Integrated Analysis of Hi-C and RNA-Seq Reveals the Molecular Mechanism of Autopolyploid Growth Advantages in Pak Choi (Brassica rapa ssp. chinensis)
Polyploids generated by the replication of a single genome (autopolyploid) or synthesis of two or more distinct genomes (allopolyploid) usually show significant advantages over their diploid progenitors in biological characteristics, including growth and development, nutrient accumulation, and plant...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2022-06-01
|
| Series: | Frontiers in Plant Science |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2022.905202/full |
| _version_ | 1811238520114642944 |
|---|---|
| author | Huiyuan Wu Xiaoming Song Shanwu Lyu Yiming Ren Tongkun Liu Xilin Hou Ying Li Changwei Zhang |
| author_facet | Huiyuan Wu Xiaoming Song Shanwu Lyu Yiming Ren Tongkun Liu Xilin Hou Ying Li Changwei Zhang |
| author_sort | Huiyuan Wu |
| collection | DOAJ |
| description | Polyploids generated by the replication of a single genome (autopolyploid) or synthesis of two or more distinct genomes (allopolyploid) usually show significant advantages over their diploid progenitors in biological characteristics, including growth and development, nutrient accumulation, and plant resistance. Whereas, the impacts of genomic replication on transcription regulation and chromatin structure in pak choi have not been explored fully. In this study, we observed the transcriptional and genomic structural alterations between diploid B. rapa (AA) and artificial autotetraploid B. rapa (AAAA) using RNA-seq and Hi-C. RNA-seq revealed 1,786 differentially expressed genes (DEGs) between the diploids and autotetraploids, including 717 down-regulated and 1,069 up-regulated genes in autotetraploids. Of all the 1,786 DEGs, 23 DEGs (10 down-regulated DEGs in autotetraploids) were involved in Compartment A-B shifts, while 28 DEGs (20 up-regulated DEGs in autotetraploids) participated in Compartment B-A shifts. Moreover, there were 15 DEGs in activated topologically associating domains (TADs) (9 up-regulated DEGs in diploids) and 80 DEGs in repressed TADs (49 down-regulated DEGs in diploids). Subsequently, eight DEGs with genomic structural variants were selected as potential candidate genes, including four DEGs involved in photosynthesis (BraA01003143, BraA09002798, BraA04002224, and BraA08000594), three DEGs related to chloroplast (BraA05002974, BraA05001662, and BraA04001148), and one DEG associated with disease resistance (BraA09004451), which all showed high expression in autotetraploids. Overall, our results demonstrated that integrative RNA-seq and Hi-C analysis can identify related genes to phenotypic traits and also provided new insights into the molecular mechanism of the growth advantage of polyploids. |
| first_indexed | 2024-04-12T12:43:49Z |
| format | Article |
| id | doaj.art-9a1f3a5cedd8451590121c5c8eb6ca94 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-12T12:43:49Z |
| publishDate | 2022-06-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-9a1f3a5cedd8451590121c5c8eb6ca942022-12-22T03:32:42ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2022-06-011310.3389/fpls.2022.905202905202Integrated Analysis of Hi-C and RNA-Seq Reveals the Molecular Mechanism of Autopolyploid Growth Advantages in Pak Choi (Brassica rapa ssp. chinensis)Huiyuan Wu0Xiaoming Song1Shanwu Lyu2Yiming Ren3Tongkun Liu4Xilin Hou5Ying Li6Changwei Zhang7State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, ChinaCenter for Genomics and Bio-Computing, School of Life Sciences, North China University of Science and Technology, Tangshan, ChinaState Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, ChinaState Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, ChinaState Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, ChinaState Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, ChinaState Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, ChinaState Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, ChinaPolyploids generated by the replication of a single genome (autopolyploid) or synthesis of two or more distinct genomes (allopolyploid) usually show significant advantages over their diploid progenitors in biological characteristics, including growth and development, nutrient accumulation, and plant resistance. Whereas, the impacts of genomic replication on transcription regulation and chromatin structure in pak choi have not been explored fully. In this study, we observed the transcriptional and genomic structural alterations between diploid B. rapa (AA) and artificial autotetraploid B. rapa (AAAA) using RNA-seq and Hi-C. RNA-seq revealed 1,786 differentially expressed genes (DEGs) between the diploids and autotetraploids, including 717 down-regulated and 1,069 up-regulated genes in autotetraploids. Of all the 1,786 DEGs, 23 DEGs (10 down-regulated DEGs in autotetraploids) were involved in Compartment A-B shifts, while 28 DEGs (20 up-regulated DEGs in autotetraploids) participated in Compartment B-A shifts. Moreover, there were 15 DEGs in activated topologically associating domains (TADs) (9 up-regulated DEGs in diploids) and 80 DEGs in repressed TADs (49 down-regulated DEGs in diploids). Subsequently, eight DEGs with genomic structural variants were selected as potential candidate genes, including four DEGs involved in photosynthesis (BraA01003143, BraA09002798, BraA04002224, and BraA08000594), three DEGs related to chloroplast (BraA05002974, BraA05001662, and BraA04001148), and one DEG associated with disease resistance (BraA09004451), which all showed high expression in autotetraploids. Overall, our results demonstrated that integrative RNA-seq and Hi-C analysis can identify related genes to phenotypic traits and also provided new insights into the molecular mechanism of the growth advantage of polyploids.https://www.frontiersin.org/articles/10.3389/fpls.2022.905202/fullRNA-seqHi-CA/B compartmentTADsautopolyploidgrowth advantage |
| spellingShingle | Huiyuan Wu Xiaoming Song Shanwu Lyu Yiming Ren Tongkun Liu Xilin Hou Ying Li Changwei Zhang Integrated Analysis of Hi-C and RNA-Seq Reveals the Molecular Mechanism of Autopolyploid Growth Advantages in Pak Choi (Brassica rapa ssp. chinensis) Frontiers in Plant Science RNA-seq Hi-C A/B compartment TADs autopolyploid growth advantage |
| title | Integrated Analysis of Hi-C and RNA-Seq Reveals the Molecular Mechanism of Autopolyploid Growth Advantages in Pak Choi (Brassica rapa ssp. chinensis) |
| title_full | Integrated Analysis of Hi-C and RNA-Seq Reveals the Molecular Mechanism of Autopolyploid Growth Advantages in Pak Choi (Brassica rapa ssp. chinensis) |
| title_fullStr | Integrated Analysis of Hi-C and RNA-Seq Reveals the Molecular Mechanism of Autopolyploid Growth Advantages in Pak Choi (Brassica rapa ssp. chinensis) |
| title_full_unstemmed | Integrated Analysis of Hi-C and RNA-Seq Reveals the Molecular Mechanism of Autopolyploid Growth Advantages in Pak Choi (Brassica rapa ssp. chinensis) |
| title_short | Integrated Analysis of Hi-C and RNA-Seq Reveals the Molecular Mechanism of Autopolyploid Growth Advantages in Pak Choi (Brassica rapa ssp. chinensis) |
| title_sort | integrated analysis of hi c and rna seq reveals the molecular mechanism of autopolyploid growth advantages in pak choi brassica rapa ssp chinensis |
| topic | RNA-seq Hi-C A/B compartment TADs autopolyploid growth advantage |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2022.905202/full |
| work_keys_str_mv | AT huiyuanwu integratedanalysisofhicandrnaseqrevealsthemolecularmechanismofautopolyploidgrowthadvantagesinpakchoibrassicarapasspchinensis AT xiaomingsong integratedanalysisofhicandrnaseqrevealsthemolecularmechanismofautopolyploidgrowthadvantagesinpakchoibrassicarapasspchinensis AT shanwulyu integratedanalysisofhicandrnaseqrevealsthemolecularmechanismofautopolyploidgrowthadvantagesinpakchoibrassicarapasspchinensis AT yimingren integratedanalysisofhicandrnaseqrevealsthemolecularmechanismofautopolyploidgrowthadvantagesinpakchoibrassicarapasspchinensis AT tongkunliu integratedanalysisofhicandrnaseqrevealsthemolecularmechanismofautopolyploidgrowthadvantagesinpakchoibrassicarapasspchinensis AT xilinhou integratedanalysisofhicandrnaseqrevealsthemolecularmechanismofautopolyploidgrowthadvantagesinpakchoibrassicarapasspchinensis AT yingli integratedanalysisofhicandrnaseqrevealsthemolecularmechanismofautopolyploidgrowthadvantagesinpakchoibrassicarapasspchinensis AT changweizhang integratedanalysisofhicandrnaseqrevealsthemolecularmechanismofautopolyploidgrowthadvantagesinpakchoibrassicarapasspchinensis |