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Article

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.)

by
Bijayalaxmi Sahoo
1,2,
Itishree Nayak
1,3,
C. Parameswaran
1,*,
Mahipal Singh Kesawat
4,*,
Khirod Kumar Sahoo
2,
H. N. Subudhi
1,
Cayalvizhi Balasubramaniasai
1,
S. R. Prabhukarthikeyan
5,
Jawahar Lal Katara
1,
Sushanta Kumar Dash
1,
Sang-Min Chung
6,
Manzer H. Siddiqui
7,
Saud Alamri
7 and
Sanghamitra Samantaray
1
1
Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack 753006, India
2
Department of Botany, Ravenshaw University, Cuttack 753006, India
3
Department of Botany, Utkal University, Bhubaneswar 751004, India
4
Department of Genetics and Plant Breeding, Faculty of Agriculture, Sri University, Cuttack 754006, India
5
Crop Protection Division, ICAR-National Rice Research Institute, Cuttack 753006, India
6
Department of Life Science, Dongguk University-Seoul, Ilsandong-gu, Goyang-si 10326, Gyeonggi-do, Republic of Korea
7
Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
*
Authors to whom correspondence should be addressed.
Plants 2023, 12(17), 3035; https://doi.org/10.3390/plants12173035
Submission received: 13 July 2023 / Revised: 17 August 2023 / Accepted: 21 August 2023 / Published: 23 August 2023
(This article belongs to the Special Issue Genetic Diversity, Germplasm Resources, and Biotechnological Applications for Sustained Crop Improvement)
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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.
Keywords: allelic variants; cytochrome P450s; expression patterns; hormones; in/del markers; grain number; grain yield and plant development allelic variants; cytochrome P450s; expression patterns; hormones; in/del markers; grain number; grain yield and plant development

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MDPI and ACS Style

Sahoo, B.; Nayak, I.; Parameswaran, C.; Kesawat, M.S.; Sahoo, K.K.; Subudhi, H.N.; Balasubramaniasai, C.; Prabhukarthikeyan, S.R.; Katara, J.L.; Dash, S.K.; et al. 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 2023, 12, 3035. https://doi.org/10.3390/plants12173035

AMA Style

Sahoo B, Nayak I, Parameswaran C, Kesawat MS, Sahoo KK, Subudhi HN, Balasubramaniasai C, Prabhukarthikeyan SR, Katara JL, Dash SK, et al. 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. 2023; 12(17):3035. https://doi.org/10.3390/plants12173035

Chicago/Turabian Style

Sahoo, Bijayalaxmi, Itishree Nayak, C. Parameswaran, Mahipal Singh Kesawat, Khirod Kumar Sahoo, H. N. Subudhi, Cayalvizhi Balasubramaniasai, S. R. Prabhukarthikeyan, Jawahar Lal Katara, Sushanta Kumar Dash, and et al. 2023. "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 12, no. 17: 3035. https://doi.org/10.3390/plants12173035

APA Style

Sahoo, B., Nayak, I., Parameswaran, C., Kesawat, M. S., Sahoo, K. K., Subudhi, H. N., Balasubramaniasai, C., Prabhukarthikeyan, S. R., Katara, J. L., Dash, S. K., Chung, S.-M., Siddiqui, M. H., Alamri, S., & Samantaray, S. (2023). 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, 12(17), 3035. https://doi.org/10.3390/plants12173035

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