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Tabassum J, Raza Q, Riaz A, Ahmad S, Rashid MAR, Javed MA, Ali Z, Kang F, Khan IA, Atif RM, Luo J. Exploration of the genomic atlas of Dof transcription factor family across genus Oryza provides novel insights on rice breeding in changing climate. FRONTIERS IN PLANT SCIENCE 2022; 13:1004359. [PMID: 36407584 PMCID: PMC9671800 DOI: 10.3389/fpls.2022.1004359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 09/05/2022] [Indexed: 06/16/2023]
Abstract
DNA-binding with one finger (Dof) transcription factors have been demonstrated to regulate various stresses and developmental processes in plants. Their identification and comparative evolutionary analyses in cultivated and wild species of genus oryza were yet to be explored. In this context, we report a comprehensive genomics atlas of DNA-binding with one finger (Dof) family genes in 13 diverse rice genomes (five cultivated and eight rice wild-relatives) through a genome-wide scanning approach. A galore of 238 Dof genes, identified across the genus Oryza, are categorized into seven distinct subgroups by comparative phylogenetic analysis with the model plant Arabidopsis. Conserved motifs and gene structure analyses unveiled the prevalence of species- and subgroups-specific structural and functional diversity that is expediating with the evolutionary period. Our results indicate that Dof genes might have undergone strong purifying selections and segmental duplications to expand their gene family members in corresponding Oryza genomes. We speculate that miR2927 potentially targets the Dof domain to regulate gene expression under different climatic conditions, which are supported by in-silico and wet-lab experiments-based expression profiles. In a nutshell, we report several superior haplotypes significantly associated with early flowering in a treasure trove of 3,010 sequenced rice accessions and have validated these haplotypes with two years of field evaluation-based flowering data of a representative subpanel. Finally, we have provided some insights on the resolution of Oryza species phylogeny discordance and divergence highlighting the mosaic evolutionary history of the genus Oryza. Overall, this study reports a complete genomic landscape of the Dof family in cultivated and wild Oryza species that could greatly facilitate in fast-track development of early maturing and climate-resilient rice cultivars through modern haplotype-led breeding.
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Affiliation(s)
- Javaria Tabassum
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
| | - Qasim Raza
- Precision Agriculture and Analytics Lab, National Centre in Big Data and Cloud Computing, Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture Faisalabad, Faisalabad, Pakistan
- Molecular Breeding Laboratory, Rice Research Institute, Kala Shah Kaku, Sheikhupura, Pakistan
| | - Awais Riaz
- Molecular Breeding Laboratory, Rice Research Institute, Kala Shah Kaku, Sheikhupura, Pakistan
- Department of Crop, Soil and Environmental Sciences, University of Arkansas, Fayetteville, AR, United States
| | - Shakeel Ahmad
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
- National Center for Genome Editing for Crop Improvement and Human Health, Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | | | - Muhammad Arshad Javed
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
| | - Zulfiqar Ali
- Department of Plant Breeding and Genetics, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Fengyu Kang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Iqrar Ahmad Khan
- Precision Agriculture and Analytics Lab, National Centre in Big Data and Cloud Computing, Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture Faisalabad, Faisalabad, Pakistan
- Institute of Horticultural Sciences, University of Agriculture, Faisalabad, Pakistan
| | - Rana Muhammad Atif
- Precision Agriculture and Analytics Lab, National Centre in Big Data and Cloud Computing, Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture Faisalabad, Faisalabad, Pakistan
- Department of Plant Breeding and Genetics, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Ju Luo
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
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Iwamoto M. In-frame editing of transcription factor gene RDD1 to suppress miR166 recognition influences nutrient uptake, photosynthesis, and grain quality in rice. Sci Rep 2022; 12:10795. [PMID: 35750704 PMCID: PMC9232572 DOI: 10.1038/s41598-022-14768-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 06/13/2022] [Indexed: 11/09/2022] Open
Abstract
The transcription factor-encoding gene RDD1 increases the uptake of nutrient ions, photosynthetic activity under ambient and high CO2 conditions, and grain productivity, and microRNA166 (miR166) regulates its transcript levels. This study found that CRISPR/Cas9 genome editing of rice plants to inhibit miR166-RDD1 transcript pairing (R1-Cas plants) increased RDD1 transcript levels, NH4+ and PO43- uptake, and photosynthetic activity under high CO2 conditions in rice. However, the panicle weight of the R1-Cas plants decreased compared with the wild-type (WT) plants. Adversely, changes in environmental conditions, such as high CO2 or high temperatures, showed insignificant differences in the panicle weight between the WT and R1-Cas plants despite a largely increased panicle weight observed in the transgenic RDD1-overexpressing plants. Moreover, both the R1-Cas and transgenic RDD1-overexpressing plants that were matured in a growth chamber demonstrated an improved grain appearance quality or a decrease in the number of chalky grains compared with the WT plants. These results suggest that the in-frame mutagenesis of RDD1 to suppress miR166-RDD1 transcript pairing contributes to the improved grain appearance of rice.
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Affiliation(s)
- Masao Iwamoto
- Division of Crop Genome Editing, Institute of Agrobiological Sciences, NARO, Tsukuba Ibaraki, 305-8604, Japan.
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