1
|
Kumar K, Kumari A, Durgesh K, Sevanthi AM, Sharma S, Singh NK, Gaikwad K. Identification of superior haplotypes for flowering time in pigeonpea through candidate gene-based association study of a diverse minicore collection. PLANT CELL REPORTS 2024; 43:156. [PMID: 38819495 DOI: 10.1007/s00299-024-03230-x] [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: 02/23/2024] [Accepted: 05/05/2024] [Indexed: 06/01/2024]
Abstract
KEY MESSAGE In current study candidate gene (261 genes) based association mapping on 144 pigeonpea accessions for flowering time and related traits and 29 MTAs producing eight superior haplotypes were identified. In the current study, we have conducted an association analysis for flowering-associated traits in a diverse pigeonpea mini-core collection comprising 144 accessions using the SNP data of 261 flowering-related genes. In total, 13,449 SNPs were detected in the current study, which ranged from 743 (ICP10228) to 1469 (ICP6668) among the individuals. The nucleotide diversity (0.28) and Watterson estimates (0.34) reflected substantial diversity, while Tajima's D (-0.70) indicated the abundance of rare alleles in the collection. A total of 29 marker trait associations (MTAs) were identified, among which 19 were unique to days to first flowering (DOF) and/or days to fifty percent flowering (DFF), 9 to plant height (PH), and 1 to determinate (Det) growth habit using 3 years of phenotypic data. Among these MTAs, six were common to DOF and/or DFF, and four were common to DOF/DFF along with the PH, reflecting their pleiotropic action. These 29 MTAs spanned 25 genes, among which 10 genes clustered in the protein-protein network analysis, indicating their concerted involvement in floral induction. Furthermore, we identified eight haplotypes, four of which regulate late flowering, while the remaining four regulate early flowering using the MTAs. Interestingly, haplotypes conferring late flowering (H001, H002, and H008) were found to be taller, while those involved in early flowering (H003) were shorter in height. The expression pattern of these genes, as inferred from the transcriptome data, also underpinned their involvement in floral induction. The haplotypes identified will be highly useful to the pigeonpea breeding community for haplotype-based breeding.
Collapse
Affiliation(s)
- Kuldeep Kumar
- ICAR-National Institute for Plant Biotechnology, Pusa, New Delhi, India
- ICAR-Indian Institute of Pulses Research, Kanpur, Uttar Pradesh, India
- The Graduate School, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi, India
| | - Anita Kumari
- Department of Botany, North Campus, University of Delhi, Delhi, New Delhi, India
| | - Kumar Durgesh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi, India
| | | | - Sandhya Sharma
- ICAR-National Institute for Plant Biotechnology, Pusa, New Delhi, India
| | | | - Kishor Gaikwad
- ICAR-National Institute for Plant Biotechnology, Pusa, New Delhi, India.
| |
Collapse
|
2
|
Sugumar T, Shen G, Smith J, Zhang H. Creating Climate-Resilient Crops by Increasing Drought, Heat, and Salt Tolerance. PLANTS (BASEL, SWITZERLAND) 2024; 13:1238. [PMID: 38732452 PMCID: PMC11085490 DOI: 10.3390/plants13091238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 05/13/2024]
Abstract
Over the years, the changes in the agriculture industry have been inevitable, considering the need to feed the growing population. As the world population continues to grow, food security has become challenged. Resources such as arable land and freshwater have become scarce due to quick urbanization in developing countries and anthropologic activities; expanding agricultural production areas is not an option. Environmental and climatic factors such as drought, heat, and salt stresses pose serious threats to food production worldwide. Therefore, the need to utilize the remaining arable land and water effectively and efficiently and to maximize the yield to support the increasing food demand has become crucial. It is essential to develop climate-resilient crops that will outperform traditional crops under any abiotic stress conditions such as heat, drought, and salt, as well as these stresses in any combinations. This review provides a glimpse of how plant breeding in agriculture has evolved to overcome the harsh environmental conditions and what the future would be like.
Collapse
Affiliation(s)
- Tharanya Sugumar
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA; (T.S.); (J.S.)
| | - Guoxin Shen
- Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China;
| | - Jennifer Smith
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA; (T.S.); (J.S.)
| | - Hong Zhang
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA; (T.S.); (J.S.)
| |
Collapse
|
3
|
Ghimire S, Hasan MM, Fang XW. Small ubiquitin-like modifiers E3 ligases in plant stress. FUNCTIONAL PLANT BIOLOGY : FPB 2024; 51:FP24032. [PMID: 38669463 DOI: 10.1071/fp24032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 04/05/2024] [Indexed: 04/28/2024]
Abstract
Plants regularly encounter various environmental stresses such as salt, drought, cold, heat, heavy metals and pathogens, leading to changes in their proteome. Of these, a post-translational modification, SUMOylation is particularly significant for its extensive involvement in regulating various plant molecular processes to counteract these external stressors. Small ubiquitin-like modifiers (SUMO) protein modification significantly contributes to various plant functions, encompassing growth, development and response to environmental stresses. The SUMO system has a limited number of ligases even in fully sequenced plant genomes but SUMO E3 ligases are pivotal in recognising substrates during the process of SUMOylation. E3 ligases play pivotal roles in numerous biological and developmental processes in plants, including DNA repair, photomorphogenesis, phytohormone signalling and responses to abiotic and biotic stress. A considerable number of targets for E3 ligases are proteins implicated in reactions to abiotic and biotic stressors. This review sheds light on how plants respond to environmental stresses by focusing on recent findings on the role of SUMO E3 ligases, contributing to a better understanding of how plants react at a molecular level to such stressors.
Collapse
Affiliation(s)
- Shantwana Ghimire
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, Gansu 730000, China
| | - Md Mahadi Hasan
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, Gansu 730000, China
| | - Xiang-Wen Fang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, Gansu 730000, China
| |
Collapse
|
4
|
De Prato L, Ansari O, Hardy GESJ, Howieson J, O'Hara G, Ruthrof KX. Physiological and cannabinoid responses of hemp ( Cannabis sativa) to rock phosphate dust under tropical conditions. FUNCTIONAL PLANT BIOLOGY : FPB 2023; 50:378-389. [PMID: 36973638 DOI: 10.1071/fp22264] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 02/27/2023] [Indexed: 05/03/2023]
Abstract
Growing a high-value crop such as industrial hemp (Cannabis sativa L.) in post-mining environments is economically and environmentally attractive but faces a range of biotic and abiotic challenges. An opportunity to investigate the cultivation of C. sativa presented itself as part of post-mining activities on Christmas Island (Australia) to profitably utilise disused phosphate (PS) quarries. Challenges to plant growth and cadmium (Cd) uptake were addressed in this study using potted plants under fully controlled conditions in a growth chamber. A complete nutritional spectrum, slow-release fertiliser was applied to all plants as a control treatment, and two levels of rock PS dust, a waste product of PS mining that contains 35% phosphorus (P) and 40ppm of naturally occurring Cd, were applied at 54 and 162gL-1 . After 12weeks, control plants (no PS dust) significantly differed in phenological development, with no flower production, lower aboveground biomass and reduced photosynthesis efficiency than those with P applied as rock dust. Compared with the controls, the 54gL-1 level of P dust increased shoot biomass by 38%, while 162gL-1 increased shoot biomass by 85%. The concentration of Δ9 -tetrahydrocannabinol also increased with the higher P levels. Cd uptake from PS dust by C. sativa was substantial and warrants further investigation. However, there was no increase in Cd content between the 54 and 162gL-1 application rates in seed and leaf. Results indicate that hemp could become a high-value crop on Christmas Island, with the readily available rock PS dust providing a source of P.
Collapse
Affiliation(s)
- Luca De Prato
- Murdoch University, Food Futures Institute, Murdoch, WA, Australia; and Medicann Health Aust Pty Ltd, Osborne Park, WA, Australia
| | - Omid Ansari
- HempGenTech Pty Ltd, Kenmore, Qld, Australia
| | - Giles E St J Hardy
- Murdoch University, Harry Butler Institute, Murdoch, WA, Australia; and ArborCarbon, Murdoch University, Murdoch, WA, Australia
| | - John Howieson
- Murdoch University, Food Futures Institute, Murdoch, WA, Australia
| | - Graham O'Hara
- Murdoch University, Food Futures Institute, Murdoch, WA, Australia
| | - Katinka X Ruthrof
- Murdoch University, Harry Butler Institute, Murdoch, WA, Australia; and Department of Biodiversity, Conservation and Attractions, Kensington, WA 6151, Australia
| |
Collapse
|
5
|
Zhang Y, Zeng L. Crosstalk between Ubiquitination and Other Post-translational Protein Modifications in Plant Immunity. PLANT COMMUNICATIONS 2020; 1:100041. [PMID: 33367245 PMCID: PMC7748009 DOI: 10.1016/j.xplc.2020.100041] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 02/07/2020] [Accepted: 03/19/2020] [Indexed: 05/05/2023]
Abstract
Post-translational modifications (PTMs) are central to the modulation of protein activity, stability, subcellular localization, and interaction with partners. They greatly expand the diversity and functionality of the proteome and have taken the center stage as key players in regulating numerous cellular and physiological processes. Increasing evidence indicates that in addition to a single regulatory PTM, many proteins are modified by multiple different types of PTMs in an orchestrated manner to collectively modulate the biological outcome. Such PTM crosstalk creates a combinatorial explosion in the number of proteoforms in a cell and greatly improves the ability of plants to rapidly mount and fine-tune responses to different external and internal cues. While PTM crosstalk has been investigated in depth in humans, animals, and yeast, the study of interplay between different PTMs in plants is still at its infant stage. In the past decade, investigations showed that PTMs are widely involved and play critical roles in the regulation of interactions between plants and pathogens. In particular, ubiquitination has emerged as a key regulator of plant immunity. This review discusses recent studies of the crosstalk between ubiquitination and six other PTMs, i.e., phosphorylation, SUMOylation, poly(ADP-ribosyl)ation, acetylation, redox modification, and glycosylation, in the regulation of plant immunity. The two basic ways by which PTMs communicate as well as the underlying mechanisms and diverse outcomes of the PTM crosstalk in plant immunity are highlighted.
Collapse
|
6
|
Rytz TC, Miller MJ, Vierstra RD. Purification of SUMO Conjugates from Arabidopsis for Mass Spectrometry Analysis. Methods Mol Biol 2018; 1475:257-81. [PMID: 27631811 DOI: 10.1007/978-1-4939-6358-4_18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The posttranslational modification of proteins with small ubiquitin-related modifier (SUMO) is a rapid, robust, and reversible mechanism that impacts a host of eukaryotic processes important to both normal cellular functions and survival during various abiotic and biotic challenges. Essential to defining the breadth of events impacted by SUMOylation is the development of full catalogues of protein targets. Here, we describe a stringent affinity method to purify native SUMO conjugates from the model plant Arabidopsis thaliana based on the expression of modified SUMOs bearing epitope tags. When combined with standard and quantitative mass spectrometric methods, deep datasets of SUMOylated proteins can be acquired. Functional analysis of these lists links SUMO to numerous regulatory events, with an emphasis on those associated with transcription, DNA replication and repair, and chromatin assembly/accessibility.
Collapse
Affiliation(s)
- Thérèse C Rytz
- Department of Genetics, University of Wisconsin, 425-G Henry Mall, Madison, Wisconsin, 53706, USA.,Department of Biology, Washington University in St. Louis, Campus Box 1137, One Brookings Drive, St. Louis, Missouri, 63130, USA
| | - Marcus J Miller
- Department of Genetics, University of Wisconsin, 425-G Henry Mall, Madison, Wisconsin, 53706, USA
| | - Richard D Vierstra
- Department of Genetics, University of Wisconsin, 425-G Henry Mall, Madison, Wisconsin, 53706, USA. .,Department of Biology, Washington University in St. Louis, Campus Box 1137, One Brookings Drive, St. Louis, Missouri, 63130, USA.
| |
Collapse
|
7
|
Liu F, Wang X, Su M, Yu M, Zhang S, Lai J, Yang C, Wang Y. Functional characterization of DnSIZ1, a SIZ/PIAS-type SUMO E3 ligase from Dendrobium. BMC PLANT BIOLOGY 2015; 15:225. [PMID: 26376625 PMCID: PMC4574183 DOI: 10.1186/s12870-015-0613-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 09/11/2015] [Indexed: 05/18/2023]
Abstract
BACKGROUND SUMOylation is an important post-translational modification of eukaryotic proteins that involves the reversible conjugation of a small ubiquitin-related modifier (SUMO) polypeptide to its specific protein substrates, thereby regulating numerous complex cellular processes. The PIAS (protein inhibitor of activated signal transducers and activators of transcription [STAT]) and SIZ (scaffold attachment factor A/B/acinus/PIAS [SAP] and MIZ) proteins are SUMO E3 ligases that modulate SUMO conjugation. The characteristic features and SUMOylation mechanisms of SIZ1 protein in monocotyledon are poorly understood. Here, we examined the functions of a homolog of Arabidopsis SIZ1, a functional SIZ/PIAS-type SUMO E3 ligase from Dendrobium. RESULTS In Dendrobium, the predicted DnSIZ1 protein has domains that are highly conserved among SIZ/PIAS-type proteins. DnSIZ1 is widely expressed in Dendrobium organs and has a up-regulated trend by treatment with cold, high temperature and wounding. The DnSIZ1 protein localizes to the nucleus and shows SUMO E3 ligase activity when expressed in an Escherichia coli reconstitution system. Moreover, ectopic expression of DnSIZ1 in the Arabidopsis siz1-2 mutant partially complements several phenotypes and results in enhanced levels of SUMO conjugates in plants exposed to heat shock conditions. We observed that DnSIZ1 acts as a negative regulator of flowering transition which may be via a vernalization-induced pathway. In addition, ABA-hypersensitivity of siz1-2 seed germination can be partially suppressed by DnSIZ1. CONCLUSIONS Our results suggest that DnSIZ1 is a functional homolog of the Arabidopsis SIZ1 with SUMO E3 ligase activity and may play an important role in the regulation of Dendrobium stress responses, flowering and development.
Collapse
Affiliation(s)
- Feng Liu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.
| | - Xiao Wang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.
| | - Mengying Su
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.
| | - Mengyuan Yu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.
| | - Shengchun Zhang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.
| | - Jianbin Lai
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.
| | - Chengwei Yang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.
| | - Yaqin Wang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.
| |
Collapse
|
8
|
Liu J, Li W, Ning Y, Shirsekar G, Cai Y, Wang X, Dai L, Wang Z, Liu W, Wang GL. The U-Box E3 ligase SPL11/PUB13 is a convergence point of defense and flowering signaling in plants. PLANT PHYSIOLOGY 2012; 160:28-37. [PMID: 22659522 PMCID: PMC3440206 DOI: 10.1104/pp.112.199430] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Accepted: 05/30/2012] [Indexed: 05/19/2023]
|
9
|
Sumoylation of transcription factor MYB30 by the small ubiquitin-like modifier E3 ligase SIZ1 mediates abscisic acid response in Arabidopsis thaliana. Proc Natl Acad Sci U S A 2012; 109:12822-7. [PMID: 22814374 DOI: 10.1073/pnas.1202630109] [Citation(s) in RCA: 136] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The phytohormone abscisic acid (ABA) plays an essential role in plant development and during the response of the plant to abiotic stress. In this study, we report that the R2R3-type transcription factor MYB30 is involved in the regulation of ABA signaling. Arabidopsis mutants lacking MYB30 are hypersensitive to ABA during germination and seedling growth. A K283R substitution in MYB30 blocks its SUMO E3 ligase SIZ1-mediated sumoylation in Arabidopsis protoplasts, indicating that MYB30 is sumoylated by SIZ1 and that K283 is the principal site for small ubiquitin-like modifier conjugation. Expression of MYB30(K283R) in myb30 partially rescues the mutant ABA-hypersensitive phenotype, but expression of wild-type MYB30 complements the mutant phenotype. Overexpression of MYB30 in wild-type results in an ABA-insensitive phenotype, whereas overexpression of MYB30 in the siz1 mutant does not alter siz1 hypersensitivity to ABA. The siz1-2 myb30-2 double-mutant exhibits greater ABA sensitivity than either single mutant, but a mutation in the SIZ1-sumoylated ABI5 transcription factor suppresses the ABA hypersensitivity of myb30-2 to wild-type levels. Our results suggest that coordination of ABI5 and MYB30 sumoylation by SIZ1 may balance gene expression, which is required for regulation of ABA signaling during seed germination.
Collapse
|