Cargando…

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.)

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 we...

Descripción completa

Detalles Bibliográficos
Autores principales: Sahoo, Bijayalaxmi, Nayak, Itishree, Parameswaran, C., Kesawat, Mahipal Singh, Sahoo, Khirod Kumar, Subudhi, H. N., Balasubramaniasai, Cayalvizhi, Prabhukarthikeyan, S. R., Katara, Jawahar Lal, Dash, Sushanta Kumar, Chung, Sang-Min, Siddiqui, Manzer H., Alamri, Saud, Samantaray, Sanghamitra
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10490456/
https://www.ncbi.nlm.nih.gov/pubmed/37687282
http://dx.doi.org/10.3390/plants12173035
_version_ 1785103844556931072
author Sahoo, Bijayalaxmi
Nayak, Itishree
Parameswaran, C.
Kesawat, Mahipal Singh
Sahoo, Khirod Kumar
Subudhi, H. N.
Balasubramaniasai, Cayalvizhi
Prabhukarthikeyan, S. R.
Katara, Jawahar Lal
Dash, Sushanta Kumar
Chung, Sang-Min
Siddiqui, Manzer H.
Alamri, Saud
Samantaray, Sanghamitra
author_facet Sahoo, Bijayalaxmi
Nayak, Itishree
Parameswaran, C.
Kesawat, Mahipal Singh
Sahoo, Khirod Kumar
Subudhi, H. N.
Balasubramaniasai, Cayalvizhi
Prabhukarthikeyan, S. R.
Katara, Jawahar Lal
Dash, Sushanta Kumar
Chung, Sang-Min
Siddiqui, Manzer H.
Alamri, Saud
Samantaray, Sanghamitra
author_sort Sahoo, Bijayalaxmi
collection PubMed
description 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.
format Online
Article
Text
id pubmed-10490456
institution National Center for Biotechnology Information
language English
publishDate 2023
publisher MDPI
record_format MEDLINE/PubMed
spelling pubmed-104904562023-09-09 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.) Sahoo, Bijayalaxmi Nayak, Itishree Parameswaran, C. Kesawat, Mahipal Singh Sahoo, Khirod Kumar Subudhi, H. N. Balasubramaniasai, Cayalvizhi Prabhukarthikeyan, S. R. Katara, Jawahar Lal Dash, Sushanta Kumar Chung, Sang-Min Siddiqui, Manzer H. Alamri, Saud Samantaray, Sanghamitra Plants (Basel) Article 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. MDPI 2023-08-23 /pmc/articles/PMC10490456/ /pubmed/37687282 http://dx.doi.org/10.3390/plants12173035 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Sahoo, Bijayalaxmi
Nayak, Itishree
Parameswaran, C.
Kesawat, Mahipal Singh
Sahoo, Khirod Kumar
Subudhi, H. N.
Balasubramaniasai, Cayalvizhi
Prabhukarthikeyan, S. R.
Katara, Jawahar Lal
Dash, Sushanta Kumar
Chung, Sang-Min
Siddiqui, Manzer H.
Alamri, Saud
Samantaray, Sanghamitra
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.)
title 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.)
title_full 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.)
title_fullStr 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.)
title_full_unstemmed 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.)
title_short 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.)
title_sort 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.)
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10490456/
https://www.ncbi.nlm.nih.gov/pubmed/37687282
http://dx.doi.org/10.3390/plants12173035
work_keys_str_mv AT sahoobijayalaxmi acomprehensivegenomewideinvestigationofthecytochrome71oscyp71genefamilyrevealingtheimpactofpromoterandgenevariantsser33leuofoscyp71p6onyieldrelatedtraitsinindicariceoryzasatival
AT nayakitishree acomprehensivegenomewideinvestigationofthecytochrome71oscyp71genefamilyrevealingtheimpactofpromoterandgenevariantsser33leuofoscyp71p6onyieldrelatedtraitsinindicariceoryzasatival
AT parameswaranc acomprehensivegenomewideinvestigationofthecytochrome71oscyp71genefamilyrevealingtheimpactofpromoterandgenevariantsser33leuofoscyp71p6onyieldrelatedtraitsinindicariceoryzasatival
AT kesawatmahipalsingh acomprehensivegenomewideinvestigationofthecytochrome71oscyp71genefamilyrevealingtheimpactofpromoterandgenevariantsser33leuofoscyp71p6onyieldrelatedtraitsinindicariceoryzasatival
AT sahookhirodkumar acomprehensivegenomewideinvestigationofthecytochrome71oscyp71genefamilyrevealingtheimpactofpromoterandgenevariantsser33leuofoscyp71p6onyieldrelatedtraitsinindicariceoryzasatival
AT subudhihn acomprehensivegenomewideinvestigationofthecytochrome71oscyp71genefamilyrevealingtheimpactofpromoterandgenevariantsser33leuofoscyp71p6onyieldrelatedtraitsinindicariceoryzasatival
AT balasubramaniasaicayalvizhi acomprehensivegenomewideinvestigationofthecytochrome71oscyp71genefamilyrevealingtheimpactofpromoterandgenevariantsser33leuofoscyp71p6onyieldrelatedtraitsinindicariceoryzasatival
AT prabhukarthikeyansr acomprehensivegenomewideinvestigationofthecytochrome71oscyp71genefamilyrevealingtheimpactofpromoterandgenevariantsser33leuofoscyp71p6onyieldrelatedtraitsinindicariceoryzasatival
AT katarajawaharlal acomprehensivegenomewideinvestigationofthecytochrome71oscyp71genefamilyrevealingtheimpactofpromoterandgenevariantsser33leuofoscyp71p6onyieldrelatedtraitsinindicariceoryzasatival
AT dashsushantakumar acomprehensivegenomewideinvestigationofthecytochrome71oscyp71genefamilyrevealingtheimpactofpromoterandgenevariantsser33leuofoscyp71p6onyieldrelatedtraitsinindicariceoryzasatival
AT chungsangmin acomprehensivegenomewideinvestigationofthecytochrome71oscyp71genefamilyrevealingtheimpactofpromoterandgenevariantsser33leuofoscyp71p6onyieldrelatedtraitsinindicariceoryzasatival
AT siddiquimanzerh acomprehensivegenomewideinvestigationofthecytochrome71oscyp71genefamilyrevealingtheimpactofpromoterandgenevariantsser33leuofoscyp71p6onyieldrelatedtraitsinindicariceoryzasatival
AT alamrisaud acomprehensivegenomewideinvestigationofthecytochrome71oscyp71genefamilyrevealingtheimpactofpromoterandgenevariantsser33leuofoscyp71p6onyieldrelatedtraitsinindicariceoryzasatival
AT samantaraysanghamitra acomprehensivegenomewideinvestigationofthecytochrome71oscyp71genefamilyrevealingtheimpactofpromoterandgenevariantsser33leuofoscyp71p6onyieldrelatedtraitsinindicariceoryzasatival
AT sahoobijayalaxmi comprehensivegenomewideinvestigationofthecytochrome71oscyp71genefamilyrevealingtheimpactofpromoterandgenevariantsser33leuofoscyp71p6onyieldrelatedtraitsinindicariceoryzasatival
AT nayakitishree comprehensivegenomewideinvestigationofthecytochrome71oscyp71genefamilyrevealingtheimpactofpromoterandgenevariantsser33leuofoscyp71p6onyieldrelatedtraitsinindicariceoryzasatival
AT parameswaranc comprehensivegenomewideinvestigationofthecytochrome71oscyp71genefamilyrevealingtheimpactofpromoterandgenevariantsser33leuofoscyp71p6onyieldrelatedtraitsinindicariceoryzasatival
AT kesawatmahipalsingh comprehensivegenomewideinvestigationofthecytochrome71oscyp71genefamilyrevealingtheimpactofpromoterandgenevariantsser33leuofoscyp71p6onyieldrelatedtraitsinindicariceoryzasatival
AT sahookhirodkumar comprehensivegenomewideinvestigationofthecytochrome71oscyp71genefamilyrevealingtheimpactofpromoterandgenevariantsser33leuofoscyp71p6onyieldrelatedtraitsinindicariceoryzasatival
AT subudhihn comprehensivegenomewideinvestigationofthecytochrome71oscyp71genefamilyrevealingtheimpactofpromoterandgenevariantsser33leuofoscyp71p6onyieldrelatedtraitsinindicariceoryzasatival
AT balasubramaniasaicayalvizhi comprehensivegenomewideinvestigationofthecytochrome71oscyp71genefamilyrevealingtheimpactofpromoterandgenevariantsser33leuofoscyp71p6onyieldrelatedtraitsinindicariceoryzasatival
AT prabhukarthikeyansr comprehensivegenomewideinvestigationofthecytochrome71oscyp71genefamilyrevealingtheimpactofpromoterandgenevariantsser33leuofoscyp71p6onyieldrelatedtraitsinindicariceoryzasatival
AT katarajawaharlal comprehensivegenomewideinvestigationofthecytochrome71oscyp71genefamilyrevealingtheimpactofpromoterandgenevariantsser33leuofoscyp71p6onyieldrelatedtraitsinindicariceoryzasatival
AT dashsushantakumar comprehensivegenomewideinvestigationofthecytochrome71oscyp71genefamilyrevealingtheimpactofpromoterandgenevariantsser33leuofoscyp71p6onyieldrelatedtraitsinindicariceoryzasatival
AT chungsangmin comprehensivegenomewideinvestigationofthecytochrome71oscyp71genefamilyrevealingtheimpactofpromoterandgenevariantsser33leuofoscyp71p6onyieldrelatedtraitsinindicariceoryzasatival
AT siddiquimanzerh comprehensivegenomewideinvestigationofthecytochrome71oscyp71genefamilyrevealingtheimpactofpromoterandgenevariantsser33leuofoscyp71p6onyieldrelatedtraitsinindicariceoryzasatival
AT alamrisaud comprehensivegenomewideinvestigationofthecytochrome71oscyp71genefamilyrevealingtheimpactofpromoterandgenevariantsser33leuofoscyp71p6onyieldrelatedtraitsinindicariceoryzasatival
AT samantaraysanghamitra comprehensivegenomewideinvestigationofthecytochrome71oscyp71genefamilyrevealingtheimpactofpromoterandgenevariantsser33leuofoscyp71p6onyieldrelatedtraitsinindicariceoryzasatival