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Zhao L, Chen J, Zhang Z, Wu W, Lin X, Gao M, Yang Y, Zhao P, Xu S, Yang C, Yao Y, Zhang A, Liu D, Wang D, Xiao J. Deciphering the Transcriptional Regulatory Network Governing Starch and Storage Protein Biosynthesis in Wheat for Breeding Improvement. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2401383. [PMID: 38943260 DOI: 10.1002/advs.202401383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 05/02/2024] [Indexed: 07/01/2024]
Abstract
Starch and seed storage protein (SSP) composition profoundly impact wheat grain yield and quality. To unveil regulatory mechanisms governing their biosynthesis, transcriptome, and epigenome profiling is conducted across key endosperm developmental stages, revealing that chromatin accessibility, H3K27ac, and H3K27me3 collectively regulate SSP and starch genes with varying impact. Population transcriptome and phenotype analyses highlight accessible promoter regions' crucial role as a genetic variation resource, influencing grain yield and quality in a core collection of wheat accessions. Integration of time-serial RNA-seq and ATAC-seq enables the construction of a hierarchical transcriptional regulatory network governing starch and SSP biosynthesis, identifying 42 high-confidence novel candidates. These candidates exhibit overlap with genetic regions associated with grain size and quality traits, and their functional significance is validated through expression-phenotype association analysis among wheat accessions and loss-of-function mutants. Functional analysis of wheat abscisic acid insensitive 3-A1 (TaABI3-A1) with genome editing knock-out lines demonstrates its role in promoting SSP accumulation while repressing starch biosynthesis through transcriptional regulation. Excellent TaABI3-A1Hap1 with enhanced grain weight is selected during the breeding process in China, linked to altered expression levels. This study unveils key regulators, advancing understanding of SSP and starch biosynthesis regulation and contributing to breeding enhancement.
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Affiliation(s)
- Long Zhao
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jinchao Chen
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhaoheng Zhang
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenying Wu
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuelei Lin
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Mingxiang Gao
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, Hebei, 071001, China
| | - Yiman Yang
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Peng Zhao
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Shengbao Xu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Changfeng Yang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), China Agricultural University, Beijing, 100193, China
| | - Yingyin Yao
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), China Agricultural University, Beijing, 100193, China
| | - Aimin Zhang
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, Hebei, 071001, China
| | - Dongcheng Liu
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, Hebei, 071001, China
| | - Dongzhi Wang
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jun Xiao
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- Centre of Excellence for Plant and Microbial Science (CEPAMS), JIC-CAS, Beijing, 100101, China
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Wu HYL, Jen J, Hsu PY. What, where, and how: Regulation of translation and the translational landscape in plants. THE PLANT CELL 2024; 36:1540-1564. [PMID: 37437121 PMCID: PMC11062462 DOI: 10.1093/plcell/koad197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/14/2023] [Accepted: 06/15/2023] [Indexed: 07/14/2023]
Abstract
Translation is a crucial step in gene expression and plays a vital role in regulating various aspects of plant development and environmental responses. It is a dynamic and complex program that involves interactions between mRNAs, transfer RNAs, and the ribosome machinery through both cis- and trans-regulation while integrating internal and external signals. Translational control can act in a global (transcriptome-wide) or mRNA-specific manner. Recent advances in genome-wide techniques, particularly ribosome profiling and proteomics, have led to numerous exciting discoveries in both global and mRNA-specific translation. In this review, we aim to provide a "primer" that introduces readers to this fascinating yet complex cellular process and provide a big picture of how essential components connect within the network. We begin with an overview of mRNA translation, followed by a discussion of the experimental approaches and recent findings in the field, focusing on unannotated translation events and translational control through cis-regulatory elements on mRNAs and trans-acting factors, as well as signaling networks through 3 conserved translational regulators TOR, SnRK1, and GCN2. Finally, we briefly touch on the spatial regulation of mRNAs in translational control. Here, we focus on cytosolic mRNAs; translation in organelles and viruses is not covered in this review.
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Affiliation(s)
- Hsin-Yen Larry Wu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Joey Jen
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Polly Yingshan Hsu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
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Zhao P, Yang S, Zheng Y, Zhang L, Li Y, Li J, Wang W, Wang Z. Polylactic acid microplastics have stronger positive effects on the qualitative traits of rice (Oryza sativa L.) than polyethylene microplastics: Evidence from a simulated field experiment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 917:170334. [PMID: 38301794 DOI: 10.1016/j.scitotenv.2024.170334] [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: 11/28/2023] [Revised: 01/17/2024] [Accepted: 01/19/2024] [Indexed: 02/03/2024]
Abstract
Soil pollution by microplastics (MPs) from different types of agricultural films has received substantial attention due to its potential effects on crop quality. To date, the effects of different types of MPs on rice grain quality and their underlying molecular mechanisms have not been clarified. In this study, we examined the effects of polyethylene MPs (PE-MPs) and biodegradable polylactic acid MPs (PLA-MPs) on rice grain quality at the environmental level (0.5 %) and evaluated the molecular mechanism through transcriptome analysis. PE- and PLA-MPs increased the number of rice grains per plant by 19.83 % and 24.66 %, respectively, and decreased the rice empty-shell rate by 55.89 % and 26.53 %, respectively. However, PLA-MPs increased the 1000-seed weight by 11.37 %, whereas PE-MPs had no obvious impact in this respect. Furthermore, MP exposure, especially that of PE-MPs, affected the content of mineral elements, fatty acids, and amino acids of rice grains by disturbing the expression of genes related to these functions and metabolism. Our findings provide insights into the response of rice grains to the stress caused by different MPs.
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Affiliation(s)
- Pengfei Zhao
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou 313000, PR China
| | - Siyu Yang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou 313000, PR China
| | - Yaoying Zheng
- Institute of Nuclear Agricultural Science, Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, Zhejiang University, Hangzhou 310058, PR China
| | - Liqin Zhang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou 313000, PR China
| | - Yongli Li
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou 313000, PR China
| | - Jiapeng Li
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou 313000, PR China
| | - Wei Wang
- Institute of Nuclear Agricultural Science, Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, Zhejiang University, Hangzhou 310058, PR China.
| | - Zhanqi Wang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou 313000, PR China.
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Chen Y, Wang W, Yang Z, Peng H, Ni Z, Sun Q, Guo W. Innovative computational tools provide new insights into the polyploid wheat genome. ABIOTECH 2024; 5:52-70. [PMID: 38576428 PMCID: PMC10987449 DOI: 10.1007/s42994-023-00131-7] [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: 09/13/2023] [Accepted: 12/14/2023] [Indexed: 04/06/2024]
Abstract
Bread wheat (Triticum aestivum) is an important crop and serves as a significant source of protein and calories for humans, worldwide. Nevertheless, its large and allopolyploid genome poses constraints on genetic improvement. The complex reticulate evolutionary history and the intricacy of genomic resources make the deciphering of the functional genome considerably more challenging. Recently, we have developed a comprehensive list of versatile computational tools with the integration of statistical models for dissecting the polyploid wheat genome. Here, we summarize the methodological innovations and applications of these tools and databases. A series of step-by-step examples illustrates how these tools can be utilized for dissecting wheat germplasm resources and unveiling functional genes associated with important agronomic traits. Furthermore, we outline future perspectives on new advanced tools and databases, taking into consideration the unique features of bread wheat, to accelerate genomic-assisted wheat breeding.
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Affiliation(s)
- Yongming Chen
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Wenxi Wang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Zhengzhao Yang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Huiru Peng
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Zhongfu Ni
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Qixin Sun
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Weilong Guo
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
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Wu HYL, Ai Q, Teixeira RT, Nguyen PHT, Song G, Montes C, Elmore JM, Walley JW, Hsu PY. Improved super-resolution ribosome profiling reveals prevalent translation of upstream ORFs and small ORFs in Arabidopsis. THE PLANT CELL 2024; 36:510-539. [PMID: 38000896 PMCID: PMC10896292 DOI: 10.1093/plcell/koad290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 10/13/2023] [Accepted: 10/17/2023] [Indexed: 11/26/2023]
Abstract
A crucial step in functional genomics is identifying actively translated ORFs and linking them to biological functions. The challenge lies in identifying short ORFs, as their identification is greatly influenced by data quality and depth. Here, we improved the coverage of super-resolution Ribo-seq in Arabidopsis (Arabidopsis thaliana), revealing uncharacterized translation events for nuclear, chloroplastic, and mitochondrial genes. Assisted by a transcriptome assembly, we identified 7,751 unconventional translation events, comprising 6,996 upstream ORFs (uORFs) and 209 downstream ORFs on annotated protein-coding genes, as well as 546 ORFs in presumed noncoding RNAs. Proteomic data confirmed the production of stable proteins from some of these unannotated translation events. We present evidence of active translation from primary transcripts of trans-acting small interfering RNAs (TAS1-4) and microRNAs (pri-MIR163 and pri-MIR169) and periodic ribosome stalling supporting cotranslational decay. Additionally, we developed a method for identifying extremely short uORFs, including 370 minimum uORFs (AUG-stop), and 2,921 tiny uORFs (2 to 10 amino acids) and 681 uORFs that overlap with each other. Remarkably, these short uORFs exhibit strong translational repression as do longer uORFs. We also systematically discovered 594 uORFs regulated by alternative splicing, suggesting widespread isoform-specific translational control. Finally, these prevalent uORFs are associated with numerous important pathways. In summary, our improved Arabidopsis translational landscape provides valuable resources to study gene expression regulation.
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Affiliation(s)
- Hsin-Yen Larry Wu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Qiaoyun Ai
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Rita Teresa Teixeira
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Phong H T Nguyen
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Gaoyuan Song
- Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, Ames, IA 50011, USA
| | - Christian Montes
- Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, Ames, IA 50011, USA
| | - J Mitch Elmore
- Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, Ames, IA 50011, USA
| | - Justin W Walley
- Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, Ames, IA 50011, USA
| | - Polly Yingshan Hsu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
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Chen Z, Wang F, Chen B, Wu G, Tian D, Yuan Q, Qiu S, Zhai Y, Chen J, Zheng H, Yan F. Turnip mosaic virus NIb weakens the function of eukaryotic translation initiation factor 6 facilitating viral infection in Nicotiana benthamiana. MOLECULAR PLANT PATHOLOGY 2024; 25:e13434. [PMID: 38388027 PMCID: PMC10883789 DOI: 10.1111/mpp.13434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 01/26/2024] [Accepted: 01/28/2024] [Indexed: 02/24/2024]
Abstract
Viruses rely completely on host translational machinery to produce the proteins encoded by their genes. Controlling translation initiation is important for gaining translational advantage in conflicts between the host and virus. The eukaryotic translation initiation factor 4E (eIF4E) has been reported to be hijacked by potyviruses for virus multiplication. The role of translation regulation in defence and anti-defence between plants and viruses is not well understood. We report that the transcript level of eIF6 was markedly increased in turnip mosaic virus (TuMV)-infected Nicotiana benthamiana. TuMV infection was impaired by overexpression of N. benthamiana eIF6 (NbeIF6) either transiently expressed in leaves or stably expressed in transgenic plants. Polysome profile assays showed that overexpression of NbeIF6 caused the accumulation of 40S and 60S ribosomal subunits, the reduction of polysomes, and also compromised TuMV UTR-mediated translation, indicating a defence role for upregulated NbeIF6 during TuMV infection. However, the polysome profile in TuMV-infected leaves was not identical to that in leaves overexpressing NbeIF6. Further analysis showed that TuMV NIb protein, the RNA-dependent RNA polymerase, interacted with NbeIF6 and interfered with its effect on the ribosomal subunits, suggesting that NIb might have a counterdefence role. The results propose a possible regulatory mechanism at the translation level during plant-virus interaction.
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Affiliation(s)
- Ziqiang Chen
- College of Life ScienceFujian Agriculture and Forestry UniversityFuzhouChina
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐productsInstitute of Plant Virology, Ningbo UniversityNingboChina
- Biotechnology Research InstituteFujian Academy of Agricultural SciencesFuzhouChina
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang ProvinceInstitute of Plant Virology, Ningbo UniversityNingboChina
| | - Feng Wang
- Biotechnology Research InstituteFujian Academy of Agricultural SciencesFuzhouChina
| | - Binghua Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐productsInstitute of Plant Virology, Ningbo UniversityNingboChina
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang ProvinceInstitute of Plant Virology, Ningbo UniversityNingboChina
| | - Guanwei Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐productsInstitute of Plant Virology, Ningbo UniversityNingboChina
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang ProvinceInstitute of Plant Virology, Ningbo UniversityNingboChina
| | - Dagang Tian
- Biotechnology Research InstituteFujian Academy of Agricultural SciencesFuzhouChina
| | - Quan Yuan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐productsInstitute of Plant Virology, Ningbo UniversityNingboChina
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang ProvinceInstitute of Plant Virology, Ningbo UniversityNingboChina
| | - Shiyou Qiu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐productsInstitute of Plant Virology, Ningbo UniversityNingboChina
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang ProvinceInstitute of Plant Virology, Ningbo UniversityNingboChina
| | - Yushan Zhai
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐productsInstitute of Plant Virology, Ningbo UniversityNingboChina
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang ProvinceInstitute of Plant Virology, Ningbo UniversityNingboChina
| | - Jianping Chen
- College of Life ScienceFujian Agriculture and Forestry UniversityFuzhouChina
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐productsInstitute of Plant Virology, Ningbo UniversityNingboChina
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang ProvinceInstitute of Plant Virology, Ningbo UniversityNingboChina
| | - Hongying Zheng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐productsInstitute of Plant Virology, Ningbo UniversityNingboChina
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang ProvinceInstitute of Plant Virology, Ningbo UniversityNingboChina
| | - Fei Yan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐productsInstitute of Plant Virology, Ningbo UniversityNingboChina
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang ProvinceInstitute of Plant Virology, Ningbo UniversityNingboChina
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An Y, Wang Z, Liu B, Cao Y, Chen L. Translational Landscape of Medicago truncatula Seedlings under Salt Stress. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:16657-16668. [PMID: 37880959 DOI: 10.1021/acs.jafc.3c03922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2023]
Abstract
The expression of plant genes under salt stress at the transcriptional level has been extensively studied. However, less attention has been paid to gene translation regulation under salt stress. In this study, Ribo-seq and RNA-seq analyses were conducted in Medicago truncatula seedlings grown under normal and salt stress conditions. The results showed that salt stress significantly altered the gene expression at the transcriptional and translational levels, with 2755 genes showing significant changes only at the translational level. Salt stress significantly inhibited the gene translation efficiency. Small ORFs (including uORFs in the 5'UTR, dORFs in 3'UTRs, and sORFs in lncRNAs) were identified throughout the genome of M. truncatula. The efficiency of gene translation was simultaneously regulated by the uORFs, dORFs, and miRNAs. In summary, our results provide valuable information about translatomic resources and new insights into plant responses to salt stress.
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Affiliation(s)
- Yixin An
- School of Grassland Science, Beijing Forestry University, Beijing 100083, China
| | - Ziqi Wang
- School of Grassland Science, Beijing Forestry University, Beijing 100083, China
| | - Baijian Liu
- School of Grassland Science, Beijing Forestry University, Beijing 100083, China
| | - Yuwei Cao
- School of Grassland Science, Beijing Forestry University, Beijing 100083, China
| | - Lin Chen
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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Wang Z, Miao L, Chen Y, Peng H, Ni Z, Sun Q, Guo W. Deciphering the evolution and complexity of wheat germplasm from a genomic perspective. J Genet Genomics 2023; 50:846-860. [PMID: 37611848 DOI: 10.1016/j.jgg.2023.08.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/29/2023] [Accepted: 08/09/2023] [Indexed: 08/25/2023]
Abstract
Bread wheat provides an essential fraction of the daily calorific intake for humanity. Due to its huge and complex genome, progress in studying on the wheat genome is substantially trailed behind those of the other two major crops, rice and maize, for at least a decade. With rapid advances in genome assembling and reduced cost of high-throughput sequencing, emerging de novo genome assemblies of wheat and whole-genome sequencing data are leading to a paradigm shift in wheat research. Here, we review recent progress in dissecting the complex genome and germplasm evolution of wheat since the release of the first high-quality wheat genome. New insights have been gained in the evolution of wheat germplasm during domestication and modern breeding progress, genomic variations at multiple scales contributing to the diversity of wheat germplasm, and complex transcriptional and epigenetic regulations of functional genes in polyploid wheat. Genomics databases and bioinformatics tools meeting the urgent needs of wheat genomics research are also summarized. The ever-increasing omics data, along with advanced tools and well-structured databases, are expected to accelerate deciphering the germplasm and gene resources in wheat for future breeding advances.
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Affiliation(s)
- Zihao Wang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Lingfeng Miao
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yongming Chen
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Huiru Peng
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zhongfu Ni
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Qixin Sun
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Weilong Guo
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China.
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