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Chen B, Shi Y, Sun Y, Lu L, Wang L, Liu Z, Cheng S. Innovations in functional genomics and molecular breeding of pea: exploring advances and opportunities. ABIOTECH 2024; 5:71-93. [PMID: 38576433 PMCID: PMC10987475 DOI: 10.1007/s42994-023-00129-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 12/05/2023] [Indexed: 04/06/2024]
Abstract
The garden pea (Pisum sativum L.) is a significant cool-season legume, serving as crucial food sources, animal feed, and industrial raw materials. The advancement of functional genomics over the past two decades has provided substantial theoretical foundations and progress to pea breeding. Notably, the release of the pea reference genome has enhanced our understanding of plant architecture, symbiotic nitrogen fixation (SNF), flowering time, floral organ development, seed development, and stress resistance. However, a considerable gap remains between pea functional genomics and molecular breeding. This review summarizes the current advancements in pea functional genomics and breeding while highlighting the future challenges in pea molecular breeding.
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Affiliation(s)
- Baizhi Chen
- Agricultural Genomics Institute at Shenzhen (AGIS), Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
| | - Yan Shi
- Agricultural Genomics Institute at Shenzhen (AGIS), Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
| | - Yuchen Sun
- Agricultural Genomics Institute at Shenzhen (AGIS), Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
| | - Lu Lu
- Agricultural Genomics Institute at Shenzhen (AGIS), Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
| | - Luyao Wang
- Agricultural Genomics Institute at Shenzhen (AGIS), Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
| | - Zijian Liu
- Agricultural Genomics Institute at Shenzhen (AGIS), Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
| | - Shifeng Cheng
- Agricultural Genomics Institute at Shenzhen (AGIS), Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
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2
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Liu S, Magne K, Zhou J, Laude J, Dalmais M, Le Signor C, Bendahmane A, Thompson R, Couzigou JM, Ratet P. The transcriptional co-regulators NBCL1 and NBCL2 redundantly coordinate aerial organ development and root nodule identity in legumes. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:194-213. [PMID: 36197099 DOI: 10.1093/jxb/erac389] [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: 05/26/2022] [Accepted: 10/03/2022] [Indexed: 06/16/2023]
Abstract
Medicago truncatula NODULE ROOT1 (MtNOOT1) and Pisum sativum COCHLEATA1 (PsCOCH1) are orthologous genes belonging to the NOOT-BOP-COCH-LIKE (NBCL) gene family which encodes key transcriptional co-regulators of plant development. In Mtnoot1 and Pscoch1 mutants, the development of stipules, flowers, and symbiotic nodules is altered. MtNOOT2 and PsCOCH2 represent the single paralogues of MtNOOT1 and PsCOCH1, respectively. In M. truncatula, MtNOOT1 and MtNOOT2 are both required for the establishment and maintenance of symbiotic nodule identity. In legumes, the role of NBCL2 in above-ground development is not known. To better understand the roles of NBCL genes in legumes, we used M. truncatula and P. sativum nbcl mutants, isolated a knockout mutant for the PsCOCH2 locus and generated Pscoch1coch2 double mutants in P. sativum. Our work shows that single Mtnoot2 and Pscoch2 mutants develop wild-type stipules, flowers, and symbiotic nodules. However, the number of flowers was increased and the pods and seeds were smaller compared to the wild type. Furthermore, in comparison to the corresponding nbcl1 single mutants, both the M. truncatula and P. sativum nbcl double mutants show a drastic alteration in stipule, inflorescence, flower, and nodule development. Remarkably, in both M. truncatula and P. sativum nbcl double mutants, stipules are transformed into a range of aberrant leaf-like structures.
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Affiliation(s)
- Shengbin Liu
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190, Gif sur Yvette, France
- Institute of Plant Sciences Paris-Saclay (IPS2), Université de Paris, 91190, Gif sur Yvette, France
| | - Kévin Magne
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190, Gif sur Yvette, France
- Institute of Plant Sciences Paris-Saclay (IPS2), Université de Paris, 91190, Gif sur Yvette, France
| | - Jing Zhou
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse INP, 31320, Auzeville Tolosane, France
| | - Juliette Laude
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190, Gif sur Yvette, France
- Institute of Plant Sciences Paris-Saclay (IPS2), Université de Paris, 91190, Gif sur Yvette, France
| | - Marion Dalmais
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190, Gif sur Yvette, France
- Institute of Plant Sciences Paris-Saclay (IPS2), Université de Paris, 91190, Gif sur Yvette, France
| | - Christine Le Signor
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique (INRAE), Université Bourgogne Franche-Comté, 21000, Dijon, France
| | - Abdelhafid Bendahmane
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190, Gif sur Yvette, France
- Institute of Plant Sciences Paris-Saclay (IPS2), Université de Paris, 91190, Gif sur Yvette, France
| | - Richard Thompson
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique (INRAE), Université Bourgogne Franche-Comté, 21000, Dijon, France
| | - Jean-Malo Couzigou
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse INP, 31320, Auzeville Tolosane, France
| | - Pascal Ratet
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190, Gif sur Yvette, France
- Institute of Plant Sciences Paris-Saclay (IPS2), Université de Paris, 91190, Gif sur Yvette, France
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3
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Lebedeva M, Azarakhsh M, Sadikova D, Lutova L. At the Root of Nodule Organogenesis: Conserved Regulatory Pathways Recruited by Rhizobia. PLANTS (BASEL, SWITZERLAND) 2021; 10:2654. [PMID: 34961125 PMCID: PMC8705049 DOI: 10.3390/plants10122654] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 11/28/2021] [Accepted: 11/30/2021] [Indexed: 05/13/2023]
Abstract
The interaction between legume plants and soil bacteria rhizobia results in the formation of new organs on the plant roots, symbiotic nodules, where rhizobia fix atmospheric nitrogen. Symbiotic nodules represent a perfect model to trace how the pre-existing regulatory pathways have been recruited and modified to control the development of evolutionary "new" organs. In particular, genes involved in the early stages of lateral root development have been co-opted to regulate nodule development. Other regulatory pathways, including the players of the KNOX-cytokinin module, the homologues of the miR172-AP2 module, and the players of the systemic response to nutrient availability, have also been recruited to a unique regulatory program effectively governing symbiotic nodule development. The role of the NIN transcription factor in the recruitment of such regulatory modules to nodulation is discussed in more details.
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Affiliation(s)
- Maria Lebedeva
- Department of Genetics and Biotechnology, Saint Petersburg State University, Universitetskaya emb.7/9, 199034 Saint Petersburg, Russia; (D.S.); (L.L.)
- Center for Genetic Technologies, N. I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), 190000 Saint Petersburg, Russia
| | - Mahboobeh Azarakhsh
- Cell and Molecular Biology Department, Kosar University of Bojnord, 9415615458 Bojnord, Iran;
| | - Darina Sadikova
- Department of Genetics and Biotechnology, Saint Petersburg State University, Universitetskaya emb.7/9, 199034 Saint Petersburg, Russia; (D.S.); (L.L.)
- Center for Genetic Technologies, N. I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), 190000 Saint Petersburg, Russia
| | - Lyudmila Lutova
- Department of Genetics and Biotechnology, Saint Petersburg State University, Universitetskaya emb.7/9, 199034 Saint Petersburg, Russia; (D.S.); (L.L.)
- Center for Genetic Technologies, N. I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), 190000 Saint Petersburg, Russia
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Tsyganov VE, Tsyganova AV. Symbiotic Regulatory Genes Controlling Nodule Development in Pisum sativum L. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1741. [PMID: 33317178 PMCID: PMC7764586 DOI: 10.3390/plants9121741] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/03/2020] [Accepted: 12/07/2020] [Indexed: 02/07/2023]
Abstract
Analyses of natural variation and the use of mutagenesis and molecular-biological approaches have revealed 50 symbiotic regulatory genes in pea (Pisum sativum L.). Studies of genomic synteny using model legumes, such as Medicago truncatula Gaertn. and Lotus japonicus (Regel) K. Larsen, have identified the sequences of 15 symbiotic regulatory genes in pea. These genes encode receptor kinases, an ion channel, a calcium/calmodulin-dependent protein kinase, transcription factors, a metal transporter, and an enzyme. This review summarizes and describes mutant alleles, their phenotypic manifestations, and the functions of all identified symbiotic regulatory genes in pea. Some examples of gene interactions are also given. In the review, all mutant alleles in genes with identified sequences are designated and still-unidentified symbiotic regulatory genes of great interest are considered. The identification of these genes will help elucidate additional components involved in infection thread growth, nodule primordium development, bacteroid differentiation and maintenance, and the autoregulation of nodulation. The significance of symbiotic mutants of pea as extremely fruitful genetic models for studying nodule development and for comparative cell biology studies of legume nodules is clearly demonstrated. Finally, it is noted that many more sequences of symbiotic regulatory genes remain to be identified. Transcriptomics approaches and genome-wide sequencing could help address this challenge.
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Affiliation(s)
- Viktor E. Tsyganov
- Laboratory of Molecular and Cellular Biology, All-Russia Research Institute for Agricultural Microbiology, Podbelsky Chaussee 3, Pushkin 8, 196608 Saint Petersburg, Russia;
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Lin J, Frank M, Reid D. No Home without Hormones: How Plant Hormones Control Legume Nodule Organogenesis. PLANT COMMUNICATIONS 2020; 1:100104. [PMID: 33367261 PMCID: PMC7747975 DOI: 10.1016/j.xplc.2020.100104] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 08/19/2020] [Accepted: 08/20/2020] [Indexed: 05/08/2023]
Abstract
The establishment of symbiotic nitrogen fixation requires the coordination of both nodule development and infection events. Despite the evolution of a variety of anatomical structures, nodule organs serve a common purpose in establishing a localized area that facilitates efficient nitrogen fixation. As in all plant developmental processes, the establishment of a new nodule organ is regulated by plant hormones. During nodule initiation, regulation of plant hormone signaling is one of the major targets of symbiotic signaling. We review the role of major developmental hormones in the initiation of the nodule organ and argue that the manipulation of plant hormones is a key requirement for engineering nitrogen fixation in non-legumes as the basis for improved food security and sustainability.
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Affiliation(s)
- Jieshun Lin
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Manuel Frank
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Dugald Reid
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
- Corresponding author
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Lei Y, Su S, He L, Hu X, Luo D. A member of the ALOG gene family has a novel role in regulating nodulation in Lotus japonicus. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:463-477. [PMID: 30129698 DOI: 10.1111/jipb.12711] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 08/19/2018] [Indexed: 06/08/2023]
Abstract
Legumes can control the number of symbiotic nodules that form on their roots, thus balancing nitrogen assimilation and energy consumption. Two major pathways participate in nodulation: the Nod factor (NF) signaling pathway which involves recognition of rhizobial bacteria by root cells and promotion of nodulation, and the autoregulation of nodulation (AON) pathway which involves long-distance negative feedback between roots and shoots. Although a handful of genes have a clear role in the maintenance of nodule number, additional unknown factors may also be involved in this process. Here, we identify a novel function for a Lotus japonicus ALOG (Arabidopsis LSH1 and Oryza G1) family member, LjALOG1, involved in positively regulating nodulation. LjALOG1 expression increased substantially after inoculation with rhizobia, with high levels of expression in whole nodule primordia and in the base of developing nodules. The ljalog1 mutants, which have an insertion of the LORE1 retroelement in LjALOG1, had significantly fewer nodules compared with wild type, along with increased expression of LjCLE-RS1 (L. japonicus CLE Root Signal 1), which encodes a nodulation suppressor in the AON pathway. In summary, our findings identified a novel factor that participates in controlling nodulation, possibly by suppressing the AON pathway.
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Affiliation(s)
- Yawen Lei
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Shihao Su
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Liang He
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Xiaohe Hu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Da Luo
- 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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Aggarwal PR, Nag P, Choudhary P, Chakraborty N, Chakraborty S. Genotype-independent Agrobacterium rhizogenes-mediated root transformation of chickpea: a rapid and efficient method for reverse genetics studies. PLANT METHODS 2018; 14:55. [PMID: 29988950 PMCID: PMC6034309 DOI: 10.1186/s13007-018-0315-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 06/02/2018] [Indexed: 05/29/2023]
Abstract
BACKGROUND Chickpea (Cicer arietinum L.), an important legume crop is one of the major source of dietary protein. Developing an efficient and reproducible transformation method is imperative to expedite functional genomics studies in this crop. Here, we present an optimized and detailed procedure for Agrobacterium rhizogenes-mediated root transformation of chickpea. RESULTS Transformation positive roots were obtained on selection medium after two weeks of A. rhizogenes inoculation. Expression of green fluorescent protein further confirmed the success of transformation. We demonstrate that our method adequately transforms chickpea roots at early developmental stage with high efficiency. In addition, root transformation was found to be genotype-independent and the efficacy of our protocol was highest in two (Annigiri and JG-62) of the seven tested chickpea genotypes. Next, we present the functional analysis of chickpea hairy roots by expressing Arabidopsis TRANSPARENT TESTA 2 (AtTT2) gene involved in proanthocyanidins biosynthesis. Overexpression of AtTT2 enhanced the level of proanthocyanidins in hairy roots that led to the decreased colonization of fungal pathogen, Fusarium oxysporum. Furthermore, the induction of transgenic roots does not affect functional studies involving infection of roots by fungal pathogen. CONCLUSIONS Transgenic roots expressing genes of interest will be useful in downstream functional characterization using reverse genetics studies. It requires 1 day to perform the root transformation protocol described in this study and the roots expressing transgene can be maintained for 3-4 weeks, providing sufficient time for further functional studies. Overall, the current methodology will greatly facilitate the functional genomics analyses of candidate genes in root-rhizosphere interaction in this recalcitrant but economically important legume crop.
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Affiliation(s)
- Pooja Rani Aggarwal
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067 India
| | - Papri Nag
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067 India
| | - Pooja Choudhary
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067 India
| | - Niranjan Chakraborty
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067 India
| | - Subhra Chakraborty
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067 India
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Magne K, George J, Berbel Tornero A, Broquet B, Madueño F, Andersen SU, Ratet P. Lotus japonicus NOOT-BOP-COCH-LIKE1 is essential for nodule, nectary, leaf and flower development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 94:880-894. [PMID: 29570881 DOI: 10.1111/tpj.13905] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 02/15/2018] [Accepted: 03/08/2018] [Indexed: 05/26/2023]
Abstract
The NOOT-BOP-COCH-LIKE (NBCL) genes are orthologs of Arabidopsis thaliana BLADE-ON-PETIOLE1/2. The NBCLs are developmental regulators essential for plant shaping, mainly through the regulation of organ boundaries, the promotion of lateral organ differentiation and the acquisition of organ identity. In addition to their roles in leaf, stipule and flower development, NBCLs are required for maintaining the identity of indeterminate nitrogen-fixing nodules with persistent meristems in legumes. In legumes forming determinate nodules, without persistent meristem, the roles of NBCL genes are not known. We thus investigated the role of Lotus japonicus NOOT-BOP-COCH-LIKE1 (LjNBCL1) in determinate nodule identity and studied its functions in aerial organ development using LORE1 insertional mutants and RNA interference-mediated silencing approaches. In Lotus, LjNBCL1 is involved in leaf patterning and participates in the regulation of axillary outgrowth. Wild-type Lotus leaves are composed of five leaflets and possess a pair of nectaries at the leaf axil. Legumes such as pea and Medicago have a pair of stipules, rather than nectaries, at the base of their leaves. In Ljnbcl1, nectary development is abolished, demonstrating that nectaries and stipules share a common evolutionary origin. In addition, ectopic roots arising from nodule vascular meristems and reorganization of the nodule vascular bundle vessels were observed on Ljnbcl1 nodules. This demonstrates that NBCL functions are conserved in both indeterminate and determinate nodules through the maintenance of nodule vascular bundle identity. In contrast to its role in floral patterning described in other plants, LjNBCL1 appears essential for the development of both secondary inflorescence meristem and floral meristem.
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Affiliation(s)
- Kévin Magne
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, 91405, Orsay, France
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405, Orsay, France
| | - Jeoffrey George
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, 91405, Orsay, France
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405, Orsay, France
| | - Ana Berbel Tornero
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV, Universidad Politécnica de Valencia, CPI Edificio 8E, Avenida de los Naranjos s/n, Valencia, 46022, Spain
| | - Blandine Broquet
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, 91405, Orsay, France
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405, Orsay, France
| | - Francisco Madueño
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV, Universidad Politécnica de Valencia, CPI Edificio 8E, Avenida de los Naranjos s/n, Valencia, 46022, Spain
| | - Stig U Andersen
- Department of Molecular Biology and Genetics, Centre for Carbohydrate Recognition and Signaling, Aarhus University, Gustav Wieds Vej 10, Aarhus C, DK-8000, Denmark
| | - Pascal Ratet
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, 91405, Orsay, France
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405, Orsay, France
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Mirzaei S, Batley J, El-Mellouki T, Liu S, Meksem K, Ferguson BJ, Gresshoff PM. Neodiversification of homeologous CLAVATA1-like receptor kinase genes in soybean leads to distinct developmental outcomes. Sci Rep 2017; 7:8878. [PMID: 28827708 PMCID: PMC5566472 DOI: 10.1038/s41598-017-08252-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 06/29/2017] [Indexed: 11/09/2022] Open
Abstract
The CLAVATA pathway that regulates stem cell numbers of the shoot apical meristem has exclusively been studied in Arabidopsis; as such insight into other species is warranted. In this study, a GmCLV1A mutant (F-S562L) with altered lateral organ development, and two mutants of GmNARK, isolated from a Forrest M2 population (EMS-mutated soybean) were studied. GmCLV1A and GmNARK encode for LRR receptor kinases, and share 92% of protein sequence. While GmNARK is critical for systemic regulation of nodulation (new organ made on the root through symbiosis), we show that GmCLV1A functions locally and has no apparent function in nodulation or root development. However, a recessive, loss-of-function mutation (S562L) in a putative S-glycosylation site of GmCLV1A causes stem nodal identity alterations as well as flower and pod abnormalities (deformed flower and pod). The mutant also exhibits a homeotic phenotype, displaying abnormal leaf development/number, vein-derived leaf emergence, and a thick, faciated stem. The mutant phenotype is also temperature-sensitive. Interestingly, a novel truncated version of GmCLV1A was identified upstream of GmCLV1A that is absent from GmNARK, but is present upstream of the GmNARK orthologues, MtSUNN and PvNARK. Taken together, our findings indicate that GmCLV1A acts on shoot architecture, whereas GmNARK, functions in controlling nodule numbers.
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Affiliation(s)
- Saeid Mirzaei
- Centre for Integrative Legume Research, School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia
- Department of Biotechnology, Institute of Science, High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran
| | - Jacqueline Batley
- School of Biological Sciences, University of Western Australia, Crawley, WA, 6009, Australia
| | - Tarik El-Mellouki
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, 62901, USA
| | - Shiming Liu
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, 62901, USA
| | - Khalid Meksem
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, 62901, USA
| | - Brett J Ferguson
- Centre for Integrative Legume Research, School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia
| | - Peter M Gresshoff
- Centre for Integrative Legume Research, School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia.
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Khan M, Xu H, Hepworth SR. BLADE-ON-PETIOLE genes: setting boundaries in development and defense. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2014; 215-216:157-71. [PMID: 24388527 DOI: 10.1016/j.plantsci.2013.10.019] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 10/19/2013] [Accepted: 10/31/2013] [Indexed: 05/19/2023]
Abstract
BLADE-ON-PETIOLE (BOP) genes encode an ancient and conserved subclade of BTB-ankryin transcriptional co-activators, divergent in the NPR1 family of plant defense regulators. Arabidopsis BOP1/2 were originally characterized as regulators of leaf and floral patterning. Recent investigation of BOP activity in a variety of land plants provides a more complete picture of their conserved functions at lateral organ boundaries in the determination of leaf, flower, inflorescence, and root nodule architecture. BOPs exert their function in part through promotion of lateral organ boundary genes including ASYMMETRIC LEAVES2, KNOTTED1-LIKE FROM ARABIDOPSIS6, and ARABIDOPSIS THALIANA HOMEOBOX GENE1 whose products restrict growth, promote differentiation, and antagonize meristem activity in various developmental contexts. Mutually antagonistic interactions between BOP and meristem factors are important in maintaining a border between meristem-organ compartments and in controlling irreversible transitions in cell fate associated with differentiation. We also examine intriguing new evidence for BOP function in plant defense. Comparisons to NPR1 highlight previously unexplored mechanisms for co-ordination of development and defense in land plants.
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Affiliation(s)
- Madiha Khan
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, Canada K1S 5B6
| | - Huasong Xu
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, Canada K1S 5B6
| | - Shelley R Hepworth
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, Canada K1S 5B6.
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11
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Couzigou JM, Mondy S, Sahl L, Gourion B, Ratet P. To be or noot to be: evolutionary tinkering for symbiotic organ identity. PLANT SIGNALING & BEHAVIOR 2013; 8:e24969. [PMID: 23733067 PMCID: PMC4004616 DOI: 10.4161/psb.24969] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 05/07/2013] [Indexed: 05/02/2023]
Abstract
Legume plants develop symbiosis specific organs on their roots as a result of their interaction with rhizobia. These organs, called nodules, house the nitrogen fixing bacteria. The molecular mechanisms governing the identity and maintenance of this organ are still poorly understood, but it is supposed that root and nodule development share common features. We have identified the Medicago truncatula nodule root (NOOT) and Pisum sativum cochleata (COCH) orthologous genes as necessary for the robust maintenance of nodule identity throughout the nodule developmental program. NOOT and COCH are Arabidopsis blade-on-petiole (BOP) orthologs and NOOT and COCH show functions in leaf and flower development in M. truncatula and P. sativum respectively that are conserved with the functions of BOP in Arabidopsis. The characterization of the noot and coch mutants highlights the root evolutionary origin of nodule vascular strands and suggests that the NOOT and COCH genes were recruited to repress root identity in the legume symbiotic organ.
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Affiliation(s)
- Jean-Malo Couzigou
- Institut des Sciences du Végétal; CNRS; Gif sur Yvette Cedex, France
- Laboratoire de Recherche en Sciences Végétales; Université Paul Sabatier CNRS; Castanet Tolosan, France
| | - Samuel Mondy
- Institut des Sciences du Végétal; CNRS; Gif sur Yvette Cedex, France
| | - Lucien Sahl
- Institut des Sciences du Végétal; CNRS; Gif sur Yvette Cedex, France
| | - Benjamin Gourion
- Institut des Sciences du Végétal; CNRS; Gif sur Yvette Cedex, France
| | - Pascal Ratet
- Institut des Sciences du Végétal; CNRS; Gif sur Yvette Cedex, France
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cell- and tissue-specific transcriptome analyses of Medicago truncatula root nodules. PLoS One 2013; 8:e64377. [PMID: 23734198 PMCID: PMC3667139 DOI: 10.1371/journal.pone.0064377] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 04/12/2013] [Indexed: 11/25/2022] Open
Abstract
Legumes have the unique ability to host nitrogen-fixing Rhizobium bacteria as symbiosomes inside root nodule cells. To get insight into this key process, which forms the heart of the endosymbiosis, we isolated specific cells/tissues at different stages of symbiosome formation from nodules of the model legume Medicago truncatula using laser-capture microdissection. Next, we determined their associated expression profiles using Affymetrix Medicago GeneChips. Cells were collected from the nodule infection zone divided into a distal (where symbiosome formation and division occur) and proximal region (where symbiosomes are mainly differentiating), as well as infected cells from the fixation zone containing mature nitrogen fixing symbiosomes. As non-infected cells/tissue we included nodule meristem cells and uninfected cells from the fixation zone. Here, we present a comprehensive gene expression map of an indeterminate Medicago nodule and selected genes that show specific enriched expression in the different cells or tissues. Validation of the obtained expression profiles, by comparison to published gene expression profiles and experimental verification, indicates that the data can be used as digital “in situ”. This digital “in situ” offers a genome-wide insight into genes specifically associated with subsequent stages of symbiosome and nodule cell development, and can serve to guide future functional studies.
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Łotocka B, Kopcińska J, Skalniak M. Review article: The meristem in indeterminate root nodules of Faboideae. Symbiosis 2012; 58:63-72. [PMID: 23482442 PMCID: PMC3589660 DOI: 10.1007/s13199-013-0225-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2012] [Accepted: 01/14/2013] [Indexed: 11/30/2022]
Abstract
In this review, the anatomy of indeterminate legume root nodule is briefly summarized. Next, the indeterminate nodule meristem activity, organization and cell ultrastructure are described in species with a distinct nodule meristem zonation. Finally, the putative primary endogenous factors controlling nodule meristem maintenance are discussed in the context of the well-studied root apical meristem (RAM) of Arabidopsis thaliana.
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Affiliation(s)
- Barbara Łotocka
- Department of Botany, Faculty of Agriculture and Biology, Warsaw University of Life Sciences – SGGW, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Joanna Kopcińska
- Department of Botany, Faculty of Agriculture and Biology, Warsaw University of Life Sciences – SGGW, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Monika Skalniak
- Department of Botany, Faculty of Agriculture and Biology, Warsaw University of Life Sciences – SGGW, Nowoursynowska 159, 02-776 Warsaw, Poland
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Osipova MA, Dolgikh EA, Lutova LA. Peculiarities of meristem-specific WOX5 gene expression during nodule organogenesis in legumes. Russ J Dev Biol 2011. [DOI: 10.1134/s1062360411010085] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Ferguson BJ, Foo E, Ross JJ, Reid JB. Relationship between gibberellin, ethylene and nodulation in Pisum sativum. THE NEW PHYTOLOGIST 2011; 189:829-842. [PMID: 21087260 DOI: 10.1111/j.1469-8137.2010.03542.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
• Gibberellin (GA) deficiency resulting from the na mutation in pea (Pisum sativum) causes a reduction in nodulation. Nodules that do form are aberrant, having poorly developed meristems and a lack of enlarged cells. Studies using additional GA-biosynthesis double mutants indicate that this results from severe GA deficiency of the roots rather than simply dwarf shoot stature. • Double mutants isolated from crosses between na and three supernodulating pea mutants exhibit a supernodulation phenotype, but the nodule structures are aberrant. This suggests that severely reduced GA concentrations are not entirely inhibitory to nodule initiation, but that higher GA concentrations are required for proper nodule development. • na mutants evolve more than double the amount of ethylene produced by wild-type plants, indicating that low GA concentrations can promote ethylene production. The excess ethylene may contribute to the reduced nodulation of na plants, as application of an ethylene biosynthesis inhibitor increased na nodule numbers. However, these nodules were still aberrant in structure. • Constitutive GA signalling mutants also form significantly fewer nodules than wild-type plants. This suggests that there is an optimum degree of GA signalling required for nodule formation and that the GA signal, and not the concentration of bioactive GA per se, is important for nodulation.
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Affiliation(s)
- Brett J Ferguson
- Australian Research Council Centre of Excellence for Integrative Legume Research, School of Plant Science, University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, Australia
| | - Eloise Foo
- School of Plant Science, University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, Australia
| | - John J Ross
- School of Plant Science, University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, Australia
| | - James B Reid
- School of Plant Science, University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, Australia
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Ferguson BJ, Indrasumunar A, Hayashi S, Lin MH, Lin YH, Reid DE, Gresshoff PM. Molecular analysis of legume nodule development and autoregulation. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2010; 52:61-76. [PMID: 20074141 DOI: 10.1111/j.1744-7909.2010.00899.x] [Citation(s) in RCA: 218] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Legumes are highly important food, feed and biofuel crops. With few exceptions, they can enter into an intricate symbiotic relationship with specific soil bacteria called rhizobia. This interaction results in the formation of a new root organ called the nodule in which the rhizobia convert atmospheric nitrogen gas into forms of nitrogen that are useable by the plant. The plant tightly controls the number of nodules it forms, via a complex root-to-shoot-to-root signaling loop called autoregulation of nodulation (AON). This regulatory process involves peptide hormones, receptor kinases and small metabolites. Using modern genetic and genomic techniques, many of the components required for nodule formation and AON have now been isolated. This review addresses these recent findings, presents detailed models of the nodulation and AON processes, and identifies gaps in our understanding of these process that have yet to be fully explained.
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Affiliation(s)
- Brett J Ferguson
- ARC Centre of Excellence for Integrative Legume Research, The University of Queensland, Brisbane, QLD 4072, Australia
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Gourion B, Sulser S, Frunzke J, Francez-Charlot A, Stiefel P, Pessi G, Vorholt JA, Fischer HM. The PhyR-sigma(EcfG) signalling cascade is involved in stress response and symbiotic efficiency in Bradyrhizobium japonicum. Mol Microbiol 2009; 73:291-305. [PMID: 19555458 DOI: 10.1111/j.1365-2958.2009.06769.x] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
PhyR is an unusual type of response regulator consisting of a receiver domain and an extracytoplasmic function (ECF) sigma factor-like domain. It was recently described as a master regulator of general stress response in Methylobacterium extorquens. Orthologues of this regulator are present in essentially all free-living Alphaproteobacteria. In most of them, phyR is genetically closely linked to a gene encoding an ECF sigma factor. Here, we investigate the role of these two regulators in the soybean symbiont Bradyrhizobium japonicum USDA110. Using deletion mutants and phenotypic assays, we showed that PhyR and the ECF sigma factor sigma(EcfG) are involved in heat shock and desiccation resistance upon carbon starvation. Both mutants had symbiotic defects on the plant hosts Glycine max (soybean) and Vigna radiata (mungbean). They induced fewer nodules than the wild type and these nodules were smaller, less pigmented, and their specific nitrogenase activity was drastically reduced 2 or 3 weeks after inoculation. Four weeks after infection, soybean nodule development caught up to a large extent whereas most mungbean nodules remained defective even 5 weeks after infection. Remarkably, both mutants triggered aberrant nodules on the different host plants with ectopically emerging roots. Microarray analysis revealed that PhyR and sigma(EcfG) control congruent regulons suggesting both regulators are part of the same signalling cascade. This finding was further substantiated by in vitro protein-protein interaction studies which are in line with a partner-switching mechanism controlling gene regulation triggered by phosphorylation of PhyR. The large number of genes of unknown function present in the PhyR/sigma(EcfG) regulon and the conspicuous symbiotic phenotype suggest that these regulators are involved in the Bradyrhizobium-legume interaction via yet undisclosed mechanisms.
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Mathesius U. Auxin: at the root of nodule development? FUNCTIONAL PLANT BIOLOGY : FPB 2008; 35:651-668. [PMID: 32688821 DOI: 10.1071/fp08177] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2008] [Accepted: 08/14/2008] [Indexed: 06/11/2023]
Abstract
Root nodules are formed as a result of an orchestrated exchange of chemical signals between symbiotic nitrogen fixing bacteria and certain plants. In plants that form nodules in symbiosis with actinorhizal bacteria, nodules are derived from lateral roots. In most legumes, nodules are formed de novo from pericycle and cortical cells that are re-stimulated for division and differentiation by rhizobia. The ability of plants to nodulate has only evolved recently and it has, therefore, been suggested that nodule development is likely to have co-opted existing mechanisms for development and differentiation from lateral root formation. Auxin is an important regulator of cell division and differentiation, and changes in auxin accumulation and transport are essential for lateral root development. There is growing evidence that rhizobia alter the root auxin balance as a prerequisite for nodule formation, and that nodule numbers are regulated by shoot-to-root auxin transport. Whereas auxin requirements appear to be similar for lateral root and nodule primordium activation and organ differentiation, the major difference between the two developmental programs lies in the specification of founder cells. It is suggested that differing ratios of auxin and cytokinin are likely to specify the precursors of the different root organs.
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Affiliation(s)
- Ulrike Mathesius
- School of Biochemistry and Molecular Biology, Australian National University and Australian Research Council Centre of Excellence for Integrative Legume Research, Linnaeus Way, Canberra, ACT 0200, Australia. Email
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Domoney C, Duc G, Ellis THN, Ferrándiz C, Firnhaber C, Gallardo K, Hofer J, Kopka J, Küster H, Madueño F, Munier-Jolain NG, Mayer K, Thompson R, Udvardi M, Salon C. Genetic and genomic analysis of legume flowers and seeds. CURRENT OPINION IN PLANT BIOLOGY 2006; 9:133-41. [PMID: 16480914 DOI: 10.1016/j.pbi.2006.01.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2005] [Accepted: 01/25/2006] [Indexed: 05/06/2023]
Abstract
New tools, such as ordered mutant libraries, microarrays and sequence based comparative maps, are available for genetic and genomic studies of legumes that are being used to shed light on seed production, the objective of most arable farming. The new information and understanding brought by these tools are revealing the biological processes that underpin and impact on seed production.
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