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Liu T, Liu H, Xian W, Liu Z, Yuan Y, Fan J, Xiang S, Yang X, Liu Y, Liu S, Zhang M, Shen Y, Jiao Y, Cheng S, Doyle JJ, Xie F, Li J, Tian Z. Duplication and sub-functionalization of flavonoid biosynthesis genes plays important role in Leguminosae root nodule symbiosis evolution. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024. [PMID: 39092779 DOI: 10.1111/jipb.13743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 06/18/2024] [Accepted: 06/25/2024] [Indexed: 08/04/2024]
Abstract
Gene innovation plays an essential role in trait evolution. Rhizobial symbioses, the most important N2-fixing agent in agricultural systems that exists mainly in Leguminosae, is one of the most attractive evolution events. However, the gene innovations underlying Leguminosae root nodule symbiosis (RNS) remain largely unknown. Here, we investigated the gene gain event in Leguminosae RNS evolution through comprehensive phylogenomic analyses. We revealed that Leguminosae-gain genes were acquired by gene duplication and underwent a strong purifying selection. Kyoto Encyclopedia of Genes and Genomes analyses showed that the innovated genes were enriched in flavonoid biosynthesis pathways, particular downstream of chalcone synthase (CHS). Among them, Leguminosae-gain type Ⅱ chalcone isomerase (CHI) could be further divided into CHI1A and CHI1B clades, which resulted from the products of tandem duplication. Furthermore, the duplicated CHI genes exhibited exon-intron structural divergences evolved through exon/intron gain/loss and insertion/deletion. Knocking down CHI1B significantly reduced nodulation in Glycine max (soybean) and Medicago truncatula; whereas, knocking down its duplication gene CHI1A had no effect on nodulation. Therefore, Leguminosae-gain type Ⅱ CHI participated in RNS and the duplicated CHI1A and CHI1B genes exhibited RNS functional divergence. This study provides functional insights into Leguminosae-gain genetic innovation and sub-functionalization after gene duplication that contribute to the evolution and adaptation of RNS in Leguminosae.
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Affiliation(s)
- Tengfei Liu
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Haiyue Liu
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Key Laboratory of Plant Carbon Capture, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Wenfei Xian
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, 72076, Germany
| | - Zhi Liu
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Hebei Key Laboratory of Crop Genetics and Breeding, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shi-jiazhuang, 050035, China
| | - Yaqin Yuan
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jingwei Fan
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shuaiying Xiang
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xia Yang
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yucheng Liu
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shulin Liu
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Min Zhang
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yanting Shen
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yuannian Jiao
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
| | - Shifeng Cheng
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Jeff J Doyle
- School of Integrative Plant Science, Sections of Plant Biology and Plant Breeding & Genetics, Cornell University, Ithaca, 14853, New York, USA
| | - Fang Xie
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Key Laboratory of Plant Carbon Capture, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Jiayang Li
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- Yazhouwan National Laboratory, Sanya, 572024, China
| | - Zhixi Tian
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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2
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Acharya S, Troell HA, Billingsley RL, Lawrence KS, McKirgan DS, Alkharouf NW, Klink VP. Glycine max polygalacturonase inhibiting protein 11 (GmPGIP11) functions in the root to suppress Heterodera glycines parasitism. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 213:108755. [PMID: 38875777 DOI: 10.1016/j.plaphy.2024.108755] [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: 03/08/2024] [Revised: 05/17/2024] [Accepted: 05/19/2024] [Indexed: 06/16/2024]
Abstract
Pathogen-secreted polygalacturonases (PGs) alter plant cell wall structure by cleaving the α-(1 → 4) linkages between D-galacturonic acid residues in homogalacturonan (HG), macerating the cell wall, facilitating infection. Plant PG inhibiting proteins (PGIPs) disengage pathogen PGs, impairing infection. The soybean cyst nematode, Heterodera glycines, obligate root parasite produces secretions, generating a multinucleate nurse cell called a syncytium, a byproduct of the merged cytoplasm of 200-250 root cells, occurring through cell wall maceration. The common cytoplasmic pool, surrounded by an intact plasma membrane, provides a source from which H. glycines derives nourishment but without killing the parasitized cell during a susceptible reaction. The syncytium is also the site of a naturally-occurring defense response that happens in specific G. max genotypes. Transcriptomic analyses of RNA isolated from the syncytium undergoing the process of defense have identified that one of the 11 G. max PGIPs, GmPGIP11, is expressed during defense. Functional transgenic analyses show roots undergoing GmPGIP11 overexpression (OE) experience an increase in its relative transcript abundance (RTA) as compared to the ribosomal protein 21 (GmRPS21) control, leading to a decrease in H. glycines parasitism as compared to the overexpression control. The GmPGIP11 undergoing RNAi experiences a decrease in its RTA as compared to the GmRPS21 control with transgenic roots experiencing an increase in H. glycines parasitism as compared to the RNAi control. Pathogen associated molecular pattern (PAMP) triggered immunity (PTI) and effector triggered immunity (ETI) components are shown to influence GmPGIP11 expression while numerous agricultural crops are shown to have homologs.
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Affiliation(s)
- Sudha Acharya
- Department of Computer and Information Sciences, Towson University, Towson, MD, 21252, USA; USDA-ARS-NEA-BARC Molecular Plant Pathology Laboratory, Building 004, Room 122, BARC-West, 10300 Baltimore Ave., Beltsville, MD, 20705, USA
| | - Hallie A Troell
- Department of Biological Sciences, Mississippi State University, MS, 39762, USA
| | - Rebecca L Billingsley
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, MS, 39762, USA
| | - Kathy S Lawrence
- Department of Entomology and Plant Pathology, Auburn University, 209 Life Science Building, Auburn, AL, 36849, USA
| | - Daniel S McKirgan
- Department of Computer and Information Sciences, Towson University, Towson, MD, 21252, USA
| | - Nadim W Alkharouf
- Department of Computer and Information Sciences, Towson University, Towson, MD, 21252, USA
| | - Vincent P Klink
- USDA-ARS-NEA-BARC Molecular Plant Pathology Laboratory, Building 004, Room 122, BARC-West, 10300 Baltimore Ave., Beltsville, MD, 20705, USA.
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Sharma S, Arpita K, Nirgude M, Srivastava H, Kumar K, Sreevathsa R, Bhattacharya R, Gaikwad K. Genomic insights into cytokinin oxidase/dehydrogenase (CKX) gene family, identification, phylogeny and synteny analysis for its possible role in regulating seed number in Pigeonpea (Cajanus cajan). Int J Biol Macromol 2024:134194. [PMID: 39097061 DOI: 10.1016/j.ijbiomac.2024.134194] [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: 04/29/2024] [Revised: 06/28/2024] [Accepted: 07/25/2024] [Indexed: 08/05/2024]
Abstract
Cytokinin oxidase/dehydrogenase (CKX) regulates cytokinin levels in plants which are vital for plant growth and development. However, there is a paucity of evidence regarding their role in controlling embryo/seed development in pigeonpea. This study is perhaps the first to provide information on the identification and characterization of CKX genes in pigeonpea. A genome-wide analysis identified 18 CKX genes, each with distinct structure, expression patterns, and possible diverse functions. Domain analysis revealed the presence of the sequences including FAD and CK-Binding domain, and subcellular localization analysis showed that almost 50 % of them reside within the nucleus. They were observed to be located unevenly on chromosome numbers 2, 4, 6, 7, and 11 with a majority of them present on the scaffold. The 8 homologous pairs and various orthologous gene pairs provided further insights into their evolution pattern. Further, SNP/Indels variation in CKX genes and haplotype groups among contrasting genotypes for SNPP (seed number per pod) were analyzed. Spatiotemporal expression analysis revealed the significant expression pattern of CcCKX15, CcCKX17, and CcCKX2 in genotypes carrying low SNPP reiterating their role as negative regulators. These genes can be potential targets to undertake crop improvement programs in pigeonpea.
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Affiliation(s)
- Sandhya Sharma
- National Institute for plant Biotechnology, New Delhi 110012, India.
| | - Kumari Arpita
- National Institute for plant Biotechnology, New Delhi 110012, India
| | | | | | - Kuldeep Kumar
- National Institute for plant Biotechnology, New Delhi 110012, India
| | | | | | - Kishor Gaikwad
- National Institute for plant Biotechnology, New Delhi 110012, India.
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Wu T, Yang S, Fang J, Ye Y, Zhang Y, Gao J, Leng J, Zhang Z, Tang K, Bhat JA, Feng X. MutL homolog 1 participates in interference-sensitive meiotic crossover formation in soybean. PLANT PHYSIOLOGY 2024; 195:2579-2595. [PMID: 38492234 PMCID: PMC11288737 DOI: 10.1093/plphys/kiae165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 02/07/2024] [Accepted: 02/15/2024] [Indexed: 03/18/2024]
Abstract
MutL homolog 1 (MLH1), a member of the MutL homolog family, is required for normal recombination in most organisms. However, its role in soybean (Glycine max) remains unclear to date. Here, we characterized the Glycine max female and male sterility 1 (Gmfms1) mutation that reduces pollen grain viability and increases embryo sac abortion in soybean. Map-based cloning revealed that the causal gene of Gmfms1 is Glycine max MutL homolog 1 (GmMLH1), and CRISPR/Cas9 knockout approach further validated that disruption of GmMLH1 confers the female-male sterility phenotype in soybean. Loss of GmMLH1 function disrupted bivalent formation, leading to univalent mis-segregation during meiosis and ultimately to female-male sterility. The Gmmlh1 mutant showed about a 78.16% decrease in meiotic crossover frequency compared to the wild type. The residual chiasmata followed a Poisson distribution, suggesting that interference-sensitive crossover formation was affected in the Gmmlh1 mutant. Furthermore, GmMLH1 could interact with GmMLH3A and GmMLH3B both in vivo and in vitro. Overall, our work demonstrates that GmMLH1 participates in interference-sensitive crossover formation in soybean, and provides additional information about the conserved functions of MLH1 across plant species.
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Affiliation(s)
- Tao Wu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Suxin Yang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Junling Fang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
- College of Life Science, Jilin Agricultural University, Changchun 130118, China
| | - Yongheng Ye
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yaohua Zhang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Jinshan Gao
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Jiantian Leng
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Zhirui Zhang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kuanqiang Tang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | | | - Xianzhong Feng
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
- Zhejiang Lab, Hangzhou 311121, China
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Li G, Zhao X, Yang J, Hu S, Ponnu J, Kimura S, Hwang I, Torii KU, Hou H. Water wisteria genome reveals environmental adaptation and heterophylly regulation in amphibious plants. PLANT, CELL & ENVIRONMENT 2024. [PMID: 39076061 DOI: 10.1111/pce.15050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 07/03/2024] [Accepted: 07/12/2024] [Indexed: 07/31/2024]
Abstract
Heterophylly is a phenomenon whereby an individual plant dramatically changes leaf shape in response to the surroundings. Hygrophila difformis (Acanthaceae; water wisteria), has recently emerged as a model plant to study heterophylly because of its striking leaf shape variation in response to various environmental factors. When submerged, H. difformis often develops complex leaves, but on land it develops simple leaves. Leaf complexity is also influenced by other factors, such as light density, humidity, and temperature. Here, we sequenced and assembled the H. difformis chromosome-level genome (scaffold N50: 60.43 Mb, genome size: 871.92 Mb), which revealed 36 099 predicted protein-coding genes distributed over 15 pseudochromosomes. H. difformis diverged from its relatives during the Oligocene climate-change period and expanded gene families related to its amphibious habit. Genes related to environmental stimuli, leaf development, and other pathways were differentially expressed in submerged and terrestrial conditions, possibly modulating morphological and physiological acclimation to changing environments. We also found that auxin plays a role in H. difformis heterophylly. Finally, we discovered candidate genes that respond to different environmental conditions and elucidated the role of LATE MERISTEM IDENTITY 1 (LMI1) in heterophylly. We established H. difformis as a model for studying interconnections between environmental adaptation and morphogenesis.
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Affiliation(s)
- Gaojie Li
- The State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xuyao Zhao
- The State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jingjing Yang
- The State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Shiqi Hu
- Laboratory of Marine Biological Resources Development and Utilization, Zhejiang Marine Development Research Institute, Zhoushan, Zhejiang, China
| | - Jathish Ponnu
- Joseph Gottlieb Kölreuter Institute for Plant Sciences, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Seisuke Kimura
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan
- Center for Plant Sciences, Kyoto Sangyo University, Kyoto, Japan
| | - Inhwan Hwang
- Department of Life Science, Pohang University of Science and Technology, Pohang, South Korea
| | - Keiko U Torii
- Institute of Transformative Biomolecules (WPI-ITbM), Nagoya University, Nagoya, Aichi, Japan
- Howard Hughes Medical Institute, The University of Texas at Austin, Austin, Texas, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Hongwei Hou
- The State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
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Khisti M, Avuthu T, Yogendra K, Kumar Valluri V, Kudapa H, Reddy PS, Tyagi W. Genome-wide identification and expression profiling of growth‑regulating factor (GRF) and GRF‑interacting factor (GIF) gene families in chickpea and pigeonpea. Sci Rep 2024; 14:17178. [PMID: 39060385 PMCID: PMC11282205 DOI: 10.1038/s41598-024-68033-2] [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: 01/19/2024] [Accepted: 07/18/2024] [Indexed: 07/28/2024] Open
Abstract
The growth-regulating factor (GRF) and GRF-interacting factor (GIF) families encode plant-specific transcription factors and play vital roles in plant development and stress response processes. Although GRF and GIF genes have been identified in various plant species, there have been no reports of the analysis and identification of the GRF and GIF transcription factor families in chickpea (Cicer arietinum) and pigeonpea (Cajanus cajan). The present study identified seven CaGRFs, eleven CcGRFs, four CaGIFs, and four CcGIFs. The identified proteins were grouped into eight and three clades for GRFs and GIFs, respectively based on their phylogenetic relationships. A comprehensive in-silico analysis was performed to determine chromosomal location, sub-cellular localization, and types of regulatory elements present in the putative promoter region. Synteny analysis revealed that GRF and GIF genes showed diploid-polyploid topology in pigeonpea, but not in chickpea. Tissue-specific expression data at the vegetative and reproductive stages of the plant showed that GRFs and GIFs were strongly expressed in tissues like embryos, pods, and seeds, indicating that GRFs and GIFs play vital roles in plant growth and development. This research characterized GRF and GIF families and hints at their primary roles in the chickpea and pigeonpea growth and developmental process. Our findings provide potential gene resources and vital information on GRF and GIF gene families in chickpea and pigeonpea, which will help further understand the regulatory role of these gene families in plant growth and development.
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Affiliation(s)
- Mitesh Khisti
- Research Program-Accelerated Crop Improvement, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Patancheru, Telangana, 502324, India
| | - Tejaswi Avuthu
- Research Program-Accelerated Crop Improvement, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Patancheru, Telangana, 502324, India
| | - Kalenahalli Yogendra
- Research Program-Accelerated Crop Improvement, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Patancheru, Telangana, 502324, India
| | - Vinod Kumar Valluri
- Research Program-Accelerated Crop Improvement, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Patancheru, Telangana, 502324, India
| | - Himabindu Kudapa
- Research Program-Accelerated Crop Improvement, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Patancheru, Telangana, 502324, India
| | - Palakolanu Sudhakar Reddy
- Research Program-Accelerated Crop Improvement, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Patancheru, Telangana, 502324, India
| | - Wricha Tyagi
- Research Program-Accelerated Crop Improvement, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Patancheru, Telangana, 502324, India.
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7
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Fang C, Sun Z, Li S, Su T, Wang L, Dong L, Li H, Li L, Kong L, Yang Z, Lin X, Zatybekov A, Liu B, Kong F, Lu S. Subfunctionalisation and self-repression of duplicated E1 homologues finetunes soybean flowering and adaptation. Nat Commun 2024; 15:6184. [PMID: 39039090 PMCID: PMC11263555 DOI: 10.1038/s41467-024-50623-3] [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: 11/15/2023] [Accepted: 07/17/2024] [Indexed: 07/24/2024] Open
Abstract
Soybean is a photoperiod-sensitive staple crop. Its photoperiodic flowering has major consequences for latitudinal adaptation and grain yield. Here, we identify and characterise a flowering locus named Time of flower 4b (Tof4b), which encodes E1-Like b (E1Lb), a homologue of the key soybean floral repressor E1. Tof4b protein physically associates with the promoters of two FLOWERING LOCUS T (FT) genes to repress their transcription and delay flowering to impart soybean adaptation to high latitudes. Three E1 homologues undergo subfunctionalisation and show differential subcellular localisation. Moreover, they all possess self-repression capability and each suppresses the two homologous counterparts. Subfunctionalisation and the transcriptional regulation of E1 genes collectively finetune flowering time and high-latitude adaptation in soybean. We propose a model for the functional fate of the three E1 genes after the soybean whole-genome duplication events, refine the molecular mechanisms underlying high-latitude adaption, and provide a potential molecular-breeding resource.
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Affiliation(s)
- Chao Fang
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, China
- The Innovative Academy of Seed Design, Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Zhihui Sun
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, China
| | - Shichen Li
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, China
| | - Tong Su
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, China
| | - Lingshuang Wang
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, China
| | - Lidong Dong
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, China
| | - Haiyang Li
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, China
| | - Lanxin Li
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, China
| | - Lingping Kong
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, China
| | - Zhiquan Yang
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, China
| | - Xiaoya Lin
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, China
| | - Alibek Zatybekov
- Laboratory of Molecular Genetics, Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
| | - Baohui Liu
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, China.
- The Innovative Academy of Seed Design, Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China.
| | - Fanjiang Kong
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, China.
- The Innovative Academy of Seed Design, Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China.
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China.
| | - Sijia Lu
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, China.
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8
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Song Q, Quigley C, He R, Wang D, Nguyen H, Miranda C, Li Z. Development and implementation of nested single-nucleotide polymorphism (SNP) assays for breeding and genetic research applications. THE PLANT GENOME 2024:e20491. [PMID: 39034885 DOI: 10.1002/tpg2.20491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 06/18/2024] [Accepted: 06/20/2024] [Indexed: 07/23/2024]
Abstract
SoySNP50K and SoySNP6K are commonly used for soybean (Glycine max) genotyping. The SoySNP50K assay has been used to genetically analyze the entire USDA Soybean Germplasm Collection, while the SoySNP6K assay, containing a subset of 6000 single-nucleotide polymorphisms (SNPs) from SoySNP50K, has been used for quantitative trait loci mapping of different traits. To meet the needs for genomic selection, selection of parents for crosses, and characterization of breeding populations, especially early selection of ideal offspring from thousands of lines, we developed two assays, SoySNP3K and SoySNP1K, containing 3072 and 1252 SNPs, respectively, based on SoySNP50K and SoySNP6K mark sets. These two assays also contained the trait markers reported or contributed by soybean breeders. The SNPs in the SoySNP3K are a subset from SoySNP6K, while the SNPs in the SoySNP1K are a subset from SoySNP3K. These SNPs were chosen to reduce the SNP number in the large linkage blocks while capturing as much of the haplotype diversity as possible. They are highly polymorphic and of high quality. The mean minor allele frequencies of the SNPs in the southern and northern US elites were 0.25 and 0.27 for SoySNP3K, respectively, and 0.29 and 0.33 for SoySNP1K. The selected SNPs are a valuable source for developing targeted amplicon sequencing assay or beadchip assay in soybean. SoySNP3K and SoySNP1K assays are commercialized by Illumina Inc. and AgriPlex Genomics, respectively. Together with SoySNP50K and SoySNP6K, a series of nested assays with different marker densities will serve as additional low-cost genomic tools for genetic, genomic, and breeding research.
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Affiliation(s)
- Qijian Song
- USDA-ARS, Soybean Genomics & Improvement Laboratory, Beltsville, Maryland, USA
| | - Charles Quigley
- USDA-ARS, Soybean Genomics & Improvement Laboratory, Beltsville, Maryland, USA
| | - Ruifeng He
- USDA-ARS, Soybean Genomics & Improvement Laboratory, Beltsville, Maryland, USA
| | - Dechun Wang
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan, USA
| | - Henry Nguyen
- Molecular Genetics and Soybean Genomics Laboratory, Division of Plant Science and Technology, University of Missouri, Columbia, Missouri, USA
| | - Carrie Miranda
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, USA
| | - Zenglu Li
- Institute of Plant Breeding, Genetics and Genomics/Department of Crop and Soil Sciences, University of Georgia, Athens, Georgia, USA
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9
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Huang T, Liu E, Cao B, Li W, Wang G, Gu W, Ma H, Dong F, Wang B, Xu G. A chromosome-level genome assembly and evolutionary analysis of Coregonus ussuriensis Berg. Sci Data 2024; 11:792. [PMID: 39025879 PMCID: PMC11258136 DOI: 10.1038/s41597-024-03642-0] [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: 09/15/2023] [Accepted: 07/12/2024] [Indexed: 07/20/2024] Open
Abstract
Coregonus ussuriensis Berg, distributed widely in cold waters above 45° N latitude, is a savored freshwater whitefish that has been included in the list of endangered animals as a consequence of overfishing. Lack of genomic information seriously hampers evolutionary and genetic research on C. ussuriensis warranting the need to assemble a high-quality reference genome to promote its genetic breeding. We assembled and constructed a reference chromosome-level C. ussuriensis genome (sequence length, 2.51 Gb; contig N50 length, 4.27 Mb) using PacBio sequencing and Hi-C assembly technology, 3,109 contigs were assembled into scaffolds, resulting in a genome assembly with 40 chromosomes and a scaffold N50 length of 62.20 Mb. In addition, 43,320 protein-coding genes were annotated. The peak Ks position in the species comparison reflects the whole-genome replication event of C. ussuriensis. This chromosome-level genome provides reference data for further studies on the molecular breeding of C. ussuriensis.
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Affiliation(s)
- Tianqing Huang
- Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, PR China
| | - Enhui Liu
- Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, PR China
| | - Baorui Cao
- Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, PR China
| | - Wenwen Li
- Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, PR China
| | - Gaochao Wang
- Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, PR China
| | - Wei Gu
- Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, PR China
| | - Haibing Ma
- Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, PR China
| | - Fulin Dong
- Yantai Jinghai Marine Fishery Co Ltd, Yantai, PR China
| | - Bingqian Wang
- Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, PR China
| | - Gefeng Xu
- Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, PR China.
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10
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Tu T, Gao Z, Li L, Chen J, Ye K, Xu T, Mai S, Han Q, Chen C, Wu S, Dong Y, Chen J, Huang L, Guan Y, Xie F, Chen X. Soybean symbiotic-nodule zonation and cell differentiation are defined by NIN2 signaling and GH3-dependent auxin homeostasis. Dev Cell 2024:S1534-5807(24)00424-6. [PMID: 39053471 DOI: 10.1016/j.devcel.2024.07.001] [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: 12/07/2023] [Revised: 04/18/2024] [Accepted: 07/02/2024] [Indexed: 07/27/2024]
Abstract
Symbiotic nodules comprise two classes, indeterminate and determinate, defined by the presence/absence of apical meristem and developmental zonation. Why meristem and zonation are absent from determinate nodules remains unclear. Here, we define cell types in developing soybean nodules, highlighting the undifferentiated infection zones and differentiated nitrogen-fixation zones. Auxin governs infection zone maintenance. GRETCHEN HAGEN 3 (GH3) enzymes deactivate auxin by conjugation and promote cell differentiation. gh3 mutants increased undifferentiated cells and enlarged infection zones. The central symbiosis-transcription factor NIN2a activates GH3.1 to reduce auxin levels and facilitates cell differentiation. High auxin promotes NIN2a protein accumulation and enhances signaling, further deactivating auxin and depleting infection zones. Our findings shed light on the NIN2a-GH3-auxin module that drives soybean nodule cell differentiation. This study challenges our understanding of determinate nodule development and proposes that the regulation of nodule zonation offers valuable insights into broader mechanisms of cell differentiation across plant species.
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Affiliation(s)
- Tianli Tu
- Haixia Institute of Science and Technology, Horticultural Plant Biology and Metabolomics Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhen Gao
- Haixia Institute of Science and Technology, Horticultural Plant Biology and Metabolomics Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Linfang Li
- Haixia Institute of Science and Technology, Horticultural Plant Biology and Metabolomics Center, Fujian Agriculture and Forestry University, Fuzhou, China; College of Agriculture and Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Jiansheng Chen
- Haixia Institute of Science and Technology, Horticultural Plant Biology and Metabolomics Center, Fujian Agriculture and Forestry University, Fuzhou, China; College of Agriculture and Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Kangzhuo Ye
- Haixia Institute of Science and Technology, Horticultural Plant Biology and Metabolomics Center, Fujian Agriculture and Forestry University, Fuzhou, China; College of Agriculture and Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Tao Xu
- Haixia Institute of Science and Technology, Horticultural Plant Biology and Metabolomics Center, Fujian Agriculture and Forestry University, Fuzhou, China; College of Agriculture and Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Siyuan Mai
- Haixia Institute of Science and Technology, Horticultural Plant Biology and Metabolomics Center, Fujian Agriculture and Forestry University, Fuzhou, China; College of Agriculture and Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Qingqing Han
- Haixia Institute of Science and Technology, Horticultural Plant Biology and Metabolomics Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chaofan Chen
- Haixia Institute of Science and Technology, Horticultural Plant Biology and Metabolomics Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shengwei Wu
- Haixia Institute of Science and Technology, Horticultural Plant Biology and Metabolomics Center, Fujian Agriculture and Forestry University, Fuzhou, China; College of Agriculture and Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Yankun Dong
- Haixia Institute of Science and Technology, Horticultural Plant Biology and Metabolomics Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiaomei Chen
- Haixia Institute of Science and Technology, Horticultural Plant Biology and Metabolomics Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Laimei Huang
- Haixia Institute of Science and Technology, Horticultural Plant Biology and Metabolomics Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuefeng Guan
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Fang Xie
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Xu Chen
- Haixia Institute of Science and Technology, Horticultural Plant Biology and Metabolomics Center, Fujian Agriculture and Forestry University, Fuzhou, China.
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11
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Yan Z, Hou J, Leng B, Yao G, Ma C, Sun Y, Zhang F, Mu C, Liu X. Genome-Wide Investigation of the CRF Gene Family in Maize and Functional Analysis of ZmCRF9 in Response to Multiple Abiotic Stresses. Int J Mol Sci 2024; 25:7650. [PMID: 39062894 PMCID: PMC11276700 DOI: 10.3390/ijms25147650] [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: 06/01/2024] [Revised: 07/08/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024] Open
Abstract
The cytokinin response factors (CRFs) are pivotal players in regulating plant growth, development, and responses to diverse stresses. Despite their significance, comprehensive information on CRF genes in the primary food crop, maize, remains scarce. In this study, a genome-wide analysis of CRF genes in maize was conducted, resulting in the identification of 12 members. Subsequently, we assessed the chromosomal locations, gene duplication events, evolutionary relationships, conserved motifs, and gene structures of all ZmCRF members. Analysis of ZmCRF promoter regions indicated the presence of cis-regulatory elements associated with plant growth regulation, hormone response, and various abiotic stress responses. The expression patterns of maize CRF genes, presented in heatmaps, exhibited distinctive patterns of tissue specificity and responsiveness to multiple abiotic stresses. qRT-PCR experiments were conducted on six selected genes and confirmed the involvement of ZmCRF genes in the plant's adaptive responses to diverse environmental challenges. In addition, ZmCRF9 was demonstrated to positively regulate cold and salt tolerance. Ultimately, we explored the putative interaction partners of ZmCRF proteins. In summary, this systematic overview and deep investigation of ZmCRF9 provides a solid foundation for further exploration into how these genes contribute to the complex interplay of plant growth, development, and responses to stress.
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Affiliation(s)
- Zhenwei Yan
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (Z.Y.); (B.L.); (G.Y.); (C.M.)
| | - Jing Hou
- School of Agriculture, Ludong University, Yantai 264001, China;
| | - Bingying Leng
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (Z.Y.); (B.L.); (G.Y.); (C.M.)
| | - Guoqi Yao
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (Z.Y.); (B.L.); (G.Y.); (C.M.)
| | - Changle Ma
- College of Life Sciences, Shandong Normal University, Jinan 250300, China;
| | - Yue Sun
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China;
| | - Fajun Zhang
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (Z.Y.); (B.L.); (G.Y.); (C.M.)
| | - Chunhua Mu
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (Z.Y.); (B.L.); (G.Y.); (C.M.)
| | - Xia Liu
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (Z.Y.); (B.L.); (G.Y.); (C.M.)
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12
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Nguyen TC, Tran HA, Lee JD, Seo HS, Jo H, Song JT. Genetic Control of Tolerance to Drought Stress in Wild Soybean ( Glycine soja) at the Vegetative and the Germination Stages. PLANTS (BASEL, SWITZERLAND) 2024; 13:1894. [PMID: 39065421 PMCID: PMC11281237 DOI: 10.3390/plants13141894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 07/05/2024] [Accepted: 07/08/2024] [Indexed: 07/28/2024]
Abstract
Drought stress, which is becoming more prevalent due to climate change, is a significant abiotic factor that adversely impacts crop production and yield stability. Cultivated soybean (Glycine max), a versatile crop for humans and animals, exhibits sensitivity to drought, resulting in reduced growth and development under drought conditions. However, few genetic studies have assessed wild soybean's (Glycine soja) response to drought stress. In this work, we conducted a genome-wide association study (GWAS) and analysis of wild soybean accessions to identify loci responsible for drought tolerance at the vegetative (n = 187) and the germination stages (n = 135) using the available resequencing data. The GWAS analysis of the leaf wilting score (LWS) identified eight single-nucleotide polymorphisms (SNPs) on chromosomes 10, 11, and 19. Of these, wild soybeans with both SNPs on chromosomes 10 (adenine) and 11 (thymine) produced lower LWS, indicating that these SNPs have an important role in the genetic effect on LWS for drought tolerance at the vegetative stage. At the germination stage, nine SNPs associated with five phenotypic measurements were identified on chromosomes 6, 9, 10, 13, 16, and 17, and the genomic regions identified at the germination stage were different from those identified for the LWS, supporting our previous finding that there may not be a robust correlation between the genes influencing phenotypes at the germination and vegetative stages. This research will benefit marker-assisted breeding programs aimed at enhancing drought tolerance in soybeans.
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Affiliation(s)
- Thi Cuc Nguyen
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea; (T.C.N.); (H.A.T.); (J.-D.L.)
| | - Hai Anh Tran
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea; (T.C.N.); (H.A.T.); (J.-D.L.)
| | - Jeong-Dong Lee
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea; (T.C.N.); (H.A.T.); (J.-D.L.)
| | - Hak Soo Seo
- Department of Agriculture, Forestry and Bioresources, Seoul National University, Seoul 08826, Republic of Korea;
| | - Hyun Jo
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea; (T.C.N.); (H.A.T.); (J.-D.L.)
| | - Jong Tae Song
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea; (T.C.N.); (H.A.T.); (J.-D.L.)
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13
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Shan Z, Chu Y, Sun G, Chen R, Yan J, He Q, Liu Y, Wang B, Luan M, Lan W. Mechanisms of vacuolar phosphate efflux supporting soybean root hair growth in response to phosphate deficiency. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024. [PMID: 38980217 DOI: 10.1111/jipb.13735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Accepted: 06/18/2024] [Indexed: 07/10/2024]
Abstract
Phosphorus is an essential macronutrient for plant growth and development. In response to phosphate (Pi) deficiency, plants rapidly produce a substitutive amount of root hairs; however, the mechanisms underlying Pi supply for root hair growth remain unclear. Here, we observed that soybean (Glycine max) plants maintain a consistent level of Pi within root hairs even under external Pi deficiency. We therefore investigated the role of vacuole-stored Pi, a major Pi reservoir in plant cells, in supporting root hair growth under Pi-deficient conditions. Our findings indicated that two vacuolar Pi efflux (VPE) transporters, GmVPE1 and GmVPE2, remobilize vacuolar stored Pi to sustain cytosolic Pi content in root hair cells. Genetic analysis showed that double mutants of GmVPE1 and GmVPE2 exhibited reduced root hair growth under low Pi conditions. Moreover, GmVPE1 and GmVPE2 were highly expressed in root hairs, with their expression levels significantly upregulated by low Pi treatment. Further analysis revealed that GmRSL2 (ROOT HAIR DEFECTIVE 6-like 2), a transcription factor involved in root hair morphogenesis, directly binds to the promoter regions of GmVPE1 and GmVPE2, and promotes their expressions under low Pi conditions. Additionally, mutants lacking both GmRSL2 and its homolog GmRSL3 exhibited impaired root hair growth under low Pi stress, which was rescued by overexpressing either GmVPE1 or GmVPE2. Taken together, our study has identified a module comprising vacuolar Pi exporters and transcription factors responsible for remobilizing vacuolar Pi to support root hair growth in response to Pi deficiency in soybean.
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Affiliation(s)
- Zhong Shan
- School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Yanli Chu
- School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Guangfang Sun
- Institute of Future Agriculture, Northwest A&F University, Yangling, 712100, China
| | - Rui Chen
- School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Jun Yan
- Institute of Future Agriculture, Northwest A&F University, Yangling, 712100, China
| | - Qiwei He
- School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Yingna Liu
- Institute of Future Agriculture, Northwest A&F University, Yangling, 712100, China
| | - Bin Wang
- School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Mingda Luan
- Institute of Future Agriculture, Northwest A&F University, Yangling, 712100, China
| | - Wenzhi Lan
- Institute of Future Agriculture, Northwest A&F University, Yangling, 712100, China
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14
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Sultan AB, Nawaz H, Saleem F, Nawaz S, Danial M, Iftikhar R, Maqsood U, Areej A, Shakoor S, Aljarba NH, Maqbool R, Rizwan M, Serfraz S. Divergent evolution of NLR genes in the genus Glycine: impacts of annuals and perennials' life history strategies. FRONTIERS IN PLANT SCIENCE 2024; 15:1383135. [PMID: 39045600 PMCID: PMC11263291 DOI: 10.3389/fpls.2024.1383135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 06/12/2024] [Indexed: 07/25/2024]
Abstract
Within the family Fabaceae, the genus Glycine is composed of two subgenera annuals (2n=40) and perennials. This life strategy transition may have differentially affected the evolution of various gene families. Its cultivated species G. max has high level of susceptibility to major pathogens including viruses, bacteria and fungi. Understanding nucleotide-binding domain leucine-rich repeat (NLR) genes evolution in soybean is of paramount importance due to their central role in plant immunity and their potential in improving disease resistance in soybean cultivars. In this study, we investigated the significance of this annual-perennial transition on the macroevolution of NLR genes in the genus Glycine. Our results reveal a remarkable distinction between annual species such as Glycine max and Glycine soja, which exhibit an expanded NLRome compared to perennial species (G. cyrtoloba, G. stenophita, G. dolichocarpa, G. falcata, G. syndetika, G. latifolia and G. tomentella). Our evolutionary timescale analysis pinpoints recent accelerated gene duplication events for this expansion, which occurred between 0.1 and 0.5 million years ago, driven predominantly by lineage-specific and terminal duplications. In contrast, perennials initially experienced significant contraction during the diploidisation phase following the Glycine-specific whole-genome duplication event (~10 million years ago). Despite the reduction in the NLRome, perennial lineages exhibit a unique and highly diversified repertoire of NLR genes with limited interspecies synteny. The investigation of gene gain and loss ratios revealed that this diversification resulted from the birth of novel genes following individual speciation events. Among perennials, G. latifolia, a well-known resistance resource, has the highest ratio of these novel genes in the tertiary gene pool. Our study suggests evolutionary mechanisms, including recombination and transposition, as potential drivers for the emergence of these novel genes. This study also provides evidence for the unbalanced expansion of the NLRome in the Dt subgenome compared with the At subgenome in the young allopolyploid G. dolichocarpa. To the best of our knowledge, this is the first study to investigate the effect of annuality and perenniality life transition on the evolution of NLR genes in the genus Glycine to identify its genomics resources for improving the resistance of soybean crop with global importance on the economy and food security.
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Affiliation(s)
- Abu Bakar Sultan
- Evolutionary Biology Lab, CABB, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Humera Nawaz
- Department of Botany, Division of Science and Technology, University of Education, Lahore, Pakistan
| | - Fozia Saleem
- Evolutionary Biology Lab, CABB, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Sehar Nawaz
- Evolutionary Biology Lab, CABB, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Muhammad Danial
- Evolutionary Biology Lab, CABB, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Romana Iftikhar
- Evolutionary Biology Lab, CABB, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Umer Maqsood
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Amna Areej
- Evolutionary Biology Lab, CABB, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Sidra Shakoor
- Evolutionary Biology Lab, CABB, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Nada H. Aljarba
- Department of Biology, College of Science, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Rizwan Maqbool
- Department of Agronomy, University of Agriculture, Faisalabad, Pakistan
| | - Muhammad Rizwan
- Evolutionary Biology Lab, CABB, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Saad Serfraz
- Evolutionary Biology Lab, CABB, University of Agriculture Faisalabad, Faisalabad, Pakistan
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15
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Feng L, Teng F, Li N, Zhang JC, Zhang BJ, Tsai SN, Yue XL, Gu LF, Meng GH, Deng TQ, Tong SW, Wang CM, Li Y, Shi W, Zeng YL, Jiang YM, Yu W, Ngai SM, An LZ, Lam HM, He JX. A reference-grade genome of the xerophyte Ammopiptanthus mongolicus sheds light on its evolution history in legumes and drought-tolerance mechanisms. PLANT COMMUNICATIONS 2024; 5:100891. [PMID: 38561965 PMCID: PMC11287142 DOI: 10.1016/j.xplc.2024.100891] [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: 09/02/2023] [Revised: 02/26/2024] [Accepted: 03/29/2024] [Indexed: 04/04/2024]
Abstract
Plants that grow in extreme environments represent unique sources of stress-resistance genes and mechanisms. Ammopiptanthus mongolicus (Leguminosae) is a xerophytic evergreen broadleaf shrub native to semi-arid and desert regions; however, its drought-tolerance mechanisms remain poorly understood. Here, we report the assembly of a reference-grade genome for A. mongolicus, describe its evolutionary history within the legume family, and examine its drought-tolerance mechanisms. The assembled genome is 843.07 Mb in length, with 98.7% of the sequences successfully anchored to the nine chromosomes of A. mongolicus. The genome is predicted to contain 47 611 protein-coding genes, and 70.71% of the genome is composed of repetitive sequences; these are dominated by transposable elements, particularly long-terminal-repeat retrotransposons. Evolutionary analyses revealed two whole-genome duplication (WGD) events at 130 and 58 million years ago (mya) that are shared by the genus Ammopiptanthus and other legumes, but no species-specific WGDs were found within this genus. Ancestral genome reconstruction revealed that the A. mongolicus genome has undergone fewer rearrangements than other genomes in the legume family, confirming its status as a "relict plant". Transcriptomic analyses demonstrated that genes involved in cuticular wax biosynthesis and transport are highly expressed, both under normal conditions and in response to polyethylene glycol-induced dehydration. Significant induction of genes related to ethylene biosynthesis and signaling was also observed in leaves under dehydration stress, suggesting that enhanced ethylene response and formation of thick waxy cuticles are two major mechanisms of drought tolerance in A. mongolicus. Ectopic expression of AmERF2, an ethylene response factor unique to A. mongolicus, can markedly increase the drought tolerance of transgenic Arabidopsis thaliana plants, demonstrating the potential for application of A. mongolicus genes in crop improvement.
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Affiliation(s)
- Lei Feng
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong, China; Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Fei Teng
- BGI-Shenzhen Tech Co., Ltd., Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Na Li
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong, China
| | - Jia-Cheng Zhang
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong, China
| | - Bian-Jiang Zhang
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong, China
| | - Sau-Na Tsai
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong, China
| | - Xiu-Le Yue
- School of Life Sciences and Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, Lanzhou University, Lanzhou 730030, China
| | - Li-Fei Gu
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong, China
| | - Guang-Hua Meng
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong, China
| | - Tian-Quan Deng
- BGI-Shenzhen Tech Co., Ltd., Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Suk-Wah Tong
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong, China
| | - Chun-Ming Wang
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong, China
| | - Yan Li
- State Key Laboratory of Subtropical Silviculture, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
| | - Wei Shi
- BGI-Shenzhen Tech Co., Ltd., Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Yong-Lun Zeng
- State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Yue-Ming Jiang
- Guangdong Provincial Key Laboratory of Applied Botany & Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Weichang Yu
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Sai-Ming Ngai
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong, China
| | - Li-Zhe An
- School of Life Sciences and Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, Lanzhou University, Lanzhou 730030, China; State Key Laboratory of Efficient Production of Forest Resources, Beijing Forestry University, Beijing 100083, China.
| | - Hon-Ming Lam
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong, China.
| | - Jun-Xian He
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong, China.
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Yang S, Han X, Li J, Luan F, Zhang S, Han D, Yang M, Chen Q, Qi Z. Oceanobacillus picturae alleviates cadmium stress and promotes growth in soybean seedlings. JOURNAL OF HAZARDOUS MATERIALS 2024; 472:134568. [PMID: 38749246 DOI: 10.1016/j.jhazmat.2024.134568] [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: 03/18/2024] [Revised: 04/24/2024] [Accepted: 05/07/2024] [Indexed: 05/30/2024]
Abstract
Cadmium (Cd) is a heavy metal that significantly impacts human health and the environment. Microorganisms play a crucial role in reducing heavy metal stress in plants; however, the mechanisms by which microorganisms enhance plant tolerance to Cd stress and the interplay between plants and microorganisms under such stress remain unclear. In this study, Oceanobacillus picturae (O. picturae) was isolated for interaction with soybean seedlings under Cd stress. Results indicated that Cd treatment alone markedly inhibited soybean seedling growth. Conversely, inoculation with O. picturae significantly improved growth indices such as plant height, root length, and fresh weight, while also promoting recovery in soil physiological indicators and pH. Metabolomic and transcriptomic analyses identified 157 genes related to aspartic acid, cysteine, and flavonoid biosynthesis pathways. Sixty-three microbial species were significantly associated with metabolites in these pathways, including pathogenic, adversity-resistant, and bioconductive bacteria. This research experimentally demonstrates, for the first time, the growth-promoting effect of the O. picturae strain on soybean seedlings under non-stress conditions. It also highlights its role in enhancing root growth and reducing Cd accumulation in the roots under Cd stress. Additionally, through the utilization of untargeted metabolomics, metagenomics, and transcriptomics for a multi-omics analysis, we investigated the impact of O. picturae on the soil microbiome and its correlation with differential gene expression in plants. This innovative approach unveils the molecular mechanisms underlying O. picturae's promotion of root growth and adaptation to Cd stress.
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Affiliation(s)
- Shangjun Yang
- National Research Center of Soybean Engineering and Technology, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Xue Han
- National Research Center of Soybean Engineering and Technology, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Jun Li
- National Research Center of Soybean Engineering and Technology, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Feng Luan
- College of Engineering, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang 163000, China
| | - Shuli Zhang
- Wuchang Branch of Heilongjiang Academy of Agricultural Sciences, Wuchang, Heilongjiang 150229, People's Republic of China
| | - Dezhi Han
- Heihe Branch of Heilongjiang Academy of Agricultural Sciences, Heihe, China
| | - Mingliang Yang
- National Research Center of Soybean Engineering and Technology, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Qingshan Chen
- National Research Center of Soybean Engineering and Technology, Northeast Agricultural University, Harbin, Heilongjiang 150030, China.
| | - Zhaoming Qi
- National Research Center of Soybean Engineering and Technology, Northeast Agricultural University, Harbin, Heilongjiang 150030, China.
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17
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Zhang X, Luo Z, Marand AP, Yan H, Jang H, Bang S, Mendieta JP, Minow MA, Schmitz RJ. A spatially resolved multiomic single-cell atlas of soybean development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.03.601616. [PMID: 39005400 PMCID: PMC11244997 DOI: 10.1101/2024.07.03.601616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Cis-regulatory elements (CREs) precisely control spatiotemporal gene expression in cells. Using a spatially resolved single-cell atlas of gene expression with chromatin accessibility across ten soybean tissues, we identified 103 distinct cell types and 303,199 accessible chromatin regions (ACRs). Nearly 40% of the ACRs showed cell-type-specific patterns and were enriched for transcription factor (TF) motifs defining diverse cell identities. We identified de novo enriched TF motifs and explored conservation of gene regulatory networks underpinning legume symbiotic nitrogen fixation. With comprehensive developmental trajectories for endosperm and embryo, we uncovered the functional transition of the three sub-cell types of endosperm, identified 13 sucrose transporters sharing the DOF11 motif that were co-up-regulated in late peripheral endosperm and identified key embryo cell-type specification regulators during embryogenesis, including a homeobox TF that promotes cotyledon parenchyma identity. This resource provides a valuable foundation for analyzing gene regulatory programs in soybean cell types across tissues and life stages.
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Affiliation(s)
- Xuan Zhang
- Department of Genetics, University of Georgia, Athens, GA, USA
- These authors contributed equally: Xuan Zhang, Ziliang Luo, Alexandre P. Marand
| | - Ziliang Luo
- Department of Genetics, University of Georgia, Athens, GA, USA
- These authors contributed equally: Xuan Zhang, Ziliang Luo, Alexandre P. Marand
| | - Alexandre P. Marand
- Department of Molecular, Cellular, and Development Biology, University of Michigan, Ann Arbor, MI, USA
- These authors contributed equally: Xuan Zhang, Ziliang Luo, Alexandre P. Marand
| | - Haidong Yan
- Department of Genetics, University of Georgia, Athens, GA, USA
- Current address: College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Hosung Jang
- Department of Genetics, University of Georgia, Athens, GA, USA
| | - Sohyun Bang
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | | | - Mark A.A. Minow
- Department of Genetics, University of Georgia, Athens, GA, USA
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18
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Bish MD, Ramachandran SR, Wright A, Lincoln LM, Whitham SA, Graham MA, Pedley KF. The Soybean Rpp3 Gene Encodes a TIR-NBS-LRR Protein that Confers Resistance to Phakopsora pachyrhizi. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:561-570. [PMID: 38569009 DOI: 10.1094/mpmi-01-24-0007-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
Soybean rust is an economically significant disease caused by the fungus Phakopsora pachyrhizi that negatively impacts soybean (Glycine max [L.] Merr.) production throughout the world. Susceptible plants infected by P. pachyrhizi develop tan-colored lesions on the leaf surface that give rise to funnel-shaped uredinia as the disease progresses. While most soybean germplasm is susceptible, seven genetic loci (Rpp1 to Rpp7) that provide race-specific resistance to P. pachyrhizi (Rpp) have been identified. Rpp3 was first discovered and characterized in the soybean accession PI 462312 (Ankur), and it was also determined to be one of two Rpp genes present in PI 506764 (Hyuuga). Genetic crosses with PI 506764 were later used to fine-map the Rpp3 locus to a 371-kb region on chromosome 6. The corresponding region in the susceptible Williams 82 (Wm82) reference genome contains several homologous nucleotide binding site-leucine rich repeat (NBS-LRR) genes. To identify Rpp3, we designed oligonucleotide primers to amplify Rpp3 candidate (Rpp3C) NBS-LRR genes at this locus from PI 462312, PI 506764, and Wm82 using polymerase chain reaction (PCR). Five Rpp3C genes were identified in both Rpp3-resistant soybean lines, and co-silencing these genes compromised resistance to P. pachyrhizi. Gene expression analysis and sequence comparisons of the Rpp3C genes in PI 462312 and PI 506764 suggest that a single candidate gene, Rpp3C3, is responsible for Rpp3-mediated resistance. [Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 "No Rights Reserved" license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2024.
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Affiliation(s)
- Mandy D Bish
- Foreign Disease-Weed Science Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Fort Detrick, MD 21702, U.S.A
| | - Sowmya R Ramachandran
- Foreign Disease-Weed Science Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Fort Detrick, MD 21702, U.S.A
- Oak Ridge Institute for Science and Education, ARS Research Participation Program, Oak Ridge, TN, U.S.A
| | - Amy Wright
- Foreign Disease-Weed Science Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Fort Detrick, MD 21702, U.S.A
| | - Lori M Lincoln
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA 50011, U.S.A
| | - Steven A Whitham
- Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, Ames, IA 50011, U.S.A
| | - Michelle A Graham
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA 50011, U.S.A
- Department of Agronomy, Iowa State University, Ames, IA 50011, U.S.A
| | - Kerry F Pedley
- Foreign Disease-Weed Science Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Fort Detrick, MD 21702, U.S.A
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19
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Canales Holzeis C, Gepts P, Koebner R, Mathur PN, Morgan S, Muñoz-Amatriaín M, Parker TA, Southern EM, Timko MP. The Kirkhouse Trust: Successes and Challenges in Twenty Years of Supporting Independent, Contemporary Grain Legume Breeding Projects in India and African Countries. PLANTS (BASEL, SWITZERLAND) 2024; 13:1818. [PMID: 38999658 PMCID: PMC11243813 DOI: 10.3390/plants13131818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 06/19/2024] [Accepted: 06/25/2024] [Indexed: 07/14/2024]
Abstract
This manuscript reviews two decades of projects funded by the Kirkhouse Trust (KT), a charity registered in the UK. KT was established to improve the productivity of legume crops important in African countries and in India. KT's requirements for support are: (1) the research must be conducted by national scientists in their home institution, either a publicly funded agricultural research institute or a university; (2) the projects need to include a molecular biology component, which to date has mostly comprised the use of molecular markers for the selection of one or more target traits in a crop improvement programme; (3) the projects funded are included in consortia, to foster the creation of scientific communities and the sharing of knowledge and breeding resources. This account relates to the key achievements and challenges, reflects on the lessons learned and outlines future research priorities.
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Affiliation(s)
| | - Paul Gepts
- Section of Crop & Ecosystem Sciences, Department of Plant Sciences, University of California, 1 Shields Avenue, Davis, CA 95616, USA
| | - Robert Koebner
- The Kirkhouse Trust, Unit 6 Fenlock Court, Long Hanborough OX29 8LN, UK
| | | | - Sonia Morgan
- The Kirkhouse Trust, Unit 6 Fenlock Court, Long Hanborough OX29 8LN, UK
| | - María Muñoz-Amatriaín
- Departamento de Biología Molecular (Área Genética), Universidad de León, 24071 León, Spain
| | - Travis A Parker
- Section of Crop & Ecosystem Sciences, Department of Plant Sciences, University of California, 1 Shields Avenue, Davis, CA 95616, USA
| | - Edwin M Southern
- The Kirkhouse Trust, Unit 6 Fenlock Court, Long Hanborough OX29 8LN, UK
| | - Michael P Timko
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
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20
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He J, Weng L, Xu X, Chen R, Peng B, Li N, Xie Z, Sun L, Han Q, He P, Wang F, Yu H, Bhat JA, Feng X. DEKR-SPrior: An Efficient Bottom-Up Keypoint Detection Model for Accurate Pod Phenotyping in Soybean. PLANT PHENOMICS (WASHINGTON, D.C.) 2024; 6:0198. [PMID: 38939747 PMCID: PMC11209727 DOI: 10.34133/plantphenomics.0198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 05/16/2024] [Indexed: 06/29/2024]
Abstract
The pod and seed counts are important yield-related traits in soybean. High-precision soybean breeders face the major challenge of accurately phenotyping the number of pods and seeds in a high-throughput manner. Recent advances in artificial intelligence, especially deep learning (DL) models, have provided new avenues for high-throughput phenotyping of crop traits with increased precision. However, the available DL models are less effective for phenotyping pods that are densely packed and overlap in in situ soybean plants; thus, accurate phenotyping of the number of pods and seeds in soybean plant is an important challenge. To address this challenge, the present study proposed a bottom-up model, DEKR-SPrior (disentangled keypoint regression with structural prior), for in situ soybean pod phenotyping, which considers soybean pods and seeds analogous to human people and joints, respectively. In particular, we designed a novel structural prior (SPrior) module that utilizes cosine similarity to improve feature discrimination, which is important for differentiating closely located seeds from highly similar seeds. To further enhance the accuracy of pod location, we cropped full-sized images into smaller and high-resolution subimages for analysis. The results on our image datasets revealed that DEKR-SPrior outperformed multiple bottom-up models, viz., Lightweight-OpenPose, OpenPose, HigherHRNet, and DEKR, reducing the mean absolute error from 25.81 (in the original DEKR) to 21.11 (in the DEKR-SPrior) in pod phenotyping. This paper demonstrated the great potential of DEKR-SPrior for plant phenotyping, and we hope that DEKR-SPrior will help future plant phenotyping.
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Affiliation(s)
- Jingjing He
- Zhejiang Laboratory, Hangzhou 311100, Zhejiang, China
| | - Lin Weng
- Zhejiang Laboratory, Hangzhou 311100, Zhejiang, China
| | - Xiaogang Xu
- School of Computer Science and Technology,
Zhejiang Gongshang University, Hangzhou 310012, Zhejiang, China
| | - Ruochen Chen
- Zhejiang Laboratory, Hangzhou 311100, Zhejiang, China
| | - Bo Peng
- Zhejiang Laboratory, Hangzhou 311100, Zhejiang, China
| | - Nannan Li
- Zhejiang Laboratory, Hangzhou 311100, Zhejiang, China
| | - Zhengchao Xie
- Zhejiang Laboratory, Hangzhou 311100, Zhejiang, China
| | - Lijian Sun
- Zhejiang Laboratory, Hangzhou 311100, Zhejiang, China
| | - Qiang Han
- Zhejiang Laboratory, Hangzhou 311100, Zhejiang, China
| | - Pengfei He
- Zhejiang Laboratory, Hangzhou 311100, Zhejiang, China
| | - Fangfang Wang
- Zhejiang Laboratory, Hangzhou 311100, Zhejiang, China
| | - Hui Yu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology,
Chinese Academy of Sciences, Changchun 130102, Jilin, China
| | | | - Xianzhong Feng
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology,
Chinese Academy of Sciences, Changchun 130102, Jilin, China
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21
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Li D, Wang Q, Tian Y, Lyv X, Zhang H, Hong H, Gao H, Li YF, Zhao C, Wang J, Wang R, Yang J, Liu B, Schnable PS, Schnable JC, Li YH, Qiu LJ. TWAS facilitates gene-scale trait genetic dissection through gene expression, structural variations, and alternative splicing in soybean. PLANT COMMUNICATIONS 2024:101010. [PMID: 38918950 DOI: 10.1016/j.xplc.2024.101010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 05/15/2024] [Accepted: 06/23/2024] [Indexed: 06/27/2024]
Abstract
A genome-wide association study (GWAS) identifies trait-associated loci, but identifying the causal genes can be a bottleneck, due in part to slow decay of linkage disequilibrium (LD). A transcriptome-wide association study (TWAS) addresses this issue by identifying gene expression-phenotype associations or integrating gene expression quantitative trait loci with GWAS results. Here, we used self-pollinated soybean (Glycine max [L.] Merr.) as a model to evaluate the application of TWAS to the genetic dissection of traits in plant species with slow LD decay. We generated RNA sequencing data for a soybean diversity panel and identified the genetic expression regulation of 29 286 soybean genes. Different TWAS solutions were less affected by LD and were robust to the source of expression, identifing known genes related to traits from different tissues and developmental stages. The novel pod-color gene L2 was identified via TWAS and functionally validated by genome editing. By introducing a new exon proportion feature, we significantly improved the detection of expression variations that resulted from structural variations and alternative splicing. As a result, the genes identified through our TWAS approach exhibited a diverse range of causal variations, including SNPs, insertions or deletions, gene fusion, copy number variations, and alternative splicing. Using this approach, we identified genes associated with flowering time, including both previously known genes and novel genes that had not previously been linked to this trait, providing insights complementary to those from GWAS. In summary, this study supports the application of TWAS for candidate gene identification in species with low rates of LD decay.
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Affiliation(s)
- Delin Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qi Wang
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China; College of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Yu Tian
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiangguang Lyv
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Hao Zhang
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Huilong Hong
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Huawei Gao
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China; National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China
| | - Yan-Fei Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chaosen Zhao
- Crops Research Institute of Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Jiajun Wang
- Soybean Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China
| | - Ruizhen Wang
- Crops Research Institute of Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Jinliang Yang
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Bin Liu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | | | - James C Schnable
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583, USA.
| | - Ying-Hui Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Li-Juan Qiu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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22
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Liu C, Huang R, Zhao X, Xu R, Zhang J, Li X, Liu G, Dong R, Liu P. Comparative analysis of lipid and flavonoid biosynthesis between Pongamia and soybean seeds: genomic, transcriptional, and metabolic perspectives. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:86. [PMID: 38915078 PMCID: PMC11197198 DOI: 10.1186/s13068-024-02538-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 06/18/2024] [Indexed: 06/26/2024]
Abstract
BACKGROUND Soybean (Glycine max) is a vital oil-producing crop. Augmenting oleic acid (OA) levels in soybean oil enhances its oxidative stability and health benefits, representing a key objective in soybean breeding. Pongamia (Pongamia pinnata), known for its abundant oil, OA, and flavonoid in the seeds, holds promise as a biofuel and medicinal plant. A comparative analysis of the lipid and flavonoid biosynthesis pathways in Pongamia and soybean seeds would facilitate the assessment of the potential value of Pongamia seeds and advance the genetic improvements of seed traits in both species. RESULTS The study employed multi-omics analysis to systematically compare differences in metabolite accumulation and associated biosynthetic genes between Pongamia seeds and soybean seeds at the transcriptional, metabolic, and genomic levels. The results revealed that OA is the predominant free fatty acid in Pongamia seeds, being 8.3 times more abundant than in soybean seeds. Lipidomics unveiled a notably higher accumulation of triacylglycerols (TAGs) in Pongamia seeds compared to soybean seeds, with 23 TAG species containing OA. Subsequently, we identified orthologous groups (OGs) involved in lipid biosynthesis across 25 gene families in the genomes of Pongamia and soybean, and compared the expression levels of these OGs in the seeds of the two species. Among the OGs with expression levels in Pongamia seeds more than twice as high as in soybean seeds, we identified one fatty acyl-ACP thioesterase A (FATA) and two stearoyl-ACP desaturases (SADs), responsible for OA biosynthesis, along with two phospholipid:diacylglycerol acyltransferases (PDATs) and three acyl-CoA:diacylglycerol acyltransferases (DGATs), responsible for TAG biosynthesis. Furthermore, we observed a significantly higher content of the flavonoid formononetin in Pongamia seeds compared to soybean seeds, by over 2000-fold. This difference may be attributed to the tandem duplication expansions of 2,7,4'-trihydroxyisoflavanone 4'-O-methyltransferases (HI4'OMTs) in the Pongamia genome, which are responsible for the final step of formononetin biosynthesis, combined with their high expression levels in Pongamia seeds. CONCLUSIONS This study extends beyond observations made in single-species research by offering novel insights into the molecular basis of differences in lipid and flavonoid biosynthetic pathways between Pongamia and soybean, from a cross-species comparative perspective.
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Affiliation(s)
- Chun Liu
- Tropical Crops Genetic Resources Institute & National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture and Rual Affairs, Haikou, 571101, China
- Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, Haikou, 571101, China
- School of Tropical Agriculture and Forestry & Sanya Institute Breeding and Multiplication, Hainan University, Haikou, 570228/572025, Sanya, China
| | - Rui Huang
- Tropical Crops Genetic Resources Institute & National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Xingkun Zhao
- School of Tropical Agriculture and Forestry & Sanya Institute Breeding and Multiplication, Hainan University, Haikou, 570228/572025, Sanya, China
| | - Ranran Xu
- School of Tropical Agriculture and Forestry & Sanya Institute Breeding and Multiplication, Hainan University, Haikou, 570228/572025, Sanya, China
| | - Jianyu Zhang
- School of Tropical Agriculture and Forestry & Sanya Institute Breeding and Multiplication, Hainan University, Haikou, 570228/572025, Sanya, China
| | - Xinyong Li
- Tropical Crops Genetic Resources Institute & National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Guodao Liu
- Tropical Crops Genetic Resources Institute & National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China.
| | - Rongshu Dong
- Tropical Crops Genetic Resources Institute & National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China.
| | - Pandao Liu
- Tropical Crops Genetic Resources Institute & National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China.
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture and Rual Affairs, Haikou, 571101, China.
- Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, Haikou, 571101, China.
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23
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Ma Z, Hu L. WRKY Transcription Factor Responses and Tolerance to Abiotic Stresses in Plants. Int J Mol Sci 2024; 25:6845. [PMID: 38999954 PMCID: PMC11241455 DOI: 10.3390/ijms25136845] [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: 06/02/2024] [Revised: 06/16/2024] [Accepted: 06/20/2024] [Indexed: 07/14/2024] Open
Abstract
Plants are subjected to abiotic stresses throughout their developmental period. Abiotic stresses include drought, salt, heat, cold, heavy metals, nutritional elements, and oxidative stresses. Improving plant responses to various environmental stresses is critical for plant survival and perpetuation. WRKY transcription factors have special structures (WRKY structural domains), which enable the WRKY transcription factors to have different transcriptional regulatory functions. WRKY transcription factors can not only regulate abiotic stress responses and plant growth and development by regulating phytohormone signalling pathways but also promote or suppress the expression of downstream genes by binding to the W-box [TGACCA/TGACCT] in the promoters of their target genes. In addition, WRKY transcription factors not only interact with other families of transcription factors to regulate plant defence responses to abiotic stresses but also self-regulate by recognising and binding to W-boxes in their own target genes to regulate their defence responses to abiotic stresses. However, in recent years, research reviews on the regulatory roles of WRKY transcription factors in higher plants have been scarce and shallow. In this review, we focus on the structure and classification of WRKY transcription factors, as well as the identification of their downstream target genes and molecular mechanisms involved in the response to abiotic stresses, which can improve the tolerance ability of plants under abiotic stress, and we also look forward to their future research directions, with a view of providing theoretical support for the genetic improvement of crop abiotic stress tolerance.
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Affiliation(s)
- Ziming Ma
- Jilin Provincial Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun 130062, China
- Max-Planck-Institute of Molecular Plant Physiology, Am Muehlenberg 1, Golm, 14476 Potsdam, Germany
- Plant Genetics, TUM School of Life Sciences, Technical University of Munich (TUM), Emil Ramann Str. 4, 85354 Freising, Germany
| | - Lanjuan Hu
- Jilin Provincial Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun 130062, China
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He L, Liu Q, Han S. Genome-Wide Analysis of Serine Carboxypeptidase-like Genes in Soybean and Their Roles in Stress Resistance. Int J Mol Sci 2024; 25:6712. [PMID: 38928417 PMCID: PMC11203753 DOI: 10.3390/ijms25126712] [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: 05/13/2024] [Revised: 06/11/2024] [Accepted: 06/15/2024] [Indexed: 06/28/2024] Open
Abstract
The serine carboxypeptidase-like (SCPL) gene family plays a crucial role in the regulation of plant growth, development, and stress response through activities such as acyltransferases in plant secondary metabolism pathways. Although SCPL genes have been identified in various plant species, their specific functions and characteristics in soybean (Glycine max) have not yet been studied. We identified and characterized 73 SCPL genes, grouped into three subgroups based on gene structure and phylogenetic relationships. These genes are distributed unevenly across 20 soybean chromosomes and show varied codon usage patterns influenced by both mutation and selection pressures. Gene ontology (GO) enrichment suggests these genes are involved in plant cell wall regulation and stress responses. Expression analysis in various tissues and under stress conditions, including the presence of numerous stress-related cis-acting elements, indicated that these genes have varied expression patterns. This suggests that they play specialized roles such as modulating plant defense mechanisms against nematode infections, enhancing tolerance to drought and high salinity, and responding to cold stress, thereby helping soybean adapt to environmental stresses. Moreover, the expression of specific GmSCPLs was significantly affected following exposure to nematode infection, drought, high salt (NaCl), and cold stresses. Our findings underscore the potential of SCPL genes in enhancing stress resistance in soybean, providing a valuable resource for future genetic improvement and breeding strategies.
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Affiliation(s)
- Long He
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (L.H.); (Q.L.)
- Zhejiang Lab, Hangzhou 310058, China
| | - Qiannan Liu
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (L.H.); (Q.L.)
| | - Shaojie Han
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (L.H.); (Q.L.)
- Zhejiang Lab, Hangzhou 310058, China
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25
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Sun J, Liu Y, Zheng Y, Xue Y, Fan Y, Ma X, Ji Y, Liu G, Zhang X, Li Y, Wang S, Tian Z, Zhao L. The MADS-box transcription factor GmFULc promotes GmZTL4 gene transcription to modulate maturity in soybean. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024. [PMID: 38869305 DOI: 10.1111/jipb.13682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 04/26/2024] [Accepted: 05/04/2024] [Indexed: 06/14/2024]
Abstract
Flowering time and maturity are crucial agronomic traits that affect the regional adaptability of soybean plants. The development of soybean cultivars with early maturity adapted to longer days and colder climates of high latitudes is very important for ensuring normal ripening before frost begins. FUL belongs to the MADS-box transcription factor family and has several duplicated members in soybeans. In this study, we observed that overexpression of GmFULc in the Dongnong 50 cultivar promoted soybean maturity, while GmFULc knockout mutants exhibited late maturity. Chromatin immunoprecipitation sequencing (ChIP-seq) and RNA sequencing (RNA-seq) revealed that GmFULc could bind to the CArG, bHLH and homeobox motifs. Further investigation revealed that GmFULc could directly bind to the CArG motif in the promoters of the GmZTL3 and GmZTL4 genes. Overexpression of GmZTL4 promoted soybean maturity, whereas the ztl4 mutants exhibited delayed maturity. Moreover, we found that the cis element box 4 motif of the GmZTL4 promoter, a motif of light response elements, played an important role in controlling the growth period. Deletion of this motif shortened the growth period by increasing the expression levels of GmZTL4. Functional investigations revealed that short-day treatment promoted the binding of GmFULc to the promoter of GmZTL4 and inhibited the expression of E1 and E1Lb, ultimately resulting in the promotion of flowering and early maturation. Taken together, these findings suggest a novel photoperiod regulatory pathway in which GmFULc directly activates GmZTL4 to promote earlier maturity in soybean.
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Affiliation(s)
- Jingzhe Sun
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin, 150030, China
- Qingdao Institute of Bioenergy and Bioprocess Technology, The Chinese Academy of Sciences, Qingdao, 266101, China
| | - Yucheng Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, The Chinese Academy of Sciences, Beijing, 100101, China
| | - Yuhong Zheng
- Jilin Academy of Agricultural Sciences, China Agricultural Science and Technology Northeast Innovation Center, Changchun, 130033, China
| | - Yongguo Xue
- Institute of Soybean Research, Heilongjiang Provincial Academy of Agricultural Sciences, Harbin, 150086, China
| | - Yuhuan Fan
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin, 150030, China
| | - Xiaofei Ma
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin, 150030, China
| | - Yujia Ji
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin, 150030, China
| | - Gaoyuan Liu
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin, 150030, China
| | - Xiaoming Zhang
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin, 150030, China
| | - Yang Li
- Depatment of Environmental and Plant Biology, Ohio University, Athens, 45701, Ohio, USA
| | - Shuming Wang
- Jilin Academy of Agricultural Sciences, China Agricultural Science and Technology Northeast Innovation Center, Changchun, 130033, China
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, The Chinese Academy of Sciences, Beijing, 100101, China
| | - Lin Zhao
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin, 150030, China
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Su T, Liu H, Wu Y, Wang J, He F, Li H, Li S, Wang L, Li L, Cao J, Lu Q, Zhao X, Xiang H, Lin C, Lu S, Liu B, Kong F, Fang C. Soybean hypocotyl elongation is regulated by a MYB33-SWEET11/21-GA2ox8c module involving long-distance sucrose transport. PLANT BIOTECHNOLOGY JOURNAL 2024. [PMID: 38861663 DOI: 10.1111/pbi.14409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 04/01/2024] [Accepted: 05/27/2024] [Indexed: 06/13/2024]
Abstract
The length of hypocotyl affects the height of soybean and lodging resistance, thus determining the final grain yield. However, research on soybean hypocotyl length is scarce, and the regulatory mechanisms are not fully understood. Here, we identified a module controlling the transport of sucrose, where sucrose acts as a messenger moved from cotyledon to hypocotyl, regulating hypocotyl elongation. This module comprises four key genes, namely MYB33, SWEET11, SWEET21 and GA2ox8c in soybean. In cotyledon, MYB33 is responsive to sucrose and promotes the expression of SWEET11 and SWEET21, thereby facilitating sucrose transport from the cotyledon to the hypocotyl. Subsequently, sucrose transported from the cotyledon up-regulates the expression of GA2ox8c in the hypocotyl, which ultimately affects the length of the hypocotyl. During the domestication and improvement of soybean, an allele of MYB33 with enhanced abilities to promote SWEET11 and SWEET21 has gradually become enriched in landraces and cultivated varieties, SWEET11 and SWEET21 exhibit high conservation and have undergone a strong purified selection and GA2ox8c is under a strong artificial selection. Our findings identify a new molecular pathway in controlling soybean hypocotyl elongation and provide new insights into the molecular mechanism of sugar transport in soybean.
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Affiliation(s)
- Tong Su
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Huan Liu
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Yichun Wu
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Jianhao Wang
- Vegetables Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, China
| | - Fanglei He
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
- Institute of Improvement and Utilization of Characteristic Resource Plants, College of Agriculture and Biotechnology, Yunnan Agricultural University, Kunming, China
| | - Haiyang Li
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Shichen Li
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Lingshuang Wang
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Lanxin Li
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Jie Cao
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Qiulian Lu
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Xiaohui Zhao
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Hongtao Xiang
- Heilongjiang Academy of Agricultural Sciences, Harbin, China
- Suihua Branch, Heilongjiang Academy of Agricultural Machinery Sciences, Suihua, China
| | - Chun Lin
- Institute of Improvement and Utilization of Characteristic Resource Plants, College of Agriculture and Biotechnology, Yunnan Agricultural University, Kunming, China
| | - Sijia Lu
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Baohui Liu
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Fanjiang Kong
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Chao Fang
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
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Li J, Zhang W, Lu Q, Sun J, Cheng C, Huang S, Li S, Li Q, Zhang W, Zhou C, Liu B, Xiang F. GmDFB1, an ARM-repeat superfamily protein, regulates floral organ identity through repressing siRNA- and miRNA-mediated gene silencing in soybean. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024. [PMID: 38860597 DOI: 10.1111/jipb.13709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 05/04/2024] [Indexed: 06/12/2024]
Abstract
The development of flowers in soybean (Glycine max) is essential for determining the yield potential of the plant. Gene silencing pathways are involved in modulating flower development, but their full elucidation is still incomplete. Here, we conducted a forward genetic screen and identified an abnormal flower mutant, deformed floral bud1-1 (Gmdfb1-1), in soybean. We mapped and identified the causal gene, which encodes a member of the armadillo (ARM)-repeat superfamily. Using small RNA sequencing (sRNA-seq), we found an abnormal accumulation of small interfering RNAs (siRNAs) and microRNA (miRNAs) in the Gmdfb1 mutants. We further demonstrated that GmDFB1 interacts with the RNA exosome cofactor SUPER KILLER7 (GmSKI7). Additionally, GmDFB1 interacts with the PIWI domain of ARGONAUTE 1 (GmAGO1) to inhibit the cleavage efficiency on the target genes of sRNAs. The enhanced gene silencing mediated by siRNA and miRNA in the Gmdfb1 mutants leads to the downregulation of their target genes associated with flower development. This study revealed the crucial role of GmDFB1 in regulating floral organ identity in soybean probably by participating in two distinct gene silencing pathways.
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Affiliation(s)
- Jie Li
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Wenxiao Zhang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Qing Lu
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Jiaqi Sun
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Chuang Cheng
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Shiyu Huang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Shuo Li
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Qiang Li
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Wei Zhang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Chuanen Zhou
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Bin Liu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Fengning Xiang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
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28
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Rodrigues JCM, Carrijo J, Anjos RM, Cunha NB, Grynberg P, Aragão FJL, Vianna GR. The role of microRNAs in NBS-LRR gene expression and its implications for plant immunity and crop development. Transgenic Res 2024:10.1007/s11248-024-00387-9. [PMID: 38856866 DOI: 10.1007/s11248-024-00387-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 05/15/2024] [Indexed: 06/11/2024]
Abstract
Plants evolved, over millions of years, complex defense systems against pathogens. Once infected, the interaction between pathogen effector molecules and host receptors triggers plant immune responses, which include apoptosis, systemic immune response, among others. An important protein family responsible for pathogen effector recognition is the nucleotide binding site-leucine repeat rich (NBS-LRR) proteins. The NBS-LRR gene family is the largest disease resistance gene class in plants. These proteins are widely distributed in vascular plants and have a complex multigenic cluster distribution in plant genomes. To counteract the genetic load of such a large gene family on fitness cost, plants evolved a mechanism using post transcriptional gene silencing induced by small RNAs, particularly microRNAs. For the NBS-LRR gene family, the small RNAs involved in this silencing mechanism are mainly the microRNA482/2118 superfamily. This suppression mechanism is relieved upon pathogen infection, thus allowing increased NBS-LRR expression and triggering plant immunity. In this review, we will discuss the biogenesis of microRNAs and secondary RNAs involved in this silencing mechanism, biochemical and structural features of NBS-LRR proteins in response to pathogen effectors and the evolution of microRNA-based silencing mechanism with a focus on the miR482/2118 family. Furthermore, the biotechnological manipulation of microRNA expression, using both transgenic or genome editing approaches to improve cultivated plants will be discussed, with a focus on the miR482/2118 family in soybean.
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Affiliation(s)
- J C M Rodrigues
- Embrapa Genetic Resources and Biotechnology, Brasília, Brazil.
| | - J Carrijo
- Embrapa Genetic Resources and Biotechnology, Brasília, Brazil
| | - R M Anjos
- University of Brasília, Brasília, Brazil
| | - N B Cunha
- University of Brasília, Brasília, Brazil
| | - P Grynberg
- Embrapa Genetic Resources and Biotechnology, Brasília, Brazil
| | - F J L Aragão
- Embrapa Genetic Resources and Biotechnology, Brasília, Brazil
| | - G R Vianna
- Embrapa Genetic Resources and Biotechnology, Brasília, Brazil
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Xu P, Meng M, Wu F, Zhang J. A comparative plastome approach enhances the assessment of genetic variation in the Melilotus genus. BMC Genomics 2024; 25:556. [PMID: 38831327 PMCID: PMC11149310 DOI: 10.1186/s12864-024-10476-y] [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: 11/29/2023] [Accepted: 05/29/2024] [Indexed: 06/05/2024] Open
Abstract
BACKGROUND Melilotus, a member of the Fabaceae family, is a pivotal forage crop that is extensively cultivated in livestock regions globally due to its notable productivity and ability to withstand abiotic stress. However, the genetic attributes of the chloroplast genome and the evolutionary connections among different Melilotus species remain unresolved. RESULTS In this study, we compiled the chloroplast genomes of 18 Melilotus species and performed a comprehensive comparative analysis. Through the examination of protein-coding genes, we successfully established a robust phylogenetic tree for these species. This conclusion is further supported by the phylogeny derived from single-nucleotide polymorphisms (SNPs) across the entire chloroplast genome. Notably, our findings revealed that M. infestus, M. siculus, M. sulcatus, and M. speciosus formed a distinct subgroup within the phylogenetic tree. Additionally, the chloroplast genomes of these four species exhibit two shared inversions. Moreover, inverted repeats were observed to have reemerged in six species within the IRLC. The distribution patterns of single-nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) within protein-coding genes indicated that ycf1 and ycf2 accumulated nonconservative alterations during evolutionary development. Furthermore, an examination of the evolutionary rate of protein-coding genes revealed that rps18, rps7, and rpl16 underwent positive selection specifically in Melilotus. CONCLUSIONS We present a comparative analysis of the complete chloroplast genomes of Melilotus species. This study represents the most thorough and detailed exploration of the evolution and variability within the genus Melilotus to date. Our study provides valuable chloroplast genomic information for improving phylogenetic reconstructions and making biogeographic inferences about Melilotus and other Papilionoideae species.
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Affiliation(s)
- Pan Xu
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, College of Pastoral Agriculture Science and Technology, Ministry of Education, Lanzhou University, Lanzhou, 730000, China
| | - Minghui Meng
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, College of Pastoral Agriculture Science and Technology, Ministry of Education, Lanzhou University, Lanzhou, 730000, China
| | - Fan Wu
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, College of Pastoral Agriculture Science and Technology, Ministry of Education, Lanzhou University, Lanzhou, 730000, China
| | - Jiyu Zhang
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, College of Pastoral Agriculture Science and Technology, Ministry of Education, Lanzhou University, Lanzhou, 730000, China.
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30
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Huang XZ, Gong SD, Shang XH, Gao M, Zhao BY, Xiao L, Shi PL, Zeng WD, Cao S, Wu ZD, Song JM, Chen LL, Yan HB. High-integrity Pueraria montana var. lobata genome and population analysis revealed the genetic diversity of Pueraria genus. DNA Res 2024; 31:dsae017. [PMID: 38809753 PMCID: PMC11149379 DOI: 10.1093/dnares/dsae017] [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: 06/26/2023] [Revised: 04/23/2024] [Accepted: 05/24/2024] [Indexed: 05/31/2024] Open
Abstract
Pueraria montana var. lobata (P. lobata) is a traditional medicinal plant belonging to the Pueraria genus of Fabaceae family. Pueraria montana var. thomsonii (P. thomsonii) and Pueraria montana var. montana (P. montana) are its related species. However, evolutionary history of the Pueraria genus is still largely unknown. Here, a high-integrity, chromosome-level genome of P. lobata and an improved genome of P. thomsonii were reported. It found evidence for an ancient whole-genome triplication and a recent whole-genome duplication shared with Fabaceae in three Pueraria species. Population genomics of 121 Pueraria accessions demonstrated that P. lobata populations had substantially higher genetic diversity, and P. thomsonii was probably derived from P. lobata by domestication as a subspecies. Selection sweep analysis identified candidate genes in P. thomsonii populations associated with the synthesis of auxin and gibberellin, which potentially play a role in the expansion and starch accumulation of tubers in P. thomsonii. Overall, the findings provide new insights into the evolutionary and domestication history of the Pueraria genome and offer a valuable genomic resource for the genetic improvement of these species.
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Affiliation(s)
- Xuan-Zhao Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi 530004, China
| | - Shao-Da Gong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi 530004, China
| | - Xiao-hong Shang
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences (GXAAS), Nanning, Guangxi 530007, China
| | - Min Gao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi 530004, China
| | - Bo-Yuan Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi 530004, China
| | - Liang Xiao
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences (GXAAS), Nanning, Guangxi 530007, China
| | - Ping-li Shi
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences (GXAAS), Nanning, Guangxi 530007, China
| | - Wen-dan Zeng
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences (GXAAS), Nanning, Guangxi 530007, China
| | - Sheng Cao
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences (GXAAS), Nanning, Guangxi 530007, China
| | - Zheng-dan Wu
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences (GXAAS), Nanning, Guangxi 530007, China
| | - Jia-Ming Song
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi 530004, China
| | - Ling-Ling Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi 530004, China
| | - Hua-bing Yan
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences (GXAAS), Nanning, Guangxi 530007, China
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Nishimura K, Kokaji H, Motoki K, Yamazaki A, Nagasaka K, Mori T, Takisawa R, Yasui Y, Kawai T, Ushijima K, Yamasaki M, Saito H, Nakano R, Nakazaki T. Degenerate oligonucleotide primer MIG-seq: an effective PCR-based method for high-throughput genotyping. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:2296-2317. [PMID: 38459738 DOI: 10.1111/tpj.16708] [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: 09/20/2023] [Revised: 01/14/2024] [Accepted: 02/14/2024] [Indexed: 03/10/2024]
Abstract
Next-generation sequencing (NGS) library construction often involves using restriction enzymes to decrease genome complexity, enabling versatile polymorphism detection in plants. However, plant leaves frequently contain impurities, such as polyphenols, necessitating DNA purification before enzymatic reactions. To overcome this problem, we developed a PCR-based method for expeditious NGS library preparation, offering flexibility in number of detected polymorphisms. By substituting a segment of the simple sequence repeat sequence in the MIG-seq primer set (MIG-seq being a PCR method enabling library construction with low-quality DNA) with degenerate oligonucleotides, we introduced variability in detectable polymorphisms across various crops. This innovation, named degenerate oligonucleotide primer MIG-seq (dpMIG-seq), enabled a streamlined protocol for constructing dpMIG-seq libraries from unpurified DNA, which was implemented stably in several crop species, including fruit trees. Furthermore, dpMIG-seq facilitated efficient lineage selection in wheat and enabled linkage map construction and quantitative trait loci analysis in tomato, rice, and soybean without necessitating DNA concentration adjustments. These findings underscore the potential of the dpMIG-seq protocol for advancing genetic analyses across diverse plant species.
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Affiliation(s)
- Kazusa Nishimura
- Graduate School of Agriculture, Kyoto University, 4-2-1, Shiroyamadai, Kizugawa City, Kyoto, 619-0218, Japan
- Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, 1-1-1 Tsushima-naka, Kita-ku, Okayama City, 700-8530, Okayama, Japan
| | - Hiroyuki Kokaji
- Graduate School of Agriculture, Kyoto University, 4-2-1, Shiroyamadai, Kizugawa City, Kyoto, 619-0218, Japan
| | - Ko Motoki
- Graduate School of Agriculture, Kyoto University, 4-2-1, Shiroyamadai, Kizugawa City, Kyoto, 619-0218, Japan
- Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, 1-1-1 Tsushima-naka, Kita-ku, Okayama City, 700-8530, Okayama, Japan
| | - Akira Yamazaki
- Faculty of Agriculture, Kindai University, 3327-204, Nakamachi, Nara City, Nara, 631-8505, Japan
| | - Kyoka Nagasaka
- Graduate School of Agriculture, Kyoto University, 4-2-1, Shiroyamadai, Kizugawa City, Kyoto, 619-0218, Japan
| | - Takashi Mori
- Graduate School of Agriculture, Kyoto University, 4-2-1, Shiroyamadai, Kizugawa City, Kyoto, 619-0218, Japan
| | - Rihito Takisawa
- Faculty of Agriculture, Ryukoku University, 1-5 Yokotani, Seta Oe-cho, Otsu City, Shiga, 520-2194, Japan
| | - Yasuo Yasui
- Graduate School of Agriculture, Kyoto University, 4-2-1, Shiroyamadai, Kizugawa City, Kyoto, 619-0218, Japan
| | - Takashi Kawai
- Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, 1-1-1 Tsushima-naka, Kita-ku, Okayama City, 700-8530, Okayama, Japan
| | - Koichiro Ushijima
- Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, 1-1-1 Tsushima-naka, Kita-ku, Okayama City, 700-8530, Okayama, Japan
| | - Masanori Yamasaki
- Graduate School of Science and Technology, Niigata University, 8050 Ikarashi 2 no-cho, Nishi-ku, Niigata City, Niigata, 950-2181, Japan
| | - Hiroki Saito
- Tropical Agriculture Research Front, Japan International Research Center for Agricultural Sciences, 1091-1 Maezato-Kawarabaru, Ishigaki, Okinawa, 907-0002, Japan
| | - Ryohei Nakano
- Graduate School of Agriculture, Kyoto University, 4-2-1, Shiroyamadai, Kizugawa City, Kyoto, 619-0218, Japan
| | - Tetsuya Nakazaki
- Graduate School of Agriculture, Kyoto University, 4-2-1, Shiroyamadai, Kizugawa City, Kyoto, 619-0218, Japan
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Li S, Li Y, Zhu H, Chen L, Zhang H, Lian L, Xu M, Feng X, Hou R, Yao X, Lin Y, Wang H, Wang X. Deciphering PDH1's role in mung bean domestication: a genomic perspective on pod dehiscence. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:1413-1422. [PMID: 38341804 DOI: 10.1111/tpj.16680] [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: 09/12/2023] [Revised: 01/02/2024] [Accepted: 01/29/2024] [Indexed: 02/13/2024]
Abstract
Mung bean (Vigna radiata) stands as a crucial legume crop in Asia, contributing to food security. However, our understanding of the underlying genetic foundation governing domesticated agronomic traits, especially those linked to pod architecture, remains largely unexplored. In this study, we delved into the genomic divergence between wild and domesticated mung bean varieties, leveraging germplasm obtained from diverse sources. Our findings unveiled pronounced variation in promoter regions (35%) between the two mung bean subpopulations, suggesting substantial changes in gene expression patterns during domestication. Leveraging transcriptome analysis using distinct reproductive stage pods and subpopulations, we identified candidate genes responsible for pod and seed architecture development, along with Genome-Wide Association Studies (GWAS) and Quantitative Trait Locus (QTL) analysis. Notably, our research conclusively confirmed PDH1 as a parallel domesticated gene governing pod dehiscence in legumes. This study imparts valuable insights into the genetic underpinnings of domesticated agronomic traits in mung bean, and simultaneously highlighting the parallel domestication of pivotal traits within the realm of legume crops.
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Affiliation(s)
- Shuai Li
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yaling Li
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Hongshan District, Wuhan, Hubei, 430070, China
| | - Hong Zhu
- College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, China
| | - Liyang Chen
- Department of Agronomy, Purdue University, West Lafayette, Indiana, 47907, USA
| | - Huiying Zhang
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China
| | - Lijie Lian
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Hongshan District, Wuhan, Hubei, 430070, China
| | - Miaomiao Xu
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China
| | - Xilong Feng
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Hongshan District, Wuhan, Hubei, 430070, China
| | - Rui Hou
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China
| | - Xiaolin Yao
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yifan Lin
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Hongshan District, Wuhan, Hubei, 430070, China
| | - Huaying Wang
- Northeast Normal University, Changchun, 130024, China
| | - Xutong Wang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Hongshan District, Wuhan, Hubei, 430070, China
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Cao J, Zhu H, Gao Y, Hu Y, Li X, Shi J, Chen L, Kang H, Ru D, Ren B, Liu B. Chromosome-level genome assembly and characterization of the Calophaca sinica genome. DNA Res 2024; 31:dsae011. [PMID: 38590243 DOI: 10.1093/dnares/dsae011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 03/26/2024] [Accepted: 04/06/2024] [Indexed: 04/10/2024] Open
Abstract
Calophaca sinica is a rare plant endemic to northern China which belongs to the Fabaceae family and possesses rich nutritional value. To support the preservation of the genetic resources of this plant, we have successfully generated a high-quality genome of C. sinica (1.06 Gb). Notably, transposable elements (TEs) constituted ~73% of the genome, with long terminal repeat retrotransposons (LTR-RTs) dominating this group of elements (~54% of the genome). The average intron length of the C. sinica genome was noticeably longer than what has been observed for closely related species. The expansion of LTR-RTs and elongated introns emerged had the largest influence on the enlarged genome size of C. sinica in comparison to other Fabaceae species. The proliferation of TEs could be explained by certain modes of gene duplication, namely, whole genome duplication (WGD) and dispersed duplication (DSD). Gene family expansion, which was found to enhance genes associated with metabolism, genetic maintenance, and environmental stress resistance, was a result of transposed duplicated genes (TRD) and WGD. The presented genomic analysis sheds light on the genetic architecture of C. sinica, as well as provides a starting point for future evolutionary biology, ecology, and functional genomics studies centred around C. sinica and closely related species.
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Affiliation(s)
| | - Hui Zhu
- State Key Laboratory of Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Yingqi Gao
- Institute of Loess Plateau, Shanxi University, Taiyuan, Shanxi, China
| | - Yue Hu
- Institute of Loess Plateau, Shanxi University, Taiyuan, Shanxi, China
| | - Xuejiao Li
- Institute of Loess Plateau, Shanxi University, Taiyuan, Shanxi, China
| | - Jianwei Shi
- Institute of Loess Plateau, Shanxi University, Taiyuan, Shanxi, China
| | - Luqin Chen
- Taiyuan Botanical Garden, Taiyuan, China
| | - Hao Kang
- Taiyuan Botanical Garden, Taiyuan, China
| | - Dafu Ru
- State Key Laboratory of Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | | | - Bingbing Liu
- Institute of Loess Plateau, Shanxi University, Taiyuan, Shanxi, China
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Wang W, Duan J, Wang X, Feng X, Chen L, Clark CB, Swarm SA, Wang J, Lin S, Nelson RL, Meyers BC, Feng X, Ma J. Long noncoding RNAs underlie multiple domestication traits and leafhopper resistance in soybean. Nat Genet 2024; 56:1270-1277. [PMID: 38684899 DOI: 10.1038/s41588-024-01738-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 03/28/2024] [Indexed: 05/02/2024]
Abstract
The origin and functionality of long noncoding RNA (lncRNA) remain poorly understood. Here, we show that multiple quantitative trait loci modulating distinct domestication traits in soybeans are pleiotropic effects of a locus composed of two tandem lncRNA genes. These lncRNA genes, each containing two inverted repeats, originating from coding sequences of the MYB genes, function in wild soybeans by generating clusters of small RNA (sRNA) species that inhibit the expression of their MYB gene relatives through post-transcriptional regulation. By contrast, the expression of lncRNA genes in cultivated soybeans is severely repressed, and, consequently, the corresponding MYB genes are highly expressed, shaping multiple distinct domestication traits as well as leafhopper resistance. The inverted repeats were formed before the divergence of the Glycine genus from the Phaseolus-Vigna lineage and exhibit strong structure-function constraints. This study exemplifies a type of target for selection during plant domestication and identifies mechanisms of lncRNA formation and action.
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Affiliation(s)
- Weidong Wang
- Department of Agronomy, Purdue University, West Lafayette, IN, USA
- Center for Plant Biology, Purdue University, West Lafayette, IN, USA
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Jingbo Duan
- Department of Agronomy, Purdue University, West Lafayette, IN, USA
- Center for Plant Biology, Purdue University, West Lafayette, IN, USA
| | - Xutong Wang
- Department of Agronomy, Purdue University, West Lafayette, IN, USA
- Center for Plant Biology, Purdue University, West Lafayette, IN, USA
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xingxing Feng
- Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Liyang Chen
- Department of Agronomy, Purdue University, West Lafayette, IN, USA
- Center for Plant Biology, Purdue University, West Lafayette, IN, USA
| | - Chancelor B Clark
- Department of Agronomy, Purdue University, West Lafayette, IN, USA
- Center for Plant Biology, Purdue University, West Lafayette, IN, USA
| | - Stephen A Swarm
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Beck's Hybrids, Atlanta, IN, USA
| | - Jinbin Wang
- Department of Agronomy, Purdue University, West Lafayette, IN, USA
- Center for Plant Biology, Purdue University, West Lafayette, IN, USA
| | - Sen Lin
- Department of Agronomy, Purdue University, West Lafayette, IN, USA
- Center for Plant Biology, Purdue University, West Lafayette, IN, USA
| | - Randall L Nelson
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Blake C Meyers
- Genome Center and Department of Plant Sciences, University of California, Davis, Davis, CA, USA
| | - Xianzhong Feng
- Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China.
| | - Jianxin Ma
- Department of Agronomy, Purdue University, West Lafayette, IN, USA.
- Center for Plant Biology, Purdue University, West Lafayette, IN, USA.
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Li S, Wang J, Ren G. CircRNA: An emerging star in plant research: A review. Int J Biol Macromol 2024; 272:132800. [PMID: 38825271 DOI: 10.1016/j.ijbiomac.2024.132800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 05/27/2024] [Accepted: 05/30/2024] [Indexed: 06/04/2024]
Abstract
CircRNAs are a class of covalently closed non-coding RNA formed by linking the 5' terminus and the 3' terminus after reverse splicing. CircRNAs are widely found in eukaryotes, and they are highly conserved, with spatio-temporal expression specificity and stability. CircRNAs can act as miRNA sponges to regulate the expression of downstream target genes, regulating the transcription of parental genes and some can even be translated into peptides or proteins. Research on circRNAs in plants is still in its infancy compared to that in animals. With the deepening of research, the results of a variety of plant circRNAs suggest that they play an important role in growth and development, and tolerance towards abiotic stresses such as salt, drought, low temperature, high temperature and other adverse environments. In this review paper, we elaborated the molecular characteristics, mechanism of action, function and bioinformatics databases of plant circRNAs, combined with the progress of circRNA research in animals, discussed the potential mechanism of action of plant circRNAs, and proposed the unsolved problems and prospects for future application of plant circRNAs.
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Affiliation(s)
- Simin Li
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Jingyi Wang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Guocheng Ren
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan 250014, China; Dongying Institute, Shandong Normal University, Dongying 257000, China.
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Sreedasyam A, Lovell JT, Mamidi S, Khanal S, Jenkins JW, Plott C, Bryan KB, Li Z, Shu S, Carlson J, Goodstein D, De Santiago L, Kirkbride RC, Calleja S, Campbell T, Koebernick JC, Dever JK, Scheffler JA, Pauli D, Jenkins JN, McCarty JC, Williams M, Boston L, Webber J, Udall JA, Chen ZJ, Bourland F, Stiller WN, Saski CA, Grimwood J, Chee PW, Jones DC, Schmutz J. Genome resources for three modern cotton lines guide future breeding efforts. NATURE PLANTS 2024; 10:1039-1051. [PMID: 38816498 PMCID: PMC11208153 DOI: 10.1038/s41477-024-01713-z] [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: 10/27/2023] [Accepted: 04/27/2024] [Indexed: 06/01/2024]
Abstract
Cotton (Gossypium hirsutum L.) is the key renewable fibre crop worldwide, yet its yield and fibre quality show high variability due to genotype-specific traits and complex interactions among cultivars, management practices and environmental factors. Modern breeding practices may limit future yield gains due to a narrow founding gene pool. Precision breeding and biotechnological approaches offer potential solutions, contingent on accurate cultivar-specific data. Here we address this need by generating high-quality reference genomes for three modern cotton cultivars ('UGA230', 'UA48' and 'CSX8308') and updating the 'TM-1' cotton genetic standard reference. Despite hypothesized genetic uniformity, considerable sequence and structural variation was observed among the four genomes, which overlap with ancient and ongoing genomic introgressions from 'Pima' cotton, gene regulatory mechanisms and phenotypic trait divergence. Differentially expressed genes across fibre development correlate with fibre production, potentially contributing to the distinctive fibre quality traits observed in modern cotton cultivars. These genomes and comparative analyses provide a valuable foundation for future genetic endeavours to enhance global cotton yield and sustainability.
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Affiliation(s)
- Avinash Sreedasyam
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
- DOE Joint Genome Institute, Berkeley, CA, USA.
| | - John T Lovell
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- DOE Joint Genome Institute, Berkeley, CA, USA
| | - Sujan Mamidi
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Sameer Khanal
- Department of Crop and Soil Sciences and Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Tifton, GA, USA
| | - Jerry W Jenkins
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Christopher Plott
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Kempton B Bryan
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, USA
| | - Zhigang Li
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, USA
| | | | | | | | - Luis De Santiago
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Ryan C Kirkbride
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | | | - Todd Campbell
- USDA-ARS, Coastal Plains Soil Water and Plant Research Center, Florence, SC, USA
| | - Jenny C Koebernick
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL, USA
| | - Jane K Dever
- Texas A&M AgriLife Research, Lubbock, TX, USA
- Pee Dee Research and Education Center, Clemson University, Florence, SC, USA
| | | | - Duke Pauli
- School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | - Johnie N Jenkins
- USDA-ARS, Genetics and Sustainable Agriculture Research Unit, Mississippi State, MS, USA
| | - Jack C McCarty
- USDA-ARS, Genetics and Sustainable Agriculture Research Unit, Mississippi State, MS, USA
| | - Melissa Williams
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - LoriBeth Boston
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Jenell Webber
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Joshua A Udall
- USDA-ARS, Crop Germplasm Research Unit, College Station, TX, USA
| | - Z Jeffrey Chen
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Fred Bourland
- Northeast Research and Extension Center (NEREC), University of Arkansas, Keiser, AR, USA
| | - Warwick N Stiller
- CSIRO Agriculture and Food Cotton Research Unit, Narrabri, New South Wales, Australia
| | - Christopher A Saski
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, USA
| | - Jane Grimwood
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Peng W Chee
- Department of Crop and Soil Sciences and Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Tifton, GA, USA
| | - Don C Jones
- Agriculture and Environmental Research Cotton Incorporated, Cary, NC, USA
| | - Jeremy Schmutz
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
- DOE Joint Genome Institute, Berkeley, CA, USA.
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Wen Z, Lu X, Wen J, Wang Z, Chai M. Physical Seed Dormancy in Legumes: Molecular Advances and Perspectives. PLANTS (BASEL, SWITZERLAND) 2024; 13:1473. [PMID: 38891282 PMCID: PMC11174410 DOI: 10.3390/plants13111473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Revised: 05/14/2024] [Accepted: 05/17/2024] [Indexed: 06/21/2024]
Abstract
Physical dormancy of seeds is a form of dormancy due to the presence of an impermeable seed coat layer, and it represents a feature for plants to adapt to environmental changes over an extended period of phylogenetic evolution. However, in agricultural practice, physical dormancy is problematic. because it prevents timely and uniform seed germination. Therefore, physical dormancy is an important agronomical trait to target in breeding and domestication, especially for many leguminous crops. Compared to the well-characterized physiological dormancy, research progress on physical dormancy at the molecular level has been limited until recent years, due to the lack of suitable research materials. This review focuses on the structure of seed coat, factors affecting physical dormancy, genes controlling physical dormancy, and plants suitable for studying physical dormancy at the molecular level. Our goal is to provide a plethora of information for further molecular research on physical dormancy.
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Affiliation(s)
- Zhaozhu Wen
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China
- Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Xuran Lu
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China
- Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China
| | - Jiangqi Wen
- Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, OK 73401, USA
| | - Zengyu Wang
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China
- Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China
| | - Maofeng Chai
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China
- Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China
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Ye Z, Mao D, Wang Y, Deng H, Liu X, Zhang T, Han Z, Zhang X. Comparative Genome-Wide Identification of the Fatty Acid Desaturase Gene Family in Tea and Oil Tea. PLANTS (BASEL, SWITZERLAND) 2024; 13:1444. [PMID: 38891253 PMCID: PMC11174766 DOI: 10.3390/plants13111444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/07/2024] [Accepted: 05/16/2024] [Indexed: 06/21/2024]
Abstract
Camellia oil is valuable as an edible oil and serves as a base material for a range of high-value products. Camellia plants of significant economic importance, such as Camellia sinensis and Camellia oleifera, have been classified into sect. Thea and sect. Oleifera, respectively. Fatty acid desaturases play a crucial role in catalyzing the formation of double bonds at specific positions of fatty acid chains, leading to the production of unsaturated fatty acids and contributing to lipid synthesis. Comparative genomics results have revealed that expanded gene families in oil tea are enriched in functions related to lipid, fatty acid, and seed processes. To explore the function of the FAD gene family, a total of 82 FAD genes were identified in tea and oil tea. Transcriptome data showed the differential expression of the FAD gene family in mature seeds of tea tree and oil tea tree. Furthermore, the structural analysis and clustering of FAD proteins provided insights for the further exploration of the function of the FAD gene family and its role in lipid synthesis. Overall, these findings shed light on the role of the FAD gene family in Camellia plants and their involvement in lipid metabolism, as well as provide a reference for understanding their function in oil synthesis.
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Affiliation(s)
- Ziqi Ye
- The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha 410004, China; (Z.Y.); (H.D.); (X.L.); (T.Z.)
| | - Dan Mao
- National Forest and Seedling Workstation of Hunan Province, The Forestry Department of Hunan Province, Changsha 410004, China; (D.M.); (Y.W.)
| | - Yujian Wang
- National Forest and Seedling Workstation of Hunan Province, The Forestry Department of Hunan Province, Changsha 410004, China; (D.M.); (Y.W.)
| | - Hongda Deng
- The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha 410004, China; (Z.Y.); (H.D.); (X.L.); (T.Z.)
| | - Xing Liu
- The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha 410004, China; (Z.Y.); (H.D.); (X.L.); (T.Z.)
| | - Tongyue Zhang
- The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha 410004, China; (Z.Y.); (H.D.); (X.L.); (T.Z.)
| | - Zhiqiang Han
- The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha 410004, China; (Z.Y.); (H.D.); (X.L.); (T.Z.)
| | - Xingtan Zhang
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
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Kim WS, Gillman JD, Kim S, Liu J, Janga MR, Stupar RM, Krishnan HB. Bowman-Birk Inhibitor Mutants of Soybean Generated by CRISPR-Cas9 Reveal Drastic Reductions in Trypsin and Chymotrypsin Inhibitor Activities. Int J Mol Sci 2024; 25:5578. [PMID: 38891766 PMCID: PMC11171862 DOI: 10.3390/ijms25115578] [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: 04/12/2024] [Revised: 05/07/2024] [Accepted: 05/15/2024] [Indexed: 06/21/2024] Open
Abstract
Despite the high quality of soybean protein, raw soybeans and soybean meal cannot be directly included in animal feed mixtures due to the presence of Kunitz (KTi) and Bowman-Birk protease inhibitors (BBis), which reduces animal productivity. Heat treatment can substantially inactivate trypsin and chymotrypsin inhibitors (BBis), but such treatment is energy-intensive, adds expense, and negatively impacts the quality of seed proteins. As an alternative approach, we have employed CRISPR/Cas9 gene editing to create mutations in BBi genes to drastically lower the protease inhibitor content in soybean seed. Agrobacterium-mediated transformation was used to generate several stable transgenic soybean events. These independent CRISPR/Cas9 events were examined in comparison to wild-type plants using Sanger sequencing, proteomic analysis, trypsin/chymotrypsin inhibitor activity assays, and qRT-PCR. Collectively, our results demonstrate the creation of an allelic series of loss-of-function mutations affecting the major BBi gene in soybean. Mutations in two of the highly expressed seed-specific BBi genes lead to substantial reductions in both trypsin and chymotrypsin inhibitor activities.
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Affiliation(s)
- Won-Seok Kim
- Division of Plant Science and Technology, University of Missouri, Columbia, MO 65211, USA; (W.-S.K.); (S.K.)
| | - Jason D. Gillman
- Plant Genetics Research Unit, US Department of Agriculture-Agricultural Research Service, Columbia, MO 65211, USA;
| | - Sunhyung Kim
- Division of Plant Science and Technology, University of Missouri, Columbia, MO 65211, USA; (W.-S.K.); (S.K.)
| | - Junqi Liu
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA; (J.L.); (R.M.S.)
| | - Madhusudhana R. Janga
- Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, TX 79409, USA;
| | - Robert M. Stupar
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA; (J.L.); (R.M.S.)
| | - Hari B. Krishnan
- Plant Genetics Research Unit, US Department of Agriculture-Agricultural Research Service, Columbia, MO 65211, USA;
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Wang W, Zhang T, Liu C, Liu C, Jiang Z, Zhang Z, Ali S, Li Z, Wang J, Sun S, Chen Q, Zhang Q, Xie L. A DNA demethylase reduces seed size by decreasing the DNA methylation of AT-rich transposable elements in soybean. Commun Biol 2024; 7:613. [PMID: 38773248 PMCID: PMC11109123 DOI: 10.1038/s42003-024-06306-2] [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: 09/24/2023] [Accepted: 05/08/2024] [Indexed: 05/23/2024] Open
Abstract
Understanding how to increase soybean yield is crucial for global food security. The genetic and epigenetic factors influencing seed size, a major crop yield determinant, are not fully understood. We explore the role of DNA demethylase GmDMEa in soybean seed size. Our research indicates that GmDMEa negatively correlates with soybean seed size. Using CRISPR-Cas9, we edited GmDMEa in the Dongnong soybean cultivar, known for small seeds. Modified plants had larger seeds and greater yields without altering plant architecture or seed nutrition. GmDMEa preferentially demethylates AT-rich transposable elements, thus activating genes and transcription factors associated with the abscisic acid pathway, which typically decreases seed size. Chromosomal substitution lines confirm that these modifications are inheritable, suggesting a stable epigenetic method to boost seed size in future breeding. Our findings provide insights into epigenetic seed size control and suggest a strategy for improving crop yields through the epigenetic regulation of crucial genes. This work implies that targeted epigenetic modification has practical agricultural applications, potentially enhancing food production without compromising crop quality.
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Affiliation(s)
- Wanpeng Wang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, Heilongjiang, China
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
| | - Tianxu Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Chunyu Liu
- College of Life Science, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Chunyan Liu
- College of Agriculture, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Zhenfeng Jiang
- College of Agriculture, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Zhaohan Zhang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Shahid Ali
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Zhuozheng Li
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Jiang Wang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, Heilongjiang, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Shanwen Sun
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, Heilongjiang, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Qingshan Chen
- College of Agriculture, Northeast Agricultural University, Harbin, Heilongjiang, China.
| | - Qingzhu Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, China.
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, Heilongjiang, China.
- College of Life Science, Northeast Forestry University, Harbin, Heilongjiang, China.
| | - Linan Xie
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, Heilongjiang, China.
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, Heilongjiang, China.
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41
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Salazar OR, Chen K, Melino VJ, Reddy MP, Hřibová E, Čížková J, Beránková D, Arciniegas Vega JP, Cáceres Leal LM, Aranda M, Jaremko L, Jaremko M, Fedoroff NV, Tester M, Schmöckel SM. SOS1 tonoplast neo-localization and the RGG protein SALTY are important in the extreme salinity tolerance of Salicornia bigelovii. Nat Commun 2024; 15:4279. [PMID: 38769297 PMCID: PMC11106269 DOI: 10.1038/s41467-024-48595-5] [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: 05/01/2023] [Accepted: 05/07/2024] [Indexed: 05/22/2024] Open
Abstract
The identification of genes involved in salinity tolerance has primarily focused on model plants and crops. However, plants naturally adapted to highly saline environments offer valuable insights into tolerance to extreme salinity. Salicornia plants grow in coastal salt marshes, stimulated by NaCl. To understand this tolerance, we generated genome sequences of two Salicornia species and analyzed the transcriptomic and proteomic responses of Salicornia bigelovii to NaCl. Subcellular membrane proteomes reveal that SbiSOS1, a homolog of the well-known SALT-OVERLY-SENSITIVE 1 (SOS1) protein, appears to localize to the tonoplast, consistent with subcellular localization assays in tobacco. This neo-localized protein can pump Na+ into the vacuole, preventing toxicity in the cytosol. We further identify 11 proteins of interest, of which SbiSALTY, substantially improves yeast growth on saline media. Structural characterization using NMR identified it as an intrinsically disordered protein, localizing to the endoplasmic reticulum in planta, where it can interact with ribosomes and RNA, stabilizing or protecting them during salt stress.
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Affiliation(s)
- Octavio R Salazar
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
- Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Ke Chen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Vanessa J Melino
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
- Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Muppala P Reddy
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
- Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Eva Hřibová
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900, Olomouc, Czech Republic
| | - Jana Čížková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900, Olomouc, Czech Republic
| | - Denisa Beránková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900, Olomouc, Czech Republic
| | - Juan Pablo Arciniegas Vega
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
- Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Lina María Cáceres Leal
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
- Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Manuel Aranda
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Lukasz Jaremko
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Mariusz Jaremko
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Nina V Fedoroff
- Department of Biology, Penn State University, University Park, PA, 16801, US
| | - Mark Tester
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia.
- Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia.
| | - Sandra M Schmöckel
- Department Physiology of Yield Stability, Institute of Crop Science, University of Hohenheim, Fruwirthstr. 21, 70599, Stuttgart, Germany
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Li Z, Sun L, Xu X, Liu Y, He H, Deng XW. Light control of three-dimensional chromatin organization in soybean. PLANT BIOTECHNOLOGY JOURNAL 2024. [PMID: 38762905 DOI: 10.1111/pbi.14372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 03/24/2024] [Accepted: 04/24/2024] [Indexed: 05/21/2024]
Abstract
Higher-order chromatin structure is critical for regulation of gene expression. In plants, light profoundly affects the morphogenesis of emerging seedlings as well as global gene expression to ensure optimal adaptation to environmental conditions. However, the changes and functional significance of chromatin organization in response to light during seedling development are not well documented. We constructed Hi-C contact maps for the cotyledon, apical hook and hypocotyl of soybean subjected to dark and light conditions. The resulting high-resolution Hi-C contact maps identified chromosome territories, A/B compartments, A/B sub-compartments, TADs (Topologically Associated Domains) and chromatin loops in each organ. We observed increased chromatin compaction under light and we found that domains that switched from B sub-compartments in darkness to A sub-compartments under light contained genes that were activated during photomorphogenesis. At the local scale, we identified a group of TADs constructed by gene clusters consisting of different numbers of Small Auxin-Upregulated RNAs (SAURs), which exhibited strict co-expression in the hook and hypocotyl in response to light stimulation. In the hypocotyl, RNA polymerase II (RNAPII) regulated the transcription of a SAURs cluster under light via TAD condensation. Our results suggest that the 3D genome is involved in the regulation of light-related gene expression in a tissue-specific manner.
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Affiliation(s)
- Zhu Li
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong, China
- School of Plant Science and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Linhua Sun
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong, China
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, China
| | - Xiao Xu
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong, China
| | - Yutong Liu
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong, China
| | - Hang He
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong, China
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, China
| | - Xing Wang Deng
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong, China
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, China
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43
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Wang F, Han T, Jeffrey Chen Z. Circadian and photoperiodic regulation of the vegetative to reproductive transition in plants. Commun Biol 2024; 7:579. [PMID: 38755402 PMCID: PMC11098820 DOI: 10.1038/s42003-024-06275-6] [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: 10/29/2023] [Accepted: 05/01/2024] [Indexed: 05/18/2024] Open
Abstract
As sessile organisms, plants must respond constantly to ever-changing environments to complete their life cycle; this includes the transition from vegetative growth to reproductive development. This process is mediated by photoperiodic response to sensing the length of night or day through circadian regulation of light-signaling molecules, such as phytochromes, to measure the length of night to initiate flowering. Flowering time is the most important trait to optimize crop performance in adaptive regions. In this review, we focus on interplays between circadian and light signaling pathways that allow plants to optimize timing for flowering and seed production in Arabidopsis, rice, soybean, and cotton. Many crops are polyploids and domesticated under natural selection and breeding. In response to adaptation and polyploidization, circadian and flowering pathway genes are epigenetically reprogrammed. Understanding the genetic and epigenetic bases for photoperiodic flowering will help improve crop yield and resilience in response to climate change.
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Affiliation(s)
- Fang Wang
- State Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Tongwen Han
- State Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Z Jeffrey Chen
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA.
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Su J, Liu K, Cui H, Shen T, Fu X, Han W. Integrating Computational and Experimental Methods to Identify Novel Sweet Peptides from Egg and Soy Proteins. Int J Mol Sci 2024; 25:5430. [PMID: 38791474 PMCID: PMC11121995 DOI: 10.3390/ijms25105430] [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: 04/09/2024] [Revised: 05/11/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024] Open
Abstract
Sweetness in food delivers a delightful sensory experience, underscoring the crucial role of sweeteners in the food industry. However, the widespread use of sweeteners has sparked health concerns. This underscores the importance of developing and screening natural, health-conscious sweeteners. Our study represents a groundbreaking venture into the discovery of such sweeteners derived from egg and soy proteins. Employing virtual hydrolysis as a novel technique, our research entailed a comprehensive screening process that evaluated biological activity, solubility, and toxicity of the derived compounds. We harnessed cutting-edge machine learning methodologies, specifically the latest graph neural network models, for predicting the sweetness of molecules. Subsequent refinements were made through molecular docking screenings and molecular dynamics simulations. This meticulous research approach culminated in the identification of three promising sweet peptides: DCY(Asp-Cys-Tyr), GGR(Gly-Gly-Arg), and IGR(Ile-Gly-Arg). Their binding affinity with T1R2/T1R3 was lower than -15 kcal/mol. Using an electronic tongue, we verified the taste profiles of these peptides, with IGR emerging as the most favorable in terms of taste with a sweetness value of 19.29 and bitterness value of 1.71. This study not only reveals the potential of these natural peptides as healthier alternatives to traditional sweeteners in food applications but also demonstrates the successful synergy of computational predictions and experimental validations in the realm of flavor science.
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Affiliation(s)
- Jinhao Su
- School of Chemical Science and Engineering, Yunnan University, South Outer Ring Road, Chenggong District, Kunming 650000, China; (J.S.); (T.S.)
| | - Kaifeng Liu
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, Edmond H. Fischer Signal Transduction Laboratory, School of Life Sciences, Jilin University, 2699 Qianjin Street, Changchun 130012, China; (K.L.); (H.C.); (X.F.)
| | - Huizi Cui
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, Edmond H. Fischer Signal Transduction Laboratory, School of Life Sciences, Jilin University, 2699 Qianjin Street, Changchun 130012, China; (K.L.); (H.C.); (X.F.)
| | - Tianze Shen
- School of Chemical Science and Engineering, Yunnan University, South Outer Ring Road, Chenggong District, Kunming 650000, China; (J.S.); (T.S.)
| | - Xueqi Fu
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, Edmond H. Fischer Signal Transduction Laboratory, School of Life Sciences, Jilin University, 2699 Qianjin Street, Changchun 130012, China; (K.L.); (H.C.); (X.F.)
| | - Weiwei Han
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, Edmond H. Fischer Signal Transduction Laboratory, School of Life Sciences, Jilin University, 2699 Qianjin Street, Changchun 130012, China; (K.L.); (H.C.); (X.F.)
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45
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Chen R, Meng S, Wang A, Jiang F, Yuan L, Lei L, Wang H, Fan W. The genomes of seven economic Caesalpinioideae trees provide insights into polyploidization history and secondary metabolite biosynthesis. PLANT COMMUNICATIONS 2024:100944. [PMID: 38733080 DOI: 10.1016/j.xplc.2024.100944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 03/29/2024] [Accepted: 05/08/2024] [Indexed: 05/13/2024]
Abstract
The Caesalpinioideae subfamily contains many well-known trees that are important for economic sustainability and human health, but a lack of genomic resources has hindered their breeding and utilization. Here, we present chromosome-level reference genomes for the two food and industrial trees Gleditsia sinensis (921 Mb) and Biancaea sappan (872 Mb), the three shade and ornamental trees Albizia julibrissin (705 Mb), Delonix regia (580 Mb), and Acacia confusa (566 Mb), and the two pioneer and hedgerow trees Leucaena leucocephala (1338 Mb) and Mimosa bimucronata (641 Mb). Phylogenetic inference shows that the mimosoid clade has a much higher evolutionary rate than the other clades of Caesalpinioideae. Macrosynteny comparison suggests that the fusion and breakage of an unstable chromosome are responsible for the difference in basic chromosome number (13 or 14) for Caesalpinioideae. After an ancient whole-genome duplication (WGD) shared by all Caesalpinioideae species (CWGD, ∼72.0 million years ago [MYA]), there were two recent successive WGD events, LWGD-1 (16.2-19.5 MYA) and LWGD-2 (7.1-9.5 MYA), in L. leucocephala. Thereafter, ∼40% gene loss and genome-size contraction have occurred during the diploidization process in L. leucocephala. To investigate secondary metabolites, we identified all gene copies involved in mimosine metabolism in these species and found that the abundance of mimosine biosynthesis genes in L. leucocephala largely explains its high mimosine production. We also identified the set of all potential genes involved in triterpenoid saponin biosynthesis in G. sinensis, which is more complete than that based on previous transcriptome-derived unigenes. Our results and genomic resources will facilitate biological studies of Caesalpinioideae and promote the utilization of valuable secondary metabolites.
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Affiliation(s)
- Rong Chen
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Sihan Meng
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Anqi Wang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Fan Jiang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Lihua Yuan
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Lihong Lei
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Hengchao Wang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Wei Fan
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China.
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Sun Y, Chen J, Yuan Y, Jiang N, Liu C, Zhang Y, Mao X, Zhang Q, Fang Y, Sun Z, Gai S. Auxin efflux carrier PsPIN4 identified through genome-wide analysis as vital factor of petal abscission. FRONTIERS IN PLANT SCIENCE 2024; 15:1380417. [PMID: 38799094 PMCID: PMC11116700 DOI: 10.3389/fpls.2024.1380417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 04/24/2024] [Indexed: 05/29/2024]
Abstract
PIN-FORMED (PIN) proteins, which function as efflux transporters, play many crucial roles in the polar transportation of auxin within plants. In this study, the exogenous applications of auxin IAA and TIBA were found to significantly prolong and shorten the florescence of tree peony (Paeonia suffruticosa Andr.) flowers. This finding suggests that auxin has some regulatory influence in petal senescence and abscission. Further analysis revealed a total of 8 PsPINs distributed across three chromosomes, which could be categorized into two classes based on phylogenetic and structural analysis. PsPIN1, PsPIN2a-b, and PsPIN4 were separated into the "long" PIN category, while PsPIN5, PsPIN6a-b, and PsPIN8 belonged to the "short" one. Additionally, the cis-regulatory elements of PsPIN promoters were associated with plant development, phytohormones, and environmental stress. These genes displayed tissue-specific expression, and phosphorylation sites were abundant throughout the protein family. Notably, PsPIN4 displayed distinct and elevated expression levels in roots, leaves, and flower organs. Expression patterns among the abscission zone (AZ) and adjacent areas during various flowering stages and IAA treatment indicate that PsPIN4 likely influences the initiation of peony petal abscission. The PsPIN4 protein was observed to be co-localized on both the plasma membrane and the cell nucleus. The ectopic expression of PsPIN4 reversed the premature flower organs abscission in the Atpin4 and significantly protracted florescence when introduced to Col Arabidopsis. Our findings established a strong basis for further investigation of PIN gene biological functions, particularly concerning intrinsic relationship between PIN-mediated auxin polar.
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Affiliation(s)
- Yin Sun
- State Key Laboratory of Efficient Production of Forest Resources, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Shandong Provincial Key Laboratory of Forest Genetic Improvement, Yellow River delta forest ecosystem positioning research station, Shandong Provincial Academy of Forestry, Jinan, China
| | - Junqiang Chen
- Shandong Provincial Key Laboratory of Forest Genetic Improvement, Yellow River delta forest ecosystem positioning research station, Shandong Provincial Academy of Forestry, Jinan, China
| | - Yanchao Yuan
- University Key Laboratory of Plant Biotechnology in Shandong Province, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Nannan Jiang
- Shandong Provincial Key Laboratory of Forest Genetic Improvement, Yellow River delta forest ecosystem positioning research station, Shandong Provincial Academy of Forestry, Jinan, China
| | - Chunying Liu
- University Key Laboratory of Plant Biotechnology in Shandong Province, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Yuxi Zhang
- University Key Laboratory of Plant Biotechnology in Shandong Province, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Xiuhong Mao
- Shandong Provincial Key Laboratory of Forest Genetic Improvement, Yellow River delta forest ecosystem positioning research station, Shandong Provincial Academy of Forestry, Jinan, China
| | - Qian Zhang
- Shandong Provincial Key Laboratory of Forest Genetic Improvement, Yellow River delta forest ecosystem positioning research station, Shandong Provincial Academy of Forestry, Jinan, China
| | - Yifu Fang
- Shandong Provincial Key Laboratory of Forest Genetic Improvement, Yellow River delta forest ecosystem positioning research station, Shandong Provincial Academy of Forestry, Jinan, China
| | - Zhenyuan Sun
- State Key Laboratory of Efficient Production of Forest Resources, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Shupeng Gai
- University Key Laboratory of Plant Biotechnology in Shandong Province, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
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Jiao F, Zhang D, Chen Y, Wu J. Genome-Wide Identification of Members of the Soybean CBL Gene Family and Characterization of the Functional Role of GmCBL1 in Responses to Saline and Alkaline Stress. PLANTS (BASEL, SWITZERLAND) 2024; 13:1304. [PMID: 38794375 PMCID: PMC11124892 DOI: 10.3390/plants13101304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 04/25/2024] [Accepted: 05/04/2024] [Indexed: 05/26/2024]
Abstract
Calcium ions function as key messengers in the context of intracellular signal transduction. The ability of plants to respond to biotic and abiotic stressors is highly dependent on the calcineurin B-like protein (CBL) and CBL-interacting protein kinase (CIPK) signaling network. Here, a comprehensive effort was made to identify all members of the soybean CBL gene family, leading to the identification of 15 total genes distributed randomly across nine chromosomes, including 13 segmental duplicates. All the GmCBL gene subfamilies presented with similar gene structures and conserved motifs. Analyses of the expression of these genes in different tissues revealed that the majority of these GmCBLs were predominantly expressed in the roots. Significant GmCBL expression and activity increases were also observed in response to a range of stress-related treatments, including salt stress, alkaline stress, osmotic stress, or exposure to salicylic acid, brassinosteroids, or abscisic acid. Striking increases in GmCBL1 expression were observed in response to alkaline and salt stress. Subsequent analyses revealed that GmCBL1 was capable of enhancing soybean salt and alkali tolerance through the regulation of redox reactions. These results offer new insight into the complex mechanisms through which the soybean CBL gene family regulates the responses of these plants to environmental stressors, highlighting promising targets for efforts aimed at enhancing soybean stress tolerance.
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Affiliation(s)
| | | | | | - Jinhua Wu
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163319, China; (F.J.); (D.Z.); (Y.C.)
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Paterson AH, Queitsch C. Genome organization and botanical diversity. THE PLANT CELL 2024; 36:1186-1204. [PMID: 38382084 PMCID: PMC11062460 DOI: 10.1093/plcell/koae045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 02/07/2024] [Accepted: 02/07/2024] [Indexed: 02/23/2024]
Abstract
The rich diversity of angiosperms, both the planet's dominant flora and the cornerstone of agriculture, is integrally intertwined with a distinctive evolutionary history. Here, we explore the interplay between angiosperm genome organization and botanical diversity, empowered by genomic approaches ranging from genetic linkage mapping to analysis of gene regulation. Commonality in the genetic hardware of plants has enabled robust comparative genomics that has provided a broad picture of angiosperm evolution and implicated both general processes and specific elements in contributing to botanical diversity. We argue that the hardware of plant genomes-both in content and in dynamics-has been shaped by selection for rather substantial differences in gene regulation between plants and animals such as maize and human, organisms of comparable genome size and gene number. Their distinctive genome content and dynamics may reflect in part the indeterminate development of plants that puts strikingly different demands on gene regulation than in animals. Repeated polyploidization of plant genomes and multiplication of individual genes together with extensive rearrangement and differential retention provide rich raw material for selection of morphological and/or physiological variations conferring fitness in specific niches, whether natural or artificial. These findings exemplify the burgeoning information available to employ in increasing knowledge of plant biology and in modifying selected plants to better meet human needs.
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Affiliation(s)
- Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, USA
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
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Sobrino-Mengual G, Alvarez D, Twyman RM, Gerrish C, Fraser PD, Capell T, Christou P. Activation of the native PHYTOENE SYNTHASE 1 promoter by modifying near-miss cis-acting elements induces carotenoid biosynthesis in embryogenic rice callus. PLANT CELL REPORTS 2024; 43:118. [PMID: 38632121 PMCID: PMC11024007 DOI: 10.1007/s00299-024-03199-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 03/13/2024] [Indexed: 04/19/2024]
Abstract
KEY MESSAGE Modification of silent latent endosperm-enabled promoters (SLEEPERs) allows the ectopic activation of non-expressed metabolic genes in rice callus Metabolic engineering in plants typically involves transgene expression or the mutation of endogenous genes. An alternative is promoter modification, where small changes in the promoter sequence allow genes to be switched on or off in particular tissues. To activate silent genes in rice endosperm, we screened native promoters for near-miss cis-acting elements that can be converted to endosperm-active regulatory motifs. We chose rice PHYTOENE SYNTHASE 1 (PSY1), encoding the enzyme responsible for the first committed step in the carotenoid biosynthesis pathway, because it is not expressed in rice endosperm. We identified six motifs within a 120-bp region, upstream of the transcriptional start site, which differed from endosperm-active elements by up to four nucleotides. We mutated four motifs to match functional elements in the endosperm-active BCH2 promoter, and this promoter was able to drive GFP expression in callus and in seeds of regenerated plants. The 4 M promoter was not sufficient to drive PSY1 expression, so we mutated the remaining two elements and used the resulting 6 M promoter to drive PSY1 expression in combination with a PDS transgene. This resulted in deep orange callus tissue indicating the accumulation of carotenoids, which was subsequently confirmed by targeted metabolomics analysis. PSY1 expression driven by the uncorrected or 4 M variants of the promoter plus a PDS transgene produced callus that lacked carotenoids. These results confirm that the adjustment of promoter elements can facilitate the ectopic activation of endogenous plant promoters in rice callus and endosperm and most likely in other tissues and plant species.
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Affiliation(s)
- Guillermo Sobrino-Mengual
- Applied Plant Biotechnology Group, Department of Agricultural and Forest Sciences and Engineering, University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
| | - Derry Alvarez
- Applied Plant Biotechnology Group, Department of Agricultural and Forest Sciences and Engineering, University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
- Division of Biological and Environmental Sciences and Engineering, Center for Desert Agriculture, BioActives Lab, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | | | - Christopher Gerrish
- Department of Biological Sciences, Royal Holloway University of London, Egham Hill, Egham, Surrey, TW20 0EX, UK
| | - Paul D Fraser
- Department of Biological Sciences, Royal Holloway University of London, Egham Hill, Egham, Surrey, TW20 0EX, UK
| | - Teresa Capell
- Applied Plant Biotechnology Group, Department of Agricultural and Forest Sciences and Engineering, University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
| | - Paul Christou
- Applied Plant Biotechnology Group, Department of Agricultural and Forest Sciences and Engineering, University of Lleida-Agrotecnio CERCA Center, Lleida, Spain.
- ICREA, Catalan Institute for Research and Advanced Studies, Barcelona, Spain.
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50
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Kumawat G, Cao D, Park C, Xu D. C-terminally encoded peptide-like genes are associated with the development of primary root at qRL16.1 in soybean. FRONTIERS IN PLANT SCIENCE 2024; 15:1387954. [PMID: 38685962 PMCID: PMC11056954 DOI: 10.3389/fpls.2024.1387954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 03/29/2024] [Indexed: 05/02/2024]
Abstract
Root architecture traits are belowground traits that harness moisture and nutrients from the soil and are equally important to above-ground traits in crop improvement. In soybean, the root length locus qRL16.1 was previously mapped on chromosome 16. The qRL16.1 has been characterized by transcriptome analysis of roots in near-isogenic lines (NILs), gene expression analysis in a pair of lines contrasting with alleles of qRL16.1, and differential gene expression analysis in germplasm accessions contrasting with root length. Two candidate genes, Glyma.16g108500 and Glyma.16g108700, have shown relatively higher expression in longer root accessions than in shorter rooting accessions. The C-terminal domain of Glyma.16g108500 and Glyma.16g108700 is similar to the conserved domain of C-terminally encoded peptides (CEPs) that regulate root length and nutrient response in Arabidopsis. Two polymorphisms upstream of Glyma.16g108500 showed a significant association with primary root length and total root length traits in a germplasm set. Synthetic peptide assay with predicted CEP variants of Glyma.16g108500 and Glyma.16g108700 demonstrated their positive effect on primary root length. The two genes are root-specific in the early stage of soybean growth and showed differential expression only in the primary root. These genes will be useful for improving soybean to develop a deep and robust root system to withstand low moisture and nutrient regimes.
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Affiliation(s)
- Giriraj Kumawat
- Japan International Research Center for Agricultural Sciences, Tsukuba, Ibaraki, Japan
- Crop Improvement Section, ICAR-Indian Institute of Soybean Research, Indore, Madhya Pradesh, India
| | - Dong Cao
- Japan International Research Center for Agricultural Sciences, Tsukuba, Ibaraki, Japan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Cheolwoo Park
- Japan International Research Center for Agricultural Sciences, Tsukuba, Ibaraki, Japan
| | - Donghe Xu
- Japan International Research Center for Agricultural Sciences, Tsukuba, Ibaraki, Japan
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