Identification of miRNAs and their target genes in genic male sterility lines in Brassica napus by small RNA sequencing
Abstract Background Brassica napus is the third leading source of edible oil in the world. Genic male sterility (GMS) lines provide crucial material for harnessing heterosis for rapeseed. GMS lines have been used successfully for rapeseed hybrid production in China. MicroRNAs (miRNAs) play crucial r...
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| Format: | Article |
| Language: | English |
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BMC
2021-11-01
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| Series: | BMC Plant Biology |
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| Online Access: | https://doi.org/10.1186/s12870-021-03306-w |
| _version_ | 1819045572856774656 |
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| author | Jianxia Jiang Pengfei Xu Yajie Li Yanli Li Xirong Zhou Meiyan Jiang Junying Zhang Jifeng Zhu Weirong Wang Liyong Yang |
| author_facet | Jianxia Jiang Pengfei Xu Yajie Li Yanli Li Xirong Zhou Meiyan Jiang Junying Zhang Jifeng Zhu Weirong Wang Liyong Yang |
| author_sort | Jianxia Jiang |
| collection | DOAJ |
| description | Abstract Background Brassica napus is the third leading source of edible oil in the world. Genic male sterility (GMS) lines provide crucial material for harnessing heterosis for rapeseed. GMS lines have been used successfully for rapeseed hybrid production in China. MicroRNAs (miRNAs) play crucial regulatory roles in various plant growth, development, and stress response processes. However, reports on miRNAs that regulate the pollen development of GMS lines in B. napus are few. Results In this study, 12 small RNA and transcriptome libraries were constructed and sequenced for the flower buds from the fertile and sterile lines of two recessive GMS (RGMS) lines, namely, “6251AB” and “6284AB”. At the same time, 12 small RNA and transcriptome libraries were also constructed and sequenced for the flower buds from the fertile and sterile lines of two dominant GMS (DGMS) lines, namely, “4001AB” and “4006AB”. Based on the results, 46 known miRNAs, 27 novel miRNAs on the other arm of known pre-miRNAs, and 44 new conserved miRNAs were identified. Thirty-five pairs of novel miRNA-3p/miRNA-5p were found. Among all the identified miRNAs, fifteen differentially expressed miRNAs with over 1.5-fold change between flower buds of sterile and fertile lines were identified, including six differentially expressed miRNAs between “4001A” and “4001B”, two differentially expressed miRNAs between “4006A” and “4006B”, four differentially expressed miRNAs between “6251A” and “6251B”, and ten differentially expressed miRNAs between “6284A” and “6284B”. The correlation analysis of small RNA and transcriptome sequencing was conducted. And 257 candidate target genes were predicted for the 15 differentially expressed miRNAs. The results of 5′ modified RACE indicated that BnaA09g48720D, BnaA09g11120D, and BnaCnng51960D were cleaved by bna-miR398a-3p, bna-miR158-3p and bna-miR159a, respectively. Among the differentially expressed miRNAs, miR159 was chosen to analyze its function. Overexpression of bna-miR159 in Arabidopsis resulted in decreased seed setting rate, and shortened siliques, illustrating that miR159 may regulate the fertility and silique development in rapeseed. Conclusions Our findings provide an overview of miRNAs that are potentially involved in GMS and pollen development. New information on miRNAs and their related target genes are provided to exploit the GMS mechanism and reveal the miRNA networks in B. napus. |
| first_indexed | 2024-12-21T10:30:43Z |
| format | Article |
| id | doaj.art-97d9bfe992044f2eb42623497d58586a |
| institution | Directory Open Access Journal |
| issn | 1471-2229 |
| language | English |
| last_indexed | 2024-12-21T10:30:43Z |
| publishDate | 2021-11-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj.art-97d9bfe992044f2eb42623497d58586a2022-12-21T19:07:13ZengBMCBMC Plant Biology1471-22292021-11-0121111810.1186/s12870-021-03306-wIdentification of miRNAs and their target genes in genic male sterility lines in Brassica napus by small RNA sequencingJianxia Jiang0Pengfei Xu1Yajie Li2Yanli Li3Xirong Zhou4Meiyan Jiang5Junying Zhang6Jifeng Zhu7Weirong Wang8Liyong Yang9Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural SciencesNational Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of SciencesSchool of Agriculture and Biology, Shanghai Jiao Tong UniversityCrop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural SciencesCrop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural SciencesCrop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural SciencesCrop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural SciencesCrop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural SciencesCrop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural SciencesCrop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural SciencesAbstract Background Brassica napus is the third leading source of edible oil in the world. Genic male sterility (GMS) lines provide crucial material for harnessing heterosis for rapeseed. GMS lines have been used successfully for rapeseed hybrid production in China. MicroRNAs (miRNAs) play crucial regulatory roles in various plant growth, development, and stress response processes. However, reports on miRNAs that regulate the pollen development of GMS lines in B. napus are few. Results In this study, 12 small RNA and transcriptome libraries were constructed and sequenced for the flower buds from the fertile and sterile lines of two recessive GMS (RGMS) lines, namely, “6251AB” and “6284AB”. At the same time, 12 small RNA and transcriptome libraries were also constructed and sequenced for the flower buds from the fertile and sterile lines of two dominant GMS (DGMS) lines, namely, “4001AB” and “4006AB”. Based on the results, 46 known miRNAs, 27 novel miRNAs on the other arm of known pre-miRNAs, and 44 new conserved miRNAs were identified. Thirty-five pairs of novel miRNA-3p/miRNA-5p were found. Among all the identified miRNAs, fifteen differentially expressed miRNAs with over 1.5-fold change between flower buds of sterile and fertile lines were identified, including six differentially expressed miRNAs between “4001A” and “4001B”, two differentially expressed miRNAs between “4006A” and “4006B”, four differentially expressed miRNAs between “6251A” and “6251B”, and ten differentially expressed miRNAs between “6284A” and “6284B”. The correlation analysis of small RNA and transcriptome sequencing was conducted. And 257 candidate target genes were predicted for the 15 differentially expressed miRNAs. The results of 5′ modified RACE indicated that BnaA09g48720D, BnaA09g11120D, and BnaCnng51960D were cleaved by bna-miR398a-3p, bna-miR158-3p and bna-miR159a, respectively. Among the differentially expressed miRNAs, miR159 was chosen to analyze its function. Overexpression of bna-miR159 in Arabidopsis resulted in decreased seed setting rate, and shortened siliques, illustrating that miR159 may regulate the fertility and silique development in rapeseed. Conclusions Our findings provide an overview of miRNAs that are potentially involved in GMS and pollen development. New information on miRNAs and their related target genes are provided to exploit the GMS mechanism and reveal the miRNA networks in B. napus.https://doi.org/10.1186/s12870-021-03306-wBrassica napusmiRNAsGenic male sterilityPollen developmentmiR159Silique development |
| spellingShingle | Jianxia Jiang Pengfei Xu Yajie Li Yanli Li Xirong Zhou Meiyan Jiang Junying Zhang Jifeng Zhu Weirong Wang Liyong Yang Identification of miRNAs and their target genes in genic male sterility lines in Brassica napus by small RNA sequencing BMC Plant Biology Brassica napus miRNAs Genic male sterility Pollen development miR159 Silique development |
| title | Identification of miRNAs and their target genes in genic male sterility lines in Brassica napus by small RNA sequencing |
| title_full | Identification of miRNAs and their target genes in genic male sterility lines in Brassica napus by small RNA sequencing |
| title_fullStr | Identification of miRNAs and their target genes in genic male sterility lines in Brassica napus by small RNA sequencing |
| title_full_unstemmed | Identification of miRNAs and their target genes in genic male sterility lines in Brassica napus by small RNA sequencing |
| title_short | Identification of miRNAs and their target genes in genic male sterility lines in Brassica napus by small RNA sequencing |
| title_sort | identification of mirnas and their target genes in genic male sterility lines in brassica napus by small rna sequencing |
| topic | Brassica napus miRNAs Genic male sterility Pollen development miR159 Silique development |
| url | https://doi.org/10.1186/s12870-021-03306-w |
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