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Huang Q, Wen C, Gu S, Jie Y, Li G, Yan Y, Tian C, Wu G, Yang N. Synergy of gut microbiota and host genome in driving heterosis expression of chickens. J Genet Genomics 2024; 51:1121-1134. [PMID: 38950856 DOI: 10.1016/j.jgg.2024.06.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 06/18/2024] [Accepted: 06/19/2024] [Indexed: 07/03/2024]
Abstract
Heterosis has been widely utilized in agricultural production. Despite over a century of extensive research, the underlying mechanisms of heterosis remain elusive. Most hypotheses and research have focused on the genetic basis of heterosis. However, the potential role of gut microbiota in heterosis has been largely ignored. Here, we carefully design a crossbreeding experiment with two distinct broiler breeds and conduct 16S rRNA amplicon and transcriptome sequencing to investigate the synergistic role of gut microbiota and host genes in driving heterosis. We find that the breast muscle weight of hybrids exhibits a high heterosis, 6.28% higher than the mid-parent value. A notable difference is observed in the composition and potential function of cecal microbiota between hybrids and their parents. Over 90% of differentially colonized microbiota and differentially expressed genes exhibit nonadditive patterns. Integrative analyses uncover associations between nonadditive genes and nonadditive microbiota, including a connection between the expression of cellular signaling pathways and metabolism-related genes and the abundance of Odoribacter, Oscillibacter, and Alistipes in hybrids. Moreover, higher abundances of these microbiota are related to better meat yield. In summary, these findings highlight the importance of gut microbiota in heterosis, serving as crucial factors that modulate heterosis expression in chickens.
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Affiliation(s)
- Qiang Huang
- State Key Laboratory of Animal Biotech Breeding and Frontier Science Center for Molecular Design Breeding, China Agricultural University, Beijing 100193, China; National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Chaoliang Wen
- State Key Laboratory of Animal Biotech Breeding and Frontier Science Center for Molecular Design Breeding, China Agricultural University, Beijing 100193, China; National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; Sanya Institute of China Agricultural University, Hainan 572025, China.
| | - Shuang Gu
- State Key Laboratory of Animal Biotech Breeding and Frontier Science Center for Molecular Design Breeding, China Agricultural University, Beijing 100193, China; National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Yuchen Jie
- State Key Laboratory of Animal Biotech Breeding and Frontier Science Center for Molecular Design Breeding, China Agricultural University, Beijing 100193, China; National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Guangqi Li
- Beijing Huadu Yukou Poultry Industry Co. Ltd., Beijing 101206, China
| | - Yiyuan Yan
- Beijing Huadu Yukou Poultry Industry Co. Ltd., Beijing 101206, China
| | - Chuanyao Tian
- Beijing Huadu Yukou Poultry Industry Co. Ltd., Beijing 101206, China
| | - Guiqin Wu
- Beijing Huadu Yukou Poultry Industry Co. Ltd., Beijing 101206, China
| | - Ning Yang
- State Key Laboratory of Animal Biotech Breeding and Frontier Science Center for Molecular Design Breeding, China Agricultural University, Beijing 100193, China; National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; Sanya Institute of China Agricultural University, Hainan 572025, China.
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Ren Y, Wu L, Zhong Y, Zhao X, Xu M, Wang J. Transcriptome Analysis Revealed the Paternal Importance to Vegetative Growth Heterosis in Populus. PLANTS (BASEL, SWITZERLAND) 2024; 13:2278. [PMID: 39204714 PMCID: PMC11359908 DOI: 10.3390/plants13162278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 06/30/2024] [Accepted: 08/14/2024] [Indexed: 09/04/2024]
Abstract
Parental selection is important for heterosis formation during crossbreeding of Populus. However, in poplar hybrids, the effect of parents on vegetative growth heterosis is not well understood. In this study, one female parent (P. simonii XY4) and two male parents (P. nigra OH and P. deltoides × P. nigra BJLY3#) were used to produce two progenies (Hyb1 and Hyb2). Vegetative growth investigation showed that both Hyb1 and Hyb2 performed heterosis in plant growth and ground diameter. The vegetative growth of hybrids was strongly correlated with the male parents but not with the female parents. The gene expression levels in the hybrids were more biased toward the male parents. In Hyb1 and Hyb2, 51.93% and 45.03% of the expressed genes showed the non-additive effect, respectively, and over 65% of the non-additively expressed genes showed the dominant effect. It is noteworthy that genes of paternal expression dominant effect (ELD_♂) account for the majority of dominantly expressed genes, suggesting the paternal contribution to heterosis. KEGG enrichment analysis indicated that a large number of non-additively expressed genes were enriched in the plant hormone signal transduction pathway. WGCNA analysis showed that MEcyan was significantly correlated with the traits of hybrids, and 12 plant hormone signal transduction pathway genes were enriched in this module. Transcription factors (TFs) MYB88, LHY, and TCP4 may be involved in the regulation of these pathway genes. This finding supported that the male parents play an important role in the formation of vegetative growth heterosis of Populus. In addition, the non-additively expressed genes of the signal transduction pathway and the regulation of TFs related to these pathway genes may be one of the reasons for the generation of heterosis.
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Affiliation(s)
- Yuxin Ren
- State Key Laboratory of Tree Genetics and Breeding, Beijing Forestry University, Beijing 100083, China; (Y.R.)
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing 100083, China
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Lixia Wu
- State Key Laboratory of Tree Genetics and Breeding, Beijing Forestry University, Beijing 100083, China; (Y.R.)
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing 100083, China
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Yuhang Zhong
- State Key Laboratory of Tree Genetics and Breeding, Beijing Forestry University, Beijing 100083, China; (Y.R.)
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing 100083, China
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Xinwen Zhao
- Liaoning Provincial Institute of Poplar, Gaizhou 115213, China
| | - Meng Xu
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Jun Wang
- State Key Laboratory of Tree Genetics and Breeding, Beijing Forestry University, Beijing 100083, China; (Y.R.)
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing 100083, China
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
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Lu A, Zeng S, Pi K, Long B, Mo Z, Liu R. Transcriptome analysis reveals the key role of overdominant expression of photosynthetic and respiration-related genes in the formation of tobacco(Nicotiana tabacum L.) biomass heterosis. BMC Genomics 2024; 25:598. [PMID: 38877410 PMCID: PMC11177473 DOI: 10.1186/s12864-024-10507-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 06/06/2024] [Indexed: 06/16/2024] Open
Abstract
BACKGROUND Leaves are the nutritional and economic organs of tobacco, and their biomass directly affects tobacco yield and the economic benefits of farmers. In the early stage, our research found that tobacco hybrids have more leaves and larger leaf areas, but the performance and formation reasons of biomass heterosis are not yet clear. RESULTS This study selected 5 parents with significant differences in tobacco biomass and paired them with hybrid varieties. It was found that tobacco hybrid varieties have a common biomass heterosis, and 45 days after transplantation is the key period for the formation of tobacco biomass heterosis; By analyzing the biomass heterosis of hybrids, Va116×GDH94 and its parents were selected for transcriptome analysis. 76.69% of the differentially expressed genes between Va116×GDH94 and its parents showed overdominant expression pattern, and these overdominant expression genes were significantly enriched in the biological processes of photosynthesis and TCA cycle; During the process of photosynthesis, the overdominant up-regulation of genes such as Lhc, Psa, and rbcl promotes the progress of photosynthesis, thereby increasing the accumulation of tobacco biomass; During the respiratory process, genes such as MDH, ACO, and OGDH are overedominantly down-regulated, inhibiting the TCA cycle and reducing substrate consumption in hybrid offspring; The photosynthetic characteristics of the hybrid and its parents were measured, and the net photosynthetic capacity of the hybrid was significantly higher than that of the parents. CONCLUSION These results indicate that the overdominant expression effect of differentially expressed genes in Va116×GDH94 and its parents plays a crucial role in the formation of tobacco biomass heterosis. The overdominant expression of genes related to photosynthesis and respiration enhances the photosynthetic ability of Va116×GDH94, reduces respiratory consumption, promotes the increase of biomass, and exhibits obvious heterosis.
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Affiliation(s)
- Anbin Lu
- College of Tobacco Science, Guizhou University, Guiyang, China
- Key Laboratory of Tobacco Quality in Guizhou Province, Guiyang, China
| | - Shuaibo Zeng
- College of Tobacco Science, Guizhou University, Guiyang, China
- Key Laboratory of Tobacco Quality in Guizhou Province, Guiyang, China
| | - Kai Pi
- College of Tobacco Science, Guizhou University, Guiyang, China
- Key Laboratory of Tobacco Quality in Guizhou Province, Guiyang, China
| | - Benshan Long
- College of Tobacco Science, Guizhou University, Guiyang, China
- Key Laboratory of Tobacco Quality in Guizhou Province, Guiyang, China
| | - Zejun Mo
- College of Agriculture, Guizhou University, Guiyang, China
- Key Laboratory of Tobacco Quality in Guizhou Province, Guiyang, China
| | - Renxiang Liu
- College of Tobacco Science, Guizhou University, Guiyang, China.
- Key Laboratory of Tobacco Quality in Guizhou Province, Guiyang, China.
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Su J, Zhao L, Yang Y, Yang Y, Zhang X, Guan Z, Fang W, Chen F, Zhang F. Comparative transcriptome analysis provides molecular insights into heterosis of waterlogging tolerance in Chrysanthemum indicum. BMC PLANT BIOLOGY 2024; 24:259. [PMID: 38594635 PMCID: PMC11005212 DOI: 10.1186/s12870-024-04954-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 03/27/2024] [Indexed: 04/11/2024]
Abstract
BACKGROUND Heterosis breeding is one of the most important breeding methods for chrysanthemum. To date, the genetic mechanisms of heterosis for waterlogging tolerance in chrysanthemum are still unclear. This study aims to analyze the expression profiles and potential heterosis-related genes of two hybrid lines and their parents with extreme differences in waterlogging tolerance under control and waterlogging stress conditions by RNA-seq. RESULTS A population of 140 F1 progeny derived from Chrysanthemum indicum (Nanchang) (waterlogging-tolerant) and Chrysanthemum indicum (Nanjing) (waterlogging-sensitive) was used to characterize the extent of genetic variation in terms of seven waterlogging tolerance-related traits across two years. Lines 98 and 95, respectively displaying positive and negative overdominance heterosis for the waterlogging tolerance traits together with their parents under control and waterlogging stress conditions, were used for RNA-seq. In consequence, the maximal number of differentially expressed genes (DEGs) occurred in line 98. Gene ontology (GO) enrichment analysis revealed multiple stress-related biological processes for the common up-regulated genes. Line 98 had a significant increase in non-additive genes under waterlogging stress, with transgressive up-regulation and paternal-expression dominant patterns being the major gene expression profiles. Further, GO analysis identified 55 and 95 transgressive up-regulation genes that overlapped with the up-regulated genes shared by two parents in terms of responses to stress and stimulus, respectively. 6,640 genes in total displaying maternal-expression dominance patterns were observed in line 95. In addition, 16 key candidate genes, including SAP12, DOX1, and ERF017 which might be of significant importance for the formation of waterlogging tolerance heterosis in line 98, were highlighted. CONCLUSION The current study provides a comprehensive overview of the root transcriptomes among F1 hybrids and their parents under waterlogging stress. These findings lay the foundation for further studies on molecular mechanisms underlying chrysanthemum heterosis on waterlogging tolerance.
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Affiliation(s)
- Jiangshuo Su
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, College of Horticulture, National Forestry and Grassland Administration, Nanjing Agricultural University, Weigang No.1, Nanjing, Jiangsu Province, 210095, P.R. China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, China
| | - Limin Zhao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, College of Horticulture, National Forestry and Grassland Administration, Nanjing Agricultural University, Weigang No.1, Nanjing, Jiangsu Province, 210095, P.R. China
| | - Yingnan Yang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, College of Horticulture, National Forestry and Grassland Administration, Nanjing Agricultural University, Weigang No.1, Nanjing, Jiangsu Province, 210095, P.R. China
| | - Yang Yang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, College of Horticulture, National Forestry and Grassland Administration, Nanjing Agricultural University, Weigang No.1, Nanjing, Jiangsu Province, 210095, P.R. China
| | - Xuefeng Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, College of Horticulture, National Forestry and Grassland Administration, Nanjing Agricultural University, Weigang No.1, Nanjing, Jiangsu Province, 210095, P.R. China
| | - Zhiyong Guan
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, College of Horticulture, National Forestry and Grassland Administration, Nanjing Agricultural University, Weigang No.1, Nanjing, Jiangsu Province, 210095, P.R. China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, China
| | - Weimin Fang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, College of Horticulture, National Forestry and Grassland Administration, Nanjing Agricultural University, Weigang No.1, Nanjing, Jiangsu Province, 210095, P.R. China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, China
| | - Fadi Chen
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, College of Horticulture, National Forestry and Grassland Administration, Nanjing Agricultural University, Weigang No.1, Nanjing, Jiangsu Province, 210095, P.R. China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, China
| | - Fei Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, College of Horticulture, National Forestry and Grassland Administration, Nanjing Agricultural University, Weigang No.1, Nanjing, Jiangsu Province, 210095, P.R. China.
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, China.
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Liu C, Mao B, Zhang Y, Tian L, Ma B, Chen Z, Wei Z, Li A, Shao Y, Cheng G, Li L, Li W, Zhang D, Ding X, Peng J, Peng Y, He J, Ye N, Yuan D, Chu C, Duan M. The OsWRKY72-OsAAT30/OsGSTU26 module mediates reactive oxygen species scavenging to drive heterosis for salt tolerance in hybrid rice. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:709-730. [PMID: 38483018 DOI: 10.1111/jipb.13640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 02/23/2024] [Indexed: 04/11/2024]
Abstract
Hybrid rice (Oryza sativa) generally outperforms its inbred parents in yield and stress tolerance, a phenomenon termed heterosis, but the underlying mechanism is not completely understood. Here, we combined transcriptome, proteome, physiological, and heterosis analyses to examine the salt response of super hybrid rice Chaoyou1000 (CY1000). In addition to surpassing the mean values for its two parents (mid-parent heterosis), CY1000 exhibited a higher reactive oxygen species scavenging ability than both its parents (over-parent heterosis or heterobeltiosis). Nonadditive expression and allele-specific gene expression assays showed that the glutathione S-transferase gene OsGSTU26 and the amino acid transporter gene OsAAT30 may have major roles in heterosis for salt tolerance, acting in an overdominant fashion in CY1000. Furthermore, we identified OsWRKY72 as a common transcription factor that binds and regulates OsGSTU26 and OsAAT30. The salt-sensitive phenotypes were associated with the OsWRKY72paternal genotype or the OsAAT30maternal genotype in core rice germplasm varieties. OsWRKY72paternal specifically repressed the expression of OsGSTU26 under salt stress, leading to salinity sensitivity, while OsWRKY72maternal specifically repressed OsAAT30, resulting in salinity tolerance. These results suggest that the OsWRKY72-OsAAT30/OsGSTU26 module may play an important role in heterosis for salt tolerance in an overdominant fashion in CY1000 hybrid rice, providing valuable clues to elucidate the mechanism of heterosis for salinity tolerance in hybrid rice.
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Affiliation(s)
- Citao Liu
- Hunan Provincial Key Laboratory of Stress Biology, College of Agriculture, Hunan Agricultural University, Changsha, 410128, China
| | - Bigang Mao
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125, China
| | - Yanxia Zhang
- College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Lei Tian
- State Key Laboratory of Wheat and Maize Crop Science, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Biao Ma
- College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Zhuo Chen
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhongwei Wei
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125, China
| | - Aifu Li
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Ye Shao
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125, China
| | - Gongye Cheng
- Hunan Provincial Key Laboratory of Stress Biology, College of Agriculture, Hunan Agricultural University, Changsha, 410128, China
| | - Lingling Li
- Hunan Provincial Key Laboratory of Stress Biology, College of Agriculture, Hunan Agricultural University, Changsha, 410128, China
| | - Wenyu Li
- Hunan Provincial Key Laboratory of Stress Biology, College of Agriculture, Hunan Agricultural University, Changsha, 410128, China
| | - Di Zhang
- Hunan Provincial Key Laboratory of Stress Biology, College of Agriculture, Hunan Agricultural University, Changsha, 410128, China
| | - Xiaoping Ding
- Hunan Provincial Key Laboratory of Stress Biology, College of Agriculture, Hunan Agricultural University, Changsha, 410128, China
| | | | - Yulin Peng
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125, China
| | - Jiwai He
- Hunan Provincial Key Laboratory of Stress Biology, College of Agriculture, Hunan Agricultural University, Changsha, 410128, China
| | - Nenghui Ye
- Hunan Provincial Key Laboratory of Stress Biology, College of Agriculture, Hunan Agricultural University, Changsha, 410128, China
| | - Dingyang Yuan
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125, China
| | - Chengcai Chu
- College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Meijuan Duan
- Hunan Provincial Key Laboratory of Stress Biology, College of Agriculture, Hunan Agricultural University, Changsha, 410128, China
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Wang S, Wu H, Lu Z, Liu W, Wang X, Fang Z, He X. Combining Ability Analysis of Yield-Related Traits of Two Elite Rice Restorer Lines in Chinese Hybrid Rice. Int J Mol Sci 2023; 24:12395. [PMID: 37569770 PMCID: PMC10418745 DOI: 10.3390/ijms241512395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/30/2023] [Accepted: 07/31/2023] [Indexed: 08/13/2023] Open
Abstract
Hybrid rice breeding is an important strategy for enhancing grain yield. Breeding high-performance parental lines and identifying combining abilities is a top priority for hybrid breeding. Yuenongsimiao (YNSM) and its derivative variety Yuehesimiao (YHSM) are elite restorer lines with a high ability of fertility restoration, from which 67 derived hybrid combinations have been authorized to different degrees in more than 110 instances in China. In this study, we found that YNSM and YHSM contained three candidate restorer-of-fertility (Rf) genes, Rf3, Rf4, and Rf5/Rf1a, that might confer their restoration ability. Subsequently, we investigated heterosis and combining ability of YNSM and YHSM using 50 F1 hybrids from a 5 × 10 incomplete diallelic mating design. Our results indicated that hybrid combinations exhibited significant genetic differences, and the additive effects of the parental genes played a preponderant role in the inheritance of observed traits. The metrics of plant height (PH), 1000-grain weight (TGW), panicle length (PL), and the number of spikelets per panicle (NSP) were mainly affected by genetic inheritance with higher heritability. Notably, the general combining ability (GCA) of YHSM exhibited the largest positive effect on the number of grains per panicle (NGP), NSP, PL, and TGW. Thus, YHSM had the largest GCA effect on yield per plant (YPP). In addition, the GCA of YNSM exhibited a positive impact on YPP, mainly due to the critical contribution of seed setting percentage (SSP). Moreover, YNSM and YHSM exhibited negative GCA effects on PH, implying that YNSM and YHSM could effectively enhance plant lodging resistance by reducing the plant height of the derived hybrids. Remarkably, among the hybrids, Yuanxiang A/YNSM (YXA/YNSM), Shen 08S/Yuemeizhan (S08S/YMZ), and Quan 9311A/YHSM (Q9311A/YHSM) represent promising new combinations with a higher specific combining ability (SCA) effect value on YPP with a value more than 3.50. Our research thus highlights the promising application for the rational utilization of YNSM and YHSM in hybrid rice breeding.
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Affiliation(s)
- Shiguang Wang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (S.W.); (H.W.); (Z.L.); (W.L.); (X.W.); (Z.F.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| | - Haoxiang Wu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (S.W.); (H.W.); (Z.L.); (W.L.); (X.W.); (Z.F.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| | - Zhanhua Lu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (S.W.); (H.W.); (Z.L.); (W.L.); (X.W.); (Z.F.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| | - Wei Liu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (S.W.); (H.W.); (Z.L.); (W.L.); (X.W.); (Z.F.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| | - Xiaofei Wang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (S.W.); (H.W.); (Z.L.); (W.L.); (X.W.); (Z.F.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| | - Zhiqiang Fang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (S.W.); (H.W.); (Z.L.); (W.L.); (X.W.); (Z.F.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| | - Xiuying He
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (S.W.); (H.W.); (Z.L.); (W.L.); (X.W.); (Z.F.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
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7
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Sun Z, Peng J, Lv Q, Ding J, Chen S, Duan M, He Q, Wu J, Tian Y, Yu D, Tan Y, Sheng X, Chen J, Sun X, Liu L, Peng R, Liu H, Zhou T, Xu N, Lou J, Yuan L, Wang B, Yuan D. Dissecting the genetic basis of heterosis in elite super-hybrid rice. PLANT PHYSIOLOGY 2023; 192:307-325. [PMID: 36755501 PMCID: PMC10152689 DOI: 10.1093/plphys/kiad078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 01/06/2023] [Accepted: 01/18/2023] [Indexed: 05/03/2023]
Abstract
Y900 is one of the top hybrid rice (Oryza sativa) varieties, with its yield exceeding 15 t·hm-2. To dissect the mechanism of heterosis, we sequenced the male parent line R900 and female parent line Y58S using long-read and Hi-C technology. High-quality reference genomes of 396.41 Mb and 398.24 Mb were obtained for R900 and Y58S, respectively. Genome-wide variations between the parents were systematically identified, including 1,367,758 single-nucleotide polymorphisms, 299,149 insertions/deletions, and 4,757 structural variations. The level of variation between Y58S and R900 was the lowest among the comparisons of Y58S with other rice genomes. More than 75% of genes exhibited variation between the two parents. Compared with other two-line hybrids sharing the same female parent, the portion of Geng/japonica (GJ)-type genetic components from different male parents increased with yield increasing in their corresponding hybrids. Transcriptome analysis revealed that the partial dominance effect was the main genetic effect that constituted the heterosis of Y900. In the hybrid, both alleles from the two parents were expressed, and their expression patterns were dynamically regulated in different tissues. The cis-regulation was dominant for young panicle tissues, while trans-regulation was more common in leaf tissues. Overdominance was surprisingly prevalent in stems and more likely regulated by the trans-regulation mechanism. Additionally, R900 contained many excellent GJ haplotypes, such as NARROW LEAF1, Oryza sativa SQUAMOSA PROMOTER BINDING PROTEIN-LIKE13, and Grain number, plant height, and heading date8, making it a good complement to Y58S. The fine-tuned mechanism of heterosis involves genome-wide variation, GJ introgression, key functional genes, and dynamic gene/allele expression and regulation pattern changes in different tissues and growth stages.
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Affiliation(s)
- Zhizhong Sun
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410125, China
- Longping Branch, College of Biology, Hunan University, Changsha 410125, China
| | | | - Qiming Lv
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410125, China
- Longping Branch, College of Biology, Hunan University, Changsha 410125, China
| | - Jia Ding
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410125, China
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Siyang Chen
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Meijuan Duan
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Qiang He
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Jun Wu
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Yan Tian
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Dong Yu
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Yanning Tan
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Xiabing Sheng
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Jin Chen
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Xuewu Sun
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Ling Liu
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Rui Peng
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Hai Liu
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Tianshun Zhou
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410125, China
- Longping Branch, College of Biology, Hunan University, Changsha 410125, China
| | - Na Xu
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Jianhang Lou
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Longping Yuan
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Bingbing Wang
- Biobin Data Sciences Co., Ltd., Changsha 410221, China
| | - Dingyang Yuan
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410125, China
- Longping Branch, College of Biology, Hunan University, Changsha 410125, China
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8
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Zhang F, Ding Y, Zhang J, Tang M, Cao Y, Zhang L, Ma Z, Qi J, Mu X, Xia L, Tang B. Comparative transcriptomic reveals the molecular mechanism of maize hybrid Zhengdan538 in response to water deficit. PHYSIOLOGIA PLANTARUM 2022; 174:e13818. [PMID: 36345780 DOI: 10.1111/ppl.13818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 09/23/2022] [Accepted: 10/31/2022] [Indexed: 06/16/2023]
Abstract
Heterosis, known as one of the most successful strategies for increasing grain yield and abiotic/biotic stress tolerance, has been widely exploited in maize breeding. However, the underlying molecular processes are still to be elucidated. The maize hybrid "Zhengdan538" shows high tolerance to drought stress. The transcriptomes of the seedling leaves of its parents, "ZhengA88" and "ZhengT22" and their reciprocal F1 hybrid under well-watered and water deficit conditions, were analyzed by RNA sequencing (RNA-Seq). Transcriptome profiling of the reciprocal hybrid revealed 2994-4692 differentially expressed genes (DEGs) under well-watered and water-deficit conditions, which were identified by comparing with their parents. The reciprocal hybrid was more closely related to the parental line "ZhengT22" than to the parental line "ZhengA88" in terms of gene expression patterns under water-deficit condition. Furthermore, genes showed expression level dominance (ELD), especially the high-parental ELD (Class 3 and 5), accounted for the largest proportion of DEGs between the reciprocal F1 hybrid and their parental lines under water deficit. These ELD genes mainly participated in photosynthesis, energy biosynthesis, and metabolism processes. The results indicated that ELD genes played important roles in hybrid tolerance to water deficit. Moreover, a set of important drought-responsive transcription factors were found to be encoded by the identified ELD genes and are thought to function in improving drought tolerance in maize hybrid plants. Our results provide a better understanding of the molecular mechanism of drought tolerance in hybrid maize.
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Affiliation(s)
- Fengqi Zhang
- Cereal Crops Research Institute, Henan Academy of Agricultural Sciences/Henan Provincial Key Laboratory of Maize Biology/Henan International Joint Laboratory on Maize Precision Production, Zhengzhou, China
| | - Yong Ding
- Cereal Crops Research Institute, Henan Academy of Agricultural Sciences/Henan Provincial Key Laboratory of Maize Biology/Henan International Joint Laboratory on Maize Precision Production, Zhengzhou, China
| | - Jun Zhang
- Cereal Crops Research Institute, Henan Academy of Agricultural Sciences/Henan Provincial Key Laboratory of Maize Biology/Henan International Joint Laboratory on Maize Precision Production, Zhengzhou, China
| | - Minqiang Tang
- The Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), College of Forestry, Hainan University, Haikou, China
| | - Yanyong Cao
- Cereal Crops Research Institute, Henan Academy of Agricultural Sciences/Henan Provincial Key Laboratory of Maize Biology/Henan International Joint Laboratory on Maize Precision Production, Zhengzhou, China
| | - Lanxun Zhang
- Cereal Crops Research Institute, Henan Academy of Agricultural Sciences/Henan Provincial Key Laboratory of Maize Biology/Henan International Joint Laboratory on Maize Precision Production, Zhengzhou, China
| | - Zhiyan Ma
- Cereal Crops Research Institute, Henan Academy of Agricultural Sciences/Henan Provincial Key Laboratory of Maize Biology/Henan International Joint Laboratory on Maize Precision Production, Zhengzhou, China
| | - Jianshuang Qi
- Cereal Crops Research Institute, Henan Academy of Agricultural Sciences/Henan Provincial Key Laboratory of Maize Biology/Henan International Joint Laboratory on Maize Precision Production, Zhengzhou, China
| | - Xinyuan Mu
- Cereal Crops Research Institute, Henan Academy of Agricultural Sciences/Henan Provincial Key Laboratory of Maize Biology/Henan International Joint Laboratory on Maize Precision Production, Zhengzhou, China
| | - Laikun Xia
- Cereal Crops Research Institute, Henan Academy of Agricultural Sciences/Henan Provincial Key Laboratory of Maize Biology/Henan International Joint Laboratory on Maize Precision Production, Zhengzhou, China
| | - Baojun Tang
- Cereal Crops Research Institute, Henan Academy of Agricultural Sciences/Henan Provincial Key Laboratory of Maize Biology/Henan International Joint Laboratory on Maize Precision Production, Zhengzhou, China
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9
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Zhou D, Zhou X, Sun C, Tang G, Liu L, Chen L, He H, Xiong Q. Transcriptome and Metabolome Analysis Provides Insights into the Heterosis of Yield and Quality Traits in Two Hybrid Rice Varieties (Oryza sativa L.). Int J Mol Sci 2022; 23:ijms232112934. [PMID: 36361748 PMCID: PMC9654843 DOI: 10.3390/ijms232112934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/18/2022] [Accepted: 10/20/2022] [Indexed: 11/24/2022] Open
Abstract
Heterosis is a common biological phenomenon that is useful for breeding superior lines. Using heterosis to increase the yield and quality of crops is one of the main achievements of modern agricultural science. In this study, we analysed the transcriptome and metabolome of two three-line hybrid rice varieties, Taiyou 871 (TY871), and Taiyou 398 (TY398) and the parental grain endosperm using RNA-seq (three biological repeats per variety) and untargeted metabolomic (six biological repeats per variety) methods. TY871 and TY398 showed specific heterosis in yield and quality. Transcriptome analysis of the hybrids revealed 638 to 4059 differentially expressed genes in the grain when compared to the parents. Metabolome analysis of the hybrids revealed 657 to 3714 differential grain metabolites when compared to the parents. The honeydew1 and grey60 module core genes Os04g0350700 and Os05g0154700 are involved in the regulation of awn development, grain size, and grain number, as well as the regulation of grain length and plant height, respectively. Rice grain length may be an important indicator for improving the quality of three-line hybrid rice. In addition, the rice quality-related metabolite NEG_M341T662 was highly connected to the module core genes Os06g0254300 and Os03g0168100. The functions of Os06g0254300 and Os03g0168100 are EF-hand calcium binding protein and late embroideries absolute protein repeat containing protein, respectively. These genes may play a role in the formation of rice quality. We constructed a gene and metabolite coexpression network, which provides a scientific basis for the utilization of heterosis in producing high-yield and high-quality hybrid rice.
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Affiliation(s)
- Dahu Zhou
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China
| | - Xinyi Zhou
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China
| | - Changhui Sun
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology, Agricultural College of Yangzhou University, Yangzhou 225009, China
| | - Guoping Tang
- Jiangxi Academy of Agricultural Sciences Rice Research Institute, Nanchang 330200, China
| | - Lin Liu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China
| | - Le Chen
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology, Agricultural College of Yangzhou University, Yangzhou 225009, China
| | - Haohua He
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China
- Correspondence: (H.H.); (Q.X.)
| | - Qiangqiang Xiong
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology, Agricultural College of Yangzhou University, Yangzhou 225009, China
- Correspondence: (H.H.); (Q.X.)
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