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Sheoran S, Gupta M, Kumari S, Kumar S, Rakshit S. Meta-QTL analysis and candidate genes identification for various abiotic stresses in maize ( Zea mays L.) and their implications in breeding programs. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:26. [PMID: 37309532 PMCID: PMC10248626 DOI: 10.1007/s11032-022-01294-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 03/26/2022] [Indexed: 06/14/2023]
Abstract
Global climate change leads to the concurrence of a number of abiotic stresses including moisture stress (drought, waterlogging), temperature stress (heat, cold), and salinity stress, which are the major factors affecting maize production. To develop abiotic stress tolerance in maize, many quantitative trait loci (QTL) have been identified, but very few of them have been utilized successfully in breeding programs. In this context, the meta-QTL analysis of the reported QTL will enable the identification of stable/real QTL which will pave a reliable way to introgress these QTL into elite cultivars through marker-assisted selection. In this study, a total of 542 QTL were summarized from 33 published studies for tolerance to different abiotic stresses in maize to conduct meta-QTL analysis using BiomercatorV4.2.3. Among those, only 244 major QTL with more than 10% phenotypic variance were preferably utilised to carry out meta-QTL analysis. In total, 32 meta-QTL possessing 1907 candidate genes were detected for different abiotic stresses over diverse genetic and environmental backgrounds. The MQTL2.1, 5.1, 5.2, 5.6, 7.1, 9.1, and 9.2 control different stress-related traits for combined abiotic stress tolerance. The candidate genes for important transcription factor families such as ERF, MYB, bZIP, bHLH, NAC, LRR, ZF, MAPK, HSP, peroxidase, and WRKY have been detected for different stress tolerances. The identified meta-QTL are valuable for future climate-resilient maize breeding programs and functional validation of candidate genes studies, which will help to deepen our understanding of the complexity of these abiotic stresses. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01294-9.
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Affiliation(s)
- Seema Sheoran
- ICAR-Indian Institute of Maize Research, PAU Campus, Ludhiana, 141004 India
- Present Address: ICAR-Indian Agricultural Research Institute, Regional Station, Karnal, 132001 India
| | - Mamta Gupta
- ICAR-Indian Institute of Maize Research, PAU Campus, Ludhiana, 141004 India
| | - Shweta Kumari
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012 India
| | - Sandeep Kumar
- Present Address: ICAR-Indian Agricultural Research Institute, Regional Station, Karnal, 132001 India
- ICAR-Indian Institute of Pulses Research, Regional Station, Phanda, Bhopal, 462030 India
| | - Sujay Rakshit
- ICAR-Indian Institute of Maize Research, PAU Campus, Ludhiana, 141004 India
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Jin H, Liu S, Zenda T, Wang X, Liu G, Duan H. Maize leaves drought-responsive genes revealed by comparative transcriptome of two cultivars during the filling stage. PLoS One 2019; 14:e0223786. [PMID: 31665169 PMCID: PMC6821100 DOI: 10.1371/journal.pone.0223786] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 09/27/2019] [Indexed: 02/03/2023] Open
Abstract
Like other important cereal crop in modern agricultural production, maize is also threatened by drought. And the drought stress during maize filling stage will directly affect the quality (protein or oil concentration) and also the weight of grain. Therefore, different from previous studies focusing on inbred lines and pot experiment at seedling stage, current study selected filling stage of the adult plant and planting maize in the experimental field. Two hybrids cultivars with different drought tolerant were used for drought and water treatment respectively. We performed transcriptome sequencing analysis of 4 groups, 12 samples, and obtained 651.08 million raw reads. Then the data were further processed by mapping to a reference genome, GO annotation, enrichment analysis and so on. Among them we focus on the different change trends of water treatment and drought treatment, and the different responses of two drought-tolerant cultivars to drought treatment. Through the analysis, several transcripts which encode nitrogen metabolic, protein phosphorylation, MYB,AP2/ERF, HB transcriptional factor, O-glycosyl hydrolases and organic acid metabolic process were implicated with maize drought stress. Our data will offer insights of the identification of genes involved in maize drought stress tolerance, which provides a theoretical basis for maize drought resistance breeding.
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Affiliation(s)
- Hongyu Jin
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, China
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding, China
| | - Songtao Liu
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, China
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding, China
| | - Tinashe Zenda
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, China
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding, China
| | - Xuan Wang
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, China
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding, China
| | - Guo Liu
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, China
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding, China
| | - Huijun Duan
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, China
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding, China
- * E-mail:
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Mittal S, Banduni P, Mallikarjuna MG, Rao AR, Jain PA, Dash PK, Thirunavukkarasu N. Structural, Functional, and Evolutionary Characterization of Major Drought Transcription Factors Families in Maize. Front Chem 2018; 6:177. [PMID: 29876347 PMCID: PMC5974147 DOI: 10.3389/fchem.2018.00177] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 05/03/2018] [Indexed: 01/22/2023] Open
Abstract
Drought is one of the major threats to the maize yield especially in subtropical production systems. Understanding the genes and regulatory mechanisms of drought tolerance is important to sustain the yield. Transcription factors (TFs) play a major role in gene regulation under drought stress. In the present study, a set of 15 major TF families comprising 1,436 genes was structurally and functionally characterized. The functional annotation indicated that the genes were involved in ABA signaling, ROS scavenging, photosynthesis, stomatal regulation, and sucrose metabolism. Duplication was identified as the primary force in divergence and expansion of TF families. Phylogenetic relationship was developed for individual TF and combined TF families. Phylogenetic analysis clustered the genes into specific and mixed groups. Gene structure analysis revealed that more number of genes were intron-rich as compared to intron-less. Drought-responsive cis-regulatory elements such as ABREA, ABREB, DRE1, and DRECRTCOREAT have been identified. Expression and interaction analyses identified leaf-specific bZIP TF, GRMZM2G140355, as a potential contributor toward drought tolerance in maize. Protein-protein interaction network of 269 drought-responsive genes belonging to different TFs has been provided. The information generated on structural and functional characteristics, expression, and interaction of the drought-related TF families will be useful to decipher the drought tolerance mechanisms and to breed drought-tolerant genotypes in maize.
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Affiliation(s)
- Shikha Mittal
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Pooja Banduni
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | - Atmakuri R Rao
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Prashant A Jain
- Department of Computational Biology & Bioinformatics, J.I.B.B., Sam Higginbottom University of Agriculture, Technology and Sciences, Allahabad, India
| | - Prasanta K Dash
- National Research Centre on Plant Biotechnology, New Delhi, India
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Chupeau MC, Granier F, Pichon O, Renou JP, Gaudin V, Chupeau Y. Characterization of the early events leading to totipotency in an Arabidopsis protoplast liquid culture by temporal transcript profiling. THE PLANT CELL 2013; 25:2444-63. [PMID: 23903317 PMCID: PMC3753376 DOI: 10.1105/tpc.113.109538] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Revised: 05/31/2013] [Accepted: 07/03/2013] [Indexed: 05/19/2023]
Abstract
The molecular mechanisms underlying plant cell totipotency are largely unknown. Here, we present a protocol for the efficient regeneration of plants from Arabidopsis thaliana protoplasts. The specific liquid medium used in our study leads to a high rate of reentry into the cell cycle of most cell types, providing a powerful system to study dedifferentiation/regeneration processes in independent somatic cells. To identify the early events in the establishment of totipotency, we monitored the genome-wide transcript profiles of plantlets and protoplast-derived cells (PdCs) during the first week of culture. Plant cells rapidly dedifferentiated. Then, we observed the reinitiation and reorientation of protein synthesis, accompanied by the reinitiation of cell division and de novo cell wall synthesis. Marked changes in the expression of chromatin-associated genes, especially of those in the histone variant family, were observed during protoplast culture. Surprisingly, the epigenetic status of PdCs and well-established cell cultures differed, with PdCs exhibiting rare reactivated transposons and epigenetic changes. The differentially expressed genes identified in this study are interesting candidates for investigating the molecular mechanisms underlying plant cell plasticity and totipotency. One of these genes, the plant-specific transcription factor ABERRANT LATERAL ROOT FORMATION4, is required for the initiation of protoplast division.
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Affiliation(s)
- Marie-Christine Chupeau
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1318–AgroParisTech, Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique–Centre de Versailles-Grignon, F-78026 Versailles cedex, France
| | - Fabienne Granier
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1318–AgroParisTech, Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique–Centre de Versailles-Grignon, F-78026 Versailles cedex, France
| | - Olivier Pichon
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1165, Unité Mixte de Recherche en Génomique Végétale, F-91057 Évry cedex 2, France
| | - Jean-Pierre Renou
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1165, Unité Mixte de Recherche en Génomique Végétale, F-91057 Évry cedex 2, France
| | - Valérie Gaudin
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1318–AgroParisTech, Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique–Centre de Versailles-Grignon, F-78026 Versailles cedex, France
| | - Yves Chupeau
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1318–AgroParisTech, Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique–Centre de Versailles-Grignon, F-78026 Versailles cedex, France
- Address correspondence to
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