Genome-Wide Identification and Expression Analysis of NCED Gene Family in Pear and Its Response to Exogenous Gibberellin and Paclobutrazol
The 9-<i>cis</i>-epoxycarotenoid dioxygenase (<i>NCED</i>) is a key enzyme for the process of ABA synthesis that plays key roles in a variety of biological processes. In the current investigation, genome-wide identification and comprehensive analysis of the <i>NCED</...
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2023-04-01
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| author | Jinming Liu Xing Yuan Shaowen Quan Meng Zhang Chao Kang Caihua Guo Zhongrong Zhang Jianxin Niu |
| author_facet | Jinming Liu Xing Yuan Shaowen Quan Meng Zhang Chao Kang Caihua Guo Zhongrong Zhang Jianxin Niu |
| author_sort | Jinming Liu |
| collection | DOAJ |
| description | The 9-<i>cis</i>-epoxycarotenoid dioxygenase (<i>NCED</i>) is a key enzyme for the process of ABA synthesis that plays key roles in a variety of biological processes. In the current investigation, genome-wide identification and comprehensive analysis of the <i>NCED</i> gene family in ‘Kuerle Xiangli’ (<i>Pyrus sinkiangensis</i> Yu) were conducted using the pear genomic sequence. In total, nineteen members of <i>PbNCED</i> genes were identified from the whole genome of pear, which are not evenly distributed over the scaffolds, and most of which were focussed in the chloroplasts. Sequence analysis of promoters showed many <i>cis</i>-regulatory elements, which presumably responded to phytohormones such as abscisic acid, auxin, etc. Synteny block indicated that the <i>PbNCED</i> genes have experienced strong purifying selection. Multiple sequence alignment demonstrated that these members are highly similar and conserved. In addition, we found that <i>PbNCED</i> genes were differentially expressed in various tissues, and three <i>PbNCED</i> genes (<i>PbNCED1</i>, <i>PbNCED2</i>, and <i>PbNCED13</i>) were differentially expressed in response to exogenous Gibberellin (GA<sub>3</sub>) and Paclobutrazol (PP<sub>333</sub>). <i>PbNCED1</i> and <i>PbNCED13</i> positively promote ABA synthesis in sepals after GA<sub>3</sub> and PP<sub>333</sub> treatment, whereas <i>PbNCED2</i> positively regulated ABA synthesis in ovaries after GA<sub>3</sub> treatment, and <i>PbNCED13</i> positively regulated ABA synthesis in the ovaries after PP<sub>333</sub> treatment. This study was the first genome-wide report of the pear <i>NCED</i> gene family, which could improve our understanding of pear NCED proteins and provide a solid foundation for future cloning and functional analyses of this gene family. Meanwhile, our results also give a better understanding of the important genes and regulation pathways related to calyx abscission in ‘Kuerle Xiangli’. |
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| spelling | doaj.art-f267b3f7129947ef8f5dc4e8d8e6f8ed2023-11-17T19:42:41ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-04-01248756610.3390/ijms24087566Genome-Wide Identification and Expression Analysis of NCED Gene Family in Pear and Its Response to Exogenous Gibberellin and PaclobutrazolJinming Liu0Xing Yuan1Shaowen Quan2Meng Zhang3Chao Kang4Caihua Guo5Zhongrong Zhang6Jianxin Niu7Department of Horticulture, College of Agriculture, Shihezi University, Shihezi 832003, ChinaDepartment of Horticulture, College of Agriculture, Shihezi University, Shihezi 832003, ChinaDepartment of Horticulture, College of Agriculture, Shihezi University, Shihezi 832003, ChinaDepartment of Horticulture, College of Agriculture, Shihezi University, Shihezi 832003, ChinaDepartment of Horticulture, College of Agriculture, Shihezi University, Shihezi 832003, ChinaDepartment of Horticulture, College of Agriculture, Shihezi University, Shihezi 832003, ChinaDepartment of Horticulture, College of Agriculture, Shihezi University, Shihezi 832003, ChinaDepartment of Horticulture, College of Agriculture, Shihezi University, Shihezi 832003, ChinaThe 9-<i>cis</i>-epoxycarotenoid dioxygenase (<i>NCED</i>) is a key enzyme for the process of ABA synthesis that plays key roles in a variety of biological processes. In the current investigation, genome-wide identification and comprehensive analysis of the <i>NCED</i> gene family in ‘Kuerle Xiangli’ (<i>Pyrus sinkiangensis</i> Yu) were conducted using the pear genomic sequence. In total, nineteen members of <i>PbNCED</i> genes were identified from the whole genome of pear, which are not evenly distributed over the scaffolds, and most of which were focussed in the chloroplasts. Sequence analysis of promoters showed many <i>cis</i>-regulatory elements, which presumably responded to phytohormones such as abscisic acid, auxin, etc. Synteny block indicated that the <i>PbNCED</i> genes have experienced strong purifying selection. Multiple sequence alignment demonstrated that these members are highly similar and conserved. In addition, we found that <i>PbNCED</i> genes were differentially expressed in various tissues, and three <i>PbNCED</i> genes (<i>PbNCED1</i>, <i>PbNCED2</i>, and <i>PbNCED13</i>) were differentially expressed in response to exogenous Gibberellin (GA<sub>3</sub>) and Paclobutrazol (PP<sub>333</sub>). <i>PbNCED1</i> and <i>PbNCED13</i> positively promote ABA synthesis in sepals after GA<sub>3</sub> and PP<sub>333</sub> treatment, whereas <i>PbNCED2</i> positively regulated ABA synthesis in ovaries after GA<sub>3</sub> treatment, and <i>PbNCED13</i> positively regulated ABA synthesis in the ovaries after PP<sub>333</sub> treatment. This study was the first genome-wide report of the pear <i>NCED</i> gene family, which could improve our understanding of pear NCED proteins and provide a solid foundation for future cloning and functional analyses of this gene family. Meanwhile, our results also give a better understanding of the important genes and regulation pathways related to calyx abscission in ‘Kuerle Xiangli’.https://www.mdpi.com/1422-0067/24/8/7566‘Kuerle Xiangli’genome-wide<i>NCED</i> gene familyexpression analysis |
| spellingShingle | Jinming Liu Xing Yuan Shaowen Quan Meng Zhang Chao Kang Caihua Guo Zhongrong Zhang Jianxin Niu Genome-Wide Identification and Expression Analysis of NCED Gene Family in Pear and Its Response to Exogenous Gibberellin and Paclobutrazol International Journal of Molecular Sciences ‘Kuerle Xiangli’ genome-wide <i>NCED</i> gene family expression analysis |
| title | Genome-Wide Identification and Expression Analysis of NCED Gene Family in Pear and Its Response to Exogenous Gibberellin and Paclobutrazol |
| title_full | Genome-Wide Identification and Expression Analysis of NCED Gene Family in Pear and Its Response to Exogenous Gibberellin and Paclobutrazol |
| title_fullStr | Genome-Wide Identification and Expression Analysis of NCED Gene Family in Pear and Its Response to Exogenous Gibberellin and Paclobutrazol |
| title_full_unstemmed | Genome-Wide Identification and Expression Analysis of NCED Gene Family in Pear and Its Response to Exogenous Gibberellin and Paclobutrazol |
| title_short | Genome-Wide Identification and Expression Analysis of NCED Gene Family in Pear and Its Response to Exogenous Gibberellin and Paclobutrazol |
| title_sort | genome wide identification and expression analysis of nced gene family in pear and its response to exogenous gibberellin and paclobutrazol |
| topic | ‘Kuerle Xiangli’ genome-wide <i>NCED</i> gene family expression analysis |
| url | https://www.mdpi.com/1422-0067/24/8/7566 |
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