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Liu S, Wu Z, Yang T, Xu J, Aishan S, Qin E, Ma K, Liu J, Qin R, Wang J, Tie J, Liu H. The Chrysosplenium sinicum genome provides insights into adaptive evolution of shade plants. Commun Biol 2024; 7:1004. [PMID: 39152309 PMCID: PMC11329650 DOI: 10.1038/s42003-024-06701-9] [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: 01/14/2024] [Accepted: 08/08/2024] [Indexed: 08/19/2024] Open
Abstract
Chrysosplenium sinicum, a traditional Tibetan medicinal plant, can successfully thrive in low-light environments for long periods of time. To investigate the adaptive evolution of shade plants in low-light environments, we generated a chromosome-scale genome assembly (~320 Mb) for C. sinicum by combining PacBio sequencing and Hi-C technologies. Based on our results, gene families related to photosynthesis and cell respiration greatly expanded and evolved in C. sinicum genome due to intracellular DNA transfer from organelle genome to nuclear genome. Under positive selective pressure, adaptive evolution of light-harvesting complex II (LHCII) component protein CsLhcb1s resulted in the expansion of threonine residues at the phosphorylation site of STN7 kinase, potentially establishing a crucial genomic foundation for enhancing C. sinicum's adaptability in low-light environments. Through transcriptome and metabolome analysis, we identified chrysosplenol and chrysosplenoside as predominant flavonoid metabolites of C. sinicum and predicted their synthesis pathways. In addition, analysis of alternative splicing (AS) revealed that AS events help regulate state transition and flavonoid biosynthesis. The present study provides new insights into the genomes of shade plants exposed to low-light conditions and adaptive evolution of these genomes; in addition, the results improve our current knowledge on the biosynthetic and regulatory processes of chrysosplenol and chrysosplenoside.
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Affiliation(s)
- Shuo Liu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan, China
| | - Zhihua Wu
- College of Life Sciences, Zhejiang Normal University, Jinhua, China
| | - Tiange Yang
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan, China
| | - Jindong Xu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan, China
| | - Saimire Aishan
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan, China
| | - Erdai Qin
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan, China
| | - Kang Ma
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan, China
| | - Jiao Liu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan, China
| | - Rui Qin
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan, China
| | - Jiangqing Wang
- College of Computer Science, South-Central Minzu University, Wuhan, China
| | - Jun Tie
- College of Computer Science, South-Central Minzu University, Wuhan, China.
| | - Hong Liu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan, China.
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Yu X, Liu J, Qin Q, Zribi I, Yu J, Yang S, Dinkins RD, Fei Z, Kereszt A, Zhu H. Species-specific microsymbiont discrimination mediated by a Medicago receptor kinase. SCIENCE ADVANCES 2024; 10:eadp6436. [PMID: 39083610 PMCID: PMC11290524 DOI: 10.1126/sciadv.adp6436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 06/26/2024] [Indexed: 08/02/2024]
Abstract
Host range specificity is a prominent feature of the legume-rhizobial symbiosis. Sinorhizobium meliloti and Sinorhizobium medicae are two closely related species that engage in root nodule symbiosis with legume plants of the Medicago genus, but certain Medicago species exhibit selectivity in their interactions with the two rhizobial species. We have identified a Medicago receptor-like kinase, which can discriminate between the two bacterial species, acting as a genetic barrier against infection by most S. medicae strains. Activation of this receptor-mediated nodulation restriction requires a bacterial gene that encodes a glycine-rich octapeptide repeat protein with distinct variants capable of distinguishing S. medicae from S. meliloti. This study sheds light on the coevolution of host plants and rhizobia, shaping symbiotic selectivity in their respective ecological niches.
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Affiliation(s)
- Xiaocheng Yu
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546, USA
| | - Jinge Liu
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546, USA
| | - Qiulin Qin
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546, USA
| | - Ikram Zribi
- Institute of Plant Biology, HUN-REN Biological Research Centre, Szeged 6726, Hungary
| | - Jingyin Yu
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14853, USA
| | - Shengming Yang
- Cereal Crops Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Fargo, ND 58102, USA
| | - Randy D. Dinkins
- Forage-Animal Production Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Lexington, KY 40546, USA
| | - Zhangjun Fei
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14853, USA
- Robert W. Holley Center for Agriculture and Health, U.S. Department of Agriculture-Agricultural Research Service, Ithaca, NY 14853, USA
| | - Attila Kereszt
- Institute of Plant Biology, HUN-REN Biological Research Centre, Szeged 6726, Hungary
| | - Hongyan Zhu
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546, USA
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Tayeh N, Hofer JMI, Aubert G, Jacquin F, Turner L, Kreplak J, Paajanen P, Le Signor C, Dalmais M, Pflieger S, Geffroy V, Ellis N, Burstin J. afila, the origin and nature of a major innovation in the history of pea breeding. THE NEW PHYTOLOGIST 2024; 243:1247-1261. [PMID: 38837425 DOI: 10.1111/nph.19800] [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: 08/24/2023] [Accepted: 03/22/2024] [Indexed: 06/07/2024]
Abstract
The afila (af) mutation causes the replacement of leaflets by a branched mass of tendrils in the compound leaves of pea - Pisum sativum L. This mutation was first described in 1953, and several reports of spontaneous af mutations and induced mutants with a similar phenotype exist. Despite widespread introgression into breeding material, the nature of af and the origin of the alleles used remain unknown. Here, we combine comparative genomics with reverse genetic approaches to elucidate the genetic determinants of af. We also investigate haplotype diversity using a set of AfAf and afaf cultivars and breeding lines and molecular markers linked to seven consecutive genes. Our results show that deletion of two tandemly arranged genes encoding Q-type Cys(2)His(2) zinc finger transcription factors, PsPALM1a and PsPALM1b, is responsible for the af phenotype in pea. Eight haplotypes were identified in the af-harbouring genomic region on chromosome 2. These haplotypes differ in the size of the deletion, covering more or less genes. Diversity at the af locus is valuable for crop improvement and sheds light on the history of pea breeding for improved standing ability. The results will be used to understand the function of PsPALM1a/b and to transfer the knowledge for innovation in related crops.
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Affiliation(s)
- Nadim Tayeh
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, F-21000, France
| | - Julie M I Hofer
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - Grégoire Aubert
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, F-21000, France
| | - Françoise Jacquin
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, F-21000, France
| | - Lynda Turner
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - Jonathan Kreplak
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, F-21000, France
| | - Pirita Paajanen
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - Christine Le Signor
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, F-21000, France
| | - Marion Dalmais
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, 91190, France
- Université Paris-Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, 91190, France
| | - Stéphanie Pflieger
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, 91190, France
- Université Paris-Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, 91190, France
| | - Valérie Geffroy
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, 91190, France
- Université Paris-Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, 91190, France
| | - Noel Ellis
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - Judith Burstin
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, F-21000, France
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Jiu S, Lv Z, Liu M, Xu Y, Chen B, Dong X, Zhang X, Cao J, Manzoor MA, Xia M, Li F, Li H, Chen L, Zhang X, Wang S, Dong Y, Zhang C. Haplotype-resolved genome assembly for tetraploid Chinese cherry ( Prunus pseudocerasus) offers insights into fruit firmness. HORTICULTURE RESEARCH 2024; 11:uhae142. [PMID: 38988622 PMCID: PMC11233885 DOI: 10.1093/hr/uhae142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 05/11/2024] [Indexed: 07/12/2024]
Abstract
Chinese cherry (Prunus pseudocerasus) holds considerable importance as one of the primary stone fruit crops in China. However, artificially improving its traits and genetic analysis are challenging due to lack of high-quality genomic resources, which mainly result from difficulties associated with resolving its tetraploid and highly heterozygous genome. Herein, we assembled a chromosome-level, haplotype-resolved genome of the cultivar 'Zhuji Duanbing', comprising 993.69 Mb assembled into 32 pseudochromosomes using PacBio HiFi, Oxford Nanopore, and Hi-C. Intra-haplotype comparative analyses revealed extensive intra-genomic sequence and expression consistency. Phylogenetic and comparative genomic analyses demonstrated that P. pseudocerasus was a stable autotetraploid species, closely related to wild P. pusilliflora, with the two diverging ~18.34 million years ago. Similar to other Prunus species, P. pseudocerasus underwent a common whole-genome duplication event that occurred ~139.96 million years ago. Because of its low fruit firmness, P. pseudocerasus is unsuitable for long-distance transportation, thereby restricting its rapid development throughout China. At the ripe fruit stage, P. pseudocerasus cv. 'Zhuji Duanbing' was significantly less firm than P. avium cv. 'Heizhenzhu'. The difference in firmness is attributed to the degree of alteration in pectin, cellulose, and hemicellulose contents. In addition, comparative transcriptomic analyses identified GalAK-like and Stv1, two genes involved in pectin biosynthesis, which potentially caused the difference in firmness between 'Zhuji Duanbing' and 'Heizhenzhu'. Transient transformations of PpsGalAK-like and PpsStv1 increase protopectin content and thereby enhance fruit firmness. Our study lays a solid foundation for functional genomic studies and the enhancement of important horticultural traits in Chinese cherries.
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Affiliation(s)
- Songtao Jiu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zhengxin Lv
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Moyang Liu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yan Xu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Baozheng Chen
- Province Key Laboratory, Biological Big Data College, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Xiao Dong
- Province Key Laboratory, Biological Big Data College, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Xinyu Zhang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jun Cao
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Muhammad Aamir Manzoor
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Mingxu Xia
- School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Fangdong Li
- Yantai Academy of Agricultural Sciences, Yantai, Shandong, 265500, China
| | - Hongwen Li
- Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, 610066, China
| | - Lijuan Chen
- Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, 610066, China
| | - Xu Zhang
- Yantai Academy of Agricultural Sciences, Yantai, Shandong, 265500, China
| | - Shiping Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yang Dong
- Province Key Laboratory, Biological Big Data College, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Caixi Zhang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
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Dhabalia Ashok A, de Vries S, Darienko T, Irisarri I, de Vries J. Evolutionary assembly of the plant terrestrialization toolkit from protein domains. Proc Biol Sci 2024; 291:20240985. [PMID: 39081174 PMCID: PMC11289646 DOI: 10.1098/rspb.2024.0985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 06/26/2024] [Accepted: 06/27/2024] [Indexed: 08/02/2024] Open
Abstract
Land plants (embryophytes) came about in a momentous evolutionary singularity: plant terrestrialization. This event marks not only the conquest of land by plants but also the massive radiation of embryophytes into a diverse array of novel forms and functions. The unique suite of traits present in the earliest land plants is thought to have been ushered in by a burst in genomic novelty. Here, we asked the question of how these bursts were possible. For this, we explored: (i) the initial emergence and (ii) the reshuffling of domains to give rise to hallmark environmental response genes of land plants. We pinpoint that a quarter of the embryophytic genes for stress physiology are specific to the lineage, yet a significant portion of this novelty arises not de novo but from reshuffling and recombining of pre-existing domains. Our data suggest that novel combinations of old genomic substrate shaped the plant terrestrialization toolkit, including hallmark processes in signalling, biotic interactions and specialized metabolism.
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Affiliation(s)
- Amra Dhabalia Ashok
- Department of Applied Bioinformatics, University of Goettingen, Institute for Microbiology and Genetics, Goldschmidtstr. 1, Goettingen37077, Germany
| | - Sophie de Vries
- Department of Applied Bioinformatics, University of Goettingen, Institute for Microbiology and Genetics, Goldschmidtstr. 1, Goettingen37077, Germany
| | - Tatyana Darienko
- Department of Applied Bioinformatics, University of Goettingen, Institute for Microbiology and Genetics, Goldschmidtstr. 1, Goettingen37077, Germany
| | - Iker Irisarri
- Department of Applied Bioinformatics, University of Goettingen, Institute for Microbiology and Genetics, Goldschmidtstr. 1, Goettingen37077, Germany
- University of Goettingen, Campus Institute Data Science (CIDAS), Goldschmidstr. 1, Goettingen37077, Germany
- Section Phylogenomics, Centre for Molecular biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change (LIB), Museum of Nature Hamburg, Martin-Luther-King-Platz 3, Hamburg20146, Germany
| | - Jan de Vries
- Department of Applied Bioinformatics, University of Goettingen, Institute for Microbiology and Genetics, Goldschmidtstr. 1, Goettingen37077, Germany
- University of Goettingen, Campus Institute Data Science (CIDAS), Goldschmidstr. 1, Goettingen37077, Germany
- Department of Applied Bioinformatics, University of Goettingen, Goettingen Center for Molecular Biosciences (GZMB), Goldschmidtstr. 1, Goettingen37077, Germany
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Xu Y, Feng T, Ding Z, Li L, Li Z, Cui K, Chen W, Pan H, Zhu P, Liu Q. Age-related compositional and functional changes in the adult and breastfed buffalo rumen microbiome. Front Microbiol 2024; 15:1342804. [PMID: 38881655 PMCID: PMC11177756 DOI: 10.3389/fmicb.2024.1342804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 05/07/2024] [Indexed: 06/18/2024] Open
Abstract
Introduction The buffalo is an important domestic animal globally, providing milk, meat, and labor to more than 2 billion people in 67 countries. The rumen microorganisms of buffaloes play an indispensable role in enabling the healthy functionality and digestive function of buffalo organisms. Currently, there is a lack of clarity regarding the differences in the composition and function of rumen microorganisms among buffaloes at different growth stages. Methods In this study, metagenomics sequencing technology was applied to examine the compositional and functional differences of rumen microorganisms in adult and breastfed buffaloes. Results The results revealed that the rumen of adult buffaloes had significantly higher levels of the following dominant genera: Prevotella, UBA1711, RF16, Saccharofermentans, F23-D06, UBA1777, RUG472, and Methanobrevibacter_A. Interestingly, the dominant genera specific to the rumen of adult buffaloes showed a significant positive correlation (correlation>0.5, p-value<0.05) with both lignocellulose degradation-related carbohydrate-active enzymes (CAZymes) and immune signaling pathways activated by antigenic stimulation. The rumen of breastfed buffaloes had significantly higher levels of the following dominant genera: UBA629, CAG- 791, Selenomonas_C, Treponema_D, Succinivibrio, and RC9. Simultaneously, the rumen-dominant genera specific to breastfed buffaloes were significantly positively correlated (correlation>0.5, p-value<0.05) with CAZymes associated with lactose degradation, amino acid synthesis pathways, and antibiotic-producing pathways. Discussion This indicates that rumen microorganisms in adult buffaloes are more engaged in lignocellulose degradation, whereas rumen microorganisms in breastfed buffaloes are more involved in lactose and amino acid degradation, as well as antibiotic production. In conclusion, these findings suggest a close relationship between differences in rumen microbes and the survival needs of buffaloes at different growth stages.
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Affiliation(s)
- Yixue Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Tong Feng
- Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Zixu Ding
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Ling Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
- Guangxi Key Laboratory of Buffalo Genetics, Nanning, China
| | - Zhipeng Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Kuiqing Cui
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, China
| | - Weihua Chen
- Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Hongping Pan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Peng Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf Marine Ecological Environment Field Observation and Research Station of Guangxi, Beibu Gulf University, Qinzhou, China
| | - Qingyou Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, China
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Pegler JL, Patrick JW, McDermott B, Brown A, Oultram JMJ, Grof CPL, Ward JM. Phaseolus vulgaris STP13.1 is an H +-coupled monosaccharide transporter, present in source leaves and seed coats, with higher substrate affinity at depolarized potentials. PLANT DIRECT 2024; 8:e585. [PMID: 38651017 PMCID: PMC11033725 DOI: 10.1002/pld3.585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 03/25/2024] [Accepted: 03/28/2024] [Indexed: 04/25/2024]
Abstract
Sugar transport proteins (STPs) are high-affinity H+-coupled hexose symporters. Recently, the contribution of STP13 to bacterial and fungal pathogen resistance across multiple plant species has garnered significant interest. Quantitative PCR analysis of source leaves, developing embryos, and seed coats of Phaseolus vulgaris L. (common bean) revealed that PvSTP13.1 was expressed in source leaves and seed coats throughout seed development. In contrast, PvSTP13.1 transcripts were detected at exceedingly low levels in developing embryos. To characterize the transport mechanism, PvSTP13.1 was expressed in Xenopus laevis oocytes, and inward-directed currents were analyzed using two-electrode voltage clamping. PvSTP13.1 was shown to function as an H+-coupled monosaccharide symporter exhibiting a unique high affinity for hexoses and aldopentoses at depolarized membrane potentials. Specifically, of the 31 assessed substrates, which included aldohexoses, deoxyhexoses, fructose, 3-O-methyl-D-glucose, aldopentoses, polyols, glycosides, disaccharides, trisaccharides, and glucuronic acid, PvSTP13.1 displayed the highest affinity (K 0.5) for glucose (43 μM), mannose (92 μM), galactose (145 μM), fructose (224 μM), xylose (1.0 mM), and fucose (3.7 mM) at pH 5.6 at a depolarized membrane potential of -40 mV. The results presented here suggest PvSTP13.1 contributes to retrieval of hexoses from the apoplasmic space in source leaves and coats of developing seeds.
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Affiliation(s)
- Joseph L. Pegler
- Centre for Plant Science, School of Environmental and Life Sciences, College of Engineering, Science and EnvironmentUniversity of NewcastleCallaghanNew South WalesAustralia
| | - John W. Patrick
- Centre for Plant Science, School of Environmental and Life Sciences, College of Engineering, Science and EnvironmentUniversity of NewcastleCallaghanNew South WalesAustralia
| | - Benjamin McDermott
- Centre for Plant Science, School of Environmental and Life Sciences, College of Engineering, Science and EnvironmentUniversity of NewcastleCallaghanNew South WalesAustralia
| | - Anthony Brown
- Centre for Plant Science, School of Environmental and Life Sciences, College of Engineering, Science and EnvironmentUniversity of NewcastleCallaghanNew South WalesAustralia
| | - Jackson M. J. Oultram
- Centre for Plant Science, School of Environmental and Life Sciences, College of Engineering, Science and EnvironmentUniversity of NewcastleCallaghanNew South WalesAustralia
| | - Christopher P. L. Grof
- Centre for Plant Science, School of Environmental and Life Sciences, College of Engineering, Science and EnvironmentUniversity of NewcastleCallaghanNew South WalesAustralia
| | - John M. Ward
- Plant and Microbial BiologyUniversity of Minnesota Twin CitiesSt. PaulMinnesotaUSA
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8
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Serrano K, Bezrutczyk M, Goudeau D, Dao T, O'Malley R, Malmstrom RR, Visel A, Scheller HV, Cole B. Spatial co-transcriptomics reveals discrete stages of the arbuscular mycorrhizal symbiosis. NATURE PLANTS 2024; 10:673-688. [PMID: 38589485 PMCID: PMC11035146 DOI: 10.1038/s41477-024-01666-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 03/06/2024] [Indexed: 04/10/2024]
Abstract
The symbiotic interaction of plants with arbuscular mycorrhizal (AM) fungi is ancient and widespread. Plants provide AM fungi with carbon in exchange for nutrients and water, making this interaction a prime target for crop improvement. However, plant-fungal interactions are restricted to a small subset of root cells, precluding the application of most conventional functional genomic techniques to study the molecular bases of these interactions. Here we used single-nucleus and spatial RNA sequencing to explore both Medicago truncatula and Rhizophagus irregularis transcriptomes in AM symbiosis at cellular and spatial resolution. Integrated, spatially registered single-cell maps revealed infected and uninfected plant root cell types. We observed that cortex cells exhibit distinct transcriptome profiles during different stages of colonization by AM fungi, indicating dynamic interplay between both organisms during establishment of the cellular interface enabling successful symbiosis. Our study provides insight into a symbiotic relationship of major agricultural and environmental importance and demonstrates a paradigm combining single-cell and spatial transcriptomics for the analysis of complex organismal interactions.
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Affiliation(s)
- Karen Serrano
- Joint Bioenergy Institute, Emeryville, CA, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Margaret Bezrutczyk
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Danielle Goudeau
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Thai Dao
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ronan O'Malley
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Rex R Malmstrom
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Axel Visel
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- School of Natural Sciences, University of California Merced, Merced, CA, USA
| | - Henrik V Scheller
- Joint Bioenergy Institute, Emeryville, CA, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Benjamin Cole
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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Lu Y, Chen X, Yu H, Zhang C, Xue Y, Zhang Q, Wang H. Haplotype-resolved genome assembly of Phanera championii reveals molecular mechanisms of flavonoid synthesis and adaptive evolution. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:488-505. [PMID: 38173092 DOI: 10.1111/tpj.16620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 12/15/2023] [Accepted: 12/20/2023] [Indexed: 01/05/2024]
Abstract
Phanera championii is a medicinal liana plant that has successfully adapted to hostile karst habitats. Despite extensive research on its medicinal components and pharmacological effects, the molecular mechanisms underlying the biosynthesis of critical flavonoids and its adaptation to karst habitats remain elusive. In this study, we performed high-coverage PacBio and Hi-C sequencing of P. championii, which revealed its high heterozygosity and phased the genome into two haplotypes: Hap1 (384.60 Mb) and Hap2 (383.70 Mb), encompassing a total of 58 612 annotated genes. Comparative genomes analysis revealed that P. championii experienced two whole-genome duplications (WGDs), with approximately 59.59% of genes originating from WGD events, thereby providing a valuable genetic resource for P. championii. Moreover, we identified a total of 112 genes that were strongly positively selected. Additionally, about 81.60 Mb of structural variations between the two haplotypes. The allele-specific expression patterns suggested that the dominant effect of P. championii was the elimination of deleterious mutations and the promotion of beneficial mutations to enhance fitness. Moreover, our transcriptome and metabolome analysis revealed alleles in different tissues or different haplotypes collectively regulate the synthesis of flavonoid metabolites. In summary, our comprehensive study highlights the significance of genomic and morphological adaptation in the successful adaptation of P. championii to karst habitats. The high-quality phased genomes obtained in this study serve as invaluable genomic resources for various applications, including germplasm conservation, breeding, evolutionary studies, and elucidation of pathways governing key biological traits of P. championii.
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Affiliation(s)
- Yongbin Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, China
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and the Chinese Academy of Sciences, Yanshan, Guilin, 541006, China
| | - Xiao Chen
- 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, 518120, China
| | - Hang Yu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, China
- Key Laboratory of Crop Cultivation and Physiology, Education Department of Guangxi Zhuang Autonomous Region, Guangxi University, Nanning, 530004, China
| | - Chao Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, China
- Key Laboratory of Crop Cultivation and Physiology, Education Department of Guangxi Zhuang Autonomous Region, Guangxi University, Nanning, 530004, China
| | - Yajie Xue
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, China
- Key Laboratory of Crop Cultivation and Physiology, Education Department of Guangxi Zhuang Autonomous Region, Guangxi University, Nanning, 530004, China
| | - Qiang Zhang
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and the Chinese Academy of Sciences, Yanshan, Guilin, 541006, China
| | - Haifeng Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, China
- Key Laboratory of Crop Cultivation and Physiology, Education Department of Guangxi Zhuang Autonomous Region, Guangxi University, Nanning, 530004, China
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10
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Massaro I, Poethig RS, Sinha NR, Leichty AR. Chromosome-level genome of the transformable northern wattle, Acacia crassicarpa. G3 (BETHESDA, MD.) 2024; 14:jkad284. [PMID: 38096217 PMCID: PMC10917515 DOI: 10.1093/g3journal/jkad284] [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: 09/13/2023] [Accepted: 12/01/2023] [Indexed: 03/08/2024]
Abstract
The genus Acacia is a large group of woody legumes containing an enormous amount of morphological diversity in leaf shape. This diversity is at least in part the result of an innovation in leaf development where many Acacia species are capable of developing leaves of both bifacial and unifacial morphologies. While not unique in the plant kingdom, unifaciality is most commonly associated with monocots, and its developmental genetic mechanisms have yet to be explored beyond this group. In this study, we identify an accession of Acacia crassicarpa with high regeneration rates and isolate a clone for genome sequencing. We generate a chromosome-level assembly of this readily transformable clone, and using comparative analyses, confirm a whole-genome duplication unique to Caesalpinoid legumes. This resource will be important for future work examining genome evolution in legumes and the unique developmental genetic mechanisms underlying unifacial morphogenesis in Acacia.
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Affiliation(s)
- Isabelle Massaro
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | | | - Neelima R Sinha
- Department of Plant Biology, University of California Davis, Davis, CA 95616, USA
| | - Aaron R Leichty
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
- Department of Plant Biology, University of California Davis, Davis, CA 95616, USA
- USDA Plant Gene Expression Center, 800 Buchanan Street, Albany, CA 94710, USA
- 800 Buchanan Street, Albany, CA 94710, USA
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11
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Dhabalia Ashok A, Freitag JN, Irisarri I, de Vries S, de Vries J. Sequence similarity networks bear out hierarchical relationships of green cytochrome P450. PHYSIOLOGIA PLANTARUM 2024; 176:e14244. [PMID: 38480467 DOI: 10.1111/ppl.14244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 02/14/2024] [Accepted: 02/16/2024] [Indexed: 03/24/2024]
Abstract
Land plants have diversified enzyme families. One of the most prominent is the cytochrome P450 (CYP or CYP450) family. With over 443,000 CYP proteins sequenced across the tree of life, CYPs are ubiquitous in archaea, bacteria, and eukaryotes. Here, we focused on land plants and algae to study the role of CYP diversification. CYPs, acting as monooxygenases, catalyze hydroxylation reactions crucial for specialized plant metabolic pathways, including detoxification and phytohormone production; the CYPome consists of one enormous superfamily that is divided into clans and families. Their evolutionary history speaks of high substrate promiscuity; radiation and functional diversification have yielded numerous CYP families. To understand the evolutionary relationships within the CYPs, we employed sequence similarity network analyses. We recovered distinct clusters representing different CYP families, reflecting their diversified sequences that we link to the prediction of functionalities. Hierarchical clustering and phylogenetic analysis further elucidated relationships between CYP clans, uncovering their shared deep evolutionary history. We explored the distribution and diversification of CYP subfamilies across plant and algal lineages, uncovering novel candidates and providing insights into the evolution of these enzyme families. This identified unexpected relationships between CYP families, such as the link between CYP82 and CYP74, shedding light on their roles in plant defense signaling pathways. Our approach provides a methodology that brings insights into the emergence of new functions within the CYP450 family, contributing to the evolutionary history of plants and algae. These insights can be further validated and implemented via experimental setups under various external conditions.
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Affiliation(s)
- Amra Dhabalia Ashok
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Jella N Freitag
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Iker Irisarri
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
- Section Phylogenomics, Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change (LIB), Museum of Nature, Hamburg, Germany
| | - Sophie de Vries
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Jan de Vries
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
- Campus Institute Data Science (CIDAS), University of Goettingen, Goettingen, Germany
- Goettingen Center for Molecular Biosciences (GZMB), Department of Applied Bioinformatics, University of Goettinzgen, Goettingen, Germany
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12
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Williams OR, Vander Schoor JK, Butler JB, Hecht VFG, Weller JL. Physical seed dormancy in pea is genetically separable from seed coat thickness and roughness. FRONTIERS IN PLANT SCIENCE 2024; 15:1359226. [PMID: 38476691 PMCID: PMC10927720 DOI: 10.3389/fpls.2024.1359226] [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: 12/22/2023] [Accepted: 02/09/2024] [Indexed: 03/14/2024]
Abstract
Introduction The seeds of wild pea (Pisum) exhibit marked physical dormancy due to impermeability of the seed coat to water, and the loss of this dormancy is thought to have been critical for domestication. Wild pea seed coats are also notably thick and rough, traits that have also reduced during domestication and are anecdotally linked to increased permeability. However, how these traits specifically interact with permeability is unclear. Methods To investigate this, we examined the genetic control of differences in seed coat characteristics between wild P. sativum ssp. humile and a non-dormant domesticated P. s. sativum accession in a recombinant inbred population. QTL effects were confirmed and their locations refined in segregating F4/5 populations. Results In this population we found a moderate correlation between testa thickness and permeability, and identified loci that affect them independently, suggesting no close functional association. However, the major loci affecting both testa thickness and permeability collocated closely with Mendel's pigmentation locus A, suggesting flavonoid compounds under its control might contribute significantly to both traits. We also show that seed coat roughness is oligogenic in this population, with the major locus independent of both testa thickness and permeability, suggesting selection for smooth seed was unlikely to be due to effects on either of these traits. Discussion Results indicate loss of seed coat dormancy during domestication was not primarily driven by reduced testa thickness or smooth seededness. The close association between major permeability and thickness QTL and Mendel's 'A' warrant further study, particularly regarding the role of flavonoids.
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Affiliation(s)
- Owen R. Williams
- School of Natural Sciences, University of Tasmania, Hobart, TAS, Australia
| | - Jacqueline K. Vander Schoor
- School of Natural Sciences, University of Tasmania, Hobart, TAS, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, University of Tasmania, Hobart, TAS, Australia
| | - Jakob B. Butler
- School of Natural Sciences, University of Tasmania, Hobart, TAS, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, University of Tasmania, Hobart, TAS, Australia
| | | | - James L. Weller
- School of Natural Sciences, University of Tasmania, Hobart, TAS, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, University of Tasmania, Hobart, TAS, Australia
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13
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Lee T, Orvosova M, Batzenschlager M, Bueno Batista M, Bailey PC, Mohd-Radzman NA, Gurzadyan A, Stuer N, Mysore KS, Wen J, Ott T, Oldroyd GED, Schiessl K. Light-sensitive short hypocotyl genes confer symbiotic nodule identity in the legume Medicago truncatula. Curr Biol 2024; 34:825-840.e7. [PMID: 38301650 DOI: 10.1016/j.cub.2024.01.018] [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: 08/16/2023] [Revised: 09/29/2023] [Accepted: 01/08/2024] [Indexed: 02/03/2024]
Abstract
Legumes produce specialized root nodules that are distinct from lateral roots in morphology and function, with nodules intracellularly hosting nitrogen-fixing bacteria. We have previously shown that a lateral root program underpins nodule initiation, but there must be additional developmental regulators that confer nodule identity. Here, we show two members of the LIGHT-SENSITIVE SHORT HYPOCOTYL (LSH) transcription factor family, predominantly known to define shoot meristem complexity and organ boundaries, function as regulators of nodule organ identity. In parallel to the root initiation program, LSH1/LSH2 recruit a program into the root cortex that mediates the divergence into nodules, in particular with cell divisions in the mid-cortex. This includes regulation of auxin and cytokinin, promotion of NODULE ROOT1/2 and Nuclear Factor YA1, and suppression of the lateral root program. A principal outcome of LSH1/LSH2 function is the production of cells able to accommodate nitrogen-fixing bacteria, a key feature unique to nodules.
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Affiliation(s)
- Tak Lee
- Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK; Crop Science Centre, Department of Plant Sciences, University of Cambridge, 93 Lawrence Weaver Road, Cambridge CB3 0LE, UK
| | - Martina Orvosova
- Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK; Crop Science Centre, Department of Plant Sciences, University of Cambridge, 93 Lawrence Weaver Road, Cambridge CB3 0LE, UK
| | | | - Marcelo Bueno Batista
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Paul C Bailey
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond TW9 3DS, UK
| | - Nadia A Mohd-Radzman
- Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK
| | - Aram Gurzadyan
- Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK
| | - Naomi Stuer
- Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK
| | - Kirankumar S Mysore
- Noble Research Institute, LLC, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
| | - Jiangqi Wen
- Noble Research Institute, LLC, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
| | - Thomas Ott
- University of Freiburg, Faculty of Biology, Schänzlestrasse, 79104 Freiburg, Germany; CIBSS - Centre of Integrative Biological Signalling Studies, University of Freiburg, Schänzlestrasse, 79104 Freiburg, Germany
| | - Giles E D Oldroyd
- Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK; Crop Science Centre, Department of Plant Sciences, University of Cambridge, 93 Lawrence Weaver Road, Cambridge CB3 0LE, UK.
| | - Katharina Schiessl
- Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK.
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14
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Poulet A, Zhao M, Peng Y, Tham F, Jaudal M, Zhang L, van Wolfswinkel JC, Putterill J. Gene-edited Mtsoc1 triple mutant Medicago plants do not flower. FRONTIERS IN PLANT SCIENCE 2024; 15:1357924. [PMID: 38469328 PMCID: PMC10926907 DOI: 10.3389/fpls.2024.1357924] [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: 12/19/2023] [Accepted: 02/02/2024] [Indexed: 03/13/2024]
Abstract
Optimized flowering time is an important trait that ensures successful plant adaptation and crop productivity. SOC1-like genes encode MADS transcription factors, which are known to play important roles in flowering control in many plants. This includes the best-characterized eudicot model Arabidopsis thaliana (Arabidopsis), where SOC1 promotes flowering and functions as a floral integrator gene integrating signals from different flowering-time regulatory pathways. Medicago truncatula (Medicago) is a temperate reference legume with strong genomic and genetic resources used to study flowering pathways in legumes. Interestingly, despite responding to similar floral-inductive cues of extended cold (vernalization) followed by warm long days (VLD), such as in winter annual Arabidopsis, Medicago lacks FLC and CO which are key regulators of flowering in Arabidopsis. Unlike Arabidopsis with one SOC1 gene, multiple gene duplication events have given rise to three MtSOC1 paralogs within the Medicago genus in legumes: one Fabaceae group A SOC1 gene, MtSOC1a, and two tandemly repeated Fabaceae group B SOC1 genes, MtSOC1b and MtSOC1c. Previously, we showed that MtSOC1a has unique functions in floral promotion in Medicago. The Mtsoc1a Tnt1 retroelement insertion single mutant showed moderately delayed flowering in long- and short-day photoperiods, with and without prior vernalization, compared to the wild-type. In contrast, Mtsoc1b Tnt1 single mutants did not have altered flowering time or flower development, indicating that it was redundant in an otherwise wild-type background. Here, we describe the generation of Mtsoc1a Mtsoc1b Mtsoc1c triple mutant lines using CRISPR-Cas9 gene editing. We studied two independent triple mutant lines that segregated plants that did not flower and were bushy under floral inductive VLD. Genotyping indicated that these non-flowering plants were homozygous for the predicted strong mutant alleles of the three MtSOC1 genes. Gene expression analyses using RNA-seq and RT-qPCR indicated that these plants remained vegetative. Overall, the non-flowering triple mutants were dramatically different from the single Mtsoc1a mutant and the Arabidopsis soc1 mutant; implicating multiple MtSOC1 genes in critical overlapping roles in the transition to flowering in Medicago.
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Affiliation(s)
- Axel Poulet
- Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, Yale University, New Haven, CT, United States
| | - Min Zhao
- Flowering Lab, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Yongyan Peng
- Flowering Lab, School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Mt Albert Research Centre, The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - FangFei Tham
- Flowering Lab, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Mauren Jaudal
- Flowering Lab, School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Mt Albert Research Centre, The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Lulu Zhang
- Flowering Lab, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Josien C. van Wolfswinkel
- Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, Yale University, New Haven, CT, United States
| | - Joanna Putterill
- Flowering Lab, School of Biological Sciences, University of Auckland, Auckland, New Zealand
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15
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Botkin JR, Farmer AD, Young ND, Curtin SJ. Genome assembly of Medicago truncatula accession SA27063 provides insight into spring black stem and leaf spot disease resistance. BMC Genomics 2024; 25:204. [PMID: 38395768 PMCID: PMC10885650 DOI: 10.1186/s12864-024-10112-9] [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: 01/02/2024] [Accepted: 02/10/2024] [Indexed: 02/25/2024] Open
Abstract
Medicago truncatula, model legume and alfalfa relative, has served as an essential resource for advancing our understanding of legume physiology, functional genetics, and crop improvement traits. Necrotrophic fungus, Ascochyta medicaginicola, the causal agent of spring black stem (SBS) and leaf spot is a devasting foliar disease of alfalfa affecting stand survival, yield, and forage quality. Host resistance to SBS disease is poorly understood, and control methods rely on cultural practices. Resistance has been observed in M. truncatula accession SA27063 (HM078) with two recessively inherited quantitative-trait loci (QTL), rnpm1 and rnpm2, previously reported. To shed light on host resistance, we carried out a de novo genome assembly of HM078. The genome, referred to as MtHM078 v1.0, is comprised of 23 contigs totaling 481.19 Mbp. Notably, this assembly contains a substantial amount of novel centromere-related repeat sequences due to deep long-read sequencing. Genome annotation resulted in 98.4% of BUSCO fabales proteins being complete. The assembly enabled sequence-level analysis of rnpm1 and rnpm2 for gene content, synteny, and structural variation between SBS-resistant accession SA27063 (HM078) and SBS-susceptible accession A17 (HM101). Fourteen candidate genes were identified, and some have been implicated in resistance to necrotrophic fungi. Especially interesting candidates include loss-of-function events in HM078 because they fit the inverse gene-for-gene model, where resistance is recessively inherited. In rnpm1, these include a loss-of-function in a disease resistance gene due to a premature stop codon, and a 10.85 kbp retrotransposon-like insertion disrupting a ubiquitin conjugating E2. In rnpm2, we identified a frameshift mutation causing a loss-of-function in a glycosidase, as well as a missense and frameshift mutation altering an F-box family protein. This study generated a high-quality genome of HM078 and has identified promising candidates, that once validated, could be further studied in alfalfa to enhance disease resistance.
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Affiliation(s)
- Jacob R Botkin
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Andrew D Farmer
- National Center for Genome Resources, Santa Fe, NM, 87505, USA
| | - Nevin D Young
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Shaun J Curtin
- United States Department of Agriculture, Plant Science Research Unit, St Paul, MN, 55108, USA.
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA.
- Center for Plant Precision Genomics, University of Minnesota, St. Paul, MN, 55108, USA.
- Center for Genome Engineering, University of Minnesota, St. Paul, MN, 55108, USA.
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16
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Kangben F, Kumar S, Li Z, Sreedasyam A, Dardick C, Jones D, Saski CA. Phylogenetic and functional analysis of tiller angle control homeologs in allotetraploid cotton. FRONTIERS IN PLANT SCIENCE 2024; 14:1320638. [PMID: 38356867 PMCID: PMC10864623 DOI: 10.3389/fpls.2023.1320638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 12/20/2023] [Indexed: 02/16/2024]
Abstract
Introduction Plants can adapt their growth to optimize light capture in competitive environments, with branch angle being a crucial factor influencing plant phenotype and physiology. Decreased branch angles in cereal crops have been shown to enhance productivity in high-density plantings. The Tiller Angle Control (TAC1) gene, known for regulating tiller inclination in rice and corn, has been found to control branch angle in eudicots. Manipulating TAC1 in field crops like cotton offers the potential for improving crop productivity. Methods Using a homolog-based methodology, we examined the distribution of TAC1-related genes in cotton compared to other angiosperms. Furthermore, tissue-specific qPCR analysis unveiled distinct expression patterns of TAC1 genes in various cotton tissues. To silence highly expressed specific TAC1 homeologs in the stem, we applied CRISPR-Cas9 gene editing and Agrobacterium-mediated transformation, followed by genotyping and subsequent phenotypic validation of the mutants. Results Gene duplication events of TAC1 specific to the Gossypium lineage were identified, with 3 copies in diploid progenitors and 6 copies in allotetraploid cottons. Sequence analysis of the TAC1 homeologs in Gossypium hirsutum revealed divergence from other angiosperms with 1-2 copies, suggesting possible neo- or sub-functionalization for the duplicated copies. These TAC1 homeologs exhibited distinct gene expression patterns in various tissues over developmental time, with elevated expression of A11G109300 and D11G112200, specifically in flowers and stems, respectively. CRISPR-mediated loss of these TAC1 homeologous genes resulted in a reduction in branch angle and altered petiole angles, and a 5 to 10-fold reduction in TAC1 expression in the mutants, confirming their role in controlling branch and petiole angles. This research provides a promising strategy for genetically engineering branch and petiole angles in commercial cotton varieties, potentially leading to increased productivity.
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Affiliation(s)
- Foster Kangben
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, United States
| | - Sonika Kumar
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, United States
| | - Zhigang Li
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, United States
| | - Avinash Sreedasyam
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Chris Dardick
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Appalachian Fruit Research Station, Kearneysville, WV, United States
| | - Don Jones
- Department of Agricultural Research, Cotton Incorporated, Cary, NC, United States
| | - Christopher A. Saski
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, United States
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17
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Zhang CX, Li RJ, Baude L, Reinhardt D, Xie ZP, Staehelin C. CRISPR/Cas9-Mediated Generation of Mutant Lines in Medicago truncatula Indicates a Symbiotic Role of MtLYK10 during Nodule Formation. BIOLOGY 2024; 13:53. [PMID: 38275729 PMCID: PMC10812973 DOI: 10.3390/biology13010053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 01/12/2024] [Accepted: 01/15/2024] [Indexed: 01/27/2024]
Abstract
CRISPR/Cas9 systems are commonly used for plant genome editing; however, the generation of homozygous mutant lines in Medicago truncatula remains challenging. Here, we present a CRISPR/Cas9-based protocol that allows the efficient generation of M. truncatula mutants. Gene editing was performed for the LysM receptor kinase gene MtLYK10 and two major facilitator superfamily transporter genes. The functionality of CRISPR/Cas9 vectors was tested in Nicotiana benthamiana leaves by editing a co-transformed GUSPlus gene. Transformed M. truncatula leaf explants were regenerated to whole plants at high efficiency (80%). An editing efficiency (frequency of mutations at a given target site) of up to 70% was reached in the regenerated plants. Plants with MtLYK10 knockout mutations were propagated, and three independent homozygous mutant lines were further characterized. No off-target mutations were identified in these lyk10 mutants. Finally, the lyk10 mutants and wild-type plants were compared with respect to the formation of root nodules induced by nitrogen-fixing Sinorhizobium meliloti bacteria. Nodule formation was considerably delayed in the three lyk10 mutant lines. Surprisingly, the size of the rare nodules in mutant plants was higher than in wild-type plants. In conclusion, the symbiotic characterization of lyk10 mutants generated with the developed CRISPR/Cas9 protocol indicated a role of MtLYK10 in nodule formation.
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Affiliation(s)
- Chun-Xiao Zhang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Ru-Jie Li
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Laura Baude
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | - Didier Reinhardt
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | - Zhi-Ping Xie
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Christian Staehelin
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
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18
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Yakovleva DV, Efremova EP, Smirnov KV, Simonova VY, Konstantinov ZS, Tvorogova VE, Lutova LA. The WOX Genes from the Intermediate Clade: Influence on the Somatic Embryogenesis in Medicago truncatula. PLANTS (BASEL, SWITZERLAND) 2024; 13:223. [PMID: 38256776 PMCID: PMC10819790 DOI: 10.3390/plants13020223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/18/2023] [Accepted: 01/10/2024] [Indexed: 01/24/2024]
Abstract
Transcription factors from the WOX family are well-known regulators of cell proliferation and differentiation in plants. Herein, we focused on several WOX genes from the intermediate clade and checked their impact on somatic embryogenesis using the model legume object Medicago truncatula. As a result, we show that MtWOX9-1 overexpression not only stimulates somatic embryogenesis in the embryogenic M. truncatula line, as it was shown previously, but can also induce somatic embryogenesis in the non-embryogenic line. Other intermediate clade WOX, including the close paralog of MtWOX9-1, as well as WOX11 homologs, did not have any significant impact on somatic embryogenesis in our in vitro cultivation system. Together, our results give new information about the diversity of the WOX family proteins and their specific functions. These data can be used for the search of new regeneration stimulators.
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Affiliation(s)
- Daria V. Yakovleva
- Department of Genetics and Biotechnology, Saint Petersburg State University, 7/9 Universitetskaya emb, Saint Petersburg 199034, Russia; (D.V.Y.); (E.P.E.); (L.A.L.)
| | - Elena P. Efremova
- Department of Genetics and Biotechnology, Saint Petersburg State University, 7/9 Universitetskaya emb, Saint Petersburg 199034, Russia; (D.V.Y.); (E.P.E.); (L.A.L.)
| | - Kirill V. Smirnov
- All-Russia Research Institute for Agricultural Microbiology, Podbelsky Chausse 3, Pushkin, Saint Petersburg 196608, Russia;
| | - Veronika Y. Simonova
- Plant Biology and Biotechnology Department, Sirius University of Science and Technology, 1 Olympic Avenue, Sochi 354340, Russia; (V.Y.S.); (Z.S.K.)
| | - Zakhar S. Konstantinov
- Plant Biology and Biotechnology Department, Sirius University of Science and Technology, 1 Olympic Avenue, Sochi 354340, Russia; (V.Y.S.); (Z.S.K.)
| | - Varvara E. Tvorogova
- Department of Genetics and Biotechnology, Saint Petersburg State University, 7/9 Universitetskaya emb, Saint Petersburg 199034, Russia; (D.V.Y.); (E.P.E.); (L.A.L.)
- Plant Biology and Biotechnology Department, Sirius University of Science and Technology, 1 Olympic Avenue, Sochi 354340, Russia; (V.Y.S.); (Z.S.K.)
- Center for Genetic Technologies, N. I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), 42 Bolshaya Morskaya Street, Saint Petersburg 190000, Russia
| | - Ludmila A. Lutova
- Department of Genetics and Biotechnology, Saint Petersburg State University, 7/9 Universitetskaya emb, Saint Petersburg 199034, Russia; (D.V.Y.); (E.P.E.); (L.A.L.)
- Plant Biology and Biotechnology Department, Sirius University of Science and Technology, 1 Olympic Avenue, Sochi 354340, Russia; (V.Y.S.); (Z.S.K.)
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19
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Sharma S, Ganotra J, Samantaray J, Sahoo RK, Bhardwaj D, Tuteja N. An emerging role of heterotrimeric G-proteins in nodulation and nitrogen sensing. PLANTA 2023; 258:101. [PMID: 37847414 DOI: 10.1007/s00425-023-04251-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 09/25/2023] [Indexed: 10/18/2023]
Abstract
MAIN CONCLUSION A comprehensive understanding of nitrogen signaling cascades involving heterotrimeric G-proteins and their putative receptors can assist in the production of nitrogen-efficient plants. Plants are immobile in nature, so they must endure abiotic stresses including nutrient stress. Plant development and agricultural productivity are frequently constrained by the restricted availability of nitrogen in the soil. Non-legume plants acquire nitrogen from the soil through root membrane-bound transporters. In depleted soil nitrogen conditions, legumes are naturally conditioned to fix atmospheric nitrogen with the aid of nodulation elicited by nitrogen-fixing bacteria. Moreover, apart from the symbiotic nitrogen fixation process, nitrogen uptake from the soil can also be a significant secondary source to satisfy the nitrogen requirements of legumes. Heterotrimeric G-proteins function as molecular switches to help plant cells relay diverse stimuli emanating from external stress conditions. They are comprised of Gα, Gβ and Gγ subunits, which cooperate with several downstream effectors to regulate multiple plant signaling events. In the present review, we concentrate on signaling mechanisms that regulate plant nitrogen nutrition. Our review highlights the potential of heterotrimeric G-proteins, together with their putative receptors, to assist the legume root nodule symbiosis (RNS) cascade, particularly during calcium spiking and nodulation. Additionally, the functions of heterotrimeric G-proteins in nitrogen acquisition by plant roots as well as in improving nitrogen use efficiency (NUE) have also been discussed. Future research oriented towards heterotrimeric G-proteins through genome editing tools can be a game changer in the enhancement of the nitrogen fixation process. This will foster the precise manipulation and production of plants to ensure global food security in an era of climate change by enhancing crop productivity and minimizing reliance on external inputs.
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Affiliation(s)
- Suvriti Sharma
- Department of Botany, Central University of Jammu, Jammu, Jammu and Kashmir, 181143, India
| | - Jahanvi Ganotra
- Department of Botany, Central University of Jammu, Jammu, Jammu and Kashmir, 181143, India
| | - Jyotipriya Samantaray
- Department of Botany, Central University of Jammu, Jammu, Jammu and Kashmir, 181143, India
| | - Ranjan Kumar Sahoo
- Department of Biotechnology, Centurion University of Technology and Management, Bhubaneswar, Odisha, 752050, India
| | - Deepak Bhardwaj
- Department of Botany, Central University of Jammu, Jammu, Jammu and Kashmir, 181143, India.
| | - Narendra Tuteja
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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20
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Cao Y, Feng T, Wu Y, Xu Y, Du L, Wang T, Luo Y, Wang Y, Li Z, Xuan Z, Chen S, Yao N, Gao NL, Xiao Q, Huang K, Wang X, Cui K, Rehman SU, Tang X, Liu D, Han H, Li Y, Chen WH, Liu Q. The multi-kingdom microbiome of the goat gastrointestinal tract. MICROBIOME 2023; 11:219. [PMID: 37779211 PMCID: PMC10544373 DOI: 10.1186/s40168-023-01651-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 08/14/2023] [Indexed: 10/03/2023]
Abstract
BACKGROUND Goat is an important livestock worldwide, which plays an indispensable role in human life by providing meat, milk, fiber, and pelts. Despite recent significant advances in microbiome studies, a comprehensive survey on the goat microbiomes covering gastrointestinal tract (GIT) sites, developmental stages, feeding styles, and geographical factors is still unavailable. Here, we surveyed its multi-kingdom microbial communities using 497 samples from ten sites along the goat GIT. RESULTS We reconstructed a goat multi-kingdom microbiome catalog (GMMC) including 4004 bacterial, 71 archaeal, and 7204 viral genomes and annotated over 4,817,256 non-redundant protein-coding genes. We revealed patterns of feeding-driven microbial community dynamics along the goat GIT sites which were likely associated with gastrointestinal food digestion and absorption capabilities and disease risks, and identified an abundance of large intestine-enriched genera involved in plant fiber digestion. We quantified the effects of various factors affecting the distribution and abundance of methane-producing microbes including the GIT site, age, feeding style, and geography, and identified 68 virulent viruses targeting the methane producers via a comprehensive virus-bacterium/archaea interaction network. CONCLUSIONS Together, our GMMC catalog provides functional insights of the goat GIT microbiota through microbiome-host interactions and paves the way to microbial interventions for better goat and eco-environmental qualities. Video Abstract.
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Affiliation(s)
- Yanhong Cao
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China
- Guangxi Vocational University of Agriculture, Nanning, Guangxi, 530007, China
| | - Tong Feng
- Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China.
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China.
| | - Yingjian Wu
- Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Yixue Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Li Du
- Hainan Key Lab of Tropical Animal Reproduction and Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou, 570000, Hainan, China
| | - Teng Wang
- Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Yuhong Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Yan Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Zhipeng Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Zeyi Xuan
- Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning, 530001, Guangxi, China
| | - Shaomei Chen
- Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning, 530001, Guangxi, China
| | - Na Yao
- Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning, 530001, Guangxi, China
| | - Na L Gao
- Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Qian Xiao
- Hainan Key Lab of Tropical Animal Reproduction and Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou, 570000, Hainan, China
| | - Kongwei Huang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China
| | - Xiaobo Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Kuiqing Cui
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Saif Ur Rehman
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Xiangfang Tang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Dewu Liu
- South China Agricultural University, Guangzhou, 510642, China
| | - Hongbing Han
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Ying Li
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China
| | - Wei-Hua Chen
- Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China.
- Institution of Medical Artificial Intelligence, Binzhou Medical University, Yantai, 264003, China.
| | - Qingyou Liu
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China.
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China.
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21
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Shen Y, Ma Y, Li D, Kang M, Pei Y, Zhang R, Tao W, Huang S, Song W, Li Y, Huang W, Wang D, Chen Y. Biological and genomic analysis of a symbiotic nitrogen fixation defective mutant in Medicago truncatula. FRONTIERS IN PLANT SCIENCE 2023; 14:1209664. [PMID: 37457346 PMCID: PMC10345209 DOI: 10.3389/fpls.2023.1209664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 06/13/2023] [Indexed: 07/18/2023]
Abstract
Medicago truncatula has been selected as one of the model legume species for gene functional studies. To elucidate the functions of the very large number of genes present in plant genomes, genetic mutant resources are very useful and necessary tools. Fast Neutron (FN) mutagenesis is effective in inducing deletion mutations in genomes of diverse species. Through this method, we have generated a large mutant resource in M. truncatula. This mutant resources have been used to screen for different mutant using a forward genetics methods. We have isolated and identified a large amount of symbiotic nitrogen fixation (SNF) deficiency mutants. Here, we describe the detail procedures that are being used to characterize symbiotic mutants in M. truncatula. In recent years, whole genome sequencing has been used to speed up and scale up the deletion identification in the mutant. Using this method, we have successfully isolated a SNF defective mutant FN007 and identified that it has a large segment deletion on chromosome 3. The causal deletion in the mutant was confirmed by tail PCR amplication and sequencing. Our results illustrate the utility of whole genome sequencing analysis in the characterization of FN induced deletion mutants for gene discovery and functional studies in the M. truncatula. It is expected to improve our understanding of molecular mechanisms underlying symbiotic nitrogen fixation in legume plants to a great extent.
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22
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Rahmat Z, Sohail MN, Perrine-Walker F, Kaiser BN. Balancing nitrate acquisition strategies in symbiotic legumes. PLANTA 2023; 258:12. [PMID: 37296318 DOI: 10.1007/s00425-023-04175-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 06/01/2023] [Indexed: 06/12/2023]
Abstract
MAIN CONCLUSION Legumes manage both symbiotic (indirect) and non-symbiotic (direct) nitrogen acquisition pathways. Understanding and optimising the direct pathway for nitrate uptake will support greater legume growth and seed yields. Legumes have multiple pathways to acquire reduced nitrogen to grow and set seed. Apart from the symbiotic N2-fixation pathway involving soil-borne rhizobia bacteria, the acquisition of nitrate and ammonia from the soil can also be an important secondary nitrogen source to meet plant N demand. The balance in N delivery between symbiotic N (indirect) and inorganic N uptake (direct) remains less clear over the growing cycle and with the type of legume under cultivation. In fertile, pH balanced agricultural soils, NO3- is often the predominant form of reduced N available to crop plants and will be a major contributor to whole plant N supply if provided at sufficient levels. The transport processes for NO3- uptake into legume root cells and its transport between root and shoot tissues involves both high and low-affinity transport systems called HATS and LATS, respectively. These proteins are regulated by external NO3- availability and by the N status of the cell. Other proteins also play a role in NO3- transport, including the voltage dependent chloride/nitrate channel family (CLC) and the S-type anion channels of the SLAC/SLAH family. CLC's are linked to NO3- transport across the tonoplast of vacuoles and the SLAC/SLAH's with NO3- efflux across the plasma membrane and out of the cell. An important step in managing the N requirements of a plant are the mechanisms involved in root N uptake and the subsequent cellular distribution within the plant. In this review, we will present the current knowledge of these proteins and what is understood on how they function in key model legumes (Lotus japonicus, Medicago truncatula and Glycine sp.). The review will examine their regulation and role in N signalling, discuss how post-translational modification affects NO3- transport in roots and aerial tissues and its translocation to vegetative tissues and storage/remobilization in reproductive tissues. Lastly, we will present how NO3-influences the autoregulation of nodulation and nitrogen fixation and its role in mitigating salt and other abiotic stresses.
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Affiliation(s)
- Zainab Rahmat
- Sydney Institute of Agriculture, The Faculty of Science, University of Sydney, 380 Werombi Road, Brownlow Hill, NSW, 2570, Australia
- School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia
| | - Muhammad N Sohail
- Sydney Institute of Agriculture, The Faculty of Science, University of Sydney, 380 Werombi Road, Brownlow Hill, NSW, 2570, Australia
- School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia
| | - Francine Perrine-Walker
- Sydney Institute of Agriculture, The Faculty of Science, University of Sydney, 380 Werombi Road, Brownlow Hill, NSW, 2570, Australia.
| | - Brent N Kaiser
- Sydney Institute of Agriculture, The Faculty of Science, University of Sydney, 380 Werombi Road, Brownlow Hill, NSW, 2570, Australia.
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23
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Jia Y, Li Y. Genome-Wide Identification and Comparative Analysis of RALF Gene Family in Legume and Non-Legume Species. Int J Mol Sci 2023; 24:ijms24108842. [PMID: 37240187 DOI: 10.3390/ijms24108842] [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: 04/05/2023] [Revised: 05/05/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
Rapid alkalinization factor (RALF) are small secreted peptide hormones that can induce rapid alkalinization in a medium. They act as signaling molecules in plants, playing a critical role in plant development and growth, especially in plant immunity. Although the function of RALF peptides has been comprehensively analyzed, the evolutionary mechanism of RALFs in symbiosis has not been studied. In this study, 41, 24, 17 and 12 RALFs were identified in Arabidopsis, soybean, Lotus and Medicago, respectively. A comparative analysis including the molecular characteristics and conserved motifs suggested that the RALF pre-peptides in soybean represented a higher value of isoelectric point and more conservative motifs/residues composition than other species. All 94 RALFs were divided into two clades according to the phylogenetic analysis. Chromosome distribution and synteny analysis suggested that the expansion of the RALF gene family in Arabidopsis mainly depended on tandem duplication, while segment duplication played a dominant role in legume species. The expression levels of most RALFs in soybean were significantly affected by the treatment of rhizobia. Seven GmRALFs are potentially involved in the release of rhizobia in the cortex cells. Overall, our research provides novel insights into the understanding of the role of the RALF gene family in nodule symbiosis.
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Affiliation(s)
- Yancui Jia
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Hongshan District, Wuhan 430070, China
| | - Youguo Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Hongshan District, Wuhan 430070, China
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24
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Watts-Williams SJ, Wege S, Ramesh SA, Berkowitz O, Xu B, Gilliham M, Whelan J, Tyerman SD. The function of the Medicago truncatula ZIP transporter MtZIP14 is linked to arbuscular mycorrhizal fungal colonization. PLANT, CELL & ENVIRONMENT 2023; 46:1691-1704. [PMID: 36654510 DOI: 10.1111/pce.14545] [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: 11/18/2022] [Revised: 01/09/2023] [Accepted: 01/17/2023] [Indexed: 06/17/2023]
Abstract
Soil micronutrient availability, including zinc (Zn), is a limiting factor for crop yield. Arbuscular mycorrhizal (AM) fungi can improve host plant growth and nutrition through the mycorrhizal pathway of nutrient uptake. Although the physiology of Zn uptake through the mycorrhizal pathway is well established, the identity of the related molecular components are unknown. Here, RNA-seq analysis was used to identify genes differentially-regulated by AM colonization and soil Zn concentration in roots of Medicago truncatula. The putative Zn transporter gene MtZIP14 was markedly up-regulated in M. truncatula roots when colonized by Rhizophagus irregularis. MtZIP14 restored yeast growth under low Zn availability. Loss-of-function mutant plants (mtzip14) had reduced shoot biomass compared to the wild-type when colonized by AM fungi and grown under low and sufficient soil Zn concentration; at high soil Zn concentration, there were no genotypic differences in shoot biomass. The vesicular and arbuscular colonization of roots was lower in the mtzip14 plants regardless of soil Zn concentration. We propose that MtZIP14 is linked to AM colonization in M. truncatula plants, with the possibility that MtZIP14 function with AM colonization is linked to plant Zn nutrition.
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Affiliation(s)
- Stephanie J Watts-Williams
- The Waite Research Institute and The School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, South Australia, Australia
- The Australian Research Council Centre of Excellence in Plant Energy Biology, Australia
| | - Stefanie Wege
- The Waite Research Institute and The School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, South Australia, Australia
- The Australian Research Council Centre of Excellence in Plant Energy Biology, Australia
| | - Sunita A Ramesh
- The Australian Research Council Centre of Excellence in Plant Energy Biology, Australia
- College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
| | - Oliver Berkowitz
- The Australian Research Council Centre of Excellence in Plant Energy Biology, Australia
- Department of Animal Plant and Soil Science, School of Life Science, La Trobe University, Bundoora, Victoria, Australia
| | - Bo Xu
- The Waite Research Institute and The School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, South Australia, Australia
- The Australian Research Council Centre of Excellence in Plant Energy Biology, Australia
| | - Matthew Gilliham
- The Waite Research Institute and The School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, South Australia, Australia
- The Australian Research Council Centre of Excellence in Plant Energy Biology, Australia
| | - James Whelan
- The Australian Research Council Centre of Excellence in Plant Energy Biology, Australia
| | - Stephen D Tyerman
- The Waite Research Institute and The School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, South Australia, Australia
- The Australian Research Council Centre of Excellence in Plant Energy Biology, Australia
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25
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Kenchanmane Raju SK, Ledford M, Niederhuth CE. DNA methylation signatures of duplicate gene evolution in angiosperms. PLANT PHYSIOLOGY 2023:kiad220. [PMID: 37061825 PMCID: PMC10400039 DOI: 10.1093/plphys/kiad220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/03/2023] [Accepted: 04/12/2023] [Indexed: 06/19/2023]
Abstract
Gene duplication is a source of evolutionary novelty. DNA methylation may play a role in the evolution of duplicate genes (paralogs) through its association with gene expression. While this relationship has been examined to varying extents in a few individual species, the generalizability of these results at either a broad phylogenetic scale with species of differing duplication histories or across a population remains unknown. We applied a comparative epigenomics approach to 43 angiosperm species across the phylogeny and a population of 928 Arabidopsis (Arabidopsis thaliana) accessions, examining the association of DNA methylation with paralog evolution. Genic DNA methylation was differentially associated with duplication type, the age of duplication, sequence evolution, and gene expression. Whole genome duplicates were typically enriched for CG-only gene-body methylated or unmethylated genes, while single-gene duplications were typically enriched for non-CG methylated or unmethylated genes. Non-CG methylation, in particular, was characteristic of more recent single-gene duplicates. Core angiosperm gene families differentiated into those which preferentially retain paralogs and 'duplication-resistant' families, which convergently reverted to singletons following duplication. Duplication-resistant families that still have paralogous copies were, uncharacteristically for core angiosperm genes, enriched for non-CG methylation. Non-CG methylated paralogs had higher rates of sequence evolution, higher frequency of presence-absence variation, and more limited expression. This suggests that silencing by non-CG methylation may be important to maintaining dosage following duplication and be a precursor to fractionation. Our results indicate that genic methylation marks differing evolutionary trajectories and fates between paralogous genes and have a role in maintaining dosage following duplication.
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Affiliation(s)
| | | | - Chad E Niederhuth
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
- AgBioResearch, Michigan State University, East Lansing, MI 48824, USA
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26
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Badri M, Ayadi A, Mahjoub A, Benltoufa A, Chaouachi M, Ranouch R, Ben Cheikh N, Abdelguerfi A, Laouar M, Abdelly C, Ludidi N, Djébali N. Variability in Responses to Phoma medicaginis Infection in a Tunisian Collection of Three Annual Medicago Species. THE PLANT PATHOLOGY JOURNAL 2023; 39:171-180. [PMID: 37019827 PMCID: PMC10102567 DOI: 10.5423/ppj.oa.09.2022.0134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 12/05/2022] [Accepted: 12/12/2022] [Indexed: 06/19/2023]
Abstract
Spring black stem and leaf spot, caused by Phoma medicaginis, is an issue in annual Medicago species. Therefore, in this study, we analyzed the response to P. medicaginis infection in a collection of 46 lines of three annual Medicago species (M. truncatula, M. ciliaris, and M. polymorpha) showing different geographic distribution in Tunisia. The reaction in the host to the disease is explained by the effects based on plant species, lines nested within species, treatment, the interaction of species × treatment, and the interaction of lines nested within species × treatment. Medicago ciliaris was the least affected for aerial growth under infection. Furthermore, the largest variation within species was found for M. truncatula under both conditions. Principal component analysis and hierarchical classification showed that M. ciliaris lines formed a separate group under control treatment and P. medicaginis infection and they are the most vigorous in growth. These results indicate that M. ciliaris is the least susceptible in response to P. medicaginis infection among the three Medicago species investigated here, which can be used as a good candidate in crop rotation to reduce disease pressure in the field and as a source of P. medicaginis resistance for the improvement of forage legumes.
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Affiliation(s)
- Mounawer Badri
- Laboratory of Extremophile Plants, Centre of Biotechnology of Borj Cedria, B.P. 901, Hammam-Lif 2050,
Tunisia
| | - Amina Ayadi
- Laboratory of Extremophile Plants, Centre of Biotechnology of Borj Cedria, B.P. 901, Hammam-Lif 2050,
Tunisia
- Faculty of Mathematical, Physical and Natural Sciences of Tunis, Campus Universitaire El-Manar, University of Tunis El Manar, El Manar 2092,
Tunisia
| | - Asma Mahjoub
- Laboratory of Extremophile Plants, Centre of Biotechnology of Borj Cedria, B.P. 901, Hammam-Lif 2050,
Tunisia
| | - Amani Benltoufa
- Laboratory of Extremophile Plants, Centre of Biotechnology of Borj Cedria, B.P. 901, Hammam-Lif 2050,
Tunisia
| | - Manel Chaouachi
- Laboratory of Bioactive Substances, Centre of Biotechnology of Borj Cedria, B.P. 901, Hammam-Lif 2050,
Tunisia
| | - Rania Ranouch
- Laboratory of Bioactive Substances, Centre of Biotechnology of Borj Cedria, B.P. 901, Hammam-Lif 2050,
Tunisia
| | - Najah Ben Cheikh
- Laboratory of Extremophile Plants, Centre of Biotechnology of Borj Cedria, B.P. 901, Hammam-Lif 2050,
Tunisia
| | - Aissa Abdelguerfi
- Ecole Nationale Supérieure Agronomique d’Alger, Rue Hassen Badi, El Harrach 16200, Algiers,
Algeria
| | - Meriem Laouar
- Ecole Nationale Supérieure Agronomique d’Alger, Rue Hassen Badi, El Harrach 16200, Algiers,
Algeria
| | - Chedly Abdelly
- Laboratory of Extremophile Plants, Centre of Biotechnology of Borj Cedria, B.P. 901, Hammam-Lif 2050,
Tunisia
| | - Ndiko Ludidi
- Plant Biotechnology Research Group, Department of Biotechnology, University of the Western Cape, Robert Sobukwe Road, Bellville 7530,
South Africa
- DSI-NRF Centre of Excellence in Food Security, University of the Western Cape, Robert Sobukwe Road, Bellville 7530,
South Africa
| | - Naceur Djébali
- Laboratory of Bioactive Substances, Centre of Biotechnology of Borj Cedria, B.P. 901, Hammam-Lif 2050,
Tunisia
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27
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Cai Z, Zhao X, Zhou C, Fang T, Liu G, Luo J. Genome-Wide Mining of the Tandem Duplicated Type III Polyketide Synthases and Their Expression, Structure Analysis of Senna tora. Int J Mol Sci 2023; 24:ijms24054837. [PMID: 36902267 PMCID: PMC10003783 DOI: 10.3390/ijms24054837] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 02/26/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
Senna tora is one of the homologous crops used as a medicinal food containing an abundance of anthraquinones. Type III polyketide synthases (PKSs) are key enzymes that catalyze polyketide formation; in particular, the chalcone synthase-like (CHS-L) genes are involved in anthraquinone production. Tandem duplication is a fundamental mechanism for gene family expansion. However, the analysis of the tandem duplicated genes (TDGs) and the identification and characterization of PKSs have not been reported for S. tora. Herein, we identified 3087 TDGs in the S. tora genome; the synonymous substitution rates (Ks) analysis indicated that the TDGs had recently undergone duplication. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that the type III PKSs were the most enriched TDGs involved in the biosynthesis of the secondary metabolite pathways, as evidenced by 14 tandem duplicated CHS-L genes. Subsequently, we identified 30 type III PKSs with complete sequences in the S. tora genome. Based on the phylogenetic analysis, the type III PKSs were classified into three groups. The protein conserved motifs and key active residues showed similar patterns in the same group. The transcriptome analysis showed that the chalcone synthase (CHS) genes were more highly expressed in the leaves than in the seeds in S. tora. The transcriptome and qRT-PCR analysis showed that the CHS-L genes had a higher expression in the seeds than in other tissues, particularly seven tandem duplicated CHS-L2/3/5/6/9/10/13 genes. The key active-site residues and three-dimensional models of the CHS-L2/3/5/6/9/10/13 proteins showed slight variation. These results indicated that the rich anthraquinones in S. tora seeds might be ascribed to the PKSs' expansion from tandem duplication, and the seven key CHS-L2/3/5/6/9/10/13 genes provide candidate genes for further research. Our study provides an important basis for further research on the regulation of anthraquinones' biosynthesis in S. tora.
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Affiliation(s)
- Zeping Cai
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou 570228, China
| | - Xingkun Zhao
- College of Tropical Crops & College of Life Sciences, Hainan University, Haikou 570228, China
| | - Chaoye Zhou
- College of Tropical Crops & College of Life Sciences, Hainan University, Haikou 570228, China
| | - Ting Fang
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou 570228, China
| | - Guodao Liu
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Correspondence: (G.L.); (J.L.)
| | - Jiajia Luo
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Correspondence: (G.L.); (J.L.)
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Nandety RS, Wen J, Mysore KS. Medicago truncatula resources to study legume biology and symbiotic nitrogen fixation. FUNDAMENTAL RESEARCH 2023; 3:219-224. [PMID: 38932916 PMCID: PMC11197554 DOI: 10.1016/j.fmre.2022.06.018] [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: 03/28/2022] [Revised: 06/01/2022] [Accepted: 06/19/2022] [Indexed: 10/17/2022] Open
Abstract
Medicago truncatula is a chosen model for legumes towards deciphering fundamental legume biology, especially symbiotic nitrogen fixation. Current genomic resources for M. truncatula include a completed whole genome sequence information for R108 and Jemalong A17 accessions along with the sparse draft genome sequences for other 226 M. truncatula accessions. These genomic resources are complemented by the availability of mutant resources such as retrotransposon (Tnt1) insertion mutants in R108 and fast neutron bombardment (FNB) mutants in A17. In addition, several M. truncatula databases such as small secreted peptides (SSPs) database, transporter protein database, gene expression atlas, proteomic atlas, and metabolite atlas are available to the research community. This review describes these resources and provide information regarding how to access these resources.
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Affiliation(s)
- Raja Sekhar Nandety
- Institute for Agricultural Biosciences, Oklahoma State University, 3210 Sam Noble Parkway, Ardmore, OK 73401, United States
- USDA-ARS, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND 58102, United States
| | - Jiangqi Wen
- Institute for Agricultural Biosciences, Oklahoma State University, 3210 Sam Noble Parkway, Ardmore, OK 73401, United States
| | - Kirankumar S. Mysore
- Institute for Agricultural Biosciences, Oklahoma State University, 3210 Sam Noble Parkway, Ardmore, OK 73401, United States
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, United States
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Volpe V, Chialva M, Mazzarella T, Crosino A, Capitanio S, Costamagna L, Kohlen W, Genre A. Long-lasting impact of chitooligosaccharide application on strigolactone biosynthesis and fungal accommodation promotes arbuscular mycorrhiza in Medicago truncatula. THE NEW PHYTOLOGIST 2023; 237:2316-2331. [PMID: 36564991 DOI: 10.1111/nph.18697] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 12/13/2022] [Indexed: 06/17/2023]
Abstract
The establishment of arbuscular mycorrhiza (AM) between plants and Glomeromycotina fungi is preceded by the exchange of chemical signals: fungal released Myc-factors, including chitooligosaccharides (CO) and lipo-chitooligosaccharides (LCO), activate plant symbiotic responses, while root-exuded strigolactones stimulate hyphal branching and boost CO release. Furthermore, fungal signaling reinforcement through CO application was shown to promote AM development in Medicago truncatula, but the cellular and molecular bases of this effect remained unclear. Here, we focused on long-term M. truncatula responses to CO treatment, demonstrating its impact on the transcriptome of both mycorrhizal and nonmycorrhizal roots over several weeks and providing an insight into the mechanistic bases of the CO-dependent promotion of AM colonization. CO treatment caused the long-lasting regulation of strigolactone biosynthesis and fungal accommodation-related genes. This was mirrored by an increase in root didehydro-orobanchol content, and the promotion of accommodation responses to AM fungi in root epidermal cells. Lastly, an advanced downregulation of AM symbiosis marker genes was observed at the latest time point in CO-treated plants, in line with an increased number of senescent arbuscules. Overall, CO treatment triggered molecular, metabolic, and cellular responses underpinning a protracted acceleration of AM development.
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Affiliation(s)
- Veronica Volpe
- Department of Life Sciences and Systems Biology, University of Turin, Viale Mattioli 25, 10125, Torino, Italy
| | - Matteo Chialva
- Department of Life Sciences and Systems Biology, University of Turin, Viale Mattioli 25, 10125, Torino, Italy
| | - Teresa Mazzarella
- Department of Life Sciences and Systems Biology, University of Turin, Viale Mattioli 25, 10125, Torino, Italy
| | - Andrea Crosino
- Department of Life Sciences and Systems Biology, University of Turin, Viale Mattioli 25, 10125, Torino, Italy
| | - Serena Capitanio
- Department of Life Sciences and Systems Biology, University of Turin, Viale Mattioli 25, 10125, Torino, Italy
| | - Lorenzo Costamagna
- Department of Life Sciences and Systems Biology, University of Turin, Viale Mattioli 25, 10125, Torino, Italy
| | - Wouter Kohlen
- Laboratory of Molecular Biology, Wageningen University & Research, Wageningen, 6708, PB, the Netherlands
| | - Andrea Genre
- Department of Life Sciences and Systems Biology, University of Turin, Viale Mattioli 25, 10125, Torino, Italy
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Yang W, Dong X, Yuan Z, Zhang Y, Li X, Wang Y. Genome-Wide Identification and Expression Analysis of the Ammonium Transporter Family Genes in Soybean. Int J Mol Sci 2023; 24:ijms24043991. [PMID: 36835403 PMCID: PMC9960152 DOI: 10.3390/ijms24043991] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 02/04/2023] [Accepted: 02/14/2023] [Indexed: 02/18/2023] Open
Abstract
Ammonium transporters (AMTs) are responsible for ammonium absorption and utilization in plants. As a high-nitrogen-demand crop and a legume, soybean can also obtain ammonium from symbiotic root nodules in which nitrogen-fixing rhizobia convert atmospheric nitrogen (N2) into ammonium. Although increasing evidence implicates vital roles of ammonium transport in soybean, no systematic analyses of AMTs in soybean (named GmAMTs) or functional analyses of GmAMTs are available. In this study, we aimed to identify all GmAMT family genes and gain a better understanding of the characteristics of GmAMT genes in soybean. Here, due to the improved genome assembly and annotation of soybean, we tried to generate a phylogenetic tree of 16 GmAMTs based on new information. Consistent with reported data, GmAMT family members can be divided into two subfamilies of GmAMT1 (6 genes) and GmAMT2 (10 genes). Interestingly, unlike Arabidopsis, which has only one AMT2, soybean has substantially increased the number of GmAMT2s, suggesting enhanced demand for ammonium transport. These genes were distributed on nine chromosomes, of which GmAMT1.3, GmAMT1.4, and GmAMT1.5 were three tandem repeat genes. The gene structures and conserved protein motifs of the GmAMT1 and GmAMT2 subfamilies were different. All the GmAMTs were membrane proteins with varying numbers of transmembrane domains ranging from 4 to 11. Promoter analysis found that these GmAMT genes have phytohormone-, circadian control-, and organ expression-related cis-elements in their promoters, and notably, there were nodulation-specific and nitrogen-responsive elements in the promoters of the GmAMT1 and GmAMT2 genes. Further expression data showed that these GmAMT family genes exhibited different spatiotemporal expression patterns across tissues and organs. In addition, GmAMT1.1, GmAMT1.2, GmAMT2.2, and GmAMT2.3 were responsive to nitrogen treatment, while GmAMT1.2, GmAMT1.3, GmAMT1.4, GmAMT1.5, GmAMT1.6, GmAMT2.1, GmAMT2.2, GmAMT2.3, GmAMT3.1, and GmAMT4.6 showed circadian rhythms in transcription. RT-qPCR validated the expression patterns of GmAMTs in response to different forms of nitrogen and exogenous ABA treatments. Gene expression analysis also confirmed that GmAMTs are regulated by key nodulation gene GmNINa, indicating a role of GmAMTs in symbiosis. Together, these data indicate that GmAMTs may differentially and/or redundantly regulate ammonium transport during plant development and in response to environmental factors. These findings provide a basis for future research on the functions of GmAMTs and the mechanisms through which GmAMTs regulate ammonium metabolism and nodulation in soybean.
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Affiliation(s)
- Wei Yang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaoxu Dong
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhanxin Yuan
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yan Zhang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xia Li
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Correspondence: (X.L.); (Y.W.)
| | - Youning Wang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Correspondence: (X.L.); (Y.W.)
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A Germin-Like Protein GLP1 of Legumes Mediates Symbiotic Nodulation by Interacting with an Outer Membrane Protein of Rhizobia. Microbiol Spectr 2023; 11:e0335022. [PMID: 36633436 PMCID: PMC9927233 DOI: 10.1128/spectrum.03350-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Rhizobia can infect legumes and induce the coordinated expression of symbiosis and defense genes for the establishment of mutualistic symbiosis. Numerous studies have elucidated the molecular interactions between rhizobia and host plants, which are associated with Nod factor, exopolysaccharide, and T3SS effector proteins. However, there have been relatively few reports about how the host plant recognizes the outer membrane proteins (OMPs) of rhizobia to mediate symbiotic nodulation. In our previous work, a gene (Mhopa22) encoding an OMP was identified in Mesorhizobium huakuii 7653R, whose homologous genes are widely distributed in Rhizobiales. In this study, a germin-like protein GLP1 interacting with Mhopa22 was identified in Astragalus sinicus. RNA interference of AsGLP1 resulted in a decrease in nodule number, whereas overexpression of AsGLP1 increased the number of nodules in the hairy roots of A. sinicus. Consistent symbiotic phenotypes were identified in Medicago truncatula with MtGLPx (refer to medtr7g111240.1, the isogeny of AsGLP1) overexpression or Tnt1 mutant (glpx-1) in symbiosis with Sinorhizobium meliloti 1021. The glpx-1 mutant displayed hyperinfection and the formation of more infection threads but a decrease in root nodules. RNA sequencing analysis showed that many differentially expressed genes were involved in hormone signaling and symbiosis. Taken together, AsGLP1 and its homology play an essential role in mediating the early symbiotic process through interacting with the OMPs of rhizobia. IMPORTANCE This study is the first report to characterize a legume host plant protein to sense and interact with an outer membrane protein (OMP) of rhizobia. It can be speculated that GLP1 plays an essential role to mediate early symbiotic process through interacting with OMPs of rhizobia. The results provide deeper understanding and novel insights into the molecular interactive mechanism of a legume symbiosis signaling pathway in recognition with rhizobial OMPs. Our findings may also provide a new perspective to improve the symbiotic compatibility and nodulation of legume.
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Liu Y, Huang Y, Li Z, Feng M, Ge W, Zhong C, Xue R. Genome-wide identification of the TGA genes in common bean ( Phaseolus vulgaris) and revealing their functions in response to Fusarium oxysporum f. sp. phaseoli infection. Front Genet 2023; 14:1137634. [PMID: 36755571 PMCID: PMC9901207 DOI: 10.3389/fgene.2023.1137634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 01/12/2023] [Indexed: 01/22/2023] Open
Abstract
Fusarium wilt, which affects common bean all across the world, is caused by Fusarium oxysporum f. sp. Phaseoli (Fop). It is necessary to have functional genes in response to Fop infection because they might be used to manage disease. As a crucial regulator, TGA-binding transcription factor (TGA) is engaged in the defense mechanism of plants against pathogens. The role of TGA regulators in common bean in response to Fop infection, however, has not been documented. Hence, we performed genome-wide identified and characterized eight TGA genes in common bean. In this study, eight PvTGA genes were distributed on six chromosomes and classified into four subgroups. The PvTGA genes have the same conserved bZIP and DOG1 domains, but there are specific sequence structures in different PvTGAs. Phylogenetic and synteny analysis explained that PvTGA gene has a close genetic relationship with legume TGAs and that PvTGA03 and PvTGA05 may play an important role in evolution. Transcriptome data explained that expression levels of PvTGA genes showed diversity in different tissues. After Fop inoculation, the expression levels of PvTGA03 and PvTGA07 were significantly different between resistant and susceptible genotypes. Under SA treatment, the expression levels of PvTGA03, PvTGA04, PvTGA06, PvTGA07 and PvTGA08 were significantly different. These results imply that PvTGA03 and PvTGA07 play key roles in SA-mediated resistance to Fusarium wilt. Together, these findings advance knowledge of the PvTGA gene family in common bean and will help future studies aimed at reducing Fusarium wilt.
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Affiliation(s)
- Yu Liu
- College of Agronomy, Shenyang Agricultural University, Shenyang, China,Crop Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang, Liaoning, China,Liaoning Provincial Key Laboratory of Miscellaneous Grain Germplasm Innovation and Genetic Breeding, Shenyang, China
| | - Yuning Huang
- Crop Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang, Liaoning, China,Liaoning Provincial Key Laboratory of Miscellaneous Grain Germplasm Innovation and Genetic Breeding, Shenyang, China
| | - Zhao Li
- College of Agronomy, Shenyang Agricultural University, Shenyang, China
| | - Ming Feng
- Crop Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang, Liaoning, China,Liaoning Provincial Key Laboratory of Miscellaneous Grain Germplasm Innovation and Genetic Breeding, Shenyang, China
| | - Weide Ge
- Crop Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang, Liaoning, China,Liaoning Provincial Key Laboratory of Miscellaneous Grain Germplasm Innovation and Genetic Breeding, Shenyang, China
| | - Chao Zhong
- College of Agronomy, Shenyang Agricultural University, Shenyang, China,*Correspondence: Chao Zhong, ; Renfeng Xue,
| | - Renfeng Xue
- Crop Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang, Liaoning, China,Liaoning Provincial Key Laboratory of Miscellaneous Grain Germplasm Innovation and Genetic Breeding, Shenyang, China,*Correspondence: Chao Zhong, ; Renfeng Xue,
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Kudriashov AA, Zlydneva NS, Efremova EP, Tvorogova VE, Lutova LA. MtCLE08, MtCLE16, and MtCLE18 Transcription Patterns and Their Possible Functions in the Embryogenic Calli of Medicago truncatula. PLANTS (BASEL, SWITZERLAND) 2023; 12:435. [PMID: 36771520 PMCID: PMC9921462 DOI: 10.3390/plants12030435] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/05/2023] [Accepted: 01/13/2023] [Indexed: 06/18/2023]
Abstract
CLE peptides are well-known hormonal regulators of plant development, but their role in somatic embryogenesis remains undetermined. CLE genes are often regulated by WOX transcription factors and, in their turn, regulate the expression level of WOX genes. In this study, we used in vitro cultivation, as well as qPCR and transcriptomic analysis, to find CLE peptides which could regulate the MtWOX9-1 gene, stimulating somatic embryogenesis in Medicago truncatula. Three CLE peptides were found which could probably be such regulators, but none of them was found to influence MtWOX9-1 expression in the embryogenic calli. Nevertheless, overexpression of one of CLE genes under study, MtCLE16, decreased somatic embryogenesis intensity. Additionally, overexpression of MtCLE08 was found to suppress expression of MtWOX13a, a supposed antagonist of somatic embryo development. Our findings can be helpful for the search for new regeneration regulators which could be used for plant transformation.
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Affiliation(s)
- Andrei A. Kudriashov
- Department of Genetics and Biotechnology, Saint Petersburg State University, 7/9 Universitetskaya Emb, 199034 Saint Petersburg, Russia
| | - Natalia S. Zlydneva
- Department of Genetics and Biotechnology, Saint Petersburg State University, 7/9 Universitetskaya Emb, 199034 Saint Petersburg, Russia
- Center for Genetic Technologies, N. I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), 42 Bolshaya Morskaya Street, 190000 Saint Petersburg, Russia
| | - Elena P. Efremova
- Department of Genetics and Biotechnology, Saint Petersburg State University, 7/9 Universitetskaya Emb, 199034 Saint Petersburg, Russia
- Center for Genetic Technologies, N. I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), 42 Bolshaya Morskaya Street, 190000 Saint Petersburg, Russia
| | - Varvara E. Tvorogova
- Department of Genetics and Biotechnology, Saint Petersburg State University, 7/9 Universitetskaya Emb, 199034 Saint Petersburg, Russia
- Center for Genetic Technologies, N. I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), 42 Bolshaya Morskaya Street, 190000 Saint Petersburg, Russia
- Plant Biology and Biotechnology Department, Sirius University of Science and Technology, 1 Olympic Avenue, 354340 Sochi, Russia
| | - Ludmila A. Lutova
- Department of Genetics and Biotechnology, Saint Petersburg State University, 7/9 Universitetskaya Emb, 199034 Saint Petersburg, Russia
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Wang L, Zhang J, Wang R, Huang Z, Cui R, Zhu H, Yang Y, Zhang D. Genome-wide identification, evolution, and expression analysis of carbonic anhydrases genes in soybean (Glycine max). Funct Integr Genomics 2023; 23:37. [PMID: 36639600 DOI: 10.1007/s10142-023-00966-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/04/2023] [Accepted: 01/05/2023] [Indexed: 01/15/2023]
Abstract
Carbonic anhydrases (CAs), as zinc metalloenzymes, are ubiquitous in nature and play essential roles in diverse biological processes. Although CAs have been broadly explored and studied, comprehensive characteristics of CA gene family members in the soybean (Glycine max) are still lacking. A total of 35 CA genes (GmCAs) were identified; they distributed on sixteen chromosomes of the soybean genome and can be divided into three subfamilies (α-type, β-type, and γ-type). Bioinformatics analysis showed that the specific GmCA gene subfamily or clade exhibited similar characteristics and that segmental duplications took the major role in generating new GmCAs. Furthermore, the synteny and evolutionary constraints analyses of CAs among soybean and distinct species provided more detailed evidence for GmCA gene family evolution. Cis-element analysis of promoter indicated that GmCAs may be responsive to abiotic stress and regulate photosynthesis. Moreover, the expression patterns of GmCAs varied in different tissues at diverse developmental stages in soybean. Additionally, we found that eight representative GmCAs may be involved in the response of soybean to low phosphorus stress. The systematic investigation of the GmCA gene family in this study will provide a valuable basis for further functional research on soybean CA genes.
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Affiliation(s)
- Li Wang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Jinyu Zhang
- Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Ruiyang Wang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Zhongwen Huang
- Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Ruifan Cui
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Hongqing Zhu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Yuming Yang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China.
| | - Dan Zhang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China.
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Gavgani HN, Grotewold E, Gray J. Methodology for Constructing a Knowledgebase for Plant Gene Regulation Information. Methods Mol Biol 2023; 2698:277-300. [PMID: 37682481 DOI: 10.1007/978-1-0716-3354-0_17] [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] [Indexed: 09/09/2023]
Abstract
The amount of biological data is growing at a rapid pace as many high-throughput omics technologies and data pipelines are developed. This is resulting in the growth of databases for DNA and protein sequences, gene expression, protein accumulation, structural, and localization information. The diversity and multi-omics nature of such bioinformatic data requires well-designed databases for flexible organization and presentation. Besides general-purpose online bioinformatic databases, users need narrowly focused online databases to quickly access a meaningful collection of related data for their research. Here, we describe the methodology used to implement a plant gene regulatory knowledgebase, with data, query, and tool features, as well as the ability to expand to accommodate future datasets. We exemplify this methodology for the GRASSIUS knowledgebase, but it is applicable to developing and updating similar plant gene regulatory knowledgebases. GRASSIUS organizes and presents gene regulatory data from grass species with a central focus on maize (Zea mays). The main class of data presented include not only the families of transcription factors (TFs) and co-regulators (CRs) but also protein-DNA interaction data, where available.
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Affiliation(s)
- Hadi Nayebi Gavgani
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
- Dandelions Therapeutics Inc., San Francisco, CA, USA
| | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - John Gray
- Department of Biological Sciences, University of Toledo, Toledo, OH, USA.
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36
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Fartash AH, Ben C, Mazurier M, Ebrahimi A, Ghalandar M, Gentzbittel L, Rickauer M. Medicago truncatula quantitative resistance to a new strain of Verticillium alfalfae from Iran revealed by a genome-wide association study. FRONTIERS IN PLANT SCIENCE 2023; 14:1125551. [PMID: 37123855 PMCID: PMC10140629 DOI: 10.3389/fpls.2023.1125551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 03/20/2023] [Indexed: 05/03/2023]
Abstract
Verticillium wilt is a major threat to many crops, among them alfalfa (Medicago sativa). The model plant Medicago truncatula, a close relative of alfalfa was used to study the genetic control of resistance towards a new Verticillium alfalfae isolate. The accidental introduction of pathogen strains through global trade is a threat to crop production and such new strains might also be better adapted to global warming. Isolates of V. alfalfae were obtained from alfalfa fields in Iran and characterized. The Iranian isolate AF1 was used in a genome-wide association study (GWAS) involving 242 accessions from the Mediterranean region. Root inoculations were performed with conidia at 25°C and symptoms were scored regularly. Maximum Symptom Score and Area under Disease Progess Curve were computed as phenotypic traits to be used in GWAS and for comparison to a previous study with French isolate V31.2 at 20°C. This comparison showed high correlation with a shift to higher susceptibility, and similar geographical distribution of resistant and susceptible accessions to AF1 at 25°C, with resistant accessions mainly in the western part. GWAS revealed 30 significant SNPs linked to resistance towards isolate AF1. None of them were common to the previous study with isolate V31.2 at 20°C. To confirm these loci, the expression of nine underlying genes was studied. All genes were induced in roots following inoculation, in susceptible and resistant plants. However, in resistant plants induction was higher and lasted longer. Taken together, the use of a new pathogen strain and a shift in temperature revealed a completely different genetic control compared to a previous study that demonstrated the existence of two major QTLs. These results can be useful for Medicago breeding programs to obtain varieties better adapted to future conditions.
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Affiliation(s)
- Amir Hossein Fartash
- Laboratoire écologie fonctionnelle et environnement, Université de Toulouse, Centre National de Recherche Scientifique, Toulouse Institut National Polytechnique, Université Toulouse 3 – Paul Sabatier (UPS), Toulouse, France
| | - Cécile Ben
- Laboratoire écologie fonctionnelle et environnement, Université de Toulouse, Centre National de Recherche Scientifique, Toulouse Institut National Polytechnique, Université Toulouse 3 – Paul Sabatier (UPS), Toulouse, France
- Project Center for Agro Technologies, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Mélanie Mazurier
- Laboratoire écologie fonctionnelle et environnement, Université de Toulouse, Centre National de Recherche Scientifique, Toulouse Institut National Polytechnique, Université Toulouse 3 – Paul Sabatier (UPS), Toulouse, France
| | - Asa Ebrahimi
- Department of Plant Breeding and Biotechnology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Mojtaba Ghalandar
- Plant Protection Department, Markazi Agricultural and Natural Resources Research and Education Center, Arak, Iran
| | - Laurent Gentzbittel
- Laboratoire écologie fonctionnelle et environnement, Université de Toulouse, Centre National de Recherche Scientifique, Toulouse Institut National Polytechnique, Université Toulouse 3 – Paul Sabatier (UPS), Toulouse, France
- Project Center for Agro Technologies, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Martina Rickauer
- Laboratoire écologie fonctionnelle et environnement, Université de Toulouse, Centre National de Recherche Scientifique, Toulouse Institut National Polytechnique, Université Toulouse 3 – Paul Sabatier (UPS), Toulouse, France
- *Correspondence: Martina Rickauer,
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Annicchiarico P, Nazzicari N, Bouizgaren A, Hayek T, Laouar M, Cornacchione M, Basigalup D, Monterrubio Martin C, Brummer EC, Pecetti L. Alfalfa genomic selection for different stress-prone growing regions. THE PLANT GENOME 2022; 15:e20264. [PMID: 36222346 DOI: 10.1002/tpg2.20264] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 08/25/2022] [Indexed: 06/16/2023]
Abstract
Alfalfa (Medicago sativa L.) selection for stress-prone regions has high priority for sustainable crop-livestock systems. This study assessed the genomic selection (GS) ability to predict alfalfa breeding values for drought-prone agricultural sites of Algeria, Morocco, and Argentina; managed-stress (MS) environments of Italy featuring moderate or intense drought; and one Tunisian site irrigated with moderately saline water. Additional aims were to investigate genotype × environment interaction (GEI) patterns and the effect on GS predictions of three single-nucleotide polymorphism (SNP) calling procedures, 12 statistical models that exclude or incorporate GEI, and allele dosage information. Our study included 127 genotypes from a Mediterranean reference population originated from three geographically contrasting populations, genotyped via genotyping-by-sequencing and phenotyped based on multi-year biomass dry matter yield of their dense-planted half-sib progenies. The GEI was very large, as shown by 27-fold greater additive genetic variance × environment interaction relative to the additive genetic variance and low genetic correlation for progeny yield responses across environments. The predictive ability of GS (using at least 37,969 SNP markers) exceeded 0.20 for moderate MS (representing Italian stress-prone sites) and the sites of Algeria and Argentina while being quite low for the Tunisian site and intense MS. Predictions of GS were complicated by rapid linkage disequilibrium decay. The weighted GBLUP model, GEI incorporation into GS models, and SNP calling based on a mock reference genome exhibited a predictive ability advantage for some environments. Our results support the specific breeding for each target region and suggest a positive role for GS in most regions when considering the challenges associated with phenotypic selection.
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Affiliation(s)
- Paolo Annicchiarico
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Centro di ricerca Zootecnia e Acquacoltura, 29 viale Piacenza, Lodi, 26900, Italy
| | - Nelson Nazzicari
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Centro di ricerca Zootecnia e Acquacoltura, 29 viale Piacenza, Lodi, 26900, Italy
| | - Abdelaziz Bouizgaren
- Institut National de la Recherche Agronomique, Centre Régional de Marrakech, BP 533, Marrakech, 40000, Morocco
| | - Taoufik Hayek
- Institut des Régions Arides, Route du Jorf, Médenine, 4119, Tunisia
| | - Meriem Laouar
- Ecole Nationale Supérieure Agronomique, Dép. de Productions Végétales. Laboratoire d'Amélioration Intégrative des Productions Végétales (C2711100), Rue Hassen Badi, El Harrach 16200, Alger, Algérie
| | - Monica Cornacchione
- Instituto Nacional de Tecnología Agropecuaria, Estación Experimental Santiago del Estero, Jujuy 850, Santiago del Estero, 4200, Argentina
| | - Daniel Basigalup
- Instituto Nacional de Tecnología Agropecuaria, Estación Experimental Manfredi, Ruta Nacional no. 9 km 636, Manfredi, Córdoba, X5988, Argentina
| | - Cristina Monterrubio Martin
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Centro di ricerca Zootecnia e Acquacoltura, 29 viale Piacenza, Lodi, 26900, Italy
| | - Edward Charles Brummer
- Plant Breeding Center, Dep. of Plant Sciences, Univ. of California, Davis, CA, 95616, USA
| | - Luciano Pecetti
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Centro di ricerca Zootecnia e Acquacoltura, 29 viale Piacenza, Lodi, 26900, Italy
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38
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Siritapetawee J, Attarataya J, Charoenwattanasatien R. Sequence analysis and crystal structure of a glycosylated protease from Euphorbia resinifera latex for its proteolytic activity aspect. Biotechnol Appl Biochem 2022; 69:2580-2591. [PMID: 34967474 DOI: 10.1002/bab.2307] [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: 07/22/2021] [Accepted: 12/19/2021] [Indexed: 12/27/2022]
Abstract
The investigation of a plant glycosylated serine protease (EuRP-61) isolated from Euphorbia resinifera latex for potential antiplatelet and anticoagulation activities has been previously reported. In the present study, the protein sequence and native crystal structure of EuRP-61 were characterized. The structure was identified using single-wavelength anomalous diffraction with a refinement resolution of 1.7 Å (PDB ID: 7EOX). The main structural components of EuRP-61 were composed of three domains: catalytic, protease-associated (PA), and fibronectin type III (Fn3)-like domains. The crystal structure revealed that some loops in the PA and catalytic domains of EuRP-61 were different from the other subtilisin-like proteases (cucumisin and SBT3). These different loops might be involved in the general monomer formation of EuRP-61, substrate specificity, and maintenance of the catalytic domain. The Fn3-like domain may provide flexibility to the enzyme to bind with various substrates and cell receptors. Additionally, the active site of EuRP-61 consisted of the catalytic triad of Ser434, His106, and Asp32, similar to other serine proteases. The present study provides additional information and insight into the protease and antithrombotic activities of EuRP-61, which could contribute to further development of this enzyme for biomedical treatment.
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Affiliation(s)
- Jaruwan Siritapetawee
- Biochemistry-Electrochemistry Research Unit, School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Jakrada Attarataya
- Synchrotron Light Research Institute (Public Organization), Nakhon Ratchasima, Thailand
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Frey LA, Vleugels T, Ruttink T, Schubiger FX, Pégard M, Skøt L, Grieder C, Studer B, Roldán-Ruiz I, Kölliker R. Phenotypic variation and quantitative trait loci for resistance to southern anthracnose and clover rot in red clover. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:4337-4349. [PMID: 36153770 PMCID: PMC9734235 DOI: 10.1007/s00122-022-04223-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 09/14/2022] [Indexed: 06/02/2023]
Abstract
High variability for and candidate loci associated with resistance to southern anthracnose and clover rot in a worldwide collection of red clover provide a first basis for genomics-assisted breeding. Red clover (Trifolium pratense L.) is an important forage legume of temperate regions, particularly valued for its high yield potential and its high forage quality. Despite substantial breeding progress during the last decades, continuous improvement of cultivars is crucial to ensure yield stability in view of newly emerging diseases or changing climatic conditions. The high amount of genetic diversity present in red clover ecotypes, landraces, and cultivars provides an invaluable, but often unexploited resource for the improvement of key traits such as yield, quality, and resistance to biotic and abiotic stresses. A collection of 397 red clover accessions was genotyped using a pooled genotyping-by-sequencing approach with 200 plants per accession. Resistance to the two most pertinent diseases in red clover production, southern anthracnose caused by Colletotrichum trifolii, and clover rot caused by Sclerotinia trifoliorum, was assessed using spray inoculation. The mean survival rate for southern anthracnose was 22.9% and the mean resistance index for clover rot was 34.0%. Genome-wide association analysis revealed several loci significantly associated with resistance to southern anthracnose and clover rot. Most of these loci are in coding regions. One quantitative trait locus (QTL) on chromosome 1 explained 16.8% of the variation in resistance to southern anthracnose. For clover rot resistance we found eight QTL, explaining together 80.2% of the total phenotypic variation. The SNPs associated with these QTL provide a promising resource for marker-assisted selection in existing breeding programs, facilitating the development of novel cultivars with increased resistance against two devastating fungal diseases of red clover.
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Affiliation(s)
- Lea A Frey
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, 8092, Zurich, Switzerland
| | - Tim Vleugels
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Caritasstraat 39, 9090, Melle, Belgium
| | - Tom Ruttink
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Caritasstraat 39, 9090, Melle, Belgium
| | - Franz X Schubiger
- Agroscope, Plant Breeding, Reckenholzstrasse 191, 8046, Zurich, Switzerland
| | - Marie Pégard
- INRAE, Centre Nouvelle-Aquitaine-Poitiers, UR4 (UR P3F), 86600, Lusignan, France
| | - Leif Skøt
- Institute of Biological, Environmental & Rural Sciences, Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, SY23 3EE, UK
| | - Christoph Grieder
- Agroscope, Plant Breeding, Reckenholzstrasse 191, 8046, Zurich, Switzerland
| | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, 8092, Zurich, Switzerland
| | - Isabel Roldán-Ruiz
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Caritasstraat 39, 9090, Melle, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Roland Kölliker
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, 8092, Zurich, Switzerland.
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40
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Validation of a QTL on Chromosome 1DS Showing a Major Effect on Salt Tolerance in Winter Wheat. Int J Mol Sci 2022; 23:ijms232213745. [PMID: 36430224 PMCID: PMC9691212 DOI: 10.3390/ijms232213745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 10/28/2022] [Accepted: 11/04/2022] [Indexed: 11/11/2022] Open
Abstract
Salt stress is one the most destructive abiotic stressors, causing yield losses in wheat worldwide. A prerequisite for improving salt tolerance is the identification of traits for screening genotypes and uncovering causative genes. Two populations of F3 lines developed from crosses between sensitive and tolerant parents were tested for salt tolerance at the seedling stage. Based on their response, the offspring were classified as salt sensitive and tolerant. Under saline conditions, tolerant genotypes showed lower Na+ and proline content but higher K+, higher chlorophyll content, higher K+/Na+ ratio, higher PSII activity levels, and higher photochemical efficiency, and were selected for further molecular analysis. Five stress responsive QTL identified in a previous study were validated in the populations. A QTL on the short arm of chromosome 1D showed large allelic effects in several salt tolerant related traits. An expression analysis of associated candidate genes showed that TraesCS1D02G052200 and TraesCS5B02G368800 had the highest expression in most tissues. Furthermore, qRT-PCR expression analysis revealed that ZIP-7 had higher differential expressions under saline conditions compared to KefC, AtABC8 and 6-SFT. This study provides information on the genetic and molecular basis of salt tolerance that could be useful in development of salt-tolerant wheat varieties.
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Jaudal M, Mayo‐Smith M, Poulet A, Whibley A, Peng Y, Zhang L, Thomson G, Trimborn L, Jacob Y, van Wolfswinkel JC, Goldstone DC, Wen J, Mysore KS, Putterill J. MtING2 encodes an ING domain PHD finger protein which affects Medicago growth, flowering, global patterns of H3K4me3, and gene expression. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:1029-1050. [PMID: 36178149 PMCID: PMC9828230 DOI: 10.1111/tpj.15994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 09/04/2022] [Accepted: 09/24/2022] [Indexed: 06/16/2023]
Abstract
Flowering of the reference legume Medicago truncatula is promoted by winter cold (vernalization) followed by long-day photoperiods (VLD) similar to winter annual Arabidopsis. However, Medicago lacks FLC and CO, key regulators of Arabidopsis VLD flowering. Most plants have two INHIBITOR OF GROWTH (ING) genes (ING1 and ING2), encoding proteins with an ING domain with two anti-parallel alpha-helices and a plant homeodomain (PHD) finger, but their genetic role has not been previously described. In Medicago, Mting1 gene-edited mutants developed and flowered normally, but an Mting2-1 Tnt1 insertion mutant and gene-edited Mting2 mutants had developmental abnormalities including delayed flowering particularly in VLD, compact architecture, abnormal leaves with extra leaflets but no trichomes, and smaller seeds and barrels. Mting2 mutants had reduced expression of activators of flowering, including the FT-like gene MtFTa1, and increased expression of the candidate repressor MtTFL1c, consistent with the delayed flowering of the mutant. MtING2 overexpression complemented Mting2-1, but did not accelerate flowering in wild type. The MtING2 PHD finger bound H3K4me2/3 peptides weakly in vitro, but analysis of gene-edited mutants indicated that it was dispensable to MtING2 function in wild-type plants. RNA sequencing experiments indicated that >7000 genes are mis-expressed in the Mting2-1 mutant, consistent with its strong mutant phenotypes. Interestingly, ChIP-seq analysis identified >5000 novel H3K4me3 locations in the genome of Mting2-1 mutants compared to wild type R108. Overall, our mutant study has uncovered an important physiological role of a plant ING2 gene in development, flowering, and gene expression, which likely involves an epigenetic mechanism.
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Affiliation(s)
- Mauren Jaudal
- School of Biological SciencesUniversity of AucklandPrivate Bag 92019Auckland1142New Zealand
| | - Matthew Mayo‐Smith
- School of Biological SciencesUniversity of AucklandPrivate Bag 92019Auckland1142New Zealand
| | - Axel Poulet
- Yale UniversityDepartment of MolecularCellular and Developmental BiologyFaculty of Arts and Sciences260 Whitney AvenueNew HavenCT06511USA
| | - Annabel Whibley
- School of Biological SciencesUniversity of AucklandPrivate Bag 92019Auckland1142New Zealand
| | - Yongyan Peng
- School of Biological SciencesUniversity of AucklandPrivate Bag 92019Auckland1142New Zealand
| | - Lulu Zhang
- School of Biological SciencesUniversity of AucklandPrivate Bag 92019Auckland1142New Zealand
| | - Geoffrey Thomson
- School of Biological SciencesUniversity of AucklandPrivate Bag 92019Auckland1142New Zealand
- Yale UniversityDepartment of MolecularCellular and Developmental BiologyFaculty of Arts and Sciences260 Whitney AvenueNew HavenCT06511USA
| | - Laura Trimborn
- School of Biological SciencesUniversity of AucklandPrivate Bag 92019Auckland1142New Zealand
- Institute for Plant Sciences, BiocenterUniversity of CologneZülpicher Str. 47b50674CologneGermany
| | - Yannick Jacob
- Yale UniversityDepartment of MolecularCellular and Developmental BiologyFaculty of Arts and Sciences260 Whitney AvenueNew HavenCT06511USA
| | - Josien C. van Wolfswinkel
- Yale UniversityDepartment of MolecularCellular and Developmental BiologyFaculty of Arts and Sciences260 Whitney AvenueNew HavenCT06511USA
| | - David C. Goldstone
- School of Biological SciencesUniversity of AucklandPrivate Bag 92019Auckland1142New Zealand
| | - Jiangqi Wen
- Institute for Agricultural BiosciencesOklahoma State University3210 Sam Noble ParkwayArdmoreOK73401USA
| | - Kirankumar S. Mysore
- Institute for Agricultural BiosciencesOklahoma State University3210 Sam Noble ParkwayArdmoreOK73401USA
| | - Joanna Putterill
- School of Biological SciencesUniversity of AucklandPrivate Bag 92019Auckland1142New Zealand
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Li XR, Sun J, Albinsky D, Zarrabian D, Hull R, Lee T, Jarratt-Barnham E, Chiu CH, Jacobsen A, Soumpourou E, Albanese A, Kohlen W, Luginbuehl LH, Guillotin B, Lawrensen T, Lin H, Murray J, Wallington E, Harwood W, Choi J, Paszkowski U, Oldroyd GED. Nutrient regulation of lipochitooligosaccharide recognition in plants via NSP1 and NSP2. Nat Commun 2022; 13:6421. [PMID: 36307431 PMCID: PMC9616857 DOI: 10.1038/s41467-022-33908-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 10/07/2022] [Indexed: 12/25/2022] Open
Abstract
Many plants associate with arbuscular mycorrhizal fungi for nutrient acquisition, while legumes also associate with nitrogen-fixing rhizobial bacteria. Both associations rely on symbiosis signaling and here we show that cereals can perceive lipochitooligosaccharides (LCOs) for activation of symbiosis signaling, surprisingly including Nod factors produced by nitrogen-fixing bacteria. However, legumes show stringent perception of specifically decorated LCOs, that is absent in cereals. LCO perception in plants is activated by nutrient starvation, through transcriptional regulation of Nodulation Signaling Pathway (NSP)1 and NSP2. These transcription factors induce expression of an LCO receptor and act through the control of strigolactone biosynthesis and the karrikin-like receptor DWARF14-LIKE. We conclude that LCO production and perception is coordinately regulated by nutrient starvation to promote engagement with mycorrhizal fungi. Our work has implications for the use of both mycorrhizal and rhizobial associations for sustainable productivity in cereals.
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Affiliation(s)
- Xin-Ran Li
- grid.5335.00000000121885934Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge, CB2 1LR UK
| | - Jongho Sun
- grid.5335.00000000121885934Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge, CB2 1LR UK
| | - Doris Albinsky
- grid.5335.00000000121885934Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
| | - Darius Zarrabian
- grid.5335.00000000121885934Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
| | - Raphaella Hull
- grid.5335.00000000121885934Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
| | - Tak Lee
- grid.5335.00000000121885934Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge, CB2 1LR UK ,grid.5335.00000000121885934Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
| | - Edwin Jarratt-Barnham
- grid.5335.00000000121885934Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
| | - Chai Hao Chiu
- grid.5335.00000000121885934Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
| | - Amy Jacobsen
- grid.5335.00000000121885934Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
| | - Eleni Soumpourou
- grid.5335.00000000121885934Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
| | - Alessio Albanese
- grid.5335.00000000121885934Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
| | - Wouter Kohlen
- grid.4818.50000 0001 0791 5666Laboratory for Molecular Biology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
| | - Leonie H. Luginbuehl
- grid.14830.3e0000 0001 2175 7246John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Bruno Guillotin
- grid.503344.50000 0004 0445 6769Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Castanet-Tolosan, France ,grid.137628.90000 0004 1936 8753Present Address: NYU-Center of Genomic and System Biology, 12 Waverly Place, New York, NY USA
| | - Tom Lawrensen
- grid.14830.3e0000 0001 2175 7246John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Hui Lin
- grid.14830.3e0000 0001 2175 7246John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Jeremy Murray
- grid.14830.3e0000 0001 2175 7246John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Emma Wallington
- grid.17595.3f0000 0004 0383 6532NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
| | - Wendy Harwood
- grid.14830.3e0000 0001 2175 7246John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Jeongmin Choi
- grid.5335.00000000121885934Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
| | - Uta Paszkowski
- grid.5335.00000000121885934Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
| | - Giles E. D. Oldroyd
- grid.5335.00000000121885934Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge, CB2 1LR UK ,grid.5335.00000000121885934Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
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43
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Langella E, Di Fiore A, Alterio V, Monti SM, De Simone G, D’Ambrosio K. α-CAs from Photosynthetic Organisms. Int J Mol Sci 2022; 23:ijms231912045. [PMID: 36233343 PMCID: PMC9570166 DOI: 10.3390/ijms231912045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/19/2022] [Accepted: 09/26/2022] [Indexed: 11/17/2022] Open
Abstract
Carbonic anhydrases (CAs) are ubiquitous enzymes that catalyze the reversible carbon dioxide hydration reaction. Among the eight different CA classes existing in nature, the α-class is the largest one being present in animals, bacteria, protozoa, fungi, and photosynthetic organisms. Although many studies have been reported on these enzymes, few functional, biochemical, and structural data are currently available on α-CAs isolated from photosynthetic organisms. Here, we give an overview of the most recent literature on the topic. In higher plants, these enzymes are engaged in both supplying CO2 at the Rubisco and determining proton concentration in PSII membranes, while in algae and cyanobacteria they are involved in carbon-concentrating mechanism (CCM), photosynthetic reactions and in detecting or signaling changes in the CO2 level in the environment. Crystal structures are only available for three algal α-CAs, thus not allowing to associate specific structural features to cellular localizations or physiological roles. Therefore, further studies on α-CAs from photosynthetic organisms are strongly needed to provide insights into their structure–function relationship.
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Yang T, Liu R, Luo Y, Hu S, Wang D, Wang C, Pandey MK, Ge S, Xu Q, Li N, Li G, Huang Y, Saxena RK, Ji Y, Li M, Yan X, He Y, Liu Y, Wang X, Xiang C, Varshney RK, Ding H, Gao S, Zong X. Improved pea reference genome and pan-genome highlight genomic features and evolutionary characteristics. Nat Genet 2022; 54:1553-1563. [PMID: 36138232 PMCID: PMC9534762 DOI: 10.1038/s41588-022-01172-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 07/26/2022] [Indexed: 12/21/2022]
Abstract
Complete and accurate reference genomes and annotations provide fundamental resources for functional genomics and crop breeding. Here we report a de novo assembly and annotation of a pea cultivar ZW6 with contig N50 of 8.98 Mb, which features a 243-fold increase in contig length and evident improvements in the continuity and quality of sequence in complex repeat regions compared with the existing one. Genome diversity of 118 cultivated and wild pea demonstrated that Pisum abyssinicum is a separate species different from P. fulvum and P. sativum within Pisum. Quantitative trait locus analyses uncovered two known Mendel's genes related to stem length (Le/le) and seed shape (R/r) as well as some candidate genes for pod form studied by Mendel. A pan-genome of 116 pea accessions was constructed, and pan-genes preferred in P. abyssinicum and P. fulvum showed distinct functional enrichment, indicating the potential value of them as pea breeding resources in the future.
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Affiliation(s)
- Tao Yang
- National Key Facility for Crop Gene Resources and Genetic Improvement / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Rong Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yingfeng Luo
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Songnian Hu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Dong Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences / Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
| | - Chenyu Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Manish K Pandey
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Song Ge
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Quanle Xu
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Nana Li
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences / Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
- College of Life Science, Shandong Normal University, Jinan, China
| | - Guan Li
- National Key Facility for Crop Gene Resources and Genetic Improvement / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuning Huang
- National Key Facility for Crop Gene Resources and Genetic Improvement / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Rachit K Saxena
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Yishan Ji
- National Key Facility for Crop Gene Resources and Genetic Improvement / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mengwei Li
- National Key Facility for Crop Gene Resources and Genetic Improvement / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xin Yan
- National Key Facility for Crop Gene Resources and Genetic Improvement / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuhua He
- Institute of Grain Crops, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Yujiao Liu
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
- Qinghai Academy of Agricultural and Forestry Sciences, Xining, China
| | - Xuejun Wang
- Jiangsu Yanjiang Institute of Agricultural Sciences, Nantong, China
| | - Chao Xiang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Rajeev K Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
- Murdoch's Centre for Crop and Food Innovation, WA State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia.
| | - Hanfeng Ding
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences / Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China.
- College of Life Science, Shandong Normal University, Jinan, China.
| | - Shenghan Gao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
| | - Xuxiao Zong
- National Key Facility for Crop Gene Resources and Genetic Improvement / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
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45
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Ribeiro B, Erffelinck ML, Lacchini E, Ceulemans E, Colinas M, Williams C, Van Hamme E, De Clercq R, Perassolo M, Goossens A. Interference between ER stress-related bZIP-type and jasmonate-inducible bHLH-type transcription factors in the regulation of triterpene saponin biosynthesis in Medicago truncatula. FRONTIERS IN PLANT SCIENCE 2022; 13:903793. [PMID: 36247618 PMCID: PMC9562455 DOI: 10.3389/fpls.2022.903793] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 09/07/2022] [Indexed: 06/01/2023]
Abstract
Triterpene saponins (TS) are a structurally diverse group of metabolites that are widely distributed in plants. They primarily serve as defense compounds and their production is often triggered by biotic stresses through signaling cascades that are modulated by phytohormones such as the jasmonates (JA). Two JA-modulated basic helix-loop-helix (bHLH) transcription factors (TFs), triterpene saponin biosynthesis activating regulator 1 (TSAR1) and TSAR2, have previously been identified as direct activators of TS biosynthesis in the model legume Medicago truncatula. Here, we report on the involvement of the core endoplasmic reticulum (ER) stress-related basic leucine zipper (bZIP) TFs bZIP17 and bZIP60 in the regulation of TS biosynthesis. Expression and processing of M. truncatula bZIP17 and bZIP60 proteins were altered in roots with perturbed TS biosynthesis or treated with JA. Accordingly, such roots displayed an altered ER network structure. M. truncatula bZIP17 and bZIP60 proteins were shown to localize in the nucleus and appeared to be capable of interfering with the TSAR-mediated transactivation of TS biosynthesis genes. Furthermore, interference between ER stress-related bZIP and JA-modulated bHLH TFs in the regulation of JA-dependent terpene biosynthetic pathways may be widespread in the plant kingdom, as we demonstrate that it also occurs in the regulation of monoterpene indole alkaloid biosynthesis in the medicinal plant Catharanthus roseus.
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Affiliation(s)
- Bianca Ribeiro
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Marie-Laure Erffelinck
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Elia Lacchini
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Evi Ceulemans
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Maite Colinas
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Clara Williams
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | | | - Rebecca De Clercq
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Maria Perassolo
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Cátedra de Biotecnología, Departamento de Microbiología, Inmunología y Biotecnología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Nanobiotecnología (NANOBIOTEC), Consejo Nacional de Investigaciones Científicas y Técnicas-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Alain Goossens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
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46
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Deng C, Li CJ, Hsieh CY, Liu LY, Chen YA, Lin WY. MtNF-YC6 and MtNF-YC11 are involved in regulating the transcriptional program of arbuscular mycorrhizal symbiosis. FRONTIERS IN PLANT SCIENCE 2022; 13:976280. [PMID: 36247647 PMCID: PMC9554486 DOI: 10.3389/fpls.2022.976280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 09/06/2022] [Indexed: 06/16/2023]
Abstract
Arbuscular mycorrhizal fungi are obligate symbionts that transfer mineral nutrients to host plants through arbuscules, a fungal structure specialized for exchange for photosynthetic products. MtNF-YC6 and MtNF-YC11, which encode the C subunits of nuclear factor Y (NF-Y) family in Medicago truncatula are induced specifically by arbuscular mycorrhizal symbiosis (AMS). A previous study showed that MtNF-YC6 and MtNF-YC11 are activated in cortical cells of mycorrhizal roots, but the gene functions were unknown. Herein, we identified both MtNF-YB17 and MtNF-YB12 as the interacting partners of MtNF-YC6 and MtNF-YC11 in yeast and plants. MtNF-YB17 was highly induced by AMS and activated in cortical cells only in mycorrhizal roots but MtNF-YB12 was not affected. The formation of B/C heterodimers led the protein complexes to transfer from the cytoplasm to the nucleus. Silencing MtNF-YC6 and C11 by RNA interference (RNAi) resulted in decreased colonization efficiency and arbuscule richness. Coincidently, genes associated with arbuscule development and degeneration in RNAi roots were also downregulated. In silico analysis showed CCAAT-binding motifs in the promoter regions of downregulated genes, further supporting the involvement of NF-Y complexes in transcriptional regulation of symbiosis. Taken together, this study identifies MtNF-YC6- or MtNF-YC11-containing protein complexes as novel transcriptional regulators of symbiotic program and provides a list of potential downstream target genes. These data will help to further dissect the AMS regulatory network.
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Affiliation(s)
- Chen Deng
- Department of Horticulture and Landscape and Architecture, National Taiwan University, Taipei, Taiwan
| | - Chun-Jui Li
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
| | - Chen-Yun Hsieh
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
| | - Li-Yu Daisy Liu
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
| | - Yi-An Chen
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
| | - Wei-Yi Lin
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
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47
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Urra M, Buezo J, Royo B, Cornejo A, López-Gómez P, Cerdán D, Esteban R, Martínez-Merino V, Gogorcena Y, Tavladoraki P, Moran JF. The importance of the urea cycle and its relationships to polyamine metabolism during ammonium stress in Medicago truncatula. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:5581-5595. [PMID: 35608836 PMCID: PMC9467648 DOI: 10.1093/jxb/erac235] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 05/20/2022] [Indexed: 05/26/2023]
Abstract
The ornithine-urea cycle (urea cycle) makes a significant contribution to the metabolic responses of lower photosynthetic eukaryotes to episodes of high nitrogen availability. In this study, we compared the role of the plant urea cycle and its relationships to polyamine metabolism in ammonium-fed and nitrate-fed Medicago truncatula plants. High ammonium resulted in the accumulation of ammonium and pathway intermediates, particularly glutamine, arginine, ornithine, and putrescine. Arginine decarboxylase activity was decreased in roots, suggesting that the ornithine decarboxylase-dependent production of putrescine was important in situations of ammonium stress. The activity of copper amine oxidase, which releases ammonium from putrescine, was significantly decreased in both shoots and roots. In addition, physiological concentrations of ammonium inhibited copper amine oxidase activity in in vitro assays, supporting the conclusion that high ammonium accumulation favors putrescine synthesis. Moreover, early supplementation of plants with putrescine avoided ammonium toxicity. The levels of transcripts encoding urea-cycle-related proteins were increased and transcripts involved in polyamine catabolism were decreased under high ammonium concentrations. We conclude that the urea cycle and associated polyamine metabolism function as important protective mechanisms limiting ammonium toxicity in M. truncatula. These findings demonstrate the relevance of the urea cycle to polyamine metabolism in higher plants.
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Affiliation(s)
- Marina Urra
- Present address: Department of Forest Engineering, Forest Management Planning and Terrestrial Measurements, University of Transilvania, 1, Ludwig van Beethoven Str., 500123 Brașov, Romania
| | - Javier Buezo
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Department of Sciences, Public University of Navarre (UPNA), Avda. de Pamplona 123, 31192 Mutilva, Spain
| | - Beatriz Royo
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Department of Sciences, Public University of Navarre (UPNA), Avda. de Pamplona 123, 31192 Mutilva, Spain
| | - Alfonso Cornejo
- Institute for Advanced Materials and Mathematics (INAMAT2), Department of Sciences, Public University of Navarre (UPNA), Campus de Arrosadía, 31006 Pamplona, Spain
| | - Pedro López-Gómez
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Department of Sciences, Public University of Navarre (UPNA), Avda. de Pamplona 123, 31192 Mutilva, Spain
| | - Daniel Cerdán
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Department of Sciences, Public University of Navarre (UPNA), Avda. de Pamplona 123, 31192 Mutilva, Spain
| | - Raquel Esteban
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), Sarriena s/n, Apdo. 644, 48080 Bilbao, Spain
| | - Víctor Martínez-Merino
- Institute for Advanced Materials and Mathematics (INAMAT2), Department of Sciences, Public University of Navarre (UPNA), Campus de Arrosadía, 31006 Pamplona, Spain
| | - Yolanda Gogorcena
- Department of Pomology, Aula Dei Experimental Station, Consejo Superior de Investigaciones Científicas (CSIC), Avda. de Montañana 1005, 50059 Zaragoza, Spain
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48
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Zhang X, Sun Y, Qiu X, Lu H, Hwang I, Wang T. Tolerant mechanism of model legume plant Medicago truncatula to drought, salt, and cold stresses. FRONTIERS IN PLANT SCIENCE 2022; 13:847166. [PMID: 36160994 PMCID: PMC9490062 DOI: 10.3389/fpls.2022.847166] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Accepted: 08/15/2022] [Indexed: 06/16/2023]
Abstract
Legume plants produce one-third of the total yield of primary crops and are important food sources for both humans and animals worldwide. Frequent exposure to abiotic stresses, such as drought, salt, and cold, greatly limits the production of legume crops. Several morphological, physiological, and molecular studies have been conducted to characterize the response and adaptation mechanism to abiotic stresses. The tolerant mechanisms of the model legume plant Medicago truncatula to abiotic stresses have been extensively studied. Although many potential genes and integrated networks underlying the M. truncatula in responding to abiotic stresses have been identified and described, a comprehensive summary of the tolerant mechanism is lacking. In this review, we provide a comprehensive summary of the adaptive mechanism by which M. truncatula responds to drought, salt, and cold stress. We also discuss future research that need to be explored to improve the abiotic tolerance of legume plants.
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Affiliation(s)
- Xiuxiu Zhang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciencess, Beijing, China
| | - Yu Sun
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciencess, Changchun, China
| | - Xiao Qiu
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Hai Lu
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Inhwan Hwang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, South Korea
| | - Tianzuo Wang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciencess, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
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49
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Alvarez-Rivera G, Sanz A, Cifuentes A, Ibánez E, Paape T, Lucas MM, Pueyo JJ. Flavonoid Accumulation Varies in Medicago truncatula in Response to Mercury Stress. FRONTIERS IN PLANT SCIENCE 2022; 13:933209. [PMID: 35874019 PMCID: PMC9301243 DOI: 10.3389/fpls.2022.933209] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 06/21/2022] [Indexed: 06/15/2023]
Abstract
Mercury (Hg) contamination is increasing worldwide in both wild ecosystems and agricultural soils due to natural processes, but mostly to anthropic activities. The molecular mechanisms involved in Hg toxicity and tolerance in plants have been extensively studied; however, the role of flavonoids in response to Hg stress remains to be investigated. We conducted a metabolomic study to analyze the changes induced at the secondary metabolite level in three Hg-tolerant and one Hg-sensitive Medicago truncatula cultivars. A total of 46 flavonoid compounds, classified into five different flavonoid families: anthocyanidins, flavones, isoflavones, pterocarpan flavonoids, and flavanones, along with their respective glycoconjugate derivatives, were identified in leaf and root tissues. The synthesis of free isoflavones, followed by monoglycosylation and further malonylation was shown to be characteristic of root samples, whereas higher glycosylation, followed by further acylation with coumaric and ferulic acid was characteristic of leaf tissues. While minor changes were observed in leaves, significant quantitative changes could be observed in roots upon Hg treatment. Some flavonoids were strongly upregulated in roots, including malonylglucosides of biochanin A, formononetin and medicarpin, and aglycones biochanin, daidzein, and irisolidone. Hg tolerance appeared to be mainly associated to the accumulation of formononetin MalGlc, tricin GlcAGlcA, and afrormosin Glc II in leaves, whereas aglycone accumulation was associated with tolerance to Hg stress in roots. The results evidence the alteration of the flavonoid metabolic profile and their glycosylation processes in response to Hg stress. However, notable differences existed between varieties, both in the basal metabolic profile and in the response to treatment with Hg. Overall, we observed an increase in flavonoid production in response to Hg stress, and Hg tolerance appeared to be associated to a characteristic glycosylation pattern in roots, associated with the accumulation of aglycones and monoglycosylated flavonoids. The findings are discussed in the context of the flavonoid biosynthetic pathway to provide a better understanding of the role of these secondary metabolites in the response and tolerance to Hg stress in M. truncatula.
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Affiliation(s)
| | - Aurora Sanz
- Institute of Agricultural Sciences, ICA-CSIC, Madrid, Spain
| | - Alejandro Cifuentes
- Laboratory of Foodomics, CIAL-CSIC, Institute of Food Science Research, Madrid, Spain
| | - Elena Ibánez
- Laboratory of Foodomics, CIAL-CSIC, Institute of Food Science Research, Madrid, Spain
| | - Timothy Paape
- Brookhaven National Laboratory, Upton, NY, United States
| | | | - José J. Pueyo
- Institute of Agricultural Sciences, ICA-CSIC, Madrid, Spain
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50
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Cheng X, Xie H, Zhang K, Wen J. Enabling Medicago truncatula forward genetics: identification of genetic crossing partner for R108 and development of mapping resources for Tnt1 mutants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:608-616. [PMID: 35510429 DOI: 10.1111/tpj.15797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/19/2022] [Accepted: 05/01/2022] [Indexed: 06/14/2023]
Abstract
Though Medicago truncatula Tnt1 mutants are widely used by researchers in the legume community, they are mainly used for reverse genetics because of the availability of the BLAST-searchable large-scale flanking sequence tags database. However, these mutants should have also been used extensively for forward genetic screens, an effort that has been hindered due to the lack of a compatible genetic crossing partner for the M. truncatula genotype R108, from which Tnt1 mutants were generated. In this study, we selected three Medicago HapMap lines (HM017, HM018 and HM022) and performed reciprocal genetic crosses with R108. After phenotypic analyses in F1 and F2 progenies, HM017 was identified as a compatible crossing partner with R108. By comparing the assembled genomic sequences of HM017 and R108, we developed and confirmed 318 Indel markers evenly distributed across the eight chromosomes of the M. truncatula genome. To validate the effectiveness of these markers, by employing the map-based cloning approach, we cloned the causative gene in the dwarf mutant crs isolated from the Tnt1 mutant population, identifying it as gibberellin 3-β-dioxygenase 1, using some of the confirmed Indel markers. The primer sequences and the size difference of each marker were made available for users in the web-based database. The identification of the crossing partner for R108 and the generation of Indel markers will enhance the forward genetics and the overall usage of the Tnt1 mutants.
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Affiliation(s)
- Xiaofei Cheng
- Noble Research Institute, LLC, Ardmore, OK, 73401, USA
| | - Hongli Xie
- 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, Shandong, 266109, China
| | - Kuihua Zhang
- Noble Research Institute, LLC, Ardmore, OK, 73401, USA
| | - Jiangqi Wen
- Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, OK, 74078, USA
- Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, OK, 73401, USA
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