Integrated SMRT Technology with UMI RNA-Seq Reveals the Hub Genes in Stamen Petalody in <i>Camellia oleifera</i>
Male sterility caused by stamen petalody is a key factor for a low fruit set rate and a low yield of <i>Camellia oleifera</i> but can serve as a useful genetic tool because it eliminates the need for artificial emasculation. However, its molecular regulation mechanism still remains uncle...
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MDPI AG
2021-06-01
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| Series: | Forests |
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| Online Access: | https://www.mdpi.com/1999-4907/12/6/749 |
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| author | Huie Li Yang Hu Chao Gao Qiqiang Guo Quanen Deng Hong Nan Lan Yang Hongli Wei Jie Qiu Lu Yang |
| author_facet | Huie Li Yang Hu Chao Gao Qiqiang Guo Quanen Deng Hong Nan Lan Yang Hongli Wei Jie Qiu Lu Yang |
| author_sort | Huie Li |
| collection | DOAJ |
| description | Male sterility caused by stamen petalody is a key factor for a low fruit set rate and a low yield of <i>Camellia oleifera</i> but can serve as a useful genetic tool because it eliminates the need for artificial emasculation. However, its molecular regulation mechanism still remains unclear. In this study, transcriptome was sequenced and analyzed on two types of bud materials, stamen petalody mutants and normal materials, at six stages of stamen development based on integrated single-molecule real-time (SMRT) technology with unique molecular identifiers (UMI) and RNA-seq technology to identify the hub genes responsible for stamen petalody in <i>C. oleifera</i>. The results show that a large number of alternative splicing events were identified in the transcriptome. A co-expression network analysis of <i>MADSs</i> and all the differentially expressed genes between the mutant stamens and the normal materials showed that four <i>MADS</i> transcription factor genes, <i>CoSEP3.1</i>, <i>CoAGL6</i>, <i>CoSEP3.2</i>, and <i>CoAP3</i>, were predicted to be the hub genes responsible for stamen petalody. Among these four, the expression patterns of <i>CoAGL6</i> and <i>CoSEP3.2</i> were consistently high in the mutant samples, but relatively low in the normal samples at six stages, while the patterns of <i>CoSEP3.1</i> and <i>CoAP3</i> were initially low in mutants and then were upregulated during development but remained relatively high in the normal materials. Furthermore, the genes with high connectivity to the hub genes showed significantly different expression patterns between the mutant stamens and the normal materials at different stages. qRT-PCR results showed a similar expression pattern of the hub genes in the RNA-seq. These results lay a solid foundation for the directive breeding of <i>C. oleifera</i> varieties and provide references for the genetic breeding of ornamental <i>Camellia</i> varieties. |
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| institution | Directory Open Access Journal |
| issn | 1999-4907 |
| language | English |
| last_indexed | 2024-03-10T10:40:09Z |
| publishDate | 2021-06-01 |
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| spelling | doaj.art-8fb6ebdb50014639ac70209d146602682023-11-21T23:00:04ZengMDPI AGForests1999-49072021-06-0112674910.3390/f12060749Integrated SMRT Technology with UMI RNA-Seq Reveals the Hub Genes in Stamen Petalody in <i>Camellia oleifera</i>Huie Li0Yang Hu1Chao Gao2Qiqiang Guo3Quanen Deng4Hong Nan5Lan Yang6Hongli Wei7Jie Qiu8Lu Yang9College of Agriculture, Guizhou University, Guiyang 550025, ChinaInstitute for Forest Resources and Environment of Guizhou, Guizhou University, Guiyang 550025, ChinaInstitute for Forest Resources and Environment of Guizhou, Guizhou University, Guiyang 550025, ChinaInstitute for Forest Resources and Environment of Guizhou, Guizhou University, Guiyang 550025, ChinaInstitute for Forest Resources and Environment of Guizhou, Guizhou University, Guiyang 550025, ChinaCollege of Agriculture, Guizhou University, Guiyang 550025, ChinaCollege of Agriculture, Guizhou University, Guiyang 550025, ChinaInstitute for Forest Resources and Environment of Guizhou, Guizhou University, Guiyang 550025, ChinaInstitute for Forest Resources and Environment of Guizhou, Guizhou University, Guiyang 550025, ChinaInstitute for Forest Resources and Environment of Guizhou, Guizhou University, Guiyang 550025, ChinaMale sterility caused by stamen petalody is a key factor for a low fruit set rate and a low yield of <i>Camellia oleifera</i> but can serve as a useful genetic tool because it eliminates the need for artificial emasculation. However, its molecular regulation mechanism still remains unclear. In this study, transcriptome was sequenced and analyzed on two types of bud materials, stamen petalody mutants and normal materials, at six stages of stamen development based on integrated single-molecule real-time (SMRT) technology with unique molecular identifiers (UMI) and RNA-seq technology to identify the hub genes responsible for stamen petalody in <i>C. oleifera</i>. The results show that a large number of alternative splicing events were identified in the transcriptome. A co-expression network analysis of <i>MADSs</i> and all the differentially expressed genes between the mutant stamens and the normal materials showed that four <i>MADS</i> transcription factor genes, <i>CoSEP3.1</i>, <i>CoAGL6</i>, <i>CoSEP3.2</i>, and <i>CoAP3</i>, were predicted to be the hub genes responsible for stamen petalody. Among these four, the expression patterns of <i>CoAGL6</i> and <i>CoSEP3.2</i> were consistently high in the mutant samples, but relatively low in the normal samples at six stages, while the patterns of <i>CoSEP3.1</i> and <i>CoAP3</i> were initially low in mutants and then were upregulated during development but remained relatively high in the normal materials. Furthermore, the genes with high connectivity to the hub genes showed significantly different expression patterns between the mutant stamens and the normal materials at different stages. qRT-PCR results showed a similar expression pattern of the hub genes in the RNA-seq. These results lay a solid foundation for the directive breeding of <i>C. oleifera</i> varieties and provide references for the genetic breeding of ornamental <i>Camellia</i> varieties.https://www.mdpi.com/1999-4907/12/6/749petaloid stamenmale sterilitydouble flowertranscriptomeWGCNA |
| spellingShingle | Huie Li Yang Hu Chao Gao Qiqiang Guo Quanen Deng Hong Nan Lan Yang Hongli Wei Jie Qiu Lu Yang Integrated SMRT Technology with UMI RNA-Seq Reveals the Hub Genes in Stamen Petalody in <i>Camellia oleifera</i> Forests petaloid stamen male sterility double flower transcriptome WGCNA |
| title | Integrated SMRT Technology with UMI RNA-Seq Reveals the Hub Genes in Stamen Petalody in <i>Camellia oleifera</i> |
| title_full | Integrated SMRT Technology with UMI RNA-Seq Reveals the Hub Genes in Stamen Petalody in <i>Camellia oleifera</i> |
| title_fullStr | Integrated SMRT Technology with UMI RNA-Seq Reveals the Hub Genes in Stamen Petalody in <i>Camellia oleifera</i> |
| title_full_unstemmed | Integrated SMRT Technology with UMI RNA-Seq Reveals the Hub Genes in Stamen Petalody in <i>Camellia oleifera</i> |
| title_short | Integrated SMRT Technology with UMI RNA-Seq Reveals the Hub Genes in Stamen Petalody in <i>Camellia oleifera</i> |
| title_sort | integrated smrt technology with umi rna seq reveals the hub genes in stamen petalody in i camellia oleifera i |
| topic | petaloid stamen male sterility double flower transcriptome WGCNA |
| url | https://www.mdpi.com/1999-4907/12/6/749 |
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