1
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Evans C, Mogg SL, Soraru C, Wallington E, Coates J, Borrill P. Wheat NAC transcription factor NAC5-1 is a positive regulator of senescence. PLANT DIRECT 2024; 8:e620. [PMID: 38962173 PMCID: PMC11217990 DOI: 10.1002/pld3.620] [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: 02/02/2024] [Revised: 06/04/2024] [Accepted: 06/10/2024] [Indexed: 07/05/2024]
Abstract
Wheat (Triticum aestivum L.) is an important source of both calories and protein in global diets, but there is a trade-off between grain yield and protein content. The timing of leaf senescence could mediate this trade-off as it is associated with both declines in photosynthesis and nitrogen remobilization from leaves to grain. NAC transcription factors play key roles in regulating senescence timing. In rice, OsNAC5 expression is correlated with increased protein content and upregulated in senescing leaves, but the role of the wheat ortholog in senescence had not been characterized. We verified that NAC5-1 is the ortholog of OsNAC5 and that it is expressed in senescing flag leaves in wheat. To characterize NAC5-1, we combined missense mutations in NAC5-A1 and NAC5-B1 from a TILLING mutant population and overexpressed NAC5-A1 in wheat. Mutation in NAC5-1 was associated with delayed onset of flag leaf senescence, while overexpression of NAC5-A1 was associated with slightly earlier onset of leaf senescence. DAP-seq was performed to locate transcription factor binding sites of NAC5-1. Analysis of DAP-seq and comparison with other studies identified putative downstream target genes of NAC5-1 which could be associated with senescence. This work showed that NAC5-1 is a positive transcriptional regulator of leaf senescence in wheat. Further research is needed to test the effect of NAC5-1 on yield and protein content in field trials, to assess the potential to exploit this senescence regulator to develop high-yielding wheat while maintaining grain protein content.
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Affiliation(s)
- Catherine Evans
- Department of Crop GeneticsJohn Innes CentreNorwichUK
- School of BiosciencesUniversity of BirminghamBirminghamUK
| | | | | | | | - Juliet Coates
- School of BiosciencesUniversity of BirminghamBirminghamUK
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2
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Yu G, Zhang B, Chen Q, Huang Z, Zhang B, Wang K, Han J. Dynamic DNA methylation modifications in the cold stress response of cassava. Genomics 2024; 116:110871. [PMID: 38806102 DOI: 10.1016/j.ygeno.2024.110871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Revised: 05/21/2024] [Accepted: 05/25/2024] [Indexed: 05/30/2024]
Abstract
Cassava, a crucial tropical crop, faces challenges from cold stress, necessitating an exploration of its molecular response. Here, we investigated the role of DNA methylation in moderating the response to moderate cold stress (10 °C) in cassava. Using whole-genome bisulfite sequencing, we examined DNA methylation patterns in leaf blades and petioles under control conditions, 5 h, and 48 h of cold stress. Tissue-specific responses were observed, with leaf blades exhibiting subtle changes, while petioles displayed a pronounced decrease in methylation levels under cold stress. We identified cold stress-induced differentially methylated regions (DMRs) that demonstrated both tissue and treatment specificity. Importantly, these DMRs were enriched in genes with altered expression, implying functional relevance. The cold-response transcription factor ERF105 associated with DMRs emerged as a significant and conserved regulator across tissues and treatments. Furthermore, we investigated DNA methylation dynamics in transposable elements, emphasizing the sensitivity of MITEs with bHLH binding motifs to cold stress. These findings provide insights into the epigenetic regulation of response to cold stress in cassava, contributing to an understanding of the molecular mechanisms underlying stress adaptation in this tropical plant.
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Affiliation(s)
- Guangrun Yu
- School of Life Sciences, Nantong University, Nantong 226019, China; Xinglin College, Nantong University, Qidong 226236, China
| | - Baowang Zhang
- Qingdao Smart Rural Development Service Center, Qingdao 266000, China
| | - Qi Chen
- School of Life Sciences, Nantong University, Nantong 226019, China; Xinglin College, Nantong University, Qidong 226236, China
| | - Zequan Huang
- Xinglin College, Nantong University, Qidong 226236, China
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
| | - Kai Wang
- School of Life Sciences, Nantong University, Nantong 226019, China.
| | - Jinlei Han
- School of Life Sciences, Nantong University, Nantong 226019, China.
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3
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Huo Q, Song R, Ma Z. Recent advances in exploring transcriptional regulatory landscape of crops. FRONTIERS IN PLANT SCIENCE 2024; 15:1421503. [PMID: 38903438 PMCID: PMC11188431 DOI: 10.3389/fpls.2024.1421503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 05/23/2024] [Indexed: 06/22/2024]
Abstract
Crop breeding entails developing and selecting plant varieties with improved agronomic traits. Modern molecular techniques, such as genome editing, enable more efficient manipulation of plant phenotype by altering the expression of particular regulatory or functional genes. Hence, it is essential to thoroughly comprehend the transcriptional regulatory mechanisms that underpin these traits. In the multi-omics era, a large amount of omics data has been generated for diverse crop species, including genomics, epigenomics, transcriptomics, proteomics, and single-cell omics. The abundant data resources and the emergence of advanced computational tools offer unprecedented opportunities for obtaining a holistic view and profound understanding of the regulatory processes linked to desirable traits. This review focuses on integrated network approaches that utilize multi-omics data to investigate gene expression regulation. Various types of regulatory networks and their inference methods are discussed, focusing on recent advancements in crop plants. The integration of multi-omics data has been proven to be crucial for the construction of high-confidence regulatory networks. With the refinement of these methodologies, they will significantly enhance crop breeding efforts and contribute to global food security.
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Affiliation(s)
| | | | - Zeyang Ma
- State Key Laboratory of Maize Bio-breeding, Frontiers Science Center for Molecular Design Breeding, Joint International Research Laboratory of Crop Molecular Breeding, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
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4
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Galli M, Chen Z, Ghandour T, Chaudhry A, Gregory J, Li M, Zhang X, Dong Y, Song G, Walley JW, Chuck G, Whipple C, Kaeppler HF, Huang SSC, Gallavotti A. Transcription factor binding site divergence across maize inbred lines drives transcriptional and phenotypic variation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.31.596834. [PMID: 38895211 PMCID: PMC11185568 DOI: 10.1101/2024.05.31.596834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Regulatory elements are important constituents of plant genomes that have shaped ancient and modern crops. Their identification, function, and diversity in crop genomes however are poorly characterized, thus limiting our ability to harness their power for further agricultural advances using induced or natural variation. Here, we use DNA affinity purification-sequencing (DAP-seq) to map transcription factor (TF) binding events for 200 maize TFs belonging to 30 distinct families and heterodimer pairs in two distinct inbred lines historically used for maize hybrid plant production, providing empirical binding site annotation for 5.3% of the maize genome. TF binding site comparison in B73 and Mo17 inbreds reveals widespread differences, driven largely by structural variation, that correlate with gene expression changes. TF binding site presence-absence variation helps clarify complex QTL such as vgt1, an important determinant of maize flowering time, and DICE, a distal enhancer involved in herbivore resistance. Modification of TF binding regions via CRISPR-Cas9 mediated editing alters target gene expression and phenotype. Our functional catalog of maize TF binding events enables collective and comparative TF binding analysis, and highlights its value for agricultural improvement.
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Affiliation(s)
- Mary Galli
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854-8020, USA
| | - Zongliang Chen
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854-8020, USA
| | - Tara Ghandour
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Amina Chaudhry
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854-8020, USA
| | - Jason Gregory
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854-8020, USA
| | - Miaomiao Li
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Xuan Zhang
- Department of Genetics, University of Georgia, Athens, GA, USA
| | - Yinxin Dong
- Department of Genetics, University of Georgia, Athens, GA, USA
| | - Gaoyuan Song
- Department of Plant Pathology, Entomology, and Microbiology, Iowa State University; Ames, IA, 50011
| | - Justin W. Walley
- Department of Plant Pathology, Entomology, and Microbiology, Iowa State University; Ames, IA, 50011
| | - George Chuck
- Plant Gene Expression Center, Albany, CA 94710, USA
| | - Clinton Whipple
- Department of Biology, Brigham Young University, 4102 LSB, Provo, UT 84602, USA
| | - Heidi F. Kaeppler
- Department of Agronomy, University of Wisconsin, Madison, WI, USA
- Wisconsin Crop Innovation Center, University of Wisconsin, Middleton, WI, USA
| | - Shao-shan Carol Huang
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Andrea Gallavotti
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854-8020, USA
- Department of Plant Biology, Rutgers University, New Brunswick, NJ, 08901, USA
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5
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Wang M, Cheng J, Wu J, Chen J, Liu D, Wang C, Ma S, Guo W, Li G, Di D, Zhang Y, Han D, Kronzucker HJ, Xia G, Shi W. Variation in TaSPL6-D confers salinity tolerance in bread wheat by activating TaHKT1;5-D while preserving yield-related traits. Nat Genet 2024; 56:1257-1269. [PMID: 38802564 DOI: 10.1038/s41588-024-01762-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 04/19/2024] [Indexed: 05/29/2024]
Abstract
Na+ exclusion from above-ground tissues via the Na+-selective transporter HKT1;5 is a major salt-tolerance mechanism in crops. Using the expression genome-wide association study and yeast-one-hybrid screening, we identified TaSPL6-D, a transcriptional suppressor of TaHKT1;5-D in bread wheat. SPL6 also targeted HKT1;5 in rice and Brachypodium. A 47-bp insertion in the first exon of TaSPL6-D resulted in a truncated peptide, TaSPL6-DIn, disrupting TaHKT1;5-D repression exhibited by TaSPL6-DDel. Overexpressing TaSPL6-DDel, but not TaSPL6-DIn, led to inhibited TaHKT1;5-D expression and increased salt sensitivity. Knockout of TaSPL6-DDel in two wheat genotypes enhanced salinity tolerance, which was attenuated by a further TaHKT1;5-D knockdown. Spike development was preserved in Taspl6-dd mutants but not in Taspl6-aabbdd mutants. TaSPL6-DIn was mainly present in landraces, and molecular-assisted introduction of TaSPL6-DIn from a landrace into a leading wheat cultivar successfully improved yield on saline soils. The SPL6-HKT1;5 module offers a target for the molecular breeding of salt-tolerant crops.
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Affiliation(s)
- Meng Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, P. R. China.
- University of Chinese Academy of Sciences, Beijing, P. R. China.
| | - Jie Cheng
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, P. R. China
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, College of Agronomy, Northwest A&F University, Yangling, P. R. China
| | - Jianhui Wu
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, College of Agronomy, Northwest A&F University, Yangling, P. R. China
| | - Jiefei Chen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, P. R. China
- University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Dan Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, P. R. China
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, College of Agronomy, Northwest A&F University, Yangling, P. R. China
| | - Chenyang Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, P. R. China
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, College of Agronomy, Northwest A&F University, Yangling, P. R. China
| | - Shengwei Ma
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, P. R. China
- Hainan Yazhou Bay Seed Laboratory, Sanya, P. R. China
| | - Weiwei Guo
- Shandong Engineering Research Center of Germplasm Innovation and Utilization of Salt-Tolerant Crops, College of Agronomy, Qingdao Agricultural University, Qingdao, P. R. China
| | - Guangjie Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, P. R. China
| | - Dongwei Di
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, P. R. China
| | - Yumei Zhang
- Shandong Engineering Research Center of Germplasm Innovation and Utilization of Salt-Tolerant Crops, College of Agronomy, Qingdao Agricultural University, Qingdao, P. R. China
| | - Dejun Han
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, College of Agronomy, Northwest A&F University, Yangling, P. R. China
| | - Herbert J Kronzucker
- School of BioSciences, Faculty of Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Guangmin Xia
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, P. R. China
| | - Weiming Shi
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, P. R. China
- University of Chinese Academy of Sciences, Beijing, P. R. China
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan, P. R. China
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6
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Long Y, Wendel JF, Zhang X, Wang M. Evolutionary insights into the organization of chromatin structure and landscape of transcriptional regulation in plants. TRENDS IN PLANT SCIENCE 2024; 29:638-649. [PMID: 38061928 DOI: 10.1016/j.tplants.2023.11.009] [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: 08/24/2023] [Revised: 11/06/2023] [Accepted: 11/09/2023] [Indexed: 06/09/2024]
Abstract
Development of complex traits necessitates the functioning and coordination of intricate regulatory networks involving multiple genes. Understanding 3D chromatin structure can facilitate insight into the regulation of gene expression by regulatory elements. This potential, of visualizing the role of chromatin organization in the evolution and function of regulatory elements, remains largely unexplored. Here, we describe new perspectives that arise from the dual considerations of sequence variation of regulatory elements and chromatin structure, with a special focus on whole-genome doubling or polyploidy. We underscore the significance of hierarchical chromatin organization in gene regulation during evolution. In addition, we describe strategies for exploring chromatin organization in future investigations of regulatory evolution in plants, enabling insights into the evolutionary influence of regulatory elements on gene expression and, hence, phenotypes.
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Affiliation(s)
- Yuexuan Long
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Maojun Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China.
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7
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Gupta S, Kesarwani V, Bhati U, Jyoti, Shankar R. PTFSpot: deep co-learning on transcription factors and their binding regions attains impeccable universality in plants. Brief Bioinform 2024; 25:bbae324. [PMID: 39013383 PMCID: PMC11250369 DOI: 10.1093/bib/bbae324] [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: 03/19/2024] [Revised: 06/07/2024] [Accepted: 06/19/2024] [Indexed: 07/18/2024] Open
Abstract
Unlike animals, variability in transcription factors (TFs) and their binding regions (TFBRs) across the plants species is a major problem that most of the existing TFBR finding software fail to tackle, rendering them hardly of any use. This limitation has resulted into underdevelopment of plant regulatory research and rampant use of Arabidopsis-like model species, generating misleading results. Here, we report a revolutionary transformers-based deep-learning approach, PTFSpot, which learns from TF structures and their binding regions' co-variability to bring a universal TF-DNA interaction model to detect TFBR with complete freedom from TF and species-specific models' limitations. During a series of extensive benchmarking studies over multiple experimentally validated data, it not only outperformed the existing software by >30% lead but also delivered consistently >90% accuracy even for those species and TF families that were never encountered during the model-building process. PTFSpot makes it possible now to accurately annotate TFBRs across any plant genome even in the total lack of any TF information, completely free from the bottlenecks of species and TF-specific models.
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Affiliation(s)
- Sagar Gupta
- Studio of Computational Biology & Bioinformatics, The Himalayan Centre for High-throughput Computational Biology, (HiCHiCoB, A BIC supported by DBT, India), Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Veerbhan Kesarwani
- Studio of Computational Biology & Bioinformatics, The Himalayan Centre for High-throughput Computational Biology, (HiCHiCoB, A BIC supported by DBT, India), Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Umesh Bhati
- Studio of Computational Biology & Bioinformatics, The Himalayan Centre for High-throughput Computational Biology, (HiCHiCoB, A BIC supported by DBT, India), Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Jyoti
- Studio of Computational Biology & Bioinformatics, The Himalayan Centre for High-throughput Computational Biology, (HiCHiCoB, A BIC supported by DBT, India), Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Ravi Shankar
- Studio of Computational Biology & Bioinformatics, The Himalayan Centre for High-throughput Computational Biology, (HiCHiCoB, A BIC supported by DBT, India), Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
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8
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Miao L, Xu W, Liu Y, Huang X, Chen Z, Wang H, Wang Z, Chen Y, Song Q, Zhang J, Han F, Peng H, Yao Y, Xin M, Hu Z, Ni Z, Sun Q, Xing J, Guo W. Reshaped DNA methylation cooperating with homoeolog-divergent expression promotes improved root traits in synthesized tetraploid wheat. THE NEW PHYTOLOGIST 2024; 242:507-523. [PMID: 38362849 DOI: 10.1111/nph.19593] [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: 11/01/2023] [Accepted: 01/27/2024] [Indexed: 02/17/2024]
Abstract
Polyploidization is a major event driving plant evolution and domestication. However, how reshaped epigenetic modifications coordinate gene transcription to generate phenotypic variations during wheat polyploidization is currently elusive. Here, we profiled transcriptomes and DNA methylomes of two diploid wheat accessions (SlSl and AA) and their synthetic allotetraploid wheat line (SlSlAA), which displayed elongated root hair and improved root capability for nitrate uptake and assimilation after tetraploidization. Globally decreased DNA methylation levels with a reduced difference between subgenomes were observed in the roots of SlSlAA. DNA methylation changes in first exon showed strong connections with altered transcription during tetraploidization. Homoeolog-specific transcription was associated with biased DNA methylation as shaped by homoeologous sequence variation. The hypomethylated promoters showed significantly enriched binding sites for MYB, which may affect gene transcription in response to root hair growth. Two master regulators in root hair elongation pathway, AlCPC and TuRSL4, exhibited upregulated transcription levels accompanied by hypomethylation in promoter, which may contribute to the elongated root hair. The upregulated nitrate transporter genes, including NPFs and NRTs, also are significantly associated with hypomethylation, indicating an epigenetic-incorporated regulation manner in improving nitrogen use efficiency. Collectively, these results provided new insights into epigenetic changes in response to crop polyploidization and underscored the importance of epigenetic regulation in improving crop traits.
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Affiliation(s)
- 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
| | - Weiya Xu
- 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
| | - Yanhong Liu
- 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
| | - Xiangyi Huang
- 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
| | - Zhe 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
| | - Huifang 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
- Shandong Provincial Key Laboratory of Dryland Farming Technology, Qingdao Agricultural University, Qingdao, 266000, China
| | - 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
| | - 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
| | - Qingxin Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jing Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Fangpu Han
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, 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
| | - Yingyin Yao
- 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
| | - Mingming Xin
- 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
| | - Zhaorong Hu
- 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
| | - Jiewen Xing
- 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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9
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Wen C, Yuan Z, Zhang X, Chen H, Luo L, Li W, Li T, Ma N, Mao F, Lin D, Lin Z, Lin C, Xu T, Lü P, Lin J, Zhu F. Sea-ATI unravels novel vocabularies of plant active cistrome. Nucleic Acids Res 2023; 51:11568-11583. [PMID: 37850650 PMCID: PMC10681729 DOI: 10.1093/nar/gkad853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 08/11/2023] [Accepted: 09/25/2023] [Indexed: 10/19/2023] Open
Abstract
The cistrome consists of all cis-acting regulatory elements recognized by transcription factors (TFs). However, only a portion of the cistrome is active for TF binding in a specific tissue. Resolving the active cistrome in plants remains challenging. In this study, we report the assay sequential extraction assisted-active TF identification (sea-ATI), a low-input method that profiles the DNA sequences recognized by TFs in a target tissue. We applied sea-ATI to seven plant tissues to survey their active cistrome and generated 41 motif models, including 15 new models that represent previously unidentified cis-regulatory vocabularies. ATAC-seq and RNA-seq analyses confirmed the functionality of the cis-elements from the new models, in that they are actively bound in vivo, located near the transcription start site, and influence chromatin accessibility and transcription. Furthermore, comparing dimeric WRKY CREs between sea-ATI and DAP-seq libraries revealed that thermodynamics and genetic drifts cooperatively shaped their evolution. Notably, sea-ATI can identify not only positive but also negative regulatory cis-elements, thereby providing unique insights into the functional non-coding genome of plants.
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Affiliation(s)
- Chenjin Wen
- College of Life Science, Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Zhen Yuan
- College of Life Science, Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Xiaotian Zhang
- College of Life Science, Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Hao Chen
- College of Life Science, Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Lin Luo
- College of Life Science, Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Wanying Li
- College of Life Science, Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Tian Li
- College of Life Science, Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Nana Ma
- College of Life Science, Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Fei Mao
- College of Life Science, Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Dongmei Lin
- College of Life Science, Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Zhanxi Lin
- College of Life Science, Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Chentao Lin
- College of Life Science, Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Tongda Xu
- College of Life Science, Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Peitao Lü
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Juncheng Lin
- College of Life Science, Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Fangjie Zhu
- College of Life Science, Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
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10
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Xie Y, Ying S, Li Z, Zhang Y, Zhu J, Zhang J, Wang M, Diao H, Wang H, Zhang Y, Ye L, Zhuang Y, Zhao F, Teng W, Zhang W, Tong Y, Cho J, Dong Z, Xue Y, Zhang Y. Transposable element-initiated enhancer-like elements generate the subgenome-biased spike specificity of polyploid wheat. Nat Commun 2023; 14:7465. [PMID: 37978184 PMCID: PMC10656477 DOI: 10.1038/s41467-023-42771-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 10/20/2023] [Indexed: 11/19/2023] Open
Abstract
Transposable elements (TEs) comprise ~85% of the common wheat genome, which are highly diverse among subgenomes, possibly contribute to polyploid plasticity, but the causality is only assumed. Here, by integrating data from gene expression cap analysis and epigenome profiling via hidden Markov model in common wheat, we detect a large proportion of enhancer-like elements (ELEs) derived from TEs producing nascent noncoding transcripts, namely ELE-RNAs, which are well indicative of the regulatory activity of ELEs. Quantifying ELE-RNA transcriptome across typical developmental stages reveals that TE-initiated ELE-RNAs are mainly from RLG_famc7.3 specifically expanded in subgenome A. Acquisition of spike-specific transcription factor binding likely confers spike-specific expression of RLG_famc7.3-initiated ELE-RNAs. Knockdown of RLG_famc7.3-initiated ELE-RNAs resulted in global downregulation of spike-specific genes and abnormal spike development. These findings link TE expansion to regulatory specificity and polyploid developmental plasticity, highlighting the functional impact of TE-driven regulatory innovation on polyploid evolution.
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Affiliation(s)
- Yilin Xie
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Songbei Ying
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Zijuan Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Yu'e Zhang
- University of the Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, and The Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jiafu Zhu
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Jinyu Zhang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Meiyue Wang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Huishan Diao
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Haoyu Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
- Henan University, School of Life Science, Kaifeng, Henan, 457000, China
| | - Yuyun Zhang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Luhuan Ye
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Yili Zhuang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Fei Zhao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Wan Teng
- University of the Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, and The Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wenli Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, CIC-MCP, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu, 210095, China
| | - Yiping Tong
- University of the Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, and The Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jungnam Cho
- Department of Biosciences, Durham University, Durham, DH1 3LE, United Kingdom.
| | - Zhicheng Dong
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China.
| | - Yongbiao Xue
- University of the Chinese Academy of Sciences, Beijing, 100049, China.
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, and The Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Centre for Bioinformation, Beijing, 100101, China.
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China.
| | - Yijing Zhang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China.
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11
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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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12
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Liu P, Liu R, Xu Y, Zhang C, Niu Q, Lang Z. DNA cytosine methylation dynamics and functional roles in horticultural crops. HORTICULTURE RESEARCH 2023; 10:uhad170. [PMID: 38025976 PMCID: PMC10660380 DOI: 10.1093/hr/uhad170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 08/20/2023] [Indexed: 12/01/2023]
Abstract
Methylation of cytosine is a conserved epigenetic modification that maintains the dynamic balance of methylation in plants under the regulation of methyltransferases and demethylases. In recent years, the study of DNA methylation in regulating the growth and development of plants and animals has become a key area of research. This review describes the regulatory mechanisms of DNA cytosine methylation in plants. It summarizes studies on epigenetic modifications of DNA methylation in fruit ripening, development, senescence, plant height, organ size, and under biotic and abiotic stresses in horticultural crops. The review provides a theoretical basis for understanding the mechanisms of DNA methylation and their relevance to breeding, genetic improvement, research, innovation, and exploitation of new cultivars of horticultural crops.
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Affiliation(s)
- Peipei Liu
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Ruie Liu
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yaping Xu
- Shanghai Center for Plant Stress Biology, National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Caixi Zhang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qingfeng Niu
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Zhaobo Lang
- Institute of Advanced Biotechnology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
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13
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Cui Y, Cao Q, Li Y, He M, Liu X. Advances in cis-element- and natural variation-mediated transcriptional regulation and applications in gene editing of major crops. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:5441-5457. [PMID: 37402253 DOI: 10.1093/jxb/erad248] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 06/28/2023] [Indexed: 07/06/2023]
Abstract
Transcriptional regulation is crucial to control of gene expression. Both spatio-temporal expression patterns and expression levels of genes are determined by the interaction between cis-acting elements and trans-acting factors. Numerous studies have focused on the trans-acting factors that mediate transcriptional regulatory networks. However, cis-acting elements, such as enhancers, silencers, transposons, and natural variations in the genome, are also vital for gene expression regulation and could be utilized by clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9)-mediated gene editing to improve crop quality and yield. In this review, we discuss current understanding of cis-element-mediated transcriptional regulation in major crops, including rice (Oryza sativa), wheat (Triticum aestivum), and maize (Zea mays), as well as the latest advancements in gene editing techniques and their applications in crops to highlight prospective strategies for crop breeding.
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Affiliation(s)
- Yue Cui
- College of Teacher Education, Molecular and Cellular Postdoctoral Research Station, Hebei Normal University, Shijiazhuang 050024, China
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling, Hebei Research Center of the Basic Discipline Cell Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Qiao Cao
- Shijiazhuang Academy of Agricultural and Forestry Sciences, Shijiazhuang, Hebei Province 050041, China
| | - Yongpeng Li
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling, Hebei Research Center of the Basic Discipline Cell Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Mingqi He
- Shijiazhuang Academy of Agricultural and Forestry Sciences, Shijiazhuang, Hebei Province 050041, China
| | - Xigang Liu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling, Hebei Research Center of the Basic Discipline Cell Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
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14
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Zhang J, Xiong H, Burguener GF, Vasquez-Gross H, Liu Q, Debernardi JM, Akhunova A, Garland-Campbell K, Kianian SF, Brown-Guedira G, Pozniak C, Faris JD, Akhunov E, Dubcovsky J. Sequencing 4.3 million mutations in wheat promoters to understand and modify gene expression. Proc Natl Acad Sci U S A 2023; 120:e2306494120. [PMID: 37703281 PMCID: PMC10515147 DOI: 10.1073/pnas.2306494120] [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: 04/24/2023] [Accepted: 08/03/2023] [Indexed: 09/15/2023] Open
Abstract
Wheat is an important contributor to global food security, and further improvements are required to feed a growing human population. Functional genetics and genomics tools can help us to understand the function of different genes and to engineer beneficial changes. In this study, we used a promoter capture assay to sequence 2-kb regions upstream of all high-confidence annotated genes from 1,513 mutagenized plants from the tetraploid wheat variety Kronos. We identified 4.3 million induced mutations with an accuracy of 99.8%, resulting in a mutation density of 41.9 mutations per kb. We also remapped Kronos exome capture reads to Chinese Spring RefSeq v1.1, identified 4.7 million mutations, and predicted their effects on annotated genes. Using these predictions, we identified 59% more nonsynonymous substitutions and 49% more truncation mutations than in the original study. To show the biological value of the promoter dataset, we selected two mutations within the promoter of the VRN-A1 vernalization gene. Both mutations, located within transcription factor binding sites, significantly altered VRN-A1 expression, and one reduced the number of spikelets per spike. These publicly available sequenced mutant datasets provide rapid and inexpensive access to induced variation in the promoters and coding regions of most wheat genes. These mutations can be used to understand and modulate gene expression and phenotypes for both basic and commercial applications, where limited governmental regulations can facilitate deployment. These mutant collections, together with gene editing, provide valuable tools to accelerate functional genetic studies in this economically important crop.
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Affiliation(s)
- Junli Zhang
- Department of Plant Sciences, University of California, Davis, CA95616
| | - Hongchun Xiong
- Department of Plant Sciences, University of California, Davis, CA95616
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing100081, China
| | - Germán F. Burguener
- Department of Plant Sciences, University of California, Davis, CA95616
- HHMI, Chevy Chase, MD20815
| | - Hans Vasquez-Gross
- Department of Plant Sciences, University of California, Davis, CA95616
- Nevada Bioinformatics Center, University of Nevada, Reno, NV89557
| | - Qiujie Liu
- Department of Plant Sciences, University of California, Davis, CA95616
- HHMI, Chevy Chase, MD20815
| | - Juan M. Debernardi
- Department of Plant Sciences, University of California, Davis, CA95616
- HHMI, Chevy Chase, MD20815
| | - Alina Akhunova
- Department of Plant Pathology, Kansas State University, Manhattan, KS66506
| | - Kimberly Garland-Campbell
- United States Department of Agriculture - Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit, Pullman, WA99164
| | - Shahryar F. Kianian
- United States Department of Agriculture - Agricultural Research Service, Cereal Disease Laboratory, Saint Paul, MN55108-6086
| | - Gina Brown-Guedira
- United States Department of Agriculture - Agricultural Research Service, Plant Science Research Unit, Raleigh, NC27695
| | - Curtis Pozniak
- Crop Development Centre, University of Saskatchewan, SaskatoonS7N 5A8, Canada
| | - Justin D. Faris
- United States Department of Agriculture - Agricultural Research Service, Cereal Crops Research Unit, Northern Crop Science Laboratory, Fargo, ND58102
| | - Eduard Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS66506
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, CA95616
- HHMI, Chevy Chase, MD20815
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15
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Zhao P, Peng C, Fang L, Wang Z, Liu GE. Taming transposable elements in livestock and poultry: a review of their roles and applications. Genet Sel Evol 2023; 55:50. [PMID: 37479995 PMCID: PMC10362595 DOI: 10.1186/s12711-023-00821-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 06/30/2023] [Indexed: 07/23/2023] Open
Abstract
Livestock and poultry play a significant role in human nutrition by converting agricultural by-products into high-quality proteins. To meet the growing demand for safe animal protein, genetic improvement of livestock must be done sustainably while minimizing negative environmental impacts. Transposable elements (TE) are important components of livestock and poultry genomes, contributing to their genetic diversity, chromatin states, gene regulatory networks, and complex traits of economic value. However, compared to other species, research on TE in livestock and poultry is still in its early stages. In this review, we analyze 72 studies published in the past 20 years, summarize the TE composition in livestock and poultry genomes, and focus on their potential roles in functional genomics. We also discuss bioinformatic tools and strategies for integrating multi-omics data with TE, and explore future directions, feasibility, and challenges of TE research in livestock and poultry. In addition, we suggest strategies to apply TE in basic biological research and animal breeding. Our goal is to provide a new perspective on the importance of TE in livestock and poultry genomes.
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Affiliation(s)
- Pengju Zhao
- Hainan Institute of Zhejiang University, Hainan Sanya, 572000, China
- College of Animal Sciences, Zhejiang University, Zhejiang, Hangzhou, People's Republic of China
| | - Chen Peng
- Hainan Institute of Zhejiang University, Hainan Sanya, 572000, China
- College of Animal Sciences, Zhejiang University, Zhejiang, Hangzhou, People's Republic of China
| | - Lingzhao Fang
- Center for Quantitative Genetics and Genomics, Aarhus University, 8000, Aarhus, Denmark.
| | - Zhengguang Wang
- Hainan Institute of Zhejiang University, Hainan Sanya, 572000, China.
- College of Animal Sciences, Zhejiang University, Zhejiang, Hangzhou, People's Republic of China.
| | - George E Liu
- Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA.
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16
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Ma J, Wang R, Zhao H, Li L, Zeng F, Wang Y, Chen M, Chang J, He G, Yang G, Li Y. Genome-wide characterization of the VQ genes in Triticeae and their functionalization driven by polyploidization and gene duplication events in wheat. Int J Biol Macromol 2023:125264. [PMID: 37302635 DOI: 10.1016/j.ijbiomac.2023.125264] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 06/03/2023] [Accepted: 06/06/2023] [Indexed: 06/13/2023]
Abstract
Valine-glutamine motif-containing (VQ) proteins are transcriptional cofactors widely involved in plant growth, development, and response to various stresses. Although the VQ family has been genome-wide identified in some species, but the knowledge regarding duplication-driven functionalization of VQ genes among evolutionarily related species is still lacking. Here, 952 VQ genes have been identified from 16 species, emphasizing seven Triticeae species including the bread wheat. Comprehensive phylogenetic and syntenic analyses allow us to establish the orthologous relationship of VQ genes from rice (Oryza sativa) to bread wheat (Triticum aestivum). The evolutionary analysis revealed that whole-genome duplication (WGD) drives the expansion of OsVQs, while TaVQs expansion is associated with a recent burst of gene duplication (RBGD). We also analyzed the motif composition and molecular properties of TaVQ proteins, enriched biological functions, and expression patterns of TaVQs. We demonstrate that WGD-derived TaVQs have become divergent in both protein motif composition and expression pattern, while RBGD-derived TaVQs tend to adopt specific expression patterns, suggesting their functionalization in certain biological processes or in response to specific stresses. Furthermore, some RBGD-derived TaVQs are found to be associated with salt tolerance. Several of the identified salt-related TaVQ proteins were located in the cytoplasm and nucleus and their salt-responsive expression patterns were validated by qPCR analysis. Yeast-based functional experiments confirmed that TaVQ27 may be a new regulator to salt response and regulation. Overall, this study lays the foundation for further functional validation of VQ family members within the Triticeae species.
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Affiliation(s)
- Jingfei Ma
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China
| | - Ruibin Wang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China
| | - Hongyan Zhao
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China
| | - Li Li
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China
| | - Fang Zeng
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China
| | - Yuesheng Wang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China
| | - Mingjie Chen
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China
| | - Junli Chang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China
| | - Guangyuan He
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China.
| | - Guangxiao Yang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China.
| | - Yin Li
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China.
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17
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Kong C, Zhao G, Gao L, Kong X, Wang D, Liu X, Jia J. Epigenetic Landscape Is Largely Shaped by Diversiform Transposons in Aegilops tauschii. Int J Mol Sci 2023; 24:ijms24119349. [PMID: 37298301 DOI: 10.3390/ijms24119349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/21/2023] [Accepted: 05/23/2023] [Indexed: 06/12/2023] Open
Abstract
Transposons (TEs) account for more than 80% of the wheat genome, the highest among all known crop species. They play an important role in shaping the elaborate genomic landscape, which is the key to the speciation of wheat. In this study, we analyzed the association between TEs, chromatin states, and chromatin accessibility in Aegilops tauschii, the D genome donor of bread wheat. We found that TEs contributed to the complex but orderly epigenetic landscape as chromatin states showed diverse distributions on TEs of different orders or superfamilies. TEs also contributed to the chromatin state and openness of potential regulatory elements, affecting the expression of TE-related genes. Some TE superfamilies, such as hAT-Ac, carry active/open chromatin regions. In addition, the histone mark H3K9ac was found to be associated with the accessibility shaped by TEs. These results suggest the role of diversiform TEs in shaping the epigenetic landscape and in gene expression regulation in Aegilops tauschii. This has positive implications for understanding the transposon roles in Aegilops tauschii or the wheat D genome.
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Affiliation(s)
- Chuizheng Kong
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Guangyao Zhao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Lifeng Gao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiuying Kong
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Daowen Wang
- State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Xu Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jizeng Jia
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
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18
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Guo Z, Guo L, Bai Y, Kang S, Sun D, Qin J, Ye F, Wang S, Wu Q, Xie W, Yang X, Crickmore N, Zhou X, Zhang Y. Retrotransposon-mediated evolutionary rewiring of a pathogen response orchestrates a resistance phenotype in an insect host. Proc Natl Acad Sci U S A 2023; 120:e2300439120. [PMID: 36996102 PMCID: PMC10083559 DOI: 10.1073/pnas.2300439120] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 02/23/2023] [Indexed: 03/31/2023] Open
Abstract
Ongoing host-pathogen interactions can trigger a coevolutionary arms race, while genetic diversity within the host can facilitate its adaptation to pathogens. Here, we used the diamondback moth (Plutella xylostella) and its pathogen Bacillus thuringiensis (Bt) as a model for exploring an adaptive evolutionary mechanism. We found that insect host adaptation to the primary Bt virulence factors was tightly associated with a short interspersed nuclear element (SINE - named SE2) insertion into the promoter of the transcriptionally activated MAP4K4 gene. This retrotransposon insertion coopts and potentiates the effect of the transcription factor forkhead box O (FOXO) in inducing a hormone-modulated Mitogen-activated protein kinase (MAPK) signaling cascade, leading to an enhancement of a host defense mechanism against the pathogen. This work demonstrates that reconstructing a cis-trans interaction can escalate a host response mechanism into a more stringent resistance phenotype to resist pathogen infection, providing a new insight into the coevolutionary mechanism of host organisms and their microbial pathogens.
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Affiliation(s)
- Zhaojiang Guo
- State Key Laboratory of Vegetable Biobreeding, Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing100081, China
| | - Le Guo
- State Key Laboratory of Vegetable Biobreeding, Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing100081, China
| | - Yang Bai
- State Key Laboratory of Vegetable Biobreeding, Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing100081, China
| | - Shi Kang
- State Key Laboratory of Vegetable Biobreeding, Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing100081, China
| | - Dan Sun
- State Key Laboratory of Vegetable Biobreeding, Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing100081, China
| | - Jianying Qin
- State Key Laboratory of Vegetable Biobreeding, Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing100081, China
| | - Fan Ye
- State Key Laboratory of Vegetable Biobreeding, Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing100081, China
| | - Shaoli Wang
- State Key Laboratory of Vegetable Biobreeding, Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing100081, China
| | - Qingjun Wu
- State Key Laboratory of Vegetable Biobreeding, Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing100081, China
| | - Wen Xie
- State Key Laboratory of Vegetable Biobreeding, Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing100081, China
| | - Xin Yang
- State Key Laboratory of Vegetable Biobreeding, Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing100081, China
| | - Neil Crickmore
- School of Life Sciences, University of Sussex, BrightonBN1 9QG, UK
| | - Xuguo Zhou
- Department of Entomology, University of Kentucky, Lexington, KY40546-0091
| | - Youjun Zhang
- State Key Laboratory of Vegetable Biobreeding, Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing100081, China
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19
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Chen Y, Guo Y, Guan P, Wang Y, Wang X, Wang Z, Qin Z, Ma S, Xin M, Hu Z, Yao Y, Ni Z, Sun Q, Guo W, Peng H. A wheat integrative regulatory network from large-scale complementary functional datasets enables trait-associated gene discovery for crop improvement. MOLECULAR PLANT 2023; 16:393-414. [PMID: 36575796 DOI: 10.1016/j.molp.2022.12.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 11/28/2022] [Accepted: 12/18/2022] [Indexed: 06/17/2023]
Abstract
Gene regulation is central to all aspects of organism growth, and understanding it using large-scale functional datasets can provide a whole view of biological processes controlling complex phenotypic traits in crops. However, the connection between massive functional datasets and trait-associated gene discovery for crop improvement is still lacking. In this study, we constructed a wheat integrative gene regulatory network (wGRN) by combining an updated genome annotation and diverse complementary functional datasets, including gene expression, sequence motif, transcription factor (TF) binding, chromatin accessibility, and evolutionarily conserved regulation. wGRN contains 7.2 million genome-wide interactions covering 5947 TFs and 127 439 target genes, which were further verified using known regulatory relationships, condition-specific expression, gene functional information, and experiments. We used wGRN to assign genome-wide genes to 3891 specific biological pathways and accurately prioritize candidate genes associated with complex phenotypic traits in genome-wide association studies. In addition, wGRN was used to enhance the interpretation of a spike temporal transcriptome dataset to construct high-resolution networks. We further unveiled novel regulators that enhance the power of spike phenotypic trait prediction using machine learning and contribute to the spike phenotypic differences among modern wheat accessions. Finally, we developed an interactive webserver, wGRN (http://wheat.cau.edu.cn/wGRN), for the community to explore gene regulation and discover trait-associated genes. Collectively, this community resource establishes the foundation for using large-scale functional datasets to guide trait-associated gene discovery for crop improvement.
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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
| | - Yiwen 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
| | - Panfeng Guan
- 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
| | - Yongfa 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
| | - Xiaobo 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
| | - 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
| | - Zhen Qin
- 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
| | - Shengwei Ma
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, China; State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Mingming Xin
- 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
| | - Zhaorong Hu
- 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
| | - Yingyin Yao
- 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.
| | - 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.
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20
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Bariah I, Gribun L, Kashkush K. Transposable elements are associated with genome-specific gene expression in bread wheat. FRONTIERS IN PLANT SCIENCE 2023; 13:1072232. [PMID: 36714723 PMCID: PMC9878150 DOI: 10.3389/fpls.2022.1072232] [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: 10/17/2022] [Accepted: 12/20/2022] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Recent studies in wheat emphasized the importance of TEs, which occupy ~85% of the wheat genome, as a major source of intraspecific genetic variation due to their recent activity and involvement in genomic rearrangements. The contribution of TEs to structural and functional variations in bread wheat genes is not fully understood. METHODS Here, publicly available RNA-Seq databases of bread wheat were integrated to identify TE insertions within gene bodies (exons\ introns) and assess the impact of TE insertions on gene expression variations of homoeologs gene groups. Overall, 70,818 homoeologs genes were analyzed: 55,170 genes appeared in each one of the three subgenomes (termed ABD), named triads; 12,640 genes appeared in two of the three subgenomes (in A and B only, termed AB; or in A and D only, termed AD; or in B and D only, termed BD);, named dyads; and 3,008 genes underwent duplication in one of the three subgenomes (two copies in: subgenome A, termed AABD; subgenome B, termed ABBD; or subgenome D, termed ABDD), named tetrads. RESULTS To this end, we found that ~36% of the 70,818 genes contained at least one TE insertion within the gene body, mostly in triads. Analysis of 14,258 triads revealed that the presence of TE insertion in at least one of the triad genes (7,439 triads) was associated with balanced expression (similar expression levels) between the homoeolog genes. TE insertions within the exon or in the untranslated regions (UTRs) of one or more of the homoeologs in a triad were significantly associated with homoeolog expression bias. Furthermore, we found a statistically significant correlation between the presence\absence of TEs insertions belonging to six TE superfamilies and 17 TE subfamilies and the suppression of a single homoeolog gene. A significant association was observed between the presence of TE insertions from specific superfamilies and the expression of genes that are associated with biotic and abiotic stress responses. CONCLUSION Our data strongly indicate that TEs might play a prominent role in controlling gene expression in a genome-specific manner in bread wheat.
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21
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Vandepoele K, Kaufmann K. Characterization of Gene Regulatory Networks in Plants Using New Methods and Data Types. Methods Mol Biol 2023; 2698:1-11. [PMID: 37682465 DOI: 10.1007/978-1-0716-3354-0_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
A major question in plant biology is to understand how plant growth, development, and environmental responses are controlled and coordinated by the activities of regulatory factors. Gene regulatory network (GRN) analyses require integrated approaches that combine experimental approaches with computational analyses. A wide range of experimental approaches and tools are now available, such as targeted perturbation of gene activities, quantitative and cell-type specific measurements of dynamic gene activities, and systematic analysis of the molecular 'hard-wiring' of the systems. At the computational level, different tools and databases are available to study regulatory sequences, including intuitive visualizations to explore data-driven gene regulatory networks in different plant species. Furthermore, advanced data integration approaches have recently been developed to efficiently leverage complementary regulatory data types and learn context-specific networks.
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Affiliation(s)
- Klaas Vandepoele
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium.
- VIB-UGent Center for Plant Systems Biology, Ghent, Belgium.
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium.
| | - Kerstin Kaufmann
- Institute of Biology, Humboldt-Universitaet zu Berlin, Berlin, Germany
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22
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Wang M, Li J, Qi Z, Long Y, Pei L, Huang X, Grover CE, Du X, Xia C, Wang P, Liu Z, You J, Tian X, Ma Y, Wang R, Chen X, He X, Fang DD, Sun Y, Tu L, Jin S, Zhu L, Wendel JF, Zhang X. Genomic innovation and regulatory rewiring during evolution of the cotton genus Gossypium. Nat Genet 2022; 54:1959-1971. [PMID: 36474047 DOI: 10.1038/s41588-022-01237-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 10/20/2022] [Indexed: 12/13/2022]
Abstract
Phenotypic diversity and evolutionary innovation ultimately trace to variation in genomic sequence and rewiring of regulatory networks. Here, we constructed a pan-genome of the Gossypium genus using ten representative diploid genomes. We document the genomic evolutionary history and the impact of lineage-specific transposon amplification on differential genome composition. The pan-3D genome reveals evolutionary connections between transposon-driven genome size variation and both higher-order chromatin structure reorganization and the rewiring of chromatin interactome. We linked changes in chromatin structures to phenotypic differences in cotton fiber and identified regulatory variations that decode the genetic basis of fiber length, the latter enabled by sequencing 1,005 transcriptomes during fiber development. We showcase how pan-genomic, pan-3D genomic and genetic regulatory data serve as a resource for delineating the evolutionary basis of spinnable cotton fiber. Our work provides insights into the evolution of genome organization and regulation and will inform cotton improvement by enabling regulome-based approaches.
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Affiliation(s)
- Maojun Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Jianying Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Zhengyang Qi
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yuexuan Long
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Liuling Pei
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xianhui Huang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Corrinne E Grover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Xiongming Du
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Chunjiao Xia
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Pengcheng Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Zhenping Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Jiaqi You
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xuehan Tian
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yizan Ma
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Ruipeng Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xinyuan Chen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xin He
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - David D Fang
- Cotton Fiber Bioscience Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, LA, USA
| | - Yuqiang Sun
- Zhejiang Sci-Tech University College of Life Sciences, Zhejiang, Hangzhou, China
| | - Lili Tu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Shuangxia Jin
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Longfu Zhu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA.
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China.
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23
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Pei H, Teng W, Gao L, Gao H, Ren X, Liu Y, Jia J, Tong Y, Wang Y, Lu Z. Low-affinity SPL binding sites contribute to subgenome expression divergence in allohexaploid wheat. SCIENCE CHINA LIFE SCIENCES 2022; 66:819-834. [PMID: 36417050 DOI: 10.1007/s11427-022-2202-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 09/22/2022] [Indexed: 11/24/2022]
Abstract
Expression divergence caused by genetic variation and crosstalks among subgenomes of the allohexaploid bread wheat (Triticum aestivum. L., BBAADD) is hypothesized to increase its adaptability and/or plasticity. However, the molecular basis of expression divergence remains unclear. Squamosa promoter-binding protein-like (SPL) transcription factors are critical for a wide array of biological processes. In this study, we constructed expression regulatory networks by combining DAP-seq for 40 SPLs, ATAC-seq, and RNA-seq. Our findings indicate that a group of low-affinity SPL binding regions (SBRs) were targeted by diverse SPLs and caused different sequence preferences around the core GTAC motif. The SBRs including the low-affinity ones are evolutionarily conserved, enriched GWAS signals related to important agricultural traits. However, those SBRs are highly diversified among the cis-regulatory regions (CREs) of syntenic genes, with less than 8% SBRs coexisting in triad genes, suggesting that CRE variations are critical for subgenome differentiations. Knocking out of TaSPL7A/B/D and TaSPL15A/B/D subfamily further proved that both high- and low-affinity SBRs played critical roles in the differential expression of genes regulating tiller number and spike sizes. Our results have provided baseline data for downstream networks of SPLs and wheat improvements and revealed that CRE variations are critical sources for subgenome divergence in the allohexaploid wheat.
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24
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Zhang Y, Li Z, Liu J, Zhang Y, Ye L, Peng Y, Wang H, Diao H, Ma Y, Wang M, Xie Y, Tang T, Zhuang Y, Teng W, Tong Y, Zhang W, Lang Z, Xue Y, Zhang Y. Transposable elements orchestrate subgenome-convergent and -divergent transcription in common wheat. Nat Commun 2022; 13:6940. [PMID: 36376315 PMCID: PMC9663577 DOI: 10.1038/s41467-022-34290-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 10/15/2022] [Indexed: 11/16/2022] Open
Abstract
The success of common wheat as a global staple crop was largely attributed to its genomic diversity and redundancy due to the merge of different genomes, giving rise to the major question how subgenome-divergent and -convergent transcription is mediated and harmonized in a single cell. Here, we create a catalog of genome-wide transcription factor-binding sites (TFBSs) to assemble a common wheat regulatory network on an unprecedented scale. A significant proportion of subgenome-divergent TFBSs are derived from differential expansions of particular transposable elements (TEs) in diploid progenitors, which contribute to subgenome-divergent transcription. Whereas subgenome-convergent transcription is associated with balanced TF binding at loci derived from TE expansions before diploid divergence. These TFBSs have retained in parallel during evolution of each diploid, despite extensive unbalanced turnover of the flanking TEs. Thus, the differential evolutionary selection of paleo- and neo-TEs contribute to subgenome-convergent and -divergent regulation in common wheat, highlighting the influence of TE repertory plasticity on transcriptional plasticity in polyploid.
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Affiliation(s)
- Yuyun Zhang
- grid.9227.e0000000119573309National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032 China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, Beijing, 100049 China ,grid.8547.e0000 0001 0125 2443State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438 China
| | - Zijuan Li
- grid.9227.e0000000119573309National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032 China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, Beijing, 100049 China ,grid.8547.e0000 0001 0125 2443State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438 China
| | - Jinyi Liu
- grid.9227.e0000000119573309National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032 China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, Beijing, 100049 China
| | - Yu’e Zhang
- grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, Beijing, 100049 China ,grid.9227.e0000000119573309The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101 China
| | - Luhuan Ye
- grid.9227.e0000000119573309National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032 China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, Beijing, 100049 China
| | - Yuan Peng
- grid.9227.e0000000119573309National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032 China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, Beijing, 100049 China ,grid.9227.e0000000119573309Shanghai Center for Plant Stress Biology, National Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
| | - Haoyu Wang
- grid.9227.e0000000119573309National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032 China ,grid.256922.80000 0000 9139 560XHenan University, School of Life Science, Kaifeng, Henan 457000 China
| | - Huishan Diao
- grid.8547.e0000 0001 0125 2443State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438 China
| | - Yu Ma
- grid.9227.e0000000119573309National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032 China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, Beijing, 100049 China ,grid.9227.e0000000119573309Shanghai Center for Plant Stress Biology, National Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
| | - Meiyue Wang
- grid.8547.e0000 0001 0125 2443State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438 China
| | - Yilin Xie
- grid.9227.e0000000119573309National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032 China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, Beijing, 100049 China
| | - Tengfei Tang
- grid.9227.e0000000119573309National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032 China ,grid.256922.80000 0000 9139 560XHenan University, School of Life Science, Kaifeng, Henan 457000 China
| | - Yili Zhuang
- grid.9227.e0000000119573309National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032 China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, Beijing, 100049 China
| | - Wan Teng
- grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, Beijing, 100049 China ,grid.9227.e0000000119573309The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101 China
| | - Yiping Tong
- grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, Beijing, 100049 China ,grid.9227.e0000000119573309The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101 China
| | - Wenli Zhang
- grid.27871.3b0000 0000 9750 7019State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095 China
| | - Zhaobo Lang
- grid.9227.e0000000119573309National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032 China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, Beijing, 100049 China ,grid.9227.e0000000119573309Shanghai Center for Plant Stress Biology, National Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032 China ,grid.263817.90000 0004 1773 1790Institute of Advanced Biotechnology and School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055 China
| | - Yongbiao Xue
- grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, Beijing, 100049 China ,grid.9227.e0000000119573309The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101 China ,grid.9227.e0000000119573309Beijing Institute of Genomics, Chinese Academy of Sciences, and National Centre for Bioinformation, Beijing, 100101 China ,grid.268415.cJiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009 China
| | - Yijing Zhang
- grid.8547.e0000 0001 0125 2443State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438 China
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Klein SP, Anderson SN. The evolution and function of transposons in epigenetic regulation in response to the environment. CURRENT OPINION IN PLANT BIOLOGY 2022; 69:102277. [PMID: 35961279 DOI: 10.1016/j.pbi.2022.102277] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 06/21/2022] [Accepted: 07/07/2022] [Indexed: 06/15/2023]
Abstract
Transposable elements (TEs) make up a major proportion of plant genomes. Despite their prevalence genome-wide, TEs are often tossed aside as "junk DNA" since they rarely cause phenotypes, and epigenetic mechanisms silence TEs to prevent them from causing deleterious mutations through movement. While this bleak picture of TEs in genomes is true on average, a growing number of examples across many plant species point to TEs as drivers of phenotypic diversity and novel stress responses. Examples of TE-influenced phenotypes illustrate the many ways that novel transposition events can alter local gene expression and how this relates to potential variation in plant responses to environmental stress. Since TE families and insertions at the locus level lack evolutionary conservation, advancements in the field will require TE experts across diverse species to identify and utilize TE variation in their own systems as a means of crop improvement.
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Affiliation(s)
- Stephanie P Klein
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
| | - Sarah N Anderson
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA.
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Wheat genomic study for genetic improvement of traits in China. SCIENCE CHINA. LIFE SCIENCES 2022; 65:1718-1775. [PMID: 36018491 DOI: 10.1007/s11427-022-2178-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/10/2022] [Indexed: 01/17/2023]
Abstract
Bread wheat (Triticum aestivum L.) is a major crop that feeds 40% of the world's population. Over the past several decades, advances in genomics have led to tremendous achievements in understanding the origin and domestication of wheat, and the genetic basis of agronomically important traits, which promote the breeding of elite varieties. In this review, we focus on progress that has been made in genomic research and genetic improvement of traits such as grain yield, end-use traits, flowering regulation, nutrient use efficiency, and biotic and abiotic stress responses, and various breeding strategies that contributed mainly by Chinese scientists. Functional genomic research in wheat is entering a new era with the availability of multiple reference wheat genome assemblies and the development of cutting-edge technologies such as precise genome editing tools, high-throughput phenotyping platforms, sequencing-based cloning strategies, high-efficiency genetic transformation systems, and speed-breeding facilities. These insights will further extend our understanding of the molecular mechanisms and regulatory networks underlying agronomic traits and facilitate the breeding process, ultimately contributing to more sustainable agriculture in China and throughout the world.
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Characterization of Transposon-Derived Accessible Chromatin Regions in Rice (Oryza Sativa). Int J Mol Sci 2022; 23:ijms23168947. [PMID: 36012213 PMCID: PMC9408979 DOI: 10.3390/ijms23168947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/05/2022] [Accepted: 08/08/2022] [Indexed: 11/17/2022] Open
Abstract
Growing evidence indicates that transposons or transposable elements (TEs)-derived accessible chromatin regions (ACRs) play essential roles in multiple biological processes by interacting with trans-acting factors. However, the function of TE-derived ACRs in the regulation of gene expression in the rice genome has not been well characterized. In this study, we examined the chromatin dynamics in six types of rice tissues and found that ~8% of ACRs were derived from TEs and exhibited distinct levels of accessibility and conservation as compared to those without TEs. TEs exhibited a TE subtype-dependent impact on ACR formation, which can be mediated by changes in the underlying DNA methylation levels. Moreover, we found that tissue-specific TE-derived ACRs might function in the tissue development through the modulation of nearby gene expression. Interestingly, many genes in domestication sweeps were found to overlap with TE-derived ACRs, suggesting their potential functions in the rice domestication. In addition, we found that the expression divergence of 1070 duplicate gene pairs were associated with TE-derived ACRs and had distinct distributions of TEs and ACRs around the transcription start sites (TSSs), which may experience different selection pressures. Thus, our study provides some insights into the biological implications of TE-derived ACRs in the rice genome. Our results imply that these ACRs are likely involved in the regulation of tissue development, rice domestication and functional divergence of duplicated genes.
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Yang JS, Qian ZH, Shi T, Li ZZ, Chen JM. Chromosome-level genome assembly of the aquatic plant Nymphoides indica reveals transposable element bursts and NBS-LRR gene family expansion shedding light on its invasiveness. DNA Res 2022; 29:6617837. [PMID: 35751614 PMCID: PMC9267246 DOI: 10.1093/dnares/dsac022] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 06/24/2022] [Indexed: 11/19/2022] Open
Abstract
Nymphoides indica, an aquatic plant, is an invasive species that causes both ecological and economic damage in North America and elsewhere. However, the lack of genomic data of N. indica limits the in-depth analysis of this invasive species. Here, we report a chromosome-level genome assembly of nine pseudochromosomes of N. indica with a total size of ∼ 520 Mb. More than half of the N. indica genome consists of transposable elements (TEs), and a higher density of TEs around genes may play a significant role in response to an ever-changing environment by regulating the nearby gene. Additionally, our analysis revealed that N. indica only experienced a gamma (γ) whole-genome triplication event. Functional enrichment of the N. indica-specific and expanded gene families highlighted genes involved in the responses to hypoxia and plant–pathogen interactions, which may strengthen the ability to adapt to external challenges and improve ecological fitness. Furthermore, we identified 160 members of the nucleotide-binding site and leucine-rich repeat gene family, which may be linked to the defence response. Collectively, the high-quality N. indica genome reported here opens a novel avenue to understand the evolution and rapid invasion of Nymphoides spp.
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Affiliation(s)
- Jing-Shan Yang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences , Wuhan 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences , Wuhan 430074, China
- University of Chinese Academy of Sciences , Beijing 100049, China
| | - Zhi-Hao Qian
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences , Wuhan 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences , Wuhan 430074, China
- University of Chinese Academy of Sciences , Beijing 100049, China
| | - Tao Shi
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences , Wuhan 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences , Wuhan 430074, China
| | - Zhi-Zhong Li
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences , Wuhan 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences , Wuhan 430074, China
| | - Jin-Ming Chen
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences , Wuhan 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences , Wuhan 430074, China
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29
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Shapiro JA. What we have learned about evolutionary genome change in the past 7 decades. Biosystems 2022; 215-216:104669. [DOI: 10.1016/j.biosystems.2022.104669] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 03/23/2022] [Accepted: 03/23/2022] [Indexed: 12/12/2022]
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30
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Flavell RB. Wheat Breeding, Transcription Factories, and Genetic Interactions: New Perspectives. FRONTIERS IN PLANT SCIENCE 2022; 13:807884. [PMID: 35283934 PMCID: PMC8905190 DOI: 10.3389/fpls.2022.807884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 01/24/2022] [Indexed: 06/14/2023]
Abstract
Epistatic interactions and negative heterosis have been shown to be associated with interchromosomal interactions in wheat. Physical gene-gene interactions between co-regulated genes clustered in "transcription factories" have been documented, and a genome-wide atlas of functionally paired, interacting regulatory elements and genes of wheat recently produced. Integration of these new studies on gene and regulatory element interactions, co-regulation of gene expression in "transcription factories," and epigenetics generates new perspectives for wheat breeding and trait enhancement.
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Huang Y, Liu Y, Liu C, Birchler JA, Han F. Prospects and challenges of epigenomics in crop improvement. Genes Genomics 2021; 44:251-257. [PMID: 34837632 DOI: 10.1007/s13258-021-01187-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 11/04/2021] [Indexed: 12/17/2022]
Abstract
BACKGROUND The advent of high-throughput epigenome mapping techniques has ushered in a new era of multiomics with powerful tools now available to map and record genomic output at different levels. Integrating the different components of the epigenome from these multiomics measures allows investigations of cis-regulatory elements on a genome-scale. Mapping of chromatin state, chromatin accessibility dynamics, and higher-order chromatin structure enables a new level of understanding of cell fate determination, identity and function in normal growth and development, disease resistance, and yield. OBJECTIVE In this paper, the recent advances in epigenomics research of rice, maize, and wheat are reviewed, and the development trends of epigenomics of major crops in the coming years are projected. METHODS We highlight the role of epigenomics in regulating growth and development and identifying potential distal cis-regulatory elements in three major crops, and discuss the prospects and challenges for new epigenetics-mediated breeding technologies in crop improvement. CONCLUSION In this review, we summarize and analyze recent epigenomic advances in three major crops epigenomics and discuss possibilities and challenges for future research in the field.
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Affiliation(s)
- Yuhong Huang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yang Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chang Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - James A Birchler
- Division of Biological Sciences, University of Missouri at Columbia, Columbia, MO, 65211, USA
| | - Fangpu Han
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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