1
|
Mishra S, Srivastava AK, Khan AW, Tran LSP, Nguyen HT. The era of panomics-driven gene discovery in plants. TRENDS IN PLANT SCIENCE 2024; 29:995-1005. [PMID: 38658292 DOI: 10.1016/j.tplants.2024.03.007] [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: 12/06/2023] [Revised: 03/01/2024] [Accepted: 03/08/2024] [Indexed: 04/26/2024]
Abstract
Panomics is an approach to integrate multiple 'omics' datasets, generated using different individuals or natural variations. Considering their diverse phenotypic spectrum, the phenome is inherently associated with panomics-based science, which is further combined with genomics, transcriptomics, metabolomics, and other omics techniques, either independently or collectively. Panomics has been accelerated through recent technological advancements in the field of genomics that enable the detection of population-wide structural variations (SVs) and hence offer unprecedented insights into the genetic variations contributing to important agronomic traits. The present review provides the recent trends of panomics-driven gene discovery toward various traits related to plant development, stress tolerance, accumulation of specialized metabolites, and domestication/dedomestication. In addition, the success stories are highlighted in the broader context of enhancing crop productivity.
Collapse
Affiliation(s)
- Shefali Mishra
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, Maharashtra 400085, India
| | - Ashish Kumar Srivastava
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, Maharashtra 400085, India; Homi Bhabha National Institute, Mumbai 400094, India.
| | - Aamir W Khan
- Division of Plant Science and Technology and National Center for Soybean Biotechnology, University of Missouri-Columbia, Columbia, MO 65211, USA
| | - Lam-Son Phan Tran
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, USA
| | - Henry T Nguyen
- Division of Plant Science and Technology and National Center for Soybean Biotechnology, University of Missouri-Columbia, Columbia, MO 65211, USA.
| |
Collapse
|
2
|
Hochholdinger F, Yu P. Molecular concepts to explain heterosis in crops. TRENDS IN PLANT SCIENCE 2024:S1360-1385(24)00215-2. [PMID: 39191625 DOI: 10.1016/j.tplants.2024.07.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Revised: 07/31/2024] [Accepted: 07/31/2024] [Indexed: 08/29/2024]
Abstract
Heterosis describes the superior performance of hybrid plants compared with their genetically distinct parents and is a pillar of global food security. Here we review the current status of the molecular dissection of heterosis. We discuss how extensive intraspecific structural genomic variation between parental genotypes leads to heterosis by genetic complementation in hybrids. Moreover, we survey how global gene expression complementation contributes to heterosis by hundreds of additionally active genes in hybrids and how overdominant single genes mediate heterosis in several species. Furthermore, we highlight the prominent role of the microbiome in improving the performance of hybrids. Taken together, the molecular understanding of heterosis will pave the way to accelerate hybrid productivity and a more sustainable agriculture.
Collapse
Affiliation(s)
- Frank Hochholdinger
- INRES, Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113 Bonn, Germany.
| | - Peng Yu
- INRES, Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113 Bonn, Germany; INRES, Institute of Crop Science and Resource Conservation, Root Functional Biology, University of Bonn, 53113 Bonn, Germany.
| |
Collapse
|
3
|
Mangal V, Verma LK, Singh SK, Saxena K, Roy A, Karn A, Rohit R, Kashyap S, Bhatt A, Sood S. Triumphs of genomic-assisted breeding in crop improvement. Heliyon 2024; 10:e35513. [PMID: 39170454 PMCID: PMC11336775 DOI: 10.1016/j.heliyon.2024.e35513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 07/23/2024] [Accepted: 07/30/2024] [Indexed: 08/23/2024] Open
Abstract
Conventional breeding approaches have played a significant role in meeting the food demand remarkably well until now. However, the increasing population, yield plateaus in certain crops, and limited recombination necessitate using genomic resources for genomics-assisted crop improvement programs. As a result of advancements in the next-generation sequence technology, GABs have developed dramatically to characterize allelic variants and facilitate their rapid and efficient incorporation in crop improvement programs. Genomics-assisted breeding (GAB) has played an important role in harnessing the potential of modern genomic tools, exploiting allelic variation from genetic resources and developing cultivars over the past decade. The availability of pangenomes for major crops has been a significant development, albeit with varying degrees of completeness. Even though adopting these technologies is essentially determined on economic grounds and cost-effective assays, which create a wealth of information that can be successfully used to exploit the latent potential of crops. GAB has been instrumental in harnessing the potential of modern genomic resources and exploiting allelic variation for genetic enhancement and cultivar development. GAB strategies will be indispensable for designing future crops and are expected to play a crucial role in breeding climate-smart crop cultivars with higher nutritional value.
Collapse
Affiliation(s)
- Vikas Mangal
- ICAR-Central Potato Research Institute (CPRI), Shimla, Himachal Pradesh, 171001, India
| | | | - Sandeep Kumar Singh
- Department of Genetics and Plant Breeding, Faculty of Agricultural Sciences, Siksha ‘O’ Anusandhan University, Bhubaneswar, Odisha, 751030, India
| | - Kanak Saxena
- Department of Genetics and Plant Breeding, Rabindranath Tagore University, Raisen, Madhya Pradesh, India
| | - Anirban Roy
- Division of Genetics and Plant Breeding, Ramakrishna Mission Vivekananda Educational and Research Institute (RKMVERI), Narendrapur, Kolkata, 700103, India
| | - Anandi Karn
- Plant Breeding & Graduate Program, IFAS - University of Florida, Gainesville, USA
| | - Rohit Rohit
- Department of Genetics and Plant Breeding, GBPUA&T, Pantnagar, Uttarakhand, 263145, India
| | - Shruti Kashyap
- Department of Genetics and Plant Breeding, GBPUA&T, Pantnagar, Uttarakhand, 263145, India
| | - Ashish Bhatt
- Department of Genetics and Plant Breeding, GBPUA&T, Pantnagar, Uttarakhand, 263145, India
| | - Salej Sood
- ICAR-Central Potato Research Institute (CPRI), Shimla, Himachal Pradesh, 171001, India
| |
Collapse
|
4
|
Liu L, Zhan J, Yan J. Engineering the future cereal crops with big biological data: toward intelligence-driven breeding by design. J Genet Genomics 2024; 51:781-789. [PMID: 38531485 DOI: 10.1016/j.jgg.2024.03.005] [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: 10/30/2023] [Revised: 03/17/2024] [Accepted: 03/17/2024] [Indexed: 03/28/2024]
Abstract
How to feed 10 billion human populations is one of the challenges that need to be addressed in the following decades, especially under an unpredicted climate change. Crop breeding, initiating from the phenotype-based selection by local farmers and developing into current biotechnology-based breeding, has played a critical role in securing the global food supply. However, regarding the changing environment and ever-increasing human population, can we breed outstanding crop varieties fast enough to achieve high productivity, good quality, and widespread adaptability? This review outlines the recent achievements in understanding cereal crop breeding, including the current knowledge about crop agronomic traits, newly developed techniques, crop big biological data research, and the possibility of integrating them for intelligence-driven breeding by design, which ushers in a new era of crop breeding practice and shapes the novel architecture of future crops. This review focuses on the major cereal crops, including rice, maize, and wheat, to explain how intelligence-driven breeding by design is becoming a reality.
Collapse
Affiliation(s)
- Lei Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
| | - Jimin Zhan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| |
Collapse
|
5
|
Jamil S, Ahmad S, Shahzad R, Umer N, Kanwal S, Rehman HM, Rana IA, Atif RM. Leveraging Multiomics Insights and Exploiting Wild Relatives' Potential for Drought and Heat Tolerance in Maize. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:16048-16075. [PMID: 38980762 DOI: 10.1021/acs.jafc.4c01375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2024]
Abstract
Climate change, particularly drought and heat stress, may slash agricultural productivity by 25.7% by 2080, with maize being the hardest hit. Therefore, unraveling the molecular nature of plant responses to these stressors is vital for the development of climate-smart maize. This manuscript's primary objective was to examine how maize plants respond to these stresses, both individually and in combination. Additionally, the paper delved into harnessing the potential of maize wild relatives as a valuable genetic resource and leveraging AI-based technologies to boost maize resilience. The role of multiomics approaches particularly genomics and transcriptomics in dissecting the genetic basis of stress tolerance was also highlighted. The way forward was proposed to utilize a bunch of information obtained through omics technologies by an interdisciplinary state-of-the-art forward-looking big-data, cyberagriculture system, and AI-based approach to orchestrate the development of climate resilient maize genotypes.
Collapse
Affiliation(s)
- Shakra Jamil
- Agricultural Biotechnology Research Institute, Ayub Agricultural Research Institute, Faisalabad 38000, Pakistan
| | - Shakeel Ahmad
- Seed Centre and Plant Genetic Resources Bank Ministry of Environment, Water and Agriculture, Riyadh 14712, Saudi Arabia
| | - Rahil Shahzad
- Agricultural Biotechnology Research Institute, Ayub Agricultural Research Institute, Faisalabad 38000, Pakistan
| | - Noroza Umer
- Dr. Ikram ul Haq - Institute of Industrial Biotechnology, Government College University, Lahore 54590, Pakistan
| | - Shamsa Kanwal
- Agricultural Biotechnology Research Institute, Ayub Agricultural Research Institute, Faisalabad 38000, Pakistan
| | - Hafiz Mamoon Rehman
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad 38000, Pakistan
| | - Iqrar Ahmad Rana
- Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture, Faisalabad 38000, Pakistan
| | - Rana Muhammad Atif
- Department of Plant Sciences, University of California Davis, California 95616, United States
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad 38000, Pakistan
- Precision Agriculture and Analytics Lab, Centre for Advanced Studies in Agriculture and Food Security, National Centre in Big Data and Cloud Computing, University of Agriculture, Faisalabad 38000, Pakistan
| |
Collapse
|
6
|
Cannon EK, Portwood JL, Hayford RK, Haley OC, Gardiner JM, Andorf CM, Woodhouse MR. Enhanced pan-genomic resources at the maize genetics and genomics database. Genetics 2024; 227:iyae036. [PMID: 38577974 DOI: 10.1093/genetics/iyae036] [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: 11/13/2023] [Accepted: 01/13/2024] [Indexed: 04/06/2024] Open
Abstract
Pan-genomes, encompassing the entirety of genetic sequences found in a collection of genomes within a clade, are more useful than single reference genomes for studying species diversity. This is especially true for a species like Zea mays, which has a particularly diverse and complex genome. Presenting pan-genome data, analyses, and visualization is challenging, especially for a diverse species, but more so when pan-genomic data is linked to extensive gene model and gene data, including classical gene information, markers, insertions, expression and proteomic data, and protein structures as is the case at MaizeGDB. Here, we describe MaizeGDB's expansion to include the genic subset of the Zea pan-genome in a pan-gene data center featuring the maize genomes hosted at MaizeGDB, and the outgroup teosinte Zea genomes from the Pan-Andropoganeae project. The new data center offers a variety of browsing and visualization tools, including sequence alignment visualization, gene trees and other tools, to explore pan-genes in Zea that were calculated by the pipeline Pandagma. Combined, these data will help maize researchers study the complexity and diversity of Zea, and to use the comparative functions to validate pan-gene relationships for a selected gene model.
Collapse
Affiliation(s)
- Ethalinda K Cannon
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, USA
| | - John L Portwood
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, USA
| | - Rita K Hayford
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, USA
| | - Olivia C Haley
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, USA
| | - Jack M Gardiner
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Carson M Andorf
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, USA
- Department of Computer Science, Iowa State University, Ames, IA 50011, USA
| | | |
Collapse
|
7
|
Chen K, Yang H, Wu D, Peng Y, Lian L, Bai L, Wang L. Weed biology and management in the multi-omics era: Progress and perspectives. PLANT COMMUNICATIONS 2024; 5:100816. [PMID: 38219012 PMCID: PMC11009161 DOI: 10.1016/j.xplc.2024.100816] [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: 09/13/2023] [Revised: 11/20/2023] [Accepted: 01/08/2024] [Indexed: 01/15/2024]
Abstract
Weeds pose a significant threat to crop production, resulting in substantial yield reduction. In addition, they possess robust weedy traits that enable them to survive in extreme environments and evade human control. In recent years, the application of multi-omics biotechnologies has helped to reveal the molecular mechanisms underlying these weedy traits. In this review, we systematically describe diverse applications of multi-omics platforms for characterizing key aspects of weed biology, including the origins of weed species, weed classification, and the underlying genetic and molecular bases of important weedy traits such as crop-weed interactions, adaptability to different environments, photoperiodic flowering responses, and herbicide resistance. In addition, we discuss limitations to the application of multi-omics techniques in weed science, particularly compared with their extensive use in model plants and crops. In this regard, we provide a forward-looking perspective on the future application of multi-omics technologies to weed science research. These powerful tools hold great promise for comprehensively and efficiently unraveling the intricate molecular genetic mechanisms that underlie weedy traits. The resulting advances will facilitate the development of sustainable and highly effective weed management strategies, promoting greener practices in agriculture.
Collapse
Affiliation(s)
- Ke Chen
- Key Laboratory of Indica Rice Genetics and Breeding in the Middle and Lower Reaches of Yangtze River Valley, Ministry of Agriculture and Rural Affairs, Hunan Rice Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China; State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha 410125, China; Longping Branch, College of Biology, Hunan University, Changsha 410125, China; Hunan Weed Science Key Laboratory, Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Haona Yang
- State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha 410125, China; Hunan Weed Science Key Laboratory, Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Di Wu
- State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Yajun Peng
- State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha 410125, China; Hunan Weed Science Key Laboratory, Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Lei Lian
- Qingdao Kingagroot Compounds Co. Ltd, Qingdao 266000, China
| | - Lianyang Bai
- Key Laboratory of Indica Rice Genetics and Breeding in the Middle and Lower Reaches of Yangtze River Valley, Ministry of Agriculture and Rural Affairs, Hunan Rice Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China; State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha 410125, China; Longping Branch, College of Biology, Hunan University, Changsha 410125, China; Huangpu Research Institute of Longping Agricultural Science and Technology, Guangzhou 510715, China; Hunan Weed Science Key Laboratory, Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China.
| | - Lifeng Wang
- Key Laboratory of Indica Rice Genetics and Breeding in the Middle and Lower Reaches of Yangtze River Valley, Ministry of Agriculture and Rural Affairs, Hunan Rice Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China; State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha 410125, China; Longping Branch, College of Biology, Hunan University, Changsha 410125, China; Huangpu Research Institute of Longping Agricultural Science and Technology, Guangzhou 510715, China; Hunan Weed Science Key Laboratory, Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China.
| |
Collapse
|
8
|
Wang H, Huang Y, Li Y, Cui Y, Xiang X, Zhu Y, Wang Q, Wang X, Ma G, Xiao Q, Huang X, Gao X, Wang J, Lu X, Larkins BA, Wang W, Wu Y. An ARF gene mutation creates flint kernel architecture in dent maize. Nat Commun 2024; 15:2565. [PMID: 38519520 PMCID: PMC10960022 DOI: 10.1038/s41467-024-46955-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 03/14/2024] [Indexed: 03/25/2024] Open
Abstract
Dent and flint kernel architectures are important characteristics that affect the physical properties of maize kernels and their grain end uses. The genes controlling these traits are unknown, so it is difficult to combine the advantageous kernel traits of both. We found mutation of ARFTF17 in a dent genetic background reduces IAA content in the seed pericarp, creating a flint-like kernel phenotype. ARFTF17 is highly expressed in the pericarp and encodes a protein that interacts with and inhibits MYB40, a transcription factor with the dual functions of repressing PIN1 expression and transactivating genes for flavonoid biosynthesis. Enhanced flavonoid biosynthesis could reduce the metabolic flux responsible for auxin biosynthesis. The decreased IAA content of the dent pericarp appears to reduce cell division and expansion, creating a shorter, denser kernel. Introgression of the ARFTF17 mutation into dent inbreds and hybrids improved their kernel texture, integrity, and desiccation, without affecting yield.
Collapse
Affiliation(s)
- Haihai Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yongcai Huang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yujie Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Yahui Cui
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Xiaoli Xiang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yidong Zhu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiong Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Xiaoqing Wang
- Forestry and Pomology Research Institute, Shanghai Academy of Agriculture Sciences, Shanghai, 201403, China
| | - Guangjin Ma
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiao Xiao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Xing Huang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoyan Gao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Jiechen Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Xiaoduo Lu
- Institute of Molecular Breeding for Maize, Qilu Normal University, Jinan, 250200, China
| | - Brian A Larkins
- School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Wenqin Wang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China.
| | - Yongrui Wu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.
| |
Collapse
|
9
|
Berdan EL, Aubier TG, Cozzolino S, Faria R, Feder JL, Giménez MD, Joron M, Searle JB, Mérot C. Structural Variants and Speciation: Multiple Processes at Play. Cold Spring Harb Perspect Biol 2024; 16:a041446. [PMID: 38052499 PMCID: PMC10910405 DOI: 10.1101/cshperspect.a041446] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Research on the genomic architecture of speciation has increasingly revealed the importance of structural variants (SVs) that affect the presence, abundance, position, and/or direction of a nucleotide sequence. SVs include large chromosomal rearrangements such as fusion/fissions and inversions and translocations, as well as smaller variants such as duplications, insertions, and deletions (CNVs). Although we have ample evidence that SVs play a key role in speciation, the underlying mechanisms differ depending on the type and length of the SV, as well as the ecological, demographic, and historical context. We review predictions and empirical evidence for classic processes such as underdominance due to meiotic aberrations and the coupling effect of recombination suppression before exploring how recent sequencing methodologies illuminate the prevalence and diversity of SVs. We discuss specific properties of SVs and their impact throughout the genome, highlighting that multiple processes are at play, and possibly interacting, in the relationship between SVs and speciation.
Collapse
Affiliation(s)
- Emma L Berdan
- Department of Marine Sciences, Gothenburg University, Gothenburg 40530, Sweden
- Bioinformatics Core, Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Thomas G Aubier
- Laboratoire Évolution & Diversité Biologique, Université Paul Sabatier Toulouse III, UMR 5174, CNRS/IRD, 31077 Toulouse, France
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Salvatore Cozzolino
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, 80126 Napoli, Italia
| | - Rui Faria
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, 4485-661 Vairão, Portugal
| | - Jeffrey L Feder
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Mabel D Giménez
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Genética Humana de Misiones (IGeHM), Parque de la Salud de la Provincia de Misiones "Dr. Ramón Madariaga," N3300KAZ Posadas, Misiones, Argentina
- Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, N3300LQH Posadas, Misiones, Argentina
| | - Mathieu Joron
- Centre d'Ecologie Fonctionnelle et Evolutive, Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York 14853, USA
| | - Claire Mérot
- CNRS, UMR 6553 Ecobio, OSUR, Université de Rennes, 35000 Rennes, France
| |
Collapse
|
10
|
Aversano R, Iovene M, Esposito S, L'Abbate A, Villano C, Di Serio E, Cardone MF, Bergamini C, Cigliano RA, D'Amelia V, Frusciante L, Carputo D. Distinct structural variants and repeat landscape shape the genomes of the ancient grapes Aglianico and Falanghina. BMC PLANT BIOLOGY 2024; 24:88. [PMID: 38317087 PMCID: PMC10845522 DOI: 10.1186/s12870-024-04778-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 01/29/2024] [Indexed: 02/07/2024]
Abstract
Mounting evidence recognizes structural variations (SVs) and repetitive DNA sequences as crucial players in shaping the existing grape phenotypic diversity at intra- and inter-species levels. To deepen our understanding on the abundance, diversity, and distribution of SVs and repetitive DNAs, including transposable elements (TEs) and tandemly repeated satellite DNA (satDNAs), we re-sequenced the genomes of the ancient grapes Aglianico and Falanghina. The analysis of large copy number variants (CNVs) detected candidate polymorphic genes that are involved in the enological features of these varieties. In a comparative analysis of Aglianico and Falanghina sequences with 21 publicly available genomes of cultivated grapes, we provided a genome-wide annotation of grape TEs at the lineage level. We disclosed that at least two main clusters of grape cultivars could be identified based on the TEs content. Multiple TEs families appeared either significantly enriched or depleted. In addition, in silico and cytological analyses provided evidence for a diverse chromosomal distribution of several satellite repeats between Aglianico, Falanghina, and other grapes. Overall, our data further improved our understanding of the intricate grape diversity held by two Italian traditional varieties, unveiling a pool of unique candidate genes never so far exploited in breeding for improved fruit quality.
Collapse
Affiliation(s)
- Riccardo Aversano
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy.
| | - Marina Iovene
- Institute of Biosciences and Bioresources, National Research Council of Italy (CNR-IBBR), Portici, Italy.
| | - Salvatore Esposito
- Institute of Biosciences and Bioresources, National Research Council of Italy (CNR-IBBR), Portici, Italy
- Research Centre for Cereal and Industrial Crops, Council for Agricultural Research and Economics (CREA-CI), Foggia, Italy
| | - Alberto L'Abbate
- Institute of Biomembranes, Bioenergetics, and Molecular Biotechnologies, National Research Council (IBIOM-CNR), Bari, Italy
| | - Clizia Villano
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Ermanno Di Serio
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Maria Francesca Cardone
- Research Centre for Viticulture and Enology, Council for Agricultural Research and Economics (CREA-VE), Turi, Italy
| | - Carlo Bergamini
- Research Centre for Viticulture and Enology, Council for Agricultural Research and Economics (CREA-VE), Turi, Italy
| | | | - Vincenzo D'Amelia
- Institute of Biosciences and Bioresources, National Research Council of Italy (CNR-IBBR), Portici, Italy
| | - Luigi Frusciante
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Domenico Carputo
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| |
Collapse
|
11
|
Andorf CM, Haley OC, Hayford RK, Portwood JL, Harding S, Sen S, Cannon EK, Gardiner JM, Kim HS, Woodhouse MR. PanEffect: a pan-genome visualization tool for variant effects in maize. Bioinformatics 2024; 40:btae073. [PMID: 38337024 PMCID: PMC10881103 DOI: 10.1093/bioinformatics/btae073] [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: 12/16/2023] [Revised: 01/30/2024] [Accepted: 02/06/2024] [Indexed: 02/12/2024] Open
Abstract
SUMMARY Understanding the effects of genetic variants is crucial for accurately predicting traits and functional outcomes. Recent approaches have utilized artificial intelligence and protein language models to score all possible missense variant effects at the proteome level for a single genome, but a reliable tool is needed to explore these effects at the pan-genome level. To address this gap, we introduce a new tool called PanEffect. We implemented PanEffect at MaizeGDB to enable a comprehensive examination of the potential effects of coding variants across 50 maize genomes. The tool allows users to visualize over 550 million possible amino acid substitutions in the B73 maize reference genome and to observe the effects of the 2.3 million natural variations in the maize pan-genome. Each variant effect score, calculated from the Evolutionary Scale Modeling (ESM) protein language model, shows the log-likelihood ratio difference between B73 and all variants in the pan-genome. These scores are shown using heatmaps spanning benign outcomes to potential functional consequences. In addition, PanEffect displays secondary structures and functional domains along with the variant effects, offering additional functional and structural context. Using PanEffect, researchers now have a platform to explore protein variants and identify genetic targets for crop enhancement. AVAILABILITY AND IMPLEMENTATION The PanEffect code is freely available on GitHub (https://github.com/Maize-Genetics-and-Genomics-Database/PanEffect). A maize implementation of PanEffect and underlying datasets are available at MaizeGDB (https://www.maizegdb.org/effect/maize/).
Collapse
Affiliation(s)
- Carson M Andorf
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, United States
- Department of Computer Science, Iowa State University, Ames, IA 50011, United States
| | - Olivia C Haley
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, United States
| | - Rita K Hayford
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, United States
| | - John L Portwood
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, United States
| | - Stephen Harding
- USDA-ARS, Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, Peoria, IL 61604, United States
| | - Shatabdi Sen
- Department of Plant Pathology & Microbiology, Iowa State University, Ames, IA 50011, United States
| | - Ethalinda K Cannon
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, United States
| | - Jack M Gardiner
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, United States
| | - Hye-Seon Kim
- USDA-ARS, Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, Peoria, IL 61604, United States
| | - Margaret R Woodhouse
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, United States
| |
Collapse
|
12
|
Chen S, Wang P, Kong W, Chai K, Zhang S, Yu J, Wang Y, Jiang M, Lei W, Chen X, Wang W, Gao Y, Qu S, Wang F, Wang Y, Zhang Q, Gu M, Fang K, Ma C, Sun W, Ye N, Wu H, Zhang X. Gene mining and genomics-assisted breeding empowered by the pangenome of tea plant Camellia sinensis. NATURE PLANTS 2023; 9:1986-1999. [PMID: 38012346 DOI: 10.1038/s41477-023-01565-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 10/20/2023] [Indexed: 11/29/2023]
Abstract
Tea is one of the world's oldest crops and is cultivated to produce beverages with various flavours. Despite advances in sequencing technologies, the genetic mechanisms underlying key agronomic traits of tea remain unclear. In this study, we present a high-quality pangenome of 22 elite cultivars, representing broad genetic diversity in the species. Our analysis reveals that a recent long terminal repeat burst contributed nearly 20% of gene copies, introducing functional genetic variants that affect phenotypes such as leaf colour. Our graphical pangenome improves the efficiency of genome-wide association studies and allows the identification of key genes controlling bud flush timing. We also identified strong correlations between allelic variants and flavour-related chemistries. These findings deepen our understanding of the genetic basis of tea quality and provide valuable genomic resources to facilitate its genomics-assisted breeding.
Collapse
Affiliation(s)
- Shuai Chen
- National Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Pengjie Wang
- National Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Weilong Kong
- National Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Kun Chai
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shengcheng Zhang
- National Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Jiaxin Yu
- National Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yibin Wang
- National Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Mengwei Jiang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wenlong Lei
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiao Chen
- National Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Wenling Wang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yingying Gao
- National Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Shenyang Qu
- National Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Fang Wang
- National Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yinghao Wang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qing Zhang
- National Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Mengya Gu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Kaixing Fang
- Tea Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of Tea Plant Resources Innovation and Utilization, Guangzhou, China
| | - Chunlei Ma
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Weijiang Sun
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Naixing Ye
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China.
| | - Hualing Wu
- Tea Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of Tea Plant Resources Innovation and Utilization, Guangzhou, China.
| | - Xingtan Zhang
- National Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
| |
Collapse
|
13
|
Munasinghe M, Read A, Stitzer MC, Song B, Menard CC, Ma KY, Brandvain Y, Hirsch CN, Springer N. Combined analysis of transposable elements and structural variation in maize genomes reveals genome contraction outpaces expansion. PLoS Genet 2023; 19:e1011086. [PMID: 38134220 PMCID: PMC10773942 DOI: 10.1371/journal.pgen.1011086] [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: 04/11/2023] [Revised: 01/08/2024] [Accepted: 11/28/2023] [Indexed: 12/24/2023] Open
Abstract
Structural differences between genomes are a major source of genetic variation that contributes to phenotypic differences. Transposable elements, mobile genetic sequences capable of increasing their copy number and propagating themselves within genomes, can generate structural variation. However, their repetitive nature makes it difficult to characterize fine-scale differences in their presence at specific positions, limiting our understanding of their impact on genome variation. Domesticated maize is a particularly good system for exploring the impact of transposable element proliferation as over 70% of the genome is annotated as transposable elements. High-quality transposable element annotations were recently generated for de novo genome assemblies of 26 diverse inbred maize lines. We generated base-pair resolved pairwise alignments between the B73 maize reference genome and the remaining 25 inbred maize line assemblies. From this data, we classified transposable elements as either shared or polymorphic in a given pairwise comparison. Our analysis uncovered substantial structural variation between lines, representing both simple and complex connections between TEs and structural variants. Putative insertions in SNP depleted regions, which represent recently diverged identity by state blocks, suggest some TE families may still be active. However, our analysis reveals that within these recently diverged genomic regions, deletions of transposable elements likely account for more structural variation events and base pairs than insertions. These deletions are often large structural variants containing multiple transposable elements. Combined, our results highlight how transposable elements contribute to structural variation and demonstrate that deletion events are a major contributor to genomic differences.
Collapse
Affiliation(s)
- Manisha Munasinghe
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Andrew Read
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, United States of America
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Michelle C. Stitzer
- Institute for Genomic Diversity, Cornell University, Ithaca, New York, United States of America
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Baoxing Song
- Peking University Institute of Advanced Agricultural Sciences, Weifang, China
| | - Claire C. Menard
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Kristy Yubo Ma
- Department of Mathematics, Statistics, and Computer Science, Macalester College, St. Paul, Minnesota, United States of America
| | - Yaniv Brandvain
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, United States of America
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Candice N. Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Nathan Springer
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, United States of America
| |
Collapse
|
14
|
Wang Z, Miao L, Chen Y, Peng H, Ni Z, Sun Q, Guo W. Deciphering the evolution and complexity of wheat germplasm from a genomic perspective. J Genet Genomics 2023; 50:846-860. [PMID: 37611848 DOI: 10.1016/j.jgg.2023.08.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/29/2023] [Accepted: 08/09/2023] [Indexed: 08/25/2023]
Abstract
Bread wheat provides an essential fraction of the daily calorific intake for humanity. Due to its huge and complex genome, progress in studying on the wheat genome is substantially trailed behind those of the other two major crops, rice and maize, for at least a decade. With rapid advances in genome assembling and reduced cost of high-throughput sequencing, emerging de novo genome assemblies of wheat and whole-genome sequencing data are leading to a paradigm shift in wheat research. Here, we review recent progress in dissecting the complex genome and germplasm evolution of wheat since the release of the first high-quality wheat genome. New insights have been gained in the evolution of wheat germplasm during domestication and modern breeding progress, genomic variations at multiple scales contributing to the diversity of wheat germplasm, and complex transcriptional and epigenetic regulations of functional genes in polyploid wheat. Genomics databases and bioinformatics tools meeting the urgent needs of wheat genomics research are also summarized. The ever-increasing omics data, along with advanced tools and well-structured databases, are expected to accelerate deciphering the germplasm and gene resources in wheat for future breeding advances.
Collapse
Affiliation(s)
- Zihao Wang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Lingfeng Miao
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yongming Chen
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Huiru Peng
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zhongfu Ni
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Qixin Sun
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Weilong Guo
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China.
| |
Collapse
|
15
|
Bapat AR, Moran Lauter AN, Hufford MB, Boerman NA, Scott MP. The Ga1 locus of the genus Zea is associated with novel genome structures derived from multiple, independent nonhomologous recombination events. G3 (BETHESDA, MD.) 2023; 13:jkad196. [PMID: 37652030 PMCID: PMC10627281 DOI: 10.1093/g3journal/jkad196] [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: 05/17/2023] [Revised: 08/11/2023] [Accepted: 08/16/2023] [Indexed: 09/02/2023]
Abstract
The Ga1 locus controls cross-incompatibility between field corn and popcorn. The Ga1-S haplotype contains 2 types of pectin methylesterase (PME) genes, ZmPme3 and several copies of ZmGa1P that are expressed in silk and pollen, respectively. The ga1 haplotype contains nonfunctional tandem repeat sequences related to ZmPme3 and ZmGa1P. This haplotype can cross-pollinate freely and is widely present in field corn. The primary objective of this study is to characterize the repeat sequences from a diverse collection of maize and teosinte lines and use this information to understand the evolution of the Ga1 locus. First, we characterized the complexity of the Ga1 genome region in high-quality maize genome assemblies that led to their categorization into 5 groups based on the number and type of PME-like sequences found at this region. Second, we studied duplication events that led to the ga1 and Ga1-S repeats using maximum likelihood phylogenetic reconstruction. Divergence estimates of the ga1 haplotype suggest that the duplication events occurred more than 600 KYA whereas those in Ga1-S occurred at 3 time points, i.e. >600, ∼260, and ∼100 KYA. These estimates suggest that the ga1 and Ga1-S tandem duplication events occurred independently. Finally, analysis of ZmPme3 and ZmGa1P homologs in Zea and Tripsacum genomes suggests that ga1 and Ga1-S repeats originated from an ancestral pair of PME genes that duplicated and diverged through 2 evolutionary branches prior to the domestication of maize.
Collapse
Affiliation(s)
- Amruta R Bapat
- Interdepartmental Genetics and Genomics Program, Iowa State University, Ames, IA 50011, USA
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA
| | | | - Matthew B Hufford
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | | | - M Paul Scott
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA 50011, USA
| |
Collapse
|
16
|
Lanzl T, Melchinger AE, Schön CC. Influence of the mating design on the additive genetic variance in plant breeding populations. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:236. [PMID: 37906322 PMCID: PMC10618341 DOI: 10.1007/s00122-023-04447-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 08/14/2023] [Indexed: 11/02/2023]
Abstract
KEY MESSAGE Mating designs determine the realized additive genetic variance in a population sample. Deflated or inflated variances can lead to reduced or overly optimistic assessment of future selection gains. The additive genetic variance [Formula: see text] inherent to a breeding population is a major determinant of short- and long-term genetic gain. When estimated from experimental data, it is not only the additive variances at individual loci (QTL) but also covariances between QTL pairs that contribute to estimates of [Formula: see text]. Thus, estimates of [Formula: see text] depend on the genetic structure of the data source and vary between population samples. Here, we provide a theoretical framework for calculating the expectation and variance of [Formula: see text] from genotypic data of a given population sample. In addition, we simulated breeding populations derived from different numbers of parents (P = 2, 4, 8, 16) and crossed according to three different mating designs (disjoint, factorial and half-diallel crosses). We calculated the variance of [Formula: see text] and of the parameter b reflecting the covariance component in [Formula: see text] standardized by the genic variance. Our results show that mating designs resulting in large biparental families derived from few disjoint crosses carry a high risk of generating progenies exhibiting strong covariances between QTL pairs on different chromosomes. We discuss the consequences of the resulting deflated or inflated [Formula: see text] estimates for phenotypic and genome-based selection as well as for applying the usefulness criterion in selection. We show that already one round of recombination can effectively break negative and positive covariances between QTL pairs induced by the mating design. We suggest to obtain reliable estimates of [Formula: see text] and its components in a population sample by applying statistical methods differing in their treatment of QTL covariances.
Collapse
Affiliation(s)
- Tobias Lanzl
- Plant Breeding, TUM School of Life Sciences, Technical University of Munich, 85354, Freising, Germany
| | - Albrecht E Melchinger
- Plant Breeding, TUM School of Life Sciences, Technical University of Munich, 85354, Freising, Germany
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, 70599, Stuttgart, Germany
| | - Chris-Carolin Schön
- Plant Breeding, TUM School of Life Sciences, Technical University of Munich, 85354, Freising, Germany.
| |
Collapse
|
17
|
Chen Y, Guo Y, Xie X, Wang Z, Miao L, Yang Z, Jiao Y, Xie C, Liu J, Hu Z, Xin M, Yao Y, Ni Z, Sun Q, Peng H, Guo W. Pangenome-based trajectories of intracellular gene transfers in Poaceae unveil high cumulation in Triticeae. PLANT PHYSIOLOGY 2023; 193:578-594. [PMID: 37249052 PMCID: PMC10469385 DOI: 10.1093/plphys/kiad319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 05/04/2023] [Indexed: 05/31/2023]
Abstract
Intracellular gene transfers (IGTs) between the nucleus and organelles, including plastids and mitochondria, constantly reshape the nuclear genome during evolution. Despite the substantial contribution of IGTs to genome variation, the dynamic trajectories of IGTs at the pangenomic level remain elusive. Here, we developed an approach, IGTminer, that maps the evolutionary trajectories of IGTs using collinearity and gene reannotation across multiple genome assemblies. We applied IGTminer to create a nuclear organellar gene (NOG) map across 67 genomes covering 15 Poaceae species, including important crops. The resulting NOGs were verified by experiments and sequencing data sets. Our analysis revealed that most NOGs were recently transferred and lineage specific and that Triticeae species tended to have more NOGs than other Poaceae species. Wheat (Triticum aestivum) had a higher retention rate of NOGs than maize (Zea mays) and rice (Oryza sativa), and the retained NOGs were likely involved in photosynthesis and translation pathways. Large numbers of NOG clusters were aggregated in hexaploid wheat during 2 rounds of polyploidization, contributing to the genetic diversity among modern wheat accessions. We implemented an interactive web server to facilitate the exploration of NOGs in Poaceae. In summary, this study provides resources and insights into the roles of IGTs in shaping interspecies and intraspecies genome variation and driving plant genome evolution.
Collapse
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
| | - Xiaoming Xie
- 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
| | - Lingfeng Miao
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zhengzhao Yang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yuannian Jiao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chaojie Xie
- 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
| | - Jie Liu
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - 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
| | - 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
| | - 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
| | - 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
| | - 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
| |
Collapse
|
18
|
Glick L, Mayrose I. The Effect of Methodological Considerations on the Construction of Gene-Based Plant Pan-genomes. Genome Biol Evol 2023; 15:evad121. [PMID: 37401440 PMCID: PMC10340445 DOI: 10.1093/gbe/evad121] [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: 01/29/2023] [Revised: 06/21/2023] [Accepted: 06/28/2023] [Indexed: 07/05/2023] Open
Abstract
Pan-genomics is an emerging approach for studying the genetic diversity within plant populations. In contrast to common resequencing studies that compare whole genome sequencing data with a single reference genome, the construction of a pan-genome (PG) involves the direct comparison of multiple genomes to one another, thereby enabling the detection of genomic sequences and genes not present in the reference, as well as the analysis of gene content diversity. Although multiple studies describing PGs of various plant species have been published in recent years, a better understanding regarding the effect of the computational procedures used for PG construction could guide researchers in making more informed methodological decisions. Here, we examine the effect of several key methodological factors on the obtained gene pool and on gene presence-absence detections by constructing and comparing multiple PGs of Arabidopsis thaliana and cultivated soybean, as well as conducting a meta-analysis on published PGs. These factors include the construction method, the sequencing depth, and the extent of input data used for gene annotation. We observe substantial differences between PGs constructed using three common procedures (de novo assembly and annotation, map-to-pan, and iterative assembly) and that results are dependent on the extent of the input data. Specifically, we report low agreement between the gene content inferred using different procedures and input data. Our results should increase the awareness of the community to the consequences of methodological decisions made during the process of PG construction and emphasize the need for further investigation of commonly applied methodologies.
Collapse
Affiliation(s)
- Lior Glick
- Department of Life Sciences, School of Plant Sciences and Food Security, Tel-Aviv University, Tel Aviv, Israel
| | - Itay Mayrose
- Department of Life Sciences, School of Plant Sciences and Food Security, Tel-Aviv University, Tel Aviv, Israel
| |
Collapse
|
19
|
Chen J, Wang Z, Tan K, Huang W, Shi J, Li T, Hu J, Wang K, Wang C, Xin B, Zhao H, Song W, Hufford MB, Schnable JC, Jin W, Lai J. A complete telomere-to-telomere assembly of the maize genome. Nat Genet 2023:10.1038/s41588-023-01419-6. [PMID: 37322109 DOI: 10.1038/s41588-023-01419-6] [Citation(s) in RCA: 56] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/05/2023] [Indexed: 06/17/2023]
Abstract
A complete telomere-to-telomere (T2T) finished genome has been the long pursuit of genomic research. Through generating deep coverage ultralong Oxford Nanopore Technology (ONT) and PacBio HiFi reads, we report here a complete genome assembly of maize with each chromosome entirely traversed in a single contig. The 2,178.6 Mb T2T Mo17 genome with a base accuracy of over 99.99% unveiled the structural features of all repetitive regions of the genome. There were several super-long simple-sequence-repeat arrays having consecutive thymine-adenine-guanine (TAG) tri-nucleotide repeats up to 235 kb. The assembly of the entire nucleolar organizer region of the 26.8 Mb array with 2,974 45S rDNA copies revealed the enormously complex patterns of rDNA duplications and transposon insertions. Additionally, complete assemblies of all ten centromeres enabled us to precisely dissect the repeat compositions of both CentC-rich and CentC-poor centromeres. The complete Mo17 genome represents a major step forward in understanding the complexity of the highly recalcitrant repetitive regions of higher plant genomes.
Collapse
Affiliation(s)
- Jian Chen
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, P. R. China
| | - Zijian Wang
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, P. R. China
| | - Kaiwen Tan
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, P. R. China
| | - Wei Huang
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, P. R. China
| | - Junpeng Shi
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, P. R. China
| | - Tong Li
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, P. R. China
| | - Jiang Hu
- Grandomics Biosciences, Wuhan, P. R. China
| | - Kai Wang
- Grandomics Biosciences, Wuhan, P. R. China
| | - Chao Wang
- Grandomics Biosciences, Wuhan, P. R. China
| | - Beibei Xin
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, P. R. China
| | - Haiming Zhao
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, P. R. China
| | - Weibin Song
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, P. R. China
| | - Matthew B Hufford
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - James C Schnable
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Weiwei Jin
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, P. R. China
| | - Jinsheng Lai
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, P. R. China.
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, P. R. China.
- Sanya Institute of China Agricultural University, Sanya, P. R. China.
- Hainan Yazhou Bay Seed Laboratory, Sanya, P. R. China.
| |
Collapse
|
20
|
Tian T, Wang S, Yang S, Yang Z, Liu S, Wang Y, Gao H, Zhang S, Yang X, Jiang C, Qin F. Genome assembly and genetic dissection of a prominent drought-resistant maize germplasm. Nat Genet 2023; 55:496-506. [PMID: 36806841 DOI: 10.1038/s41588-023-01297-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 01/11/2023] [Indexed: 02/22/2023]
Abstract
In the context of climate change, drought is one of the most limiting factors that influence crop production. Maize, as a major crop, is highly vulnerable to water deficit, which causes significant yield loss. Thus, identification and utilization of drought-resistant germplasm are crucial for the genetic improvement of the trait. Here we report on a high-quality genome assembly of a prominent drought-resistant genotype, CIMBL55. Genomic and genetic variation analyses revealed that 65 favorable alleles of 108 previously identified drought-resistant candidate genes were found in CIMBL55, which may constitute the genetic basis for its excellent drought resistance. Notably, ZmRtn16, encoding a reticulon-like protein, was found to contribute to drought resistance by facilitating the vacuole H+-ATPase activity, which highlights the role of vacuole proton pumps in maize drought resistance. The assembled CIMBL55 genome provided a basis for genetic dissection and improvement of plant drought resistance, in support of global food security.
Collapse
Affiliation(s)
- Tian Tian
- State Key Laboratory of Plant Environmental Resilience, College of Biological Science, China Agricultural University, Beijing, China
| | - Shuhui Wang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Science, China Agricultural University, Beijing, China
| | - Shiping Yang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Science, China Agricultural University, Beijing, China
| | - Zhirui Yang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Science, China Agricultural University, Beijing, China
| | - Shengxue Liu
- State Key Laboratory of Plant Environmental Resilience, College of Biological Science, China Agricultural University, Beijing, China
| | - Yijie Wang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Science, China Agricultural University, Beijing, China
| | - Huajian Gao
- State Key Laboratory of Plant Environmental Resilience, College of Biological Science, China Agricultural University, Beijing, China
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, China
| | - Shuaisong Zhang
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, China
| | - Xiaohong Yang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Science, China Agricultural University, Beijing, China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, China
- National Maize Improvement Center of China, China Agricultural University, Beijing, China
| | - Caifu Jiang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Science, China Agricultural University, Beijing, China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, China
| | - Feng Qin
- State Key Laboratory of Plant Environmental Resilience, College of Biological Science, China Agricultural University, Beijing, China.
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, China.
| |
Collapse
|
21
|
Liu J, Dawe RK. Large haplotypes highlight a complex age structure within the maize pan-genome. Genome Res 2023; 33:359-370. [PMID: 36854668 PMCID: PMC10078284 DOI: 10.1101/gr.276705.122] [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: 02/22/2022] [Accepted: 02/21/2023] [Indexed: 03/02/2023]
Abstract
The genomes of maize and other eukaryotes contain stable haplotypes in regions of low recombination. These regions, including centromeres, long heterochromatic blocks, and rDNA arrays, have been difficult to analyze with respect to their diversity and origin. Greatly improved genome assemblies are now available that enable comparative genomics over these and other nongenic spaces. Using 26 complete maize genomes, we developed methods to align intergenic sequences while excluding genes and regulatory regions. The centromere haplotypes (cenhaps) extend for megabases on either side of the functional centromere regions and appear as evolutionary strata, with haplotype divergence/coalescence times dating as far back as 450 thousand years ago (kya). Application of the same methods to other low recombination regions (heterochromatic knobs and rDNA) and all intergenic spaces revealed that deep coalescence times are ubiquitous across the maize pan-genome. Divergence estimates vary over a broad timescale with peaks at ∼16 and 300 kya, reflecting a complex history of gene flow among diverging populations and changes in population size associated with domestication. Cenhaps and other long haplotypes provide vivid displays of this ancient diversity.
Collapse
Affiliation(s)
- Jianing Liu
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
| | - R Kelly Dawe
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA;
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA
| |
Collapse
|
22
|
Nawae W, Naktang C, Charoensri S, U-thoomporn S, Narong N, Chusri O, Tangphatsornruang S, Pootakham W. Resequencing of durian genomes reveals large genetic variations among different cultivars. FRONTIERS IN PLANT SCIENCE 2023; 14:1137077. [PMID: 36875624 PMCID: PMC9978785 DOI: 10.3389/fpls.2023.1137077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
Durian (Durio zibethinus), which yields the fruit known as the "King of Fruits," is an important economic crop in Southeast Asia. Several durian cultivars have been developed in this region. In this study, we resequenced the genomes of three popular durian cultivars in Thailand, including Kradumthong (KD), Monthong (MT), and Puangmanee (PM) to investigate genetic diversities of cultivated durians. KD, MT, and PM genome assemblies were 832.7, 762.6, and 821.6 Mb, and their annotations covered 95.7, 92.4, and 92.7% of the embryophyta core proteins, respectively. We constructed the draft durian pangenome and analyzed comparative genomes with related species in Malvales. Long terminal repeat (LTR) sequences and protein families in durian genomes had slower evolution rates than that in cotton genomes. However, protein families with transcriptional regulation function and protein phosphorylation function involved in abiotic and biotic stress responses appeared to evolve faster in durians. The analyses of phylogenetic relationships, copy number variations (CNVs), and presence/absence variations (PAVs) suggested that the genome evolution of Thai durians was different from that of the Malaysian durian, Musang King (MK). Among the three newly sequenced genomes, the PAV and CNV profiles of disease resistance genes and the expressions of methylesterase inhibitor domain containing genes involved in flowering and fruit maturation in MT were different from those in KD and PM. These genome assemblies and their analyses provide valuable resources to gain a better understanding of the genetic diversity of cultivated durians, which may be useful for the future development of new durian cultivars.
Collapse
Affiliation(s)
- Wanapinun Nawae
- National Omics Center (NOC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathum Thani, Thailand
| | - Chaiwat Naktang
- National Omics Center (NOC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathum Thani, Thailand
| | - Salisa Charoensri
- National Omics Center (NOC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathum Thani, Thailand
| | - Sonicha U-thoomporn
- National Omics Center (NOC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathum Thani, Thailand
| | - Nattapol Narong
- National Omics Center (NOC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathum Thani, Thailand
| | - Orwintinee Chusri
- Chantaburi Horticulture Research Center, Horticulture Research Institute, Department of Agriculture, Chantaburi, Thailand
| | - Sithichoke Tangphatsornruang
- National Omics Center (NOC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathum Thani, Thailand
| | - Wirulda Pootakham
- National Omics Center (NOC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathum Thani, Thailand
| |
Collapse
|
23
|
Wang B, Hou M, Shi J, Ku L, Song W, Li C, Ning Q, Li X, Li C, Zhao B, Zhang R, Xu H, Bai Z, Xia Z, Wang H, Kong D, Wei H, Jing Y, Dai Z, Wang HH, Zhu X, Li C, Sun X, Wang S, Yao W, Hou G, Qi Z, Dai H, Li X, Zheng H, Zhang Z, Li Y, Wang T, Jiang T, Wan Z, Chen Y, Zhao J, Lai J, Wang H. De novo genome assembly and analyses of 12 founder inbred lines provide insights into maize heterosis. Nat Genet 2023; 55:312-323. [PMID: 36646891 DOI: 10.1038/s41588-022-01283-w] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 12/09/2022] [Indexed: 01/18/2023]
Abstract
Hybrid maize displays superior heterosis and contributes over 30% of total worldwide cereal production. However, the molecular mechanisms of heterosis remain obscure. Here we show that structural variants (SVs) between the parental lines have a predominant role underpinning maize heterosis. De novo assembly and analyses of 12 maize founder inbred lines (FILs) reveal abundant genetic variations among these FILs and, through expression quantitative trait loci and association analyses, we identify several SVs contributing to genomic and phenotypic differentiations of various heterotic groups. Using a set of 91 diallel-cross F1 hybrids, we found strong positive correlations between better-parent heterosis of the F1 hybrids and the numbers of SVs between the parental lines, providing concrete genomic support for a prevalent role of genetic complementation underlying heterosis. Further, we document evidence that SVs in both ZAR1 and ZmACO2 contribute to yield heterosis in an overdominance fashion. Our results should promote genomics-based breeding of hybrid maize.
Collapse
Affiliation(s)
- Baobao Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mei Hou
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, Inner Mongolia University, Hohhot, China
| | - Junpeng Shi
- State Key Laboratory of Plant Physiology and Biochemistry & National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
| | - Lixia Ku
- College of Agronomy and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Wei Song
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Center, Beijing Academy of Agriculture & Forestry Sciences, Beijing, China
| | - Chunhui Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qiang Ning
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xin Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Changyu Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Binbin Zhao
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ruyang Zhang
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Center, Beijing Academy of Agriculture & Forestry Sciences, Beijing, China
| | - Hua Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhijing Bai
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhanchao Xia
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hai Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dexin Kong
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
| | - Hongbin Wei
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
| | - Yifeng Jing
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
| | - Zhouyan Dai
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
| | - Hu Hailing Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
| | - Xinyu Zhu
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
| | - Chunhui Li
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Center, Beijing Academy of Agriculture & Forestry Sciences, Beijing, China
| | - Xuan Sun
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Center, Beijing Academy of Agriculture & Forestry Sciences, Beijing, China
| | - Shuaishuai Wang
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Center, Beijing Academy of Agriculture & Forestry Sciences, Beijing, China
| | - Wen Yao
- College of Agronomy and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Gege Hou
- College of Agronomy and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Zhi Qi
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, Inner Mongolia University, Hohhot, China
| | - He Dai
- Biomarker Technologies Corporation, Beijing, China
| | - Xuming Li
- Biomarker Technologies Corporation, Beijing, China
| | | | - Zuxin Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yu Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tianyu Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Taijiao Jiang
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou, China.,Guangzhou Laboratory, Guangzhou, China
| | - Zhaoman Wan
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou, China
| | - Yanhui Chen
- College of Agronomy and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China.
| | - Jiuran Zhao
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Center, Beijing Academy of Agriculture & Forestry Sciences, Beijing, China.
| | - Jinsheng Lai
- State Key Laboratory of Plant Physiology and Biochemistry & National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China.
| | - Haiyang Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China.
| |
Collapse
|
24
|
Yang Z, Qin F. The battle of crops against drought: Genetic dissection and improvement. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:496-525. [PMID: 36639908 DOI: 10.1111/jipb.13451] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 01/12/2023] [Indexed: 06/17/2023]
Abstract
With ongoing global climate change, water scarcity-induced drought stress remains a major threat to agricultural productivity. Plants undergo a series of physiological and morphological changes to cope with drought stress, including stomatal closure to reduce transpiration and changes in root architecture to optimize water uptake. Combined phenotypic and multi-omics studies have recently identified a number of drought-related genetic resources in different crop species. The functional dissection of these genes using molecular techniques has enriched our understanding of drought responses in crops and has provided genetic targets for enhancing resistance to drought. Here, we review recent advances in the cloning and functional analysis of drought resistance genes and the development of technologies to mitigate the threat of drought to crop production.
Collapse
Affiliation(s)
- Zhirui Yang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Feng Qin
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| |
Collapse
|
25
|
Zhao Y, Zhao B, Xie Y, Jia H, Li Y, Xu M, Wu G, Ma X, Li Q, Hou M, Li C, Xia Z, He G, Xu H, Bai Z, Kong D, Zheng Z, Liu Q, Liu Y, Zhong J, Tian F, Wang B, Wang H. The evening complex promotes maize flowering and adaptation to temperate regions. THE PLANT CELL 2023; 35:369-389. [PMID: 36173348 PMCID: PMC9806612 DOI: 10.1093/plcell/koac296] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 09/16/2022] [Indexed: 05/30/2023]
Abstract
Maize (Zea mays) originated in southern Mexico and has spread over a wide latitudinal range. Maize expansion from tropical to temperate regions has necessitated a reduction of its photoperiod sensitivity. In this study, we cloned a quantitative trait locus (QTL) regulating flowering time in maize and show that the maize ortholog of Arabidopsis thaliana EARLY FLOWERING3, ZmELF3.1, is the causal locus. We demonstrate that ZmELF3.1 and ZmELF3.2 proteins can physically interact with ZmELF4.1/4.2 and ZmLUX1/2, to form evening complex(es; ECs) in the maize circadian clock. Loss-of-function mutants for ZmELF3.1/3.2 and ZmLUX1/2 exhibited delayed flowering under long-day and short-day conditions. We show that EC directly represses the expression of several flowering suppressor genes, such as the CONSTANS, CONSTANS-LIKE, TOC1 (CCT) genes ZmCCT9 and ZmCCT10, ZmCONSTANS-LIKE 3, and the PSEUDORESPONSE REGULATOR (PRR) genes ZmPRR37a and ZmPRR73, thus alleviating their inhibition, allowing florigen gene expression and promoting flowering. Further, we identify two closely linked retrotransposons located in the ZmELF3.1 promoter that regulate the expression levels of ZmELF3.1 and may have been positively selected during postdomestication spread of maize from tropical to temperate regions during the pre-Columbian era. These findings provide insights into circadian clock-mediated regulation of photoperiodic flowering in maize and new targets of genetic improvement for breeding.
Collapse
Affiliation(s)
- Yongping Zhao
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Binbin Zhao
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yurong Xie
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- HainanYazhou Bay Seed Lab, Sanya, 572025, China
| | - Hong Jia
- Department of Plant Genetics and Breeding, State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, China Agricultural University, Beijing, 100193, China
| | - Yongxiang Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 10008, China
| | - Miaoyun Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- HainanYazhou Bay Seed Lab, Sanya, 572025, China
| | - Guangxia Wu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaojing Ma
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Quanquan Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Mei Hou
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Changyu Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhanchao Xia
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Gang He
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hua Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhijing Bai
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Dexin Kong
- School of Life Sciences, and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Zhigang Zheng
- School of Life Sciences, and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Qing Liu
- School of Life Sciences, and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Yuting Liu
- School of Life Sciences, and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Jinshun Zhong
- School of Life Sciences, and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Feng Tian
- Department of Plant Genetics and Breeding, State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, China Agricultural University, Beijing, 100193, China
| | - Baobao Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- HainanYazhou Bay Seed Lab, Sanya, 572025, China
| | - Haiyang Wang
- School of Life Sciences, and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| |
Collapse
|
26
|
Shi J, Tian Z, Lai J, Huang X. Plant pan-genomics and its applications. MOLECULAR PLANT 2023; 16:168-186. [PMID: 36523157 DOI: 10.1016/j.molp.2022.12.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 12/07/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
Plant genomes are so highly diverse that a substantial proportion of genomic sequences are not shared among individuals. The variable DNA sequences, along with the conserved core sequences, compose the more sophisticated pan-genome that represents the collection of all non-redundant DNA in a species. With rapid progress in genome sequencing technologies, pan-genome research in plants is now accelerating. Here we review recent advances in plant pan-genomics, including major driving forces of structural variations that constitute the variable sequences, methodological innovations for representing the pan-genome, and major successes in constructing plant pan-genomes. We also summarize recent efforts toward decoding the remaining dark matter in telomere-to-telomere or gapless plant genomes. These new genome resources, which have remarkable advantages over numerous previously assembled less-than-perfect genomes, are expected to become new references for genetic studies and plant breeding.
Collapse
Affiliation(s)
- Junpeng Shi
- State Key Laboratory of Biocontrol, School of Agriculture, Sun Yat-sen University, Shenzhen 518107, China.
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Jinsheng Lai
- State Key Laboratory of Plant Physiology and Biochemistry and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Xuehui Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China.
| |
Collapse
|
27
|
Vourlaki IT, Castanera R, Ramos-Onsins SE, Casacuberta JM, Pérez-Enciso M. Transposable element polymorphisms improve prediction of complex agronomic traits in rice. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3211-3222. [PMID: 35931838 PMCID: PMC9482605 DOI: 10.1007/s00122-022-04180-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 07/12/2022] [Indexed: 06/15/2023]
Abstract
Transposon insertion polymorphisms can improve prediction of complex agronomic traits in rice compared to using SNPs only, especially when accessions to be predicted are less related to the training set. Transposon insertion polymorphisms (TIPs) are significant sources of genetic variation. Previous work has shown that TIPs can improve detection of causative loci on agronomic traits in rice. Here, we quantify the fraction of variance explained by single nucleotide polymorphisms (SNPs) compared to TIPs, and we explore whether TIPs can improve prediction of traits when compared to using only SNPs. We used eleven traits of agronomic relevance from by five different rice population groups (Aus, Indica, Aromatic, Japonica, and Admixed), 738 accessions in total. We assess prediction by applying data split validation in two scenarios. In the within-population scenario, we predicted performance of improved Indica varieties using the rest of Indica accessions. In the across population scenario, we predicted all Aromatic and Admixed accessions using the rest of populations. In each scenario, Bayes C and a Bayesian reproducible kernel Hilbert space regression were compared. We find that TIPs can explain an important fraction of total genetic variance and that they also improve genomic prediction. In the across population prediction scenario, TIPs outperformed SNPs in nine out of the eleven traits analyzed. In some traits like leaf senescence or grain width, using TIPs increased predictive correlation by 30-50%. Our results evidence, for the first time, that TIPs genotyping can improve prediction on complex agronomic traits in rice, especially when accessions to be predicted are less related to training accessions.
Collapse
Affiliation(s)
- Ioanna-Theoni Vourlaki
- Universitat Autònoma de Barcelona, Department of Animal Production, 08193, Bellaterra, Barcelona, Spain.
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, 08193, Bellaterra, Barcelona, Spain.
| | - Raúl Castanera
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, 08193, Bellaterra, Barcelona, Spain
| | - Sebastián E Ramos-Onsins
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, 08193, Bellaterra, Barcelona, Spain
| | - Josep M Casacuberta
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, 08193, Bellaterra, Barcelona, Spain
| | - Miguel Pérez-Enciso
- Universitat Autònoma de Barcelona, Department of Animal Production, 08193, Bellaterra, Barcelona, Spain.
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, 08193, Bellaterra, Barcelona, Spain.
- Catalan Institute for Research and Advanced studies, ICREA, 08010, Barcelona, Spain.
| |
Collapse
|
28
|
Chapman MA, He Y, Zhou M. Beyond a reference genome: pangenomes and population genomics of underutilized and orphan crops for future food and nutrition security. THE NEW PHYTOLOGIST 2022; 234:1583-1597. [PMID: 35318683 PMCID: PMC9994440 DOI: 10.1111/nph.18021] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 01/22/2022] [Indexed: 04/14/2023]
Abstract
Underutilized crops are, by definition, under-researched compared to staple crops yet come with traits that may be especially important given climate change and the need to feed a globally increasing population. These crops are often stress-tolerant, and this combined with unique and beneficial nutritional profiles. Whilst progress is being made by generating reference genome sequences, in this Tansley Review, we show how this is only the very first step. We advocate that going 'beyond a reference genome' should be a priority, as it is only at this stage one can identify the specific genes and the adaptive alleles that underpin the valuable traits. We sum up how population genomic and pangenomic approaches have led to the identification of stress- and disease-tolerant alleles in staple crops and compare this to the small number of examples from underutilized crops. We also demonstrate how previously underutilized crops have benefitted from genomic advances and that many breeding targets in underutilized crops are often well studied in staple crops. This cross-crop population-level resequencing could lead to an understanding of the genetic basis of adaptive traits in underutilized crops. This level of investment may be crucial for fully understanding the value of these crops before they are lost.
Collapse
Affiliation(s)
- Mark A. Chapman
- Biological SciencesUniversity of SouthamptonLife Sciences Building 85, Highfield CampusSouthamptonSO17 1BJUK
| | - Yuqi He
- Institute of Crop SciencesChinese Academy of Agricultural SciencesRoom 405, National Crop Gene Bank BuildingZhongguancun South Street No. 12Haidian DistrictBeijing100081China
| | - Meiliang Zhou
- Institute of Crop SciencesChinese Academy of Agricultural SciencesRoom 405, National Crop Gene Bank BuildingZhongguancun South Street No. 12Haidian DistrictBeijing100081China
| |
Collapse
|
29
|
Song JM, Zhang Y, Zhou ZW, Lu S, Ma W, Lu C, Chen LL, Guo L. Oil plant genomes: current state of the science. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:2859-2874. [PMID: 35560205 DOI: 10.1093/jxb/erab472] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 10/22/2021] [Indexed: 05/25/2023]
Abstract
Vegetable oils are an indispensable nutritional component of the human diet as well as important raw materials for a variety of industrial applications such as pharmaceuticals, cosmetics, oleochemicals, and biofuels. Oil plant genomes are highly diverse, and their genetic variation leads to a diversity in oil biosynthesis and accumulation along with agronomic traits. This review discusses plant oil biosynthetic pathways, current state of genome assembly, polyploidy and asymmetric evolution of genomes of oil plants and their wild relatives, and research progress of pan-genomics in oil plants. The availability of complete high-resolution genomes and pan-genomes has enabled the identification of structural variations in the genomes that are associated with the diversity of agronomic and environment fitness traits. These and future genomes also provide powerful tools to understand crop evolution and to harvest the rich natural variations to improve oil crops for enhanced productivity, oil quality, and adaptability to changing environments.
Collapse
Affiliation(s)
- Jia-Ming Song
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Yuting Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Zhi-Wei Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Shaoping Lu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Wei Ma
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Chaofu Lu
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717, USA
| | - Ling-Ling Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Liang Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| |
Collapse
|
30
|
Yang Z, Wang Z, Wang W, Xie X, Chai L, Wang X, Feng X, Li J, Peng H, Su Z, You M, Yao Y, Xin M, Hu Z, Liu J, Liang R, Ni Z, Sun Q, Guo W. ggComp enables dissection of germplasm resources and construction of a multiscale germplasm network in wheat. PLANT PHYSIOLOGY 2022; 188:1950-1965. [PMID: 35088857 PMCID: PMC8968352 DOI: 10.1093/plphys/kiac029] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 12/10/2021] [Indexed: 05/31/2023]
Abstract
Accurate germplasm characterization is a vital step for accelerating crop genetic improvement, which remains largely infeasible for crops such as bread wheat (Triticum aestivum L.), which has a complex genome that undergoes frequent introgression and contains many structural variations. Here, we propose a genomic strategy called ggComp, which integrates resequencing data with copy number variations and stratified single-nucleotide polymorphism densities to enable unsupervised identification of pairwise germplasm resource-based Identity-By-Descent (gIBD) blocks. The reliability of ggComp was verified in wheat cultivar Nongda5181 by dissecting parental-descent patterns represented by inherited genomic blocks. With gIBD blocks identified among 212 wheat accessions, we constructed a multi-scale genomic-based germplasm network. At the whole-genome level, the network helps to clarify pedigree relationship, demonstrate genetic flow, and identify key founder lines. At the chromosome level, we were able to trace the utilization of 1RS introgression in modern wheat breeding by hitchhiked segments. At the single block scale, the dissected germplasm-based haplotypes nicely matched with previously identified alleles of "Green Revolution" genes and can guide allele mining and dissect the trajectory of beneficial alleles in wheat breeding. Our work presents a model-based framework for precisely evaluating germplasm resources with genomic data. A database, WheatCompDB (http://wheat.cau.edu.cn/WheatCompDB/), is available for researchers to exploit the identified gIBDs with a multi-scale network.
Collapse
Affiliation(s)
| | | | | | - Xiaoming Xie
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Lingling Chai
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Xiaobo Wang
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Xibo Feng
- Tibet Key Experiments of Crop Cultivation and Farming/College of Plant Science, Tibet Agriculture and Animal Husbandry University, Linzhi 860000, China
| | - Jinghui Li
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
- Wheat Center, Henan Institute of Science and Technology/Henan Provincial Key Laboratory of Hybrid Wheat, Xinxiang 453003, China
| | - Huiru Peng
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Zhenqi Su
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Mingshan You
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Yingyin Yao
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Mingming Xin
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Zhaorong Hu
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Jie Liu
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Rongqi Liang
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | | |
Collapse
|
31
|
Carvalho RF, Aguiar-Perecin MLR, Clarindo WR, Fristche-Neto R, Mondin M. A Heterochromatic Knob Reducing the Flowering Time in Maize. Front Genet 2022; 12:799681. [PMID: 35280927 PMCID: PMC8908004 DOI: 10.3389/fgene.2021.799681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 12/22/2021] [Indexed: 11/13/2022] Open
Abstract
Maize flowering time is an important agronomic trait, which has been associated with variations in the genome size and heterochromatic knobs content. We integrated three steps to show this association. Firstly, we selected inbred lines varying for heterochromatic knob composition at specific sites in the homozygous state. Then, we produced homozygous and heterozygous hybrids for knobs. Second, we measured the genome size and flowering time for all materials. Knob composition did not affect the genome size and flowering time. Finally, we developed an association study and identified a knob marker on chromosome 9 showing the strongest association with flowering time. Indeed, modelling allele substitution and dominance effects could offer only one heterochromatic knob locus that could affect flowering time, making it earlier rather than the knob composition.
Collapse
Affiliation(s)
- Renata Flávia Carvalho
- “Luiz de Queiroz” College of Agriculture, ESALQ, University of São Paulo, Piracicaba, Brazil
| | | | | | - Roberto Fristche-Neto
- “Luiz de Queiroz” College of Agriculture, ESALQ, University of São Paulo, Piracicaba, Brazil
- International Rice Research Institute (IRRI) - Breeding Analytics and Data, Management Unit, Laguna, Philippines
| | - Mateus Mondin
- “Luiz de Queiroz” College of Agriculture, ESALQ, University of São Paulo, Piracicaba, Brazil
| |
Collapse
|
32
|
Oren E, Tzuri G, Dafna A, Rees ER, Song B, Freilich S, Elkind Y, Isaacson T, Schaffer AA, Tadmor Y, Burger J, Buckler ES, Gur A. QTL mapping and genomic analyses of earliness and fruit ripening traits in a melon Recombinant Inbred Lines population supported by de novo assembly of their parental genomes. HORTICULTURE RESEARCH 2022; 9:uhab081. [PMID: 35043206 PMCID: PMC8968493 DOI: 10.1093/hr/uhab081] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 11/01/2021] [Accepted: 11/04/2021] [Indexed: 05/27/2023]
Abstract
Earliness and ripening behavior are important attributes of fruits on and off the vine, and affect quality and preference of both growers and consumers. Fruit ripening is a complex physiological process that involves metabolic shifts affecting fruit color, firmness, and aroma production. Melon is a promising model crop for the study of fruit ripening, as the full spectrum of climacteric behavior is represented across the natural variation. Using Recombinant Inbred Lines (RILs) population derived from the parental lines "Dulce" (reticulatus, climacteric) and "Tam Dew" (inodorus, non-climacteric) that vary in earliness and ripening traits, we mapped QTLs for ethylene emission, fruit firmness and days to flowering and maturity. To further annotate the main QTL intervals and identify candidate genes, we used Oxford Nanopore long-read sequencing in combination with Illumina short-read resequencing, to assemble the parental genomes de-novo. In addition to 2.5 million genome-wide SNPs and short InDels detected between the parents, we also highlight here the structural variation between these lines and the reference melon genome. Through systematic multi-layered prioritization process, we identified 18 potential polymorphisms in candidate genes within multi-trait QTLs. The associations of selected SNPs with earliness and ripening traits were further validated across a panel of 177 diverse melon accessions and across a diallel population of 190 F1 hybrids derived from a core subset of 20 diverse parents. The combination of advanced genomic tools with diverse germplasm and targeted mapping populations is demonstrated as a way to leverage forward genetics strategies to dissect complex horticulturally important traits.
Collapse
Affiliation(s)
- Elad Oren
- Plant Science Institute, Agricultural Research Organization, Newe Ya’ar Research Center, P.O. Box 1021, Ramat Yishay 3009500, Israel
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Galil Tzuri
- Plant Science Institute, Agricultural Research Organization, Newe Ya’ar Research Center, P.O. Box 1021, Ramat Yishay 3009500, Israel
| | - Asaf Dafna
- Plant Science Institute, Agricultural Research Organization, Newe Ya’ar Research Center, P.O. Box 1021, Ramat Yishay 3009500, Israel
| | - Evan R Rees
- Plant Breeding and Genetics Section, Cornell University, Ithaca, NY 14853, USA
| | - Baoxing Song
- Plant Breeding and Genetics Section, Cornell University, Ithaca, NY 14853, USA
| | - Shiri Freilich
- Plant Science Institute, Agricultural Research Organization, Newe Ya’ar Research Center, P.O. Box 1021, Ramat Yishay 3009500, Israel
| | - Yonatan Elkind
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Tal Isaacson
- Plant Science Institute, Agricultural Research Organization, Newe Ya’ar Research Center, P.O. Box 1021, Ramat Yishay 3009500, Israel
| | - Arthur A Schaffer
- Plant Science Institute, Agricultural Research Organization, The Volcani Center, P.O. Box 15159, Rishon LeZiyyon 7507101, Israel
| | - Yaakov Tadmor
- Plant Science Institute, Agricultural Research Organization, Newe Ya’ar Research Center, P.O. Box 1021, Ramat Yishay 3009500, Israel
| | - Joseph Burger
- Plant Science Institute, Agricultural Research Organization, Newe Ya’ar Research Center, P.O. Box 1021, Ramat Yishay 3009500, Israel
| | - Edward S Buckler
- Plant Breeding and Genetics Section, Cornell University, Ithaca, NY 14853, USA
- United States Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA
| | - Amit Gur
- Plant Science Institute, Agricultural Research Organization, Newe Ya’ar Research Center, P.O. Box 1021, Ramat Yishay 3009500, Israel
| |
Collapse
|
33
|
Hu Y, Resende Jr. M. Maize Genome Assembly with PacBio Reads. Bio Protoc 2022. [DOI: 10.21769/bioprotoc.4456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
|
34
|
Vargas-Chavez C, Longo Pendy NM, Nsango SE, Aguilera L, Ayala D, González J. Transposable element variants and their potential adaptive impact in urban populations of the malaria vector Anopheles coluzzii. Genome Res 2021; 32:189-202. [PMID: 34965939 PMCID: PMC8744685 DOI: 10.1101/gr.275761.121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 11/24/2021] [Indexed: 11/28/2022]
Abstract
Anopheles coluzzii is one of the primary vectors of human malaria in sub-Saharan Africa. Recently, it has spread into the main cities of Central Africa threatening vector control programs. The adaptation of An. coluzzii to urban environments partly results from an increased tolerance to organic pollution and insecticides. Some of the molecular mechanisms for ecological adaptation are known, but the role of transposable elements (TEs) in the adaptive processes of this species has not been studied yet. As a first step toward assessing the role of TEs in rapid urban adaptation, we sequenced using long reads six An. coluzzii genomes from natural breeding sites in two major Central Africa cities. We de novo annotated TEs in these genomes and in an additional high-quality An. coluzzii genome, and we identified 64 new TE families. TEs were nonrandomly distributed throughout the genome with significant differences in the number of insertions of several superfamilies across the studied genomes. We identified seven putatively active families with insertions near genes with functions related to vectorial capacity, and several TEs that may provide promoter and transcription factor binding sites to insecticide resistance and immune-related genes. Overall, the analysis of multiple high-quality genomes allowed us to generate the most comprehensive TE annotation in this species to date and identify several TE insertions that could potentially impact both genome architecture and the regulation of functionally relevant genes. These results provide a basis for future studies of the impact of TEs on the biology of An. coluzzii.
Collapse
Affiliation(s)
- Carlos Vargas-Chavez
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003 Barcelona, Spain
| | - Neil Michel Longo Pendy
- Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), BP 769, Franceville, Gabon.,École Doctorale Régional (EDR) en Infectiologie Tropicale d'Afrique Centrale, BP 876, Franceville, Gabon
| | - Sandrine E Nsango
- Faculté de Médecine et des Sciences Pharmaceutiques, Université de Douala, BP 2701, Douala, Cameroun
| | - Laura Aguilera
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003 Barcelona, Spain
| | - Diego Ayala
- Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), BP 769, Franceville, Gabon.,Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle (MIVEGEC), Université Montpellier, CNRS, IRD, 64501 Montpellier, France
| | - Josefa González
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003 Barcelona, Spain
| |
Collapse
|
35
|
Bornowski N, Michel KJ, Hamilton JP, Ou S, Seetharam AS, Jenkins J, Grimwood J, Plott C, Shu S, Talag J, Kennedy M, Hundley H, Singan VR, Barry K, Daum C, Yoshinaga Y, Schmutz J, Hirsch CN, Hufford MB, de Leon N, Kaeppler SM, Buell CR. Genomic variation within the maize stiff-stalk heterotic germplasm pool. THE PLANT GENOME 2021; 14:e20114. [PMID: 34275202 DOI: 10.1002/tpg2.20114] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 05/06/2021] [Indexed: 05/28/2023]
Abstract
The stiff-stalk heterotic group in Maize (Zea mays L.) is an important source of inbreds used in U.S. commercial hybrid production. Founder inbreds B14, B37, B73, and, to a lesser extent, B84, are found in the pedigrees of a majority of commercial seed parent inbred lines. We created high-quality genome assemblies of B84 and four expired Plant Variety Protection (ex-PVP) lines LH145 representing B14, NKH8431 of mixed descent, PHB47 representing B37, and PHJ40, which is a Pioneer Hi-Bred International (PHI) early stiff-stalk type. Sequence was generated using long-read sequencing achieving highly contiguous assemblies of 2.13-2.18 Gbp with N50 scaffold lengths >200 Mbp. Inbred-specific gene annotations were generated using a core five-tissue gene expression atlas, whereas transposable element (TE) annotation was conducted using de novo and homology-directed methodologies. Compared with the reference inbred B73, synteny analyses revealed extensive collinearity across the five stiff-stalk genomes, although unique components of the maize pangenome were detected. Comparison of this set of stiff-stalk inbreds with the original Iowa Stiff Stalk Synthetic breeding population revealed that these inbreds represent only a proportion of variation in the original stiff-stalk pool and there are highly conserved haplotypes in released public and ex-Plant Variety Protection inbreds. Despite the reduction in variation from the original stiff-stalk population, substantial genetic and genomic variation was identified supporting the potential for continued breeding success in this pool. The assemblies described here represent stiff-stalk inbreds that have historical and commercial relevance and provide further insight into the emerging maize pangenome.
Collapse
Affiliation(s)
- Nolan Bornowski
- Dep. of Plant Biology, Michigan State Univ., 612 Wilson Road, East Lansing, MI, 48824, USA
| | - Kathryn J Michel
- Dep. of Agronomy, Univ. of Wisconsin - Madison, 1575 Linden Drive, Madison, WI, 53706, USA
| | - John P Hamilton
- Dep. of Plant Biology, Michigan State Univ., 612 Wilson Road, East Lansing, MI, 48824, USA
| | - Shujun Ou
- Dep. of Ecology, Evolution, and Organismal Biology, Iowa State Univ., 2200 Osborn Drive, Ames, IA, 50011, USA
| | - Arun S Seetharam
- Dep. of Ecology, Evolution, and Organismal Biology, Iowa State Univ., 2200 Osborn Drive, Ames, IA, 50011, USA
| | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, 601 Genome Way Northwest, Huntsville, AL, 35806, USA
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, 601 Genome Way Northwest, Huntsville, AL, 35806, USA
| | - Chris Plott
- HudsonAlpha Institute for Biotechnology, 601 Genome Way Northwest, Huntsville, AL, 35806, USA
| | - Shengqiang Shu
- U.S. Dep. of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Jayson Talag
- Arizona Genomics Institute, School of Plant Sciences, Univ. of Arizona, 1657 E Helen Street, Tucson, AZ, 85721, USA
| | - Megan Kennedy
- U.S. Dep. of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Hope Hundley
- U.S. Dep. of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Vasanth R Singan
- U.S. Dep. of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Kerrie Barry
- U.S. Dep. of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Chris Daum
- U.S. Dep. of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Yuko Yoshinaga
- U.S. Dep. of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, 601 Genome Way Northwest, Huntsville, AL, 35806, USA
- U.S. Dep. of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Candice N Hirsch
- Dep. of Agronomy and Plant Genetics, Univ. of Minnesota, 1991 Upper Buford Circle, Saint Paul, MN, 55108, USA
| | - Matthew B Hufford
- Dep. of Ecology, Evolution, and Organismal Biology, Iowa State Univ., 2200 Osborn Drive, Ames, IA, 50011, USA
| | - Natalia de Leon
- Dep. of Agronomy, Univ. of Wisconsin - Madison, 1575 Linden Drive, Madison, WI, 53706, USA
- Dep. of Energy, Great Lakes Bioenergy Research Center, Univ. of Wisconsin - Madison, 1575 Linden Drive, Madison, WI, 53706, USA
| | - Shawn M Kaeppler
- Dep. of Agronomy, Univ. of Wisconsin - Madison, 1575 Linden Drive, Madison, WI, 53706, USA
- Dep. of Energy, Great Lakes Bioenergy Research Center, Univ. of Wisconsin - Madison, 1575 Linden Drive, Madison, WI, 53706, USA
- Wisconsin Crop Innovation Center, Univ. of Wisconsin - Madison, 8520 University Green, Middleton, WI, 53562, USA
| | - C Robin Buell
- Dep. of Plant Biology, Michigan State Univ., 612 Wilson Road, East Lansing, MI, 48824, USA
- Dep. of Energy, Great Lakes Bioenergy Research Center, Michigan State Univ., 612 Wilson Road, East Lansing, MI, 48824, USA
| |
Collapse
|
36
|
The Dynamism of Transposon Methylation for Plant Development and Stress Adaptation. Int J Mol Sci 2021; 22:ijms222111387. [PMID: 34768817 PMCID: PMC8583499 DOI: 10.3390/ijms222111387] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 10/13/2021] [Accepted: 10/19/2021] [Indexed: 02/06/2023] Open
Abstract
Plant development processes are regulated by epigenetic alterations that shape nuclear structure, gene expression, and phenotypic plasticity; these alterations can provide the plant with protection from environmental stresses. During plant growth and development, these processes play a significant role in regulating gene expression to remodel chromatin structure. These epigenetic alterations are mainly regulated by transposable elements (TEs) whose abundance in plant genomes results in their interaction with genomes. Thus, TEs are the main source of epigenetic changes and form a substantial part of the plant genome. Furthermore, TEs can be activated under stress conditions, and activated elements cause mutagenic effects and substantial genetic variability. This introduces novel gene functions and structural variation in the insertion sites and primarily contributes to epigenetic modifications. Altogether, these modifications indirectly or directly provide the ability to withstand environmental stresses. In recent years, many studies have shown that TE methylation plays a major role in the evolution of the plant genome through epigenetic process that regulate gene imprinting, thereby upholding genome stability. The induced genetic rearrangements and insertions of mobile genetic elements in regions of active euchromatin contribute to genome alteration, leading to genomic stress. These TE-mediated epigenetic modifications lead to phenotypic diversity, genetic variation, and environmental stress tolerance. Thus, TE methylation is essential for plant evolution and stress adaptation, and TEs hold a relevant military position in the plant genome. High-throughput techniques have greatly advanced the understanding of TE-mediated gene expression and its associations with genome methylation and suggest that controlled mobilization of TEs could be used for crop breeding. However, development application in this area has been limited, and an integrated view of TE function and subsequent processes is lacking. In this review, we explore the enormous diversity and likely functions of the TE repertoire in adaptive evolution and discuss some recent examples of how TEs impact gene expression in plant development and stress adaptation.
Collapse
|
37
|
Tsugawa H, Rai A, Saito K, Nakabayashi R. Metabolomics and complementary techniques to investigate the plant phytochemical cosmos. Nat Prod Rep 2021; 38:1729-1759. [PMID: 34668509 DOI: 10.1039/d1np00014d] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Covering: up to 2021Plants and their associated microbial communities are known to produce millions of metabolites, a majority of which are still not characterized and are speculated to possess novel bioactive properties. In addition to their role in plant physiology, these metabolites are also relevant as existing and next-generation medicine candidates. Elucidation of the plant metabolite diversity is thus valuable for the successful exploitation of natural resources for humankind. Herein, we present a comprehensive review on recent metabolomics approaches to illuminate molecular networks in plants, including chemical isolation and enzymatic production as well as the modern metabolomics approaches such as stable isotope labeling, ultrahigh-resolution mass spectrometry, metabolome imaging (spatial metabolomics), single-cell analysis, cheminformatics, and computational mass spectrometry. Mass spectrometry-based strategies to characterize plant metabolomes through metabolite identification and annotation are described in detail. We also highlight the use of phytochemical genomics to mine genes associated with specialized metabolites' biosynthesis. Understanding the metabolic diversity through biotechnological advances is fundamental to elucidate the functions of the plant-derived specialized metabolome.
Collapse
Affiliation(s)
- Hiroshi Tsugawa
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan. .,RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.,Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Nakamachi, Koganei, Tokyo 184-8588, Japan.,Graduate School of Medical Life Science, Yokohama City University, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Amit Rai
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan. .,Plant Molecular Science Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
| | - Kazuki Saito
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan. .,Plant Molecular Science Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
| | - Ryo Nakabayashi
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| |
Collapse
|
38
|
Nie S, Wang B, Ding H, Lin H, Zhang L, Li Q, Wang Y, Zhang B, Liang A, Zheng Q, Wang H, Lv H, Zhu K, Jia M, Wang X, Du J, Zhao R, Jiang Z, Xia C, Qiao Z, Li X, Liu B, Zhu H, An R, Li Y, Jiang Q, Chen B, Zhang H, Wang D, Tang C, Yuan Y, Dai J, Zhan J, He W, Wang X, Shi J, Wang B, Gong M, He X, Li P, Huang L, Li H, Pan C, Huang H, Yuan G, Lan H, Nie Y, Li X, Zhao X, Zhang X, Pan G, Wu Q, Xu F, Zhang Z. Genome assembly of the Chinese maize elite inbred line RP125 and its EMS mutant collection provide new resources for maize genetics research and crop improvement. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:40-54. [PMID: 34252236 DOI: 10.1111/tpj.15421] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 07/06/2021] [Indexed: 06/13/2023]
Abstract
Maize is an important crop worldwide, as well as a valuable model with vast genetic diversity. Accurate genome and annotation information for a wide range of inbred lines would provide valuable resources for crop improvement and pan-genome characterization. In this study, we generated a high-quality de novo genome assembly (contig N50 of 15.43 Mb) of the Chinese elite inbred line RP125 using Nanopore long-read sequencing and Hi-C scaffolding, which yield highly contiguous, chromosome-length scaffolds. Global comparison of the RP125 genome with those of B73, W22, and Mo17 revealed a large number of structural variations. To create new germplasm for maize research and crop improvement, we carried out an EMS mutagenesis screen on RP125. In total, we obtained 5818 independent M2 families, with 946 mutants showing heritable phenotypes. Taking advantage of the high-quality RP125 genome, we successfully cloned 10 mutants from the EMS library, including the novel kernel mutant qk1 (quekou: "missing a small part" in Chinese), which exhibited partial loss of endosperm and a starch accumulation defect. QK1 encodes a predicted metal tolerance protein, which is specifically required for Fe transport. Increased accumulation of Fe and reactive oxygen species as well as ferroptosis-like cell death were detected in qk1 endosperm. Our study provides the community with a high-quality genome sequence and a large collection of mutant germplasm.
Collapse
Affiliation(s)
- Shujun Nie
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| | - Bo Wang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 11724, USA
| | - Haiping Ding
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
| | - Haijian Lin
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| | - Li Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| | - Qigui Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| | - Yujiao Wang
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| | - Bin Zhang
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| | - Anping Liang
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| | - Qi Zheng
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
- The Key Laboratory of Plant Development and Environmental Adaption Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Hui Wang
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| | - Huayang Lv
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| | - Kun Zhu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
| | - Minghui Jia
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
| | - Xiaotong Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
| | - Jiyuan Du
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
| | - Runtai Zhao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
| | - Zhenzhen Jiang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
| | - Caina Xia
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
| | - Zhenghao Qiao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
| | - Xiaohu Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
| | - Boyan Liu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
| | - Hongbo Zhu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
| | - Rong An
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| | - Yucui Li
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| | - Qian Jiang
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| | - Benfang Chen
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| | - Hongkai Zhang
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| | - Dening Wang
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| | - Changxiao Tang
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| | - Yang Yuan
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| | - Jie Dai
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| | - Jing Zhan
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| | - Weiqiang He
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| | - Xuebo Wang
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| | - Jian Shi
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| | - Bin Wang
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| | - Min Gong
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| | - Xiujing He
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| | - Peng Li
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| | - Li Huang
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| | - Hui Li
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| | - Chao Pan
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| | - Hong Huang
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| | - Guangsheng Yuan
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| | - Hai Lan
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| | - Yongxin Nie
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
| | - Xinzheng Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
| | - Xiangyu Zhao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
| | - Xiansheng Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
| | - Guangtang Pan
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| | - Qingyu Wu
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Fang Xu
- The Key Laboratory of Plant Development and Environmental Adaption Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Zhiming Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| |
Collapse
|
39
|
Becher H, Powell RF, Brown MR, Metherell C, Pellicer J, Leitch IJ, Twyford AD. The nature of intraspecific and interspecific genome size variation in taxonomically complex eyebrights. ANNALS OF BOTANY 2021; 128:639-651. [PMID: 34318876 PMCID: PMC8422891 DOI: 10.1093/aob/mcab102] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 07/27/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND AND AIMS Genome size varies considerably across the diversity of plant life. Although genome size is, by definition, affected by genetic presence/absence variants, which are ubiquitous in population sequencing studies, genome size is often treated as an intrinsic property of a species. Here, we studied intra- and interspecific genome size variation in taxonomically complex British eyebrights (Euphrasia, Orobanchaceae). Our aim is to document genome size diversity and investigate underlying evolutionary processes shaping variation between individuals, populations and species. METHODS We generated genome size data for 192 individuals of diploid and tetraploid Euphrasia and analysed genome size variation in relation to ploidy, taxonomy, population affiliation and geography. We further compared the genomic repeat content of 30 samples. KEY RESULTS We found considerable intraspecific genome size variation, and observed isolation-by-distance for genome size in outcrossing diploids. Tetraploid Euphrasia showed contrasting patterns, with genome size increasing with latitude in outcrossing Euphrasia arctica, but with little genome size variation in the highly selfing Euphrasia micrantha. Interspecific differences in genome size and the genomic proportions of repeat sequences were small. CONCLUSIONS We show the utility of treating genome size as the outcome of polygenic variation. Like other types of genetic variation, such as single nucleotide polymorphisms, genome size variation may be affected by ongoing hybridization and the extent of population subdivision. In addition to selection on associated traits, genome size is predicted to be affected indirectly by selection due to pleiotropy of the underlying presence/absence variants.
Collapse
Affiliation(s)
- Hannes Becher
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Max R Brown
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
- Wellcome Trust Genome Campus, Hinxton, Saffron Walden, UK
| | - Chris Metherell
- Botanical Society of Britain and Ireland, Harpenden, Hertfordshire, UK
| | - Jaume Pellicer
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Barcelona, Spain
| | | | - Alex D Twyford
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
- Royal Botanic Garden Edinburgh, Edinburgh, UK
| |
Collapse
|
40
|
Woodhouse MR, Cannon EK, Portwood JL, Harper LC, Gardiner JM, Schaeffer ML, Andorf CM. A pan-genomic approach to genome databases using maize as a model system. BMC PLANT BIOLOGY 2021; 21:385. [PMID: 34416864 PMCID: PMC8377966 DOI: 10.1186/s12870-021-03173-5] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 08/11/2021] [Indexed: 05/21/2023]
Abstract
Research in the past decade has demonstrated that a single reference genome is not representative of a species' diversity. MaizeGDB introduces a pan-genomic approach to hosting genomic data, leveraging the large number of diverse maize genomes and their associated datasets to quickly and efficiently connect genomes, gene models, expression, epigenome, sequence variation, structural variation, transposable elements, and diversity data across genomes so that researchers can easily track the structural and functional differences of a locus and its orthologs across maize. We believe our framework is unique and provides a template for any genomic database poised to host large-scale pan-genomic data.
Collapse
Affiliation(s)
| | - Ethalinda K Cannon
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, 50011, USA
| | - John L Portwood
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, 50011, USA
| | - Lisa C Harper
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, 50011, USA
| | - Jack M Gardiner
- Division of Animal Sciences, University of Missouri, 65211, Columbia, MO, USA
| | - Mary L Schaeffer
- Division of Plant Sciences, University of Missouri, 65211, Columbia, MO, USA
| | - Carson M Andorf
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, 50011, USA
- Department of Computer Science, Iowa State University, Ames, IA, 50011, USA
| |
Collapse
|
41
|
Noshay JM, Liang Z, Zhou P, Crisp PA, Marand AP, Hirsch CN, Schmitz RJ, Springer NM. Stability of DNA methylation and chromatin accessibility in structurally diverse maize genomes. G3 (BETHESDA, MD.) 2021; 11:6288454. [PMID: 34849810 PMCID: PMC8496265 DOI: 10.1093/g3journal/jkab190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 05/27/2021] [Indexed: 06/13/2023]
Abstract
Accessible chromatin and unmethylated DNA are associated with many genes and cis-regulatory elements. Attempts to understand natural variation for accessible chromatin regions (ACRs) and unmethylated regions (UMRs) often rely upon alignments to a single reference genome. This limits the ability to assess regions that are absent in the reference genome assembly and monitor how nearby structural variants influence variation in chromatin state. In this study, de novo genome assemblies for four maize inbreds (B73, Mo17, Oh43, and W22) are utilized to assess chromatin accessibility and DNA methylation patterns in a pan-genome context. A more complete set of UMRs and ACRs can be identified when chromatin data are aligned to the matched genome rather than a single reference genome. While there are UMRs and ACRs present within genomic regions that are not shared between genotypes, these features are 6- to 12-fold enriched within regions between genomes. Characterization of UMRs present within shared genomic regions reveals that most UMRs maintain the unmethylated state in other genotypes with only ∼5% being polymorphic between genotypes. However, the majority (71%) of UMRs that are shared between genotypes only exhibit partial overlaps suggesting that the boundaries between methylated and unmethylated DNA are dynamic. This instability is not solely due to sequence variation as these partially overlapping UMRs are frequently found within genomic regions that lack sequence variation. The ability to compare chromatin properties among individuals with structural variation enables pan-epigenome analyses to study the sources of variation for accessible chromatin and unmethylated DNA.
Collapse
Affiliation(s)
- Jaclyn M Noshay
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN 55108, USA
| | - Zhikai Liang
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN 55108, USA
| | - Peng Zhou
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN 55108, USA
| | - Peter A Crisp
- School of Agriculture and Food Sciences, University of Queensland, St Lucia, QLD 4072, Australia
| | | | - Candice N Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN 55108, USA
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Nathan M Springer
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN 55108, USA
| |
Collapse
|
42
|
Hufford MB, Seetharam AS, Woodhouse MR, Chougule KM, Ou S, Liu J, Ricci WA, Guo T, Olson A, Qiu Y, Della Coletta R, Tittes S, Hudson AI, Marand AP, Wei S, Lu Z, Wang B, Tello-Ruiz MK, Piri RD, Wang N, Kim DW, Zeng Y, O'Connor CH, Li X, Gilbert AM, Baggs E, Krasileva KV, Portwood JL, Cannon EKS, Andorf CM, Manchanda N, Snodgrass SJ, Hufnagel DE, Jiang Q, Pedersen S, Syring ML, Kudrna DA, Llaca V, Fengler K, Schmitz RJ, Ross-Ibarra J, Yu J, Gent JI, Hirsch CN, Ware D, Dawe RK. De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes. Science 2021; 373:655-662. [PMID: 34353948 PMCID: PMC8733867 DOI: 10.1126/science.abg5289] [Citation(s) in RCA: 233] [Impact Index Per Article: 77.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 06/24/2021] [Indexed: 12/24/2022]
Abstract
We report de novo genome assemblies, transcriptomes, annotations, and methylomes for the 26 inbreds that serve as the founders for the maize nested association mapping population. The number of pan-genes in these diverse genomes exceeds 103,000, with approximately a third found across all genotypes. The results demonstrate that the ancient tetraploid character of maize continues to degrade by fractionation to the present day. Excellent contiguity over repeat arrays and complete annotation of centromeres revealed additional variation in major cytological landmarks. We show that combining structural variation with single-nucleotide polymorphisms can improve the power of quantitative mapping studies. We also document variation at the level of DNA methylation and demonstrate that unmethylated regions are enriched for cis-regulatory elements that contribute to phenotypic variation.
Collapse
Affiliation(s)
- Matthew B Hufford
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Arun S Seetharam
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
- Genome Informatics Facility, Iowa State University, Ames, IA 50011, USA
| | - Margaret R Woodhouse
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA 50011, USA
| | | | - Shujun Ou
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Jianing Liu
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - William A Ricci
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Tingting Guo
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA
| | - Andrew Olson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Yinjie Qiu
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
| | - Rafael Della Coletta
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
| | - Silas Tittes
- Center for Population Biology, University of California, Davis, CA 95616, USA
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - Asher I Hudson
- Center for Population Biology, University of California, Davis, CA 95616, USA
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | | | - Sharon Wei
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Zhenyuan Lu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Bo Wang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | | | - Rebecca D Piri
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Na Wang
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Dong Won Kim
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Yibing Zeng
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Christine H O'Connor
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN 55108, USA
| | - Xianran Li
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA
| | - Amanda M Gilbert
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
| | - Erin Baggs
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Ksenia V Krasileva
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - John L Portwood
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA 50011, USA
| | - Ethalinda K S Cannon
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA 50011, USA
| | - Carson M Andorf
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA 50011, USA
| | - Nancy Manchanda
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Samantha J Snodgrass
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - David E Hufnagel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, IA, 50010, USA
| | - Qiuhan Jiang
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Sarah Pedersen
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Michael L Syring
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - David A Kudrna
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | | | | | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Jeffrey Ross-Ibarra
- Center for Population Biology, University of California, Davis, CA 95616, USA
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
- Genome Center, University of California, Davis, CA 95616, USA
| | - Jianming Yu
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA
| | - Jonathan I Gent
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Candice N Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
| | - Doreen Ware
- USDA-ARS NAA Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, Ithaca, NY 14853, USA
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - R Kelly Dawe
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA.
| |
Collapse
|
43
|
Gogolev YV, Ahmar S, Akpinar BA, Budak H, Kiryushkin AS, Gorshkov VY, Hensel G, Demchenko KN, Kovalchuk I, Mora-Poblete F, Muslu T, Tsers ID, Yadav NS, Korzun V. OMICs, Epigenetics, and Genome Editing Techniques for Food and Nutritional Security. PLANTS (BASEL, SWITZERLAND) 2021; 10:1423. [PMID: 34371624 PMCID: PMC8309286 DOI: 10.3390/plants10071423] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/30/2021] [Accepted: 07/07/2021] [Indexed: 12/22/2022]
Abstract
The incredible success of crop breeding and agricultural innovation in the last century greatly contributed to the Green Revolution, which significantly increased yields and ensures food security, despite the population explosion. However, new challenges such as rapid climate change, deteriorating soil, and the accumulation of pollutants require much faster responses and more effective solutions that cannot be achieved through traditional breeding. Further prospects for increasing the efficiency of agriculture are undoubtedly associated with the inclusion in the breeding strategy of new knowledge obtained using high-throughput technologies and new tools in the future to ensure the design of new plant genomes and predict the desired phenotype. This article provides an overview of the current state of research in these areas, as well as the study of soil and plant microbiomes, and the prospective use of their potential in a new field of microbiome engineering. In terms of genomic and phenomic predictions, we also propose an integrated approach that combines high-density genotyping and high-throughput phenotyping techniques, which can improve the prediction accuracy of quantitative traits in crop species.
Collapse
Affiliation(s)
- Yuri V. Gogolev
- Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Kazan Institute of Biochemistry and Biophysics, 420111 Kazan, Russia;
- Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Laboratory of Plant Infectious Diseases, 420111 Kazan, Russia;
| | - Sunny Ahmar
- Institute of Biological Sciences, University of Talca, 1 Poniente 1141, Talca 3460000, Chile; (S.A.); (F.M.-P.)
| | | | - Hikmet Budak
- Montana BioAg Inc., Missoula, MT 59802, USA; (B.A.A.); (H.B.)
| | - Alexey S. Kiryushkin
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute of the Russian Academy of Sciences, 197376 Saint Petersburg, Russia; (A.S.K.); (K.N.D.)
| | - Vladimir Y. Gorshkov
- Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Kazan Institute of Biochemistry and Biophysics, 420111 Kazan, Russia;
- Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Laboratory of Plant Infectious Diseases, 420111 Kazan, Russia;
| | - Goetz Hensel
- Centre for Plant Genome Engineering, Institute of Plant Biochemistry, Heinrich-Heine-University, 40225 Dusseldorf, Germany;
- Centre of the Region Haná for Biotechnological and Agricultural Research, Czech Advanced Technology and Research Institute, Palacký University Olomouc, 78371 Olomouc, Czech Republic
| | - Kirill N. Demchenko
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute of the Russian Academy of Sciences, 197376 Saint Petersburg, Russia; (A.S.K.); (K.N.D.)
| | - Igor Kovalchuk
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada; (I.K.); (N.S.Y.)
| | - Freddy Mora-Poblete
- Institute of Biological Sciences, University of Talca, 1 Poniente 1141, Talca 3460000, Chile; (S.A.); (F.M.-P.)
| | - Tugdem Muslu
- Faculty of Engineering and Natural Sciences, Sabanci University, 34956 Istanbul, Turkey;
| | - Ivan D. Tsers
- Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Laboratory of Plant Infectious Diseases, 420111 Kazan, Russia;
| | - Narendra Singh Yadav
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada; (I.K.); (N.S.Y.)
| | - Viktor Korzun
- Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Laboratory of Plant Infectious Diseases, 420111 Kazan, Russia;
- KWS SAAT SE & Co. KGaA, Grimsehlstr. 31, 37555 Einbeck, Germany
| |
Collapse
|
44
|
Jayakodi M, Schreiber M, Stein N, Mascher M. Building pan-genome infrastructures for crop plants and their use in association genetics. DNA Res 2021; 28:6117190. [PMID: 33484244 PMCID: PMC7934568 DOI: 10.1093/dnares/dsaa030] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Indexed: 12/20/2022] Open
Abstract
Pan-genomic studies aim at representing the entire sequence diversity within a species to provide useful resources for evolutionary studies, functional genomics and breeding of cultivated plants. Cost reductions in high-throughput sequencing and advances in sequence assembly algorithms have made it possible to create multiple reference genomes along with a catalogue of all forms of genetic variations in plant species with large and complex or polyploid genomes. In this review, we summarize the current approaches to building pan-genomes as an in silico representation of plant sequence diversity and outline relevant methods for their effective utilization in linking structural with phenotypic variation. We propose as future research avenues (i) transcriptomic and epigenomic studies across multiple reference genomes and (ii) the development of user-friendly and feature-rich pan-genome browsers.
Collapse
Affiliation(s)
- Murukarthick Jayakodi
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Mona Schreiber
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Nils Stein
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.,Center for Integrated Breeding Research (CiBreed), Georg-August-University Göttingen, Göttingen, Germany
| | - Martin Mascher
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Saxony, Germany
| |
Collapse
|
45
|
Li Z, Han L, Luo Z, Li L. Single-molecule long-read sequencing reveals extensive genomic and transcriptomic variation between maize and its wild relative teosinte (Zea mays ssp. parviglumis). Mol Ecol Resour 2021; 22:272-282. [PMID: 34157795 DOI: 10.1111/1755-0998.13454] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 06/10/2021] [Accepted: 06/11/2021] [Indexed: 11/27/2022]
Abstract
Teosinte (Zea mays ssp. parviglumis), the wild progenitor of maize (Zea mays L.), is an important germplasm resource for improvement of modern maize lines. However, we have limited genetic and genomic information about teosinte and lack state-of-the-art tools to annotate transcriptomes assembled by single-molecule long-read sequencing without a reference genome. Here, we employed single-molecule long-read sequencing of cDNA libraries from five tissues of the teosinte inbred line TIL11 and identified 70,044 nonredundant transcript isoforms. We devised a state-of-the-art, machine learning-based bioinformatics pipeline DenovoAS_Finder to annotate the TIL11 transcriptome without a complete reference genome with an accuracy of up to 91%, providing a robust gene classifier of complex genomes. Additionally, we constructed a draft TIL11 genome with 16,633 high-quality contigs and a N50 of 112 kb by Nanopore sequencing. Genes from families that expanded from teosinte to maize were significantly enriched in the gene ontology (GO) term "RNA modification pathway" and had more transcript isoforms in TIL11 than in the maize inbred line B73. Genes showed collinearity between TIL11 and B73, and intergenic regions were extensively altered by transposable elements. Our study furthers the understanding of maize domestication and provides a resource for the utilization of wild germplasm in maize breeding.
Collapse
Affiliation(s)
- Zhao Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Linqian Han
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Zi Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Lin Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| |
Collapse
|
46
|
Lin G, He C, Zheng J, Koo DH, Le H, Zheng H, Tamang TM, Lin J, Liu Y, Zhao M, Hao Y, McFraland F, Wang B, Qin Y, Tang H, McCarty DR, Wei H, Cho MJ, Park S, Kaeppler H, Kaeppler SM, Liu Y, Springer N, Schnable PS, Wang G, White FF, Liu S. Chromosome-level genome assembly of a regenerable maize inbred line A188. Genome Biol 2021; 22:175. [PMID: 34108023 PMCID: PMC8188678 DOI: 10.1186/s13059-021-02396-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 05/28/2021] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND The maize inbred line A188 is an attractive model for elucidation of gene function and improvement due to its high embryogenic capacity and many contrasting traits to the first maize reference genome, B73, and other elite lines. The lack of a genome assembly of A188 limits its use as a model for functional studies. RESULTS Here, we present a chromosome-level genome assembly of A188 using long reads and optical maps. Comparison of A188 with B73 using both whole-genome alignments and read depths from sequencing reads identify approximately 1.1 Gb of syntenic sequences as well as extensive structural variation, including a 1.8-Mb duplication containing the Gametophyte factor1 locus for unilateral cross-incompatibility, and six inversions of 0.7 Mb or greater. Increased copy number of carotenoid cleavage dioxygenase 1 (ccd1) in A188 is associated with elevated expression during seed development. High ccd1 expression in seeds together with low expression of yellow endosperm 1 (y1) reduces carotenoid accumulation, accounting for the white seed phenotype of A188. Furthermore, transcriptome and epigenome analyses reveal enhanced expression of defense pathways and altered DNA methylation patterns of the embryonic callus. CONCLUSIONS The A188 genome assembly provides a high-resolution sequence for a complex genome species and a foundational resource for analyses of genome variation and gene function in maize. The genome, in comparison to B73, contains extensive intra-species structural variations and other genetic differences. Expression and network analyses identify discrete profiles for embryonic callus and other tissues.
Collapse
Affiliation(s)
- Guifang Lin
- Department of Plant Pathology, Kansas State University, 4024 Throckmorton Center, Manhattan, KS, 66506-5502, USA
| | - Cheng He
- Department of Plant Pathology, Kansas State University, 4024 Throckmorton Center, Manhattan, KS, 66506-5502, USA
| | - Jun Zheng
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Dal-Hoe Koo
- Department of Plant Pathology, Kansas State University, 4024 Throckmorton Center, Manhattan, KS, 66506-5502, USA
| | - Ha Le
- Department of Plant Pathology, Kansas State University, 4024 Throckmorton Center, Manhattan, KS, 66506-5502, USA
| | - Huakun Zheng
- Department of Plant Pathology, Kansas State University, 4024 Throckmorton Center, Manhattan, KS, 66506-5502, USA
| | - Tej Man Tamang
- Department of Horticulture and Natural Resources, Kansas State University, Manhattan, KS, 66506-5502, USA
| | - Jinguang Lin
- Department of Plant Pathology, Kansas State University, 4024 Throckmorton Center, Manhattan, KS, 66506-5502, USA
- Present Address, Corvallis, OR, 97330, USA
| | - Yan Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Mingxia Zhao
- Department of Plant Pathology, Kansas State University, 4024 Throckmorton Center, Manhattan, KS, 66506-5502, USA
| | - Yangfan Hao
- Department of Plant Pathology, Kansas State University, 4024 Throckmorton Center, Manhattan, KS, 66506-5502, USA
| | - Frank McFraland
- Department of Agronomy, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Bo Wang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Yang Qin
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Haibao Tang
- Center for Genomics and Biotechnology and Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Donald R McCarty
- Department of Horticulture, University of Florida, Gainesville, FL, 32611-0680, USA
| | - Hairong Wei
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA
| | - Myeong-Je Cho
- Innovative Genomics Institute, University of California-Berkeley, Sunnyvale, CA, 94704, USA
| | - Sunghun Park
- Department of Horticulture and Natural Resources, Kansas State University, Manhattan, KS, 66506-5502, USA
| | - Heidi Kaeppler
- Department of Agronomy, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Shawn M Kaeppler
- Department of Agronomy, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Yunjun Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Nathan Springer
- Department of Plant Biology, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Patrick S Schnable
- Department of Agronomy, Iowa State University, Ames, IA, 50011-3605, USA
| | - Guoying Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Frank F White
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611-0680, USA
| | - Sanzhen Liu
- Department of Plant Pathology, Kansas State University, 4024 Throckmorton Center, Manhattan, KS, 66506-5502, USA.
| |
Collapse
|
47
|
Jocković M, Jocić S, Cvejić S, Marjanović-Jeromela A, Jocković J, Radanović A, Miladinović D. Genetic Improvement in Sunflower Breeding—Integrated Omics Approach. PLANTS 2021; 10:plants10061150. [PMID: 34200113 PMCID: PMC8228292 DOI: 10.3390/plants10061150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/31/2021] [Accepted: 06/01/2021] [Indexed: 01/23/2023]
Abstract
Foresight in climate change and the challenges ahead requires a systematic approach to sunflower breeding that will encompass all available technologies. There is a great scarcity of desirable genetic variation, which is in fact undiscovered because it has not been sufficiently researched as detection and designing favorable genetic variation largely depends on thorough genome sequencing through broad and deep resequencing. Basic exploration of genomes is insufficient to find insight about important physiological and molecular mechanisms unique to crops. That is why integrating information from genomics, epigenomics, transcriptomics, proteomics, metabolomics and phenomics enables a comprehensive understanding of the molecular mechanisms in the background of architecture of many important quantitative traits. Omics technologies offer novel possibilities for deciphering the complex pathways and molecular profiling through the level of systems biology and can provide important answers that can be utilized for more efficient breeding of sunflower. In this review, we present omics profiling approaches in order to address their possibilities and usefulness as a potential breeding tools in sunflower genetic improvement.
Collapse
Affiliation(s)
- Milan Jocković
- Institute of Field and Vegetable Crops, Maksima Gorkog 30, 21000 Novi Sad, Serbia; (S.J.); (S.C.); (A.M.-J.); (A.R.); (D.M.)
- Correspondence:
| | - Siniša Jocić
- Institute of Field and Vegetable Crops, Maksima Gorkog 30, 21000 Novi Sad, Serbia; (S.J.); (S.C.); (A.M.-J.); (A.R.); (D.M.)
| | - Sandra Cvejić
- Institute of Field and Vegetable Crops, Maksima Gorkog 30, 21000 Novi Sad, Serbia; (S.J.); (S.C.); (A.M.-J.); (A.R.); (D.M.)
| | - Ana Marjanović-Jeromela
- Institute of Field and Vegetable Crops, Maksima Gorkog 30, 21000 Novi Sad, Serbia; (S.J.); (S.C.); (A.M.-J.); (A.R.); (D.M.)
| | - Jelena Jocković
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Dositeja Obradovića 3, 21000 Novi Sad, Serbia;
| | - Aleksandra Radanović
- Institute of Field and Vegetable Crops, Maksima Gorkog 30, 21000 Novi Sad, Serbia; (S.J.); (S.C.); (A.M.-J.); (A.R.); (D.M.)
| | - Dragana Miladinović
- Institute of Field and Vegetable Crops, Maksima Gorkog 30, 21000 Novi Sad, Serbia; (S.J.); (S.C.); (A.M.-J.); (A.R.); (D.M.)
| |
Collapse
|
48
|
Barragan AC, Weigel D. Plant NLR diversity: the known unknowns of pan-NLRomes. THE PLANT CELL 2021; 33:814-831. [PMID: 33793812 PMCID: PMC8226294 DOI: 10.1093/plcell/koaa002] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 10/23/2020] [Indexed: 05/20/2023]
Abstract
Plants and pathogens constantly adapt to each other. As a consequence, many members of the plant immune system, and especially the intracellular nucleotide-binding site leucine-rich repeat receptors, also known as NOD-like receptors (NLRs), are highly diversified, both among family members in the same genome, and between individuals in the same species. While this diversity has long been appreciated, its true extent has remained unknown. With pan-genome and pan-NLRome studies becoming more and more comprehensive, our knowledge of NLR sequence diversity is growing rapidly, and pan-NLRomes provide powerful platforms for assigning function to NLRs. These efforts are an important step toward the goal of comprehensively predicting from sequence alone whether an NLR provides disease resistance, and if so, to which pathogens.
Collapse
Affiliation(s)
- A Cristina Barragan
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | | |
Collapse
|
49
|
Li M, Noshay JM, Dong X, Springer NM, Li Q. A capture-based assay for detection and characterization of transposon polymorphisms in maize. G3-GENES GENOMES GENETICS 2021; 11:6255745. [PMID: 33905487 PMCID: PMC8495914 DOI: 10.1093/g3journal/jkab138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 04/15/2021] [Indexed: 11/14/2022]
Abstract
Transposons can create allelic diversity that affects gene expression and phenotypic diversity. The detection of transposon polymorphisms at a genome-wide scale across a large population is difficult. Here we developed a targeted sequencing approach to monitor transposon polymorphisms of interest. This approach can interrogate the presence or absence of transposons reliably across various genotypes. Using this approach, we genotyped a set of 965 transposon-related presence/absence polymorphisms in a diverse panel of 16 maize (Zea mays L.) inbred lines that are representative of the major maize breeding groups. About 70% of the selected regions can be effectively assayed in each genotype. The consistency between the capture-based assay and PCR-based assay are 98.6% based on analysis of 24 randomly selected transposon polymorphisms. By integrating the transposon polymorphisms data with gene expression data, ∼18% of the assayed transposon polymorphisms were found to be associated with variable gene expression levels. A detailed analysis of 18 polymorphisms in a larger association panel confirmed the effects of 10 polymorphisms, with one of them having stronger association with expression than nearby SNP markers. The effects of seven polymorphisms were tested using a luciferase-based expression assay, and one was confirmed. Together, this study demonstrates that the targeted sequencing assay is an effective way to explore transposon function in a high-throughput manner.
Collapse
Affiliation(s)
- Minqi Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jaclyn M Noshay
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN 55108, USA
| | - Xiaoxiao Dong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Nathan M Springer
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN 55108, USA
| | - Qing Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| |
Collapse
|
50
|
Zhan S, Griswold C, Lukens L. Zea mays RNA-seq estimated transcript abundances are strongly affected by read mapping bias. BMC Genomics 2021; 22:285. [PMID: 33874908 PMCID: PMC8056621 DOI: 10.1186/s12864-021-07577-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 03/30/2021] [Indexed: 11/27/2022] Open
Abstract
Background Genetic variation for gene expression is a source of phenotypic variation for natural and agricultural species. The common approach to map and to quantify gene expression from genetically distinct individuals is to assign their RNA-seq reads to a single reference genome. However, RNA-seq reads from alleles dissimilar to this reference genome may fail to map correctly, causing transcript levels to be underestimated. Presently, the extent of this mapping problem is not clear, particularly in highly diverse species. We investigated if mapping bias occurred and if chromosomal features associated with mapping bias. Zea mays presents a model species to assess these questions, given it has genotypically distinct and well-studied genetic lines. Results In Zea mays, the inbred B73 genome is the standard reference genome and template for RNA-seq read assignments. In the absence of mapping bias, B73 and a second inbred line, Mo17, would each have an approximately equal number of regulatory alleles that increase gene expression. Remarkably, Mo17 had 2–4 times fewer such positively acting alleles than did B73 when RNA-seq reads were aligned to the B73 reference genome. Reciprocally, over one-half of the B73 alleles that increased gene expression were not detected when reads were aligned to the Mo17 genome template. Genes at dissimilar chromosomal ends were strongly affected by mapping bias, and genes at more similar pericentromeric regions were less affected. Biased transcript estimates were higher in untranslated regions and lower in splice junctions. Bias occurred across software and alignment parameters. Conclusions Mapping bias very strongly affects gene transcript abundance estimates in maize, and bias varies across chromosomal features. Individual genome or transcriptome templates are likely necessary for accurate transcript estimation across genetically variable individuals in maize and other species. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07577-3.
Collapse
Affiliation(s)
- Shuhua Zhan
- Department of Plant Agriculture, University of Guelph, Guelph, Ontario, Canada
| | - Cortland Griswold
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Lewis Lukens
- Department of Plant Agriculture, University of Guelph, Guelph, Ontario, Canada.
| |
Collapse
|