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Zhao J, Chen M, Luo Z, Cui P, Ren P, Wang Y. Strand-Specific RNA Sequencing Reveals Gene Expression Patterns in F1 Chick Breast Muscle and Liver after Hatching. Animals (Basel) 2024; 14:1335. [PMID: 38731340 PMCID: PMC11083249 DOI: 10.3390/ani14091335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 04/25/2024] [Accepted: 04/26/2024] [Indexed: 05/13/2024] Open
Abstract
Heterosis refers to the phenomenon where hybrids exhibit superior performance compared to the parental phenotypes and has been widely utilized in crossbreeding programs for animals and crops, yet the molecular mechanisms underlying this phenomenon remain enigmatic. A better understanding of the gene expression patterns in post-hatch chickens is very important for exploring the genetic basis underlying economically important traits in the crossbreeding of chickens. In this study, breast muscle and liver tissues (n = 36) from full-sib F1 birds and their parental pure lines were selected to identify gene expression patterns and differentially expressed genes (DEGs) at 28 days of age by strand-specific RNA sequencing (ssRNA-seq). This study indicates that additivity is the predominant gene expression pattern in the F1 chicken post-hatch breast muscle (80.6% genes with additivity) and liver (94.2% genes with additivity). In breast muscle, Gene Ontology (GO) enrichment analysis revealed that a total of 11 biological process (BP) terms closely associated with growth and development were annotated in the identified DEG sets and non-additive gene sets, including STAT5A, TGFB2, FGF1, IGF2, DMA, FGF16, FGF12, STAC3, GSK3A, and GRB2. Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation presented that a total of six growth- and development-related pathways were identified, involving key genes such as SLC27A4, GLUL, TGFB2, COX17, and GSK3A, including the PPAR signaling pathway, TGF-beta signaling pathway, and mTOR signaling pathway. Our results may provide a theoretical basis for crossbreeding in domestic animals.
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Affiliation(s)
- Jianfei Zhao
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621010, China; (J.Z.); (M.C.); (Z.L.); (P.C.)
| | - Meiying Chen
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621010, China; (J.Z.); (M.C.); (Z.L.); (P.C.)
| | - Zhengwei Luo
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621010, China; (J.Z.); (M.C.); (Z.L.); (P.C.)
| | - Pengxin Cui
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621010, China; (J.Z.); (M.C.); (Z.L.); (P.C.)
| | - Peng Ren
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621010, China; (J.Z.); (M.C.); (Z.L.); (P.C.)
| | - Ye Wang
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China
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E L, Lyu S, Wang Y, Xiao D, Liu T, Hou X, Li Y, Zhang C. Integrating Dynamic 3D Chromatin Architecture and Gene Expression Alterations Reveal Heterosis in Brassica rapa. Int J Mol Sci 2024; 25:2568. [PMID: 38473815 DOI: 10.3390/ijms25052568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 01/25/2024] [Accepted: 02/09/2024] [Indexed: 03/14/2024] Open
Abstract
Heterosis plays a significant role in enhancing variety, boosting yield, and raising economic value in crops, but the molecular mechanism is still unclear. We analyzed the transcriptomes and 3D genomes of a hybrid (F1) and its parents (w30 and 082). The analysis of the expression revealed a total of 485 specially expressed genes (SEGs), 173 differentially expressed genes (DEGs) above the parental expression level, more actively expressed genes, and up-regulated DEGs in the F1. Further study revealed that the DEGs detected in the F1 and its parents were mainly involved in the response to auxin, plant hormone signal transduction, DNA metabolic process, purine metabolism, starch, and sucrose metabolism, which suggested that these biological processes may play a crucial role in the heterosis of Brassica rapa. The analysis of 3D genome data revealed that hybrid F1 plants tend to contain more transcriptionally active A chromatin compartments after hybridization. Supplementaryly, the F1 had a smaller TAD (topologically associated domain) genome length, but the number was the highest, and the expression change in activated TAD was higher than that of repressed TAD. More specific TAD boundaries were detected between the parents and F1. Subsequently, 140 DEGs with genomic structural variants were selected as potential candidate genes. We found two DEGs with consistent expression changes in A/B compartments and TADs. Our findings suggested that genomic structural variants, such as TADs and A/B chromatin compartments, may affect gene expression and contribute to heterosis in Brassica rapa. This study provides further insight into the molecular mechanism of heterosis in Brassica rapa.
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Affiliation(s)
- Liu E
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Shanwu Lyu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Yaolong Wang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Dong Xiao
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Tongkun Liu
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Xilin Hou
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Ying Li
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Changwei Zhang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
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Liu S, Xiong Z, Zhang Z, Wei Y, Xiong D, Wang F, Huang J. Exploration of chlorophyll fluorescence characteristics gene regulatory in rice ( Oryza sativa L.): a genome-wide association study. FRONTIERS IN PLANT SCIENCE 2023; 14:1234866. [PMID: 37746023 PMCID: PMC10513790 DOI: 10.3389/fpls.2023.1234866] [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: 06/05/2023] [Accepted: 08/21/2023] [Indexed: 09/26/2023]
Abstract
Chlorophyll content and fluorescence parameters are crucial indicators to evaluate the light use efficiency in rice; however, the correlations among these parameters and the underlying genetic mechanisms remain poorly understood. Here, to clarify these issues, we conducted a genome-wide association study (GWAS) on 225 rice accessions. In the phenotypic and Mendelian randomization (MR) analysis, a weak negative correlation was observed between the chlorophyll content and actual quantum yield of photosystem II (Φ I I ). The phenotypic diversity observed in SPAD, N P Q t , Φ N P Q , and F v / F m among accessions was affected by genetic background. Furthermore, the GWAS identified 78 SNPs and 17 candidate genes significantly associated with SPAD, N P Q t , Φ I I , Φ N P Q , q L and q P . Combining GWAS on 225 rice accessions with transcriptome analysis of two varieties exhibiting distinct fluorescence characteristics revealed two potential candidate genes (Os03g0583000 from Φ I I & q P traits and Os06g0587200 from N P Q t trait), which are respectively associated with peroxisomes, and protein kinase catalytic domains might involve in regulating the chlorophyll content and chlorophyll fluorescence. This study provides novel insights into the correlation among chlorophyll content and fluorescence parameters and the genetic mechanisms in rice, and offers valuable information for the breeding of rice with enhanced photosynthetic efficiency.
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Affiliation(s)
- Sicheng Liu
- Ministry of Agriculture Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zhuang Xiong
- Ministry of Agriculture Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zuolin Zhang
- Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Youbo Wei
- Ministry of Agriculture Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Dongliang Xiong
- Ministry of Agriculture Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Fei Wang
- Ministry of Agriculture Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jianliang Huang
- Ministry of Agriculture Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
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Kamara N, Jiao Y, Huang W, Cao L, Zhu L, Zhao C, Huang X, Shivute FN, Liu X, Wu J, Shahid MQ. Comparative cytological and transcriptome analyses of ny2 mutant delayed degeneration of tapetal cells and promotes abnormal microspore development in neo-tetraploid rice. FRONTIERS IN PLANT SCIENCE 2023; 14:1229870. [PMID: 37528969 PMCID: PMC10387629 DOI: 10.3389/fpls.2023.1229870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 06/26/2023] [Indexed: 08/03/2023]
Abstract
We aimed to investigate the genetic defects related to pollen development and infertility in NY2, a novel tetraploid rice germplasm known as Neo-tetraploid rice. This rice variety was created through the crossbreeding and selective breeding of various autotetraploid rice lines and has previously shown high fertility. Our previous research has revealed that the NY2 gene, encoding a eukaryotic translation initiation factor 3 subunit E, regulates pollen fertility. However, the underlying mechanism behind this fertility is yet to be understood. To shed light on this matter, we performed a combined cytological and transcriptome analysis of the NY2 gene. Cytological analysis indicated that ny2 underwent abnormal tapetal cells, microspore, and middle layer development, which led to pollen abortion and ultimately to male sterility. Genetic analysis revealed that the F1 plants showed normal fertility and an obvious advantage for seed setting compared to ny2. Global gene expression analysis in ny2 revealed a total of 7545 genes were detected at the meiosis stage, and 3925 and 3620 displayed upregulation and downregulation, respectively. The genes were significantly enriched for the gene ontology (GO) term "carbohydrate metabolic process. Moreover, 9 genes related to tapetum or pollen fertility showed down-regulation, such as OsABCG26 (ATP Binding Cassette G26), TMS9-1 (Thermosensitive Male Sterility), EAT1 (Programmed cell death regulatory), KIN14M (Kinesin Motor), OsMT1a (Metallothionein), and OsSTRL2 (Atypical strictosidine synthase), which were validated by qRT-PCR. Further analyses of DEGs identified nine down-regulated transcription factor genes related to pollen development. NY2 is an important regulator of the development of tapetum and microspore. The regulatory gene network described in this study may offer important understandings into the molecular processes that underlie fertility control in tetraploid rice.
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Affiliation(s)
- Nabieu Kamara
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- College of Agriculture, South China Agricultural University, Guangzhou, China
- Crop Improvement Programme, Rokupr Agricultural Research Center, Rokupr - Sierra Leone Agricultural Research Institute (SLARI), Freetown, Sierra Leone
| | - Yamin Jiao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Weicong Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Lichong Cao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Lianjun Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Chongchong Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Xu Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Fimanekeni Ndaitavela Shivute
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- College of Agriculture, South China Agricultural University, Guangzhou, China
- Multi-disciplinary Research Services, University of Namibia, Windhoek, Namibia
| | - Xiangdong Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Jinwen Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- College of Agriculture, South China Agricultural University, Guangzhou, China
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5
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Zhong Z, Wu Y, Zhang P, Hu G, Fu D, Yu G, Tong H. Transcriptomic Analysis Reveals Panicle Heterosis in an Elite Hybrid Rice ZZY10 and Its Parental Lines. PLANTS (BASEL, SWITZERLAND) 2023; 12:1309. [PMID: 36987003 PMCID: PMC10059593 DOI: 10.3390/plants12061309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 03/10/2023] [Accepted: 03/12/2023] [Indexed: 06/19/2023]
Abstract
Heterosis is the phenomenon in which some hybrid traits are superior to those of their parents. Most studies have analyzed the heterosis of agronomic traits of crops; however, heterosis of the panicles can improve yield and is important for crop breeding. Therefore, a systematic study of panicle heterosis is needed, especially during the reproductive stage. RNA sequencing (RNA Seq) and transcriptome analysis are suitable for further study of heterosis. Using the Illumina Nova Seq platform, the transcriptome of ZhongZheYou 10 (ZZY10), an elite rice hybrid, the maintainer line ZhongZhe B (ZZB), and the restorer line Z7-10 were analyzed at the heading date in Hangzhou, 2022. 581 million high-quality short reads were obtained by sequencing and were aligned against the Nipponbare reference genome. A total of 9000 differential expression genes were found between the hybrids and their parents (DGHP). Of the DGHP, 60.71% were up-regulated and 39.29% were down-regulated in the hybrid. Comparative transcriptome analysis revealed that 5235 and 3765 DGHP were between ZZY10 and ZhongZhe B and between ZZY10 and Z7-10, respectively. This result is consistent with the transcriptome profile of ZZY10 and was similar to Z7-10. The expression patterns of DGHP mainly exhibited over-dominance, under-dominance, and additivity. Among the DGHP-involved GO terms, pathways such as photosynthesis, DNA integration, cell wall modification, thylakoid, and photosystem were significant. 21 DGHP, which were involved in photosynthesis, and 17 random DGHP were selected for qRT-PCR validation. The up-regulated PsbQ and down-regulated subunits of PSI and PSII and photosynthetic electron transport in the photosynthesis pathway were observed in our study. Extensive transcriptome data were obtained by RNA-Seq, providing a comprehensive overview of panicle transcriptomes at the heading stage in a heterotic hybrid.
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Affiliation(s)
- Zhengzheng Zhong
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China
| | - Yawen Wu
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China
| | - Peng Zhang
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China
| | - Guocheng Hu
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China
| | - Dong Fu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Guoping Yu
- National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya 572025, China
| | - Hanhua Tong
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China
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Li R, Nie S, Zhang N, Tian M, Zhang L. Transcriptome Analysis Reveals a Major Gene Expression Pattern and Important Metabolic Pathways in the Control of Heterosis in Chinese Cabbage. PLANTS (BASEL, SWITZERLAND) 2023; 12:1195. [PMID: 36904055 PMCID: PMC10005390 DOI: 10.3390/plants12051195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 03/02/2023] [Accepted: 03/03/2023] [Indexed: 06/18/2023]
Abstract
Although heterosis is commonly used in Chinese cabbage, its molecular basis is poorly understood. In this study, 16Chinese cabbage hybrids were utilized as test subjects to explore the potential molecular mechanism of heterosis. RNA sequencing revealed 5815-10,252 differentially expressed genes (DEGs) (female parent vs. male parent), 1796-5990 DEGs (female parent-vs-hybrid), and 2244-7063 DEGs (male parent vs. hybrid) in 16 cross combinations at the middle stage of heading. Among of them, 72.83-84.20% DEGs conformed to the dominant expression pattern, which is the predominant expression pattern in hybrids. There were 13 pathways in which DEGs were significantly enriched in most cross combinations. Among them, the plant-pathogen interaction (ko04626) and circadian rhythm-plant (ko04712)were significantly enriched by DEGs in strong heterosis hybrids. WGCNA also proved that the two pathways were significantly related to heterosis in Chinese cabbage.
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Ma M, Zhong W, Zhang Q, Deng L, Wen J, Yi B, Tu J, Fu T, Zhao L, Shen J. Genome-wide analysis of transcriptome and histone modifications in Brassica napus hybrid. FRONTIERS IN PLANT SCIENCE 2023; 14:1123729. [PMID: 36778699 PMCID: PMC9911877 DOI: 10.3389/fpls.2023.1123729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
Although utilization of heterosis has largely improved the yield of many crops worldwide, the underlying molecular mechanism of heterosis, particularly for allopolyploids, remains unclear. Here, we compared epigenome and transcriptome data of an elite hybrid and its parental lines in three assessed tissues (seedling, flower bud, and silique) to explore their contribution to heterosis in allopolyploid B. napus. Transcriptome analysis illustrated that a small proportion of non-additive genes in the hybrid compared with its parents, as well as parental expression level dominance, might have a significant effect on heterosis. We identified histone modification (H3K4me3 and H3K27me3) variation between the parents and hybrid, most of which resulted from the differences between parents. H3K4me3 variations were positively correlated with gene expression differences among the hybrid and its parents. Furthermore, H3K4me3 and H3K27me3 were rather stable in hybridization and were mainly inherited additively in the B. napus hybrid. Together, our data revealed that transcriptome reprogramming and histone modification remodeling in the hybrid could serve as valuable resources for better understanding heterosis in allopolyploid crops.
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Huang Z, Ye J, Zhai R, Wu M, Yu F, Zhu G, Wang Z, Zhang X, Ye S. Comparative Transcriptome Analysis of the Heterosis of Salt Tolerance in Inter-Subspecific Hybrid Rice. Int J Mol Sci 2023; 24:ijms24032212. [PMID: 36768538 PMCID: PMC9916944 DOI: 10.3390/ijms24032212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/25/2022] [Accepted: 01/02/2023] [Indexed: 01/27/2023] Open
Abstract
Soil salinity is one of the major abiotic stresses limiting rice growth. Hybrids outperform their parents in salt tolerance in rice, while its mechanism is not completely understood. In this study, a higher seedling survival was observed after salt treatment in an inter-subspecific hybrid rice, Zhegengyou1578 (ZGY1578), compared with its maternal japonica Zhegeng7A (ZG7A) and paternal indica Zhehui1578 (ZH1578). A total of 2584 and 3061 differentially expressed genes (DEGs) with at least twofold changes were identified between ZGY1578 and ZG7A and between ZGY1578 and ZH1578, respectively, in roots under salt stress using the RNA sequencing (RNA-Seq) approach. The expressions of a larger number of DEGs in hybrid were lower or higher than those of both parents. The DEGs associated with transcription factors, hormones, and reactive oxygen species (ROS)-related genes might be involved in the heterosis of salt tolerance. The expressions of the majority of transcription factors and ethylene-, auxin-, and gibberellin-related genes, as well as peroxidase genes, were significantly higher in the hybrid ZGY1578 compared with those of both parents. The identified genes provide valuable clues to elucidate the heterosis of salt tolerance in inter-subspecific hybrid rice.
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Affiliation(s)
- Zhibo Huang
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Jing Ye
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Rongrong Zhai
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Mingming Wu
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Faming Yu
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Guofu Zhu
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Zhoufei Wang
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Xiaoming Zhang
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
- Correspondence: (X.Z.); (S.Y.)
| | - Shenghai Ye
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
- Correspondence: (X.Z.); (S.Y.)
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9
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Hackauf B, Siekmann D, Fromme FJ. Improving Yield and Yield Stability in Winter Rye by Hybrid Breeding. PLANTS (BASEL, SWITZERLAND) 2022; 11:2666. [PMID: 36235531 PMCID: PMC9571156 DOI: 10.3390/plants11192666] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 09/27/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
Rye is the only cross-pollinating small-grain cereal. The unique reproduction biology results in an exceptional complexity concerning genetic improvement of rye by breeding. Rye is a close relative of wheat and has a strong adaptation potential that refers to its mating system, making this overlooked cereal readily adjustable to a changing environment. Rye breeding addresses the emerging challenges of food security associated with climate change. The systematic identification, management, and use of its valuable natural diversity became a feasible option in outbreeding rye only following the establishment of hybrid breeding late in the 20th century. In this article, we review the most recent technological advances to improve yield and yield stability in winter rye. Based on recently released reference genome sequences, SMART breeding approaches are described to counterbalance undesired linkage drag effects of major restorer genes on grain yield. We present the development of gibberellin-sensitive semidwarf hybrids as a novel plant breeding innovation based on an approach that is different from current methods of increasing productivity in rye and wheat. Breeding of new rye cultivars with improved performance and resilience is indispensable for a renaissance of this healthy minor cereal as a homogeneous commodity with cultural relevance in Europe that allows for comparatively smooth but substantial complementation of wheat with rye-based diets, supporting the necessary restoration of the balance between human action and nature.
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Affiliation(s)
- Bernd Hackauf
- Julius Kühn Institute, Institute for Breeding Research on Agricultural Crops, Rudolf-Schick-Platz 3a, 18190 Sanitz, Germany
| | - Dörthe Siekmann
- Hybro Saatzucht GmbH & Co. KG, Langlinger Straße 3, 29565 Wriedel, Germany
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Mbebi AJ, Breitler JC, Bordeaux M, Sulpice R, McHale M, Tong H, Toniutti L, Castillo JA, Bertrand B, Nikoloski Z. A comparative analysis of genomic and phenomic predictions of growth-related traits in 3-way coffee hybrids. G3 GENES|GENOMES|GENETICS 2022; 12:6632664. [PMID: 35792875 PMCID: PMC9434219 DOI: 10.1093/g3journal/jkac170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 06/14/2022] [Indexed: 11/14/2022]
Abstract
Abstract
Genomic prediction has revolutionized crop breeding despite remaining issues of transferability of models to unseen environmental conditions and environments. Usage of endophenotypes rather than genomic markers leads to the possibility of building phenomic prediction models that can account, in part, for this challenge. Here, we compare and contrast genomic prediction and phenomic prediction models for 3 growth-related traits, namely, leaf count, tree height, and trunk diameter, from 2 coffee 3-way hybrid populations exposed to a series of treatment-inducing environmental conditions. The models are based on 7 different statistical methods built with genomic markers and ChlF data used as predictors. This comparative analysis demonstrates that the best-performing phenomic prediction models show higher predictability than the best genomic prediction models for the considered traits and environments in the vast majority of comparisons within 3-way hybrid populations. In addition, we show that phenomic prediction models are transferrable between conditions but to a lower extent between populations and we conclude that chlorophyll a fluorescence data can serve as alternative predictors in statistical models of coffee hybrid performance. Future directions will explore their combination with other endophenotypes to further improve the prediction of growth-related traits for crops.
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Affiliation(s)
- Alain J Mbebi
- Bioinformatics Group, Institute of Biochemistry and Biology, University of Potsdam , Potsdam-Golm 14476, Germany
- Systems Biology and Mathematical Modeling Group, Max Planck Institute of Molecular Plant Physiology , Potsdam-Golm 14476, Germany
| | - Jean-Christophe Breitler
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Montpellier 34398, France
| | - Mélanie Bordeaux
- Fundación Nicafrance , Finca La Cumplida Km. 147 Carretera Matagalpa - La Dalia, 3 Km al Noreste, Matagalpa, Nicaragua
| | - Ronan Sulpice
- National University Ireland Galway, Plant Systems Biology Laboratory, Ryan Institute, School of Natural Sciences , Galway H91 TK33, Ireland
| | - Marcus McHale
- National University Ireland Galway, Plant Systems Biology Laboratory, Ryan Institute, School of Natural Sciences , Galway H91 TK33, Ireland
| | - Hao Tong
- Bioinformatics Group, Institute of Biochemistry and Biology, University of Potsdam , Potsdam-Golm 14476, Germany
- Systems Biology and Mathematical Modeling Group, Max Planck Institute of Molecular Plant Physiology , Potsdam-Golm 14476, Germany
- Center for Plant Systems Biology and Biotechnology , Plovdiv 4000, Bulgaria
| | - Lucile Toniutti
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Montpellier 34398, France
| | - Jonny Alonso Castillo
- Fundación Nicafrance , Finca La Cumplida Km. 147 Carretera Matagalpa - La Dalia, 3 Km al Noreste, Matagalpa, Nicaragua
| | - Benoît Bertrand
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Montpellier 34398, France
| | - Zoran Nikoloski
- Bioinformatics Group, Institute of Biochemistry and Biology, University of Potsdam , Potsdam-Golm 14476, Germany
- Systems Biology and Mathematical Modeling Group, Max Planck Institute of Molecular Plant Physiology , Potsdam-Golm 14476, Germany
- Center for Plant Systems Biology and Biotechnology , Plovdiv 4000, Bulgaria
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11
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Fu J, Zhang Y, Yan T, Li Y, Jiang N, Zhou Y, Zhou Q, Qin P, Fu C, Lin H, Zhong J, Han X, Lin Z, Wang F, He H, Wang K, Yang Y. Transcriptome profiling of two super hybrid rice provides insights into the genetic basis of heterosis. BMC PLANT BIOLOGY 2022; 22:314. [PMID: 35773646 PMCID: PMC9245205 DOI: 10.1186/s12870-022-03697-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 06/15/2022] [Indexed: 05/19/2023]
Abstract
BACKGROUND Heterosis is a phenomenon that hybrids show superior performance over their parents. The successful utilization of heterosis has greatly improved rice productivity, but the molecular basis of heterosis remains largely unclear. RESULTS Here, the transcriptomes of young panicles and leaves of the two widely grown two-line super hybrid rice varieties (Jing-Liang-You-Hua-Zhan (JLYHZ) and Long-Liang-You-Hua-Zhan (LLYHZ)) and their parents were analyzed by RNA-seq. Transcriptome profiling of the hybrids revealed 1,778 ~ 9,404 differentially expressed genes (DEGs) in two tissues, which were identified by comparing with their parents. GO, and KEGG enrichment analysis showed that the pathways significantly enriched in both tissues of two hybrids were all related to yield and resistance, like circadian rhythm (GO:0,007,623), response to water deprivation (GO:0,009,414), and photosynthetic genes (osa00196). Allele-specific expression genes (ASEGs) were also identified in hybrids. The ASEGs were most significantly enriched in ionotropic glutamate receptor signaling pathway, which was hypothesized to be potential amino acid sensors in plants. Moreover, the ASEGs were also differentially expressed between parents. The number of variations in ASEGs is higher than expected, especially for large effect variations. The DEGs and ASEGs are the potential reasons for the formation of heterosis in the two elite super hybrid rice. CONCLUSIONS Our results provide a comprehensive understanding of the heterosis of two-line super hybrid rice and facilitate the exploitation of heterosis in hybrid rice breeding with high yield heterosis.
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Affiliation(s)
- Jun Fu
- Key Laboratory of Southern Rice Innovation & Improvement, Ministry of Agriculture and Rural Affairs, Hunan Engineering Laboratory of Disease and Pest Resistant Rice Breeding, Yuan Longping High-Tech Agriculture Co., Ltd, Changsha, 410128, China
| | - Yilin Zhang
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Tianze Yan
- Key Laboratory of Southern Rice Innovation & Improvement, Ministry of Agriculture and Rural Affairs, Hunan Engineering Laboratory of Disease and Pest Resistant Rice Breeding, Yuan Longping High-Tech Agriculture Co., Ltd, Changsha, 410128, China
| | - Yanfeng Li
- Key Laboratory of Southern Rice Innovation & Improvement, Ministry of Agriculture and Rural Affairs, Hunan Engineering Laboratory of Disease and Pest Resistant Rice Breeding, Yuan Longping High-Tech Agriculture Co., Ltd, Changsha, 410128, China
| | - Nan Jiang
- Key Laboratory of Southern Rice Innovation & Improvement, Ministry of Agriculture and Rural Affairs, Hunan Engineering Laboratory of Disease and Pest Resistant Rice Breeding, Yuan Longping High-Tech Agriculture Co., Ltd, Changsha, 410128, China
| | - Yanbiao Zhou
- Key Laboratory of Southern Rice Innovation & Improvement, Ministry of Agriculture and Rural Affairs, Hunan Engineering Laboratory of Disease and Pest Resistant Rice Breeding, Yuan Longping High-Tech Agriculture Co., Ltd, Changsha, 410128, China
| | - Qunfeng Zhou
- Key Laboratory of Southern Rice Innovation & Improvement, Ministry of Agriculture and Rural Affairs, Hunan Engineering Laboratory of Disease and Pest Resistant Rice Breeding, Yuan Longping High-Tech Agriculture Co., Ltd, Changsha, 410128, China
| | - Peng Qin
- Key Laboratory of Southern Rice Innovation & Improvement, Ministry of Agriculture and Rural Affairs, Hunan Engineering Laboratory of Disease and Pest Resistant Rice Breeding, Yuan Longping High-Tech Agriculture Co., Ltd, Changsha, 410128, China
| | - Chenjian Fu
- Key Laboratory of Southern Rice Innovation & Improvement, Ministry of Agriculture and Rural Affairs, Hunan Engineering Laboratory of Disease and Pest Resistant Rice Breeding, Yuan Longping High-Tech Agriculture Co., Ltd, Changsha, 410128, China
| | - Haiyan Lin
- Key Laboratory of Southern Rice Innovation & Improvement, Ministry of Agriculture and Rural Affairs, Hunan Engineering Laboratory of Disease and Pest Resistant Rice Breeding, Yuan Longping High-Tech Agriculture Co., Ltd, Changsha, 410128, China
| | - Jing Zhong
- Key Laboratory of Southern Rice Innovation & Improvement, Ministry of Agriculture and Rural Affairs, Hunan Engineering Laboratory of Disease and Pest Resistant Rice Breeding, Yuan Longping High-Tech Agriculture Co., Ltd, Changsha, 410128, China
| | - Xue Han
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Zechuan Lin
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Fei Wang
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hang He
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.
| | - Kai Wang
- Key Laboratory of Southern Rice Innovation & Improvement, Ministry of Agriculture and Rural Affairs, Hunan Engineering Laboratory of Disease and Pest Resistant Rice Breeding, Yuan Longping High-Tech Agriculture Co., Ltd, Changsha, 410128, China.
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China.
- Longping Hi-Tech (Sanya) Overseas Seed Industry R&D Co., Ltd, Sanya, 572099, China.
| | - Yuanzhu Yang
- Key Laboratory of Southern Rice Innovation & Improvement, Ministry of Agriculture and Rural Affairs, Hunan Engineering Laboratory of Disease and Pest Resistant Rice Breeding, Yuan Longping High-Tech Agriculture Co., Ltd, Changsha, 410128, China.
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China.
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125, China.
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12
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Lee JS, Jahani M, Huang K, Mandel JR, Marek LF, Burke JM, Langlade NB, Owens GL, Rieseberg LH. Expression complementation of gene presence/absence polymorphisms in hybrids contributes importantly to heterosis in sunflower. J Adv Res 2022; 42:83-98. [PMID: 36513422 PMCID: PMC9788961 DOI: 10.1016/j.jare.2022.04.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 04/01/2022] [Accepted: 04/16/2022] [Indexed: 12/27/2022] Open
Abstract
INTRODUCTION Numerous crops have transitioned to hybrid seed production to increase yields and yield stability through heterosis. However, the molecular mechanisms underlying heterosis and its stability across environments are not yet fully understood. OBJECTIVES This study aimed to (1) elucidate the genetic and molecular mechanisms underlying heterosis in sunflower, and (2) determine how heterosis is maintained under different environments. METHODS Genome-wide association (GWA) analyses were employed to assess the effects of presence/absence variants (PAVs) and stop codons on 16 traits phenotyped in the sunflower association mapping population at three locations. To link the GWA results to transcriptomic variation, we sequenced the transcriptomes of two sunflower cultivars and their F1 hybrid (INEDI) under both control and drought conditions and analyzed patterns of gene expression and alternative splicing. RESULTS Thousands of PAVs were found to affect phenotypic variation using a relaxed significance threshold, and at most such loci the "absence" allele reduced values of heterotic traits, but not those of non-heterotic traits. This pattern was strengthened for PAVs that showed expression complementation in INEDI. Stop codons were much rarer than PAVs and less likely to reduce heterotic trait values. Hybrid expression patterns were enriched for the GO category, sensitivity to stimulus, but all genotypes responded to drought similarily - by up-regulating water stress response pathways and down-regulating metabolic pathways. Changes in alternative splicing were strongly negatively correlated with expression variation, implying that alternative splicing in this system largely acts to reinforce expression responses. CONCLUSION Our results imply that complementation of expression of PAVs in hybrids is a major contributor to heterosis in sunflower, consistent with the dominance model of heterosis. This mechanism can account for yield stability across different environments. Moreover, given the much larger numbers of PAVs in plant vs. animal genomes, it also offers an explanation for the stronger heterotic responses seen in the former.
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Affiliation(s)
- Joon Seon Lee
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Mojtaba Jahani
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Kaichi Huang
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Jennifer R. Mandel
- Department of Biological Sciences and Center for Biodiversity, University of Memphis, Memphis, TN 38152, USA
| | - Laura F. Marek
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA
| | - John M. Burke
- Department of Plant Biology, Miller Plant Sciences, University of Georgia, Athens 30602, Georgia
| | | | - Gregory L. Owens
- Department of Biology, University of Victoria, Victoria, BC V8P 5C2, Canada
| | - Loren H. Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada,Corresponding author.
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13
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Wang M, Wang J. Transcriptome and DNA methylome analyses provide insight into the heterosis in flag leaf of inter-subspecific hybrid rice. PLANT MOLECULAR BIOLOGY 2022; 108:105-125. [PMID: 34855066 DOI: 10.1007/s11103-021-01228-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 11/22/2021] [Indexed: 05/26/2023]
Abstract
Flag leaf heterosis of inter-subspecific hybrid rice is suggested to be related to leaf area, gene expression pattern and allele-specific expression, putatively related to DNA methylation differences between the hybrid and its parents. Inter-subspecific hybrid rice combinations of indica × japonica have great potential to broaden genetic diversity and enhance the heterosis. The genetic and epigenetic molecular mechanism of its heterosis is not completely understood. Here, the dissection of gene expression and epigenetic regulation of an elite inter-subspecific hybrid rice were reported. In the hybrid, plant height, flag leaf area and Pn showed significant heterosis at the heading stage. Chloroplast-related differentially expressed genes (DEGs) and 530 allele-specific expression genes in hybrid were identified. Analysis of the genome-wide distribution of DNA methylation (5-methylcytosine, 5mC) and its association with transcription showed that there were variant DNA methylation maps and that the regulation of gene expression levels was negatively regulated by DNA methylation in the inter-subspecific hybrid rice. Differentially methylated DEGs were significantly enriched in photosynthetic functions. Moreover, distinct 5mC sequence contexts and distinct functional elements (promoter/gene body) may have different influences on heterosis related genes. The data identified heterosis related molecular mechanisms in inter-subspecific hybrid rice and suggested that epigenetic changes could extensively influence the flag leaf gene expression and heterosis.
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Affiliation(s)
- Mengyao Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Jianbo Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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14
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Wu X, Liu Y, Zhang Y, Gu R. Advances in Research on the Mechanism of Heterosis in Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:745726. [PMID: 34646291 PMCID: PMC8502865 DOI: 10.3389/fpls.2021.745726] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/06/2021] [Indexed: 05/13/2023]
Abstract
Heterosis is a common biological phenomenon in nature. It substantially contributes to the biomass yield and grain yield of plants. Moreover, this phenomenon results in high economic returns in agricultural production. However, the utilization of heterosis far exceeds the level of theoretical research on this phenomenon. In this review, the recent progress in research on heterosis in plants was reviewed from the aspects of classical genetics, parental genetic distance, quantitative trait loci, transcriptomes, proteomes, epigenetics (DNA methylation, histone modification, and small RNA), and hormone regulation. A regulatory network of various heterosis-related genes under the action of different regulatory factors was summarized. This review lays a foundation for the in-depth study of the molecular and physiological aspects of this phenomenon to promote its effects on increasing the yield of agricultural production.
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Affiliation(s)
- Xilin Wu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Yan Liu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Yaowei Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Ran Gu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
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15
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Yu D, Gu X, Zhang S, Dong S, Miao H, Gebretsadik K, Bo K. Molecular basis of heterosis and related breeding strategies reveal its importance in vegetable breeding. HORTICULTURE RESEARCH 2021; 8:120. [PMID: 34059656 PMCID: PMC8166827 DOI: 10.1038/s41438-021-00552-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 03/07/2021] [Accepted: 03/22/2021] [Indexed: 05/02/2023]
Abstract
Heterosis has historically been exploited in plants; however, its underlying genetic mechanisms and molecular basis remain elusive. In recent years, due to advances in molecular biotechnology at the genome, transcriptome, proteome, and epigenome levels, the study of heterosis in vegetables has made significant progress. Here, we present an extensive literature review on the genetic and epigenetic regulation of heterosis in vegetables. We summarize six hypotheses to explain the mechanism by which genes regulate heterosis, improve upon a possible model of heterosis that is triggered by epigenetics, and analyze previous studies on quantitative trait locus effects and gene actions related to heterosis based on analyses of differential gene expression in vegetables. We also discuss the contributions of yield-related traits, including flower, fruit, and plant architecture traits, during heterosis development in vegetables (e.g., cabbage, cucumber, and tomato). More importantly, we propose a comprehensive breeding strategy based on heterosis studies in vegetables and crop plants. The description of the strategy details how to obtain F1 hybrids that exhibit heterosis based on heterosis prediction, how to obtain elite lines based on molecular biotechnology, and how to maintain heterosis by diploid seed breeding and the selection of hybrid simulation lines that are suitable for heterosis research and utilization in vegetables. Finally, we briefly provide suggestions and perspectives on the role of heterosis in the future of vegetable breeding.
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Affiliation(s)
- Daoliang Yu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xingfang Gu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shengping Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shaoyun Dong
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Han Miao
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Kiros Gebretsadik
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Department of Plant Science, Aksum University, Shire Campus, Shire, Ethiopia
| | - Kailiang Bo
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China.
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16
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Pei L, Li G, Lindsey K, Zhang X, Wang M. Plant 3D genomics: the exploration and application of chromatin organization. THE NEW PHYTOLOGIST 2021; 230:1772-1786. [PMID: 33560539 PMCID: PMC8252774 DOI: 10.1111/nph.17262] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 02/01/2021] [Indexed: 05/29/2023]
Abstract
Eukaryotic genomes are highly folded for packing into higher-order chromatin structures in the nucleus. With the emergence of state-of-the-art chromosome conformation capture methods and microscopic imaging techniques, the spatial organization of chromatin and its functional implications have been interrogated. Our knowledge of 3D chromatin organization in plants has improved dramatically in the past few years, building on the early advances in animal systems. Here, we review recent advances in 3D genome mapping approaches, our understanding of the sophisticated organization of spatial structures, and the application of 3D genomic principles in plants. We also discuss directions for future developments in 3D genomics in plants.
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Affiliation(s)
- Liuling Pei
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubei430070China
| | - Guoliang Li
- Hubei Key Laboratory of Agricultural BioinformaticsCollege of InformaticsHuazhong Agricultural UniversityWuhanHubei430070China
| | - Keith Lindsey
- Department of BiosciencesDurham UniversitySouth RoadDurhamDH1 3LEUK
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubei430070China
| | - Maojun Wang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubei430070China
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17
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Allotetraploidization in Brachypodium May Have Led to the Dominance of One Parent's Metabolome in Germinating Seeds. Cells 2021; 10:cells10040828. [PMID: 33917018 PMCID: PMC8067749 DOI: 10.3390/cells10040828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 04/01/2021] [Accepted: 04/02/2021] [Indexed: 11/26/2022] Open
Abstract
Seed germination is a complex process during which a mature seed resumes metabolic activity to prepare for seedling growth. In this study, we performed a comparative metabolomic analysis of the embryo and endosperm using the community standard lines of three annual Brachypodium species, i.e., B. distachyon (Bd) and B. stacei (Bs) and their natural allotetraploid B. hybridum (BdBs) that has wider ecological range than the other two species. We explored how far the metabolomic impact of allotetraploidization would be observable as over-lapping changes at 4, 12, and 24 h after imbibition (HAI) with water when germination was initiated. Metabolic changes during germination were more prominent in Brachypodium embryos than in the endosperm. The embryo and endosperm metabolomes of Bs and BdBs were similar, and those of Bd were distinctive. The Bs and BdBs embryos showed increased levels of sugars and the tricarboxylic acid cycle compared to Bd, which could have been indicative of better nutrient mobilization from the endosperm. Bs and BdBs also showed higher oxalate levels that could aid nutrient transfer through altered cellular events. In Brachypodium endosperm, the thick cell wall, in addition to starch, has been suggested to be a source of nutrients to the embryo. Metabolites indicative of sugar metabolism in the endosperm of all three species were not prominent, suggesting that mobilization mostly occurred prior to 4 HAI. Hydroxycinnamic and monolignol changes in Bs and BdBs were consistent with cell wall remodeling that arose following the release of nutrients to the respective embryos. Amino acid changes in both the embryo and endosperm were broadly consistent across the species. Taking our data together, the formation of BdBs may have maintained much of the Bs metabolome in both the embryo and endosperm during the early stages of germination. In the embryo, this conserved Bs metabolome appeared to include an elevated sugar metabolism that played a vital role in germination. If these observations are confirmed in the future with more Brachypodium accessions, it would substantiate the dominance of the Bs metabolome in BdBs allotetraploidization and the use of metabolomics to suggest important adaptive changes.
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18
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Li Y, Lu Y, Zhou Y, Wei X, Peng Y, Dai Y, Zhang L, Zhu Z. Diurnal transcriptomics analysis reveals the regulatory role of the circadian rhythm in super-hybrid rice LY2186. Genomics 2021; 113:1281-1290. [PMID: 33705889 DOI: 10.1016/j.ygeno.2020.12.046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 11/23/2020] [Accepted: 12/09/2020] [Indexed: 12/13/2022]
Abstract
Heterosis, an important biological phenomenon wherein F1 hybrids exhibit better performance than any of their parents, has been widely applied; however, its underlying mechanism remains largely unknown. Here, we studied and compared the dynamic transcriptional profiles of super-hybrid rice LY2186 and its parents at 17 time points during 2 day/night cycles and identified 1552 rhythmic differentially expressed genes (RDGs). Cluster and functional enrichment analyses revealed that the day- and night-phased RDGs were mainly enriched in the photosynthesis and stress response categories, respectively. Regulatory network analysis indicated that circadian-related RDGs are core components in both the day and night phases and extensively regulate downstream genes involved in photosynthesis, starch synthesis, plant hormone signal transduction, and other pathways. Furthermore, among the 282 RDGs mapped onto the quantitative tract loci of small intervals (≤100 genes), 72.3% were significantly enriched in the yield, vigor, and anatomy categories. These findings provide valuable information for exploring heterosis mechanisms further and guiding breeding practices.
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Affiliation(s)
- Yue Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Yufei Lu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Yun Zhou
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaoli Wei
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Yonggang Peng
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Yan Dai
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.
| | - Lei Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.
| | - Zhen Zhu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.
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19
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Meena RK, Reddy KS, Gautam R, Maddela S, Reddy AR, Gudipalli P. Improved photosynthetic characteristics correlated with enhanced biomass in a heterotic F 1 hybrid of maize (Zea mays L.). PHOTOSYNTHESIS RESEARCH 2021; 147:253-267. [PMID: 33555518 DOI: 10.1007/s11120-021-00822-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 01/15/2021] [Indexed: 05/13/2023]
Abstract
Heterosis is a phenomenon wherein F1 hybrid often displays phenotypic superiority and surpasses its parents in terms of growth and agronomic traits. Investigations on the physiological and biochemical properties of the heterotic F1 hybrid are important to uncover the mechanisms underlying heterosis in plants. In the present study, the photosynthetic capacity of a heterotic F1 hybrid of Zea mays L. (DHM 117) that exhibited a higher growth rate and increased biomass was compared with its parental inbreds at vegetative and reproductive stages in the field during 2017 and 2018. The net photosynthetic rate (Pn), stomatal conductance (gs), transpiration rate (E) as well as foliar carbohydrates were higher in F1 hybrid than parental inbreds at vegetative and reproductive stages. An increase in total chlorophyll content along with better chlorophyll a fluorescence characteristics including effective quantum yield of photosystem II (ΔF/Fm'), maximum quantum yield of PSII (Fv/Fm), photochemical quenching (qp) and decreased non-photochemical quenching (NPQ) was observed in F1 hybrid than the parental inbreds. Further, the expression of potential genes related to C4 photosynthesis was considerably upregulated in F1 hybrid than the parental inbreds during vegetative and reproductive stages. Moreover, the F1 hybrid exhibited distinct heterosis in yield with 63% and 62% increase relative to parental inbreds during 2017 and 2018. We conclude that improved photosynthetic efficiency associated with increased foliar carbohydrates could have contributed to higher growth rate, biomass and yield in the F1 hybrid.
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Affiliation(s)
- Rajesh Kumar Meena
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, 500 046, Telangana, India
| | - Kanubothula Sitarami Reddy
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, 500 046, Telangana, India
| | - Ranjana Gautam
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, 500 046, Telangana, India
| | - Surender Maddela
- Institute of Biotechnology, Prof. Jayashankar Telangana State Agricultural University, Hyderabad, 500 030, Telangana, India
| | - Attipalli Ramachandra Reddy
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, 500 046, Telangana, India
| | - Padmaja Gudipalli
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, 500 046, Telangana, India.
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20
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Zhang X, Ma C, Wang X, Wu M, Shao J, Huang L, Yuan L, Fu Z, Li W, Zhang X, Guo Z, Tang J. Global transcriptional profiling between inbred parents and hybrids provides comprehensive insights into ear-length heterosis of maize (Zea mays). BMC PLANT BIOLOGY 2021; 21:118. [PMID: 33637040 PMCID: PMC7908659 DOI: 10.1186/s12870-021-02890-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 02/09/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Maize (Zea mays) ear length, which is an important yield component, exhibits strong heterosis. Understanding the potential molecular mechanisms of ear-length heterosis is critical for efficient yield-related breeding. RESULTS Here, a joint netted pattern, including six parent-hybrid triplets, was designed on the basis of two maize lines harboring long (T121 line) and short (T126 line) ears. Global transcriptional profiling of young ears (containing meristem) was performed. Multiple comparative analyses revealed that 874 differentially expressed genes are mainly responsible for the ear-length variation between T121 and T126 lines. Among them, four key genes, Zm00001d049958, Zm00001d027359, Zm00001d048502 and Zm00001d052138, were identified as being related to meristem development, which corroborated their roles in the superior additive genetic effects on ear length in T121 line. Non-additive expression patterns were used to identify candidate genes related to ear-length heterosis. A non-additively expressed gene (Zm00001d050649) was associated with the timing of meristematic phase transition and was determined to be the homolog of tomato SELF PRUNING, which assists SINGLE FLOWER TRUSS in driving yield-related heterosis, indicating that Zm00001d050649 is a potential contributor to drive heterotic effect on ear length. CONCLUSION Our results suggest that inbred parents provide genetic and heterotic effects on the ear lengths of their corresponding F1 hybrids through two independent pathways. These findings provide comprehensive insights into the transcriptional regulation of ear length and improve the understanding of ear-length heterosis in maize.
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Affiliation(s)
- Xiangge Zhang
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450018, China
| | - Chenchen Ma
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450018, China
| | - Xiaoqing Wang
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450018, China
| | - Mingbo Wu
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450018, China
| | - Jingkuan Shao
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450018, China
| | - Li Huang
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450018, China
| | - Liang Yuan
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450018, China
| | - Zhiyuan Fu
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450018, China
| | - Weihua Li
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450018, China
| | - Xuehai Zhang
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450018, China
| | - Zhanyong Guo
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450018, China.
| | - Jihua Tang
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450018, China.
- Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, 433200, China.
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21
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Hou G, Dong Y, Zhu F, Zhao Q, Li T, Dou D, Ma X, Wu L, Ku L, Chen Y. MicroRNA transcriptomic analysis of the sixth leaf of maize (Zea mays L.) revealed a regulatory mechanism of jointing stage heterosis. BMC PLANT BIOLOGY 2020; 20:541. [PMID: 33256592 PMCID: PMC7708177 DOI: 10.1186/s12870-020-02751-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 11/22/2020] [Indexed: 05/27/2023]
Abstract
BACKGROUND Zhengdan 958 (Zheng 58 × Chang 7-2), a commercial hybrid that is produced in a large area in China, is the result of the successful use of the heterotic pattern of Reid × Tang-SPT. The jointing stage of maize is the key period from vegetative to reproductive growth, which determines development at later stages and heterosis to a certain degree. MicroRNAs (miRNAs) play vital roles in the regulation of plant development, but how they function in the sixth leaf at the six-leaf (V6) stage to influence jointing stage heterosis is still unclear. RESULT Our objective was to study miRNAs in four hybrid combinations developed in accordance with the Reid × Tang-SPT pattern, Zhengdan 958, Anyu 5 (Ye 478 × Chang 7-2), Ye 478 × Huangzaosi, Zheng 58 × Huangzaosi, and their parental inbred lines to explore the mechanism related to heterosis. A total of 234 miRNAs were identified in the sixth leaf at the V6 stage, and 85 miRNAs were differentially expressed between the hybrid combinations and their parental inbred lines. Most of the differentially expressed miRNAs were non-additively expressed, which indicates that miRNAs may participate in heterosis at the jointing stage. miR164, miR1432 and miR528 families were repressed in the four hybrid combinations, and some miRNAs, such as miR156, miR399, and miR395 families, exhibited different expression trends in different hybrid combinations, which may result in varying effects on the heterosis regulatory mechanism. CONCLUSIONS The potential targets of the identified miRNAs are related to photosynthesis, the response to plant hormones, and nutrient use. Different hybrid combinations employ different mature miRNAs of the same miRNA family and exhibit different expression trends that may result in enhanced or repressed gene expression to regulate heterosis. Taken together, our results reveal a miRNA-mediated network that plays a key role in jointing stage heterosis via posttranscriptional regulation.
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Affiliation(s)
- Gege Hou
- College of Agronomy, State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, #15 Longzi Lake University District, Zhengdong New District, Zhengzhou, 450046, Henan, People's Republic of China
| | - Yahui Dong
- College of Agronomy, State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, #15 Longzi Lake University District, Zhengdong New District, Zhengzhou, 450046, Henan, People's Republic of China
| | - Fangfang Zhu
- College of Agronomy, State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, #15 Longzi Lake University District, Zhengdong New District, Zhengzhou, 450046, Henan, People's Republic of China
| | - Qiannan Zhao
- College of Agronomy, State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, #15 Longzi Lake University District, Zhengdong New District, Zhengzhou, 450046, Henan, People's Republic of China
| | - Tianyi Li
- College of Agronomy, State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, #15 Longzi Lake University District, Zhengdong New District, Zhengzhou, 450046, Henan, People's Republic of China
| | - Dandan Dou
- College of Agronomy, State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, #15 Longzi Lake University District, Zhengdong New District, Zhengzhou, 450046, Henan, People's Republic of China
| | - Xingli Ma
- College of Agronomy, State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, #15 Longzi Lake University District, Zhengdong New District, Zhengzhou, 450046, Henan, People's Republic of China
| | - Liancheng Wu
- College of Agronomy, State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, #15 Longzi Lake University District, Zhengdong New District, Zhengzhou, 450046, Henan, People's Republic of China
| | - Lixia Ku
- College of Agronomy, State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, #15 Longzi Lake University District, Zhengdong New District, Zhengzhou, 450046, Henan, People's Republic of China
| | - Yanhui Chen
- College of Agronomy, State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, #15 Longzi Lake University District, Zhengdong New District, Zhengzhou, 450046, Henan, People's Republic of China.
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22
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Liu T, Duan W, Chen Z, Yuan J, Xiao D, Hou X, Li Y. Enhanced photosynthetic activity in pak choi hybrids is associated with increased grana thylakoids in chloroplasts. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:2211-2224. [PMID: 32573878 DOI: 10.1111/tpj.14893] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 06/01/2020] [Accepted: 06/12/2020] [Indexed: 05/12/2023]
Abstract
Increased photosynthetic activity is closely linked to heterosis in plants, but the underlying molecular mechanisms remain elusive. Pak choi (Brassica rapa ssp. chinensis) is a widely grown vegetable in Asia, and the most commercial cultivars are F1 hybrids. Here, the inbred pak choi lines WTC and 2Q, and their reciprocal F1 hybrids WQ and QW, were used to characterize the increased photosynthetic activity in these hybrids at the physiological, cellular and molecular levels. We found that the hybrids had larger leaves, with more grana thylakoids. Additionally, these hybrids had significantly increased net photosynthetic rates (Pn ) under both saturating and low irradiance conditions. These data indicate that the increased photosynthetic activity in pak choi hybrids was associated with an improved photosynthetic mechanism and larger leaves. Next, we obtained genome-wide data using transcriptome and bisulfite sequencing. Gene ontology (GO) analysis showed that the differentially expressed genes among the parents and hybrids were mostly enriched in the 'photosynthesis', 'thylakoid', and 'chloroplast' categories, indicating that the increased number of grana thylakoids contributes to the enhanced photosynthetic capacity in hybrids. Furthermore, we found that the increased number of grana thylakoids was associated with the upregulation of light-harvesting complex of photosystem II 1 (BrLhcb1). Yeast one-hybrid and transient assay showed that the BrLhcb1 promoter was directly bound by CIRCADIAN CLOCK ASSOCIATED 1 (BrCCA1), resulting in increased BrLhcb1 expression and enhanced carbon fixation in hybrids. Finally, our findings provide new insight into molecular mechanisms underlying enhanced photosynthesis in pak choi hybrids.
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Affiliation(s)
- Tongkun Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Weike Duan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Department of Life science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003, China
| | - Zhongwen Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jingping Yuan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Dong Xiao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xilin Hou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ying Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
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23
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Kong X, Chen L, Wei T, Zhou H, Bai C, Yan X, Miao Z, Xie J, Zhang L. Transcriptome analysis of biological pathways associated with heterosis in Chinese cabbage. Genomics 2020; 112:4732-4741. [PMID: 32798717 DOI: 10.1016/j.ygeno.2020.08.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 07/25/2020] [Accepted: 08/10/2020] [Indexed: 12/01/2022]
Abstract
Chinese cabbage is an important vegetable in Asia, and high-yielding hybrids are needed to cope with the growing demand. A comparative transcriptome profiling was conducted to reveal the differentially expressed genes (DEGs) associated with heterosis in two hybrids relative to their parents. Our data suggests that heterosis is underlined by a significant upregulation of gene expression. High expression of DEGs in glycolysis and photosynthesis pathways in hybrids depicted their relation with growth and hybrid vigor. Besides, DEGs related to auxin, abscisic acid, ethylene and gibberellin were identified, implying that these hormones may boost the mechanisms of growth and developmental processes in the hybrids. Furthermore, transcription factors, including bHLH, ERF, MYB and WRKY were predicted to regulate downstream genes linked to hybrid vigor. Collectively, the present study will be helpful for a better understanding of the regulation mechanisms of heterosis to aid cabbage yield improvement.
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Affiliation(s)
- Xiaoping Kong
- Horticulture College, Gansu Agricultural University, China; Xining Vegetable Technical Service Center, China
| | - Lin Chen
- Horticulture College, Northwest A & F Sci-tech University, China
| | - Tingzhen Wei
- Xining Vegetable Technical Service Center, China
| | - Hongwei Zhou
- Xining Vegetable Technical Service Center, China
| | | | | | - Zenjian Miao
- Xining Vegetable Technical Service Center, China
| | - Jianming Xie
- Horticulture College, Gansu Agricultural University, China.
| | - Lugang Zhang
- Horticulture College, Northwest A & F Sci-tech University, China.
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24
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Sinha P, Singh VK, Saxena RK, Kale SM, Li Y, Garg V, Meifang T, Khan AW, Kim KD, Chitikineni A, Saxena KB, Sameer Kumar CV, Liu X, Xu X, Jackson S, Powell W, Nevo E, Searle IR, Lodha M, Varshney RK. Genome-wide analysis of epigenetic and transcriptional changes associated with heterosis in pigeonpea. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:1697-1710. [PMID: 31925873 PMCID: PMC7336283 DOI: 10.1111/pbi.13333] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Accepted: 12/26/2019] [Indexed: 05/20/2023]
Abstract
Hybrids are extensively used in agriculture to deliver an increase in yield, yet the molecular basis of heterosis is not well understood. Global DNA methylation analysis, transcriptome analysis and small RNA profiling were aimed to understand the epigenetic effect of the changes in gene expression level in the two hybrids and their parental lines. Increased DNA methylation was observed in both the hybrids as compared to their parents. This increased DNA methylation in hybrids showed that majority of the 24-nt siRNA clusters had higher expression in hybrids than the parents. Transcriptome analysis revealed that various phytohormones (auxin and salicylic acid) responsive hybrid-MPV DEGs were significantly altered in both the hybrids in comparison to MPV. DEGs associated with plant immunity and growth were overexpressed whereas DEGs associated with basal defence level were repressed. This antagonistic patterns of gene expression might contribute to the greater growth of the hybrids. It was also noticed that some common as well as unique changes in the regulatory pathways were associated with heterotic growth in both the hybrids. Approximately 70% and 67% of down-regulated hybrid-MPV DEGs were found to be differentially methylated in ICPH 2671 and ICPH 2740 hybrid, respectively. This reflected the association of epigenetic regulation in altered gene expressions. Our findings also revealed that miRNAs might play important roles in hybrid vigour in both the hybrids by regulating their target genes, especially in controlling plant growth and development, defence and stress response pathways. The above finding provides an insight into the molecular mechanism of pigeonpea heterosis.
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Affiliation(s)
- Pallavi Sinha
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruIndia
| | - Vikas K. Singh
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruIndia
- International Rice Research Institute, South‐Asia HubPatancheruIndia
| | - Rachit K. Saxena
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruIndia
| | - Sandip M. Kale
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruIndia
- The Leibniz Institute of Plant Genetics and Crop Plant ResearchGaterslebenGermany
| | | | - Vanika Garg
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruIndia
| | | | - Aamir W. Khan
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruIndia
| | - Kyung Do Kim
- University of GeorgiaAthensUSA
- Myongji UniversityYonginRepublic of Korea
| | - Annapurna Chitikineni
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruIndia
| | - K. B. Saxena
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruIndia
| | - C. V. Sameer Kumar
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruIndia
| | | | - Xun Xu
- BGI‐ShenzhenShenzhenChina
| | | | | | | | | | - Mukesh Lodha
- Centre for Cellular and Molecular Biology (CSIR)HyderabadIndia
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruIndia
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Selva C, Riboni M, Baumann U, Würschum T, Whitford R, Tucker MR. Hybrid breeding in wheat: how shaping floral biology can offer new perspectives. FUNCTIONAL PLANT BIOLOGY : FPB 2020; 47:675-694. [PMID: 32534601 DOI: 10.1071/fp19372] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 03/21/2020] [Indexed: 06/11/2023]
Abstract
Hybrid breeding in wheat (Triticum aestivum L.) has the potential to deliver major yield increases. This is a requisite to guarantee food security for increasing population demands and to counterbalance the effects of extreme environmental conditions. Successful hybrid breeding in wheat relies on forced outcrossing while preventing self-pollination. To achieve this, research has been directed towards identifying and improving fertility control systems. To maximise cross-pollination and seed set, however, fertility control systems need to be complemented by breeding phenotypically distinct male and female lines. This review summarises existing and novel male sterility systems for wheat hybridisation. We also consider the genetic resources that can be used to alter wheat's floral development and spike morphology, with a focus on the genetic variation already available. Exploiting these resources can lead to enhanced outcrossing, a key requirement in the progress towards hybrid wheat breeding.
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Affiliation(s)
- Caterina Selva
- School of Agriculture Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA 5064, Australia
| | - Matteo Riboni
- School of Agriculture Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA 5064, Australia
| | - Ute Baumann
- School of Agriculture Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA 5064, Australia
| | - Tobias Würschum
- State Plant Breeding Institute, University of Hohenheim, 70593 Stuttgart, Germany
| | - Ryan Whitford
- School of Agriculture Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA 5064, Australia; and Corresponding authors. ;
| | - Matthew R Tucker
- School of Agriculture Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA 5064, Australia; and Corresponding authors. ;
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26
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Yi G, Shin H, Park HR, Park JE, Ahn JH, Lim S, Lee JG, Lee EJ, Huh JH. Revealing biomass heterosis in the allodiploid xBrassicoraphanus, a hybrid between Brassica rapa and Raphanus sativus, through integrated transcriptome and metabolites analysis. BMC PLANT BIOLOGY 2020; 20:252. [PMID: 32493222 PMCID: PMC7268423 DOI: 10.1186/s12870-020-02470-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 05/26/2020] [Indexed: 05/15/2023]
Abstract
BACKGROUND Heterosis is biologically important but the molecular basis of the phenomenon is poorly understood. We characterized intergeneric hybrids between B. rapa cv. Chiifu and R. sativus cv. WK10039 as an extreme example of heterosis. Taking advantage of clear heterosis phenotypes and the genetic distance between parents, we performed transcriptome and metabolite analysis to decipher the molecular basis of heterosis. RESULTS The heterosis was expressed as fresh weight in the field and as inflorescence stem length in the glass house. Flowering time, distributed as a normal segregating population, ranged from the early flowering of one parent to the late flowering of the other, in contrast to the homogeneous flowering time in a typical F1 population, indicating unstable allelic interactions. The transcriptome and metabolome both indicated that sugar metabolism was altered, suggesting that the change in metabolism was linked to the heterosis. Because alleles were not shared between the hybridized genomes, classic models only partly explain this heterosis, indicating that other mechanisms are involved. CONCLUSION The differential expression of genes for primary and secondary metabolism, along with the altered metabolite profiles, suggests that heterosis could involve a change in balance between primary and secondary metabolism.
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Affiliation(s)
- Gibum Yi
- Department of Plant Science, Seoul National University, Gwanak-gu, Seoul, 08826 South Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 South Korea
- Department of Central Area Crop Science, National Institute of Crop Science, RDA, Suwon, 16429 Republic of Korea
| | - Hosub Shin
- Department of Plant Science, Seoul National University, Gwanak-gu, Seoul, 08826 South Korea
| | - Hye Rang Park
- Department of Plant Science, Seoul National University, Gwanak-gu, Seoul, 08826 South Korea
| | - Jeong Eun Park
- Department of Plant Science, Seoul National University, Gwanak-gu, Seoul, 08826 South Korea
| | - Jong Hwa Ahn
- Department of Plant Science, Seoul National University, Gwanak-gu, Seoul, 08826 South Korea
- Illumina Korea, Yeongdeungpo-gu, Seoul, 07325 South Korea
| | - Sooyeon Lim
- Department of Plant Science, Seoul National University, Gwanak-gu, Seoul, 08826 South Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826 South Korea
- National Institute of Horticultural and Herbal Science, RDA, Wanju-gun, Jeollabuk-do 55365 South Korea
| | - Jeong Gu Lee
- Department of Plant Science, Seoul National University, Gwanak-gu, Seoul, 08826 South Korea
| | - Eun Jin Lee
- Department of Plant Science, Seoul National University, Gwanak-gu, Seoul, 08826 South Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826 South Korea
| | - Jin Hoe Huh
- Department of Plant Science, Seoul National University, Gwanak-gu, Seoul, 08826 South Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 South Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826 South Korea
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27
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Howlader J, Robin AHK, Natarajan S, Biswas MK, Sumi KR, Song CY, Park JI, Nou IS. Transcriptome Analysis by RNA-Seq Reveals Genes Related to Plant Height in Two Sets of Parent-hybrid Combinations in Easter lily (Lilium longiflorum). Sci Rep 2020; 10:9082. [PMID: 32494055 PMCID: PMC7270119 DOI: 10.1038/s41598-020-65909-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 05/12/2020] [Indexed: 11/23/2022] Open
Abstract
In this study, two different hybrids of Easter lily (Lilium longiflorum), obtained from two cross combinations, along with their four parents were sequenced by high–throughput RNA–sequencing (RNA–Seq) to find out differentially expressed gene in parent-hybrid combinations. The leaf mRNA profiles of two hybrids and their four parents were RNA–sequenced with a view to identify the potential candidate genes related to plant height heterosis. In both cross combinations, based to morphological traits mid–parent heterosis (MPH) was higher than high–parent heterosis (HPH) for plant height, leaf length, and number of flowers whereas HPH was higher than MPH for flowering time. A total of 4,327 differentially expressed genes (DEGs) were identified through RNA–Seq between the hybrids and their parents based on fold changes (FC) ≥ 2 for up– and ≤ –2 for down–regulation. Venn diagram analysis revealed that there were 703 common DEGs in two hybrid combinations, those were either up– or down–regulated. Most of the commonly expressed DEGs exhibited higher non–additive effects especially overdominance (75.9%) rather than additive (19.4%) and dominance (4.76%) effects. Among the 384 functionally annotated DEGs identified through Blast2GO tool, 12 DEGs were up–regulated and 16 of them were down–regulated in a similar fashion in both hybrids as revealed by heat map analysis. These 28 universally expressed DEGs were found to encode different types of proteins and enzymes those might regulate heterosis by modulating growth, development and stress–related functions in lily. In addition, gene ontology (GO) analysis of 260 annotated DEGs revealed that biological process might play dominant role in heterotic expression. In this first report of transcriptome sequencing in Easter lily, the notable universally up-regulated DEGs annotated ABC transporter A family member–like, B3 domain–containing, disease resistance RPP13/1, auxin–responsive SAUR68–like, and vicilin–like antimicrobial peptides 2–2 proteins those were perhaps associated with plant height heterosis. The genes expressed universally due to their overdominace function perhaps influenced MPH for greater plant height― largely by modulating biological processes involved therein. The genes identified in this study might be exploited in heterosis breeding for plant height of L. longiflorum.
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Affiliation(s)
- Jewel Howlader
- Department of Horticulture, Sunchon National University, 255, Jungang-ro, Suncheon, Jeonnam, 57922, Republic of Korea.,Department of Horticulture, Patuakhali Science and Technology University, Dumki, Patuakhali, 8602, Bangladesh
| | - Arif Hasan Khan Robin
- Department of Horticulture, Sunchon National University, 255, Jungang-ro, Suncheon, Jeonnam, 57922, Republic of Korea.,Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Sathishkumar Natarajan
- Department of Horticulture, Sunchon National University, 255, Jungang-ro, Suncheon, Jeonnam, 57922, Republic of Korea
| | - Manosh Kumar Biswas
- Department of Horticulture, Sunchon National University, 255, Jungang-ro, Suncheon, Jeonnam, 57922, Republic of Korea
| | - Kanij Rukshana Sumi
- Department of Fisheries Science, Chonnam National University, 50, Daehak-ro, Yeosu, Jeonnam, 59626, Republic of Korea.,Department of Aquaculture, Patuakhali Science and Technology University, Dumki, Patuakhali, 8602, Bangladesh
| | - Cheon Young Song
- Department of Floriculture, Korea National College of Agriculture and Fisheries, 1515, Kongjwipatjwi-ro, Wansan-gu, Jeonju-si, Jeollabuk-do, 54874, Republic of Korea
| | - Jong-In Park
- Department of Horticulture, Sunchon National University, 255, Jungang-ro, Suncheon, Jeonnam, 57922, Republic of Korea
| | - Ill-Sup Nou
- Department of Horticulture, Sunchon National University, 255, Jungang-ro, Suncheon, Jeonnam, 57922, Republic of Korea.
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Shahzad K, Zhang X, Guo L, Qi T, Bao L, Zhang M, Zhang B, Wang H, Tang H, Qiao X, Feng J, Wu J, Xing C. Comparative transcriptome analysis between inbred and hybrids reveals molecular insights into yield heterosis of upland cotton. BMC PLANT BIOLOGY 2020; 20:239. [PMID: 32460693 PMCID: PMC7251818 DOI: 10.1186/s12870-020-02442-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 05/13/2020] [Indexed: 05/12/2023]
Abstract
BACKGROUND Utilization of heterosis has greatly improved the productivity of many crops worldwide. Understanding the potential molecular mechanism about how hybridization produces superior yield in upland cotton is critical for efficient breeding programs. RESULTS In this study, high, medium, and low hybrids varying in the level of yield heterosis were screened based on field experimentation of different years and locations. Phenotypically, high hybrid produced a mean of 14% more seed cotton yield than its better parent. Whole-genome RNA sequencing of these hybrids and their four inbred parents was performed using different tissues of the squaring stage. Comparative transcriptomic differences in each hybrid parent triad revealed a higher percentage of differentially expressed genes (DEGs) in each tissue. Expression level dominance analysis identified majority of hybrids DEGs were biased towards parent like expressions. An array of DEGs involved in ATP and protein binding, membrane, cell wall, mitochondrion, and protein phosphorylation had more functional annotations in hybrids. Sugar metabolic and plant hormone signal transduction pathways were most enriched in each hybrid. Further, these two pathways had most mapped DEGs on known seed cotton yield QTLs. Integration of transcriptome, QTLs, and gene co-expression network analysis discovered genes Gh_A03G1024, Gh_D08G1440, Gh_A08G2210, Gh_A12G2183, Gh_D07G1312, Gh_D08G1467, Gh_A03G0889, Gh_A08G2199, and Gh_D05G0202 displayed a complex regulatory network of many interconnected genes. qRT-PCR of these DEGs was performed to ensure the accuracy of RNA-Seq data. CONCLUSIONS Through genome-wide comparative transcriptome analysis, the current study identified nine key genes and pathways associated with biological process of yield heterosis in upland cotton. Our results and data resources provide novel insights and will be useful for dissecting the molecular mechanism of yield heterosis in cotton.
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Affiliation(s)
- Kashif Shahzad
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture, 38 Huanghe Dadao, Anyang, 455000 Henan China
| | - Xuexian Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture, 38 Huanghe Dadao, Anyang, 455000 Henan China
| | - Liping Guo
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture, 38 Huanghe Dadao, Anyang, 455000 Henan China
| | - Tingxiang Qi
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture, 38 Huanghe Dadao, Anyang, 455000 Henan China
| | - Lisheng Bao
- Jinhua Department of Economic Special Technology Promotion, Jinhua, 321017 Zhejiang China
| | - Meng Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture, 38 Huanghe Dadao, Anyang, 455000 Henan China
| | - Bingbing Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture, 38 Huanghe Dadao, Anyang, 455000 Henan China
| | - Hailin Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture, 38 Huanghe Dadao, Anyang, 455000 Henan China
| | - Huini Tang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture, 38 Huanghe Dadao, Anyang, 455000 Henan China
| | - Xiuqin Qiao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture, 38 Huanghe Dadao, Anyang, 455000 Henan China
| | - Juanjuan Feng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture, 38 Huanghe Dadao, Anyang, 455000 Henan China
| | - Jianyong Wu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture, 38 Huanghe Dadao, Anyang, 455000 Henan China
| | - Chaozhu Xing
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture, 38 Huanghe Dadao, Anyang, 455000 Henan China
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Mehraj H, Kawanabe T, Shimizu M, Miyaji N, Akter A, Dennis ES, Fujimoto R. In Arabidopsis thaliana Heterosis Level Varies among Individuals in an F 1 Hybrid Population. PLANTS 2020; 9:plants9040414. [PMID: 32230994 PMCID: PMC7238264 DOI: 10.3390/plants9040414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 03/23/2020] [Accepted: 03/23/2020] [Indexed: 11/28/2022]
Abstract
Heterosis or hybrid vigour is a phenomenon in which hybrid progeny exhibit superior yield and biomass to parental lines and has been used to breed F1 hybrid cultivars in many crops. A similar level of heterosis in all F1 individuals is expected as they are genetically identical. However, we found variation in rosette size in individual F1 plants from a cross between C24 and Columbia-0 accessions of Arabidopsis thaliana. Big-sized F1 plants had 26.1% larger leaf area in the first and second leaves than medium-sized F1 plants at 14 days after sowing in spite of the identical genetic background. We identified differentially expressed genes between big- and medium-sized F1 plants by microarray; genes involved in the category of stress response were overrepresented. We made transgenic plants overexpressing 21 genes, which were differentially expressed between the two size classes, and some lines had increased plant size at 14 or 21 days after sowing but not at all time points during development. Change of expression levels in stress-responsive genes among individual F1 plants could generate the variation in plant size of individual F1 plants in A. thaliana.
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Affiliation(s)
- Hasan Mehraj
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada-ku, Kobe 657-8501, Japan; (H.M.); (N.M.); (A.A.)
| | - Takahiro Kawanabe
- School of Agriculture, Tokai University, Toroku, Higashi-ku, Kumamoto 862-8652, Japan
- Correspondence: (T.K.); (R.F.)
| | - Motoki Shimizu
- Iwate Biotechnology Research Center, Narita, Kitakami, Iwate 024-0003, Japan;
| | - Naomi Miyaji
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada-ku, Kobe 657-8501, Japan; (H.M.); (N.M.); (A.A.)
| | - Ayasha Akter
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada-ku, Kobe 657-8501, Japan; (H.M.); (N.M.); (A.A.)
- Department of Horticulture, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Elizabeth S. Dennis
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia;
- University of Technology, Sydney, PO Box 123, Broadway, NSW 2007, Australia
| | - Ryo Fujimoto
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada-ku, Kobe 657-8501, Japan; (H.M.); (N.M.); (A.A.)
- Correspondence: (T.K.); (R.F.)
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Genome-wide transcriptome profile of rice hybrids with and without Oryza rufipogon introgression reveals candidate genes for yield. Sci Rep 2020; 10:4873. [PMID: 32184449 PMCID: PMC7078188 DOI: 10.1038/s41598-020-60922-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 02/10/2020] [Indexed: 01/22/2023] Open
Abstract
In this study, we compared genome-wide transcriptome profile of two rice hybrids, one with (test hybrid IR79156A/IL50-13) and the other without (control hybrid IR79156A/KMR3) O. rufipogon introgressions to identify candidate genes related to grain yield in the test hybrid. IL50-13 (Chinsurah Nona2 IET21943) the male parent (restorer) used in the test hybrid, is an elite BC4F8 introgression line of KMR3 with O. rufipogon introgressions. We identified 2798 differentially expressed genes (DEGs) in flag leaf and 3706 DEGs in panicle. Overall, 78 DEGs were within the major yield QTL qyld2.1 and 25 within minor QTL qyld8.2. The DEGs were significantly (p < 0.05) enriched in starch synthesis, phenyl propanoid pathway, ubiquitin degradation and phytohormone related pathways in test hybrid compared to control hybrid. Sequence analysis of 136 DEGs from KMR3 and IL50-13 revealed 19 DEGs with SNP/InDel variations. Of the 19 DEGs only 6 showed both SNP and InDel variations in exon regions. Of these, two DEGs within qyld2.1, Phenylalanine ammonia- lyase (PAL) (Os02t0626400-01, OsPAL2) showed 184 SNPs and 11 InDel variations and Similar to phenylalanine ammonia- lyase (Os02t0627100-01, OsPAL4) showed 205 SNPs and 13 InDel variations. Both PAL genes within qyld2.1 and derived from O. rufipogon are high priority candidate genes for increasing grain yield in rice.
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Katara JL, Verma RL, Parida M, Ngangkham U, Molla KA, Barbadikar KM, Mukherjee M, C P, Samantaray S, Ravi NR, Singh ON, Mohapatra T. Differential Expression of Genes at Panicle Initiation and Grain Filling Stages Implied in Heterosis of Rice Hybrids. Int J Mol Sci 2020; 21:ijms21031080. [PMID: 32041193 PMCID: PMC7038112 DOI: 10.3390/ijms21031080] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 12/23/2019] [Accepted: 12/27/2019] [Indexed: 12/15/2022] Open
Abstract
RNA-Seq technology was used to analyze the transcriptome of two rice hybrids, Ajay (based on wild-abortive (WA)-cytoplasm) and Rajalaxmi (based on Kalinga-cytoplasm), and their respective parents at the panicle initiation (PI) and grain filling (GF) stages. Around 293 and 302 million high quality paired-end reads of Ajay and Rajalaxmi, respectively, were generated and aligned against the Nipponbare reference genome. Transcriptome profiling of Ajay revealed 2814 and 4819 differentially expressed genes (DEGs) at the PI and GF stages, respectively, as compared to its parents. In the case of Rajalaxmi, 660 and 5264 DEGs were identified at PI and GF stages, respectively. Functionally relevant DEGs were selected for validation through qRT-PCR, which were found to be co-related with the expression patterns to RNA-seq. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated significant DEGs enriched for energy metabolism pathways, such as photosynthesis, oxidative phosphorylation, and carbon fixation, at the PI stage, while carbohydrate metabolism-related pathways, such as glycolysis and starch and sucrose metabolism, were significantly involved at the GF stage. Many genes involved in energy metabolism exhibited upregulation at the PI stage, whereas the genes involved in carbohydrate biosynthesis had higher expression at the GF stage. The majority of the DEGs were successfully mapped to know yield related rice quantitative trait loci (QTLs). A set of important transcription factors (TFs) was found to be encoded by the identified DEGs. Our results indicated that a complex interplay of several genes in different pathways contributes to higher yield and vigor in rice hybrids.
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Nadir S, Li W, Zhu Q, Khan S, Zhang XL, Zhang H, Wei ZF, Li MT, Zhou L, Li CY, Chen LJ, Lee DS. A novel discovery of a long terminal repeat retrotransposon-induced hybrid weakness in rice. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:1197-1207. [PMID: 30576523 PMCID: PMC6382335 DOI: 10.1093/jxb/ery442] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 12/04/2018] [Indexed: 06/09/2023]
Abstract
Hybrid weakness is a post-zygotic hybridization barrier frequently observed in plants, including rice. In this study, we describe the genomic variation among three temperate japonica rice (Oryza sativa ssp. japonica) varieties 'Aranghyangchalbyeo' ('CH7'), 'Sanghaehyangheolua' ('CH8') and 'Shinseonchalbyeo' ('CH9'), carrying different hybrid weakness genes. The reciprocal progeny obtained from crossing any two varieties displayed characteristic hybrid weakness traits. We mapped and cloned a new locus, Hwc3 (hybrid weakness 3), on chromosome 4. Sequence analysis identified that a long terminal repeat (LTR) retrotransposon was inserted into the promoter region of the Hwc3 gene in 'CH7'. A 4-kb DNA fragment from 'CH7' containing the Hwc3 gene with the inserted LTR retrotransposon was able to induce hybrid weakness in hybrids with 'CH8' plants carrying the Hwc1 gene by genetic complementation. We investigated the differential gene expression profile of F1 plants exhibiting hybrid weakness and detected that the genes associated with energy metabolism were significantly down-regulated compared with the parents. Based on our results, we propose that LTR retrotransposons could be a potential cause of hybrid weakness in intrasubspecific hybrids in japonica rice. Understanding the molecular mechanisms underlying intrasubspecific hybrid weakness is important for increasing our knowledge on reproductive isolation and could have significant implications for rice improvement and hybrid breeding.
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Affiliation(s)
- Sadia Nadir
- Rice Research Institute, Yunnan Agriculture University, Kunming, Yunnan, China
- Department of Chemistry, University of Science and Technology, Bannu, KPK, Pakistan
- Centre for Mountain Ecosystem Studies, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Wei Li
- Rice Research Institute, Yunnan Agriculture University, Kunming, Yunnan, China
| | - Qian Zhu
- Rice Research Institute, Yunnan Agriculture University, Kunming, Yunnan, China
| | - Sehroon Khan
- Centre for Mountain Ecosystem Studies, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- World Agroforestry Centre, East and Central Asia, Kunming, Yunnan, China
| | - Xiao-Ling Zhang
- Agricultural College of Kunming University, Kunming, Yunnan, China
| | - Hui Zhang
- College of Agronomy and Biotechnology, Yunnan Agriculture University, Kunming, Yunnan, China
| | - Zhen-Fei Wei
- Maize Research Institute, Shanxi Academy of Agriculture Sciences, Xinzhou, Shanxi, China
| | - Meng-Ting Li
- Rice Research Institute, Yunnan Agriculture University, Kunming, Yunnan, China
| | - Li Zhou
- Rice Research Institute, Yunnan Agriculture University, Kunming, Yunnan, China
| | - Cheng-Yun Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Li-Juan Chen
- Rice Research Institute, Yunnan Agriculture University, Kunming, Yunnan, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Dong-Sun Lee
- Rice Research Institute, Yunnan Agriculture University, Kunming, Yunnan, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan, China
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Toniutti L, Breitler JC, Guittin C, Doulbeau S, Etienne H, Campa C, Lambot C, Herrera Pinilla JC, Bertrand B. An Altered Circadian Clock Coupled with a Higher Photosynthesis Efficiency Could Explain the Better Agronomic Performance of a New Coffee Clone When Compared with a Standard Variety. Int J Mol Sci 2019; 20:ijms20030736. [PMID: 30744144 PMCID: PMC6386876 DOI: 10.3390/ijms20030736] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 01/28/2019] [Accepted: 01/30/2019] [Indexed: 11/16/2022] Open
Abstract
In a context where climate change is threatening coffee productivity, the management of coffee leaf rust is a challenging issue. Major resistant genes, which have been used for many years, are systematically being overcome by pathogens. Developing healthy plants, able to defend themselves and be productive even when attacked by the pathogen, should be part of a more sustainable alternative approach. We compared one hybrid (GPFA124), selected for its good health in various environments including a reduced rust incidence, and the cv. 'Caturra', considered as a standard in terms of productivity and quality but highly susceptible to rust, for phenotypic variables and for the expression of genes involved in the circadian clock and in primary photosynthetic metabolism. The GPFA124 hybrid showed increased photosynthetic electron transport efficiency, better carbon partitioning, and higher chlorophyll content. A strong relationship exists between chlorophyll a fluorescence and the expression of genes related to the photosynthetic electron transport chain. We also showed an alteration of the amplitude of circadian clock genes in the clone. Our work also indicated that increased photosynthetic electron transport efficiency is related to the clone's better performance. Chlorophyll a fluorescence measurement is a good indicator of the coffee tree's physiological status for the breeder. We suggest a connection between the circadian clock and carbon metabolism in coffee tree.
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Affiliation(s)
- Lucile Toniutti
- CIRAD, IPME, 34 398 Montpellier, France.
- UMR IPME, Univ. Montpellier, IRD, CIRAD, 34 398 Montpellier, France.
- Nestlé R&D Tours, 101 AV. G. Eiffel, Notre Dame d'Oé, BP 49716, 37097 Tours CEDEX 2, France.
| | - Jean-Christophe Breitler
- CIRAD, IPME, 34 398 Montpellier, France.
- UMR IPME, Univ. Montpellier, IRD, CIRAD, 34 398 Montpellier, France.
| | - Charlie Guittin
- IRD, IPME, 34 398 Montpellier, France.
- UMR IPME, Univ. Montpellier, IRD, CIRAD, 34 398 Montpellier, France.
| | | | - Hervé Etienne
- CIRAD, IPME, 34 398 Montpellier, France.
- UMR IPME, Univ. Montpellier, IRD, CIRAD, 34 398 Montpellier, France.
| | - Claudine Campa
- IRD, IPME, 34 398 Montpellier, France.
- UMR IPME, Univ. Montpellier, IRD, CIRAD, 34 398 Montpellier, France.
| | - Charles Lambot
- Nestlé R&D Tours, 101 AV. G. Eiffel, Notre Dame d'Oé, BP 49716, 37097 Tours CEDEX 2, France.
| | | | - Benoît Bertrand
- CIRAD, IPME, 34 398 Montpellier, France.
- UMR IPME, Univ. Montpellier, IRD, CIRAD, 34 398 Montpellier, France.
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Li H, Yuan J, Wu M, Han Z, Li L, Jiang H, Jia Y, Han X, Liu M, Sun D, Chen C, Song W, Wang C. Transcriptome and DNA methylome reveal insights into yield heterosis in the curds of broccoli (Brassica oleracea L var. italic). BMC PLANT BIOLOGY 2018; 18:168. [PMID: 30103674 PMCID: PMC6090608 DOI: 10.1186/s12870-018-1384-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 08/01/2018] [Indexed: 05/21/2023]
Abstract
BACKGROUND Curds are the main edible organs, which exhibit remarkable yield heterosis in F1 hybrid broccoli. However, the molecular basis underlying heterosis in broccoli remains elusive. RESULTS In the present study, transcriptome profiles revealed that the hybridization made most genes show additive expression patterns in hybrid broccoli. The differentially expressed genes including the non-additively expressed genes detected in the hybrid broccoli and its parents were mainly involved in light, hormone and hydrogen peroxide-mediated signaling pathways, responses to stresses, and regulation of floral development, which suggested that these biological processes should play crucial roles in the yield heterosis of broccoli. Among them, light and hydrogen peroxide-mediated signaling pathways represent two novel classes of regulatory processes that could function in yield or biomass heterosis of plants. Totally, 53 candidate genes closely involved in curd yield heterosis were identified. Methylome data indicated that the DNA methylation ratio of the hybrids was higher than that of their parents. However, the DNA methylation levels of most sites also displayed additive expression patterns. These sites with differential methylation levels were predominant in the intergenic regions. In most cases, the changes of DNA methylation levels in gene regions did not significantly affect their expression levels. CONCLUSIONS The differentially expressed genes, the regulatory processes and the possible roles of DNA methylation modification in the formation of curd yield heterotic trait were discovered. These findings provided comprehensive insights into the curd yield heterosis in broccoli, and were significant for breeding high-yield broccoli varieties.
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Affiliation(s)
- Hui Li
- College of Horticulture and Landscape, Tianjin Agricultural University, Tianjin, China
| | - Jiye Yuan
- College of Life Sciences, Nankai University, Tianjin, China
| | - Mei Wu
- College of Life Sciences, Nankai University, Tianjin, China
| | - Zhanpin Han
- College of Horticulture and Landscape, Tianjin Agricultural University, Tianjin, China
| | - Lihong Li
- College of Life Sciences, Nankai University, Tianjin, China
| | - Hanmin Jiang
- Tianjin Kernel Vegetable Research Institute, Tianjin, China
| | - Yinglan Jia
- College of Life Sciences, Nankai University, Tianjin, China
| | - Xue Han
- College of Life Sciences, Nankai University, Tianjin, China
| | - Min Liu
- College of Life Sciences, Shandong Normal University, Jinan, Shandong China
| | - Deling Sun
- Tianjin Kernel Vegetable Research Institute, Tianjin, China
| | - Chengbin Chen
- College of Life Sciences, Nankai University, Tianjin, China
| | - Wenqin Song
- College of Life Sciences, Nankai University, Tianjin, China
| | - Chunguo Wang
- College of Life Sciences, Nankai University, Tianjin, China
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Chen L, Bian J, Shi S, Yu J, Khanzada H, Wassan GM, Zhu C, Luo X, Tong S, Yang X, Peng X, Yong S, Yu Q, He X, Fu J, Chen X, Hu L, Ouyang L, He H. Genetic analysis for the grain number heterosis of a super-hybrid rice WFYT025 combination using RNA-Seq. RICE (NEW YORK, N.Y.) 2018; 11:37. [PMID: 29904811 PMCID: PMC6003258 DOI: 10.1186/s12284-018-0229-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 06/06/2018] [Indexed: 05/19/2023]
Abstract
BACKGROUND Despite the great contributions of utilizing heterosis to crop productivity worldwide, the molecular mechanism of heterosis remains largely unexplored. Thus, the present research is focused on the grain number heterosis of a widely used late-cropping indica super hybrid rice combination in China using a high-throughput next-generation RNA-seq strategy. RESULTS Here, we obtained 872 million clean reads, and at least one read could maps 27,917 transcripts out of 35,679 annotations. Transcript differential expression analysis revealed a total of 5910 differentially expressed genes (DGHP) between super-hybrid rice Wufengyou T025 (WFYT025) and its parents were identified in the young panicles. Out of the 5910 DGHP, 63.1% had a genetic action mode of over-dominance, 17.3% had a complete-dominance action, 15.6% had a partial-dominance action and 4.0% had an additive action. DGHP were significantly enriched in carotenoid biosynthesis, diterpenoid biosynthesis and plant hormone signal transduction pathways, with the key genes involved in the three pathways being up-regulated in the hybrid. By comparing the DGHP enriched in the KEGG pathway with QTLs associated with grain number, several DGHP were located on the same chromosomal segment with some of these grain number QTLs. CONCLUSION Through young panicle development transcriptome analysis, we conclude that the over-dominant effect is probably the major contributor to the grain number heterosis of WFYT025. The DGHP sharing the same location with grain number QTLs could be considered a candidate gene and provide valuable targets for the cloning and functional analysis of these grain number QTLs.
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Affiliation(s)
- Liang Chen
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045 China
- College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045 China
| | - Jianmin Bian
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045 China
- College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045 China
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Changsha, China
| | - Shilai Shi
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045 China
- College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045 China
| | - Jianfeng Yu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045 China
- College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045 China
| | - Hira Khanzada
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045 China
- College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045 China
| | - Ghulam Mustafa Wassan
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045 China
- College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045 China
| | - Changlan Zhu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045 China
- College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045 China
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Changsha, China
| | - Xin Luo
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045 China
- College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045 China
| | - Shan Tong
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045 China
- College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045 China
| | - Xiaorong Yang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045 China
- College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045 China
| | - Xiaosong Peng
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045 China
- College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045 China
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Changsha, China
| | - Shuang Yong
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045 China
| | - Qiuying Yu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045 China
| | - Xiaopeng He
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045 China
- College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045 China
| | - Junru Fu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045 China
- College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045 China
| | - Xiaorong Chen
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045 China
- College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045 China
| | - Lifang Hu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045 China
- College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045 China
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Changsha, China
| | - Linjuan Ouyang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045 China
- College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045 China
| | - Haohua He
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045 China
- College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045 China
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Changsha, China
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Cis-regulated additively expressed genes play a fundamental role in the formation of triploid loquat (Eriobotrya japonica (Thunb.) Lindl.) Heterosis. Mol Genet Genomics 2018; 293:967-981. [DOI: 10.1007/s00438-018-1433-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Accepted: 03/23/2018] [Indexed: 10/17/2022]
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Fujimoto R, Uezono K, Ishikura S, Osabe K, Peacock WJ, Dennis ES. Recent research on the mechanism of heterosis is important for crop and vegetable breeding systems. BREEDING SCIENCE 2018; 68:145-158. [PMID: 29875598 PMCID: PMC5982191 DOI: 10.1270/jsbbs.17155] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Accepted: 01/29/2018] [Indexed: 05/18/2023]
Abstract
Heterosis or hybrid vigor is a phenomenon where hybrid progeny have superior performance compared to their parental inbred lines. This is important in the use of F1 hybrid cultivars in many crops and vegetables. However, the molecular mechanism of heterosis is not clearly understood. Gene interactions between the two genomes such as dominance, overdominance, and epistasis have been suggested to explain the increased biomass and yield. Genetic analyses of F1 hybrids in maize, rice, and canola have defined a large number of quantitative trait loci, which may contribute to heterosis. Recent molecular analyses of transcriptomes together with reference to the epigenome of the parents and hybrids have begun to uncover new facts about the generation of heterosis. These include the identification of gene expression changes in hybrids, which may be important for heterosis, the role of epigenetic processes in heterosis, and the development of stable high yielding lines.
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Affiliation(s)
- Ryo Fujimoto
- Graduate School of Agricultural Science, Kobe University,
Rokkodai, Nada-ku, Kobe, Hyogo 657-8501,
Japan
- Corresponding author (e-mail: )
| | - Kosuke Uezono
- Graduate School of Agricultural Science, Kobe University,
Rokkodai, Nada-ku, Kobe, Hyogo 657-8501,
Japan
| | - Sonoko Ishikura
- Graduate School of Agricultural Science, Kobe University,
Rokkodai, Nada-ku, Kobe, Hyogo 657-8501,
Japan
| | - Kenji Osabe
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University,
Onna-son, Okinawa 904-0495,
Japan
| | - W. James Peacock
- CSIRO Agriculture and Food,
Canberra, ACT 2601,
Australia
- University of Technology, Sydney,
PO Box 123, Broadway, NSW 2007,
Australia
| | - Elizabeth S. Dennis
- CSIRO Agriculture and Food,
Canberra, ACT 2601,
Australia
- University of Technology, Sydney,
PO Box 123, Broadway, NSW 2007,
Australia
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Yang H, Wang X, Wei Y, Deng Z, Liu H, Chen J, Dai L, Xia Z, He G, Li D. Transcriptomic analyses reveal molecular mechanisms underlying growth heterosis and weakness of rubber tree seedlings. BMC PLANT BIOLOGY 2018; 18:10. [PMID: 29316882 PMCID: PMC5759766 DOI: 10.1186/s12870-017-1203-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Accepted: 12/04/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Breeding rubber tree seedling with growth heterosis is vital for natural rubber production. It is the prerequisites for effectively utilizing growth heterosis to elucidate its molecular mechanisms, but the molecular mechanisms remain poorly understood in rubber tree. To elucidate seedling growth heterosis, we conducted comparative transcriptomic analyses between the two hybrids and their parents. RESULTS By identifying and comparing differently expressed genes (DEGs), we found that the hybrids (BT 3410 and WC 11) show significantly differential expression profiles from their parents (PR 107 and RRIM 600). In BT 3410-parent triad, 1092 (49.95%) and 1094 (50.05%) DEGs indicated clear underdominance or overdominance, respectively. Whereas in WC 11-parent triad, most DEGs (78.2%, 721) showed low- or high-parent dominance; 160 (17.35%) exhibited expression patterns that are not statistically distinguishable from additivity, and 8 (0.87%) and 33 (3.58%) DEGs exhibited underdominance and overdominance, respectively. Furthermore, some biological processes are differentially regulated between two hybrids. Interestingly, the pathway in response to stimulus is significantly downregulated and metabolic pathways are more highly regulated in BT 3410. CONCLUSIONS Taken together, the genotypes, transcriptomes and biological pathways (especially, carbohydrate metabolism) are highly divergent between two hybrids, which may be associated with growth heterosis and weakness. Analyzing gene action models in hybrid-parent triads, we propose that overdominance may play important roles on growth heterosis, whereas dominance on hybrid weakness in rubber tree seedlings. These findings bring new insights into our understanding of growth heterosis of rubber tree seedling.
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Affiliation(s)
- Hong Yang
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Baodao Xincun, Danzhou, Hainan 571737 China
| | - Xuncheng Wang
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, No. 5 Yiheyuan Road, Haidian District, Beijing, 100871 China
| | - Yongxuan Wei
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Agriculture, Hainan University, Haikou, Hainan 570228 China
| | - Zhi Deng
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Baodao Xincun, Danzhou, Hainan 571737 China
| | - Hui Liu
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Baodao Xincun, Danzhou, Hainan 571737 China
| | - Jiangshu Chen
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Agriculture, Hainan University, Haikou, Hainan 570228 China
| | - Longjun Dai
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Baodao Xincun, Danzhou, Hainan 571737 China
| | - Zhihui Xia
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Agriculture, Hainan University, Haikou, Hainan 570228 China
| | - Guangming He
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, No. 5 Yiheyuan Road, Haidian District, Beijing, 100871 China
| | - Dejun Li
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Baodao Xincun, Danzhou, Hainan 571737 China
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Shen Y, Sun S, Hua S, Shen E, Ye CY, Cai D, Timko MP, Zhu QH, Fan L. Analysis of transcriptional and epigenetic changes in hybrid vigor of allopolyploid Brassica napus uncovers key roles for small RNAs. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 91:874-893. [PMID: 28544196 DOI: 10.1111/tpj.13605] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 05/08/2017] [Accepted: 05/17/2017] [Indexed: 05/23/2023]
Abstract
Heterosis is a fundamental biological phenomenon characterized by the superior performance of a hybrid compared with its parents. The underlying molecular basis for heterosis, particularly for allopolyploids, remains elusive. In this study we analyzed the transcriptomes of Brassica napus parental lines and their F1 hybrids at three stages of early flower development. Phenotypically, the F1 hybrids show remarkable heterosis in silique number and grain yield. Transcriptome analysis revealed that various phytohormone (auxin and salicylic acid) response genes are significantly altered in the F1 hybrids relative to the parental lines. We also found evidence for decreased expression divergence of the homoeologous gene pairs in the allopolyploid F1 hybrids and suggest that high-parental expression-level dominance plays an important role in heterosis. Small RNA and methylation studies aimed at examining the epigenetic effect of the changes in gene expression level in the F1 hybrids showed that the majority of the small interfering RNA (siRNA) clusters had a higher expression level in the F1 hybrids than in the parents, and that there was an increase in genome-wide DNA methylation in the F1 hybrid. Transposable elements associated with siRNA clusters had a higher level of methylation and a lower expression level in the F1 hybrid, implying that the non-additively expressed siRNA clusters resulted in lower activity of the transposable elements through DNA methylation in the hybrid. Our data provide insights into the role that changes in gene expression pattern and epigenetic mechanisms contribute to heterosis during early flower development in allopolyploid B. napus.
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Affiliation(s)
- Yifei Shen
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China
| | - Shuo Sun
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China
| | - Shuijin Hua
- Institute of Crop and Utilization of Nuclear Technology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Enhui Shen
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China
| | - Chu-Yu Ye
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China
| | - Daguang Cai
- Institute of Phytopathology, Christian Albrechts University of Kiel, Hermann Rodewald Str. 9, D-24118, Kiel, Germany
| | - Michael P Timko
- Department of Biology, University of Virginia, Charlottesville, VA, 22903, USA
| | - Qian-Hao Zhu
- CSIRO Agriculture and Food, Black Mountain Laboratories, Canberra, ACT, 2601, Australia
| | - Longjiang Fan
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China
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Cao A, Jin J, Li S, Wang J. Integrated analysis of mRNA and miRNA expression profiling in rice backcrossed progenies (BC2F12) with different plant height. PLoS One 2017; 12:e0184106. [PMID: 28859136 PMCID: PMC5578646 DOI: 10.1371/journal.pone.0184106] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 08/17/2017] [Indexed: 11/18/2022] Open
Abstract
Inter-specific hybridization and backcrossing commonly occur in plants. The use of progeny generated from inter-specific hybridization and backcrossing has been developed as a novel model system to explore gene expression divergence. The present study investigated the analysis of gene expression and miRNA regulation in backcrossed introgression lines constructed from cultivated and wild rice. High-throughput sequencing was used to compare gene and miRNA expression profiles in three progeny lines (L1710, L1817 and L1730), with different plant heights resulting from the backcrossing of introgression lines (BC2F12) and their parents (O. sativa and O. longistaminata). A total of 25,387 to 26,139 mRNAs and 379 to 419 miRNAs were obtained in these rice lines. More differentially expressed genes and miRNAs were detected in progeny/O. longistaminata comparison groups than in progeny/O. sativa comparison groups. Approximately 80% of the genes and miRNAs showed expression level dominance to O. sativa, indicating that three progeny lines were closer to the recurrent parent, which might be influenced by their parental genome dosage. Approximately 16% to 64% of the differentially expressed miRNAs possessing coherent target genes were predicted, and many of these miRNAs regulated multiple target genes. Most genes were up-regulated in progeny lines compared with their parents, but down-regulated in the higher plant height line in the comparison groups among the three progeny lines. Moreover, certain genes related to cell walls and plant hormones might play crucial roles in the plant height variations of the three progeny lines. Taken together, these results provided valuable information on the molecular mechanisms of hybrid backcrossing and plant height variations based on the gene and miRNA expression levels in the three progeny lines.
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Affiliation(s)
- Aqin Cao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jie Jin
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Shaoqing Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jianbo Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
- * E-mail:
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Zhang C, Lin C, Fu F, Zhong X, Peng B, Yan H, Zhang J, Zhang W, Wang P, Ding X, Zhang W, Zhao L. Comparative transcriptome analysis of flower heterosis in two soybean F1 hybrids by RNA-seq. PLoS One 2017; 12:e0181061. [PMID: 28708857 PMCID: PMC5510844 DOI: 10.1371/journal.pone.0181061] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 06/26/2017] [Indexed: 01/05/2023] Open
Abstract
Heterosis has been widely exploited as an approach to enhance crop traits during breeding. However, its underlying molecular genetic mechanisms remain unclear. Recent advances in RNA sequencing technology (RNA-seq) have provided an opportunity to conduct transcriptome profiling for heterosis studies. We used RNA-seq to analyze the flower transcriptomes of two F1 hybrid soybeans (HYBSOY-1 and HYBSOY-5) and their parents. More than 385 million high-quality reads were generated and aligned against the soybean reference genome. A total of 681 and 899 genes were identified as being differentially expressed between HYBSOY-1 and HYBSOY-5 and their parents, respectively. These differentially expressed genes (DEGs) were categorized into four major expression categories with 12 expression patterns. Furthermore, gene ontology (GO) term analysis showed that the DEGs were enriched in the categories metabolic process and catalytic activity, while Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis found that metabolic pathway and biosynthesis of secondary metabolites were enriched in the two F1 hybrids. Comparing the DEGs of the two F1 hybrids by GO term and KEGG pathway analyses identified 26 common DEGs that showed transgressive up-regulation, and which could be considered potential candidate genes for heterosis in soybean F1 hybrids. This identification of an extensive transcriptome dataset gives a comprehensive overview of the flower transcriptomes in two F1 hybrids, and provides useful information for soybean hybrid breeding. These findings lay the foundation for future studies on molecular mechanisms underlying soybean heterosis.
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Affiliation(s)
- Chunbao Zhang
- Soybean Research Institute, National Engineering Research Center for Soybean, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Chunjing Lin
- Soybean Research Institute, National Engineering Research Center for Soybean, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Fuyou Fu
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, United States of America
| | - Xiaofang Zhong
- Agro-Biotechnology Institute, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Bao Peng
- Soybean Research Institute, National Engineering Research Center for Soybean, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Hao Yan
- Soybean Research Institute, National Engineering Research Center for Soybean, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Jingyong Zhang
- Soybean Research Institute, National Engineering Research Center for Soybean, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Weilong Zhang
- Soybean Research Institute, National Engineering Research Center for Soybean, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Pengnian Wang
- Soybean Research Institute, National Engineering Research Center for Soybean, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Xiaoyang Ding
- Soybean Research Institute, National Engineering Research Center for Soybean, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Wei Zhang
- Soybean Research Institute, National Engineering Research Center for Soybean, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Limei Zhao
- Soybean Research Institute, National Engineering Research Center for Soybean, Jilin Academy of Agricultural Sciences, Changchun, China
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Transcriptome and functional analysis reveals hybrid vigor for oil biosynthesis in oil palm. Sci Rep 2017; 7:439. [PMID: 28348403 PMCID: PMC5428490 DOI: 10.1038/s41598-017-00438-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 02/22/2017] [Indexed: 01/09/2023] Open
Abstract
Oil palm is the most productive oil crop in the world and composes 36% of the world production. However, the molecular mechanisms of hybrids vigor (or heterosis) between Dura, Pisifera and their hybrid progeny Tenera has not yet been well understood. Here we compared the temporal and spatial compositions of lipids and transcriptomes for two oil yielding organs mesocarp and endosperm from Dura, Pisifera and Tenera. Multiple lipid biosynthesis pathways are highly enriched in all non-additive expression pattern in endosperm, while cytokinine biosynthesis and cell cycle pathways are highly enriched both in endosperm and mesocarp. Compared with parental palms, the high oil content in Tenera was associated with much higher transcript levels of EgWRI1, homolog of Arabidopsis thaliana WRINKLED1. Among 338 identified genes in lipid synthesis, 207 (61%) has been identified to contain the WRI1 specific binding AW motif. We further functionally identified EgWRI1-1, one of three EgWRI1 orthologs, by genetic complementation of the Arabidopsis wri1 mutant. Ectopic expression of EgWRI1-1 in plant produced dramatically increased seed mass and oil content, with oil profile changed. Our findings provide an explanation for EgWRI1 as an important gene contributing hybrid vigor in lipid biosynthesis in oil palm.
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Koya Y, Kajiyama H, Liu W, Shibata K, Senga T, Kikkawa F. Murine Experimental Model of Original Tumor Development and Peritoneal Metastasis via Orthotopic Inoculation with Ovarian Carcinoma Cells. J Vis Exp 2016. [PMID: 28060250 DOI: 10.3791/54353] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Epithelial ovarian carcinoma (EOC) is associated with a poor prognosis because it shows peritoneal dissemination. To improve the prognosis, it is important to control peritoneal dissemination. However, it is still unclear how tumor cells detach from primary lesions and attach to the mesothelium. The establishment of an appropriate animal model is needed to gain an understanding of the mechanism of peritoneal dissemination in vivo. In the current study, we introduce the process from the local injection of EOC cells into the murine ovarian surface to the development of metastasis, including the peritoneum and distant organs. Female nude mice (BALB/c nu/nu) at 8 weeks of age were used. Under a microscopic field of view, EOC cells (1 x 105 cells/µl of medium-extracellular matrix (ECM)-based hydrogel/unilateral ovary/mouse) were injected into murine ovaries through a retroperitoneal approach from the dorsal flank. This proposed method is a less invasive procedure for the mouse and minimizes damage to the ovary. Here, we describe the methodological steps in the development of the original and metastatic tumor formation of EOC.
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Affiliation(s)
- Yoshihiro Koya
- Bell Research Center for Reproductive Health and Cancer; Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine;
| | - Hiroaki Kajiyama
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine;
| | - Wenting Liu
- Bell Research Center for Reproductive Health and Cancer; Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine
| | - Kiyosumi Shibata
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine
| | - Takeshi Senga
- Department of Cancer Biology, Nagoya University Graduate School of Medicine
| | - Fumitaka Kikkawa
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine
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Hu X, Wang H, Diao X, Liu Z, Li K, Wu Y, Liang Q, Wang H, Huang C. Transcriptome profiling and comparison of maize ear heterosis during the spikelet and floret differentiation stages. BMC Genomics 2016; 17:959. [PMID: 27875998 PMCID: PMC5120533 DOI: 10.1186/s12864-016-3296-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 11/15/2016] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Hybridization is a prominent process in the evolution of crop plants that can give rise to gene expression variation, phenotypic novelty and heterosis. Maize is the most successful crop in utilizing heterosis. The development of hybrid maize ears exhibits strong heterotic vigor and greatly affects maize yield. However, a comprehensive perspective on transcriptional variation and its correlation with heterosis during maize ear development is not available. RESULTS Using RNA sequencing technology, we investigated the transcriptome profiles of maize ears in the spikelet and floret differentiation stages of hybrid ZD808 and its parents CL11 and NG5. Our results revealed that 53.9% (21,258) of maize protein-coding genes were transcribed in at least one genotype. In both development stages, significant numbers of genes were differentially expressed between the hybrid and its parents. Gene expression inheritance analysis revealed approximately 80% of genes were expressed additively, which suggested that the complementary effect may play a foundation role in maize ear heterosis. Among non-additively expressed genes, NG5-dominant genes were predominant. Analyses of the allele-specific gene expression in hybrid identified pervasive allelic imbalance and significant preferential expression of NG5 alleles in both developmental stages. The results implied that NG5 may provide beneficial alleles that contribute greatly to heterosis. Further comparison of parental and hybrid allele-specific expression suggested that gene expression variation is largely attributable to cis-regulatory variation in maize. The cis-regulatory variations tend to preserve the allelic expression levels in hybrid and result in additive expression. Comparison between the two development stages revealed that allele-specific expression and cis-/trans-regulatory variations responded differently to developmental cues, which may lead to stage-specific vigor phenotype during maize ear development. CONCLUSION Our research suggests that cis-regulated additive expression may fine-tune gene expression level into an optimal status and play a foundation role in maize ear heterosis. Our work provides a comprehensive insight into transcriptional variation and its correlation with heterosis during maize ear development. The knowledge gained from this study presents novel opportunity to improve our maize varieties.
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Affiliation(s)
- Xiaojiao Hu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South Main Street, Beijing, 100081 China
| | - Hongwu Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South Main Street, Beijing, 100081 China
| | - Xizhou Diao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South Main Street, Beijing, 100081 China
| | - Zhifang Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South Main Street, Beijing, 100081 China
| | - Kun Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South Main Street, Beijing, 100081 China
| | - Yujin Wu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South Main Street, Beijing, 100081 China
| | - Qianjin Liang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South Main Street, Beijing, 100081 China
| | - Hui Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South Main Street, Beijing, 100081 China
| | - Changling Huang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South Main Street, Beijing, 100081 China
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Temporal Shift of Circadian-Mediated Gene Expression and Carbon Fixation Contributes to Biomass Heterosis in Maize Hybrids. PLoS Genet 2016; 12:e1006197. [PMID: 27467757 PMCID: PMC4965137 DOI: 10.1371/journal.pgen.1006197] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 06/24/2016] [Indexed: 12/31/2022] Open
Abstract
Heterosis has been widely used in agriculture, but the molecular mechanism for this remains largely elusive. In Arabidopsis hybrids and allopolyploids, increased photosynthetic and metabolic activities are linked to altered expression of circadian clock regulators, including CIRCADIAN CLOCK ASSOCIATED1 (CCA1). It is unknown whether a similar mechanism mediates heterosis in maize hybrids. Here we report that higher levels of carbon fixation and starch accumulation in the maize hybrids are associated with altered temporal gene expression. Two maize CCA1 homologs, ZmCCA1a and ZmCCA1b, are diurnally up-regulated in the hybrids. Expressing ZmCCA1 complements the cca1 mutant phenotype in Arabidopsis, and overexpressing ZmCCA1b disrupts circadian rhythms and biomass heterosis. Furthermore, overexpressing ZmCCA1b in maize reduced chlorophyll content and plant height. Reduced height stems from reduced node elongation but not total node number in both greenhouse and field conditions. Phenotypes are less severe in the field than in the greenhouse, suggesting that enhanced light and/or metabolic activities in the field can compensate for altered circadian regulation in growth vigor. Chromatin immunoprecipitation-sequencing (ChIP-seq) analysis reveals a temporal shift of ZmCCA1-binding targets to the early morning in the hybrids, suggesting that activation of morning-phased genes in the hybrids promotes photosynthesis and growth vigor. This temporal shift of ZmCCA1-binding targets correlated with nonadditive and additive gene expression in early and late stages of seedling development. These results could guide breeding better hybrid crops to meet the growing demand in food and bioenergy. All corn in the USA is grown as hybrids, which grow more vigorously and produce higher yield than their parents, a phenomenon known as heterosis. The molecular basis for heterosis remains elusive. Heterosis is predicted to arise from allelic interactions between parental genomes, leading to altered regulatory networks that promote the growth and fitness of hybrids. One such regulator is the circadian clock, which is functionally conserved in Arabidopsis and maize. Disrupting corn CCA1 expression reduces growth vigor. In corn hybrids, CCA1 proteins target thousands of output genes early in the morning, as if the hybrids wake up early to promote photosynthesis, starch metabolism and biomass accumulation. This early acting mechanism could guide breeding and selection of high-yield hybrids.
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Song Y, Zhang Z, Tan X, Jiang Y, Gao J, Lin L, Wang Z, Ren J, Wang X, Qin L, Cheng W, Qi J, Kuai B. Association of the molecular regulation of ear leaf senescence/stress response and photosynthesis/metabolism with heterosis at the reproductive stage in maize. Sci Rep 2016; 6:29843. [PMID: 27435114 PMCID: PMC4951735 DOI: 10.1038/srep29843] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 06/24/2016] [Indexed: 11/17/2022] Open
Abstract
Maize exhibits a wide range of heterotic traits, but the molecular basis of heterosis at the reproductive stage has seldom been exploited. Leaf senescence is a degenerative process which affects crop yield and quality. In this study, we observed significantly delayed ear leaf senescence in the reciprocal hybrids of B73/Mo17 and Zheng58/Chang7-2 after silking, and all the hybrids displayed larger leaf areas and higher stems with higher yields. Our time-course transcriptome analysis identified 2,826 differentially expressed genes (DEGs) between two parental lines (PP-DEGs) and 2,328 DEGs between parental lines and the hybrid (PH-DEGs) after silking. Notably, several senescence promoting genes (ZmNYE1, ZmORE1, ZmWRKY53 and ZmPIFs) exhibited underdominant expression patterns in the hybrid, whereas putative photosynthesis and carbon-fixation (ZmPEPC)-associated, starch biosynthetic (ZmAPS1, ZmAPL), gibberellin biosynthetic genes (ZmGA20OX, ZmGA3OX) expressed overdominantly. We also identified 86 transcription factors from PH-DEGs, some of which were known to regulate senescence, stress and metabolic processes. Collectively, we demonstrate a molecular association of the regulations of both ear leaf senescence/stress response and photosynthesis/metabolism with heterosis at the late developmental stage. This finding not only extends our understanding to the molecular basis of maize heterosis but also provides basic information for molecular breeding.
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Affiliation(s)
- Yi Song
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Zhe Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China.,Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Fudan University, Shanghai 200438, China
| | - Xianjie Tan
- Maize Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Yufeng Jiang
- Maize Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Jiong Gao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Li Lin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Zhenhua Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jun Ren
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xiaolei Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Lanqiu Qin
- Maize Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Weidong Cheng
- Maize Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Ji Qi
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China.,Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Fudan University, Shanghai 200438, China
| | - Benke Kuai
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China.,Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Fudan University, Shanghai 200438, China
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47
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Tazoe Y, Sazuka T, Yamaguchi M, Saito C, Ikeuchi M, Kanno K, Kojima S, Hirano K, Kitano H, Kasuga S, Endo T, Fukuda H, Makino A. Growth Properties and Biomass Production in the Hybrid C4 Crop Sorghum bicolor. PLANT & CELL PHYSIOLOGY 2016; 57:944-952. [PMID: 26508521 DOI: 10.1093/pcp/pcv158] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 10/19/2015] [Indexed: 06/05/2023]
Abstract
Hybrid vigor (heterosis) has been used as a breeding technique for crop improvement to achieve enhanced biomass production, but the physiological mechanisms underlying heterosis remain poorly understood. In this study, to find a clue to the enhancement of biomass production by heterosis, we systemically evaluated the effect of heterosis on the growth rate and photosynthetic efficiency in sorghum hybrid [Sorghum bicolor (L.) Moench cv. Tentaka] and its parental lines (restorer line and maintainer line). The final biomass of Tentaka was 10-14 times greater than that of the parental lines grown in an experimental field, but the relative growth rate during the vegetative growth stage did not differ. Tentaka exhibited a relatively enlarged leaf area with lower leaf nitrogen content per leaf area (Narea). When the plants were grown hydroponically at different N levels, daily CO2 assimilation per leaf area (A) increased with Narea, and the ratio of A to Narea (N-use efficiency) was higher in the plants grown at low N levels but not different between Tentaka and the parental lines. The relationships between the CO2 assimilation rate, the amounts of photosynthetic enzymes, including ribulose-1,5-bisphosphate carboxylase/oxygenase, phosphoenolpyruvate carboxylase and pyruvate phosphate dikinase, Chl and Narea did not differ between Tentaka and the parental lines. Thus, Tentaka tended to exhibit enlargement of leaf area with lower N content, leading to a higher N-use efficiency for CO2 assimilation, but the photosynthetic properties did not differ. The greater biomass in Tentaka was mainly due to the prolonged vegetative growth period.
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Affiliation(s)
- Youshi Tazoe
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Sendai, 981-8555 Japan CREST, JST, Gobancho, Chiyoda-ku, Tokyo, 102-0076 Japan
| | - Takashi Sazuka
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, 464-8601 Japan
| | - Miki Yamaguchi
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, 464-8601 Japan
| | - Chieko Saito
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033 Japan
| | - Masahiro Ikeuchi
- Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501 Japan
| | - Keiichi Kanno
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Sendai, 981-8555 Japan
| | - Soichi Kojima
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Sendai, 981-8555 Japan
| | - Ko Hirano
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, 464-8601 Japan
| | - Hideki Kitano
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, 464-8601 Japan
| | - Shigemitsu Kasuga
- Faculty of Agriculture, Education and Research Center of Alpine Field Science, Shinshu University, Nagano, 396-0111 Japan
| | - Tsuyoshi Endo
- Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501 Japan
| | - Hiroo Fukuda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033 Japan
| | - Amane Makino
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Sendai, 981-8555 Japan CREST, JST, Gobancho, Chiyoda-ku, Tokyo, 102-0076 Japan
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48
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Saeki N, Kawanabe T, Ying H, Shimizu M, Kojima M, Abe H, Okazaki K, Kaji M, Taylor JM, Sakakibara H, Peacock WJ, Dennis ES, Fujimoto R. Molecular and cellular characteristics of hybrid vigour in a commercial hybrid of Chinese cabbage. BMC PLANT BIOLOGY 2016; 16:45. [PMID: 26882898 PMCID: PMC4756405 DOI: 10.1186/s12870-016-0734-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 02/09/2016] [Indexed: 05/03/2023]
Abstract
BACKGROUND Heterosis or hybrid vigour is a phenomenon in which hybrid progeny exhibit superior performance compared to their parental inbred lines. Most commercial Chinese cabbage cultivars are F1 hybrids and their level of hybrid vigour is of critical importance and is a key selection criterion in the breeding system. RESULTS We have characterized the heterotic phenotype of one F1 hybrid cultivar of Chinese cabbage and its parental lines from early- to late-developmental stages of the plants. Hybrid cotyledons are larger than those of the parents at 4 days after sowing and biomass in the hybrid, determined by the fresh weight of leaves, is greater than that of the larger parent line by approximately 20% at 14 days after sowing. The final yield of the hybrid harvested at 63 days after sowing is 25% greater than the yield of the better parent. The larger leaves of the hybrid are a consequence of increased cell size and number of the photosynthetic palisade mesophyll cells and other leaf cells. The accumulation of plant hormones in the F1 was within the range of the parental levels at both 2 and 10 days after sowing. Two days after sowing, the expression levels of chloroplast-targeted genes in the cotyledon cells were upregulated in the F1 hybrid relative to their mid parent values. Shutdown of chlorophyll biosynthesis in the cotyledon by norflurazon prevented the increased leaf area in the F1 hybrid. CONCLUSIONS In the cotyledons of F1 hybrids, chloroplast-targeted genes were upregulated at 2 days after sowing. The increased activity levels of this group of genes suggested that their differential transcription levels could be important for establishing early heterosis but the increased transcription levels were transient. Inhibition of the photosynthetic process in the cotyledon reduced heterosis in later seedling stages. These observations suggest early developmental events in the germinating seedling of the hybrid may be important for later developmental vigour and yield advantage.
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Affiliation(s)
- Natsumi Saeki
- Graduate School of Science and Technology, Niigata University, Ikarashi-ninocho, Niigata, 950-2181, Japan.
| | - Takahiro Kawanabe
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada-ku, Kobe, 657-8501, Japan.
| | - Hua Ying
- CSIRO Agriculture, Canberra, ACT 2601, Australia.
| | - Motoki Shimizu
- Graduate School of Science and Technology, Niigata University, Ikarashi-ninocho, Niigata, 950-2181, Japan.
| | - Mikiko Kojima
- Center for Sustainable Resource Science, 1-7-22, Suehiro, Tsurumi, Yokohama, 230-0045, Japan.
| | - Hiroshi Abe
- Experimental Plant Division, RIKEN BioResource Center, Tsukuba, 305-0074, Japan.
| | - Keiichi Okazaki
- Graduate School of Science and Technology, Niigata University, Ikarashi-ninocho, Niigata, 950-2181, Japan.
| | - Makoto Kaji
- Watanabe Seed Co., Ltd, Machiyashiki, Misato-cho, Miyagi, 987-0003, Japan.
| | | | - Hitoshi Sakakibara
- Center for Sustainable Resource Science, 1-7-22, Suehiro, Tsurumi, Yokohama, 230-0045, Japan.
| | - W James Peacock
- CSIRO Agriculture, Canberra, ACT 2601, Australia.
- University of Technology, Broadway, Sydney, PO Box 123, NSW, 2007, Australia.
| | - Elizabeth S Dennis
- CSIRO Agriculture, Canberra, ACT 2601, Australia.
- University of Technology, Broadway, Sydney, PO Box 123, NSW, 2007, Australia.
| | - Ryo Fujimoto
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada-ku, Kobe, 657-8501, Japan.
- Japan Science and Technology Agency (JST), Precursory Research for Embryonic Science and Technology (PRESTO), Saitama, 332-0012, Japan.
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49
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Cheng S, Yang J, Liao T, Zhu X, Suo Y, Zhang P, Wang J, Kang X. Transcriptomic changes following synthesis of a Populus full-sib diploid and allotriploid population with different heterozygosities driven by three types of 2n female gamete. PLANT MOLECULAR BIOLOGY 2015; 89:493-510. [PMID: 26419948 DOI: 10.1007/s11103-015-0384-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 09/20/2015] [Indexed: 06/05/2023]
Abstract
Diploid gametes are usually applied to produce triploids of Populus [originating from first-division restitution (FDR), second-division restitution (SDR), and postmeiotic restitution (PMR) 2n eggs]. Three types of 2n gametes transmitted different parental heterozygosities in Populus. Failed spindle formation and no chromosomal separation to opposite poles during meiosis I mean that FDR 2n gametes carry nonsister chromatids that are potentially heterozygous. By contrast, SDR 2n gametes result from failed sister chromatid separation in meiosis II, and therefore, they carry sister chromatid that are potentially homozygous. Completely homozygous 2n gametes can arise from the PMR mechanism. The alteration of gene expression resulting from allopolyploidization is a prominent feature in plants. We compared gene expression in the full-sib progeny of three allotriploid Populus populations (triploid-F, triploid-S, and triploid-P) with that in its parent species, and their full-sib diploid F1 hybrid. Genome-wide expression level dominance was biased toward the maternal in the diploid F1 hybrid and three allotriploid populations, whereas our data indicated important, but different, effects of the transmission of different heterozygosity by 2n female gametes in the expression patterns of allopolyploids. Because of the higher level of heterozygosity, the triploids had higher rates of non-additive and transgressive expression patterns in the triploid-F than in triploid-S and triploid-P. Compared with diploid F1, about 30-fold more genes (251) were differently expressed in the triploid-F than in the triploid-S (9) and triploid-P (8), respectively. These findings indicate that hybridization and polyploidization have immediate and distinct effects on the large-scale patterns of gene expression, and different effects on the transmission of heterozygosity by three 2n female gametes.
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Affiliation(s)
- Shiping Cheng
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China
- Pingdingshan University, Pingdingshan, 467000, Henan Province, People's Republic of China
| | - Jun Yang
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China
| | - Ting Liao
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China
| | - Xiaohu Zhu
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China
- College of Forestry and Horticulture, Xinjiang Agricultural University, No. 311, East Nongda Road, Urumqi, 830052, People's Republic of China
| | - Yujing Suo
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China
| | - Pingdong Zhang
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China
| | - Jun Wang
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China
| | - Xiangyang Kang
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China.
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50
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Zhang Y, Verhoeff NI, Chen Z, Chen S, Wang M, Zhu Z, Ouwerkerk PBF. Functions of OsDof25 in regulation of OsC4PPDK. PLANT MOLECULAR BIOLOGY 2015; 89:229-42. [PMID: 26337938 PMCID: PMC4579267 DOI: 10.1007/s11103-015-0357-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 07/31/2015] [Indexed: 05/03/2023]
Abstract
Relative little is known about the functions of the so-called Dof zinc factors in plants. Here we report on the analysis of OsDof25 and show a function in regulation of the important C4 photosynthesis gene, OsC4PPDK in rice. Over-expression of OsDof25 enhanced the expression of OsC4PPDK in transient expression experiments by binding in a specific way to a conserved Dof binding site which was confirmed by yeast and in vitro binding studies. Expression studies using promoter GUS plants as well as qPCR experiments showed that OsDof25 expressed in different tissues including both photosynthetic and non-photosynthetic organs and that expression of OsDof25 was partially overlapping with the OsC4PPDK gene. Conclusive evidence for a role of OsDof25 in regulation of C4PPDK came from loss-of-function and gain-of-function experiments with transgenic rice, which showed that down-regulation or over-expression of OsDof25 correlated with OsC4PPDK expression and that OsDof25 has functions as transcriptional activator.
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Affiliation(s)
- Y Zhang
- Department of Molecular and Developmental Genetics, Institute of Biology (IBL), Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing, 100101, China
- Graduate School of the Chinese Academy of Sciences, Beijing, 100049, China
| | - N I Verhoeff
- Department of Molecular and Developmental Genetics, Institute of Biology (IBL), Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands
| | - Z Chen
- Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Wusi Rd 247, Fuzhou, 350003, Fujian, China
| | - S Chen
- Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Wusi Rd 247, Fuzhou, 350003, Fujian, China
| | - Mei Wang
- Department of Molecular and Developmental Genetics, Institute of Biology (IBL), Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands
- SU BioMedicine/TNO Quality of Life, Zernikedreef 9, P.O. Box 2215, 2301 CE, Leiden, The Netherlands
| | - Zhen Zhu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing, 100101, China
| | - P B F Ouwerkerk
- Department of Molecular and Developmental Genetics, Institute of Biology (IBL), Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands.
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