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Hakami MA, Khan FR, Abdulaziz O, Alshaghdali K, Hazazi A, Aleissi AF, Abalkhail A, Alotaibi BS, Alhazmi AYM, Kukreti N, Binshaya AS. Varicella-zoster virus-related neurological complications: From infection to immunomodulatory therapies. Rev Med Virol 2024; 34:e2554. [PMID: 38862398 DOI: 10.1002/rmv.2554] [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: 01/20/2024] [Revised: 05/11/2024] [Accepted: 05/27/2024] [Indexed: 06/13/2024]
Abstract
The Varicella-zoster virus (VZV), classified as a neurotropic member of the Herpesviridae family, exhibits a characteristic pathogenicity, predominantly inducing varicella, commonly known as chickenpox, during the initial infectious phase, and triggering the reactivation of herpes zoster, more commonly recognized as shingles, following its emergence from a latent state. The pathogenesis of VZV-associated neuroinflammation involves a complex interplay between viral replication within sensory ganglia and immune-mediated responses that contribute to tissue damage and dysfunction. Upon primary infection, VZV gains access to sensory ganglia, establishing latent infection within neurons. During reactivation, the virus can spread along sensory nerves, triggering a cascade of inflammatory mediators, chemokines, and immune cell infiltration in the affected neural tissues. The role of both adaptive and innate immune reactions, including the contributions of T and B cells, macrophages, and dendritic cells, in orchestrating the immune-mediated damage in the central nervous system is elucidated. Furthermore, the aberrant activation of the natural defence mechanism, characterised by the dysregulated production of immunomodulatory proteins and chemokines, has been implicated in the pathogenesis of VZV-induced neurological disorders, such as encephalitis, myelitis, and vasculopathy. The intricate balance between protective and detrimental immune responses in the context of VZV infection emphasises the necessity for an exhaustive comprehension of the immunopathogenic mechanisms propelling neuroinflammatory processes. Despite the availability of vaccines and antiviral therapies, VZV-related neurological complications remain a significant concern, particularly in immunocompromised individuals and the elderly. Elucidating these mechanisms might facilitate the emergence of innovative immunomodulatory strategies and targeted therapies aimed at mitigating VZV-induced neuroinflammatory damage and improving clinical outcomes. This comprehensive understanding enhances our grasp of viral pathogenesis and holds promise for pioneering therapeutic strategies designed to mitigate the neurological ramifications of VZV infections.
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Affiliation(s)
- Mohammed Ageeli Hakami
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Al-Quwayiyah, Shaqra University, Riyadh, Saudi Arabia
| | - Farhan R Khan
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Al-Quwayiyah, Shaqra University, Riyadh, Saudi Arabia
| | - Osama Abdulaziz
- Clinical Laboratory Sciences Department, College of Applied Medical Sciences, Taif University, Taif, Makkah Province, Saudi Arabia
| | - Khalid Alshaghdali
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hail, Hail, Saudi Arabia
| | - Ali Hazazi
- Department of Pathology and Laboratory Medicine, Security Forces Hospital Program, Riyadh, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Awad F Aleissi
- Department of Pathology and Laboratory Medicine, Security Forces Hospital Program, Riyadh, Saudi Arabia
| | - Adil Abalkhail
- Department of Public Health, College of Public Health and Health Informatics, Qassim University, Buraydah, Qassim, Saudi Arabia
| | - Bader S Alotaibi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Al-Quwayiyah, Shaqra University, Riyadh, Saudi Arabia
| | | | - Neelima Kukreti
- Graphic Era Hill University, Clement Town, Dehradun, India
- Graphic Era (Deemed to be University), Clement Town, Dehradun, India
| | - Abdulkarim S Binshaya
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj, Saudi Arabia
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Ren Y, Wu C, Zhou H, Hu X, Miao Z. Dual-extraction modeling: A multi-modal deep-learning architecture for phenotypic prediction and functional gene mining of complex traits. PLANT COMMUNICATIONS 2024:101002. [PMID: 38872306 DOI: 10.1016/j.xplc.2024.101002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 05/27/2024] [Accepted: 06/11/2024] [Indexed: 06/15/2024]
Abstract
Despite considerable advances in extracting crucial insights from bio-omics data to unravel the intricate mechanisms underlying complex traits, the absence of a universal multi-modal computational tool with robust interpretability for accurate phenotype prediction and identification of trait-associated genes remains a challenge. This study introduces the dual-extraction modeling (DEM) approach, a multi-modal deep-learning architecture designed to extract representative features from heterogeneous omics datasets, enabling the prediction of complex trait phenotypes. Through comprehensive benchmarking experiments, we demonstrate the efficacy of DEM in classification and regression prediction of complex traits. DEM consistently exhibits superior accuracy, robustness, generalizability, and flexibility. Notably, we establish its effectiveness in predicting pleiotropic genes that influence both flowering time and rosette leaf number, underscoring its commendable interpretability. In addition, we have developed user-friendly software to facilitate seamless utilization of DEM's functions. In summary, this study presents a state-of-the-art approach with the ability to effectively predict qualitative and quantitative traits and identify functional genes, confirming its potential as a valuable tool for exploring the genetic basis of complex traits.
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Affiliation(s)
- Yanlin Ren
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chenhua Wu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - He Zhou
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaona Hu
- College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Zhenyan Miao
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China.
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3
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Zhang Y, Jin J, Wang N, Sun Q, Feng D, Zhu S, Wang Z, Li S, Ye J, Chai L, Xie Z, Deng X. Cytochrome P450 CitCYP97B modulates carotenoid accumulation diversity by hydroxylating β-cryptoxanthin in Citrus. PLANT COMMUNICATIONS 2024; 5:100847. [PMID: 38379285 PMCID: PMC11211522 DOI: 10.1016/j.xplc.2024.100847] [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: 10/07/2023] [Revised: 12/21/2023] [Accepted: 02/18/2024] [Indexed: 02/22/2024]
Abstract
Carotenoids in plant foods provide health benefits by functioning as provitamin A. One of the vital provitamin A carotenoids, β-cryptoxanthin, is typically plentiful in citrus fruit. However, little is known about the genetic basis of β-cryptoxanthin accumulation in citrus. Here, we performed a widely targeted metabolomic analysis of 65 major carotenoids and carotenoid derivatives to characterize carotenoid accumulation in Citrus and determine the taxonomic profile of β-cryptoxanthin. We used data from 81 newly sequenced representative accessions and 69 previously sequenced Citrus cultivars to reveal the genetic basis of β-cryptoxanthin accumulation through a genome-wide association study. We identified a causal gene, CitCYP97B, which encodes a cytochrome P450 protein whose substrate and metabolic pathways in land plants were undetermined. We subsequently demonstrated that CitCYP97B functions as a novel monooxygenase that specifically hydroxylates the β-ring of β-cryptoxanthin in a heterologous expression system. In planta experiments provided further evidence that CitCYP97B negatively regulates β-cryptoxanthin content. Using the sequenced Citrus accessions, we found that two critical structural cis-element variations contribute to increased expression of CitCYP97B, thereby altering β-cryptoxanthin accumulation in fruit. Hybridization/introgression appear to have contributed to the prevalence of two cis-element variations in different Citrus types during citrus evolution. Overall, these findings extend our understanding of the regulation and diversity of carotenoid metabolism in fruit crops and provide a genetic target for production of β-cryptoxanthin-biofortified products.
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Affiliation(s)
- Yingzi Zhang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiajing Jin
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Nan Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Quan Sun
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Di Feng
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Shenchao Zhu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Zexin Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Shunxin Li
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Junli Ye
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Lijun Chai
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Zongzhou Xie
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiuxin Deng
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China.
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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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Zhao D, Zheng H, Li J, Wan M, Shu K, Wang W, Hu X, Hu Y, Qiu L, Wang X. Natural Variation in the Promoter of GmSPL9d Affects Branch Number in Soybean. Int J Mol Sci 2024; 25:5991. [PMID: 38892178 PMCID: PMC11172651 DOI: 10.3390/ijms25115991] [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: 04/23/2024] [Revised: 05/17/2024] [Accepted: 05/25/2024] [Indexed: 06/21/2024] Open
Abstract
The branch number is a crucial factor that influences density tolerance and is closely associated with the yield of soybean. However, its molecular regulation mechanisms remain poorly understood. This study cloned a candidate gene GmSPL9d for regulating the soybean branch number based on the rice OsSPL14 homologous gene. Meanwhile, the genetic diversity of the GmSPL9d was analyzed using 3599 resequencing data and identified 55 SNP/InDel variations, which were categorized into seven haplotypes. Evolutionary analysis classified these haplotypes into two groups: GmSPL9d H-I and GmSPL9d H-II. Soybean varieties carrying the GmSPL9d H-II haplotype exhibited a significantly lower branch number compared with those carrying the GmSPL9d H-I haplotype. Association analysis between the variation sites and branch number phenotypes revealed a significant correlation between the promoter variations and the branch number. Promoter activity assays demonstrated that the GmSPL9d H-II promoter displayed significantly higher activity than the GmSPL9d H-I promoter. Transgenic experiments confirmed that the plants that carried the GmSPL9d H-II promoter exhibited a significantly lower branch number compared with those that carried the GmSPL9d H-I promoter. These findings indicate that the variation in the GmSPL9d promoter affected its transcription level, leading to differences in the soybean branch number. This study provides valuable molecular targets for improving the soybean plant structure.
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Affiliation(s)
- Duo Zhao
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China; (D.Z.); (H.Z.); (J.L.); (M.W.); (K.S.); (W.W.); (X.H.); (Y.H.)
| | - Haowei Zheng
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China; (D.Z.); (H.Z.); (J.L.); (M.W.); (K.S.); (W.W.); (X.H.); (Y.H.)
| | - Jiajia Li
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China; (D.Z.); (H.Z.); (J.L.); (M.W.); (K.S.); (W.W.); (X.H.); (Y.H.)
| | - Mingyue Wan
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China; (D.Z.); (H.Z.); (J.L.); (M.W.); (K.S.); (W.W.); (X.H.); (Y.H.)
| | - Kuo Shu
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China; (D.Z.); (H.Z.); (J.L.); (M.W.); (K.S.); (W.W.); (X.H.); (Y.H.)
| | - Wenhui Wang
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China; (D.Z.); (H.Z.); (J.L.); (M.W.); (K.S.); (W.W.); (X.H.); (Y.H.)
| | - Xiaoyu Hu
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China; (D.Z.); (H.Z.); (J.L.); (M.W.); (K.S.); (W.W.); (X.H.); (Y.H.)
| | - Yu Hu
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China; (D.Z.); (H.Z.); (J.L.); (M.W.); (K.S.); (W.W.); (X.H.); (Y.H.)
| | - Lijuan Qiu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaobo Wang
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China; (D.Z.); (H.Z.); (J.L.); (M.W.); (K.S.); (W.W.); (X.H.); (Y.H.)
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Yu H, Liu B, Yang Q, Yang Q, Li W, Fu F. Maize ZmLAZ1-3 gene negatively regulates drought tolerance in transgenic Arabidopsis. BMC PLANT BIOLOGY 2024; 24:246. [PMID: 38575869 PMCID: PMC10996212 DOI: 10.1186/s12870-024-04923-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 03/18/2024] [Indexed: 04/06/2024]
Abstract
BACKGROUND Molecular mechanisms in response to drought stress are important for the genetic improvement of maize. In our previous study, nine ZmLAZ1 members were identified in the maize genome, but the function of ZmLAZ1 was largely unknown. RESULTS The ZmLAZ1-3 gene was cloned from B73, and its drought-tolerant function was elucidated by expression analysis in transgenic Arabidopsis. The expression of ZmLAZ1-3 was upregulated by drought stress in different maize inbred lines. The driving activity of the ZmLAZ1-3 promoter was induced by drought stress and related to the abiotic stress-responsive elements such as MYB, MBS, and MYC. The results of subcellular localization indicated that the ZmLAZ1-3 protein localized on the plasma membrane and chloroplast. The ectopic expression of the ZmLAZ1-3 gene in Arabidopsis significantly reduced germination ratio and root length, decreased biomass, and relative water content, but increased relative electrical conductivity and malondialdehyde content under drought stress. Moreover, transcriptomics analysis showed that the differentially expressed genes between the transgenic lines and wild-type were mainly associated with response to abiotic stress and biotic stimulus, and related to pathways of hormone signal transduction, phenylpropanoid biosynthesis, mitogen-activated protein kinase signaling, and plant-pathogen interaction. CONCLUSION The study suggests that the ZmLAZ1-3 gene is a negative regulator in regulating drought tolerance and can be used to improve maize drought tolerance via its silencing or knockout.
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Affiliation(s)
- Haoqiang Yu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China
| | - Bingliang Liu
- College of Food and Biological Engineering, Chengdu University, Chengdu, 610106, People's Republic of China
| | - Qinyu Yang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China
| | - Qingqing Yang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China
| | - Wanchen Li
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China.
| | - Fengling Fu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China.
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Lu C, Wei Y, Abbas M, Agula H, Wang E, Meng Z, Zhang R. Application of Single-Cell Assay for Transposase-Accessible Chromatin with High Throughput Sequencing in Plant Science: Advances, Technical Challenges, and Prospects. Int J Mol Sci 2024; 25:1479. [PMID: 38338756 PMCID: PMC10855595 DOI: 10.3390/ijms25031479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/16/2024] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
The Single-cell Assay for Transposase-Accessible Chromatin with high throughput sequencing (scATAC-seq) has gained increasing popularity in recent years, allowing for chromatin accessibility to be deciphered and gene regulatory networks (GRNs) to be inferred at single-cell resolution. This cutting-edge technology now enables the genome-wide profiling of chromatin accessibility at the cellular level and the capturing of cell-type-specific cis-regulatory elements (CREs) that are masked by cellular heterogeneity in bulk assays. Additionally, it can also facilitate the identification of rare and new cell types based on differences in chromatin accessibility and the charting of cellular developmental trajectories within lineage-related cell clusters. Due to technical challenges and limitations, the data generated from scATAC-seq exhibit unique features, often characterized by high sparsity and noise, even within the same cell type. To address these challenges, various bioinformatic tools have been developed. Furthermore, the application of scATAC-seq in plant science is still in its infancy, with most research focusing on root tissues and model plant species. In this review, we provide an overview of recent progress in scATAC-seq and its application across various fields. We first conduct scATAC-seq in plant science. Next, we highlight the current challenges of scATAC-seq in plant science and major strategies for cell type annotation. Finally, we outline several future directions to exploit scATAC-seq technologies to address critical challenges in plant science, ranging from plant ENCODE(The Encyclopedia of DNA Elements) project construction to GRN inference, to deepen our understanding of the roles of CREs in plant biology.
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Affiliation(s)
- Chao Lu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (C.L.); (Y.W.)
- Key Laboratory of Herbage & Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Yunxiao Wei
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (C.L.); (Y.W.)
| | - Mubashir Abbas
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (C.L.); (Y.W.)
| | - Hasi Agula
- Key Laboratory of Herbage & Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Edwin Wang
- Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Zhigang Meng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (C.L.); (Y.W.)
| | - Rui Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (C.L.); (Y.W.)
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8
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Chen YH, Lu J, Yang X, Huang LC, Zhang CQ, Liu QQ, Li QF. Gene editing of non-coding regulatory DNA and its application in crop improvement. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6158-6175. [PMID: 37549968 DOI: 10.1093/jxb/erad313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 08/04/2023] [Indexed: 08/09/2023]
Abstract
The development of the clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas) system has provided precise and efficient strategies to edit target genes and generate transgene-free crops. Significant progress has been made in the editing of protein-coding genes; however, studies on the editing of non-coding DNA with regulatory roles lags far behind. Non-coding regulatory DNAs, including those which can be transcribed into long non-coding RNAs (lncRNAs), and miRNAs, together with cis-regulatory elements (CREs), play crucial roles in regulating plant growth and development. Therefore, the combination of CRISPR/Cas technology and non-coding regulatory DNA has great potential to generate novel alleles that affect various agronomic traits of crops, thus providing valuable genetic resources for crop breeding. Herein, we review recent advances in the roles of non-coding regulatory DNA, attempts to edit non-coding regulatory DNA for crop improvement, and potential application of novel editing tools in modulating non-coding regulatory DNA. Finally, the existing problems, possible solutions, and future applications of gene editing of non-coding regulatory DNA in modern crop breeding practice are also discussed.
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Affiliation(s)
- Yu-Hao Chen
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, Jiangsu, China
| | - Jun Lu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, Jiangsu, China
| | - Xia Yang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, Jiangsu, China
| | - Li-Chun Huang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, Jiangsu, China
| | - Chang-Quan Zhang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, Jiangsu, China
| | - Qiao-Quan Liu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, Jiangsu, China
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Yangzhou University, Yangzhou 225009, Jiangsu, China
| | - Qian-Feng Li
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, Jiangsu, China
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Yangzhou University, Yangzhou 225009, Jiangsu, China
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Hale B, Ratnayake S, Flory A, Wijeratne R, Schmidt C, Robertson AE, Wijeratne AJ. Gene regulatory network inference in soybean upon infection by Phytophthora sojae. PLoS One 2023; 18:e0287590. [PMID: 37418376 PMCID: PMC10328377 DOI: 10.1371/journal.pone.0287590] [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: 10/28/2022] [Accepted: 06/07/2023] [Indexed: 07/09/2023] Open
Abstract
Phytophthora sojae is a soil-borne oomycete and the causal agent of Phytophthora root and stem rot (PRR) in soybean (Glycine max [L.] Merrill). Yield losses attributed to P. sojae are devastating in disease-conducive environments, with global estimates surpassing 1.1 million tonnes annually. Historically, management of PRR has entailed host genetic resistance (both vertical and horizontal) complemented by disease-suppressive cultural practices (e.g., oomicide application). However, the vast expansion of complex and/or diverse P. sojae pathotypes necessitates developing novel technologies to attenuate PRR in field environments. Therefore, the objective of the present study was to couple high-throughput sequencing data and deep learning to elucidate molecular features in soybean following infection by P. sojae. In doing so, we generated transcriptomes to identify differentially expressed genes (DEGs) during compatible and incompatible interactions with P. sojae and a mock inoculation. The expression data were then used to select two defense-related transcription factors (TFs) belonging to WRKY and RAV families. DNA Affinity Purification and sequencing (DAP-seq) data were obtained for each TF, providing putative DNA binding sites in the soybean genome. These bound sites were used to train Deep Neural Networks with convolutional and recurrent layers to predict new target sites of WRKY and RAV family members in the DEG set. Moreover, we leveraged publicly available Arabidopsis (Arabidopsis thaliana) DAP-seq data for five TF families enriched in our transcriptome analysis to train similar models. These Arabidopsis data-based models were used for cross-species TF binding site prediction on soybean. Finally, we created a gene regulatory network depicting TF-target gene interactions that orchestrate an immune response against P. sojae. Information herein provides novel insight into molecular plant-pathogen interaction and may prove useful in developing soybean cultivars with more durable resistance to P. sojae.
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Affiliation(s)
- Brett Hale
- Molecular Biosciences Graduate Program, Arkansas State University, State University, AR, United States of America
- Arkansas Biosciences Institute, Arkansas State University, State University, AR, United States of America
- College of Science and Mathematics, Arkansas State University, State University, AR, United States of America
| | - Sandaruwan Ratnayake
- Arkansas Biosciences Institute, Arkansas State University, State University, AR, United States of America
- College of Science and Mathematics, Arkansas State University, State University, AR, United States of America
| | - Ashley Flory
- Arkansas Biosciences Institute, Arkansas State University, State University, AR, United States of America
| | | | - Clarice Schmidt
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, United States of America
| | - Alison E. Robertson
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, United States of America
| | - Asela J. Wijeratne
- Arkansas Biosciences Institute, Arkansas State University, State University, AR, United States of America
- College of Science and Mathematics, Arkansas State University, State University, AR, United States of America
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10
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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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11
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Gavgani HN, Grotewold E, Gray J. Methodology for Constructing a Knowledgebase for Plant Gene Regulation Information. Methods Mol Biol 2023; 2698:277-300. [PMID: 37682481 DOI: 10.1007/978-1-0716-3354-0_17] [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
The amount of biological data is growing at a rapid pace as many high-throughput omics technologies and data pipelines are developed. This is resulting in the growth of databases for DNA and protein sequences, gene expression, protein accumulation, structural, and localization information. The diversity and multi-omics nature of such bioinformatic data requires well-designed databases for flexible organization and presentation. Besides general-purpose online bioinformatic databases, users need narrowly focused online databases to quickly access a meaningful collection of related data for their research. Here, we describe the methodology used to implement a plant gene regulatory knowledgebase, with data, query, and tool features, as well as the ability to expand to accommodate future datasets. We exemplify this methodology for the GRASSIUS knowledgebase, but it is applicable to developing and updating similar plant gene regulatory knowledgebases. GRASSIUS organizes and presents gene regulatory data from grass species with a central focus on maize (Zea mays). The main class of data presented include not only the families of transcription factors (TFs) and co-regulators (CRs) but also protein-DNA interaction data, where available.
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Affiliation(s)
- Hadi Nayebi Gavgani
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
- Dandelions Therapeutics Inc., San Francisco, CA, USA
| | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - John Gray
- Department of Biological Sciences, University of Toledo, Toledo, OH, USA.
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12
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Zheng M, Li J, Zeng C, Liu X, Chu W, Lin J, Wang F, Wang W, Guo W, Xin M, Yao Y, Peng H, Ni Z, Sun Q, Hu Z. Subgenome-biased expression and functional diversification of a Na +/H + antiporter homoeologs in salt tolerance of polyploid wheat. FRONTIERS IN PLANT SCIENCE 2022; 13:1072009. [PMID: 36570929 PMCID: PMC9768589 DOI: 10.3389/fpls.2022.1072009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
Common wheat (Triticum aestivum, BBAADD) is an allohexaploid species combines the D genome from Ae. tauschii and with the AB genomes from tetraploid wheat (Triticum turgidum). Compared with tetraploid wheat, hexaploid wheat has wide-ranging adaptability to environmental adversity such as salt stress. However, little is known about the molecular basis underlying this trait. The plasma membrane Na+/H+ transporter Salt Overly Sensitive 1 (SOS1) is a key determinant of salt tolerance in plants. Here we show that the upregulation of TaSOS1 expression is positively correlated with salt tolerance variation in polyploid wheat. Furthermore, both transcriptional analysis and GUS staining on transgenic plants indicated TaSOS1-A and TaSOS1-B exhibited higher basal expression in roots and leaves in normal conditions and further up-regulated under salt stress; while TaSOS1-D showed markedly lower expression in roots and leaves under normal conditions, but significant up-regulated in roots but not leaves under salt stress. Moreover, transgenic studies in Arabidopsis demonstrate that three TaSOS1 homoeologs display different contribution to salt tolerance and TaSOS1-D plays the prominent role in salt stress. Our findings provide insights into the subgenomic homoeologs variation potential to broad adaptability of natural polyploidy wheat, which might effective for genetic improvement of salinity tolerance in wheat and other crops.
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Affiliation(s)
- Mei Zheng
- Frontiers Science Center for Molecular Design Breeding/Key Laboratory of Crop Heterosis and Utilization (Ministry of Education), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Jinpeng Li
- Frontiers Science Center for Molecular Design Breeding/Key Laboratory of Crop Heterosis and Utilization (Ministry of Education), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Chaowu Zeng
- Frontiers Science Center for Molecular Design Breeding/Key Laboratory of Crop Heterosis and Utilization (Ministry of Education), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
- Institute of Crop Sciences, Xinjiang Academy of Agricultural Sciences, Urumuqi, China
| | - Xingbei Liu
- Frontiers Science Center for Molecular Design Breeding/Key Laboratory of Crop Heterosis and Utilization (Ministry of Education), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Wei Chu
- Frontiers Science Center for Molecular Design Breeding/Key Laboratory of Crop Heterosis and Utilization (Ministry of Education), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Jingchen Lin
- Frontiers Science Center for Molecular Design Breeding/Key Laboratory of Crop Heterosis and Utilization (Ministry of Education), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Fengzhi Wang
- Hebei Key Laboratory of Crop Salt-alkali Stress Tolerance Evaluation and Genetic Improvement, Cangzhou Academy of Agriculture and Forestry Science, Cangzhou, China
| | - Weiwei Wang
- Hebei Key Laboratory of Crop Salt-alkali Stress Tolerance Evaluation and Genetic Improvement, Cangzhou Academy of Agriculture and Forestry Science, Cangzhou, China
| | - Weilong Guo
- Frontiers Science Center for Molecular Design Breeding/Key Laboratory of Crop Heterosis and Utilization (Ministry of Education), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Mingming Xin
- Frontiers Science Center for Molecular Design Breeding/Key Laboratory of Crop Heterosis and Utilization (Ministry of Education), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Yingyin Yao
- Frontiers Science Center for Molecular Design Breeding/Key Laboratory of Crop Heterosis and Utilization (Ministry of Education), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Huiru Peng
- Frontiers Science Center for Molecular Design Breeding/Key Laboratory of Crop Heterosis and Utilization (Ministry of Education), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Zhongfu Ni
- Frontiers Science Center for Molecular Design Breeding/Key Laboratory of Crop Heterosis and Utilization (Ministry of Education), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Qixin Sun
- Frontiers Science Center for Molecular Design Breeding/Key Laboratory of Crop Heterosis and Utilization (Ministry of Education), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Zhaorong Hu
- Frontiers Science Center for Molecular Design Breeding/Key Laboratory of Crop Heterosis and Utilization (Ministry of Education), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
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13
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Kumar K, Mandal SN, Pradhan B, Kaur P, Kaur K, Neelam K. From Evolution to Revolution: Accelerating Crop Domestication through Genome Editing. PLANT & CELL PHYSIOLOGY 2022; 63:1607-1623. [PMID: 36018059 DOI: 10.1093/pcp/pcac124] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 08/25/2022] [Indexed: 06/15/2023]
Abstract
Crop domestication has a tremendous impact on socioeconomic conditions and human civilization. Modern cultivars were domesticated from their wild progenitors thousands of years ago by the selection of natural variation by humans. New cultivars are being developed by crossing two or more compatible individuals. But the limited genetic diversity in the cultivars severely affects the yield and renders the crop susceptible to many biotic and abiotic stresses. Crop wild relatives (CWRs) are the rich reservoir for many valuable agronomic traits. The incorporation of useful genes from CWR is one of the sustainable approaches for enriching the gene pool of cultivated crops. However, CWRs are not suited for urban and intensive cultivation because of several undesirable traits. Researchers have begun to study the domestication traits in the CWRs and modify them using genome-editing tools to make them suitable for extensive cultivation. Growing evidence has shown that modification in these genes is not sufficient to bring the desired change in the neodomesticated crop. However, the other dynamic genetic factors such as microRNAs (miRNAs), transposable elements, cis-regulatory elements and epigenetic changes have reshaped the domesticated crops. The creation of allelic series for many valuable domestication traits through genome editing holds great potential for the accelerated development of neodomesticated crops. The present review describes the current understanding of the genetics of domestication traits that are responsible for the agricultural revolution. The targeted mutagenesis in these domestication genes via clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 could be used for the rapid domestication of CWRs.
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Affiliation(s)
- Kishor Kumar
- Faculty Centre for Integrated Rural Development and Management, Ramakrishna Mission Vivekananda Educational and Research Institute, Narendrapur, Kolkata 700103, India
| | - Swarupa Nanda Mandal
- Department of Genetics and Plant Breeding, Bidhan Chandra Krishi Viswavidyalaya, Extended Campus, Burdwan, West Bengal 713101, India
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79415, USA
| | - Bhubaneswar Pradhan
- Faculty Centre for Integrated Rural Development and Management, Ramakrishna Mission Vivekananda Educational and Research Institute, Narendrapur, Kolkata 700103, India
| | - Pavneet Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab 141004, India
| | - Karminderbir Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab 141004, India
| | - Kumari Neelam
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab 141004, India
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14
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Shelake RM, Kadam US, Kumar R, Pramanik D, Singh AK, Kim JY. Engineering drought and salinity tolerance traits in crops through CRISPR-mediated genome editing: Targets, tools, challenges, and perspectives. PLANT COMMUNICATIONS 2022; 3:100417. [PMID: 35927945 PMCID: PMC9700172 DOI: 10.1016/j.xplc.2022.100417] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 07/07/2022] [Accepted: 07/27/2022] [Indexed: 05/10/2023]
Abstract
Prolonged periods of drought triggered by climate change hamper plant growth and cause substantial agricultural yield losses every year. In addition to drought, salinity is one of the major abiotic stresses that severely affect crop health and agricultural production. Plant responses to drought and salinity involve multiple processes that operate in a spatiotemporal manner, such as stress sensing, perception, epigenetic modifications, transcription, post-transcriptional processing, translation, and post-translational changes. Consequently, drought and salinity stress tolerance are polygenic traits influenced by genome-environment interactions. One of the ideal solutions to these challenges is the development of high-yielding crop varieties with enhanced stress tolerance, together with improved agricultural practices. Recently, genome-editing technologies, especially clustered regularly interspaced short palindromic repeats (CRISPR) tools, have been effectively applied to elucidate how plants deal with drought and saline environments. In this work, we aim to portray that the combined use of CRISPR-based genome engineering tools and modern genomic-assisted breeding approaches are gaining momentum in identifying genetic determinants of complex traits for crop improvement. This review provides a synopsis of plant responses to drought and salinity stresses at the morphological, physiological, and molecular levels. We also highlight recent advances in CRISPR-based tools and their use in understanding the multi-level nature of plant adaptations to drought and salinity stress. Integrating CRISPR tools with modern breeding approaches is ideal for identifying genetic factors that regulate plant stress-response pathways and for the introgression of beneficial traits to develop stress-resilient crops.
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Affiliation(s)
- Rahul Mahadev Shelake
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea.
| | - Ulhas Sopanrao Kadam
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea
| | - Ritesh Kumar
- Department of Agronomy & Plant Genetics, University of Minnesota, Saint Paul, MN 55108, USA
| | - Dibyajyoti Pramanik
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea
| | - Anil Kumar Singh
- ICAR-National Institute for Plant Biotechnology, LBS Centre, Pusa Campus, New Delhi 110012, India
| | - Jae-Yean Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea; Division of Life Science, Gyeongsang National University, 501 Jinju-daero, Jinju 52828, Korea.
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15
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Wu L, Luo Z, Shi Y, Jiang Y, Li R, Miao X, Yang F, Li Q, Zhao H, Xue J, Xu S, Zhang T, Li L. A cost-effective tsCUT&Tag method for profiling transcription factor binding landscape. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:2033-2038. [PMID: 36047457 DOI: 10.1111/jipb.13354] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 08/25/2022] [Indexed: 06/15/2023]
Abstract
Knowledge of the transcription factor binding landscape (TFBL) is necessary to analyze gene regulatory networks for important agronomic traits. However, a low-cost and high-throughput in vivo chromatin profiling method is still lacking in plants. Here, we developed a transient and simplified cleavage under targets and tagmentation (tsCUT&Tag) that combines transient expression of transcription factor proteins in protoplasts with a simplified CUT&Tag without nucleus extraction. Our tsCUT&Tag method provided higher data quality and signal resolution with lower sequencing depth compared with traditional ChIP-seq. Furthermore, we developed a strategy combining tsCUT&Tag with machine learning, which has great potential for profiling the TFBL across plant development.
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Affiliation(s)
- Leiming Wu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- The National Engineering Laboratory of Crop Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Zi Luo
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yanni Shi
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yizhe Jiang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ruonan Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xinxin Miao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Fang Yang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qing Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Han Zhao
- Jiangsu Provincial Key Laboratory of Agrobiology, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Jiquan Xue
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, Northwest A&F University, Yangling, 712100, China
| | - Shutu Xu
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, Northwest A&F University, Yangling, 712100, China
| | - Tifu Zhang
- Jiangsu Provincial Key Laboratory of Agrobiology, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Lin Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
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16
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Zhao N, Li C, Yan Y, Wang H, Wang L, Jiang J, Chen S, Chen F. The transcriptional coactivator CmMBF1c is required for waterlogging tolerance in Chrysanthemum morifolium. HORTICULTURE RESEARCH 2022; 9:uhac215. [PMID: 36479581 PMCID: PMC9720447 DOI: 10.1093/hr/uhac215] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 09/15/2022] [Indexed: 06/17/2023]
Abstract
Waterlogging is one of the most serious abiotic stressors affecting Chrysanthemum morifolium during its lifespan. However, the molecular mechanisms underlying the waterlogging tolerance of chrysanthemum remain unclear. In this study, we discovered that the transcriptional coactivator MULTIPROTEIN BRIDGING FACTOR 1c (CmMBF1c) was significantly induced by waterlogging stress in chrysanthemums. Promoter sequence analysis and transient dual-luciferase assay using chrysanthemum protoplasts showed that the waterlogging-tolerant cultivar 'Nannongxuefeng' carried more response elements involved in waterlogging and hypoxia stress compared with the waterlogging-sensitive cultivar 'Qinglu', conferring on 'Nannongxuefeng' a stronger hypoxia responsive activity and higher CmMBF1c expression under waterlogging conditions. Subcellular localization and transcriptional activity assays showed that CmMBF1c protein was localized to the nucleus and had no transcriptional activation activity. Overexpression of CmMBF1c in 'Qinglu' enhanced its waterlogging tolerance by promoting its reactive oxygen species (ROS) scavenging ability and maintaining low ROS levels. However, RNAi-mediated knockdown of CmMBF1c in cultivar 'Nannongxuefeng' resulted in the opposite tendency. Yeast two-hybrid screening and tobacco bimolecular fluorescence complementation assays revealed that CmHRE2, a pivotal regulator of hypoxia response, could interact with CmMBF1c. In summary, this study demonstrates that CmMBF1c improves chrysanthemum waterlogging tolerance by regulating its ROS signaling pathway and interacting with CmHRE2. These findings together offer, to our knowledge, new mechanistic insights into chrysanthemum waterlogging tolerance and provide a rational foundation for future research on the genetic improvement of horticultural crops for waterlogging stress tolerance.
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Affiliation(s)
| | | | - Yajun Yan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
| | - Haibin Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
| | - Likai Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
| | - Jiafu Jiang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
| | - Sumei Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
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17
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Duan Z, Zhang M, Zhang Z, Liang S, Fan L, Yang X, Yuan Y, Pan Y, Zhou G, Liu S, Tian Z. Natural allelic variation of GmST05 controlling seed size and quality in soybean. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1807-1818. [PMID: 35642379 PMCID: PMC9398382 DOI: 10.1111/pbi.13865] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/23/2022] [Accepted: 05/27/2022] [Indexed: 05/26/2023]
Abstract
Seed size is one of the most important agronomic traits determining the yield of crops. Cloning the key genes controlling seed size and pyramiding their elite alleles will facilitate yield improvement. To date, few genes controlling seed size have been identified in soybean, a major crop that provides half of the plant oil and one quarter of the plant protein globally. Here, through a genome-wide association study of over 1800 soybean accessions, we determined that natural allelic variation at GmST05 (Seed Thickness 05) predominantly controlled seed thickness and size in soybean germplasm. Further analyses suggested that the two major haplotypes of GmST05 differed significantly at the transcriptional level. Transgenic experiments demonstrated that GmST05 positively regulated seed size and influenced oil and protein contents, possibly by regulating the transcription of GmSWEET10a. Population genetic diversity analysis suggested that allelic variations of GmST05 were selected during geographical differentiation but have not been fixed. In summary, natural variation in GmST05 determines transcription levels and influences seed size and quality in soybean, making it an important gene resource for soybean molecular breeding.
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Affiliation(s)
- Zongbiao Duan
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Min Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Zhifang Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Shan Liang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Lei Fan
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Xia Yang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yaqin Yuan
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yi Pan
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Guoan Zhou
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Shulin Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
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18
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Chen Q, Tian F, Cheng T, Jiang J, Zhu G, Gao Z, Lin H, Hu J, Qian Q, Fang X, Chen F. Translational repression of FZP mediated by CU-rich element/OsPTB interactions modulates panicle development in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:1319-1331. [PMID: 35293072 DOI: 10.1111/tpj.15737] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 03/03/2022] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
Panicle development is an important determinant of the grain number in rice. A thorough characterization of the molecular mechanism underlying panicle development will lead to improved breeding of high-yielding rice varieties. Frizzy Panicle (FZP), a critical gene for panicle development, is regulated by OsBZR1 and OsARFs at the transcriptional stage. However, the translational modulation of FZP has not been reported. We reveal that the CU-rich elements (CUREs) in the 3' UTR of the FZP mRNA are crucial for efficient FZP translation. The knockout of CUREs in the FZP 3' UTR or the over-expression of the FZP 3' UTR fragment containing CUREs resulted in an increase in FZP mRNA translation efficiency. Moreover, the number of secondary branches (NSB) and the grain number per panicle (GNP) decreased in the transformed rice plants. The CUREs in the 3' UTR of FZP mRNA were verified as the targets of the polypyrimidine tract-binding proteins OsPTB1 and OsPTB2 in rice. Both OsPTB1 and OsPTB2 were highly expressed in young panicles. The knockout of OsPTB1/2 resulted in an increase in the FZP translational efficiency and a decrease in the NSB and GNP. Furthermore, the over-expression of OsPTB1/2 decreased the translation of the reporter gene fused to FZP 3' UTR in vivo and in vitro. These results suggest that OsPTB1/2 can mediate FZP translational repression by interacting with CUREs in the 3' UTR of FZP mRNA, leading to changes in the NSB and GNP. Accordingly, in addition to transcriptional regulation, FZP expression is also fine-tuned at the translational stage during rice panicle development.
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Affiliation(s)
- Qiong Chen
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, The Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China
| | - Fa'an Tian
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, The Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Tingting Cheng
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, The Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jun'e Jiang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, The Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Guanlin Zhu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, The Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhenyu Gao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Haiyan Lin
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Jiang Hu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Xiaohua Fang
- Genetic Resource R&D Center, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Chang Zhou, 213001, China
| | - Fan Chen
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, The Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China
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19
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Gomez-Cano F, Chu YH, Cruz-Gomez M, Abdullah HM, Lee YS, Schnell DJ, Grotewold E. Exploring Camelina sativa lipid metabolism regulation by combining gene co-expression and DNA affinity purification analyses. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:589-606. [PMID: 35064997 DOI: 10.1111/tpj.15682] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 01/18/2022] [Accepted: 01/20/2022] [Indexed: 06/14/2023]
Abstract
Camelina (Camelina sativa) is an annual oilseed plant that is gaining momentum as a biofuel cover crop. Understanding gene regulatory networks is essential to deciphering plant metabolic pathways, including lipid metabolism. Here, we take advantage of a growing collection of gene expression datasets to predict transcription factors (TFs) associated with the control of Camelina lipid metabolism. We identified approximately 350 TFs highly co-expressed with lipid-related genes (LRGs). These TFs are highly represented in the MYB, AP2/ERF, bZIP, and bHLH families, including a significant number of homologs of well-known Arabidopsis lipid and seed developmental regulators. After prioritizing the top 22 TFs for further validation, we identified DNA-binding sites and predicted target genes for 16 out of the 22 TFs tested using DNA affinity purification followed by sequencing (DAP-seq). Enrichment analyses of targets supported the co-expression prediction for most TF candidates, and the comparison to Arabidopsis revealed some common themes, but also aspects unique to Camelina. Within the top potential lipid regulators, we identified CsaMYB1, CsaABI3AVP1-2, CsaHB1, CsaNAC2, CsaMYB3, and CsaNAC1 as likely involved in the control of seed fatty acid elongation and CsaABI3AVP1-2 and CsabZIP1 as potential regulators of the synthesis and degradation of triacylglycerols (TAGs), respectively. Altogether, the integration of co-expression data and DNA-binding assays permitted us to generate a high-confidence and short list of Camelina TFs involved in the control of lipid metabolism during seed development.
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Affiliation(s)
- Fabio Gomez-Cano
- Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, Room 212, Biochemistry Building, East Lansing, MI, 48824-6473, USA
| | - Yi-Hsuan Chu
- Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, Room 212, Biochemistry Building, East Lansing, MI, 48824-6473, USA
| | - Mariel Cruz-Gomez
- Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, Room 212, Biochemistry Building, East Lansing, MI, 48824-6473, USA
| | - Hesham M Abdullah
- Department of Plant Biology, Michigan State University, 612 Wilson Road, Room 166, East Lansing, MI, 48824-1312, USA
- Biotechnology Department, Faculty of Agriculture, Al-Azhar University, Cairo, 11651, Egypt
| | - Yun Sun Lee
- Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, Room 212, Biochemistry Building, East Lansing, MI, 48824-6473, USA
| | - Danny J Schnell
- Department of Plant Biology, Michigan State University, 612 Wilson Road, Room 166, East Lansing, MI, 48824-1312, USA
| | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, Room 212, Biochemistry Building, East Lansing, MI, 48824-6473, USA
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20
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Mao H, Li S, Chen B, Jian C, Mei F, Zhang Y, Li F, Chen N, Li T, Du L, Ding L, Wang Z, Cheng X, Wang X, Kang Z. Variation in cis-regulation of a NAC transcription factor contributes to drought tolerance in wheat. MOLECULAR PLANT 2022; 15:276-292. [PMID: 34793983 DOI: 10.1016/j.molp.2021.11.007] [Citation(s) in RCA: 73] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 10/28/2021] [Accepted: 11/11/2021] [Indexed: 06/13/2023]
Abstract
Drought is a major environmental factor limiting wheat production worldwide, and developing drought-tolerant cultivars is a central challenge for wheat breeders globally. Therefore, it is important to identify genetic components determining drought tolerance in wheat. In this study, we identified a wheat NAC gene (TaNAC071-A) that is tightly associated with drought tolerance by a genome-wide association study. Knockdown of TaNAC071-A in wheat attenuated plant drought tolerance, whereas its overexpression significantly enhanced drought tolerance through improved water-use efficiency and increased expression of stress-responsive genes. This heightened water-saving mechanism mitigated the yield loss caused by water deficit. Further candidate gene association analysis showed that a 108-bp insertion in the promoter of TaNAC071-A alters its expression level and contributes to variation in drought tolerance among wheat accessions. This insertion contains two MYB cis-regulatory elements (CREs) that can be directly bound by the MYB transcription activator, TaMYBL1, thereby leading to increased TaNAC071-A expression and plant drought tolerance. Importantly, introgression of this 108-bp insertion allele, TaNAC071-AIn-693, into drought-sensitive cultivars could improve their drought tolerance, demonstrating that it is a valuable genetic resource for wheat breeding. Taken together, our findings highlight a major breakthrough in determining the genetic basis underlying phenotypic variation in wheat drought tolerance and showcase the potential of exploiting CRE-containing indels for improving important agronomical traits.
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Affiliation(s)
- Hude Mao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China; Pioneering Innovation Center for Wheat Stress Tolerance Improvement, State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, Shaanxi 712100, China.
| | - Shumin Li
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Bin Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chao Jian
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Fangming Mei
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yifang Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Fangfang Li
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Nan Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Tian Li
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Linying Du
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Science, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Li Ding
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhongxue Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xinxiu Cheng
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaojing Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Science, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China; Pioneering Innovation Center for Wheat Stress Tolerance Improvement, State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, Shaanxi 712100, China; Yangling Seed Industry Innovation Center, Yangling, Shaanxi 712100, China.
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21
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Schmitz RJ, Grotewold E, Stam M. Cis-regulatory sequences in plants: Their importance, discovery, and future challenges. THE PLANT CELL 2022; 34:718-741. [PMID: 34918159 PMCID: PMC8824567 DOI: 10.1093/plcell/koab281] [Citation(s) in RCA: 110] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 10/20/2021] [Indexed: 05/19/2023]
Abstract
The identification and characterization of cis-regulatory DNA sequences and how they function to coordinate responses to developmental and environmental cues is of paramount importance to plant biology. Key to these regulatory processes are cis-regulatory modules (CRMs), which include enhancers and silencers. Despite the extraordinary advances in high-quality sequence assemblies and genome annotations, the identification and understanding of CRMs, and how they regulate gene expression, lag significantly behind. This is especially true for their distinguishing characteristics and activity states. Here, we review the current knowledge on CRMs and breakthrough technologies enabling identification, characterization, and validation of CRMs; we compare the genomic distributions of CRMs with respect to their target genes between different plant species, and discuss the role of transposable elements harboring CRMs in the evolution of gene expression. This is an exciting time to study cis-regulomes in plants; however, significant existing challenges need to be overcome to fully understand and appreciate the role of CRMs in plant biology and in crop improvement.
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Affiliation(s)
- Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
| | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
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22
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Wu X, Liang Y, Gao H, Wang J, Zhao Y, Hua L, Yuan Y, Wang A, Zhang X, Liu J, Zhou J, Meng X, Zhang D, Lin S, Huang X, Han B, Li J, Wang Y. Enhancing rice grain production by manipulating the naturally evolved cis-regulatory element-containing inverted repeat sequence of OsREM20. MOLECULAR PLANT 2021; 14:997-1011. [PMID: 33741527 DOI: 10.1016/j.molp.2021.03.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/19/2021] [Accepted: 03/14/2021] [Indexed: 05/05/2023]
Abstract
Grain number per panicle (GNP) is an important agronomic trait that contributes to rice grain yield. Despite its importance in rice breeding, the molecular mechanism underlying GNP regulation remains largely unknown. In this study, we identified a previously unrecognized regulatory gene that controls GNP in rice, Oryza sativa REPRODUCTIVE MERISTEM 20 (OsREM20), which encodes a B3 domain transcription factor. Through genetic analysis and transgenic validation we found that genetic variation in the CArG box-containing inverted repeat (IR) sequence of the OsREM20 promoter alters its expression level and contributes to GNP variation among rice varieties. Furthermore, we revealed that the IR sequence regulates OsREM20 expression by affecting the direct binding of OsMADS34 to the CArG box within the IR sequence. Interestingly, the divergent pOsREM20IR and pOsREM20ΔIR alleles were found to originate from different Oryza rufipogon accessions, and were independently inherited into the japonica and indica subspecies, respectively, during domestication. Importantly, we demonstrated that IR sequence variations in the OsREM20 promoter can be utilized for germplasm improvement through either genome editing or traditional breeding. Taken together, our study characterizes novel genetic variations responsible for GNP diversity in rice, reveals the underlying molecular mechanism in the regulation of agronomically important gene expression, and provides a promising strategy for improving rice production by manipulating the cis-regulatory element-containing IR sequence.
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Affiliation(s)
- Xiaowei Wu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan Liang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Hengbin Gao
- College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Jiyao Wang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan Zhao
- National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Lekai Hua
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yundong Yuan
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ahong Wang
- National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Xiaohui Zhang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiafan Liu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jie Zhou
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiangbing Meng
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Dahan Zhang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shaoyang Lin
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xuehui Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Bin Han
- CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Jiayang Li
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yonghong Wang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China; College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, China.
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23
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Wang X, Aguirre L, Rodríguez-Leal D, Hendelman A, Benoit M, Lippman ZB. Dissecting cis-regulatory control of quantitative trait variation in a plant stem cell circuit. NATURE PLANTS 2021; 7:419-427. [PMID: 33846596 DOI: 10.1038/s41477-021-00898-x] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 03/10/2021] [Indexed: 05/22/2023]
Abstract
Cis-regulatory mutations underlie important crop domestication and improvement traits1,2. However, limited allelic diversity has hindered functional dissection of the large number of cis-regulatory elements and their potential interactions, thereby precluding a deeper understanding of how cis-regulatory variation impacts traits quantitatively. Here, we engineered over 60 promoter alleles in two tomato fruit size genes3,4 to characterize cis-regulatory sequences and study their functional relationships. We found that targeted mutations in conserved promoter sequences of SlCLV3, a repressor of stem cell proliferation5,6, have a weak impact on fruit locule number. Pairwise combinations of these mutations mildly enhance this phenotype, revealing additive and synergistic relationships between conserved regions and further suggesting even higher-order cis-regulatory interactions within the SlCLV3 promoter. In contrast, SlWUS, a positive regulator of stem cell proliferation repressed by SlCLV3 (refs. 5,6), is more tolerant to promoter perturbations. Our results show that complex interplay among cis-regulatory variants can shape quantitative variation, and suggest that empirical dissections of this hidden complexity can guide promoter engineering to predictably modify crop traits.
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Affiliation(s)
- Xingang Wang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Lyndsey Aguirre
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Daniel Rodríguez-Leal
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Inari Agriculture, Cambridge, MA, USA
| | - Anat Hendelman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Matthias Benoit
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Zachary B Lippman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
- School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
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24
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Hendelman A, Zebell S, Rodriguez-Leal D, Dukler N, Robitaille G, Wu X, Kostyun J, Tal L, Wang P, Bartlett ME, Eshed Y, Efroni I, Lippman ZB. Conserved pleiotropy of an ancient plant homeobox gene uncovered by cis-regulatory dissection. Cell 2021; 184:1724-1739.e16. [PMID: 33667348 DOI: 10.1016/j.cell.2021.02.001] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 01/03/2021] [Accepted: 02/01/2021] [Indexed: 01/09/2023]
Abstract
Divergence of gene function is a hallmark of evolution, but assessing functional divergence over deep time is not trivial. The few alleles available for cross-species studies often fail to expose the entire functional spectrum of genes, potentially obscuring deeply conserved pleiotropic roles. Here, we explore the functional divergence of WUSCHEL HOMEOBOX9 (WOX9), suggested to have species-specific roles in embryo and inflorescence development. Using a cis-regulatory editing drive system, we generate a comprehensive allelic series in tomato, which revealed hidden pleiotropic roles for WOX9. Analysis of accessible chromatin and conserved cis-regulatory sequences identifies the regions responsible for this pleiotropic activity, the functions of which are conserved in groundcherry, a tomato relative. Mimicking these alleles in Arabidopsis, distantly related to tomato and groundcherry, reveals new inflorescence phenotypes, exposing a deeply conserved pleiotropy. We suggest that targeted cis-regulatory mutations can uncover conserved gene functions and reduce undesirable effects in crop improvement.
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Affiliation(s)
- Anat Hendelman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Sophia Zebell
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA; Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | - Noah Dukler
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Gina Robitaille
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA; Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Xuelin Wu
- The Salk Institute for Biological Research, San Diego, CA, USA
| | - Jamie Kostyun
- Biology Department, University of Massachusetts Amherst, Amherst, MA, USA
| | - Lior Tal
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Peipei Wang
- Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, The Hebrew University, Rehovot, Israel
| | | | - Yuval Eshed
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Idan Efroni
- Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, The Hebrew University, Rehovot, Israel.
| | - Zachary B Lippman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA; Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
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25
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Shoji T, Yuan L. ERF Gene Clusters: Working Together to Regulate Metabolism. TRENDS IN PLANT SCIENCE 2021; 26:23-32. [PMID: 32883605 DOI: 10.1016/j.tplants.2020.07.015] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 07/28/2020] [Accepted: 07/30/2020] [Indexed: 05/18/2023]
Abstract
Plants produce structurally diverse specialized metabolites, including bioactive alkaloids and terpenoids, in response to biotic and abiotic environmental stresses. The APETALA2/ETHYLENE RESPONSE FACTOR (AP2/ERF) family of transcription factors (TFs) play key roles in regulating biosynthesis of specialized metabolites. Increasing genomic and functional evidence shows that a subset of the ERF genes occurs in clusters on the chromosomes. These jasmonate-responsive ERF TF gene clusters control the biosynthesis of many important metabolites, from natural products, such as nicotine and steroidal glycoalkaloids (SGAs), to pharmaceuticals, such as artemisinin, vinblastine, and vincristine. Here, we review the function, regulation, and evolution of ERF clusters and highlight recent advances in understanding the distinct roles of clustered ERF genes and their possible application in metabolic engineering.
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Affiliation(s)
- Tsubasa Shoji
- Department of Biological Science, Nara Institute of Science and Technology, Ikoma, Japan.
| | - Ling Yuan
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, USA; South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
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Guo W, Chen L, Herrera-Estrella L, Cao D, Tran LSP. Altering Plant Architecture to Improve Performance and Resistance. TRENDS IN PLANT SCIENCE 2020; 25:1154-1170. [PMID: 32595089 DOI: 10.1016/j.tplants.2020.05.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 05/11/2020] [Accepted: 05/26/2020] [Indexed: 06/11/2023]
Abstract
High-stress resistance and yield are major goals in crop cultivation, which can be addressed by modifying plant architecture. Significant progress has been made in recent years to understand how plant architecture is controlled under various growth conditions, recognizing the central role phytohormones play in response to environmental stresses. miRNAs, transcription factors, and other associated proteins regulate plant architecture, mainly via the modulation of hormone homeostasis and signaling. To generate crop plants of ideal architecture, we propose simultaneous editing of multiple genes involved in the regulatory networks associated with plant architecture as a feasible strategy. This strategy can help to address the need to increase grain yield and/or stress resistance under the pressures of the ever-increasing world population and climate change.
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Affiliation(s)
- Wei Guo
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Limiao Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Luis Herrera-Estrella
- The Unidad de Genomica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato, Mexico; Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, TX, USA
| | - Dong Cao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China.
| | - Lam-Son Phan Tran
- Institute of Research and Development, Duy Tan University, 03 Quang Trung, Da Nang 550000, Vietnam; Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan.
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Galli M, Feng F, Gallavotti A. Mapping Regulatory Determinants in Plants. Front Genet 2020; 11:591194. [PMID: 33193733 PMCID: PMC7655918 DOI: 10.3389/fgene.2020.591194] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 09/28/2020] [Indexed: 12/24/2022] Open
Abstract
The domestication and improvement of many plant species have frequently involved modulation of transcriptional outputs and continue to offer much promise for targeted trait engineering. The cis-regulatory elements (CREs) controlling these trait-associated transcriptional variants however reside within non-coding regions that are currently poorly annotated in most plant species. This is particularly true in large crop genomes where regulatory regions constitute only a small fraction of the total genomic space. Furthermore, relatively little is known about how CREs function to modulate transcription in plants. Therefore understanding where regulatory regions are located within a genome, what genes they control, and how they are structured are important factors that could be used to guide both traditional and synthetic plant breeding efforts. Here, we describe classic examples of regulatory instances as well as recent advances in plant regulatory genomics. We highlight valuable molecular tools that are enabling large-scale identification of CREs and offering unprecedented insight into how genes are regulated in diverse plant species. We focus on chromatin environment, transcription factor (TF) binding, the role of transposable elements, and the association between regulatory regions and target genes.
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Affiliation(s)
- Mary Galli
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, United States
| | - Fan Feng
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, United States
| | - Andrea Gallavotti
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, United States.,Department of Plant Biology, Rutgers University, New Brunswick, NJ, United States
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Parvathaneni RK, Bertolini E, Shamimuzzaman M, Vera DL, Lung PY, Rice BR, Zhang J, Brown PJ, Lipka AE, Bass HW, Eveland AL. The regulatory landscape of early maize inflorescence development. Genome Biol 2020; 21:165. [PMID: 32631399 PMCID: PMC7336428 DOI: 10.1186/s13059-020-02070-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Accepted: 06/11/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The functional genome of agronomically important plant species remains largely unexplored, yet presents a virtually untapped resource for targeted crop improvement. Functional elements of regulatory DNA revealed through profiles of chromatin accessibility can be harnessed for fine-tuning gene expression to optimal phenotypes in specific environments. RESULT Here, we investigate the non-coding regulatory space in the maize (Zea mays) genome during early reproductive development of pollen- and grain-bearing inflorescences. Using an assay for differential sensitivity of chromatin to micrococcal nuclease (MNase) digestion, we profile accessible chromatin and nucleosome occupancy in these largely undifferentiated tissues and classify at least 1.6% of the genome as accessible, with the majority of MNase hypersensitive sites marking proximal promoters, but also 3' ends of maize genes. This approach maps regulatory elements to footprint-level resolution. Integration of complementary transcriptome profiles and transcription factor occupancy data are used to annotate regulatory factors, such as combinatorial transcription factor binding motifs and long non-coding RNAs, that potentially contribute to organogenesis, including tissue-specific regulation between male and female inflorescence structures. Finally, genome-wide association studies for inflorescence architecture traits based solely on functional regions delineated by MNase hypersensitivity reveals new SNP-trait associations in known regulators of inflorescence development as well as new candidates. CONCLUSIONS These analyses provide a comprehensive look into the cis-regulatory landscape during inflorescence differentiation in a major cereal crop, which ultimately shapes architecture and influences yield potential.
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Affiliation(s)
| | | | - Md Shamimuzzaman
- Donald Danforth Plant Science Center, St. Louis, MO 63132 USA
- Current address: USDA-ARS Edward T. Schafer Agricultural Research Center, Fargo, ND 58102 USA
| | - Daniel L. Vera
- The Center for Genomics and Personalized Medicine, Florida State University, Tallahassee, FL 32306 USA
- Current address: Department of Genetics, Harvard Medical School, Boston, MA 02115 USA
| | - Pei-Yau Lung
- Department of Statistics, Florida State University, Tallahassee, FL 32306 USA
| | - Brian R. Rice
- Department of Crop Sciences, University of Illinois Urbana-Champaign, Urbana, IL 61801 USA
| | - Jinfeng Zhang
- Department of Statistics, Florida State University, Tallahassee, FL 32306 USA
| | - Patrick J. Brown
- Department of Plant Sciences, University of California, Davis, CA 95616 USA
| | - Alexander E. Lipka
- Department of Crop Sciences, University of Illinois Urbana-Champaign, Urbana, IL 61801 USA
| | - Hank W. Bass
- Department of Biological Science, Florida State University, Tallahassee, FL 32306 USA
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Díaz-Valenzuela E, Sawers RH, Cibrián-Jaramillo A. Cis- and Trans-Regulatory Variations in the Domestication of the Chili Pepper Fruit. Mol Biol Evol 2020; 37:1593-1603. [PMID: 32031611 PMCID: PMC7253206 DOI: 10.1093/molbev/msaa027] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The process of domestication requires the rapid transformation of the wild morphology into the cultivated forms that humans select for. This process often takes place through changes in the regulation of genes, yet, there is no definite pattern on the role of cis- and trans-acting regulatory variations in the domestication of the fruit among crops. Using allele-specific expression and network analyses, we characterized the regulatory patterns and the inheritance of gene expression in wild and cultivated accessions of chili pepper, a crop with remarkable fruit morphological variation. We propose that gene expression differences associated to the cultivated form are best explained by cis-regulatory hubs acting through trans-regulatory cascades. We show that in cultivated chili, the expression of genes associated with fruit morphology is partially recessive with respect to those in the wild relative, consistent with the hybrid fruit phenotype. Decreased expression of fruit maturation and growth genes in cultivated chili suggest that selection for loss-of-function took place in its domestication. Trans-regulatory changes underlie the majority of the genes showing regulatory divergence and had larger effect sizes on gene expression than cis-regulatory variants. Network analysis of selected cis-regulated genes, including ARP9 and MED25, indicated their interaction with many transcription factors involved in organ growth and fruit ripening. Differentially expressed genes linked to cis-regulatory variants and their interactions with downstream trans-acting genes have the potential to drive the morphological differences observed between wild and cultivated fruits and provide an attractive mechanism of morphological transformation during the domestication of the chili pepper.
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Affiliation(s)
- Erik Díaz-Valenzuela
- Ecological and Evolutionary Genomics Laboratory, Unidad de Genomica Avanzada (Langebio), Irapuato, Guanajuato, México
| | - Ruairidh H Sawers
- Department of Plant Science, The Pennsylvania State University, University Park State College, University Park, PA
| | - Angélica Cibrián-Jaramillo
- Ecological and Evolutionary Genomics Laboratory, Unidad de Genomica Avanzada (Langebio), Irapuato, Guanajuato, México
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30
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Zhou P, Li Z, Magnusson E, Gomez Cano F, Crisp PA, Noshay JM, Grotewold E, Hirsch CN, Briggs SP, Springer NM. Meta Gene Regulatory Networks in Maize Highlight Functionally Relevant Regulatory Interactions. THE PLANT CELL 2020; 32:1377-1396. [PMID: 32184350 PMCID: PMC7203921 DOI: 10.1105/tpc.20.00080] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 03/06/2020] [Accepted: 03/16/2020] [Indexed: 05/22/2023]
Abstract
The regulation of gene expression is central to many biological processes. Gene regulatory networks (GRNs) link transcription factors (TFs) to their target genes and represent maps of potential transcriptional regulation. Here, we analyzed a large number of publically available maize (Zea mays) transcriptome data sets including >6000 RNA sequencing samples to generate 45 coexpression-based GRNs that represent potential regulatory relationships between TFs and other genes in different populations of samples (cross-tissue, cross-genotype, and tissue-and-genotype samples). While these networks are all enriched for biologically relevant interactions, different networks capture distinct TF-target associations and biological processes. By examining the power of our coexpression-based GRNs to accurately predict covarying TF-target relationships in natural variation data sets, we found that presence/absence changes rather than quantitative changes in TF gene expression are more likely associated with changes in target gene expression. Integrating information from our TF-target predictions and previous expression quantitative trait loci (eQTL) mapping results provided support for 68 TFs underlying 74 previously identified trans-eQTL hotspots spanning a variety of metabolic pathways. This study highlights the utility of developing multiple GRNs within a species to detect putative regulators of important plant pathways and provides potential targets for breeding or biotechnological applications.
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Affiliation(s)
- Peng Zhou
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota 55108
| | - Zhi Li
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Erika Magnusson
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota 55108
| | - Fabio Gomez Cano
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Peter A Crisp
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota 55108
| | - Jaclyn M Noshay
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota 55108
| | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Candice N Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Steven P Briggs
- Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093
| | - Nathan M Springer
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota 55108
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