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Sahoo B, Nayak I, Parameswaran C, Kesawat MS, Sahoo KK, Subudhi HN, Balasubramaniasai C, Prabhukarthikeyan SR, Katara JL, Dash SK, Chung SM, Siddiqui MH, Alamri S, Samantaray S. A Comprehensive Genome-Wide Investigation of the Cytochrome 71 ( OsCYP71) Gene Family: Revealing the Impact of Promoter and Gene Variants (Ser33Leu) of OsCYP71P6 on Yield-Related Traits in Indica Rice ( Oryza sativa L.). PLANTS (BASEL, SWITZERLAND) 2023; 12:3035. [PMID: 37687282 PMCID: PMC10490456 DOI: 10.3390/plants12173035] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/17/2023] [Accepted: 08/21/2023] [Indexed: 09/10/2023]
Abstract
The cytochrome P450 (CYP450) gene family plays a critical role in plant growth and developmental processes, nutrition, and detoxification of xenobiotics in plants. In the present research, a comprehensive set of 105 OsCYP71 family genes was pinpointed within the genome of indica rice. These genes were categorized into twelve distinct subfamilies, where members within the same subgroup exhibited comparable gene structures and conserved motifs. In addition, 105 OsCYP71 genes were distributed across 11 chromosomes, and 36 pairs of OsCYP71 involved in gene duplication events. Within the promoter region of OsCYP71, there exists an extensive array of cis-elements that are associated with light responsiveness, hormonal regulation, and stress-related signaling. Further, transcriptome profiling revealed that a majority of the genes exhibited responsiveness to hormones and were activated across diverse tissues and developmental stages in rice. The OsCYP71P6 gene is involved in insect resistance, senescence, and yield-related traits in rice. Hence, understanding the association between OsCYP71P6 genetic variants and yield-related traits in rice varieties could provide novel insights for rice improvement. Through the utilization of linear regression models, a total of eight promoters were identified, and a specific gene variant (Ser33Leu) within OsCYP71P6 was found to be linked to spikelet fertility. Additionally, different alleles of the OsCYP71P6 gene identified through in/dels polymorphism in 131 rice varieties were validated for their allelic effects on yield-related traits. Furthermore, the single-plant yield, spikelet number, panicle length, panicle weight, and unfilled grain per panicle for the OsCYP71P6-1 promoter insertion variant were found to contribute 20.19%, 13.65%, 5.637%, 8.79%, and 36.86% more than the deletion variant, respectively. These findings establish a robust groundwork for delving deeper into the functions of OsCYP71-family genes across a range of biological processes. Moreover, these findings provide evidence that allelic variation in the promoter and amino acid substitution of Ser33Leu in the OsCYP71P6 gene could potentially impact traits related to rice yield. Therefore, the identified promoter variants in the OsCYP71P6 gene could be harnessed to amplify rice yields.
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Affiliation(s)
- Bijayalaxmi Sahoo
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack 753006, India; (B.S.); (I.N.); (H.N.S.); (C.B.); (J.L.K.); (S.K.D.); (S.S.)
- Department of Botany, Ravenshaw University, Cuttack 753006, India;
| | - Itishree Nayak
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack 753006, India; (B.S.); (I.N.); (H.N.S.); (C.B.); (J.L.K.); (S.K.D.); (S.S.)
- Department of Botany, Utkal University, Bhubaneswar 751004, India
| | - C. Parameswaran
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack 753006, India; (B.S.); (I.N.); (H.N.S.); (C.B.); (J.L.K.); (S.K.D.); (S.S.)
| | - Mahipal Singh Kesawat
- Department of Genetics and Plant Breeding, Faculty of Agriculture, Sri University, Cuttack 754006, India
| | | | - H. N. Subudhi
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack 753006, India; (B.S.); (I.N.); (H.N.S.); (C.B.); (J.L.K.); (S.K.D.); (S.S.)
| | - Cayalvizhi Balasubramaniasai
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack 753006, India; (B.S.); (I.N.); (H.N.S.); (C.B.); (J.L.K.); (S.K.D.); (S.S.)
| | | | - Jawahar Lal Katara
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack 753006, India; (B.S.); (I.N.); (H.N.S.); (C.B.); (J.L.K.); (S.K.D.); (S.S.)
| | - Sushanta Kumar Dash
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack 753006, India; (B.S.); (I.N.); (H.N.S.); (C.B.); (J.L.K.); (S.K.D.); (S.S.)
| | - Sang-Min Chung
- Department of Life Science, Dongguk University-Seoul, Ilsandong-gu, Goyang-si 10326, Gyeonggi-do, Republic of Korea;
| | - Manzer H. Siddiqui
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia; (M.H.S.); (S.A.)
| | - Saud Alamri
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia; (M.H.S.); (S.A.)
| | - Sanghamitra Samantaray
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack 753006, India; (B.S.); (I.N.); (H.N.S.); (C.B.); (J.L.K.); (S.K.D.); (S.S.)
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Eragam A, Shukla V, Kola VS, Latha P, Akkareddy S, Kommana ML, Ramireddy E, Vemireddy LR. Yield-associated putative gene regulatory networks in Oryza sativa L. subsp. indica and their association with high-yielding genotypes. Mol Biol Rep 2022; 49:7649-7663. [PMID: 35612779 DOI: 10.1007/s11033-022-07581-0] [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: 01/27/2022] [Accepted: 05/06/2022] [Indexed: 11/26/2022]
Abstract
BACKGROUND With the increase in population and economies of developing countries in Asia and Africa, the research towards securing future food demands is an imminent need. Among japonica and indica genotypes, indica rice varieties are largely cultivated across the globe. However, our present understanding of yield-contributing gene information stems mainly from japonica and studies on the yield potential of indica genotypes are limited. METHODS AND RESULTS In the present study, yield contributing orthologous genes previously characterized from japonica varieties were identified in the indica genome and analysed with binGO tool for GO biological processes categorization. Transcription factor binding site enrichment analysis in the promoters of yield-related genes of indica was performed with MEME-AME tool that revealed putative common TF regulators are enriched in flower development, two-component signalling and water deprivation biological processes. Gene regulatory networks revealed important TF-target interactions that might govern yield-related traits. Some of the identified candidate genes were validated by qRT-PCR analysis for their expression and association with yield-related traits among 16 widely cultivated popular indica genotypes. Further, SNP-metabolite-trait association analysis was performed using high-yielding indica variety Rasi. This resulted in the identification of putative SNP variations in TF regulators and targeted yield genes significantly linked with metabolite accumulation. CONCLUSIONS The study suggests some of the high yielding indica genotypes such as Ravi003, Rasi and Kavya could be used as potential donors in breeding programs based on yield gene expression analysis and SNP-metabolites associations.
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Affiliation(s)
- Aparna Eragam
- Department of Molecular Biology and Biotechnology, S.V. Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, India
- Biology Division, Indian Institute of Science Education and Research Tirupati (IISER Tirupati), Tirupati, 517507, India
| | - Vishnu Shukla
- Biology Division, Indian Institute of Science Education and Research Tirupati (IISER Tirupati), Tirupati, 517507, India
| | - Vijaya Sudhakararao Kola
- Biology Division, Indian Institute of Science Education and Research Tirupati (IISER Tirupati), Tirupati, 517507, India
| | - P Latha
- Regional Agricultural Research Station (RARS), ANGRAU, Tirupati, India
| | | | - Madhavi L Kommana
- Department of Genetics and Plant Breeding, S.V. Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, India
| | - Eswarayya Ramireddy
- Biology Division, Indian Institute of Science Education and Research Tirupati (IISER Tirupati), Tirupati, 517507, India.
| | - Lakshminarayana R Vemireddy
- Department of Molecular Biology and Biotechnology, S.V. Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, India.
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