Transcriptome Analyses Indicate Significant Association of Increased Non-Additive and Allele-Specific Gene Expression with Hybrid Weakness in Rice (<i>Oryza sativa</i> L.)
The heterosis in hybrid rice is highly affected by the environment and hybrid weakness occurs frequently depending on the genotypes of the hybrid and its parents. Hybrid weakness was also observed in our field experiments on nine rice hybrids produced by 3 × 3 incomplete diallel crosses. Among the n...
| Main Authors: | , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2022-08-01
|
| Series: | Life |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2075-1729/12/8/1278 |
| _version_ | 1797431985558257664 |
|---|---|
| author | Yingheng Wang Jing Xia Likun Huang Qiang Lin Qiuhua Cai Hongguang Xie Wei He Yidong Wei Huaan Xie Weiqi Tang Weiren Wu Jianfu Zhang |
| author_facet | Yingheng Wang Jing Xia Likun Huang Qiang Lin Qiuhua Cai Hongguang Xie Wei He Yidong Wei Huaan Xie Weiqi Tang Weiren Wu Jianfu Zhang |
| author_sort | Yingheng Wang |
| collection | DOAJ |
| description | The heterosis in hybrid rice is highly affected by the environment and hybrid weakness occurs frequently depending on the genotypes of the hybrid and its parents. Hybrid weakness was also observed in our field experiments on nine rice hybrids produced by 3 × 3 incomplete diallel crosses. Among the nine hybrids, five displayed mid-parent heterosis (MPH) for grain yield per plant, while four showed mid-parent hybrid weakness (MPHW). A sequencing analysis of transcriptomes in panicles at the seed-filling stage revealed a significant association between enhanced non-additive gene expression (NAE) and allele-specific gene expression (ASE) with hybrid weakness. High proportions of ASE genes, with most being of mono-allele expression, were detected in the four MPHW hybrids, ranging from 22.65% to 45.97%; whereas only 4.80% to 5.69% of ASE genes were found in the five MPH hybrids. Moreover, an independence test indicated that the enhancements of NAE and ASE in the MPHW hybrids were significantly correlated. Based on the results of our study, we speculated that an unfavorable environment might cause hybrid weakness by enhancing ASE and NAE at the transcriptome level. |
| first_indexed | 2024-03-09T09:54:43Z |
| format | Article |
| id | doaj.art-cff6e4c42ed54eadbd6e09bbb6b8433f |
| institution | Directory Open Access Journal |
| issn | 2075-1729 |
| language | English |
| last_indexed | 2024-03-09T09:54:43Z |
| publishDate | 2022-08-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Life |
| spelling | doaj.art-cff6e4c42ed54eadbd6e09bbb6b8433f2023-12-01T23:54:56ZengMDPI AGLife2075-17292022-08-01128127810.3390/life12081278Transcriptome Analyses Indicate Significant Association of Increased Non-Additive and Allele-Specific Gene Expression with Hybrid Weakness in Rice (<i>Oryza sativa</i> L.)Yingheng Wang0Jing Xia1Likun Huang2Qiang Lin3Qiuhua Cai4Hongguang Xie5Wei He6Yidong Wei7Huaan Xie8Weiqi Tang9Weiren Wu10Jianfu Zhang11Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350019, ChinaCollege of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, ChinaCollege of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, ChinaRice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350019, ChinaRice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350019, ChinaRice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350019, ChinaRice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350019, ChinaRice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350019, ChinaRice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350019, ChinaMarine and Agricultural Biotechnology Laboratory, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou 350108, ChinaCollege of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, ChinaRice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350019, ChinaThe heterosis in hybrid rice is highly affected by the environment and hybrid weakness occurs frequently depending on the genotypes of the hybrid and its parents. Hybrid weakness was also observed in our field experiments on nine rice hybrids produced by 3 × 3 incomplete diallel crosses. Among the nine hybrids, five displayed mid-parent heterosis (MPH) for grain yield per plant, while four showed mid-parent hybrid weakness (MPHW). A sequencing analysis of transcriptomes in panicles at the seed-filling stage revealed a significant association between enhanced non-additive gene expression (NAE) and allele-specific gene expression (ASE) with hybrid weakness. High proportions of ASE genes, with most being of mono-allele expression, were detected in the four MPHW hybrids, ranging from 22.65% to 45.97%; whereas only 4.80% to 5.69% of ASE genes were found in the five MPH hybrids. Moreover, an independence test indicated that the enhancements of NAE and ASE in the MPHW hybrids were significantly correlated. Based on the results of our study, we speculated that an unfavorable environment might cause hybrid weakness by enhancing ASE and NAE at the transcriptome level.https://www.mdpi.com/2075-1729/12/8/1278mid-parent hybrid weakness (MPHW)non-additive gene expression (NAE)allele-specific gene expression (ASE)transcriptome |
| spellingShingle | Yingheng Wang Jing Xia Likun Huang Qiang Lin Qiuhua Cai Hongguang Xie Wei He Yidong Wei Huaan Xie Weiqi Tang Weiren Wu Jianfu Zhang Transcriptome Analyses Indicate Significant Association of Increased Non-Additive and Allele-Specific Gene Expression with Hybrid Weakness in Rice (<i>Oryza sativa</i> L.) Life mid-parent hybrid weakness (MPHW) non-additive gene expression (NAE) allele-specific gene expression (ASE) transcriptome |
| title | Transcriptome Analyses Indicate Significant Association of Increased Non-Additive and Allele-Specific Gene Expression with Hybrid Weakness in Rice (<i>Oryza sativa</i> L.) |
| title_full | Transcriptome Analyses Indicate Significant Association of Increased Non-Additive and Allele-Specific Gene Expression with Hybrid Weakness in Rice (<i>Oryza sativa</i> L.) |
| title_fullStr | Transcriptome Analyses Indicate Significant Association of Increased Non-Additive and Allele-Specific Gene Expression with Hybrid Weakness in Rice (<i>Oryza sativa</i> L.) |
| title_full_unstemmed | Transcriptome Analyses Indicate Significant Association of Increased Non-Additive and Allele-Specific Gene Expression with Hybrid Weakness in Rice (<i>Oryza sativa</i> L.) |
| title_short | Transcriptome Analyses Indicate Significant Association of Increased Non-Additive and Allele-Specific Gene Expression with Hybrid Weakness in Rice (<i>Oryza sativa</i> L.) |
| title_sort | transcriptome analyses indicate significant association of increased non additive and allele specific gene expression with hybrid weakness in rice i oryza sativa i l |
| topic | mid-parent hybrid weakness (MPHW) non-additive gene expression (NAE) allele-specific gene expression (ASE) transcriptome |
| url | https://www.mdpi.com/2075-1729/12/8/1278 |
| work_keys_str_mv | AT yinghengwang transcriptomeanalysesindicatesignificantassociationofincreasednonadditiveandallelespecificgeneexpressionwithhybridweaknessinriceioryzasativail AT jingxia transcriptomeanalysesindicatesignificantassociationofincreasednonadditiveandallelespecificgeneexpressionwithhybridweaknessinriceioryzasativail AT likunhuang transcriptomeanalysesindicatesignificantassociationofincreasednonadditiveandallelespecificgeneexpressionwithhybridweaknessinriceioryzasativail AT qianglin transcriptomeanalysesindicatesignificantassociationofincreasednonadditiveandallelespecificgeneexpressionwithhybridweaknessinriceioryzasativail AT qiuhuacai transcriptomeanalysesindicatesignificantassociationofincreasednonadditiveandallelespecificgeneexpressionwithhybridweaknessinriceioryzasativail AT hongguangxie transcriptomeanalysesindicatesignificantassociationofincreasednonadditiveandallelespecificgeneexpressionwithhybridweaknessinriceioryzasativail AT weihe transcriptomeanalysesindicatesignificantassociationofincreasednonadditiveandallelespecificgeneexpressionwithhybridweaknessinriceioryzasativail AT yidongwei transcriptomeanalysesindicatesignificantassociationofincreasednonadditiveandallelespecificgeneexpressionwithhybridweaknessinriceioryzasativail AT huaanxie transcriptomeanalysesindicatesignificantassociationofincreasednonadditiveandallelespecificgeneexpressionwithhybridweaknessinriceioryzasativail AT weiqitang transcriptomeanalysesindicatesignificantassociationofincreasednonadditiveandallelespecificgeneexpressionwithhybridweaknessinriceioryzasativail AT weirenwu transcriptomeanalysesindicatesignificantassociationofincreasednonadditiveandallelespecificgeneexpressionwithhybridweaknessinriceioryzasativail AT jianfuzhang transcriptomeanalysesindicatesignificantassociationofincreasednonadditiveandallelespecificgeneexpressionwithhybridweaknessinriceioryzasativail |