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Ren X, Chen L, Deng L, Zhao Q, Yao D, Li X, Cong W, Zang Z, Zhao D, Zhang M, Yang S, Zhang J. Comparative transcriptomic analysis reveals the molecular mechanism underlying seedling heterosis and its relationship with hybrid contemporary seeds DNA methylation in soybean. FRONTIERS IN PLANT SCIENCE 2024; 15:1364284. [PMID: 38444535 PMCID: PMC10913200 DOI: 10.3389/fpls.2024.1364284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 01/31/2024] [Indexed: 03/07/2024]
Abstract
Heterosis is widely used in crop production, but phenotypic dominance and its underlying causes in soybeans, a significant grain and oil crop, remain a crucial yet unexplored issue. Here, the phenotypes and transcriptome profiles of three inbred lines and their resulting F1 seedlings were analyzed. The results suggest that F1 seedlings with superior heterosis in leaf size and biomass exhibited a more extensive recompilation in their transcriptional network and activated a greater number of genes compared to the parental lines. Furthermore, the transcriptional reprogramming observed in the four hybrid combinations was primarily non-additive, with dominant effects being more prevalent. Enrichment analysis of sets of differentially expressed genes, coupled with a weighted gene co-expression network analysis, has shown that the emergence of heterosis in seedlings can be attributed to genes related to circadian rhythms, photosynthesis, and starch synthesis. In addition, we combined DNA methylation data from previous immature seeds and observed similar recompilation patterns between DNA methylation and gene expression. We also found significant correlations between methylation levels of gene region and gene expression levels, as well as the discovery of 12 hub genes that shared or conflicted with their remodeling patterns. This suggests that DNA methylation in contemporary hybrid seeds have an impact on both the F1 seedling phenotype and gene expression to some extent. In conclusion, our study provides valuable insights into the molecular mechanisms of heterosis in soybean seedlings and its practical implications for selecting superior soybean varieties.
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Affiliation(s)
- Xiaobo Ren
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
| | - Liangyu Chen
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
- Zhanjiang City Key Laboratory for Tropical Crops Genetic Improvement, South Subtropical Crops Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, China
| | - Lin Deng
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
| | - Qiuzhu Zhao
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
| | - Dan Yao
- College of Life Science, Jilin Agricultural University, Changchun, China
| | - Xueying Li
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
| | - Weixuan Cong
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
| | - Zhenyuan Zang
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
| | - Dingyi Zhao
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
| | - Miao Zhang
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
| | - Songnan Yang
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
| | - Jun Zhang
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
- National Crop Variety Approval and Characteristic Identification Station, Jilin Agricultural University, Changchun, China
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Pi K, Huang Y, Luo W, Zeng S, Mo Z, Duan L, Liu R. Overdominant expression of genes plays a key role in root growth of tobacco hybrids. FRONTIERS IN PLANT SCIENCE 2023; 14:1107550. [PMID: 36798711 PMCID: PMC9927235 DOI: 10.3389/fpls.2023.1107550] [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: 11/25/2022] [Accepted: 01/17/2023] [Indexed: 06/18/2023]
Abstract
Heterosis has greatly improved the yield and quality of crops. However, previous studies often focused on improving the yield and quality of the shoot system, while research on the root system was neglected. We determined the root numbers of 12 F1 hybrids, all of which showed strong heterosis, indicating that tobacco F1 hybrids have general heterosis. To understand its molecular mechanism, we selected two hybrids with strong heterosis, GJ (G70 × Jiucaiping No.2) and KJ (K326 × Jiucaiping No.2), and their parents for transcriptome analysis. There were 84.22% and 90.25% of the differentially expressed genes were overdominantly expressed. The enrichment analysis of these overdominantly expressed genes showed that "Plant hormone signal transduction", "Phenylpropanoid biosynthesis", "MAPK signaling pathway - plant", and "Starch and sucrose metabolism" pathways were associated with root development. We focused on the analysis of the biosynthetic pathways of auxin(AUX), cytokinins(CTK), abscisic acid(ABA), ethylene(ET), and salicylic acid(SA), suggesting that overdominant expression of these hormone signaling pathway genes may enhance root development in hybrids. In addition, Nitab4.5_0011528g0020、Nitab4.5_0003282g0020、Nitab4.5_0004384g0070 may be the genes involved in root growth. Genome-wide comparative transcriptome analysis enhanced our understanding of the regulatory network of tobacco root development and provided new ideas for studying the molecular mechanisms of tobacco root development.
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Affiliation(s)
- Kai Pi
- College of Tobacco, Guizhou University, Guiyang, China
- Key Laboratory of Tobacco Quality in Guizhou Province, Guiyang, China
| | - Ying Huang
- College of Tobacco, Guizhou University, Guiyang, China
- Key Laboratory of Tobacco Quality in Guizhou Province, Guiyang, China
| | - Wen Luo
- College of Tobacco, Guizhou University, Guiyang, China
- Key Laboratory of Tobacco Quality in Guizhou Province, Guiyang, China
| | - Shuaibo Zeng
- College of Tobacco, Guizhou University, Guiyang, China
- Key Laboratory of Tobacco Quality in Guizhou Province, Guiyang, China
| | - Zejun Mo
- College of Agriculture, Guizhou University, Guiyang, China
| | - Lili Duan
- College of Agriculture, Guizhou University, Guiyang, China
| | - Renxiang Liu
- College of Tobacco, Guizhou University, Guiyang, China
- Key Laboratory of Tobacco Quality in Guizhou Province, Guiyang, China
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Duan H, Li J, Sun Y, Xiong X, Sun L, Li W, Gao J, Li N, Zhang J, Cui J, Fu Z, Zhang X, Tang J. Candidate loci for leaf angle in maize revealed by a combination of genome-wide association study and meta-analysis. Front Genet 2022; 13:1004211. [PMID: 36437932 PMCID: PMC9691904 DOI: 10.3389/fgene.2022.1004211] [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: 07/27/2022] [Accepted: 10/28/2022] [Indexed: 11/13/2022] Open
Abstract
Leaf angle (LA) is a key component of maize plant architecture that can simultaneously govern planting density and improve final yield. However, the genetic mechanisms underlying LA have not been fully addressed. To broaden our understanding of its genetic basis, we scored three LA-related traits on upper, middle, and low leaves of 492 maize inbred lines in five environments. Phenotypic data revealed that the three LA-related traits were normally distributed, and significant variation was observed among environments and genotypes. A genome-wide association study (GWAS) was then performed to dissect the genetic factors that control natural variation in maize LA. In total, 85 significant SNPs (involving 32 non-redundant QTLs) were detected (p ≤ 2.04 × 10-6), and individual QTL explained 4.80%-24.09% of the phenotypic variation. Five co-located QTL were detected in at least two environments, and two QTLs were co-located with multiple LA-related traits. Forty-seven meta-QTLs were identified based on meta-analysis combing 294 LA-related QTLs extracted from 18 previously published studies, 816 genes were identified within these meta-QTLs, and seven co-located QTLs were jointly identified by both GWAS and meta-analysis. ZmULA1 was located in one of the co-located QTLs, qLA7, and its haplotypes, hap1 and hap2, differed significantly in LA-related traits. Interestingly, the temperate materials with hap2 had smallest LA. Finally, we also performed haplotype analysis using the reported genes that regulate LA, and identified a lot of maize germplasms that aggregated favorable haplotypes. These results will be helpful for elucidating the genetic basis of LA and breeding new maize varieties with ideal plant architecture.
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Affiliation(s)
- Haiyang Duan
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Jianxin Li
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Yan Sun
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Xuehang Xiong
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Li Sun
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Wenlong Li
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Jionghao Gao
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Na Li
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Junli Zhang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Jiangkuan Cui
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Zhiyuan Fu
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Xuehai Zhang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Jihua Tang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
- The Shennong Laboratory, Zhengzhou, China
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Zhang F, Ding Y, Zhang J, Tang M, Cao Y, Zhang L, Ma Z, Qi J, Mu X, Xia L, Tang B. Comparative transcriptomic reveals the molecular mechanism of maize hybrid Zhengdan538 in response to water deficit. PHYSIOLOGIA PLANTARUM 2022; 174:e13818. [PMID: 36345780 DOI: 10.1111/ppl.13818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 09/23/2022] [Accepted: 10/31/2022] [Indexed: 06/16/2023]
Abstract
Heterosis, known as one of the most successful strategies for increasing grain yield and abiotic/biotic stress tolerance, has been widely exploited in maize breeding. However, the underlying molecular processes are still to be elucidated. The maize hybrid "Zhengdan538" shows high tolerance to drought stress. The transcriptomes of the seedling leaves of its parents, "ZhengA88" and "ZhengT22" and their reciprocal F1 hybrid under well-watered and water deficit conditions, were analyzed by RNA sequencing (RNA-Seq). Transcriptome profiling of the reciprocal hybrid revealed 2994-4692 differentially expressed genes (DEGs) under well-watered and water-deficit conditions, which were identified by comparing with their parents. The reciprocal hybrid was more closely related to the parental line "ZhengT22" than to the parental line "ZhengA88" in terms of gene expression patterns under water-deficit condition. Furthermore, genes showed expression level dominance (ELD), especially the high-parental ELD (Class 3 and 5), accounted for the largest proportion of DEGs between the reciprocal F1 hybrid and their parental lines under water deficit. These ELD genes mainly participated in photosynthesis, energy biosynthesis, and metabolism processes. The results indicated that ELD genes played important roles in hybrid tolerance to water deficit. Moreover, a set of important drought-responsive transcription factors were found to be encoded by the identified ELD genes and are thought to function in improving drought tolerance in maize hybrid plants. Our results provide a better understanding of the molecular mechanism of drought tolerance in hybrid maize.
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Affiliation(s)
- Fengqi Zhang
- Cereal Crops Research Institute, Henan Academy of Agricultural Sciences/Henan Provincial Key Laboratory of Maize Biology/Henan International Joint Laboratory on Maize Precision Production, Zhengzhou, China
| | - Yong Ding
- Cereal Crops Research Institute, Henan Academy of Agricultural Sciences/Henan Provincial Key Laboratory of Maize Biology/Henan International Joint Laboratory on Maize Precision Production, Zhengzhou, China
| | - Jun Zhang
- Cereal Crops Research Institute, Henan Academy of Agricultural Sciences/Henan Provincial Key Laboratory of Maize Biology/Henan International Joint Laboratory on Maize Precision Production, Zhengzhou, China
| | - Minqiang Tang
- The Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), College of Forestry, Hainan University, Haikou, China
| | - Yanyong Cao
- Cereal Crops Research Institute, Henan Academy of Agricultural Sciences/Henan Provincial Key Laboratory of Maize Biology/Henan International Joint Laboratory on Maize Precision Production, Zhengzhou, China
| | - Lanxun Zhang
- Cereal Crops Research Institute, Henan Academy of Agricultural Sciences/Henan Provincial Key Laboratory of Maize Biology/Henan International Joint Laboratory on Maize Precision Production, Zhengzhou, China
| | - Zhiyan Ma
- Cereal Crops Research Institute, Henan Academy of Agricultural Sciences/Henan Provincial Key Laboratory of Maize Biology/Henan International Joint Laboratory on Maize Precision Production, Zhengzhou, China
| | - Jianshuang Qi
- Cereal Crops Research Institute, Henan Academy of Agricultural Sciences/Henan Provincial Key Laboratory of Maize Biology/Henan International Joint Laboratory on Maize Precision Production, Zhengzhou, China
| | - Xinyuan Mu
- Cereal Crops Research Institute, Henan Academy of Agricultural Sciences/Henan Provincial Key Laboratory of Maize Biology/Henan International Joint Laboratory on Maize Precision Production, Zhengzhou, China
| | - Laikun Xia
- Cereal Crops Research Institute, Henan Academy of Agricultural Sciences/Henan Provincial Key Laboratory of Maize Biology/Henan International Joint Laboratory on Maize Precision Production, Zhengzhou, China
| | - Baojun Tang
- Cereal Crops Research Institute, Henan Academy of Agricultural Sciences/Henan Provincial Key Laboratory of Maize Biology/Henan International Joint Laboratory on Maize Precision Production, Zhengzhou, China
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Song JM, Xie WZ, Wang S, Guo YX, Koo DH, Kudrna D, Gong C, Huang Y, Feng JW, Zhang W, Zhou Y, Zuccolo A, Long E, Lee S, Talag J, Zhou R, Zhu XT, Yuan D, Udall J, Xie W, Wing RA, Zhang Q, Poland J, Zhang J, Chen LL. Two gap-free reference genomes and a global view of the centromere architecture in rice. MOLECULAR PLANT 2021; 14:1757-1767. [PMID: 34171480 DOI: 10.1016/j.molp.2021.06.018] [Citation(s) in RCA: 115] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 06/16/2021] [Accepted: 06/22/2021] [Indexed: 05/04/2023]
Abstract
Rice (Oryza sativa), a major staple throughout the world and a model system for plant genomics and breeding, was the first crop genome sequenced almost two decades ago. However, reference genomes for all higher organisms to date contain gaps and missing sequences. Here, we report the assembly and analysis of gap-free reference genome sequences for two elite O. sativa xian/indica rice varieties, Zhenshan 97 and Minghui 63, which are being used as a model system for studying heterosis and yield. Gap-free reference genomes provide the opportunity for a global view of the structure and function of centromeres. We show that all rice centromeric regions share conserved centromere-specific satellite motifs with different copy numbers and structures. In addition, the similarity of CentO repeats in the same chromosome is higher than across chromosomes, supporting a model of local expansion and homogenization. Both genomes have over 395 non-TE genes located in centromere regions, of which ∼41% are actively transcribed. Two large structural variants at the end of chromosome 11 affect the copy number of resistance genes between the two genomes. The availability of the two gap-free genomes lays a solid foundation for further understanding genome structure and function in plants and breeding climate-resilient varieties.
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Affiliation(s)
- Jia-Ming Song
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Wen-Zhao Xie
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Shuo Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yi-Xiong Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Dal-Hoe Koo
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Dave Kudrna
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Chenbo Gong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yicheng Huang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jia-Wu Feng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenhui Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yong Zhou
- Center for Desert Agriculture, Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Andrea Zuccolo
- Center for Desert Agriculture, Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Evan Long
- Plant and Wildlife Science Department, Brigham Young University, Provo, UT 84602, USA
| | - Seunghee Lee
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Jayson Talag
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Run Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Xi-Tong Zhu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Daojun Yuan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Joshua Udall
- Plant and Wildlife Science Department, Brigham Young University, Provo, UT 84602, USA
| | - Weibo Xie
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Rod A Wing
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA; Center for Desert Agriculture, Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; International Rice Research Institute (IRRI), Strategic Innovation, Los Baños, 4031 Laguna, Philippines
| | - Qifa Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jesse Poland
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, USA.
| | - Jianwei Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
| | - Ling-Ling Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; College of Life Science and Technology, Guangxi University, Nanning 530004, China.
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Overdominance at the Gene Expression Level Plays a Critical Role in the Hybrid Root Growth of Brassica napus. Int J Mol Sci 2021; 22:ijms22179246. [PMID: 34502153 PMCID: PMC8431428 DOI: 10.3390/ijms22179246] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/20/2021] [Accepted: 08/23/2021] [Indexed: 01/12/2023] Open
Abstract
Despite heterosis contributing to genetic improvements in crops, root growth heterosis in rapeseed plants is poorly understood at the molecular level. The current study was performed to discover key differentially expressed genes (DEGs) related to heterosis in two hybrids with contrasting root growth performance (FO; high hybrid and FV; low hybrid) based on analysis of the root heterosis effect. Based on comparative transcriptomic analysis, we believe that the overdominance at the gene expression level plays a critical role in hybrid roots’ early biomass heterosis. Our findings imply that a considerable increase in up-regulation of gene expression underpins heterosis. In the FO hybrid, high expression of DEGs overdominant in the starch/sucrose and galactose metabolic pathways revealed a link between hybrid vigor and root growth. DEGs linked to auxin, cytokinin, brassinosteroids, ethylene, and abscisic acid were also specified, showing that these hormones may enhance mechanisms of root growth and the development in the FO hybrid. Moreover, transcription factors such as MYB, ERF, bHLH, NAC, bZIP, and WRKY are thought to control downstream genes involved in root growth. Overall, this is the first study to provide a better understanding related to the regulation of the molecular mechanism of heterosis, which assists in rapeseed growth and yield improvement.
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Liu C, Huang R, Wang L, Liang G. Functional Identification of EjGIF1 in Arabidopsis and Preliminary Analysis of Its Regulatory Mechanisms in the Formation of Triploid Loquat Leaf Heterosis. FRONTIERS IN PLANT SCIENCE 2021; 11:612055. [PMID: 33510754 PMCID: PMC7835675 DOI: 10.3389/fpls.2020.612055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/11/2020] [Indexed: 06/12/2023]
Abstract
Although several results have been obtained in triploid loquat heterosis (i.e., leaf size of triploid loquat) studies in the past years, the underlying mechanisms of the heterosis are still largely unknown, especially the regulation effects of one specific gene on the corresponding morphology heterosis. In this study, we sought to further illustrate the regulatory mechanisms of one specific gene on the leaf size heterosis of triploid loquats. A leaf size development-related gene (EjGIF1) and its promoter were successfully cloned. Ectopic expression of EjGIF1 in Arabidopsis showed that the leaf size of transgenic plantlets was larger than that of WTs, and the transgenic plantlets had more leaves than WTs. Quantitative Reverse Transcription PCR (qRT-PCR) showed that the expression level of EjGIF1 showed an AHP expression pattern in most of the hybrids, and this was consistent with our previous phenotype observations. Structure analysis of EjGIF1 promoter showed that there were significantly more light-responsive elements than other elements. To further ascertain the regulatory mechanisms of EjGIF1 on triploid loquat heterosis, the methylation levels of EjGIF1 promoter in different ploidy loquats were analyzed by using bisulfite sequencing. Surprisingly, the total methylation levels of EjGIF1 promoter in triploid showed a decreasing trend compared with the mid-parent value (MPV), and this was also consistent with the qRT-PCR results of EjGIF1. Taken together, our results suggested that EjGIF1 played an important role in promoting leaf size development of loquat, and demethylation of EjGIF1 promoter in triploid loquats caused EjGIF1 to exhibit over-dominance expression pattern and then further to promote leaf heterosis formation. In conclusion, EjGIF1 played an important role in the formation of triploid loquat leaf size heterosis.
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Affiliation(s)
- Chao Liu
- College of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Renwei Huang
- Sichuan Provincial Key Laboratory for Development and Utilization of Characteristic Horticultural Biological Resources, College of Chemistry and Life Sciences, Chengdu Normal University, Chengdu, China
| | - Lingli Wang
- Technical Advice Station of Economic Crop, Chongqing, China
| | - Guolu Liang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
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Li Z, Zhou P, Della Coletta R, Zhang T, Brohammer AB, H O'Connor C, Vaillancourt B, Lipzen A, Daum C, Barry K, de Leon N, Hirsch CD, Buell CR, Kaeppler SM, Springer NM, Hirsch CN. Single-parent expression drives dynamic gene expression complementation in maize hybrids. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:93-107. [PMID: 33098691 DOI: 10.1111/tpj.15042] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 09/27/2020] [Accepted: 10/02/2020] [Indexed: 06/11/2023]
Abstract
Single-parent expression (SPE) is defined as gene expression in only one of the two parents. SPE can arise from differential expression between parental alleles, termed non-presence/absence (non-PAV) SPE, or from the physical absence of a gene in one parent, termed PAV SPE. We used transcriptome data of diverse Zea mays (maize) inbreds and hybrids, including 401 samples from five different tissues, to test for differences between these types of SPE genes. Although commonly observed, SPE is highly genotype and tissue specific. A positive correlation was observed between the genetic distance of the two inbred parents and the number of SPE genes identified. Regulatory analysis showed that PAV SPE and non-PAV SPE genes are mainly regulated by cis effects, with a small fraction under trans regulation. Polymorphic transposable element insertions in promoter sequences contributed to the high level of cis regulation for PAV SPE and non-PAV SPE genes. PAV SPE genes were more frequently expressed in hybrids than non-PAV SPE genes. The expression of parentally silent alleles in hybrids of non-PAV SPE genes was relatively rare but occurred in most hybrids. Non-PAV SPE genes with expression of the silent allele in hybrids are more likely to exhibit above high parent expression level than hybrids that do not express the silent allele, leading to non-additive expression. This study provides a comprehensive understanding of the nature of non-PAV SPE and PAV SPE genes and their roles in gene expression complementation in maize hybrids.
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Affiliation(s)
- Zhi Li
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Peng Zhou
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Rafael Della Coletta
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Tifu Zhang
- Jiangsu Provincial Key Laboratory of Agrobiology, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Alex B Brohammer
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Christine H O'Connor
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Brieanne Vaillancourt
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Anna Lipzen
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Chris Daum
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Kerrie Barry
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Natalia de Leon
- Department of Agronomy, University of Wisconsin, Madison, WI, 53706, USA
| | - Cory D Hirsch
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, 55108, USA
| | - C Robin Buell
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Shawn M Kaeppler
- Department of Agronomy, University of Wisconsin, Madison, WI, 53706, USA
| | - Nathan M Springer
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Candice N Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
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Zhang X, Qi Y. Single-Parent Expression of Anti-sense RNA Contributes to Transcriptome Complementation in Maize Hybrid. FRONTIERS IN PLANT SCIENCE 2020; 11:577274. [PMID: 33343593 PMCID: PMC7744309 DOI: 10.3389/fpls.2020.577274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 10/30/2020] [Indexed: 06/12/2023]
Abstract
Anti-sense transcription is increasingly being recognized as an important regulator of gene expression. But the transcriptome complementation of anti-sense RNA in hybrid relative to their inbred parents was largely unknown. In this study, we profiled strand-specific RNA sequencing (RNA-seq) in a maize hybrid and its inbred parents (B73 and Mo17) in two tissues. More anti-sense transcripts were present in the hybrid compared with the parental lines. We detected 293 and 242 single-parent expression of anti-sense (SPEA) transcripts in maize immature ear and leaf tissues, respectively. There was little overlap of the SPEA transcripts between the two maize tissues. These results suggested that SPEA is a general mechanism that drives extensive complementation in maize hybrids. More importantly, extremely high-level expression of anti-sense transcripts was associated with low-level expression of the cognate sense transcript by reducing the level of histone H3 lysine 36 methylation (H3K36me3). In summary, these SPEA transcripts increased our knowledge about the transcriptomic complementation in hybrid.
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10
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Li Z, Zhu A, Song Q, Chen HY, Harmon FG, Chen ZJ. Temporal Regulation of the Metabolome and Proteome in Photosynthetic and Photorespiratory Pathways Contributes to Maize Heterosis. THE PLANT CELL 2020; 32:3706-3722. [PMID: 33004616 PMCID: PMC7721322 DOI: 10.1105/tpc.20.00320] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 08/17/2020] [Accepted: 09/29/2020] [Indexed: 05/04/2023]
Abstract
Heterosis or hybrid vigor is widespread in plants and animals. Although the molecular basis for heterosis has been extensively studied, metabolic and proteomic contributions to heterosis remain elusive. Here we report an integrative analysis of time-series metabolome and proteome data in maize (Zea mays) hybrids and their inbred parents. Many maize metabolites and proteins are diurnally regulated, and many of these show nonadditive abundance in the hybrids, including key enzymes and metabolites involved in carbon assimilation. Compared with robust trait heterosis, metabolic heterosis is relatively mild. Interestingly, most amino acids display negative mid-parent heterosis (MPH), i.e., having lower values than the average of the parents, while sugars, alcohols, and nucleoside metabolites show positive MPH. From the network perspective, metabolites in the photosynthetic pathway show positive MPH, whereas metabolites in the photorespiratory pathway show negative MPH, which corresponds to nonadditive protein abundance and enzyme activities of key enzymes in the respective pathways in the hybrids. Moreover, diurnally expressed proteins that are upregulated in the hybrids are enriched in photosynthesis-related gene-ontology terms. Hybrids may more effectively remove toxic metabolites generated during photorespiration, and thus maintain higher photosynthetic efficiency. These metabolic and proteomic resources provide unique insight into heterosis and its utilization for high yielding maize and other crop plants.
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Affiliation(s)
- Zhi Li
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Andan Zhu
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Qingxin Song
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Helen Y Chen
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Frank G Harmon
- Plant Gene Expression Center, Agricultural Research Service, U.S. Department of Agriculture, Albany, California 94710
- Department of Plant & Microbial Biology, University of California, Berkeley, California 94720
| | - Z Jeffrey Chen
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
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11
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Fikere M, Barbulescu DM, Malmberg MM, Spangenberg GC, Cogan NOI, Daetwyler HD. Meta-analysis of GWAS in canola blackleg (Leptosphaeria maculans) disease traits demonstrates increased power from imputed whole-genome sequence. Sci Rep 2020; 10:14300. [PMID: 32868838 PMCID: PMC7459325 DOI: 10.1038/s41598-020-71274-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 08/13/2020] [Indexed: 12/21/2022] Open
Abstract
Blackleg disease causes yield losses in canola (Brassica napus L.). To identify resistance genes and genomic regions, genome-wide association studies (GWAS) of 585 diverse winter and spring canola accessions were performed using imputed whole-genome sequence (WGS) and transcriptome genotype-by-sequencing (GBSt). Blackleg disease phenotypes were collected across three years in six trials. GWAS were performed in several ways and their respective power was judged by the number of significant single nucleotide polymorphisms (SNP), the false discovery rate (FDR), and the percentage of SNP that validated in additional field trials in two subsequent years. WGS GWAS with 1,234,708 million SNP detected a larger number of significant SNP, achieved a lower FDR and a higher validation rate than GBSt with 64,072 SNP. A meta-analysis combining survival and average internal infection resulted in lower FDR but also lower validation rates. The meta-analysis GWAS identified 79 genomic regions (674 SNP) conferring potential resistance to L. maculans. While several GWAS signals localised in regions of known Rlm genes, fifty-three new potential resistance regions were detected. Seventeen regions had underlying genes with putative functions related to disease defence or stress response in Arabidopsis thaliana. This study provides insight into the genetic architecture and potential molecular mechanisms underlying canola L. maculans resistance.
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Affiliation(s)
- M Fikere
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3086, Australia.,Centre for AgriBioscience, Agriculture Victoria, AgriBio, Bundoora, VIC, 3083, Australia.,Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Brisbane, QLD, 4072, Australia
| | - D M Barbulescu
- Agriculture Victoria, Grains Innovation Park, Horsham, VIC, 3401, Australia
| | - M M Malmberg
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3086, Australia.,Centre for AgriBioscience, Agriculture Victoria, AgriBio, Bundoora, VIC, 3083, Australia
| | - G C Spangenberg
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3086, Australia.,Centre for AgriBioscience, Agriculture Victoria, AgriBio, Bundoora, VIC, 3083, Australia
| | - N O I Cogan
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3086, Australia.,Centre for AgriBioscience, Agriculture Victoria, AgriBio, Bundoora, VIC, 3083, Australia
| | - H D Daetwyler
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3086, Australia. .,Centre for AgriBioscience, Agriculture Victoria, AgriBio, Bundoora, VIC, 3083, Australia.
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12
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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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13
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Ramstein GP, Larsson SJ, Cook JP, Edwards JW, Ersoz ES, Flint-Garcia S, Gardner CA, Holland JB, Lorenz AJ, McMullen MD, Millard MJ, Rocheford TR, Tuinstra MR, Bradbury PJ, Buckler ES, Romay MC. Dominance Effects and Functional Enrichments Improve Prediction of Agronomic Traits in Hybrid Maize. Genetics 2020; 215:215-230. [PMID: 32152047 PMCID: PMC7198274 DOI: 10.1534/genetics.120.303025] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 02/26/2020] [Indexed: 01/04/2023] Open
Abstract
Single-cross hybrids have been critical to the improvement of maize (Zea mays L.), but the characterization of their genetic architectures remains challenging. Previous studies of hybrid maize have shown the contribution of within-locus complementation effects (dominance) and their differential importance across functional classes of loci. However, they have generally considered panels of limited genetic diversity, and have shown little benefit from genomic prediction based on dominance or functional enrichments. This study investigates the relevance of dominance and functional classes of variants in genomic models for agronomic traits in diverse populations of hybrid maize. We based our analyses on a diverse panel of inbred lines crossed with two testers representative of the major heterotic groups in the U.S. (1106 hybrids), as well as a collection of 24 biparental populations crossed with a single tester (1640 hybrids). We investigated three agronomic traits: days to silking (DTS), plant height (PH), and grain yield (GY). Our results point to the presence of dominance for all traits, but also among-locus complementation (epistasis) for DTS and genotype-by-environment interactions for GY. Consistently, dominance improved genomic prediction for PH only. In addition, we assessed enrichment of genetic effects in classes defined by genic regions (gene annotation), structural features (recombination rate and chromatin openness), and evolutionary features (minor allele frequency and evolutionary constraint). We found support for enrichment in genic regions and subsequent improvement of genomic prediction for all traits. Our results suggest that dominance and gene annotations improve genomic prediction across diverse populations in hybrid maize.
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Affiliation(s)
| | - Sara J Larsson
- Section of Plant Breeding and Genetics, Cornell University, Ithaca, New York 14853
| | - Jason P Cook
- Division of Plant Science, University of Missouri, Columbia, Missouri 56211
| | - Jode W Edwards
- U.S. Department of Agriculture-Agricultural Research Service, Ames, Iowa 50011
| | | | - Sherry Flint-Garcia
- U.S. Department of Agriculture-Agricultural Research Service, University of Missouri, Columbia, Missouri 56211
| | - Candice A Gardner
- U.S. Department of Agriculture-Agricultural Research Service, Ames, Iowa 50011
| | - James B Holland
- U.S. Department of Agriculture-Agricultural Research Service, Department of Crop and Soil Sciences, North Carolina State University, Raleigh, North Carolina 27695
| | - Aaron J Lorenz
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, Nebraska 68588
| | - Michael D McMullen
- U.S. Department of Agriculture-Agricultural Research Service, University of Missouri, Columbia, Missouri 56211
| | - Mark J Millard
- U.S. Department of Agriculture-Agricultural Research Service, Ames, Iowa 50011
| | | | | | - Peter J Bradbury
- U.S. Department of Agriculture-Agricultural Research Service, Ithaca, New York 14853
| | - Edward S Buckler
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853
- U.S. Department of Agriculture-Agricultural Research Service, Ithaca, New York 14853
| | - M Cinta Romay
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853
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14
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Seifert F, Thiemann A, Schrag TA, Rybka D, Melchinger AE, Frisch M, Scholten S. Small RNA-based prediction of hybrid performance in maize. BMC Genomics 2018; 19:371. [PMID: 29783940 PMCID: PMC5963143 DOI: 10.1186/s12864-018-4708-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 04/22/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Small RNA (sRNA) sequences are known to have a broad impact on gene regulation by various mechanisms. Their performance for the prediction of hybrid traits has not yet been analyzed. Our objective was to analyze the relation of parental sRNA expression with the performance of their hybrids, to develop a sRNA-based prediction approach, and to compare it to more common SNP and mRNA transcript based predictions using a factorial mating scheme of a maize hybrid breeding program. RESULTS Correlation of genomic differences and messenger RNA (mRNA) or sRNA expression differences between parental lines with hybrid performance of their hybrids revealed that sRNAs showed an inverse relationship in contrast to the other two data types. We associated differences for SNPs, mRNA and sRNA expression between parental inbred lines with the performance of their hybrid combinations and developed two prediction approaches using distance measures based on associated markers. Cross-validations revealed parental differences in sRNA expression to be strong predictors for hybrid performance for grain yield in maize, comparable to genomic and mRNA data. The integration of both positively and negatively associated markers in the prediction approaches enhanced the prediction accurary. The associated sRNAs belong predominantly to the canonical size classes of 22- and 24-nt that show specific genomic mapping characteristics. CONCLUSION Expression profiles of sRNA are a promising alternative to SNPs or mRNA expression profiles for hybrid prediction, especially for plant species without reference genome or transcriptome information. The characteristics of the sRNAs we identified suggest that association studies based on breeding populations facilitate the identification of sRNAs involved in hybrid performance.
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Affiliation(s)
- Felix Seifert
- Developmental Biology, Biocenter Klein Flottbek, University of Hamburg, 22609 Hamburg, Germany
| | - Alexander Thiemann
- Developmental Biology, Biocenter Klein Flottbek, University of Hamburg, 22609 Hamburg, Germany
| | - Tobias A. Schrag
- Institute for Plant Breeding, Seed Science and Population Genetics, Quantitative Genetics and Genomics of Crops, University of Hohenheim, Fruwirthstrasse 21, 70599 Stuttgart, Germany
| | - Dominika Rybka
- Developmental Biology, Biocenter Klein Flottbek, University of Hamburg, 22609 Hamburg, Germany
| | - Albrecht E. Melchinger
- Institute for Plant Breeding, Seed Science and Population Genetics, Quantitative Genetics and Genomics of Crops, University of Hohenheim, Fruwirthstrasse 21, 70599 Stuttgart, Germany
| | - Matthias Frisch
- Institute of Agronomy and Plant Breeding II, Justus Liebig University, 35392 Giessen, Germany
| | - Stefan Scholten
- Developmental Biology, Biocenter Klein Flottbek, University of Hamburg, 22609 Hamburg, Germany
- Institute for Plant Breeding, Seed Science and Population Genetics, Quantitative Genetics and Genomics of Crops, University of Hohenheim, Fruwirthstrasse 21, 70599 Stuttgart, Germany
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15
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Liu C, Wang M, Wang L, Guo Q, Liang G. Extensive genetic and DNA methylation variation contribute to heterosis in triploid loquat hybrids. Genome 2018; 61:437-447. [PMID: 29687741 DOI: 10.1139/gen-2017-0232] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We aim to overcome the unclear origin of the loquat and elucidate the heterosis mechanism of the triploid loquat. Here we investigated the genetic and epigenetic variations between the triploid plant and its parental lines using amplified fragment length polymorphism (AFLP) and methylation-sensitive amplified fragment length polymorphism (MSAP) analyses. We show that in addition to genetic variations, extensive DNA methylation variation occurred during the formation process of triploid loquat, with the triploid hybrid having increased DNA methylation compared to the parents. Furthermore, a correlation existed between genetic variation and DNA methylation remodeling, suggesting that genome instability may lead to DNA methylation variation or vice versa. Sequence analysis of the MSAP bands revealed that over 53% of them overlap with protein-coding genes, which may indicate a functional role of the differential DNA methylation in gene regulation and hence heterosis phenotypes. Consistent with this, the genetic and epigenetic alterations were associated closely to the heterosis phenotypes of triploid loquat, and this association varied for different traits. Our results suggested that the formation of triploid is accompanied by extensive genetic and DNA methylation variation, and these changes contribute to the heterosis phenotypes of the triploid loquats from the two cross lines.
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Affiliation(s)
- Chao Liu
- a Key Laboratory of Horticulture Science for Southern Mountainous Region, Ministry of Education/College of Horticulture and Landscape Architecture, Southwest University, Tiansheng Road 2, 400715, Chongqing, P.R. China
| | - Mingbo Wang
- b CSIRO Agriculture and Food, Clunies Ross Street, Canberra ACT 2061, Australia
| | - Lingli Wang
- c Technical Advice Station of Economic Crop, Yubei district, Chongqing, P.R. China
| | - Qigao Guo
- a Key Laboratory of Horticulture Science for Southern Mountainous Region, Ministry of Education/College of Horticulture and Landscape Architecture, Southwest University, Tiansheng Road 2, 400715, Chongqing, P.R. China
| | - Guolu Liang
- a Key Laboratory of Horticulture Science for Southern Mountainous Region, Ministry of Education/College of Horticulture and Landscape Architecture, Southwest University, Tiansheng Road 2, 400715, Chongqing, P.R. China
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16
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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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17
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Seifert F, Thiemann A, Grant-Downton R, Edelmann S, Rybka D, Schrag TA, Frisch M, Dickinson HG, Melchinger AE, Scholten S. Parental Expression Variation of Small RNAs Is Negatively Correlated with Grain Yield Heterosis in a Maize Breeding Population. FRONTIERS IN PLANT SCIENCE 2018; 9:13. [PMID: 29441076 PMCID: PMC5797689 DOI: 10.3389/fpls.2018.00013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 01/04/2018] [Indexed: 05/26/2023]
Abstract
Heterosis refers to a quantitative phenomenon in which F1 hybrid trait values exceed the mean of the parental values in a positive direction. Generally, it is dependent on a high degree of heterozygosity, which is maintained in hybrid breeding by developing parental lines in separate, genetically distinct heterotic groups. The mobility of small RNAs (sRNAs) that mediate epigenetic regulation of gene expression renders them promising candidates for modulating the action of combined diverse genomes in trans-and evidence already indicates their contribution to transgressive phenotypes. By sequencing small RNA libraries of a panel of 21 maize parental inbred lines we found a low overlap of 35% between the sRNA populations from both distinct heterotic groups. Surprisingly, in contrast to genetic or gene expression variation, parental sRNA expression variation is negatively correlated with grain yield (GY) heterosis. Among 0.595 million expressed sRNAs, we identified 9,767, predominantly 22- and 24-nt long sRNAs, which showed an association of their differential expression between parental lines and GY heterosis of the respective hybrids. Of these sRNAs, 3,485 or 6,282 showed an association with high or low GY heterosis, respectively, thus the low heterosis associated group prevailing at 64%. The heterosis associated sRNAs map more frequently to genes that show differential expression between parental lines than reference sets. Together these findings suggest that trans-chromosomal actions of sRNAs in hybrids might add up to a negative contribution in heterosis formation, mediated by unfavorable gene expression regulation. We further revealed an exclusive accumulation of 22-nt sRNAs that are associated with low GY heterosis in pericentromeric genomic regions. That recombinational suppression led to this enrichment is indicated by its close correlation with low recombination rates. The existence of this enrichment, which we hypothesize resulted from the separated breeding of inbred lines within heterotic groups, may have implications for hybrid breeding strategies addressing the recombinational constraints characteristic of complex crop genomes.
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Affiliation(s)
- Felix Seifert
- Biocenter Klein Flottbek, University of Hamburg, Hamburg, Germany
| | | | | | - Susanne Edelmann
- Biocenter Klein Flottbek, University of Hamburg, Hamburg, Germany
| | - Dominika Rybka
- Biocenter Klein Flottbek, University of Hamburg, Hamburg, Germany
| | - Tobias A. Schrag
- Institute for Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Stuttgart, Germany
| | - Matthias Frisch
- Institute of Agronomy and Plant Breeding II, Justus-Liebig University, Giessen, Germany
| | - Hugh G. Dickinson
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Albrecht E. Melchinger
- Institute for Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Stuttgart, Germany
| | - Stefan Scholten
- Biocenter Klein Flottbek, University of Hamburg, Hamburg, Germany
- Institute for Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Stuttgart, Germany
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18
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Westhues M, Schrag TA, Heuer C, Thaller G, Utz HF, Schipprack W, Thiemann A, Seifert F, Ehret A, Schlereth A, Stitt M, Nikoloski Z, Willmitzer L, Schön CC, Scholten S, Melchinger AE. Omics-based hybrid prediction in maize. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017. [PMID: 28647896 DOI: 10.1007/s00122-017-2934-0] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Complementing genomic data with other "omics" predictors can increase the probability of success for predicting the best hybrid combinations using complex agronomic traits. Accurate prediction of traits with complex genetic architecture is crucial for selecting superior candidates in animal and plant breeding and for guiding decisions in personalized medicine. Whole-genome prediction has revolutionized these areas but has inherent limitations in incorporating intricate epistatic interactions. Downstream "omics" data are expected to integrate interactions within and between different biological strata and provide the opportunity to improve trait prediction. Yet, predicting traits from parents to progeny has not been addressed by a combination of "omics" data. Here, we evaluate several "omics" predictors-genomic, transcriptomic and metabolic data-measured on parent lines at early developmental stages and demonstrate that the integration of transcriptomic with genomic data leads to higher success rates in the correct prediction of untested hybrid combinations in maize. Despite the high predictive ability of genomic data, transcriptomic data alone outperformed them and other predictors for the most complex heterotic trait, dry matter yield. An eQTL analysis revealed that transcriptomic data integrate genomic information from both, adjacent and distant sites relative to the expressed genes. Together, these findings suggest that downstream predictors capture physiological epistasis that is transmitted from parents to their hybrid offspring. We conclude that the use of downstream "omics" data in prediction can exploit important information beyond structural genomics for leveraging the efficiency of hybrid breeding.
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Affiliation(s)
- Matthias Westhues
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, 70599, Stuttgart, Germany
| | - Tobias A Schrag
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, 70599, Stuttgart, Germany
| | - Claas Heuer
- Institute of Animal Breeding and Husbandry, Christian-Albrechts-University Kiel, 24098, Kiel, Germany
- Inguran LLC dba STGenetics, 22575 SH6 South, Navasota, TX, 77868, USA
| | - Georg Thaller
- Institute of Animal Breeding and Husbandry, Christian-Albrechts-University Kiel, 24098, Kiel, Germany
| | - H Friedrich Utz
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, 70599, Stuttgart, Germany
| | - Wolfgang Schipprack
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, 70599, Stuttgart, Germany
| | - Alexander Thiemann
- Biocenter Klein Flottbek, Developmental Biology and Biotechnology, University of Hamburg, 22609, Hamburg, Germany
| | - Felix Seifert
- Biocenter Klein Flottbek, Developmental Biology and Biotechnology, University of Hamburg, 22609, Hamburg, Germany
| | - Anita Ehret
- Institute of Animal Breeding and Husbandry, Christian-Albrechts-University Kiel, 24098, Kiel, Germany
| | - Armin Schlereth
- Max-Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Mark Stitt
- Max-Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Zoran Nikoloski
- Max-Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Lothar Willmitzer
- Max-Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Chris C Schön
- Plant Breeding, Technische Universität München, 85354, Freising, Germany
| | - Stefan Scholten
- Biocenter Klein Flottbek, Developmental Biology and Biotechnology, University of Hamburg, 22609, Hamburg, Germany.
| | - Albrecht E Melchinger
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, 70599, Stuttgart, Germany.
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19
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Comparative transcriptome analysis among parental inbred and crosses reveals the role of dominance gene expression in heterosis in Drosophila melanogaster. Sci Rep 2016; 6:21124. [PMID: 26928435 PMCID: PMC4772002 DOI: 10.1038/srep21124] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 01/18/2016] [Indexed: 12/16/2022] Open
Abstract
We observed heteroses for body weight in Drosophila melanogaster after generating hybrids from three inbred lines. To better understand the mechanism for this phenomenon at the mRNA level, we compared the mRNA profiles of the parental and hybrid lines using high-throughput RNA-seq. A total of 5877 differentially expressed genes (DEGs) were found and about 92% of these exhibited parental expression level dominance. Genes in the dominance category were functionally characterized using the Kyoto Encyclopedia of Genes and Genomes (KEGG) and the gene classifications offered by the Gene Ontology (GO) Consortium. The analysis identified genes associated with crucial processes such as development and growth in all three crosses. Functional assignments involving aminoglycan metabolism, starch and sucrose metabolism, and galactose metabolism are significantly overrepresented amongst the 215 common dominance DEGs. We conclude that dominance DEGs are important in heteroses in Drosophila melanogaster and contribute specifically to body weight heterosis.
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Martinez AK, Soriano JM, Tuberosa R, Koumproglou R, Jahrmann T, Salvi S. Yield QTLome distribution correlates with gene density in maize. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 242:300-309. [PMID: 26566847 DOI: 10.1016/j.plantsci.2015.09.022] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 09/22/2015] [Accepted: 09/23/2015] [Indexed: 05/09/2023]
Abstract
The genetic control of yield and related traits in maize has been addressed by many quantitative trait locus (QTL) studies, which have produced a wealth of QTL information, also known as QTLome. In this study, we assembled a yield QTLome database and carried out QTL meta-analysis based on 44 published studies, representing 32 independent mapping populations and 49 parental lines. A total of 808 unique QTLs were condensed to 84 meta-QTLs and were projected on the 10 maize chromosomes. Seventy-four percent of QTLs showed a proportion of phenotypic variance explained (PVE) smaller than 10% confirming the high genetic complexity of grain yield. Yield QTLome projection on the genetic map suggested pericentromeric enrichment of QTLs. Conversely, pericentromeric depletion of QTLs was observed when the physical map was considered, suggesting gene density as the main driver of yield QTL distribution on chromosomes. Dominant and overdominant yield QTLs did not distribute differently from additive effect QTLs.
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Affiliation(s)
- Ana Karine Martinez
- Department of Agricultural Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy
| | - Jose Miguel Soriano
- Department of Agricultural Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy; Field Crops Programme, IRTA (Institute for Food and Agricultural Research and Technology), 25198 Lleida, Spain
| | - Roberto Tuberosa
- Department of Agricultural Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy
| | | | | | - Silvio Salvi
- Department of Agricultural Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy.
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Mindaye TT, Mace ES, Godwin ID, Jordan DR. Genetic differentiation analysis for the identification of complementary parental pools for sorghum hybrid breeding in Ethiopia. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:1765-1775. [PMID: 26024715 DOI: 10.1007/s00122-015-2545-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 04/27/2015] [Indexed: 06/04/2023]
Abstract
The potential for exploiting heterosis for sorghum hybrid production in Ethiopia with improved local adaptation and farmers preferences has been investigated and populations suitable for initial hybrid development have been identified. Hybrids in sorghum have demonstrated increased productivity and stability of performance in the developed world. In Ethiopia, the uptake of hybrid sorghum has been limited to date, primarily due to poor adaptation and absence of farmer's preferred traits in existing hybrids. This study aimed to identify complementary parental pools to develop locally adapted hybrids, through an analysis of whole genome variability of 184 locally adapted genotypes and introduced hybrid parents (R and B). Genetic variability was assessed using genetic distance, model-based STRUCTURE analysis and pair-wise comparison of groups. We observed a high degree of genetic similarity between the Ethiopian improved inbred genotypes and a subset of landraces adapted to lowland agro-ecology with the introduced R lines. This coupled with the genetic differentiation from existing B lines, indicated that these locally adapted genotype groups are expected to have similar patterns of heterotic expression as observed between introduced R and B line pools. Additionally, the hybrids derived from these locally adapted genotypes will have the benefit of containing farmers preferred traits. The groups most divergent from introduced B lines were the Ethiopian landraces adapted to highland and intermediate agro-ecologies and a subset of lowland-adapted genotypes, indicating the potential for increased heterotic response of their hybrids. However, these groups were also differentiated from the R lines, and hence are different from the existing complementary heterotic pools. This suggests that although these groups could provide highly divergent parental pools, further research is required to investigate the extent of heterosis and their hybrid performance.
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Affiliation(s)
- Taye T Mindaye
- Queensland Alliance for Agriculture and Food Innovation, Hermitage Research Facility, The University of Queensland, 604 Yangan Rd, Warwick, QLD, 4370, Australia,
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Dan Z, Hu J, Zhou W, Yao G, Zhu R, Huang W, Zhu Y. Hierarchical additive effects on heterosis in rice (Oryza sativa L.). FRONTIERS IN PLANT SCIENCE 2015; 6:738. [PMID: 26442051 PMCID: PMC4566041 DOI: 10.3389/fpls.2015.00738] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 08/31/2015] [Indexed: 05/21/2023]
Abstract
Exploitation of heterosis in crops has contributed greatly to improvement in global food and energy production. In spite of the pervasive importance of heterosis, a complete understanding of its mechanisms has remained elusive. In this study, a small test-crossed rice population was constructed to investigate the formation mechanism of heterosis for 13 traits. The results of the relative mid-parent heterosis and modes of inheritance of all investigated traits demonstrated that additive effects were the foundation of heterosis for complex traits in a hierarchical structure, and multiplicative interactions among the component traits were the framework of heterosis in complex traits. Furthermore, new balances between unit traits and related component traits provided hybrids with the opportunity to achieve an optimal degree of heterosis for complex traits. This study dissected heterosis of both reproductive and vegetative traits from the perspective of hierarchical structure for the first time. Additive multiplicative interactions of component traits were proven to be the origin of heterosis in complex traits. Meanwhile, more attention should be paid to component traits, rather than complex traits, in the process of revealing the mechanism of heterosis.
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Affiliation(s)
- Zhiwu Dan
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan UniversityWuhan, China
- Key Laboratory for Research and Utilization of Heterosis in Indica Rice, Ministry of Agriculture, Wuhan UniversityWuhan, China
- The Yangzte River Valley Hybrid Rice Collaboration Innovation Center, Wuhan UniversityWuhan, China
| | - Jun Hu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan UniversityWuhan, China
- Key Laboratory for Research and Utilization of Heterosis in Indica Rice, Ministry of Agriculture, Wuhan UniversityWuhan, China
- The Yangzte River Valley Hybrid Rice Collaboration Innovation Center, Wuhan UniversityWuhan, China
| | - Wei Zhou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan UniversityWuhan, China
- Key Laboratory for Research and Utilization of Heterosis in Indica Rice, Ministry of Agriculture, Wuhan UniversityWuhan, China
- The Yangzte River Valley Hybrid Rice Collaboration Innovation Center, Wuhan UniversityWuhan, China
| | - Guoxin Yao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan UniversityWuhan, China
- Key Laboratory for Research and Utilization of Heterosis in Indica Rice, Ministry of Agriculture, Wuhan UniversityWuhan, China
- The Yangzte River Valley Hybrid Rice Collaboration Innovation Center, Wuhan UniversityWuhan, China
| | - Renshan Zhu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan UniversityWuhan, China
- Key Laboratory for Research and Utilization of Heterosis in Indica Rice, Ministry of Agriculture, Wuhan UniversityWuhan, China
- The Yangzte River Valley Hybrid Rice Collaboration Innovation Center, Wuhan UniversityWuhan, China
| | - Wenchao Huang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan UniversityWuhan, China
- Key Laboratory for Research and Utilization of Heterosis in Indica Rice, Ministry of Agriculture, Wuhan UniversityWuhan, China
- The Yangzte River Valley Hybrid Rice Collaboration Innovation Center, Wuhan UniversityWuhan, China
- *Correspondence: Wenchao Huang and Yingguo Zhu, State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Bayi Road, Wuhan 430072, China, ;
| | - Yingguo Zhu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan UniversityWuhan, China
- Key Laboratory for Research and Utilization of Heterosis in Indica Rice, Ministry of Agriculture, Wuhan UniversityWuhan, China
- The Yangzte River Valley Hybrid Rice Collaboration Innovation Center, Wuhan UniversityWuhan, China
- *Correspondence: Wenchao Huang and Yingguo Zhu, State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Bayi Road, Wuhan 430072, China, ;
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