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La S, Li J, Ma S, Liu X, Gao L, Tian Y. Protective role of native root-associated bacterial consortium against root-knot nematode infection in susceptible plants. Nat Commun 2024; 15:6723. [PMID: 39112511 PMCID: PMC11306399 DOI: 10.1038/s41467-024-51073-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 07/26/2024] [Indexed: 08/10/2024] Open
Abstract
Root-knot nematodes (RKNs) are a global menace to agricultural crop production. The role of root-associated microbes (RAMs) in plant protection against RKN infection remains unclear. Here we observe that cucumber (highly susceptible to Meloidogyne incognita) exhibits a consistently lower susceptibility to M. incognita in the presence of native RAMs in three distinct soils. Nematode infection alters the assembly of bacterial RAMs along the life cycle of M. incognita. Particularly, the loss of bacterial diversity of RAMs exacerbates plant susceptibility to M. incognita. A diverse range of native bacterial strains isolated from M. incognita-infected roots has nematode-antagonistic activity. Increasing the number of native bacterial strains causes decreasing nematode infection, which is lowest when six or more bacterial strains are present. Multiple simplified synthetic communities consisting of six bacterial strains show pronounced inhibitory effects on M. incognita infection in plants. These inhibitory effects are underpinned via multiple mechanisms including direct inhibition of infection, secretion of anti-nematode substances, and regulation of plant defense responses. This study highlights the role of native bacterial RAMs in plant resistance against RKNs and provides a useful insight into the development of a sustainable way to protect susceptible plants.
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Affiliation(s)
- Shikai La
- College of Horticulture, China Agricultural University, Yuanmingyuan West Road No. 2, Haidian District, Beijing, 100193, China
- Institute of Economic Crops, Hebei Academy of Agricultural and Forestry Sciences, Heping West Road No. 598, Shijiazhuang, 050051, China
| | - Jiafan Li
- College of Horticulture, China Agricultural University, Yuanmingyuan West Road No. 2, Haidian District, Beijing, 100193, China
| | - Si Ma
- College of Horticulture, China Agricultural University, Yuanmingyuan West Road No. 2, Haidian District, Beijing, 100193, China
| | - Xingqun Liu
- College of Horticulture, China Agricultural University, Yuanmingyuan West Road No. 2, Haidian District, Beijing, 100193, China
| | - Lihong Gao
- College of Horticulture, China Agricultural University, Yuanmingyuan West Road No. 2, Haidian District, Beijing, 100193, China.
| | - Yongqiang Tian
- College of Horticulture, China Agricultural University, Yuanmingyuan West Road No. 2, Haidian District, Beijing, 100193, China.
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2
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Gawande ND, Bhalla H, Watts A, Shelake RM, Sankaranarayanan S. Application of genome editing in plant reproductive biology: recent advances and challenges. PLANT REPRODUCTION 2024:10.1007/s00497-024-00506-w. [PMID: 38954018 DOI: 10.1007/s00497-024-00506-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Accepted: 06/21/2024] [Indexed: 07/04/2024]
Abstract
KEY MESSAGE This comprehensive review underscores the application of genome editing in plant reproductive biology, including recent advances and challenges associated with it. Genome editing (GE) is a powerful technology that has the potential to accelerate crop improvement by enabling efficient, precise, and rapid engineering of plant genomes. Over the last decade, this technology has rapidly evolved from the use of meganucleases (homing endonucleases), zinc-finger nucleases, transcription activator-like effector nucleases to the use of clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (CRISPR/Cas), which has emerged as a popular GE tool in recent times and has been extensively used in several organisms, including plants. GE has been successfully employed in several crops to improve plant reproductive traits. Improving crop reproductive traits is essential for crop yields and securing the world's food supplies. In this review, we discuss the application of GE in various aspects of plant reproductive biology, including its potential application in haploid induction, apomixis, parthenocarpy, development of male sterile lines, and the regulation of self-incompatibility. We also discuss current challenges and future prospects of this technology for crop improvement, focusing on plant reproduction.
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Affiliation(s)
- Nilesh D Gawande
- Department of Biological Sciences and Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gujarat, 382355, India
| | - Hemal Bhalla
- Department of Biological Sciences and Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gujarat, 382355, India
| | - Anshul Watts
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - Rahul Mahadev Shelake
- Division of Applied Life Science (BK21 Four Program), Plant Molecular and Biotechnology Research Center, Gyeongsang National University, Jinju, 52828, Korea
| | - Subramanian Sankaranarayanan
- Department of Biological Sciences and Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gujarat, 382355, India.
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3
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Mizuta Y, Sakakibara D, Nagahara S, Kaneshiro I, Nagae TT, Kurihara D, Higashiyama T. Deep imaging reveals dynamics and signaling in one-to-one pollen tube guidance. EMBO Rep 2024; 25:2529-2549. [PMID: 38773320 PMCID: PMC11169409 DOI: 10.1038/s44319-024-00151-4] [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: 09/07/2023] [Revised: 04/09/2024] [Accepted: 04/18/2024] [Indexed: 05/23/2024] Open
Abstract
In the pistil of flowering plants, each ovule usually associates with a single pollen tube for fertilization. This one-to-one pollen tube guidance, which contributes to polyspermy blocking and efficient seed production, is largely different from animal chemotaxis of many sperms to one egg. However, the functional mechanisms underlying the directional cues and polytubey blocks in the depths of the pistil remain unknown. Here, we develop a two-photon live imaging method to directly observe pollen tube guidance in the pistil of Arabidopsis thaliana, clarifying signaling and cellular behaviors in the one-to-one guidance. Ovules are suggested to emit multiple signals for pollen tubes, including an integument-dependent directional signal that reaches the inner surface of the septum and adhesion signals for emerged pollen tubes on the septum. Not only FERONIA in the septum but ovular gametophytic FERONIA and LORELEI, as well as FERONIA- and LORELEI-independent repulsion signal, are involved in polytubey blocks on the ovular funiculus. However, these funicular blocks are not strictly maintained in the first 45 min, explaining previous reports of polyspermy in flowering plants.
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Affiliation(s)
- Yoko Mizuta
- Institute for Advanced Research (IAR), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan.
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan.
| | - Daigo Sakakibara
- Division of Biological Sciences, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Shiori Nagahara
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan
| | - Ikuma Kaneshiro
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan
- Department of Physics, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
- Research Center for Computational Science, Institute for Molecular Science, National Institutes of Natural Sciences, 38 Nishigo-Naka, Myodaiji, Okazaki, 444-8585, Japan
| | - Takuya T Nagae
- Division of Biological Sciences, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Daisuke Kurihara
- Institute for Advanced Research (IAR), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan
| | - Tetsuya Higashiyama
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan
- Division of Biological Sciences, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bukyo-ku, Tokyo, 113-0033, Japan
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4
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Li B, Jia Y, Xu L, Zhang S, Long Z, Wang R, Guo Y, Zhang W, Jiao C, Li C, Xu Y. Transcriptional convergence after repeated duplication of an amino acid transporter gene leads to the independent emergence of the black husk/pericarp trait in barley and rice. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1282-1298. [PMID: 38124464 PMCID: PMC11022822 DOI: 10.1111/pbi.14264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 11/09/2023] [Accepted: 11/25/2023] [Indexed: 12/23/2023]
Abstract
The repeated emergence of the same trait (convergent evolution) in distinct species is an interesting phenomenon and manifests visibly the power of natural selection. The underlying genetic mechanisms have important implications to understand how the genome evolves under environmental challenges. In cereal crops, both rice and barley can develop black-coloured husk/pericarp due to melanin accumulation. However, it is unclear if this trait shares a common origin. Here, we fine-mapped the barley HvBlp gene controlling the black husk/pericarp trait and confirmed its function by gene silencing. The result was further supported by a yellow husk/pericarp mutant with deletion of the HvBlp gene, derived from gamma ray radiation of the wild-type W1. HvBlp encodes a putative tyrosine transporter homologous to the black husk gene OsBh4 in rice. Surprisingly, synteny and phylogenetic analyses showed that HvBlp and OsBh4 belonged to different lineages resulted from dispersed and tandem duplications, respectively, suggesting that the black husk/pericarp trait has emerged independently. The dispersed duplication (dated at 21.23 MYA) yielding HvBlp occurred exclusively in the common ancestor of Triticeae. HvBlp and OsBh4 displayed converged transcription in husk/pericarp tissues, contributing to the black husk/pericarp trait. Further transcriptome and metabolome data identified critical candidate genes and metabolites related to melanin production in barley. Taken together, our study described a compelling case of convergent evolution resulted from transcriptional convergence after repeated gene duplication, providing valuable genetic insights into phenotypic evolution. The identification of the black husk/pericarp genes in barley also has great potential in breeding for stress-resilient varieties with higher nutritional values.
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Affiliation(s)
- Bo Li
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement & Key Laboratory of Ministry of Agriculture and Rural Affairs for Crop Molecular Breeding, Food Crops InstituteHubei Academy of Agricultural SciencesWuhanChina
| | - Yong Jia
- Western Crop Genetics Alliance, Future Food Institute, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Le Xu
- Hubei Collaborative Innovation Centre for the industrialization of Major Grain Crops, College of AgricultureYangtze UniversityJingzhouChina
| | - Shuo Zhang
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement & Key Laboratory of Ministry of Agriculture and Rural Affairs for Crop Molecular Breeding, Food Crops InstituteHubei Academy of Agricultural SciencesWuhanChina
| | - Zhoukai Long
- Hubei Collaborative Innovation Centre for the industrialization of Major Grain Crops, College of AgricultureYangtze UniversityJingzhouChina
| | - Rong Wang
- Hubei Collaborative Innovation Centre for the industrialization of Major Grain Crops, College of AgricultureYangtze UniversityJingzhouChina
| | - Ying Guo
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement & Key Laboratory of Ministry of Agriculture and Rural Affairs for Crop Molecular Breeding, Food Crops InstituteHubei Academy of Agricultural SciencesWuhanChina
| | - Wenying Zhang
- Hubei Collaborative Innovation Centre for the industrialization of Major Grain Crops, College of AgricultureYangtze UniversityJingzhouChina
| | - Chunhai Jiao
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement & Key Laboratory of Ministry of Agriculture and Rural Affairs for Crop Molecular Breeding, Food Crops InstituteHubei Academy of Agricultural SciencesWuhanChina
| | - Chengdao Li
- Western Crop Genetics Alliance, Future Food Institute, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWestern AustraliaAustralia
- Department of Primary Industries and Regional DevelopmentSouth PerthWestern AustraliaAustralia
| | - Yanhao Xu
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement & Key Laboratory of Ministry of Agriculture and Rural Affairs for Crop Molecular Breeding, Food Crops InstituteHubei Academy of Agricultural SciencesWuhanChina
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5
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Sun W, Chen Y, Zeng J, Li C, Yao M, Liu M, Ma Z, Huang L, Yan J, Zhan J, Chen H, Bu T, Tang Z, Li Q, Wu Q, Hou J, Huang Y. The Tartary buckwheat bHLH gene ALCATRAZ enables Arabidopsis thaliana silique dehiscence. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023:111733. [PMID: 37211220 DOI: 10.1016/j.plantsci.2023.111733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 04/02/2023] [Accepted: 05/15/2023] [Indexed: 05/23/2023]
Abstract
Tartary buckwheat is popular because of its rich nutrients. However, the difficulty in shelling restricts food production. The gene ALCATRAZ (AtALC) plays a key role in silique dehiscence in Arabidopsis thaliana. In this study, an atalc mutant was obtained by CRISPR/Cas9, and a FtALC gene homologous to AtALC was complemented into the atalc mutant to verify its function. Phenotypic observations showed that three atalc mutant lines did not dehiscence, while ComFtALC lines recovered the dehiscence phenotype. The contents of lignin, cellulose, hemicellulose, and pectin in the siliques of all the atalc mutant lines were significantly higher than those in the wild-type and ComFtALC lines. Moreover, FtALC was found to regulate the expression of cell wall pathway genes. Finally, the interaction of FtALC with FtSHP and FtIND was verified by yeast two-hybrid, bimolecular fluorescent complimentary (BIFC) and firefly luciferase completion imaging assays (LCIs). Our findings enrich the silique regulatory network and lay the foundation for the cultivation of easily shelled tartary buckwheat varieties.
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Affiliation(s)
- Wenjun Sun
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China.
| | - Ying Chen
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China.
| | - Jing Zeng
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China.
| | - Chenglei Li
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China.
| | - Min Yao
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China.
| | - Moyang Liu
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Zhaotang Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Key Laboratory of Major Crop Diseases and Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China.
| | - Li Huang
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China.
| | - Jun Yan
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, Sichuan, China.
| | - Junyi Zhan
- College of Life Science, Nanjing Agricultural University, Nanjing 210032, China.
| | - Hui Chen
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China.
| | - Tongliang Bu
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China.
| | - Zizong Tang
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China.
| | - Qingfeng Li
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China.
| | - Qi Wu
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China.
| | - Jingfei Hou
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China.
| | - Yulin Huang
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China.
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6
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Luo H, Zhang H, Wang H. Advance in sex differentiation in cucumber. FRONTIERS IN PLANT SCIENCE 2023; 14:1186904. [PMID: 37265638 PMCID: PMC10231686 DOI: 10.3389/fpls.2023.1186904] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 04/20/2023] [Indexed: 06/03/2023]
Abstract
Cucumber belongs to the family Cucurbitaceae (melon genus) and is an annual herbaceous vegetable crop. Cucumber is an important cash crop that is grown all over the world. From morphology to cytology, from canonical genetics to molecular biology, researchers have performed much research on sex differentiation and its regulatory mechanism in cucumber, mainly in terms of cucumber sex determination genes, environmental conditions, and the effects of plant hormones, revealing its genetic basis to improve the number of female flowers in cucumber, thus greatly improving the yield of cucumber. This paper reviews the research progress of sex differentiation in cucumber in recent years, mainly focusing on sex-determining genes, environmental conditions, and the influence of phytohormones in cucumber, and provides a theoretical basis and technical support for the realization of high and stable yield cultivation and molecular breeding of cucumber crop traits.
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Affiliation(s)
- Haiyan Luo
- Key Laboratory for Quality and Safety Control of Subtropical Fruits and Vegetables, Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, China
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao, China
- Hangzhou Lin’an District Agricultural and Rural Bureau, Hangzhou, China
| | - Huanchun Zhang
- Yantai Institute of Agricultural Sciences, Yantai, China
| | - Huasen Wang
- Key Laboratory for Quality and Safety Control of Subtropical Fruits and Vegetables, Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, China
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao, China
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7
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Kiryushkin AS, Ilina EL, Guseva ED, Pawlowski K, Demchenko KN. Lateral Root Initiation in Cucumber ( Cucumis sativus): What Does the Expression Pattern of Rapid Alkalinization Factor 34 ( RALF34) Tell Us? Int J Mol Sci 2023; 24:ijms24098440. [PMID: 37176146 PMCID: PMC10179419 DOI: 10.3390/ijms24098440] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/02/2023] [Accepted: 05/04/2023] [Indexed: 05/15/2023] Open
Abstract
In Arabidopsis, the small signaling peptide (peptide hormone) RALF34 is involved in the gene regulatory network of lateral root initiation. In this study, we aimed to understand the nature of the signals induced by RALF34 in the non-model plant cucumber (Cucumis sativus), where lateral root primordia are induced in the apical meristem of the parental root. The RALF family members of cucumber were identified using phylogenetic analysis. The sequence of events involved in the initiation and development of lateral root primordia in cucumber was examined in detail. To elucidate the role of the small signaling peptide CsRALF34 and its receptor CsTHESEUS1 in the initial stages of lateral root formation in the parental root meristem in cucumber, we studied the expression patterns of both genes, as well as the localization and transport of the CsRALF34 peptide. CsRALF34 is expressed in all plant organs. CsRALF34 seems to differ from AtRALF34 in that its expression is not regulated by auxin. The expression of AtRALF34, as well as CsRALF34, is regulated in part by ethylene. CsTHESEUS1 is expressed constitutively in cucumber root tissues. Our data suggest that CsRALF34 acts in a non-cell-autonomous manner and is not involved in lateral root initiation in cucumber.
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Affiliation(s)
- Alexey S Kiryushkin
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute, Russian Academy of Sciences, 197022 Saint Petersburg, Russia
| | - Elena L Ilina
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute, Russian Academy of Sciences, 197022 Saint Petersburg, Russia
| | - Elizaveta D Guseva
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute, Russian Academy of Sciences, 197022 Saint Petersburg, Russia
| | - Katharina Pawlowski
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 10691 Stockholm, Sweden
| | - Kirill N Demchenko
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute, Russian Academy of Sciences, 197022 Saint Petersburg, Russia
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