Changes in Alternative Splicing Revealed Special Metabolic Pathways Related to Heterosis of Heading Chinese Cabbage
As an important genetic improvement technique in current production practice, heterosis is widely used to enhance the productive traits of hybrid progeny from their parents. Alternative splicing (AS) analysis can be used as a method for exploring the molecular manifestations of heterosis. In our res...
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2022-12-01
|
| Series: | Horticulturae |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2311-7524/9/1/17 |
| _version_ | 1797441867856478208 |
|---|---|
| author | Ru Li Min Tian Shanshan Nie Lugang Zhang |
| author_facet | Ru Li Min Tian Shanshan Nie Lugang Zhang |
| author_sort | Ru Li |
| collection | DOAJ |
| description | As an important genetic improvement technique in current production practice, heterosis is widely used to enhance the productive traits of hybrid progeny from their parents. Alternative splicing (AS) analysis can be used as a method for exploring the molecular manifestations of heterosis. In our research, 16 hybrids and their parents were utilized to analyze the heterosis performance and AS events. Statistics of plant gross weight (PGW) showed that these hybrids had prominent heterosis, with the mid-parent heterosis values (MPV) ranging from 15.69% to 233.98%. Through pairwise comparison among the female parent, male parent, and hybrid, there were 2980–3205 AS events in each combination, with intron retention being the most common type followed by alternate 3’ splice site, alternative 5’ splice site, skipped exon, and mutually exclusive exon.There were 263–409 differential AS genes (DASGs) between the female parent and the hybrid, and 234–425 DASGs between the male parent and the hybrid in cross combinations. The DASGs were significantly enriched in 33 metabolic pathways in 16 cross combinations, and DASGs of different cross combinations were enriched in different metabolic pathways. Moreover, 76 DASGs in the strong heterosis combinations were identified and significantly enriched in the metabolic pathways related to amino acid metabolism. Further analysis revealed that most of these DASGs in amino acid metabolism were expressed differently in strong heterosis combinations. In addition, the expression levels of <i>BraA06g014310.3C</i> and <i>BraA03g041700.3C</i> in amino acid metabolism significantly correlated with PGW. These results could provide an index for future studies of the genetic and molecular mechanism of heterosis in hybrids. |
| first_indexed | 2024-03-09T12:31:13Z |
| format | Article |
| id | doaj.art-f64ea6f7c5e040cdb3bfe40355902139 |
| institution | Directory Open Access Journal |
| issn | 2311-7524 |
| language | English |
| last_indexed | 2024-03-09T12:31:13Z |
| publishDate | 2022-12-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Horticulturae |
| spelling | doaj.art-f64ea6f7c5e040cdb3bfe403559021392023-11-30T22:29:41ZengMDPI AGHorticulturae2311-75242022-12-01911710.3390/horticulturae9010017Changes in Alternative Splicing Revealed Special Metabolic Pathways Related to Heterosis of Heading Chinese CabbageRu Li0Min Tian1Shanshan Nie2Lugang Zhang3State Key Laboratory of Crop Stress Biology for Arid Area, College of Horticulture, Northwest A&F University, Xianyang 712100, ChinaState Key Laboratory of Crop Stress Biology for Arid Area, College of Horticulture, Northwest A&F University, Xianyang 712100, ChinaState Key Laboratory of Crop Stress Biology for Arid Area, College of Horticulture, Northwest A&F University, Xianyang 712100, ChinaState Key Laboratory of Crop Stress Biology for Arid Area, College of Horticulture, Northwest A&F University, Xianyang 712100, ChinaAs an important genetic improvement technique in current production practice, heterosis is widely used to enhance the productive traits of hybrid progeny from their parents. Alternative splicing (AS) analysis can be used as a method for exploring the molecular manifestations of heterosis. In our research, 16 hybrids and their parents were utilized to analyze the heterosis performance and AS events. Statistics of plant gross weight (PGW) showed that these hybrids had prominent heterosis, with the mid-parent heterosis values (MPV) ranging from 15.69% to 233.98%. Through pairwise comparison among the female parent, male parent, and hybrid, there were 2980–3205 AS events in each combination, with intron retention being the most common type followed by alternate 3’ splice site, alternative 5’ splice site, skipped exon, and mutually exclusive exon.There were 263–409 differential AS genes (DASGs) between the female parent and the hybrid, and 234–425 DASGs between the male parent and the hybrid in cross combinations. The DASGs were significantly enriched in 33 metabolic pathways in 16 cross combinations, and DASGs of different cross combinations were enriched in different metabolic pathways. Moreover, 76 DASGs in the strong heterosis combinations were identified and significantly enriched in the metabolic pathways related to amino acid metabolism. Further analysis revealed that most of these DASGs in amino acid metabolism were expressed differently in strong heterosis combinations. In addition, the expression levels of <i>BraA06g014310.3C</i> and <i>BraA03g041700.3C</i> in amino acid metabolism significantly correlated with PGW. These results could provide an index for future studies of the genetic and molecular mechanism of heterosis in hybrids.https://www.mdpi.com/2311-7524/9/1/17Chinese cabbageheterosisalternative splicingGO enrichmentKEGG enrichment |
| spellingShingle | Ru Li Min Tian Shanshan Nie Lugang Zhang Changes in Alternative Splicing Revealed Special Metabolic Pathways Related to Heterosis of Heading Chinese Cabbage Horticulturae Chinese cabbage heterosis alternative splicing GO enrichment KEGG enrichment |
| title | Changes in Alternative Splicing Revealed Special Metabolic Pathways Related to Heterosis of Heading Chinese Cabbage |
| title_full | Changes in Alternative Splicing Revealed Special Metabolic Pathways Related to Heterosis of Heading Chinese Cabbage |
| title_fullStr | Changes in Alternative Splicing Revealed Special Metabolic Pathways Related to Heterosis of Heading Chinese Cabbage |
| title_full_unstemmed | Changes in Alternative Splicing Revealed Special Metabolic Pathways Related to Heterosis of Heading Chinese Cabbage |
| title_short | Changes in Alternative Splicing Revealed Special Metabolic Pathways Related to Heterosis of Heading Chinese Cabbage |
| title_sort | changes in alternative splicing revealed special metabolic pathways related to heterosis of heading chinese cabbage |
| topic | Chinese cabbage heterosis alternative splicing GO enrichment KEGG enrichment |
| url | https://www.mdpi.com/2311-7524/9/1/17 |
| work_keys_str_mv | AT ruli changesinalternativesplicingrevealedspecialmetabolicpathwaysrelatedtoheterosisofheadingchinesecabbage AT mintian changesinalternativesplicingrevealedspecialmetabolicpathwaysrelatedtoheterosisofheadingchinesecabbage AT shanshannie changesinalternativesplicingrevealedspecialmetabolicpathwaysrelatedtoheterosisofheadingchinesecabbage AT lugangzhang changesinalternativesplicingrevealedspecialmetabolicpathwaysrelatedtoheterosisofheadingchinesecabbage |