiamen, 361021, China
| | - Tao Dong
- Institute of Fruit Tree ResearchKey Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural AffairsGuangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Yinglong Chen
- School of Agriculture and Environment, The UWA Institute of Agriculture, The University of Western Australia, Perth, 6009 WA, Australia
| | - Ping Lin
- Institute of Horticulture Science and Engineering, Huaqiao University, Xiamen, 361021, China
| | - Chuqiao Wang
- Institute of Horticulture Science and Engineering, Huaqiao University, Xiamen, 361021, China
| | - Kelin Chen
- Institute of Horticulture Science and Engineering, Huaqiao University, Xiamen, 361021, China
| | - Yi Tang
- Institute of Horticulture Science and Engineering, Huaqiao University, Xiamen, 361021, China
| | - Mingyuan Wang
- Institute of Horticulture Science and Engineering, Huaqiao University, Xiamen, 361021, China.
| | - Jianfu Liu
- Institute of Horticulture Science and Engineering, Huaqiao University, Xiamen, 361021, China.
| | - Hailing Yu
- Institute of Horticulture Science and Engineering, Huaqiao University, Xiamen, 361021, China.
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18
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Zhang A, You H, Cao L, Shi Y, Chen J, Shen Y, Tao S, Cheng Z, Zhang W. Low cell number ChIP-seq reveals chromatin state-based regulation of gene transcription in the rice male meiocytes. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:2236-2238. [PMID: 36056565 PMCID: PMC9674319 DOI: 10.1111/pbi.13921] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/27/2022] [Accepted: 08/28/2022] [Indexed: 05/26/2023]
Affiliation(s)
- Aicen Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, CIC‐MCPNanjing Agricultural UniversityNanjingJiangsuChina
| | - Hanli You
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Lei Cao
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yining Shi
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, CIC‐MCPNanjing Agricultural UniversityNanjingJiangsuChina
| | - Jiawei Chen
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yi Shen
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijingChina
| | - Shentong Tao
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, CIC‐MCPNanjing Agricultural UniversityNanjingJiangsuChina
| | - Zhukuan Cheng
- Jiangsu Co‐Innovation Center for Modern Production Technology of Grain CropsYangzhou UniversityYangzhouChina
| | - Wenli Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, CIC‐MCPNanjing Agricultural UniversityNanjingJiangsuChina
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19
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Jin S, Wang X, Dong Y, Li G, Chang X, Zhang L, Jin S. The gene LpBCP increased NaHCO 3 resistance by enhancing lignin or ROS scavenging in the Nicotiana benthamiana. PLANT BIOLOGY (STUTTGART, GERMANY) 2022; 24:1057-1065. [PMID: 35976073 DOI: 10.1111/plb.13462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 08/02/2022] [Indexed: 06/15/2023]
Abstract
Lilium pumilum is an excellent wildflower germplasm resource with high resistance to salinity stress. The gene LpBCP plays an important role in salinity tolerance of L. pumilum. Studying the molecular mechanism of salinity resistance in L. pumilum will provide insights into multiple aspects, including breeding better varieties, environmental protection, improving soil conditions, etc. Conventional methods were used to determine different physiological indicators of Nicotiana benthamiana after NaHCO3 treatment, i.e. chlorophyll content, soluble phenol content and lignin content. RT-qPCR was carried out to find expression of LpBCP in different organs and under abiotic stresses. DAB was used to detect H2 O2 in leaves in situ. A yeast two-hybrid system was used to screen for LpBCP interacting proteins. LpBCP was cloned from bulbs of L. pumilum. The highest expression of LpBCP was in roots and bulbs of transgenic plants. LpBCP-overexpressed plants showed less wilting, compared to WT plants. LpBCP transgenic plants have higher chlorophyll, soluble phenol and lignin content, and lower relative conductivity under 500 mM NaHCO3 stress. In addition, H2 O2 scavenging in transgenic plants was much improved, indicating increased resistance to NaHCO3 stress. Thirteen LpBCP-interacting proteins were screened using the yeast two-hybrid method and five were associated with salt stress. Based on our findings, LPBCP could be a key gene that can be used to improve L. pumilum salt tolerance.
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Affiliation(s)
- S Jin
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, China
- Forestry College, Northeast Forestry University, Harbin, China
| | - X Wang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, China
| | - Y Dong
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, China
- Aulin College, Northeast Forestry University, Harbin, China
| | - G Li
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, China
| | - X Chang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, China
| | - L Zhang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, China
| | - S Jin
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, China
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20
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Hou Q, Zhang T, Qi Y, Dong Z, Wan X. Epigenetic Dynamics and Regulation of Plant Male Reproduction. Int J Mol Sci 2022; 23:ijms231810420. [PMID: 36142333 PMCID: PMC9499625 DOI: 10.3390/ijms231810420] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 08/30/2022] [Accepted: 09/05/2022] [Indexed: 11/16/2022] Open
Abstract
Flowering plant male germlines develop within anthers and undergo epigenetic reprogramming with dynamic changes in DNA methylation, chromatin modifications, and small RNAs. Profiling the epigenetic status using different technologies has substantially accumulated information on specific types of cells at different stages of male reproduction. Many epigenetically related genes involved in plant gametophyte development have been identified, and the mutation of these genes often leads to male sterility. Here, we review the recent progress on dynamic epigenetic changes during pollen mother cell differentiation, microsporogenesis, microgametogenesis, and tapetal cell development. The reported epigenetic variations between male fertile and sterile lines are summarized. We also summarize the epigenetic regulation-associated male sterility genes and discuss how epigenetic mechanisms in plant male reproduction can be further revealed.
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21
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Research progress about microRNAs involved in plant secondary metabolism. Int J Biol Macromol 2022; 216:820-829. [DOI: 10.1016/j.ijbiomac.2022.07.224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 07/21/2022] [Accepted: 07/27/2022] [Indexed: 11/18/2022]
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22
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Ranjan R, Malik N, Sharma S, Agarwal P, Kapoor S, Tyagi AK. OsCPK29 interacts with MADS68 to regulate pollen development in rice. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 321:111297. [PMID: 35696904 DOI: 10.1016/j.plantsci.2022.111297] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 03/09/2022] [Accepted: 04/20/2022] [Indexed: 06/15/2023]
Abstract
Pollen development and its germination are obligatory for the reproductive success of flowering plants. Calcium-dependent protein kinases (CPKs, also known as CDPKs) regulate diverse signaling pathways controlling plant growth and development. Here, we report the functional characterization of a novel OsCPK29 from rice, which is mainly expressed during pollen maturation stages of the anther. OsCPK29 exclusively localizes in the nucleus, and its N-terminal variable domain is responsible for retaining it in the nucleus. OsCPK29 knockdown rice plants exhibit reduced fertility, set fewer seeds, and produce collapsed non-viable pollen grains that do not germinate. Cytological analysis of anther semi-thin sections during different developmental stages suggested that pollen abnormalities appear after the vacuolated pollen stage. Detailed microscopic study of pollen grains further revealed that they were lacking the functional intine layer although exine layer was present. Consistent with that, downregulation of known intine development-related rice genes was also observed in OsCPK29 silenced anthers. Furthermore, it has been demonstrated that OsCPK29 interacts in vitro as well as in vivo with the MADS68 transcription factor which is a known regulator of pollen development. Therefore, phenotypic observations and molecular studies suggest that OsCPK29 is an important regulator of pollen development in rice.
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Affiliation(s)
- Rajeev Ranjan
- National Institute of Plant Genome Research (NIPGR), New Delhi 110067, India; Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus (UDSC), New Delhi 110021, India
| | - Naveen Malik
- National Institute of Plant Genome Research (NIPGR), New Delhi 110067, India
| | - Shivam Sharma
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus (UDSC), New Delhi 110021, India
| | - Pinky Agarwal
- National Institute of Plant Genome Research (NIPGR), New Delhi 110067, India
| | - Sanjay Kapoor
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus (UDSC), New Delhi 110021, India
| | - Akhilesh K Tyagi
- National Institute of Plant Genome Research (NIPGR), New Delhi 110067, India; Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus (UDSC), New Delhi 110021, India.
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23
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Wu Y, Huang X, Zhang S, Zhang C, Yang H, Lyu L, Li W, Wu W. Small RNA and degradome sequencing reveal the role of blackberry miRNAs in flavonoid and anthocyanin synthesis during fruit ripening. Int J Biol Macromol 2022; 213:892-901. [PMID: 35691433 DOI: 10.1016/j.ijbiomac.2022.06.035] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 12/28/2022]
Abstract
Blackberry shrubs are economically important for their production of small, pulped fruits. This species has attracted much attention because of the unique flavor of its fruits and their rich nutritional and medicinal value. In this study, microRNAs (miRNAs) and their target genes related to flavonoids and anthocyanins in blackberry fruits during ripening were analyzed and identified by small RNA and degradome sequencing technology, and the expression levels of key miRNAs in unripe and ripe blackberry fruits were verified via the RT-qPCR. A total of 258 known miRNAs were identified. Eighty differentially expressed miRNAs (DEMs) were detected in the fruits of the ripe group compared with those of the unripe group. Differentially expressed miR828-x/miR828-z and unigene0086056 (unknown function) were coexpressed. Moreover, miR858 had the most target genes for the synthesis of flavonoids and anthocyanins. Taken together, these results provide important value for improving the quality of blackberry fruits and breeding blackberry plants that produce high-flavonoid fruits for the pharmaceutical industry.
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Affiliation(s)
- Yaqiong Wu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Qian Hu Hou Cun No. 1, Nanjing 210014, China
| | - Xin Huang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Qian Hu Hou Cun No. 1, Nanjing 210014, China
| | - Shanshan Zhang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Qian Hu Hou Cun No. 1, Nanjing 210014, China
| | - Chunhong Zhang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Qian Hu Hou Cun No. 1, Nanjing 210014, China
| | - Haiyan Yang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Qian Hu Hou Cun No. 1, Nanjing 210014, China
| | - Lianfei Lyu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Qian Hu Hou Cun No. 1, Nanjing 210014, China
| | - Weilin Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, 159 Longpan Road, Nanjing 210037, China.
| | - Wenlong Wu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Qian Hu Hou Cun No. 1, Nanjing 210014, China.
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Kumar K, Mandal SN, Neelam K, de los Reyes BG. MicroRNA-mediated host defense mechanisms against pathogens and herbivores in rice: balancing gains from genetic resistance with trade-offs to productivity potential. BMC PLANT BIOLOGY 2022; 22:351. [PMID: 35850632 PMCID: PMC9290239 DOI: 10.1186/s12870-022-03723-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 06/29/2022] [Indexed: 05/08/2023]
Abstract
BACKGROUND Rice (Oryza sativa L.) is the major source of daily caloric intake for more than 30% of the human population. However, the sustained productivity of this staple food crop is continuously threatened by various pathogens and herbivores. Breeding has been successful in utilizing various mechanisms of defense by gene pyramiding in elite cultivars, but the continuous resurgence of highly resistant races of pathogens and herbivores often overcomes the inherent capacity of host plant immunity. MicroRNAs (miRNAs) are endogenous, short, single-stranded, non-coding RNA molecules that regulate gene expression by sequence-specific cleavage of target mRNA or suppressing target mRNA translation. While miRNAs function as upstream regulators of plant growth, development, and host immunity, their direct effects on growth and development in the context of balancing defenses with agronomic potential have not been extensively discussed and explored as a more viable strategy in breeding for disease and pest resistant cultivars of rice with optimal agronomic potentials. RESULTS Using the available knowledge in rice and other model plants, this review examines the important roles of miRNAs in regulating host responses to various fungal, bacterial, and viral pathogens, and insect pests, in the context of gains and trade-offs to crop yield. Gains from R-gene-mediated resistance deployed in modern rice cultivars are often undermined by the rapid breakdown of resistance, negative pleiotropic effects, and linkage drags with undesirable traits. In stark contrast, several classes of miRNAs are known to efficiently balance the positive gains from host immunity without significant costs in terms of losses in agronomic potentials (i.e., yield penalty) in rice. Defense-related miRNAs such as Osa-miR156, Osa-miR159, Osa-miR162, Osa-miR396, Osa-530, Osa-miR1432, Osa-miR1871, and Osa-miR1873 are critical in fine-tuning and integrating immune responses with physiological processes that are necessary to the maintenance of grain yield. Recent research has shown that many defense-related miRNAs regulate complex and agronomically important traits. CONCLUSIONS Identification of novel immune-responsive miRNAs that orchestrate physiological processes critical to the full expression of agronomic potential will facilitate the stacking of optimal combinations of miRNA-encoding genes to develop high-yielding cultivars with durable resistance to disease and insect pests with minimal penalties to yield.
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Affiliation(s)
- Kishor Kumar
- Faculty Centre for Integrated Rural Development and Management, Ramakrishna Mission Vivekananda Educational and Research Institute, Narendrapur, Kolkata, 700103 India
| | - Swarupa Nanda Mandal
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX-79415 USA
- Department of Genetics and Plant Breeding, Bidhan Chandra Krishi Viswavidyalaya, Extended Campus, Burdwan, West Bengal 713101 India
| | - Kumari Neelam
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab 141004 India
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25
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Yao S, Kang J, Guo G, Yang Z, Huang Y, Lan Y, Zhou T, Wang L, Wei C, Xu Z, Li Y. The key micronutrient copper orchestrates broad-spectrum virus resistance in rice. SCIENCE ADVANCES 2022; 8:eabm0660. [PMID: 35776788 PMCID: PMC10883364 DOI: 10.1126/sciadv.abm0660] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Copper is a critical regulator of plant growth and development. However, the mechanisms by which copper responds to virus invasion are unclear. We previously showed that SPL9-mediated transcriptional activation of miR528 adds a previously unidentified regulatory layer to the established ARGONAUTE (AGO18)-miR528-L-ascorbate oxidase (AO) antiviral defense. Here, we report that rice promotes copper accumulation in shoots by inducing copper transporter genes, including HMA5 and COPT, to counteract viral infection. Copper suppresses the transcriptional activation of miR528 by inhibiting the protein level of SPL9, thus alleviating miR528-mediated cleavage of AO transcripts to strengthen the antiviral response. Loss-of-function mutations in HMA5, COPT1, and COPT5 caused a significant reduction in copper accumulation and plant viral resistance because of the increased SPL9-mediated miR528 transcription. Gain in viral susceptibility was mitigated when SPL9 was mutated in the hma5 mutant background. Our study elucidates the molecular mechanisms and regulatory networks of copper homeostasis and the SPL9-miR528-AO antiviral pathway.
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Affiliation(s)
- Shengze Yao
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Jinrui Kang
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Ge Guo
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Zhirui Yang
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Yu Huang
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Ying Lan
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Tong Zhou
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Liying Wang
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Chunhong Wei
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Zhihong Xu
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Yi Li
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
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26
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Wang N, Zhang B, Yao T, Shen C, Wen T, Zhang R, Li Y, Le Y, Li Z, Zhang X, Lin Z. Re enhances anthocyanin and proanthocyanidin accumulation to produce red foliated cotton and brown fiber. PLANT PHYSIOLOGY 2022; 189:1466-1481. [PMID: 35289870 PMCID: PMC9237731 DOI: 10.1093/plphys/kiac118] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 02/16/2022] [Indexed: 05/04/2023]
Abstract
Red foliated cotton is a typical dominant mutation trait in upland cotton (Gossypium hirsutum). Although mutants have been described, few responsible genes have been identified and characterized. In this study, we performed map-based cloning of the red foliated mutant gene (Re) derived from the cross between G. hirsutum cv. Emian22 and G. barbadense acc. 3-79. Through expression profiling, metabolic pathway analysis, and sequencing of candidate genes, Re was identified as an MYB113 transcription factor. A repeat sequence variation in the promoter region increased the activity of the promoter, which enhanced the expression of Re. Re expression driven by the 35S promoter produced a red foliated phenotype, as expected. When the gene was driven by a fiber elongation-specific promoter, promoter of α-expansin 2 (PGbEXPA2), Re was specifically expressed in 5- to 10-day post-anthesis fibers rather than in other tissues, resulting in brown mature fibers. Re responded to light through phytochrome-interacting factor 4 and formed a dimer with transparent testa 8, which increased its expression as well as that of anthocyanin synthase and UDP-glucose:flavonoid 3-o-glucosyl transferase, and thus activated the entire anthocyanin metabolism pathway. Our research has identified the red foliated mutant gene in cotton, which paves the way for detailed studies of anthocyanin and proanthocyanidin metabolism and pigment accumulation in cotton and provides an alternative strategy for producing brown fiber.
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Affiliation(s)
- Nian Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Beibei Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Tian Yao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Chao Shen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- College of Biological and Food Engineering, Guangdong University of Petrochemical Technology, Maoming, Guangdong 525000, China
| | - Tianwang Wen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Ruiting Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuanxue Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yu Le
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhonghua Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
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Mazurier M, Drouaud J, Bahrman N, Rau A, Lejeune-Hénaut I, Delbreil B, Legrand S. Integrated sRNA-seq and RNA-seq Analyses Reveal a microRNA Regulation Network Involved in Cold Response in Pisum sativum L. Genes (Basel) 2022; 13:1119. [PMID: 35885902 PMCID: PMC9322779 DOI: 10.3390/genes13071119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/14/2022] [Accepted: 06/20/2022] [Indexed: 12/04/2022] Open
Abstract
(1) Background: Cold stress affects growth and development in plants and is a major environmental factor that decreases productivity. Over the past two decades, the advent of next generation sequencing (NGS) technologies has opened new opportunities to understand the molecular bases of stress resistance by enabling the detection of weakly expressed transcripts and the identification of regulatory RNAs of gene expression, including microRNAs (miRNAs). (2) Methods: In this study, we performed time series sRNA and mRNA sequencing experiments on two pea (Pisum sativum L., Ps) lines, Champagne frost-tolerant and Térèse frost-sensitive, during a low temperature treatment versus a control condition. (3) Results: An integrative analysis led to the identification of 136 miRNAs and a regulation network composed of 39 miRNA/mRNA target pairs with discordant expression patterns. (4) Conclusions: Our findings indicate that the cold response in pea involves 11 miRNA families as well as their target genes related to antioxidative and multi-stress defense mechanisms and cell wall biosynthesis.
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Affiliation(s)
- Mélanie Mazurier
- BioEcoAgro Joint Research Unit, Université de Lille, INRAE, Université de Liège, Université de Picardie Jules Verne, 59000 Lille, France; (M.M.); (N.B.); (B.D.)
| | - Jan Drouaud
- BioEcoAgro Joint Research Unit, INRAE, Université de Lille, Université de Liège, Université de Picardie Jules Verne, 80200 Estrées-Mons, France; (J.D.); (A.R.); (I.L.-H.)
| | - Nasser Bahrman
- BioEcoAgro Joint Research Unit, Université de Lille, INRAE, Université de Liège, Université de Picardie Jules Verne, 59000 Lille, France; (M.M.); (N.B.); (B.D.)
- BioEcoAgro Joint Research Unit, INRAE, Université de Lille, Université de Liège, Université de Picardie Jules Verne, 80200 Estrées-Mons, France; (J.D.); (A.R.); (I.L.-H.)
| | - Andrea Rau
- BioEcoAgro Joint Research Unit, INRAE, Université de Lille, Université de Liège, Université de Picardie Jules Verne, 80200 Estrées-Mons, France; (J.D.); (A.R.); (I.L.-H.)
- Université Paris-Saclay, AgroParisTech, INRAE, GABI, 78350 Jouy-en-Josas, France
| | - Isabelle Lejeune-Hénaut
- BioEcoAgro Joint Research Unit, INRAE, Université de Lille, Université de Liège, Université de Picardie Jules Verne, 80200 Estrées-Mons, France; (J.D.); (A.R.); (I.L.-H.)
| | - Bruno Delbreil
- BioEcoAgro Joint Research Unit, Université de Lille, INRAE, Université de Liège, Université de Picardie Jules Verne, 59000 Lille, France; (M.M.); (N.B.); (B.D.)
| | - Sylvain Legrand
- Univ. Lille, CNRS, UMR 8198—Evo-Eco-Paleo, 59000 Lille, France
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28
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Ma X, Tang K, Tang Z, Dong A, Xiao H, Meng Y, Wang P. An organ-specific transcriptomic atlas of the medicinal plant Bletilla striata: Protein-coding genes, microRNAs, and regulatory networks. THE PLANT GENOME 2022; 15:e20210. [PMID: 35475547 DOI: 10.1002/tpg2.20210] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 03/14/2022] [Indexed: 06/14/2023]
Abstract
As one of the important species belonging to the Bletilla genus of Orchidaceae, Bletilla striata (Thunb.) Rchb. f., possesses both ornamental and medicinal values. Its dried tubers are used as a traditional Chinese medicine, and several secondary metabolites have been indicated to be the active ingredients. However, the molecular mechanisms related to the regulation of secondary metabolism have not been characterized in B. striata. In this study, integrated analysis of RNA sequencing (RNA-seq), small RNA sequencing (sRNA-seq), and degradome sequencing (degradome-seq) data from three organs (leaf, root, and tuber) of B. striata provided us with a comprehensive view of the microRNA (miRNA)-mediated regulatory network. Firstly, based on the RNA-seq data, the organ-specific expression patterns of the protein-coding genes, especially for those related to secondary metabolism, were investigated. Secondly, 342 conserved miRNA candidates were identified from B. striata. These miRNAs were assigned to 88 families, some of which were selected for expression pattern analysis. Additionally, 31 hairpin-structured precursors encoding 23 novel miRNAs were uncovered from the transcriptome assembly. Thirdly, based on the degradome signatures, 1,142 validated miRNA-target pairs (involving 167 conserved miRNAs and six novel miRNAs and 51 target genes) were included in the regulatory network. Organ-specific expression level comparison between the miRNAs and their targets revealed some interesting miRNA-target pairs. Fourthly, some valuable subnetworks were extracted for further functional studies. Additionally, some regulatory pathways were indicated to be monocot specific. Summarily, our results lay a solid basis for in-depth studies on the regulatory mechanisms underlying the production of the medicinal ingredients in B. striata.
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Affiliation(s)
- Xiaoxia Ma
- College of Pharmaceutical Science, Zhejiang Univ. of Technology, Hangzhou, 310014, China
- School of Pharmacy, Hangzhou Normal Univ., Hangzhou, 311121, China
| | - Kehua Tang
- Key Laboratory of Hunan Forest Products and Chemical Industry Engineering, Jishou Univ., Zhangjiajie, 427000, China
| | - Zhonghai Tang
- College of Food Science and Technology, Hunan Agricultural Univ., Changsha, 410128, China
| | - Aiwen Dong
- Key Laboratory of Hunan Forest Products and Chemical Industry Engineering, Jishou Univ., Zhangjiajie, 427000, China
| | - Hang Xiao
- Dep. of Food Science, Univ. of Massachusetts, Amherst, MA, 01003, USA
| | - Yijun Meng
- College of Life and Environmental Sciences, Hangzhou Normal Univ., Hangzhou, 311121, China
| | - Pu Wang
- College of Pharmaceutical Science, Zhejiang Univ. of Technology, Hangzhou, 310014, China
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29
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Zhao J, Liu X, Wang M, Xie L, Wu Z, Yu J, Wang Y, Zhang Z, Jia Y, Liu Q. The miR528-D3 Module Regulates Plant Height in Rice by Modulating the Gibberellin and Abscisic Acid Metabolisms. RICE (NEW YORK, N.Y.) 2022; 15:27. [PMID: 35596029 PMCID: PMC9123139 DOI: 10.1186/s12284-022-00575-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 05/13/2022] [Indexed: 05/02/2023]
Abstract
Plant height, as one of the important agronomic traits of rice, is closely related to yield. In recent years, plant height-related genes have been characterized and identified, among which the DWARF3 (D3) gene is one of the target genes of miR528, and regulates rice plant height and tillering mainly by affecting strigolactone (SL) signal transduction. However, it remains unknown whether the miR528 and D3 interaction functions in controlling plant height, and the underlying regulatory mechanism in rice. In this study, we found that the plant height, internode length, and cell length of internodes of d3 mutants and miR528-overexpressing (OE-miR528) lines were greatly shorter than WT, D3-overexpressing (OE-D3), and miR528 target mimicry (OE-MIM528) transgenic plants. Knockout of D3 gene (d3 mutants) or miR528-overexpressing (OE-miR528) triggers a substantial reduction of gibberellin (GA) content, but a significant increase of abscisic acid (ABA) accumulation than in WT. The d3 and OE-miR528 transgenic plants were much more sensitive to GA, but less sensitive to ABA than WT. Moreover, the expression level of GA biosynthesis-related key genes, including OsCPS1, OsCPS2, OsKO2 and OsKAO was remarkably higher in OE-D3 plants, while the NECD2 expression, a key gene involved in ABA biosynthesis, was significantly higher in d3 mutants than in WT and OE-D3 plants. The results indicate that the miR528-D3 module negatively regulates plant height in rice by modulating the GA and ABA homeostasis, thereby further affecting the elongation of internodes, and resulting in lower plant height, which adds a new regulatory role to the D3-mediated plant height controlling in rice.
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Affiliation(s)
- Juan Zhao
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Lin'an Hangzhou, 311300, People's Republic of China
| | - Xing Liu
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Lin'an Hangzhou, 311300, People's Republic of China
| | - Mei Wang
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Lin'an Hangzhou, 311300, People's Republic of China
| | - Lingjuan Xie
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Lin'an Hangzhou, 311300, People's Republic of China
| | - Zhengxin Wu
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Lin'an Hangzhou, 311300, People's Republic of China
| | - Jiuming Yu
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Lin'an Hangzhou, 311300, People's Republic of China
| | - Yuchen Wang
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Lin'an Hangzhou, 311300, People's Republic of China
| | - Zhiqiao Zhang
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Lin'an Hangzhou, 311300, People's Republic of China
| | - Yufang Jia
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Lin'an Hangzhou, 311300, People's Republic of China
| | - Qingpo Liu
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Lin'an Hangzhou, 311300, People's Republic of China.
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30
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Yu K, Ciais P, Seneviratne SI, Liu Z, Chen HYH, Barichivich J, Allen CD, Yang H, Huang Y, Ballantyne AP. Field-based tree mortality constraint reduces estimates of model-projected forest carbon sinks. Nat Commun 2022; 13:2094. [PMID: 35440564 PMCID: PMC9018757 DOI: 10.1038/s41467-022-29619-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 03/18/2022] [Indexed: 11/11/2022] Open
Abstract
Considerable uncertainty and debate exist in projecting the future capacity of forests to sequester atmospheric CO2. Here we estimate spatially explicit patterns of biomass loss by tree mortality (LOSS) from largely unmanaged forest plots to constrain projected (2015–2099) net primary productivity (NPP), heterotrophic respiration (HR) and net carbon sink in six dynamic global vegetation models (DGVMs) across continents. This approach relies on a strong relationship among LOSS, NPP, and HR at continental or biome scales. The DGVMs overestimated historical LOSS, particularly in tropical regions and eastern North America by as much as 5 Mg ha−1 y−1. The modeled spread of DGVM-projected NPP and HR uncertainties was substantially reduced in tropical regions after incorporating the field-based mortality constraint. The observation-constrained models show a decrease in the tropical forest carbon sink by the end of the century, particularly across South America (from 2 to 1.4 PgC y−1), and an increase in the sink in North America (from 0.8 to 1.1 PgC y−1). These results highlight the feasibility of using forest demographic data to empirically constrain forest carbon sink projections and the potential overestimation of projected tropical forest carbon sinks. Here the authors use broad-scale tree mortality data to estimate biomass loss, constraining uncertainty of projected forest net primary productivity in 6 models, finding weaker tropical forest carbon sinks with climate change.
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Affiliation(s)
- Kailiang Yu
- Le Laboratoire des Sciences du Climat et de l'Environnement, IPSL-LSCECEA/CNRS/UVSQ Saclay, Gif-sur-Yvette, France. .,Department of Ecosystem and Conservation Sciences, University of Montana, Missoula, USA.
| | - Philippe Ciais
- Le Laboratoire des Sciences du Climat et de l'Environnement, IPSL-LSCECEA/CNRS/UVSQ Saclay, Gif-sur-Yvette, France.,The Cyprus Institute, Nicosia, Cyprus
| | - Sonia I Seneviratne
- Institute for Atmospheric and Climate Science, ETH Zürich, Zürich, Switzerland
| | - Zhihua Liu
- Department of Ecosystem and Conservation Sciences, University of Montana, Missoula, USA
| | - Han Y H Chen
- Faculty of Natural Resources Management, Lakehead University, Thunder Bay, ON, Canada
| | - Jonathan Barichivich
- Le Laboratoire des Sciences du Climat et de l'Environnement, IPSL-LSCECEA/CNRS/UVSQ Saclay, Gif-sur-Yvette, France.,Instituto de Geografía, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Craig D Allen
- Department of Geography and Environmental Studies, University of New Mexico, Albuquerque, NM, USA
| | - Hui Yang
- Le Laboratoire des Sciences du Climat et de l'Environnement, IPSL-LSCECEA/CNRS/UVSQ Saclay, Gif-sur-Yvette, France.,Max Planck Institute for Biogeochemistry, Jena, Germany
| | - Yuanyuan Huang
- Le Laboratoire des Sciences du Climat et de l'Environnement, IPSL-LSCECEA/CNRS/UVSQ Saclay, Gif-sur-Yvette, France.,CSIRO Oceans and Atmosphere, Aspendale, Australia
| | - Ashley P Ballantyne
- Le Laboratoire des Sciences du Climat et de l'Environnement, IPSL-LSCECEA/CNRS/UVSQ Saclay, Gif-sur-Yvette, France.,Department of Ecosystem and Conservation Sciences, University of Montana, Missoula, USA
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31
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Mi L, Mo A, Yang J, Liu H, Ren D, Chen W, Long H, Jiang N, Zhang T, Lu P. Arabidopsis Novel Microgametophyte Defective Mutant 1 Is Required for Pollen Viability via Influencing Intine Development in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2022; 13:814870. [PMID: 35498668 PMCID: PMC9039731 DOI: 10.3389/fpls.2022.814870] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 03/03/2022] [Indexed: 05/28/2023]
Abstract
The pollen intine layer is necessary for male fertility in flowering plants. However, the mechanisms behind the developmental regulation of intine formation still remain largely unknown. Here, we identified a positive regulator, Arabidopsis novel microgametophyte defective mutant 1 (AtNMDM1), which influences male fertility by regulating intine formation. The AtNMDM1, encoding a pollen nuclei-localized protein, was highly expressed in the pollens at the late anther stages, 10-12. Both the mutations and the knock-down of AtNMDM1 resulted in pollen defects and significantly lowered the seed-setting rates. Genetic transmission analysis indicated that AtNMDM1 is a microgametophyte lethal gene. Calcofluor white staining revealed that abnormal cellulose distribution was present in the aborted pollen. Ultrastructural analyses showed that the abnormal intine rather than the exine led to pollen abortion. We further found, using transcriptome analysis, that cell wall modification was the most highly enriched gene ontology (GO) term used in the category of biological processes. Notably, two categories of genes, Arabinogalactan proteins (AGPs) and pectin methylesterases (PMEs) were greatly reduced, which were associated with pollen intine formation. In addition, we also identified another regulator, AtNMDM2, which interacted with AtNMDM1 in the pollen nuclei. Taken together, we identified a novel regulator, AtNMDM1 that affected cellulose distribution in the intine by regulating intine-related gene expression; furthermore, these results provide insights into the molecular mechanisms of pollen intine development.
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Affiliation(s)
- Limin Mi
- School of Life Sciences, Fudan University, Shanghai, China
| | - Aowei Mo
- School of Life Sciences, Fudan University, Shanghai, China
| | - Jiange Yang
- School of Life Sciences, Fudan University, Shanghai, China
| | - Hui Liu
- School of Life Sciences, Fudan University, Shanghai, China
| | - Ding Ren
- School of Life Sciences, Fudan University, Shanghai, China
| | - Wanli Chen
- School of Life Sciences, Fudan University, Shanghai, China
| | - Haifei Long
- School of Life Sciences, Fudan University, Shanghai, China
| | - Ning Jiang
- School of Life Sciences, Fudan University, Shanghai, China
| | - Tian Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Pingli Lu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
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32
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Deng Y, Wan Y, Liu W, Zhang L, Zhou K, Feng P, He G, Wang N. OsFLA1 encodes a fasciclin-like arabinogalactan protein and affects pollen exine development in rice. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1247-1262. [PMID: 34985538 DOI: 10.1007/s00122-021-04028-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 12/28/2021] [Indexed: 06/14/2023]
Abstract
OsFLA1 positively regulates pollen exine development, and locates in the cellular membrane. Arabinogalactan proteins are a type of hydroxyproline-rich glycoprotein that are present in all plant tissues and cells and play important roles in plant growth and development. Little information is available on the participation of fasciclin-like arabinogalactan proteins in sexual reproduction in rice. In this study, a rice male-sterile mutant, osfla1, was isolated from an ethylmethanesulfonate-induced mutant library. The osfla1 mutant produced withered, shrunken, and abortive pollen. The gene OsFLA1 encoded a FLA protein and was expressed strongly in the anthers in rice. Subcellular localization showed that OsFLA1 was located in the cellular membrane. In the osfla1 mutant, abnormal Ubisch bodies and a discontinuous nexine layer of the microspore wall were observed, which resulted in pollen abortion and ultimately in male sterility. The results show the important role that OsFLA1 plays in male reproductive development in rice.
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Affiliation(s)
- Yao Deng
- Key Laboratory of Application and Safety Control of Genetically Modified Crops, College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
| | - Yingchun Wan
- Key Laboratory of Application and Safety Control of Genetically Modified Crops, College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
| | - Weichi Liu
- Key Laboratory of Application and Safety Control of Genetically Modified Crops, College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
| | - Lisha Zhang
- Key Laboratory of Application and Safety Control of Genetically Modified Crops, College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
| | - Kai Zhou
- 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
| | - Guanghua He
- Key Laboratory of Application and Safety Control of Genetically Modified Crops, College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
| | - Nan Wang
- Key Laboratory of Application and Safety Control of Genetically Modified Crops, College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China.
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33
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Naik J, Misra P, Trivedi PK, Pandey A. Molecular components associated with the regulation of flavonoid biosynthesis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 317:111196. [PMID: 35193745 DOI: 10.1016/j.plantsci.2022.111196] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 01/04/2022] [Accepted: 01/21/2022] [Indexed: 06/14/2023]
Abstract
Flavonoids exhibit amazing structural diversity and play different roles in plants. Besides, these compounds have been associated with several health benefits in humans. Several exogenous and endogenous cues, for example, light, temperature, nutrient status, and phytohormones have been reported as modulators of biosynthesis and accumulation of flavonoids. Thus, multiple hormones and stress-related signaling pathways are involved in the regulation of gene expression associated with this pathway. The transcriptional regulators belonging to the MYB and bHLH family transcription factors are well documented as the direct regulators of the structural genes associated with flavonoid biosynthesis. Recent studies also suggest that some of these factors are regulated by molecular components involved in stress and hormone signaling pathways. Adapter proteins for transcriptional activation or repression via recruitment of co-activators and co-repressors, respectively, E2 ubiquitin ligases, miRNA processing complex, and DNA methylation/demethylation factors have been recently discovered in various plants to play key roles in fine-tuning flavonoids synthesis. In the present review, we aim to provide comprehensive information about the role of different factors in the regulation of flavonoid biosynthesis. Besides, we describe the potential upstream regulators involved in the regulation of flavonoid biosynthesis within the context of available information. To sum up, the present review furnishes an updated account of signal transduction pathways modulating the biosynthesis of flavonoids.
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Affiliation(s)
- Jogindra Naik
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Prashant Misra
- Plant Science and Agrotechnology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
| | | | - Ashutosh Pandey
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India.
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34
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Yang K, Han H, Li Y, Ye J, Xu F. Significance of miRNA in enhancement of flavonoid biosynthesis. PLANT BIOLOGY (STUTTGART, GERMANY) 2022; 24:217-226. [PMID: 34806280 DOI: 10.1111/plb.13361] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 10/15/2021] [Indexed: 05/20/2023]
Abstract
Flavonoid metabolism shows very strong plasticity in plant development and coping with the changing environment. Flavonoid biosynthesis is regulated by many metabolic pathways, including transcriptional regulation, post-transcriptional control, post-translational regulationand epigenetic regulation. miRNA is a form of endogenous noncoding single-strand small molecule RNA that primarily regulates the expression of target genes horizontally after transcription through splicing and translational suppression. It also plays an important role in regulating plant growth and development, secondary metabolism and biotic and abiotic stress. miRNA can regulate the formation of flavonoids by acting on structural genes or indirectly by using an MBW transcription complex comprising MYB-bHLH-WD40. This study summarizes the biosynthesis and mechanisms of miRNA, and provides a summary of the mechanisms of miRNAs involved in production of flavonoids, in order to elucidate the biosynthesis pathway and complex regulatory network of plant flavonoids. We aim to provide new insights into improving the content of flavonoid active ingredients in plants.
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Affiliation(s)
- K Yang
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
| | - H Han
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
| | - Y Li
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
| | - J Ye
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
| | - F Xu
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
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35
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Wang J, Zhang C, Li Y. Genome-Wide Identification and Expression Profiles of 13 Key Structural Gene Families Involved in the Biosynthesis of Rice Flavonoid Scaffolds. Genes (Basel) 2022; 13:genes13030410. [PMID: 35327963 PMCID: PMC8951560 DOI: 10.3390/genes13030410] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 02/18/2022] [Accepted: 02/23/2022] [Indexed: 12/31/2022] Open
Abstract
Flavonoids are a class of key polyphenolic secondary metabolites with broad functions in plants, including stress defense, growth, development and reproduction. Oryza sativa L. (rice) is a well-known model plant for monocots, with a wide range of flavonoids, but the key flavonoid biosynthesis-related genes and their molecular features in rice have not been comprehensively and systematically characterized. Here, we identified 85 key structural gene candidates associated with flavonoid biosynthesis in the rice genome. They belong to 13 families potentially encoding chalcone synthase (CHS), chalcone isomerase (CHI), flavanone 3-hydroxylase (F3H), flavonol synthase (FLS), leucoanthocyanidin dioxygenase (LDOX), anthocyanidin synthase (ANS), flavone synthase II (FNSII), flavanone 2-hydroxylase (F2H), flavonoid 3′-hydroxylase (F3′H), flavonoid 3′,5′-hydroxylase (F3′5′H), dihydroflavonol 4-reductase (DFR), anthocyanidin reductase (ANR) and leucoanthocyanidin reductase (LAR). Through structural features, motif analyses and phylogenetic relationships, these gene families were further grouped into five distinct lineages and were examined for conservation and divergence. Subsequently, 22 duplication events were identified out of a total of 85 genes, among which seven pairs were derived from segmental duplication events and 15 pairs were from tandem duplications, demonstrating that segmental and tandem duplication events play important roles in the expansion of key flavonoid biosynthesis-related genes in rice. Furthermore, these 85 genes showed spatial and temporal regulation in a tissue-specific manner and differentially responded to abiotic stress (including six hormones and cold and salt treatments). RNA-Seq, microarray analysis and qRT-PCR indicated that these genes might be involved in abiotic stress response, plant growth and development. Our results provide a valuable basis for further functional analysis of the genes involved in the flavonoid biosynthesis pathway in rice.
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36
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Lan Y, Zhang K, Wang Y, Wu J, Lin M, Yan H, Xiang Y. Comparative analysis of the stellacyanins (SCs) family and focus on drought resistance of PtSC18 in Populus trichocarpa. Gene 2021; 813:146106. [PMID: 34953936 DOI: 10.1016/j.gene.2021.146106] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/28/2021] [Accepted: 11/16/2021] [Indexed: 11/18/2022]
Abstract
Stellacyanin (SC) is a type I (blue) copper protein, which plays a crucial role in plant growth and stress response. However, the comprehensive analysis and functional research of SCs in the woody plant is still lacking. Here, a total of 74 SCs were collected and identified from Arabidopsis, papaya, grape, rice and poplar. Bioinformatics was used to analyze the gene structure, protein structure and evolutionary relationship of 74 genes, especially 19 SCs in Populus trichocarpa. Based on the RNA-seq data, expression pattern of SCs in poplar under cold, high temperature, drought and salt stress were further analyzed. Subsequently, a key candidate gene PtSC18 that strongly responded to drought stress was screened. Subcellular localization experiment exhibited that PtSC18 was localized in the nucleus and plasma membrane. Overexpression of PtSC18 enhanced drought tolerance of transgenic Arabidopsis by improving water retention and reducing oxidative damage. Measurements of physiological indicators, including chlorophyll, H2O2, malondialdehyde content, peroxidase and catalase enzyme activities and electrical conductivity, all supported this conclusion. More importantly, PtSC18 enhanced the expression of some stress-related genes in transgenic Arabidopsis. Overall, our results lay a foundation for understanding the structure and function of PtSCs and provide useful gene resources for breeding through genetic engineering.
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Affiliation(s)
- Yangang Lan
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei 230036, China
| | - Kaimei Zhang
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei 230036, China
| | - Yamei Wang
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei 230036, China
| | - Jing Wu
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei 230036, China
| | - Miao Lin
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei 230036, China
| | - Hanwei Yan
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei 230036, China.
| | - Yan Xiang
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei 230036, China.
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Zhou YF, Zhang YC, Sun YM, Yu Y, Lei MQ, Yang YW, Lian JP, Feng YZ, Zhang Z, Yang L, He RR, Huang JH, Cheng Y, Liu YW, Chen YQ. The parent-of-origin lncRNA MISSEN regulates rice endosperm development. Nat Commun 2021; 12:6525. [PMID: 34764271 PMCID: PMC8585977 DOI: 10.1038/s41467-021-26795-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 10/22/2021] [Indexed: 11/09/2022] Open
Abstract
The cereal endosperm is a major factor determining seed size and shape. However, the molecular mechanisms of endosperm development are not fully understood. Long noncoding RNAs (lncRNAs) function in various biological processes. Here we show a lncRNA, MISSEN, that plays an essential role in early endosperm development in rice (Oryza sativa). MISSEN is a parent-of-origin lncRNA expressed in endosperm, and negatively regulates endosperm development, leading to a prominent dent and bulge in the seed. Mechanistically, MISSEN functions through hijacking a helicase family protein (HeFP) to regulate tubulin function during endosperm nucleus division and endosperm cellularization, resulting in abnormal cytoskeletal polymerization. Finally, we revealed that the expression of MISSEN is inhibited by histone H3 lysine 27 trimethylation (H3K27me3) modification after pollination. Therefore, MISSEN is the first lncRNA identified as a regulator in endosperm development, highlighting the potential applications in rice breeding.
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Affiliation(s)
- Yan-Fei Zhou
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Yu-Chan Zhang
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Yu-Meng Sun
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Yang Yu
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Meng-Qi Lei
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Yu-Wei Yang
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Jian-Ping Lian
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Yan-Zhao Feng
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Zhi Zhang
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Lu Yang
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Rui-Rui He
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Jia-Hui Huang
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Yu Cheng
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Yu-Wei Liu
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Yue-Qin Chen
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, 510275, Guangzhou, China. .,MOE Key Laboratory of Gene Function and Regulation, Sun Yat-sen University, 510275, Guangzhou, China.
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You L, Lin J, Xu H, Chen C, Chen J, Zhang J, Zhang J, Li Y, Ye C, Zhang H, Jiang J, Zhu J, Li QQ, Duan C. Intragenic heterochromatin-mediated alternative polyadenylation modulates miRNA and pollen development in rice. THE NEW PHYTOLOGIST 2021; 232:835-852. [PMID: 34289124 PMCID: PMC9292364 DOI: 10.1111/nph.17635] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 06/25/2021] [Indexed: 05/02/2023]
Abstract
Despite a much higher proportion of intragenic heterochromatin-containing genes in crop genomes, the importance of intragenic heterochromatin in crop development remains unclear. Intragenic heterochromatin can be recognised by a protein complex, ASI1-AIPP1-EDM2 (AAE) complex, to regulate alternative polyadenylation. Here, we investigated the impact of rice ASI1 on global poly(A) site usage through poly(A) sequencing and ASI1-dependent regulation on rice development. We found that OsASI1 is essential for rice pollen development and flowering. OsASI1 dysfunction has an important impact on global poly(A) site usage, which is closely related to heterochromatin marks. Intriguingly, OsASI1 interacts with the intronic heterochromatin of OsXRNL, a nuclear XRN family exonuclease gene involved in the processing of an miRNA precursor, to promote the processing of full-length OsXRNL and regulate miRNA abundance. We found that OsASI1-mediated regulation of pollen development partially depends on OsXRNL. Finally, we characterised the rice AAE complex and its involvement in alternative polyadenylation and pollen development. Our findings help to elucidate an epigenetic mechanism governing miRNA abundance and rice development, and provide a valuable resource for studying the epigenetic mechanisms of many important processes in crops.
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Affiliation(s)
- Li‐Yuan You
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant SciencesChinese Academy of ScienceShanghai201602China
- University of Chinese Academy of SciencesBeijing100049China
| | - Juncheng Lin
- Key Laboratory of the Ministry of Education for Coastal and Wetland EcosystemsCollege of the Environment and EcologyXiamen UniversityXiamenFujian361102China
| | - Hua‐Wei Xu
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant SciencesChinese Academy of ScienceShanghai201602China
- College of AgricultureHenan University of Science and TechnologyLuoyang471023China
| | - Chun‐Xiang Chen
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant SciencesChinese Academy of ScienceShanghai201602China
- University of Chinese Academy of SciencesBeijing100049China
| | - Jun‐Yu Chen
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant SciencesChinese Academy of ScienceShanghai201602China
- University of Chinese Academy of SciencesBeijing100049China
| | - Jinshan Zhang
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant SciencesChinese Academy of ScienceShanghai201602China
| | - Jian Zhang
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant SciencesChinese Academy of ScienceShanghai201602China
- University of Chinese Academy of SciencesBeijing100049China
| | - Ying‐Xin Li
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant SciencesChinese Academy of ScienceShanghai201602China
- University of Chinese Academy of SciencesBeijing100049China
| | - Congting Ye
- Key Laboratory of the Ministry of Education for Coastal and Wetland EcosystemsCollege of the Environment and EcologyXiamen UniversityXiamenFujian361102China
| | - Hui Zhang
- College of Life ScienceShanghai Normal UniversityShanghai200234China
| | - Jing Jiang
- State Key Laboratory of Crop Stress Adaptation and ImprovementSchool of Life SciencesHenan UniversityKaifeng475004China
| | - Jian‐Kang Zhu
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant SciencesChinese Academy of ScienceShanghai201602China
| | - Qingshun Q. Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland EcosystemsCollege of the Environment and EcologyXiamen UniversityXiamenFujian361102China
- Graduate College of Biomedical SciencesWestern University of Health SciencesPomonaCA91766USA
| | - Cheng‐Guo Duan
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant SciencesChinese Academy of ScienceShanghai201602China
- University of Chinese Academy of SciencesBeijing100049China
- State Key Laboratory of Crop Stress Adaptation and ImprovementSchool of Life SciencesHenan UniversityKaifeng475004China
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Kan L, Liao Q, Chen Z, Wang S, Ma Y, Su Z, Zhang L. Dynamic Transcriptomic and Metabolomic Analyses of Madhuca pasquieri (Dubard) H. J. Lam During the Post-germination Stages. FRONTIERS IN PLANT SCIENCE 2021; 12:731203. [PMID: 34659296 PMCID: PMC8516028 DOI: 10.3389/fpls.2021.731203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 08/24/2021] [Indexed: 06/02/2023]
Abstract
The wild population of Madhuca pasquieri (Dubard) H. J. Lam is currently dwindling; its understory seedlings are rare, and there is a lack of molecular studies, which impedes the conservation of this species. This study exploited second-generation sequencing and widely targeted metabolomics analysis to uncover the dynamic changes in differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) in five post-germination stages of M. pasquieri whole organism. Notably, the weighted gene co-expression network analysis (WGCNA), transcriptome, and metabolome association analyses all indicated significant enrichment of the flavonoid biosynthesis pathway in stage 4 (two-leaf), and an upregulation of the genes encoding flavonol biosynthesis in this stage. In stage 5 (nine-leaf), the flavonols were significantly accumulated, indicating that the changes in metabolites were driven at the transcript level. According to the significant changes in gene expression encoding auxin transport carriers and their correlation with flavonols during stage 5, the flavonols were speculated to have a direct inhibitory effect on the expression of PIN4 encoding gene, which may inhibit the process of polar auxin transport. The results provided important insights into the molecular network relationships between the transcription and metabolism of this rare and endangered species during the post-germination stages and explained the reasons for the slow growth of its seedlings at the molecular level.
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Wang M, Guo W, Li J, Pan X, Pan L, Zhao J, Zhang Y, Cai S, Huang X, Wang A, Liu Q. The miR528- AO Module Confers Enhanced Salt Tolerance in Rice by Modulating the Ascorbic Acid and Abscisic Acid Metabolism and ROS Scavenging. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:8634-8648. [PMID: 34339211 DOI: 10.1021/acs.jafc.1c01096] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The monocot lineage-specific miR528 was previously established as a multistress regulator. However, it remains largely unclear how miR528 participates in response to salinity stress in rice. Here, we show that miR528 positively regulates rice salt tolerance by down-regulating a gene encoding l-ascorbate oxidase (AO), thereby bolstering up the AO-mediated abscisic acid (ABA) synthesis and ROS scavenging. Overexpression of miR528 caused a substantial increase in ascorbic acid (AsA) and ABA contents but a significant reduction in ROS accumulation, resulting in the enhanced salt tolerance of rice plants. Conversely, knockdown of miR528 or overexpression of AO stimulated the expression of the AO gene, hence lowering the level of AsA, a critical antioxidant that promotes the ABA content but reduces the ROS level, and then compromising rice tolerance to salinity. Together, the findings reveal a novel mechanism of the miR528-AO module-mediated salt tolerance by modulating the processes of AsA and ABA metabolism as well as ROS detoxification, which adds a new regulatory role to the miR528-AO stress defense pathway in rice.
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Affiliation(s)
- Mei Wang
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, P. R. China
| | - Wenping Guo
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, P. R. China
| | - Jun Li
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, P. R. China
| | - Xiangjian Pan
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, P. R. China
| | - Lihao Pan
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, P. R. China
| | - Juan Zhao
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, P. R. China
| | - Yiwei Zhang
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, P. R. China
| | - Shitian Cai
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, P. R. China
| | - Xia Huang
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, P. R. China
| | - An Wang
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, P. R. China
| | - Qingpo Liu
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, P. R. China
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ZmFAR1 and ZmABCG26 Regulated by microRNA Are Essential for Lipid Metabolism in Maize Anther. Int J Mol Sci 2021; 22:ijms22157916. [PMID: 34360681 PMCID: PMC8348775 DOI: 10.3390/ijms22157916] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/18/2021] [Accepted: 07/21/2021] [Indexed: 12/12/2022] Open
Abstract
The function and regulation of lipid metabolic genes are essential for plant male reproduction. However, expression regulation of lipid metabolic genic male sterility (GMS) genes by noncoding RNAs is largely unclear. Here, we systematically predicted the microRNA regulators of 34 maize white brown complex members in ATP-binding cassette transporter G subfamily (WBC/ABCG) genes using transcriptome analysis. Results indicate that the ZmABCG26 transcript was predicted to be targeted by zma-miR164h-5p, and their expression levels were negatively correlated in maize B73 and Oh43 genetic backgrounds based on both transcriptome data and qRT-PCR experiments. CRISPR/Cas9-induced gene mutagenesis was performed on ZmABCG26 and another lipid metabolic gene, ZmFAR1. DNA sequencing, phenotypic, and cytological observations demonstrated that both ZmABCG26 and ZmFAR1 are GMS genes in maize. Notably, ZmABCG26 proteins are localized in the endoplasmic reticulum (ER), chloroplast/plastid, and plasma membrane. Furthermore, ZmFAR1 shows catalytic activities to three CoA substrates in vitro with the activity order of C12:0-CoA > C16:0-CoA > C18:0-CoA, and its four key amino acid sites were critical to its catalytic activities. Lipidomics analysis revealed decreased cutin amounts and increased wax contents in anthers of both zmabcg26 and zmfar1 GMS mutants. A more detailed analysis exhibited differential changes in 54 monomer contents between wild type and mutants, as well as between zmabcg26 and zmfar1. These findings will promote a deeper understanding of miRNA-regulated lipid metabolic genes and the functional diversity of lipid metabolic genes, contributing to lipid biosynthesis in maize anthers. Additionally, cosegregating molecular markers for ZmABCG26 and ZmFAR1 were developed to facilitate the breeding of male sterile lines.
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Rawandoozi ZJ, Hartmann TP, Carpenedo S, Gasic K, da Silva Linge C, Cai L, Van de Weg E, Byrne DH. Mapping and characterization QTLs for phenological traits in seven pedigree-connected peach families. BMC Genomics 2021; 22:187. [PMID: 33726679 PMCID: PMC7962356 DOI: 10.1186/s12864-021-07483-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 02/25/2021] [Indexed: 12/02/2022] Open
Abstract
Background Environmental adaptation and expanding harvest seasons are primary goals of most peach [Prunus persica (L.) Batsch] breeding programs. Breeding perennial crops is a challenging task due to their long breeding cycles and large tree size. Pedigree-based analysis using pedigreed families followed by haplotype construction creates a platform for QTL and marker identification, validation, and the use of marker-assisted selection in breeding programs. Results Phenotypic data of seven F1 low to medium chill full-sib families were collected over 2 years at two locations and genotyped using the 9 K SNP Illumina array. Three QTLs were discovered for bloom date (BD) and mapped on linkage group 1 (LG1) (172–182 cM), LG4 (48–54 cM), and LG7 (62–70 cM), explaining 17–54%, 11–55%, and 11–18% of the phenotypic variance, respectively. The QTL for ripening date (RD) and fruit development period (FDP) on LG4 was co-localized at the central part of LG4 (40–46 cM) and explained between 40 and 75% of the phenotypic variance. Haplotype analyses revealed SNP haplotypes and predictive SNP marker(s) associated with desired QTL alleles and the presence of multiple functional alleles with different effects for a single locus for RD and FDP. Conclusions A multiple pedigree-linked families approach validated major QTLs for the three key phenological traits which were reported in previous studies across diverse materials, geographical distributions, and QTL mapping methods. Haplotype characterization of these genomic regions differentiates this study from the previous QTL studies. Our results will provide the peach breeder with the haplotypes for three BD QTLs and one RD/FDP QTL to create predictive DNA-based molecular marker tests to select parents and/or seedlings that have desired QTL alleles and cull unwanted genotypes in early seedling stages. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07483-8.
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Affiliation(s)
- Zena J Rawandoozi
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843, USA.
| | - Timothy P Hartmann
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Silvia Carpenedo
- Embrapa Clima Temperado, BR-392, km 78, Cx. Postal 403, Pelotas, Rio Grande do Sul, 96010-971, Brazil
| | - Ksenija Gasic
- Department of Agricultural and Environmental Sciences, College of Agriculture, Forestry and Life Sciences, Clemson University, Clemson, SC, 29634, USA
| | - Cassia da Silva Linge
- Department of Agricultural and Environmental Sciences, College of Agriculture, Forestry and Life Sciences, Clemson University, Clemson, SC, 29634, USA
| | - Lichun Cai
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Eric Van de Weg
- Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
| | - David H Byrne
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843, USA
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Abbas A, Yu P, Sun L, Yang Z, Chen D, Cheng S, Cao L. Exploiting Genic Male Sterility in Rice: From Molecular Dissection to Breeding Applications. FRONTIERS IN PLANT SCIENCE 2021; 12:629314. [PMID: 33763090 PMCID: PMC7982899 DOI: 10.3389/fpls.2021.629314] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 01/28/2021] [Indexed: 06/12/2023]
Abstract
Rice (Oryza sativa L.) occupies a very salient and indispensable status among cereal crops, as its vast production is used to feed nearly half of the world's population. Male sterile plants are the fundamental breeding materials needed for specific propagation in order to meet the elevated current food demands. The development of the rice varieties with desired traits has become the ultimate need of the time. Genic male sterility is a predominant system that is vastly deployed and exploited for crop improvement. Hence, the identification of new genetic elements and the cognizance of the underlying regulatory networks affecting male sterility in rice are crucial to harness heterosis and ensure global food security. Over the years, a variety of genomics studies have uncovered numerous mechanisms regulating male sterility in rice, which provided a deeper and wider understanding on the complex molecular basis of anther and pollen development. The recent advances in genomics and the emergence of multiple biotechnological methods have revolutionized the field of rice breeding. In this review, we have briefly documented the recent evolution, exploration, and exploitation of genic male sterility to the improvement of rice crop production. Furthermore, this review describes future perspectives with focus on state-of-the-art developments in the engineering of male sterility to overcome issues associated with male sterility-mediated rice breeding to address the current challenges. Finally, we provide our perspectives on diversified studies regarding the identification and characterization of genic male sterility genes, the development of new biotechnology-based male sterility systems, and their integrated applications for hybrid rice breeding.
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Affiliation(s)
- Adil Abbas
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Ping Yu
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Lianping Sun
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Zhengfu Yang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Daibo Chen
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Shihua Cheng
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Liyong Cao
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
- Northern Center of China National Rice Research Institute, Shuangyashan, China
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Dong NQ, Lin HX. Contribution of phenylpropanoid metabolism to plant development and plant-environment interactions. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:180-209. [PMID: 33325112 DOI: 10.1111/jipb.13054] [Citation(s) in RCA: 412] [Impact Index Per Article: 137.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/10/2020] [Indexed: 05/21/2023]
Abstract
Phenylpropanoid metabolism is one of the most important metabolisms in plants, yielding more than 8,000 metabolites contributing to plant development and plant-environment interplay. Phenylpropanoid metabolism materialized during the evolution of early freshwater algae that were initiating terrestrialization and land plants have evolved multiple branches of this pathway, which give rise to metabolites including lignin, flavonoids, lignans, phenylpropanoid esters, hydroxycinnamic acid amides, and sporopollenin. Recent studies have revealed that many factors participate in the regulation of phenylpropanoid metabolism, and modulate phenylpropanoid homeostasis when plants undergo successive developmental processes and are subjected to stressful environments. In this review, we summarize recent progress on elucidating the contribution of phenylpropanoid metabolism to the coordination of plant development and plant-environment interaction, and metabolic flux redirection among diverse metabolic routes. In addition, our review focuses on the regulation of phenylpropanoid metabolism at the transcriptional, post-transcriptional, post-translational, and epigenetic levels, and in response to phytohormones and biotic and abiotic stresses.
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Affiliation(s)
- Nai-Qian Dong
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics and Development, Shanghai Institute of Plant Physiology and Ecology, the Chinese Academy of Sciences, Shanghai, 200032, China
| | - Hong-Xuan Lin
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics and Development, Shanghai Institute of Plant Physiology and Ecology, the Chinese Academy of Sciences, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
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Kandpal M, Vishwakarma C, Krishnan K, Chinnusamy V, Pareek A, Sharma MK, Sharma R. Gene Expression Dynamics in Rice Peduncles at the Heading Stage. Front Genet 2020; 11:584678. [PMID: 33343630 PMCID: PMC7744745 DOI: 10.3389/fgene.2020.584678] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 11/09/2020] [Indexed: 11/16/2022] Open
Abstract
Improving grain yield in the staple food crop rice has been long sought goal of plant biotechnology. One of the traits with significant impact on rice breeding programs is peduncle elongation at the time of heading failing which leads to significant reduction in grain yield due to incomplete panicle exsertion. To decipher transcriptional dynamics and molecular players underlying peduncle elongation, we performed RNA sequencing analysis of elongating and non-elongating peduncles in two Indian cultivars, Swarna and Pokkali, at the time of heading. Along with genes associated with cell division and cell wall biosynthesis, we observed significant enrichment of genes associated with auxins, gibberellins, and brassinosteroid biosynthesis/signaling in the elongating peduncles before heading in both the genotypes. Similarly, genes associated with carbohydrate metabolism and mobilization, abiotic stress response along with cytokinin, abscisic acid, jasmonic acid, and ethylene biosynthesis/signaling were enriched in non-elongating peduncles post heading. Significant enrichment of genes belonging to key transcription factor families highlights their specialized roles in peduncle elongation and grain filling before and after heading, respectively. A comparison with anther/pollen development-related genes provided 76 candidates with overlapping roles in anther/pollen development and peduncle elongation. Some of these are important for carbohydrate remobilization to the developing grains. These can be engineered to combat with incomplete panicle exsertion in male sterile lines and manipulate carbohydrate dynamics in grasses. Overall, this study provides baseline information about potential target genes for engineering peduncle elongation with implications on plant height, biomass composition and grain yields in rice.
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Affiliation(s)
- Manu Kandpal
- Grass Genetics and Informatics Group, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Chandrapal Vishwakarma
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Kushagra Krishnan
- Grass Genetics and Informatics Group, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Viswanathan Chinnusamy
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Ashwani Pareek
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Manoj K. Sharma
- Grass Genetics and Informatics Group, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Rita Sharma
- Grass Genetics and Informatics Group, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
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