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Song M, Zhao J, Zhang C, Jia C, Yang J, Zhao H, Zhai J, Lei B, Tao S, Chen S, Su R, Ma C. PEA-m6A: an ensemble learning framework for accurately predicting N6-methyladenosine modifications in plants. PLANT PHYSIOLOGY 2024; 195:1200-1213. [PMID: 38428981 DOI: 10.1093/plphys/kiae120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 01/11/2024] [Accepted: 02/01/2024] [Indexed: 03/03/2024]
Abstract
N 6-methyladenosine (m6A), which is the mostly prevalent modification in eukaryotic mRNAs, is involved in gene expression regulation and many RNA metabolism processes. Accurate prediction of m6A modification is important for understanding its molecular mechanisms in different biological contexts. However, most existing models have limited range of application and are species-centric. Here we present PEA-m6A, a unified, modularized and parameterized framework that can streamline m6A-Seq data analysis for predicting m6A-modified regions in plant genomes. The PEA-m6A framework builds ensemble learning-based m6A prediction models with statistic-based and deep learning-driven features, achieving superior performance with an improvement of 6.7% to 23.3% in the area under precision-recall curve compared with state-of-the-art regional-scale m6A predictor WeakRM in 12 plant species. Especially, PEA-m6A is capable of leveraging knowledge from pretrained models via transfer learning, representing an innovation in that it can improve prediction accuracy of m6A modifications under small-sample training tasks. PEA-m6A also has a strong capability for generalization, making it suitable for application in within- and cross-species m6A prediction. Overall, this study presents a promising m6A prediction tool, PEA-m6A, with outstanding performance in terms of its accuracy, flexibility, transferability, and generalization ability. PEA-m6A has been packaged using Galaxy and Docker technologies for ease of use and is publicly available at https://github.com/cma2015/PEA-m6A.
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Affiliation(s)
- Minggui Song
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jiawen Zhao
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chujun Zhang
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chengchao Jia
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jing Yang
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Haonan Zhao
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jingjing Zhai
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
- Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA
| | - Beilei Lei
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Shiheng Tao
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Siqi Chen
- School of Computer Software, College of Intelligence and Computing, Tianjin University, Tianjin 300072, China
| | - Ran Su
- School of Computer Software, College of Intelligence and Computing, Tianjin University, Tianjin 300072, China
| | - Chuang Ma
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
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Chen X, Tang S, Gao X, Niu F, Yang X, Song X, Zhang L. Characterization and validation of TaAGL66, a gene related to fertility conversion of wheat in the presence of Aegilops kotschyi cytoplasm. PLANTA 2024; 260:6. [PMID: 38780795 DOI: 10.1007/s00425-024-04416-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 04/15/2024] [Indexed: 05/25/2024]
Abstract
MAIN CONCLUSION TaAGL66, a MADS-box transcription factor highly expressed in fertile anthers of KTM3315A, regulates anther and/or pollen development, as well as male fertility in wheat with Aegilops kotschyi cytoplasm. Male sterility, as a string of sophisticated biological processes in higher plants, is commonly regulated by transcription factors (TFs). Among them, MADS-box TFs are mainly participated in the processes of floral organ formation and pollen development, which are tightly related to male sterility, but they have been little studied in the reproductive development in wheat. In our study, TaAGL66, a gene that was specifically expressed in spikes and highly expressed in fertile anthers, was identified by RNA sequencing and the expression profiles data of these genes, and qRT-PCR analyses, which was localized to the nucleus. Silencing of TaAGL66 under fertility condition in KTM3315A, a thermo-sensitive male sterile line with Ae. kotschyi cytoplasm, displayed severe fertility reduction, abnormal anther dehiscence, defective pollen development, decreased viability, and low seed-setting. It can be concluded that TaAGL66 plays an important role in wheat pollen development in the presence of Ae. kotschyi cytoplasm, providing new insights into the utilization of male sterility.
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Affiliation(s)
- Xianning Chen
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Shengmei Tang
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xiaoran Gao
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Fuqiang Niu
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xinyu Yang
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xiyue Song
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| | - Lingli Zhang
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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Song P, Cai Z, Jia G. Principles, functions, and biological implications of m 6A in plants. RNA (NEW YORK, N.Y.) 2024; 30:491-499. [PMID: 38531642 PMCID: PMC11019739 DOI: 10.1261/rna.079951.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Accepted: 02/09/2024] [Indexed: 03/28/2024]
Abstract
Over the past decade, N 6-methyladenosine (m6A) has emerged as a prevalent and dynamically regulated modification across the transcriptome; it has been reversibly installed, removed, and interpreted by specific binding proteins, and has played crucial roles in molecular and biological processes. Within this scope, we consolidate recent advancements of m6A research in plants regarding gene expression regulation, diverse physiologic and pathogenic processes, as well as crop trial implications, to guide discussions on challenges associated with and leveraging epitranscriptome editing for crop improvement.
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Affiliation(s)
- Peizhe Song
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Zhihe Cai
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Guifang Jia
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- PKU-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- Beijing Advanced Center of RNA Biology, Peking University, Beijing 100871, China
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Liu W, He G, Deng XW. Toward understanding and utilizing crop heterosis in the age of biotechnology. iScience 2024; 27:108901. [PMID: 38533455 PMCID: PMC10964264 DOI: 10.1016/j.isci.2024.108901] [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] [Indexed: 03/28/2024] Open
Abstract
Heterosis, a universal phenomenon in nature, mainly reflected in the superior productivity, quality, and fitness of F1 hybrids compared with their inbred parents, has been exploited in agriculture and greatly benefited human society in terms of food security. However, the flexible and efficient utilization of heterosis has remained a challenge in hybrid breeding systems because of the limitations of "three-line" and "two-line" methods. In the past two decades, rapidly developed biotechnologies have provided unprecedented conveniences for both understanding and utilizing heterosis. Notably, "third-generation" (3G) hybrid breeding technology together with high-throughput sequencing and gene editing greatly promoted the efficiency of hybrid breeding. Here, we review emerging ideas about the genetic or molecular mechanisms of heterosis and the development of 3G hybrid breeding system in the age of biotechnology. In addition, we summarized opportunities and challenges for optimal heterosis utilization in the future.
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Affiliation(s)
- Wenwen Liu
- School of Advanced Agricultural 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
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, Shandong 261325, China
| | - Guangming He
- School of Advanced Agricultural 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
| | - Xing Wang Deng
- School of Advanced Agricultural 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
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, Shandong 261325, China
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Dong Y, Li G, Zhang X, Feng Z, Li T, Li Z, Xu S, Xu S, Liu W, Xue J. Genome-Wide Association Study for Maize Hybrid Performance in a Typical Breeder Population. Int J Mol Sci 2024; 25:1190. [PMID: 38256265 PMCID: PMC10816832 DOI: 10.3390/ijms25021190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/14/2024] [Accepted: 01/16/2024] [Indexed: 01/24/2024] Open
Abstract
Maize is one of the major crops that has demonstrated success in the utilization of heterosis. Developing high-yield hybrids is a crucial part of plant breeding to secure global food demand. In this study, we conducted a genome-wide association study (GWAS) for 10 agronomic traits using a typical breeder population comprised 442 single-cross hybrids by evaluating additive, dominance, and epistatic effects. A total of 49 significant single nucleotide polymorphisms (SNPs) and 69 significant pairs of epistasis were identified, explaining 26.2% to 64.3% of the phenotypic variation across the 10 traits. The enrichment of favorable genotypes is significantly correlated to the corresponding phenotype. In the confident region of the associated site, 532 protein-coding genes were discovered. Among these genes, the Zm00001d044211 candidate gene was found to negatively regulate starch synthesis and potentially impact yield. This typical breeding population provided a valuable resource for dissecting the genetic architecture of yield-related traits. We proposed a novel mating strategy to increase the GWAS efficiency without utilizing more resources. Finally, we analyzed the enrichment of favorable alleles in the Shaan A and Shaan B groups, as well as in each inbred line. Our breeding practice led to consistent results. Not only does this study demonstrate the feasibility of GWAS in F1 hybrid populations, it also provides a valuable basis for further molecular biology and breeding research.
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Affiliation(s)
- Yuan Dong
- Key Laboratory of Biology and Genetic Breeding of Maize in Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Guoliang Li
- National Maize Improvement Center of China, Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing 100193, China
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany
| | - Xinghua Zhang
- Key Laboratory of Biology and Genetic Breeding of Maize in Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Zhiqian Feng
- Key Laboratory of Biology and Genetic Breeding of Maize in Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Ting Li
- Key Laboratory of Biology and Genetic Breeding of Maize in Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Zhoushuai Li
- Key Laboratory of Biology and Genetic Breeding of Maize in Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Shizhong Xu
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Shutu Xu
- Key Laboratory of Biology and Genetic Breeding of Maize in Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Wenxin Liu
- National Maize Improvement Center of China, Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing 100193, China
| | - Jiquan Xue
- Key Laboratory of Biology and Genetic Breeding of Maize in Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling 712100, China
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Paril J, Reif J, Fournier-Level A, Pourkheirandish M. Heterosis in crop improvement. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:23-32. [PMID: 37971883 DOI: 10.1111/tpj.16488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 09/15/2023] [Accepted: 09/20/2023] [Indexed: 11/19/2023]
Abstract
Heterosis, also known as hybrid vigor, is the phenomenon wherein a progeny exhibits superior traits relative to one or both parents. In terms of crop breeding, this usually refers to the yield advantage of F1 hybrids over both inbred parents. The development of high-yielding hybrid cultivars across a wider range of crops is key to meeting future food demands. However, conventional hybrid breeding strategies are proving to be exceptionally challenging to apply commercially in many self-pollinating crops, particularly wheat and barley. Currently in these crops, the relative performance advantage of hybrids over inbred line cultivars does not outweigh the cost of hybrid seed production. Here, we review the genetic basis of heterosis, discuss the challenges in hybrid breeding, and propose a strategy to recruit multiple heterosis-associated genes to develop lines with improved agronomic characteristics. This strategy leverages modern genetic engineering tools to synthesize supergenes by fusing multiple heterotic alleles across multiple heterosis-associated loci. We outline a plan to assess the feasibility of this approach to improve line performance using barley (Hordeum vulgare) as the model self-pollinating crop species, and a few heterosis-associated genes. The proposed method can be applied to all crops for which heterotic gene combinations can be identified.
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Affiliation(s)
- Jefferson Paril
- Faculty of Science, University of Melbourne, Parkville, Melbourne, Victoria, Australia
- AgriBio, Centre for AgriBioscience, Agriculture Victoria Research, Bundoora, Victoria, Australia
| | - Jochen Reif
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
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Guo S, Liu Z, Sheng H, Olukayode T, Zhou Z, Liu Y, Wang M, He M, Kochian L, Qin Y. Dynamic transcriptome analysis unravels key regulatory genes of maize root growth and development in response to potassium deficiency. PLANTA 2023; 258:99. [PMID: 37837470 PMCID: PMC10576708 DOI: 10.1007/s00425-023-04260-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 10/03/2023] [Indexed: 10/16/2023]
Abstract
MAIN CONCLUSION Integrated root phenotypes and transcriptome analysis have revealed key candidate genes responsible for maize root growth and development in potassium deficiency. Potassium (K) is a vital macronutrient for plant growth, but our understanding of its regulatory mechanisms in maize root system architecture (RSA) and K+ uptake remains limited. To address this, we conducted hydroponic and field trials at different growth stages. K+ deficiency significantly inhibited maize root growth, with metrics like total root length, primary root length, width and maximum root number reduced by 50% to 80% during early seedling stages. In the field, RSA traits exhibited maximum values at the silking stage but continued to decline thereafter. Furthermore, K deprivation had a pronounced negative impact on root morphology and RSA growth and grain yield. RNA-Seq analysis identified 5972 differentially expressed genes (DEGs), including 17 associated with K+ signaling, transcription factors, and transporters. Weighted gene co-expression network analysis revealed 23 co-expressed modules, with enrichment of transcription factors at different developmental stages under K deficiency. Several DEGs and transcription factors were predicted as potential candidate genes responsible for maize root growth and development. Interestingly, some of these genes exhibited homology to well-known regulators of root architecture or development in Arabidopsis, such as Zm00001d014467 (AtRCI3), Zm00001d011237 (AtWRKY9), and Zm00001d030862 (AtAP2/ERF). Identifying these key genes helps to provide a deeper understanding of the molecular mechanisms governing maize root growth and development under nutrient deficient conditions offering potential benefits for enhancing maize production and improving stress resistance through targeted manipulation of RSA traits in modern breeding efforts.
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Affiliation(s)
- Song Guo
- Institute of Agricultural Resources and Environment, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, People's Republic of China
| | - Zhigang Liu
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, S7N 4L8, Canada
| | - Huajin Sheng
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, S7N 4L8, Canada
| | - Toluwase Olukayode
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, S7N 4L8, Canada
| | - Zijun Zhou
- Institute of Agricultural Resources and Environment, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, People's Republic of China
| | - Yonghong Liu
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, People's Republic of China
| | - Meng Wang
- Institute of Agricultural Resource and Environment, Jilin Academy of Agricultural Sciences, Changchun, 130033, People's Republic of China
| | - Mingjiang He
- Institute of Agricultural Resources and Environment, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, People's Republic of China
| | - Leon Kochian
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, S7N 4L8, Canada
| | - Yusheng Qin
- Institute of Agricultural Resources and Environment, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, People's Republic of China.
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Chen T, Wang Z, Wang J, Liu J, Zhang R, Jia X, Yu C, Yin Y, Creech D. Transcriptomic and metabolomic analyses unveil the growth advantage mechanism conferred by heterosis of Michelia 'Zhongshanhanxiao'. TREE PHYSIOLOGY 2023; 43:1454-1466. [PMID: 37099801 DOI: 10.1093/treephys/tpad046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 04/11/2023] [Indexed: 06/19/2023]
Abstract
Michelia compressa (Maxim.) Sarg. is one of the important timber trees in Taiwan province, P. R. China. Michelia 'Zhongshanhanxiao' is a group of variants found among the progeny of M. compressa that exhibit higher growth rates compared with normal individuals, with a significantly increased stem diameter and height, as well as enlarged leaves and flowers. However, the molecular mechanisms fostering the growth advantage and morphological variations are unknown and deserve further study. Through analysing the transcriptome, metabolome and physiological processes of leaves, we identified remarkable differences in gene expression and metabolic profiles between Michelia 'Zhongshanhanxiao' and both the maternal M. compressa and its normal progeny. These differences were widely associated with a plant-pathogen interaction, phenylpropanoid biosynthesis, cyanoamino acid metabolism, carbon fixation in photosynthetic organisms and plant hormone signal transduction. Additionally, physiological measurements showed that Michelia 'Zhongshanhanxiao' possesses stronger photosynthetic capacity and higher plant hormone content. These results suggest that the heterosis of Michelia 'Zhongshanhanxiao' is regulated by candidates related to cell division, resistance to pathogens and the accumulation of organic compounds. The findings of this study provide crucial information on the molecular mechanisms underlying the growth advantages conferred by heterosis in trees.
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Affiliation(s)
- Tingting Chen
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, No. 1, Qianhu Village, Zhongshan Gate, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, No. 1, Qianhu Village, Zhongshan Gate, Nanjing 210014, China
- Nanjing Botanical Garden Mem. Sun Yat-Sen, No. 1, Qianhu Village, Zhongshan Gate, Nanjing 210014, China
| | - Zhiquan Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, No. 1, Qianhu Village, Zhongshan Gate, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, No. 1, Qianhu Village, Zhongshan Gate, Nanjing 210014, China
- Nanjing Botanical Garden Mem. Sun Yat-Sen, No. 1, Qianhu Village, Zhongshan Gate, Nanjing 210014, China
| | - Junjie Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, No. 1, Qianhu Village, Zhongshan Gate, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, No. 1, Qianhu Village, Zhongshan Gate, Nanjing 210014, China
- Nanjing Botanical Garden Mem. Sun Yat-Sen, No. 1, Qianhu Village, Zhongshan Gate, Nanjing 210014, China
| | - Jiaqi Liu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, No. 1, Qianhu Village, Zhongshan Gate, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, No. 1, Qianhu Village, Zhongshan Gate, Nanjing 210014, China
- Nanjing Botanical Garden Mem. Sun Yat-Sen, No. 1, Qianhu Village, Zhongshan Gate, Nanjing 210014, China
| | - Rui Zhang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, No. 1, Qianhu Village, Zhongshan Gate, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, No. 1, Qianhu Village, Zhongshan Gate, Nanjing 210014, China
- Nanjing Botanical Garden Mem. Sun Yat-Sen, No. 1, Qianhu Village, Zhongshan Gate, Nanjing 210014, China
| | - Xiaoyu Jia
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, No. 1, Qianhu Village, Zhongshan Gate, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, No. 1, Qianhu Village, Zhongshan Gate, Nanjing 210014, China
- Nanjing Botanical Garden Mem. Sun Yat-Sen, No. 1, Qianhu Village, Zhongshan Gate, Nanjing 210014, China
| | - Chaoguang Yu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, No. 1, Qianhu Village, Zhongshan Gate, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, No. 1, Qianhu Village, Zhongshan Gate, Nanjing 210014, China
- Nanjing Botanical Garden Mem. Sun Yat-Sen, No. 1, Qianhu Village, Zhongshan Gate, Nanjing 210014, China
| | - Yunlong Yin
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, No. 1, Qianhu Village, Zhongshan Gate, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, No. 1, Qianhu Village, Zhongshan Gate, Nanjing 210014, China
- Nanjing Botanical Garden Mem. Sun Yat-Sen, No. 1, Qianhu Village, Zhongshan Gate, Nanjing 210014, China
| | - David Creech
- Arthur Temple College of Forestry and Agriculture, Stephen F. Austin State University, Nacogdoches, TX 75962, USA
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Xing K, Liu Z, Liu L, Zhang J, Qanmber G, Wang Y, Liu L, Gu Y, Zhang C, Li S, Zhang Y, Yang Z. N 6 -Methyladenosine mRNA modification regulates transcripts stability associated with cotton fiber elongation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:967-985. [PMID: 37158663 DOI: 10.1111/tpj.16274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 04/29/2023] [Accepted: 05/04/2023] [Indexed: 05/10/2023]
Abstract
N6 -Methyladenosine (m6 A) is the most abundant methylation modification in eukaryotic mRNA. The discovery of the dynamic and reversible regulatory mechanism of m6 A has greatly promoted the development of m6 A-led epitranscriptomics. However, the characterization of m6 A in cotton fiber is still unknown. Here, we reveal the potential link between m6 A modification and cotton fiber elongation by parallel m6 A-immunoprecipitation-sequencing (m6 A-seq) and RNA-seq analysis of fibers from the short fiber mutants Ligonliness-2 (Li2 ) and wild-type (WT). This study demonstrated a higher level of m6 A in the Li2 mutant, with the enrichment of m6 A modifications in the stop codon, 3'-untranslated region and coding sequence regions than in WT cotton. In the correlation analysis between genes containing differential m6 A modifications and differentially expressed genes, we identified several genes that could potentially regulate fiber elongation, including cytoskeleton, microtubule binding, cell wall and transcription factors (TFs). We further confirmed that the methylation of m6 A affected the mRNA stability of these fiber elongation-related genes including the TF GhMYB44, which showed the highest expression level in the RNA-seq data and m6 A methylation in the m6 A-seq data. Next, the overexpression of GhMYB44 reduces fiber elongation, whereas the silencing of GhMYB44 produces longer fibers. In summary, these results uncover that m6 A methylation regulated the expression of genes related to fiber development by affecting mRNA's stability, ultimately affecting cotton fiber elongation.
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Affiliation(s)
- Kun Xing
- Hebei Research Base,National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, College of Agronomy, Hebei Agricultural University, Baoding, 071001, Hebei, China
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization,Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Zhao Liu
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Le Liu
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization,Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Jie Zhang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization,Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Ghulam Qanmber
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Ye Wang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization,Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Lisen Liu
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization,Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Yu Gu
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization,Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Changsheng Zhang
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Shuaijie Li
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Yan Zhang
- Hebei Research Base,National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, College of Agronomy, Hebei Agricultural University, Baoding, 071001, Hebei, China
| | - Zuoren Yang
- Hebei Research Base,National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, College of Agronomy, Hebei Agricultural University, Baoding, 071001, Hebei, China
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization,Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, Xinjiang, China
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10
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Tang J, Chen S, Jia G. Detection, regulation, and functions of RNA N 6-methyladenosine modification in plants. PLANT COMMUNICATIONS 2023; 4:100546. [PMID: 36627844 DOI: 10.1016/j.xplc.2023.100546] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/22/2022] [Accepted: 01/05/2023] [Indexed: 05/11/2023]
Abstract
N6-Methyladenosine (m6A) is the most abundant internal chemical modification in eukaryotic mRNA and plays important roles in gene expression regulation, including transcriptional and post-transcriptional regulation. m6A is a reversible modification that is installed, removed, and recognized by methyltransferases (writers), demethylases (erasers), and m6A-binding proteins (readers), respectively. Recently, the breadth of research on m6A in plants has expanded, and the vital roles of m6A in plant development, biotic and abiotic stress responses, and crop trait improvement have been investigated. In this review, we discuss recent developments in research on m6A and highlight the detection methods, distribution, regulatory proteins, and molecular and biological functions of m6A in plants. We also offer some perspectives on future investigations, providing direction for subsequent research on m6A in plants.
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Affiliation(s)
- Jun Tang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Shuyan Chen
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Guifang Jia
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Beijing 100871, China.
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11
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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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12
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Viana JMS. The impact of epistasis in the heterosis and combining ability analyses. FRONTIERS IN PLANT SCIENCE 2023; 14:1168419. [PMID: 37143879 PMCID: PMC10151527 DOI: 10.3389/fpls.2023.1168419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 03/27/2023] [Indexed: 05/06/2023]
Abstract
The current theoretical knowledge concerning the influence of epistasis on heterosis is based on a simplified multiplicative model. The objective of this study was to assess how epistasis affects the heterosis and combining ability analyses, assuming additive model, hundreds of genes, linkage disequilibrium (LD), dominance, and seven types of digenic epistasis. We developed the quantitative genetics theory for supporting the simulation of the individual genotypic values in nine populations, the selfed populations, the 36 interpopulation crosses, 180 doubled haploids (DHs), and their 16,110 crosses, assuming 400 genes on 10 chromosomes of 200 cM. Epistasis only affects population heterosis if there is LD. Only additive × additive and dominance × dominance epistasis can affect the components of the heterosis and combining ability analyses of populations. Epistasis can have a negative impact on the heterosis and combining ability analysis of populations, leading to wrong inferences regarding the identification of superior and most divergent populations. However, this depends on the type of epistasis, percentage of epistatic genes, and magnitude of their effects. Except for duplicate genes with cumulative effects and non-epistatic genic interaction, there was a decrease in the average heterosis by increasing the percentage of epistatic genes and the magnitude of their effects. The same results are generally true for the combining ability analysis of DHs. The combining ability analyses of subsets of 20 DHs showed no significant average impact of epistasis on the identification of the most divergent ones, regardless of the number of epistatic genes and magnitude of their effects. However, a negative effect on the assessment of the superior DHs can occur assuming 100% of epistatic genes, but depending on the epistasis type and the epistatic effect magnitude.
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13
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Hu J, Cai J, Xu T, Kang H. Epitranscriptomic mRNA modifications governing plant stress responses: underlying mechanism and potential application. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:2245-2257. [PMID: 36002976 PMCID: PMC9674322 DOI: 10.1111/pbi.13913] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 08/14/2022] [Accepted: 08/16/2022] [Indexed: 06/01/2023]
Abstract
Plants inevitably encounter environmental adversities, including abiotic and biotic stresses, which significantly impede plant growth and reduce crop yield. Thus, fine-tuning the fate and function of stress-responsive RNAs is indispensable for plant survival under such adverse conditions. Recently, post-transcriptional RNA modifications have been studied as a potent route to regulate plant gene expression under stress. Among over 160 mRNA modifications identified to date, N6 -methyladenosine (m6 A) in mRNAs is notable because of its multifaceted roles in plant development and stress response. Recent transcriptome-wide mapping has revealed the distribution and patterns of m6 A in diverse stress-responsive mRNAs in plants, building a foundation for elucidating the molecular link between m6 A and stress response. Moreover, the identification and characterization of m6 A writers, readers and erasers in Arabidopsis and other model crops have offered insights into the biological roles of m6 A in plant abiotic stress responses. Here, we review the recent progress of research on mRNA modifications, particularly m6 A, and their dynamics, distribution, regulation and biological functions in plant stress responses. Further, we posit potential strategies for breeding stress-tolerant crops by engineering mRNA modifications and propose the future direction of research on RNA modifications to gain a much deeper understanding of plant stress biology.
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Affiliation(s)
- Jianzhong Hu
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life SciencesJiangsu Normal UniversityXuzhouJiangsu ProvinceChina
- Department of Applied Biology, College of Agriculture and Life SciencesChonnam National UniversityGwangjuKorea
| | - Jing Cai
- Department of Applied Biology, College of Agriculture and Life SciencesChonnam National UniversityGwangjuKorea
| | - Tao Xu
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life SciencesJiangsu Normal UniversityXuzhouJiangsu ProvinceChina
| | - Hunseung Kang
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life SciencesJiangsu Normal UniversityXuzhouJiangsu ProvinceChina
- Department of Applied Biology, College of Agriculture and Life SciencesChonnam National UniversityGwangjuKorea
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14
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Zhou L, Gao G, Tang R, Wang W, Wang Y, Tian S, Qin G. m 6 A-mediated regulation of crop development and stress responses. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1447-1455. [PMID: 35178842 PMCID: PMC9342612 DOI: 10.1111/pbi.13792] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/28/2022] [Accepted: 02/07/2022] [Indexed: 05/12/2023]
Abstract
Dynamic chemical modifications in eukaryotic messenger RNAs (mRNAs) constitute an essential layer of gene regulation, among which N6 -methyladenosine (m6 A) was unveiled to be the most abundant. m6 A functionally modulates important biological processes in various mammals and plants through the regulation of mRNA metabolism, mainly mRNA degradation and translation efficiency. Physiological functions of m6 A methylation are diversified and affected by intricate sequence contexts and m6 A machineries. A number of studies have dissected the functional roles and the underlying mechanisms of m6 A modifications in regulating plant development and stress responses. Recently, it was demonstrated that the human FTO-mediated plant m6 A removal caused dramatic yield increases in rice and potato, indicating that modulation of m6 A methylation could be an efficient strategy for crop improvement. In this review, we summarize the current progress concerning the m6 A-mediated regulation of crop development and stress responses, and provide an outlook on the potential application of m6 A epitranscriptome in the future improvement of crops.
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Affiliation(s)
- Leilei Zhou
- Key Laboratory of Plant ResourcesInstitute of BotanyChinese Academy of SciencesHaidian District, BeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Guangtong Gao
- Key Laboratory of Plant ResourcesInstitute of BotanyChinese Academy of SciencesHaidian District, BeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Renkun Tang
- Key Laboratory of Plant ResourcesInstitute of BotanyChinese Academy of SciencesHaidian District, BeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Weihao Wang
- Key Laboratory of Plant ResourcesInstitute of BotanyChinese Academy of SciencesHaidian District, BeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yuying Wang
- Key Laboratory of Plant ResourcesInstitute of BotanyChinese Academy of SciencesHaidian District, BeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Shiping Tian
- Key Laboratory of Plant ResourcesInstitute of BotanyChinese Academy of SciencesHaidian District, BeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Guozheng Qin
- Key Laboratory of Plant ResourcesInstitute of BotanyChinese Academy of SciencesHaidian District, BeijingChina
- University of Chinese Academy of SciencesBeijingChina
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15
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Govindan G, Sharma B, Li Y, Armstrong CD, Merum P, Rohila JS, Gregory BD, Sunkar R. mRNA N 6 -methyladenosine is critical for cold tolerance in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:1052-1068. [PMID: 35710867 PMCID: PMC9543165 DOI: 10.1111/tpj.15872] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 05/28/2022] [Accepted: 06/13/2022] [Indexed: 05/16/2023]
Abstract
Plants respond to low temperatures by altering the mRNA abundance of thousands of genes contributing to numerous physiological and metabolic processes that allow them to adapt. At the post-transcriptional level, these cold stress-responsive transcripts undergo alternative splicing, microRNA-mediated regulation and alternative polyadenylation, amongst others. Recently, m6 A, m5 C and other mRNA modifications that can affect the regulation and stability of RNA were discovered, thus revealing another layer of post-transcriptional regulation that plays an important role in modulating gene expression. The importance of m6 A in plant growth and development has been appreciated, although its significance under stress conditions is still underexplored. To assess the role of m6 A modifications during cold stress responses, methylated RNA immunoprecipitation sequencing was performed in Arabidopsis seedlings esposed to low temperature stress (4°C) for 24 h. This transcriptome-wide m6 A analysis revealed large-scale shifts in this modification in response to low temperature stress. Because m6 A is known to affect transcript stability/degradation and translation, we investigated these possibilities. Interestingly, we found that cold-enriched m6 A-containing transcripts demonstrated the largest increases in transcript abundance coupled with increased ribosome occupancy under cold stress. The significance of the m6 A epitranscriptome on plant cold tolerance was further assessed using the mta mutant in which the major m6 A methyltransferase gene was mutated. Compared to the wild-type, along with the differences in CBFs and COR gene expression levels, the mta mutant exhibited hypersensitivity to cold treatment as determined by primary root growth, biomass, and reactive oxygen species accumulation. Furthermore, and most importantly, both non-acclimated and cold-acclimated mta mutant demonstrated hypersensitivity to freezing tolerance. Taken together, these findings suggest a critical role for the epitranscriptome in cold tolerance of Arabidopsis.
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Affiliation(s)
- Ganesan Govindan
- Department of Biochemistry and Molecular BiologyOklahoma State UniversityStillwaterOK74078USA
| | - Bishwas Sharma
- Department of BiologyUniversity of PennsylvaniaPhiladelphiaPA19104USA
| | - Yong‐Fang Li
- Department of Biochemistry and Molecular BiologyOklahoma State UniversityStillwaterOK74078USA
| | | | - Pandrangaiah Merum
- Department of Biochemistry and Molecular BiologyOklahoma State UniversityStillwaterOK74078USA
| | - Jai S. Rohila
- Dale Bumpers National Rice Research CenterUnited States Department of Agriculture‐Agricultural Research ServicesStuttgartAR72160USA
| | - Brian D. Gregory
- Department of BiologyUniversity of PennsylvaniaPhiladelphiaPA19104USA
| | - Ramanjulu Sunkar
- Department of Biochemistry and Molecular BiologyOklahoma State UniversityStillwaterOK74078USA
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16
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Li T, Wang F, Yasir M, Li K, Qin Y, Zheng J, Luo K, Zhu S, Zhang H, Jiang Y, Zhang Y, Rong J. Expression Patterns Divergence of Reciprocal F 1 Hybrids Between Gossypium hirsutum and Gossypium barbadense Reveals Overdominance Mediating Interspecific Biomass Heterosis. FRONTIERS IN PLANT SCIENCE 2022; 13:892805. [PMID: 35845678 PMCID: PMC9284264 DOI: 10.3389/fpls.2022.892805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 06/06/2022] [Indexed: 06/15/2023]
Abstract
Hybrid breeding has provided an impetus to the process and achievement of a higher yield and quality of crops. Interspecific hybridization is critical for resolving parental genetic diversity bottleneck problems. The reciprocal interspecific hybrids and their parents (Gossypium hirsutum and Gossypium barbadense) have been applied in this study to elucidate the transcription regulatory mechanism of early biomass heterosis. Phenotypically, the seed biomass, plant height over parent heterosis, leaf area over parent heterosis, and fresh and dry biomass were found to be significantly higher in hybrids than in parents. Analysis of leaf areas revealed that the one-leaf stage exhibits the most significant performance in initial vegetative growth vigor and larger leaves in hybrids, increasing the synthesis of photosynthesis compounds and enhancing photosynthesis compound synthesis. Comparative transcriptome analysis showed that transgressive down-regulation (TDR) is the main gene expression pattern in the hybrids (G. hirsutum × G. barbadense, HB), and it was found that the genes of photosystem I and Adenosine triphosphate (ATP)-binding may promote early growth vigor. Transgressive up-regulation (TUR) is the major primary gene expression pattern in the hybrids (G. barbadense × G. hirsutum, BH), and photosystem II-related genes mediated the performance of early biomass heterosis. The above results demonstrated that overdominance mediates biomass heterosis in interspecific hybrid cotton and the supervisory mechanism divergence of hybrids with different females. Photosynthesis and other metabolic process are jointly involved in controlling early biomass heterosis in interspecific hybrid cotton. The expression pattern data of transcriptome sequencing were supported using the qRT-PCR analysis. Our findings could be useful in theoretical and practical studies of early interspecific biomass heterosis, and the results provide potential resources for the theoretical and applied research on early interspecific biomass heterosis.
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Affiliation(s)
- Tengyu Li
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, Zhejiang Agriculture and Forestry University, Hangzhou, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Fuqiu Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Muhammad Yasir
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Kui Li
- Institute of Food and Nutrition Development, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuan Qin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Jing Zheng
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Kun Luo
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Shouhong Zhu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Hua Zhang
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Yurong Jiang
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Yongshan Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Junkang Rong
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, Zhejiang Agriculture and Forestry University, Hangzhou, China
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17
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Xiong J, Hu K, Shalby N, Zhuo C, Wen J, Yi B, Shen J, Ma C, Fu T, Tu J. Comparative transcriptomic analysis reveals the molecular mechanism underlying seedling biomass heterosis in Brassica napus. BMC PLANT BIOLOGY 2022; 22:283. [PMID: 35676627 PMCID: PMC9178846 DOI: 10.1186/s12870-022-03671-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 05/16/2022] [Indexed: 05/25/2023]
Abstract
BACKGROUND Heterosis is an important biological phenomenon in which the hybrids exceed the parents in many traits. However, the molecular mechanism underlying seedling heterosis remains unclear. RESULTS In the present study, we analyzed the leaf transcriptomes of strong hybrids (AM, HM) and weak hybrids (CM, HW) and their parents (A, C, H, M, and W) at two periods. Phenotypically, hybrids had obvious biomass heterosis at the seedling stage, with statistically significant differences between the strong and weak hybrids. The transcriptomic analysis demonstrated that the number of differentially expressed genes (DEGs) between parents was the highest. Further analysis showed that most DEGs were biased toward parental expression. The biological processes of the two periods were significantly enriched in the plant hormone signal transduction and photosynthetic pathways. In the plant hormone signaling pathway, DEG expression was high in hybrids, with expression differences between strong and weak hybrids. In addition, DEGs related to cell size were identified. Similar changes were observed during photosynthesis. The enhanced leaf area of hybrids generated an increase in photosynthetic products, which was consistent with the phenotype of the biomass. Weighted gene co-expression network analysis of different hybrids and parents revealed that hub genes in vigorous hybrid were mainly enriched in the plant hormone signal transduction and regulation of plant hormones. CONCLUSION Plant hormone signaling and photosynthesis pathways, as well as differential expression of plant cell size-related genes, jointly regulate the dynamic changes between strong and weak hybrids and the generation of seedling-stage heterosis. This study may elucidate the molecular mechanism underlying early biomass heterosis and help enhance canola yield.
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Affiliation(s)
- Jie Xiong
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 China
| | - Kaining Hu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 China
| | - Nesma Shalby
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 China
| | - Chenjian Zhuo
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 China
| | - Jing Wen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 China
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 China
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 China
| | - Chaozhi Ma
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 China
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 China
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 China
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18
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Quan C, Chen G, Li S, Jia Z, Yu P, Tu J, Shen J, Yi B, Fu T, Dai C, Ma C. Transcriptome shock in interspecific F1 allotriploid hybrids between Brassica species. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:2336-2353. [PMID: 35139197 DOI: 10.1093/jxb/erac047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 02/03/2022] [Indexed: 06/14/2023]
Abstract
Interspecific hybridization drives the evolution of angiosperms and can be used to introduce novel alleles for important traits or to activate heterosis in crop breeding. Hybridization brings together gene expression networks from two different species, potentially causing global alterations of gene expression in the F1 plants which is called 'transcriptome shock'. Here, we explored such a transcriptome shock in allotriploid Brassica hybrids. We generated interspecific F1 allotriploid hybrids between the allotetraploid species Brassica napus and three accessions of the diploid species Brassica rapa. RNA-seq of the F1 hybrids and the parental plants revealed that 26.34-30.89% of genes were differentially expressed between the parents. We also analyzed expression level dominance and homoeolog expression bias between the parents and the F1 hybrids. The expression-level dominance biases of the Ar, An, and Cn subgenomes was genotype and stage dependent, whereas significant homoeolog expression bias was observed among three subgenomes from different parents. Furthermore, more genes were involved in trans regulation than in cis regulation in allotriploid F1 hybrids. Our findings provide new insights into the transcriptomic responses of cross-species hybrids and hybrids showing heterosis, as well as a new method for promoting the breeding of desirable traits in polyploid Brassica species.
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Affiliation(s)
- Chengtao Quan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Guoting Chen
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Sijia Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhibo Jia
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Pugang Yu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Cheng Dai
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Chaozhi Ma
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
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19
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Shoaib Y, Usman B, Kang H, Jung KH. Epitranscriptomics: An Additional Regulatory Layer in Plants' Development and Stress Response. PLANTS (BASEL, SWITZERLAND) 2022; 11:1033. [PMID: 35448761 PMCID: PMC9027318 DOI: 10.3390/plants11081033] [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: 03/13/2022] [Revised: 04/04/2022] [Accepted: 04/04/2022] [Indexed: 06/14/2023]
Abstract
Epitranscriptomics has added a new layer of regulatory machinery to eukaryotes, and the advancement of sequencing technology has revealed more than 170 post-transcriptional modifications in various types of RNAs, including messenger RNA (mRNA), transfer RNA (tRNA), ribosomal RNA (rRNA), and long non-coding RNA (lncRNA). Among these, N6-methyladenosine (m6A) and N5-methylcytidine (m5C) are the most prevalent internal mRNA modifications. These regulate various aspects of RNA metabolism, mainly mRNA degradation and translation. Recent advances have shown that regulation of RNA fate mediated by these epitranscriptomic marks has pervasive effects on a plant's development and responses to various biotic and abiotic stresses. Recently, it was demonstrated that the removal of human-FTO-mediated m6A from transcripts in transgenic rice and potatoes caused a dramatic increase in their yield, and that the m6A reader protein mediates stress responses in wheat and apple, indicating that regulation of m6A levels could be an efficient strategy for crop improvement. However, changing the overall m6A levels might have unpredictable effects; therefore, the identification of precise m6A levels at a single-base resolution is essential. In this review, we emphasize the roles of epitranscriptomic modifications in modulating molecular, physiological, and stress responses in plants, and provide an outlook on epitranscriptome engineering as a promising tool to ensure food security by editing specific m6A and m5C sites through robust genome-editing technology.
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Affiliation(s)
- Yasira Shoaib
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin-si 17104, Korea; (Y.S.); (B.U.)
| | - Babar Usman
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin-si 17104, Korea; (Y.S.); (B.U.)
| | - Hunseung Kang
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Korea;
| | - Ki-Hong Jung
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin-si 17104, Korea; (Y.S.); (B.U.)
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Liu W, Zhang Y, He H, He G, Deng XW. From hybrid genomes to heterotic trait output: Challenges and opportunities. CURRENT OPINION IN PLANT BIOLOGY 2022; 66:102193. [PMID: 35219140 DOI: 10.1016/j.pbi.2022.102193] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 12/19/2021] [Accepted: 01/23/2022] [Indexed: 06/14/2023]
Abstract
Heterosis (or hybrid vigor) has been widely used in crop seed breeding to improve many key economic traits. Nevertheless, the genetic and molecular basis of this important phenomenon has long remained elusive, constraining its flexible and effective exploitation. Advanced genomic approaches are efficient in characterizing the mechanism of heterosis. Here, we review how the omics approaches, including genomic, transcriptomic, and population genetics methods such as genome-wide association studies, can reveal how hybrid genomes outperform parental genomes in plants. This information opens up opportunities for genomic exploration and manipulation of heterosis in crop breeding.
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Affiliation(s)
- Wenwen Liu
- School of Advanced Agricultural 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
| | - Yilin Zhang
- School of Advanced Agricultural 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
| | - Hang He
- Peking University Institute of Advanced Agricultural Sciences, 699 Binhu Road, Xiashan Ecological and Economic Development Zone, Weifang, Shandong, 261325, China
| | - Guangming He
- School of Advanced Agricultural 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.
| | - Xing Wang Deng
- School of Advanced Agricultural 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; Peking University Institute of Advanced Agricultural Sciences, 699 Binhu Road, Xiashan Ecological and Economic Development Zone, Weifang, Shandong, 261325, China.
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21
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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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22
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Brodie ED, Gregory B, Lisch D, Riddle NC. The epigenome and beyond: How does non-genetic inheritance change our view of evolution? Integr Comp Biol 2021; 61:2199-2207. [PMID: 34028538 DOI: 10.1093/icb/icab084] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Evidence from across the tree of life suggests that epigenetic inheritance is more common than previously thought. If epigenetic inheritance is indeed as common as the data suggest, this finding has potentially important implications for evolutionary theory and our understanding of how evolution and adaptation progress. However, we currently lack an understanding of how common various epigenetic inheritance types are, and how they impact phenotypes. In this perspective, we review the open questions that need to be addressed to fully integrate epigenetic inheritance into evolutionary theory and to develop reliable predictive models for phenotypic evolution. We posit that addressing these challenges will require the collaboration of biologists from different disciplines and a focus on the exploration of data and phenomena without preconceived limits on potential mechanisms or outcomes.
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Affiliation(s)
- Edmund D Brodie
- Department of Biology, University of Virginia, Charlottesville, VA
| | - Brian Gregory
- Department of Biology, University of Pennsylvania, Philadelphia, PA
| | - Damon Lisch
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN
| | - Nicole C Riddle
- Department of Biology, The University of Alabama at Birmingham, Birmingham, AL
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23
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Xu Z, Shi X, Bao M, Song X, Zhang Y, Wang H, Xie H, Mao F, Wang S, Jin H, Dong S, Zhang F, Wu Z, Wu Y. Transcriptome-Wide Analysis of RNA m 6A Methylation and Gene Expression Changes Among Two Arabidopsis Ecotypes and Their Reciprocal Hybrids. FRONTIERS IN PLANT SCIENCE 2021; 12:685189. [PMID: 34178005 PMCID: PMC8222996 DOI: 10.3389/fpls.2021.685189] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 05/14/2021] [Indexed: 05/10/2023]
Abstract
The remodeling of transcriptome, epigenome, proteome, and metabolome in hybrids plays an important role in heterosis. N(6)-methyladenosine (m6A) methylation is the most abundant type of post-transcriptional modification for mRNAs, but the pattern of inheritance from parents to hybrids and potential impact on heterosis are largely unknown. We constructed transcriptome-wide mRNA m6A methylation maps of Arabidopsis thaliana Col-0 and Landsberg erecta (Ler) and their reciprocal F1 hybrids. Generally, the transcriptome-wide pattern of m6A methylation tends to be conserved between accessions. Approximately 74% of m6A methylation peaks are consistent between the parents and hybrids, indicating that a majority of the m6A methylation is maintained after hybridization. We found a significant association between differential expression and differential m6A modification, and between non-additive expression and non-additive methylation on the same gene. The overall RNA m6A level between Col-0 and Ler is clearly different but tended to disappear at the allelic sites in the hybrids. Interestingly, many enriched biological functions of genes with differential m6A modification between parents and hybrids are also conserved, including many heterosis-related genes involved in biosynthetic processes of starch. Collectively, our study revealed the overall pattern of inheritance of mRNA m6A modifications from parents to hybrids and a potential new layer of regulatory mechanisms related to heterosis formation.
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Affiliation(s)
- Zhihui Xu
- College of Life Science, Nanjing Agricultural University, Nanjing, China
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Key Laboratory for Information Agriculture, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China
| | - Xiaobo Shi
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Key Laboratory for Information Agriculture, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China
| | - Mengmei Bao
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Key Laboratory for Information Agriculture, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China
| | - Xiaoqian Song
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Key Laboratory for Information Agriculture, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China
| | - Yuxia Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Key Laboratory for Information Agriculture, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China
| | - Haiyan Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Key Laboratory for Information Agriculture, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China
| | - Hairong Xie
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Key Laboratory for Information Agriculture, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China
| | - Fei Mao
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Key Laboratory for Information Agriculture, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China
| | - Shuai Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Key Laboratory for Information Agriculture, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China
| | - Hongmei Jin
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Suomeng Dong
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Feng Zhang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Zhe Wu
- Department of Biology, SUSTech-PKU Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, China
| | - Yufeng Wu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Key Laboratory for Information Agriculture, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China
- *Correspondence: Yufeng Wu
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