1
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Gutaker RM, Purugganan MD. Adaptation and the Geographic Spread of Crop Species. ANNUAL REVIEW OF PLANT BIOLOGY 2024; 75:679-706. [PMID: 38012052 DOI: 10.1146/annurev-arplant-060223-030954] [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: 11/29/2023]
Abstract
Crops are plant species that were domesticated starting about 11,000 years ago from several centers of origin, most prominently the Fertile Crescent, East Asia, and Mesoamerica. From their domestication centers, these crops spread across the globe and had to adapt to differing environments as a result of this dispersal. We discuss broad patterns of crop spread, including the early diffusion of crops associated with the rise and spread of agriculture, the later movement via ancient trading networks, and the exchange between the Old and New Worlds over the last ∼550 years after the European colonization of the Americas. We also examine the various genetic mechanisms associated with the evolutionary adaptation of crops to their new environments after dispersal, most prominently seasonal adaptation associated with movement across latitudes, as well as altitudinal, temperature, and other environmental factors.
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Affiliation(s)
| | - Michael D Purugganan
- Center for Genomics and Systems Biology, New York University, New York, NY, USA;
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
- Institute for the Study of the Ancient World, New York University, New York, NY, USA
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2
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Yu P, Li C, Li M, He X, Wang D, Li H, Marcon C, Li Y, Perez-Limón S, Chen X, Delgado-Baquerizo M, Koller R, Metzner R, van Dusschoten D, Pflugfelder D, Borisjuk L, Plutenko I, Mahon A, Resende MFR, Salvi S, Akale A, Abdalla M, Ahmed MA, Bauer FM, Schnepf A, Lobet G, Heymans A, Suresh K, Schreiber L, McLaughlin CM, Li C, Mayer M, Schön CC, Bernau V, von Wirén N, Sawers RJH, Wang T, Hochholdinger F. Seedling root system adaptation to water availability during maize domestication and global expansion. Nat Genet 2024; 56:1245-1256. [PMID: 38778242 DOI: 10.1038/s41588-024-01761-3] [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: 04/28/2023] [Accepted: 04/19/2024] [Indexed: 05/25/2024]
Abstract
The maize root system has been reshaped by indirect selection during global adaptation to new agricultural environments. In this study, we characterized the root systems of more than 9,000 global maize accessions and its wild relatives, defining the geographical signature and genomic basis of variation in seminal root number. We demonstrate that seminal root number has increased during maize domestication followed by a decrease in response to limited water availability in locally adapted varieties. By combining environmental and phenotypic association analyses with linkage mapping, we identified genes linking environmental variation and seminal root number. Functional characterization of the transcription factor ZmHb77 and in silico root modeling provides evidence that reshaping root system architecture by reducing the number of seminal roots and promoting lateral root density is beneficial for the resilience of maize seedlings to drought.
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Affiliation(s)
- Peng Yu
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany.
- Emmy Noether Group Root Functional Biology, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany.
| | - Chunhui Li
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, PR China
| | - Meng Li
- Department of Plant Science, The Pennsylvania State University, State College, PA, USA
| | - Xiaoming He
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
- Emmy Noether Group Root Functional Biology, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
| | - Danning Wang
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
- Emmy Noether Group Root Functional Biology, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
| | - Hongjie Li
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
- Emmy Noether Group Root Functional Biology, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
| | - Caroline Marcon
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
| | - Yu Li
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, PR China
| | - Sergio Perez-Limón
- Department of Plant Science, The Pennsylvania State University, State College, PA, USA
| | - Xinping Chen
- College of Resources and Environment, and Academy of Agricultural Sciences, Southwest University (SWU), Chongqing, PR China
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico. Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, Spain
- Unidad Asociada CSIC-UPO (BioFun), Universidad Pablo de Olavide, Sevilla, Spain
| | - Robert Koller
- Institute of Bio- and Geosciences, Plant Sciences (IBG-2), Forschungszentrum Juelich GmbH, Juelich, Germany
| | - Ralf Metzner
- Institute of Bio- and Geosciences, Plant Sciences (IBG-2), Forschungszentrum Juelich GmbH, Juelich, Germany
| | - Dagmar van Dusschoten
- Institute of Bio- and Geosciences, Plant Sciences (IBG-2), Forschungszentrum Juelich GmbH, Juelich, Germany
| | - Daniel Pflugfelder
- Institute of Bio- and Geosciences, Plant Sciences (IBG-2), Forschungszentrum Juelich GmbH, Juelich, Germany
| | - Ljudmilla Borisjuk
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Iaroslav Plutenko
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Audrey Mahon
- Horticultural Sciences Department, University of Florida, Gainesville, FL, USA
| | - Marcio F R Resende
- Horticultural Sciences Department, University of Florida, Gainesville, FL, USA
| | - Silvio Salvi
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Asegidew Akale
- Chair of Root-Soil Interactions, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Mohanned Abdalla
- Chair of Root-Soil Interactions, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Mutez Ali Ahmed
- Chair of Root-Soil Interactions, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Felix Maximilian Bauer
- Institute of Bio- and Geosciences, Agrosphere (IBG-3), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Andrea Schnepf
- Institute of Bio- and Geosciences, Agrosphere (IBG-3), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Guillaume Lobet
- Institute of Bio- and Geosciences, Agrosphere (IBG-3), Forschungszentrum Jülich GmbH, Jülich, Germany
- Earth and Life Institute, Université catholique de Louvain, UCLouvain, Belgium
| | - Adrien Heymans
- Earth and Life Institute, Université catholique de Louvain, UCLouvain, Belgium
| | - Kiran Suresh
- Institute of Cellular and Molecular Botany (IZMB), Department of Ecophysiology, University of Bonn, Bonn, Germany
| | - Lukas Schreiber
- Institute of Cellular and Molecular Botany (IZMB), Department of Ecophysiology, University of Bonn, Bonn, Germany
| | - Chloee M McLaughlin
- Intercollege Graduate Degree Program in Plant Biology, The Pennsylvania State University, State College, PA, USA
| | - Chunjian Li
- Key Laboratory of Plant-Soil Interactions, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Ministry of Education, China Agricultural University, Beijing, PR China
| | - Manfred Mayer
- Plant Breeding, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Chris-Carolin Schön
- Plant Breeding, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Vivian Bernau
- North Central Regional Plant Introduction Station, USDA-Agriculture Research Service and Iowa State University, Ames, IA, USA
| | - Nicolaus von Wirén
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Ruairidh J H Sawers
- Department of Plant Science, The Pennsylvania State University, State College, PA, USA.
| | - Tianyu Wang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, PR China.
| | - Frank Hochholdinger
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany.
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3
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Mascher M, Marone MP, Schreiber M, Stein N. Are cereal grasses a single genetic system? NATURE PLANTS 2024; 10:719-731. [PMID: 38605239 DOI: 10.1038/s41477-024-01674-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 03/17/2024] [Indexed: 04/13/2024]
Abstract
In 1993, a passionate and provocative call to arms urged cereal researchers to consider the taxon they study as a single genetic system and collaborate with each other. Since then, that group of scientists has seen their discipline blossom. In an attempt to understand what unity of genetic systems means and how the notion was borne out by later research, we survey the progress and prospects of cereal genomics: sequence assemblies, population-scale sequencing, resistance gene cloning and domestication genetics. Gene order may not be as extraordinarily well conserved in the grasses as once thought. Still, several recurring themes have emerged. The same ancestral molecular pathways defining plant architecture have been co-opted in the evolution of different cereal crops. Such genetic convergence as much as cross-fertilization of ideas between cereal geneticists has led to a rich harvest of genes that, it is hoped, will lead to improved varieties.
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Affiliation(s)
- Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
| | - Marina Püpke Marone
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Mona Schreiber
- University of Marburg, Department of Biology, Marburg, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany.
- Martin Luther University Halle-Wittenberg, Halle (Saale), Germany.
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4
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Meiri M, Bar-Oz G. Unraveling the diversity and cultural heritage of fruit crops through paleogenomics. Trends Genet 2024; 40:398-409. [PMID: 38423916 PMCID: PMC11079635 DOI: 10.1016/j.tig.2024.02.003] [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: 11/30/2023] [Revised: 02/06/2024] [Accepted: 02/06/2024] [Indexed: 03/02/2024]
Abstract
Abundant and plentiful fruit crops are threatened by the loss of diverse legacy cultivars which are being replaced by a limited set of high-yielding ones. This article delves into the potential of paleogenomics that utilizes ancient DNA analysis to revive lost diversity. By focusing on grapevines, date palms, and tomatoes, recent studies showcase the effectiveness of paleogenomic techniques in identifying and understanding genetic traits crucial for crop resilience, disease resistance, and nutritional value. The approach not only tracks landrace dispersal and introgression but also sheds light on domestication events. In the face of major future environmental challenges, integrating paleogenomics with modern breeding strategies emerges as a promising avenue to significantly bolster fruit crop sustainability.
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Affiliation(s)
- Meirav Meiri
- The Steinhardt Museum of Natural History and Israel National Center for Biodiversity Studies, Tel Aviv University, Tel Aviv 6997801, Israel.
| | - Guy Bar-Oz
- School of Archaeology and Maritime Cultures, University of Haifa, Haifa, 3498837 Mount Carmel, Israel
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5
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Su H, Cao L, Ren Z, Sun W, Zhu B, Ma S, Sun C, Zhang D, Liu Z, Zeng H, Yang W, Liu Y, Zheng L, Yang Y, Wu Z, Zhu Y, Ku L, Chong L, Chen Y. ZmELF6-ZmPRR37 module regulates maize flowering and salt response. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:929-945. [PMID: 38009862 PMCID: PMC10955496 DOI: 10.1111/pbi.14236] [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: 06/05/2023] [Revised: 10/22/2023] [Accepted: 11/06/2023] [Indexed: 11/29/2023]
Abstract
The control of flowering time in maize is crucial for reproductive success and yield, and it can be influenced by environmental stresses. Using the approaches of Ac/Ds transposon and transposable element amplicon sequencing techniques, we identified a Ds insertion mutant in the ZmPRR37 gene. The Ds insertion showed a significant correlation with days to anthesis. Further research indicated that ZmPRR37-CR knockout mutants exhibited early flowering, whereas ZmPRR37-overexpression lines displayed delayed flowering compared to WT under long-day (LD) conditions. We demonstrated that ZmPRR37 repressed the expression of ZmNF-YC2 and ZmNF-YA3 to delay flowering. Association analysis revealed a significant correlation between flowering time and a SNP2071-C/T located upstream of ZmPRR37. The SNP2071-C/T impacted the binding capacity of ZmELF6 to the promoter of ZmPRR37. ZmELF6 also acted as a flowering suppressor in maize under LD conditions. Notably, our study unveiled that ZmPRR37 can enhance salt stress tolerance in maize by directly regulating the expression of ABA-responsive gene ZmDhn1. ZmDhn1 negatively regulated maize salt stress resistance. In summary, our findings proposed a novel pathway for regulating photoperiodic flowering and responding to salt stress based on ZmPRR37 in maize, providing novel insights into the integration of abiotic stress signals into floral pathways.
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Affiliation(s)
- Huihui Su
- National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, College of AgronomyHenan Agricultural UniversityZhengzhouHenanChina
| | - Liru Cao
- The Shennong LaboratoryZhengzhouHenanChina
| | - Zhenzhen Ren
- National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, College of AgronomyHenan Agricultural UniversityZhengzhouHenanChina
| | - Wenhao Sun
- National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, College of AgronomyHenan Agricultural UniversityZhengzhouHenanChina
| | - Bingqi Zhu
- National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, College of AgronomyHenan Agricultural UniversityZhengzhouHenanChina
| | - Shixiang Ma
- National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, College of AgronomyHenan Agricultural UniversityZhengzhouHenanChina
| | - Chongyu Sun
- National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, College of AgronomyHenan Agricultural UniversityZhengzhouHenanChina
| | - Dongling Zhang
- National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, College of AgronomyHenan Agricultural UniversityZhengzhouHenanChina
| | - Zhixue Liu
- National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, College of AgronomyHenan Agricultural UniversityZhengzhouHenanChina
| | - Haixia Zeng
- National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, College of AgronomyHenan Agricultural UniversityZhengzhouHenanChina
| | - Wenjing Yang
- National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, College of AgronomyHenan Agricultural UniversityZhengzhouHenanChina
| | - Yingpeng Liu
- National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, College of AgronomyHenan Agricultural UniversityZhengzhouHenanChina
| | - Lingling Zheng
- National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, College of AgronomyHenan Agricultural UniversityZhengzhouHenanChina
| | - Yuwei Yang
- National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, College of AgronomyHenan Agricultural UniversityZhengzhouHenanChina
| | - Zhendong Wu
- National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, College of AgronomyHenan Agricultural UniversityZhengzhouHenanChina
| | - Yingfang Zhu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life SciencesHenan UniversityKaifengChina
| | - Lixia Ku
- National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, College of AgronomyHenan Agricultural UniversityZhengzhouHenanChina
| | - Leelyn Chong
- National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, College of AgronomyHenan Agricultural UniversityZhengzhouHenanChina
| | - Yanhui Chen
- National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, College of AgronomyHenan Agricultural UniversityZhengzhouHenanChina
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6
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Cao S, Zhang H, Liu Y, Sun Y, Chen ZJ. Cytoplasmic genome contributions to domestication and improvement of modern maize. BMC Biol 2024; 22:64. [PMID: 38481288 PMCID: PMC10938767 DOI: 10.1186/s12915-024-01859-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 02/28/2024] [Indexed: 03/17/2024] Open
Abstract
BACKGROUND Studies on maize evolution and domestication are largely limited to the nuclear genomes, and the contribution of cytoplasmic genomes to selection and domestication of modern maize remains elusive. Maize cytoplasmic genomes have been classified into fertile (NA and NB) and cytoplasmic-nuclear male-sterility (CMS-S, CMS-C, and CMS-T) groups, but their contributions to modern maize breeding have not been systematically investigated. RESULTS Here we report co-selection and convergent evolution between nuclear and cytoplasmic genomes by analyzing whole genome sequencing data of 630 maize accessions modern maize and its relatives, including 24 fully assembled mitochondrial and chloroplast genomes. We show that the NB cytotype is associated with the expansion of modern maize to North America, gradually replaces the fertile NA cytotype probably through unequal division, and predominates in over 90% of modern elite inbred lines. The mode of cytoplasmic evolution is increased nucleotypic diversity among the genes involved in photosynthesis and energy metabolism, which are driven by selection and domestication. Furthermore, genome-wide association study reveals correlation of cytoplasmic nucleotypic variation with key agronomic and reproductive traits accompanied with the diversification of the nuclear genomes. CONCLUSIONS Our results indicate convergent evolution between cytoplasmic and nuclear genomes during maize domestication and breeding. These new insights into the important roles of mitochondrial and chloroplast genomes in maize domestication and improvement should help select elite inbred lines to improve yield stability and crop resilience of maize hybrids.
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Affiliation(s)
- Shuai Cao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, China
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Huanhuan Zhang
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, Shanxi Agricultural University, Shanxi, Taiyuan, 030031, China
| | - Yang Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, China
| | - Yi Sun
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, Shanxi Agricultural University, Shanxi, Taiyuan, 030031, China
| | - Z Jeffrey Chen
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA.
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7
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He Y, Zhang K, Shi Y, Lin H, Huang X, Lu X, Wang Z, Li W, Feng X, Shi T, Chen Q, Wang J, Tang Y, Chapman MA, Germ M, Luthar Z, Kreft I, Janovská D, Meglič V, Woo SH, Quinet M, Fernie AR, Liu X, Zhou M. Genomic insight into the origin, domestication, dispersal, diversification and human selection of Tartary buckwheat. Genome Biol 2024; 25:61. [PMID: 38414075 PMCID: PMC10898187 DOI: 10.1186/s13059-024-03203-z] [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: 08/15/2023] [Accepted: 02/21/2024] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND Tartary buckwheat, Fagopyrum tataricum, is a pseudocereal crop with worldwide distribution and high nutritional value. However, the origin and domestication history of this crop remain to be elucidated. RESULTS Here, by analyzing the population genomics of 567 accessions collected worldwide and reviewing historical documents, we find that Tartary buckwheat originated in the Himalayan region and then spread southwest possibly along with the migration of the Yi people, a minority in Southwestern China that has a long history of planting Tartary buckwheat. Along with the expansion of the Mongol Empire, Tartary buckwheat dispersed to Europe and ultimately to the rest of the world. The different natural growth environments resulted in adaptation, especially significant differences in salt tolerance between northern and southern Chinese Tartary buckwheat populations. By scanning for selective sweeps and using a genome-wide association study, we identify genes responsible for Tartary buckwheat domestication and differentiation, which we then experimentally validate. Comparative genomics and QTL analysis further shed light on the genetic foundation of the easily dehulled trait in a particular variety that was artificially selected by the Wa people, a minority group in Southwestern China known for cultivating Tartary buckwheat specifically for steaming as a staple food to prevent lysine deficiency. CONCLUSIONS This study provides both comprehensive insights into the origin and domestication of, and a foundation for molecular breeding for, Tartary buckwheat.
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Affiliation(s)
- Yuqi He
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Kaixuan Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yaliang Shi
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hao Lin
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xu Huang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiang Lu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhirong Wang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wei Li
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xibo Feng
- Tibet Key Experiments of Crop Cultivation and Farming/College of Plant Science, Tibet Agriculture and Animal Husbandry University, Linzhi, 860000, China
| | - Taoxiong Shi
- Research Center of Buckwheat Industry Technology, Guizhou Normal University, Guiyang, 550001, China
| | - Qingfu Chen
- Research Center of Buckwheat Industry Technology, Guizhou Normal University, Guiyang, 550001, China
| | - Junzhen Wang
- Xichang Institute of Agricultural Science, Liangshan Yi People Autonomous Prefecture, Liangshan, Sichuan, 615000, China
| | - Yu Tang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Mark A Chapman
- Biological Sciences, University of Southampton, Life Sciences Building 85, Highfield Campus, Southampton, SO17 1BJ, UK
| | - Mateja Germ
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000, Ljubljana, Slovenia
| | - Zlata Luthar
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000, Ljubljana, Slovenia
| | - Ivan Kreft
- Nutrition Institute, Koprska Ulica 98, SI-1000, Ljubljana, Slovenia
| | - Dagmar Janovská
- Gene Bank, Crop Research Institute, Drnovská 507, Prague 6, Czech Republic
| | - Vladimir Meglič
- Agricultural Institute of Slovenia, Hacquetova ulica 17, SI-1000, Ljubljana, Slovenia
| | - Sun-Hee Woo
- Department of Crop Science, Chungbuk National University, Cheong-ju, Republic of Korea
| | - Muriel Quinet
- Groupe de Recherche en Physiologie Végétale (GRPV), Earth and Life Institute-Agronomy (ELI-A), Université catholique de Louvain, Croix du Sud 45, boîte L7.07.13, B-1348, Louvain-la-Neuve, Belgium
| | - Alisdair R Fernie
- Department of Molecular Physiology, Max-Planck-Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Xu Liu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Meiliang Zhou
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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8
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Wagner S, Seguin-Orlando A, Leplé JC, Leroy T, Lalanne C, Labadie K, Aury JM, Poirier S, Wincker P, Plomion C, Kremer A, Orlando L. Tracking population structure and phenology through time using ancient genomes from waterlogged white oak wood. Mol Ecol 2024; 33:e16859. [PMID: 36748324 PMCID: PMC7615563 DOI: 10.1111/mec.16859] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 12/08/2022] [Accepted: 01/16/2023] [Indexed: 02/08/2023]
Abstract
Whole genome characterizations of crop plants based on ancient DNA have provided unique keys for a better understanding of the evolutionary origins of modern cultivars, the pace and mode of selection underlying their adaptation to new environments and the production of phenotypes of interest. Although forests are among the most biologically rich ecosystems on earth and represent a fundamental resource for human societies, no ancient genome sequences have been generated for trees. This contrasts with the generation of multiple ancient reference genomes for important crops. Here, we sequenced the first ancient tree genomes using two white oak wood remains from Germany dating to the Last Little Ice Age (15th century CE, 7.3× and 4.0×) and one from France dating to the Bronze Age (1700 BCE, 3.4×). We assessed the underlying species and identified one medieval remains as a hybrid between two common oak species (Quercus robur and Q. petraea) and the other two remains as Q. robur. We found that diversity at the global genome level had not changed over time. However, exploratory analyses suggested that a reduction of diversity took place at different time periods. Finally, we determined the timing of leaf unfolding for ancient trees for the first time. The study extends the application of ancient wood beyond the classical proxies of dendroclimatology, dendrochronology, dendroarchaeology and dendroecology, thereby enhancing resolution of inferences on the responses of forest ecosystems to past environmental changes, epidemics and silvicultural practices.
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Affiliation(s)
- Stefanie Wagner
- Plant Genomic Resources Center (CNRGV), INRAE, Castanet-Tolosan, France
- Centre for Anthropobiology and Genomics of Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse, France
| | - Andaine Seguin-Orlando
- Centre for Anthropobiology and Genomics of Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse, France
| | | | - Thibault Leroy
- IRHS UMR1345, Université d’Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, Beaucouzé, France
| | | | - Karine Labadie
- Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Jean-Marc Aury
- Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | | | - Patrick Wincker
- Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | | | | | - Ludovic Orlando
- Centre for Anthropobiology and Genomics of Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse, France
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9
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Khalaf EM, Shrestha A, Reid M, McFadyen BJ, Raizada MN. Conservation and diversity of the pollen microbiome of Pan-American maize using PacBio and MiSeq. Front Microbiol 2023; 14:1276241. [PMID: 38179444 PMCID: PMC10764481 DOI: 10.3389/fmicb.2023.1276241] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 11/21/2023] [Indexed: 01/06/2024] Open
Abstract
Pollen is a vector for diversification, fitness-selection, and transmission of plant genetic material. The extent to which the pollen microbiome may contribute to host diversification is largely unknown, because pollen microbiome diversity within a plant species has not been reported, and studies have been limited to conventional short-read 16S rRNA gene sequencing (e.g., V4-MiSeq) which suffers from poor taxonomic resolution. Here we report the pollen microbiomes of 16 primitive and traditional accessions of maize (corn) selected by indigenous peoples across the Americas, along with the modern U.S. inbred B73. The maize pollen microbiome has not previously been reported. The pollen microbiomes were identified using full-length (FL) 16S rRNA gene PacBio SMRT sequencing compared to V4-MiSeq. The Pan-American maize pollen microbiome encompasses 765 taxa spanning 39 genera and 46 species, including known plant growth promoters, insect-obligates, plant pathogens, nitrogen-fixers and biocontrol agents. Eleven genera and 13 species composed the core microbiome. Of 765 taxa, 63% belonged to only four genera: 28% were Pantoea, 15% were Lactococcus, 11% were Pseudomonas, and 10% were Erwinia. Interestingly, of the 215 Pantoea taxa, 180 belonged to a single species, P. ananatis. Surprisingly, the diversity within P. ananatis ranged nearly 10-fold amongst the maize accessions analyzed (those with ≥3 replicates), despite being grown in a common field. The highest diversity within P. ananatis occurred in accessions that originated near the center of diversity of domesticated maize, with reduced diversity associated with the north-south migration of maize. This sub-species diversity was revealed by FL-PacBio but missed by V4-MiSeq. V4-MiSeq also mis-identified some dominant genera captured by FL-PacBio. The study, though limited to a single season and common field, provides initial evidence that pollen microbiomes reflect evolutionary and migratory relationships of their host plants.
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Affiliation(s)
- Eman M. Khalaf
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
- Department of Microbiology and Immunology, Faculty of Pharmacy, Damanhour University, Damanhour, Egypt
| | - Anuja Shrestha
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
| | - Michelle Reid
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
| | | | - Manish N. Raizada
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
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10
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Kim AS, Kreiner JM, Hernández F, Bock DG, Hodgins KA, Rieseberg LH. Temporal collections to study invasion biology. Mol Ecol 2023; 32:6729-6742. [PMID: 37873879 DOI: 10.1111/mec.17176] [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: 08/22/2023] [Revised: 10/07/2023] [Accepted: 10/11/2023] [Indexed: 10/25/2023]
Abstract
Biological invasions represent an extraordinary opportunity to study evolution. This is because accidental or deliberate species introductions have taken place for centuries across large geographical scales, frequently prompting rapid evolutionary transitions in invasive populations. Until recently, however, the utility of invasions as evolutionary experiments has been hampered by limited information on the makeup of populations that were part of earlier invasion stages. Now, developments in ancient and historical DNA technologies, as well as the quickening pace of digitization for millions of specimens that are housed in herbaria and museums globally, promise to help overcome this obstacle. In this review, we first introduce the types of temporal data that can be used to study invasions, highlighting the timescale captured by each approach and their respective limitations. We then discuss how ancient and historical specimens as well as data available from prior invasion studies can be used to answer questions on mechanisms of (mal)adaptation, rates of evolution, or community-level changes during invasions. By bridging the gap between contemporary and historical invasive populations, temporal data can help us connect pattern to process in invasion science. These data will become increasingly important if invasions are to achieve their full potential as experiments of evolution in nature.
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Affiliation(s)
- Amy S Kim
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Julia M Kreiner
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Fernando Hernández
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Dan G Bock
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kathryn A Hodgins
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
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11
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Yang N, Wang Y, Liu X, Jin M, Vallebueno-Estrada M, Calfee E, Chen L, Dilkes BP, Gui S, Fan X, Harper TK, Kennett DJ, Li W, Lu Y, Ding J, Chen Z, Luo J, Mambakkam S, Menon M, Snodgrass S, Veller C, Wu S, Wu S, Zhuo L, Xiao Y, Yang X, Stitzer MC, Runcie D, Yan J, Ross-Ibarra J. Two teosintes made modern maize. Science 2023; 382:eadg8940. [PMID: 38033071 DOI: 10.1126/science.adg8940] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 10/02/2023] [Indexed: 12/02/2023]
Abstract
The origins of maize were the topic of vigorous debate for nearly a century, but neither the current genetic model nor earlier archaeological models account for the totality of available data, and recent work has highlighted the potential contribution of a wild relative, Zea mays ssp. mexicana. Our population genetic analysis reveals that the origin of modern maize can be traced to an admixture between ancient maize and Zea mays ssp. mexicana in the highlands of Mexico some 4000 years after domestication began. We show that variation in admixture is a key component of maize diversity, both at individual loci and for additive genetic variation underlying agronomic traits. Our results clarify the origin of modern maize and raise new questions about the anthropogenic mechanisms underlying dispersal throughout the Americas.
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Affiliation(s)
- Ning Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - Yuebin Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiangguo Liu
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun 130033, China
| | - Minliang Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Miguel Vallebueno-Estrada
- Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad, CINVESTAV Irapuato, 36821 Guanajuato, México
| | - Erin Calfee
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
- Center for Population Biology, University of California, Davis, CA 95616, USA
- Adaptive Biotechnologies, Seattle, WA 98109, USA
| | - Lu Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Brian P Dilkes
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Songtao Gui
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Xingming Fan
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650200, China
| | - Thomas K Harper
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802, USA
| | - Douglas J Kennett
- Department of Anthropology, University of California, Santa Barbara, CA 93106, USA
| | - Wenqiang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yanli Lu
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan 611130, China
| | - Junqiang Ding
- College of Agronomy, Henan Agricultural University, Zhengzhou, Henan 450046, China
| | - Ziqi Chen
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun 130033, China
| | - Jingyun Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Sowmya Mambakkam
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - Mitra Menon
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
- Center for Population Biology, University of California, Davis, CA 95616, USA
| | - Samantha Snodgrass
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Carl Veller
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
| | - Shenshen Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Siying Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Lin Zhuo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yingjie Xiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Xiaohong Yang
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Michelle C Stitzer
- Institute for Genomic Diversity and Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Daniel Runcie
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
- Yazhouwan National Laboratory, Sanya 572024, China
| | - Jeffrey Ross-Ibarra
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
- Center for Population Biology, University of California, Davis, CA 95616, USA
- Genome Center, University of California, Davis, CA 95616, USA
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12
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Ma Y, Yang W, Zhang H, Wang P, Liu Q, Li F, Du W. Genetic analysis of phenotypic plasticity identifies BBX6 as the candidate gene for maize adaptation to temperate regions. FRONTIERS IN PLANT SCIENCE 2023; 14:1280331. [PMID: 37964997 PMCID: PMC10642939 DOI: 10.3389/fpls.2023.1280331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 10/12/2023] [Indexed: 11/16/2023]
Abstract
Introduction Climate changes pose a significant threat to crop adaptation and production. Dissecting the genetic basis of phenotypic plasticity and uncovering the responsiveness of regulatory genes to environmental factors can significantly contribute to the improvement of climate- resilience in crops. Methods We established a BC1F3:4 population using the elite inbred lines Zheng58 and PH4CV and evaluated plant height (PH) across four environments characterized by substantial variations in environmental factors. Then, we quantified the correlation between the environmental mean of PH (the mean performance in each environment) and the environmental parameters within a specific growth window. Furthermore, we performed GWAS analysis of phenotypic plasticity, and identified QTLs and candidate gene that respond to key environment index. After that, we constructed the coexpression network involving the candidate gene, and performed selective sweep analysis of the candidate gene. Results We found that the environmental parameters demonstrated substantial variation across the environments, and genotype by environment interaction contributed to the variations of PH. Then, we identified PTT(35-48) (PTT is the abbreviation for photothermal units), the mean PTT from 35 to 48 days after planting, as the pivotal environmental index that closely correlated with environmental mean of PH. Leveraging the slopes of the response of PH to both the environmental mean and PTT(35-48), we successfully pinpointed QTLs for phenotypic plasticity on chromosomes 1 and 2. Notably, the PH4CV genotypes at these two QTLs exhibited positive contributions to phenotypic plasticity. Furthermore, our analysis demonstrated a direct correlation between the additive effects of each QTL and PTT(35-48). By analyzing transcriptome data of the parental lines in two environments, we found that the 1009 genes responding to PTT(35-48) were enriched in the biological processes related to environmental sensitivity. BBX6 was the prime candidate gene among the 13 genes in the two QTL regions. The coexpression network of BBX6 contained other genes related to flowering time and photoperiod sensitivity. Our investigation, including selective sweep analysis and genetic differentiation analysis, suggested that BBX6 underwent selection during maize domestication. Discussion Th is research substantially advances our understanding of critical environmental factors influencing maize adaptation while simultaneously provides an invaluable gene resource for the development of climate-resilient maize hybrid varieties.
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Affiliation(s)
- Yuting Ma
- College of Agronomy, Shenyang Agricultural University, Shenyang, Liaoning, China
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wenyan Yang
- College of Agronomy, Shenyang Agricultural University, Shenyang, Liaoning, China
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongwei Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Pingxi Wang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qian Liu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fenghai Li
- College of Agronomy, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Wanli Du
- College of Agronomy, Shenyang Agricultural University, Shenyang, Liaoning, China
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13
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Kohler TA, Bird D, Bocinsky RK, Reese K, Gillreath-Brown AD. Wealth inequality in the prehispanic northern US Southwest: from Malthus to Tyche. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220298. [PMID: 37381850 DOI: 10.1098/rstb.2022.0298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 03/31/2023] [Indexed: 06/30/2023] Open
Abstract
Persistent differences in wealth and power among prehispanic Pueblo societies are visible from the late AD 800s through the late 1200s, after which large portions of the northern US Southwest were depopulated. In this paper we measure these differences in wealth using Gini coefficients based on house size, and show that high Ginis (large wealth differences) are positively related to persistence in settlements and inversely related to an annual measure of the size of the unoccupied dry-farming niche. We argue that wealth inequality in this record is due first to processes inherent in village life which have internally different distributions of the most productive maize fields, exacerbated by the dynamics of systems of balanced reciprocity; and second to decreasing ability to escape village life owing to shrinking availability of unoccupied places within the maize dry-farming niche as villages get enmeshed in regional systems of tribute or taxation. We embed this analytical reconstruction in the model of an 'Abrupt imposition of Malthusian equilibrium in a natural-fertility, agrarian society' proposed by Puleston et al. (Puleston C, Tuljapurkar S, Winterhalder B. 2014 PLoS ONE 9, e87541 (doi:10.1371/journal.pone.0087541)), but show that the transition to Malthusian dynamics in this area is not abrupt but extends over centuries This article is part of the theme issue 'Evolutionary ecology of inequality'.
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Affiliation(s)
- Timothy A Kohler
- Department of Anthropology, Washington State University, Pullman, Washington 99164, USA
- Santa Fe Institute, Santa Fe, NM 87506, USA
- Crow Canyon Archaeological Center, Cortez, CO 81321, USA
- Department of Archaeology, University of Durham, Durham DH1 3LE, UK
| | - Darcy Bird
- Department of Anthropology, Washington State University, Pullman, Washington 99164, USA
| | - R Kyle Bocinsky
- Crow Canyon Archaeological Center, Cortez, CO 81321, USA
- WA Franke College of Forestry and Conservation, University of Montana, Missoula, MT 59812, USA
| | - Kelsey Reese
- Environmental Stewardship Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
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14
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Kennett DJ, Harper TK, VanDerwarker A, Thakar HB, Domic A, Blake M, Benz BF, George RJ, Scheffler TE, Culleton BJ, Kistler L, Hirth KG. Trans-Holocene Bayesian chronology for tree and field crop use from El Gigante rockshelter, Honduras. PLoS One 2023; 18:e0287195. [PMID: 37352287 PMCID: PMC10289419 DOI: 10.1371/journal.pone.0287195] [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: 11/10/2022] [Accepted: 06/01/2023] [Indexed: 06/25/2023] Open
Abstract
El Gigante rockshelter in western Honduras provides a deeply stratified archaeological record of human-environment interaction spanning the entirety of the Holocene. Botanical materials are remarkably well preserved and include important tree (e.g., ciruela (Spondias), avocado (Persea americana)) and field (maize (Zea mays), beans (Phaseolus), and squash (Cucurbita)) crops. Here we provide a major update to the chronology of tree and field crop use evident in the sequence. We report 375 radiocarbon dates, a majority of which are for short-lived botanical macrofossils (e.g., maize cobs, avocado seeds, or rinds). Radiocarbon dates were used in combination with stratigraphic details to establish a Bayesian chronology for ~9,800 identified botanical samples spanning the last 11,000 years. We estimate that at least 16 discrete intervals of use occurred during this time, separated by gaps of ~100-2,000 years. The longest hiatus in rockshelter occupation was between ~6,400 and 4,400 years ago and the deposition of botanical remains peaked at ~2,000 calendar years before present (cal BP). Tree fruits and squash appeared early in the occupational sequence (~11,000 cal BP) with most other field crops appearing later in time (e.g., maize at ~4,400 cal BP; beans at ~2,200 cal BP). The early focus on tree fruits and squash is consistent with early coevolutionary partnering with humans as seed dispersers in the wake of megafaunal extinction in Mesoamerica. Tree crops predominated through much of the Holocene, and there was an overall shift to field crops after 4,000 cal BP that was largely driven by increased reliance on maize farming.
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Affiliation(s)
- Douglas J. Kennett
- Department of Anthropology, University of California, Santa Barbara, Santa Barbara, California, United States of America
| | - Thomas K. Harper
- Department of Anthropology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Amber VanDerwarker
- Department of Anthropology, University of California, Santa Barbara, Santa Barbara, California, United States of America
| | - Heather B. Thakar
- Department of Anthropology, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Alejandra Domic
- Department of Anthropology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Michael Blake
- Department of Biology, Texas Wesleyan University, Forth Worth, Texas, United States of America
| | - Bruce F. Benz
- Department of Anthropology, Texas A & M University, College Station, Texas, United States of America
| | - Richard J. George
- Department of Anthropology, University of California, Santa Barbara, Santa Barbara, California, United States of America
| | - Timothy E. Scheffler
- Department of Anthropology, University of Hawaii at Hilo, Hilo, Hawaii, United States of America
| | - Brendan J. Culleton
- Institutes of Energy and the Environment, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Logan Kistler
- Department of Anthropology, Smithsonian Institution, Washington, DC, United States of America
| | - Kenneth G. Hirth
- Department of Anthropology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
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15
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Arca M, Gouesnard B, Mary-Huard T, Le Paslier MC, Bauland C, Combes V, Madur D, Charcosset A, Nicolas SD. Genotyping of DNA pools identifies untapped landraces and genomic regions to develop next-generation varieties. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:1123-1139. [PMID: 36740649 DOI: 10.1111/pbi.14022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 01/18/2023] [Indexed: 05/27/2023]
Abstract
Landraces, that is, traditional varieties, have a large diversity that is underexploited in modern breeding. A novel DNA pooling strategy was implemented to identify promising landraces and genomic regions to enlarge the genetic diversity of modern varieties. As proof of concept, DNA pools from 156 American and European maize landraces representing 2340 individuals were genotyped with an SNP array to assess their genome-wide diversity. They were compared to elite cultivars produced across the 20th century, represented by 327 inbred lines. Detection of selective footprints between landraces of different geographic origin identified genes involved in environmental adaptation (flowering times, growth) and tolerance to abiotic and biotic stress (drought, cold, salinity). Promising landraces were identified by developing two novel indicators that estimate their contribution to the genome of inbred lines: (i) a modified Roger's distance standardized by gene diversity and (ii) the assignation of lines to landraces using supervised analysis. It showed that most landraces do not have closely related lines and that only 10 landraces, including famous landraces as Reid's Yellow Dent, Lancaster Surecrop and Lacaune, cumulated half of the total contribution to inbred lines. Comparison of ancestral lines directly derived from landraces with lines from more advanced breeding cycles showed a decrease in the number of landraces with a large contribution. New inbred lines derived from landraces with limited contributions enriched more the haplotype diversity of reference inbred lines than those with a high contribution. Our approach opens an avenue for the identification of promising landraces for pre-breeding.
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Affiliation(s)
- Mariangela Arca
- INRAE, CNRS, AgroParisTech, GQE - Le Moulon, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Brigitte Gouesnard
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Tristan Mary-Huard
- INRAE, CNRS, AgroParisTech, GQE - Le Moulon, Université Paris-Saclay, Gif-sur-Yvette, France
| | | | - Cyril Bauland
- INRAE, CNRS, AgroParisTech, GQE - Le Moulon, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Valérie Combes
- INRAE, CNRS, AgroParisTech, GQE - Le Moulon, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Delphine Madur
- INRAE, CNRS, AgroParisTech, GQE - Le Moulon, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Alain Charcosset
- INRAE, CNRS, AgroParisTech, GQE - Le Moulon, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Stéphane D Nicolas
- INRAE, CNRS, AgroParisTech, GQE - Le Moulon, Université Paris-Saclay, Gif-sur-Yvette, France
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16
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Schmidt SB, Brown LK, Booth A, Wishart J, Hedley PE, Martin P, Husted S, George TS, Russell J. Heritage genetics for adaptation to marginal soils in barley. TRENDS IN PLANT SCIENCE 2023; 28:544-551. [PMID: 36858842 DOI: 10.1016/j.tplants.2023.01.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 01/17/2023] [Accepted: 01/23/2023] [Indexed: 05/22/2023]
Abstract
Future crops need to be sustainable in the face of climate change. Modern barley varieties have been bred for high productivity and quality; however, they have suffered considerable genetic erosion, losing crucial genetic diversity. This renders modern cultivars vulnerable to climate change and stressful environments. We highlight the potential to tailor crops to a specific environment by utilising diversity inherent in an adapted landrace population. Tapping into natural biodiversity, while incorporating information about local environmental and climatic conditions, allows targeting of key traits and genotypes, enabling crop production in marginal soils. We outline future directions for the utilisation of genetic resources maintained in landrace collections to support sustainable agriculture through germplasm development via the use of genomics technologies and big data.
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Affiliation(s)
- Sidsel Birkelund Schmidt
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK; Innovation Centre for Organic Farming, Agro Food Park 26, 8200 Aarhus N., Denmark
| | - Lawrie K Brown
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Allan Booth
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - John Wishart
- Agronomy Institute, Orkney College, University of the Highlands and Islands, Orkney, UK
| | - Pete E Hedley
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Peter Martin
- Agronomy Institute, Orkney College, University of the Highlands and Islands, Orkney, UK
| | - Søren Husted
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1879 Frederiksberg C., Denmark
| | | | - Joanne Russell
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK.
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17
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Sun G, Yu H, Wang P, Lopez-Guerrero M, Mural RV, Mizero ON, Grzybowski M, Song B, van Dijk K, Schachtman DP, Zhang C, Schnable JC. A role for heritable transcriptomic variation in maize adaptation to temperate environments. Genome Biol 2023; 24:55. [PMID: 36964601 PMCID: PMC10037803 DOI: 10.1186/s13059-023-02891-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 03/06/2023] [Indexed: 03/26/2023] Open
Abstract
Background Transcription bridges genetic information and phenotypes. Here, we evaluated how changes in transcriptional regulation enable maize (Zea mays), a crop originally domesticated in the tropics, to adapt to temperate environments. Result We generated 572 unique RNA-seq datasets from the roots of 340 maize genotypes. Genes involved in core processes such as cell division, chromosome organization and cytoskeleton organization showed lower heritability of gene expression, while genes involved in anti-oxidation activity exhibited higher expression heritability. An expression genome-wide association study (eGWAS) identified 19,602 expression quantitative trait loci (eQTLs) associated with the expression of 11,444 genes. A GWAS for alternative splicing identified 49,897 splicing QTLs (sQTLs) for 7614 genes. Genes harboring both cis-eQTLs and cis-sQTLs in linkage disequilibrium were disproportionately likely to encode transcription factors or were annotated as responding to one or more stresses. Independent component analysis of gene expression data identified loci regulating co-expression modules involved in oxidation reduction, response to water deprivation, plastid biogenesis, protein biogenesis, and plant-pathogen interaction. Several genes involved in cell proliferation, flower development, DNA replication, and gene silencing showed lower gene expression variation explained by genetic factors between temperate and tropical maize lines. A GWAS of 27 previously published phenotypes identified several candidate genes overlapping with genomic intervals showing signatures of selection during adaptation to temperate environments. Conclusion Our results illustrate how maize transcriptional regulatory networks enable changes in transcriptional regulation to adapt to temperate regions. Supplementary information The online version contains supplementary material available at 10.1186/s13059-023-02891-3.
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Affiliation(s)
- Guangchao Sun
- grid.24434.350000 0004 1937 0060Quantitative Life Sciences Initiative, University of Nebraska-Lincoln, Lincoln, USA
- grid.24434.350000 0004 1937 0060Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, USA
- grid.24434.350000 0004 1937 0060Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, USA
| | - Huihui Yu
- grid.24434.350000 0004 1937 0060Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, USA
- grid.24434.350000 0004 1937 0060School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, USA
| | - Peng Wang
- grid.24434.350000 0004 1937 0060Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, USA
| | - Martha Lopez-Guerrero
- grid.24434.350000 0004 1937 0060Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA
| | - Ravi V. Mural
- grid.24434.350000 0004 1937 0060Quantitative Life Sciences Initiative, University of Nebraska-Lincoln, Lincoln, USA
- grid.24434.350000 0004 1937 0060Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, USA
- grid.24434.350000 0004 1937 0060Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, USA
| | - Olivier N. Mizero
- grid.24434.350000 0004 1937 0060Quantitative Life Sciences Initiative, University of Nebraska-Lincoln, Lincoln, USA
- grid.24434.350000 0004 1937 0060Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, USA
- grid.24434.350000 0004 1937 0060Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, USA
| | - Marcin Grzybowski
- grid.24434.350000 0004 1937 0060Quantitative Life Sciences Initiative, University of Nebraska-Lincoln, Lincoln, USA
- grid.24434.350000 0004 1937 0060Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, USA
- grid.24434.350000 0004 1937 0060Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, USA
| | - Baoxing Song
- grid.5386.8000000041936877XInstitute for Genomic Diversity, Cornell University, Ithaca, USA
| | - Karin van Dijk
- grid.24434.350000 0004 1937 0060Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA
| | - Daniel P. Schachtman
- grid.24434.350000 0004 1937 0060Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, USA
- grid.24434.350000 0004 1937 0060Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, USA
| | - Chi Zhang
- grid.24434.350000 0004 1937 0060Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, USA
- grid.24434.350000 0004 1937 0060School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, USA
| | - James C. Schnable
- grid.24434.350000 0004 1937 0060Quantitative Life Sciences Initiative, University of Nebraska-Lincoln, Lincoln, USA
- grid.24434.350000 0004 1937 0060Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, USA
- grid.24434.350000 0004 1937 0060Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, USA
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18
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Ruperao P, Gandham P, Odeny DA, Mayes S, Selvanayagam S, Thirunavukkarasu N, Das RR, Srikanda M, Gandhi H, Habyarimana E, Manyasa E, Nebie B, Deshpande SP, Rathore A. Exploring the sorghum race level diversity utilizing 272 sorghum accessions genomic resources. FRONTIERS IN PLANT SCIENCE 2023; 14:1143512. [PMID: 37008459 PMCID: PMC10063887 DOI: 10.3389/fpls.2023.1143512] [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: 01/16/2023] [Accepted: 02/22/2023] [Indexed: 06/19/2023]
Abstract
Due to evolutionary divergence, sorghum race populations exhibit significant genetic and morphological variation. A k-mer-based sorghum race sequence comparison identified the conserved k-mers of all 272 accessions from sorghum and the race-specific genetic signatures identified the gene variability in 10,321 genes (PAVs). To understand sorghum race structure, diversity and domestication, a deep learning-based variant calling approach was employed in a set of genotypic data derived from a diverse panel of 272 sorghum accessions. The data resulted in 1.7 million high-quality genome-wide SNPs and identified selective signature (both positive and negative) regions through a genome-wide scan with different (iHS and XP-EHH) statistical methods. We discovered 2,370 genes associated with selection signatures including 179 selective sweep regions distributed over 10 chromosomes. Co-localization of these regions undergoing selective pressure with previously reported QTLs and genes revealed that the signatures of selection could be related to the domestication of important agronomic traits such as biomass and plant height. The developed k-mer signatures will be useful in the future to identify the sorghum race and for trait and SNP markers for assisting in plant breeding programs.
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Affiliation(s)
- Pradeep Ruperao
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Prasad Gandham
- School of Plant, Environmental and Soil Sciences, Louisiana State University Agricultural Center, LA, United States
| | - Damaris A. Odeny
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Sean Mayes
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Nepolean Thirunavukkarasu
- Genomics and Molecular Breeding Lab, Indian Council of Agricultural Research (ICAR) - Indian Institute of Millets Research, Hyderabad, India
| | - Roma R. Das
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Manasa Srikanda
- Department of Statistics, Osmania University, Hyderabad, India
| | - Harish Gandhi
- International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
| | - Ephrem Habyarimana
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Eric Manyasa
- Sorghum Breeding Program, International Crops Research Institute for the Semi-Arid Tropics, Nairobi, Kenya
| | - Baloua Nebie
- International Maize and Wheat Improvement Center (CIMMYT), Dakar, Senegal
| | | | - Abhishek Rathore
- Excellence in Breeding, International Maize and Wheat Improvement Center (CIMMYT), Hyderabad, India
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19
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Grzybowski MW, Mural RV, Xu G, Turkus J, Yang J, Schnable JC. A common resequencing-based genetic marker data set for global maize diversity. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:1109-1121. [PMID: 36705476 DOI: 10.1111/tpj.16123] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 01/20/2023] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
Maize (Zea mays ssp. mays) populations exhibit vast ranges of genetic and phenotypic diversity. As sequencing costs have declined, an increasing number of projects have sought to measure genetic differences between and within maize populations using whole-genome resequencing strategies, identifying millions of segregating single-nucleotide polymorphisms (SNPs) and insertions/deletions (InDels). Unlike older genotyping strategies like microarrays and genotyping by sequencing, resequencing should, in principle, frequently identify and score common genetic variants. However, in practice, different projects frequently employ different analytical pipelines, often employ different reference genome assemblies and consistently filter for minor allele frequency within the study population. This constrains the potential to reuse and remix data on genetic diversity generated from different projects to address new biological questions in new ways. Here, we employ resequencing data from 1276 previously published maize samples and 239 newly resequenced maize samples to generate a single unified marker set of approximately 366 million segregating variants and approximately 46 million high-confidence variants scored across crop wild relatives, landraces as well as tropical and temperate lines from different breeding eras. We demonstrate that the new variant set provides increased power to identify known causal flowering-time genes using previously published trait data sets, as well as the potential to track changes in the frequency of functionally distinct alleles across the global distribution of modern maize.
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Affiliation(s)
- Marcin W Grzybowski
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Department of Plant Molecular Ecophysiology, Institute of Plant Experimental Biology and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Ravi V Mural
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Gen Xu
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Jonathan Turkus
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Jinliang Yang
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - James C Schnable
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
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20
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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.
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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
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21
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Davis CC. The herbarium of the future. Trends Ecol Evol 2022; 38:412-423. [PMID: 36549958 DOI: 10.1016/j.tree.2022.11.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/24/2022]
Abstract
The ~400 million specimens deposited across ~3000 herbaria are essential for: (i) understanding where plants have lived in the past, (ii) forecasting where they may live in the future, and (iii) delineating their conservation status. An open access 'global metaherbarium' is emerging as these specimens are digitized, mobilized, and interlinked online. This virtual biodiversity resource is attracting new users who are accelerating traditional applications of herbaria and generating basic and applied scientific innovations, including e-monographs and floras produced by diverse, interdisciplinary, and inclusive teams; robust machine-learning algorithms for species identification and phenotyping; collection and synthesis of ecological trait data at large spatiotemporal and phylogenetic scales; and exhibitions and installations that convey the beauty of plants and the value of herbaria in addressing broader societal issues.
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Affiliation(s)
- Charles C Davis
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, 22 Divinity Avenue, Cambridge, MA 02138, USA.
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22
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Chen L, Luo J, Jin M, Yang N, Liu X, Peng Y, Li W, Phillips A, Cameron B, Bernal JS, Rellán-Álvarez R, Sawers RJH, Liu Q, Yin Y, Ye X, Yan J, Zhang Q, Zhang X, Wu S, Gui S, Wei W, Wang Y, Luo Y, Jiang C, Deng M, Jin M, Jian L, Yu Y, Zhang M, Yang X, Hufford MB, Fernie AR, Warburton ML, Ross-Ibarra J, Yan J. Genome sequencing reveals evidence of adaptive variation in the genus Zea. Nat Genet 2022; 54:1736-1745. [PMID: 36266506 DOI: 10.1038/s41588-022-01184-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 08/10/2022] [Indexed: 11/09/2022]
Abstract
Maize is a globally valuable commodity and one of the most extensively studied genetic model organisms. However, we know surprisingly little about the extent and potential utility of the genetic variation found in wild relatives of maize. Here, we characterize a high-density genomic variation map from 744 genomes encompassing maize and all wild taxa of the genus Zea, identifying over 70 million single-nucleotide polymorphisms. The variation map reveals evidence of selection within taxa displaying novel adaptations. We focus on adaptive alleles in highland teosinte and temperate maize, highlighting the key role of flowering-time-related pathways in their adaptation. To show the utility of variants in these data, we generate mutant alleles for two flowering-time candidate genes. This work provides an extensive sampling of the genetic diversity of Zea, resolving questions on evolution and identifying adaptive variants for direct use in modern breeding.
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Affiliation(s)
- Lu Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.,State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Jingyun Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Minliang Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Ning Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China. .,Hubei Hongshan Laboratory, Wuhan, China.
| | - Xiangguo Liu
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Yong Peng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Wenqiang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Alyssa Phillips
- Center for Population Biology, University of California Davis, Davis, CA, USA.,Department of Evolution and Ecology, University of California Davis, Davis, CA, USA
| | - Brenda Cameron
- Department of Evolution and Ecology, University of California Davis, Davis, CA, USA
| | - Julio S Bernal
- Department of Entomology, Texas A&M University, College Station, TX, USA
| | - Rubén Rellán-Álvarez
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, USA
| | - Ruairidh J H Sawers
- Department of Plant Science, The Pennsylvania State University, State College, PA, USA
| | - Qing Liu
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Yuejia Yin
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Xinnan Ye
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Jiali Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Qinghua Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Xiaoting Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Shenshen Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Songtao Gui
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Wenjie Wei
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Yuebin Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Yun Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Chenglin Jiang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Min Deng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Min Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Liumei Jian
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Yanhui Yu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Maolin Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Xiaohong Yang
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Matthew B Hufford
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Alisdair R Fernie
- Department of Molecular Physiology, Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Marilyn L Warburton
- United States Department of Agriculture-Agricultural Research Service: Western Regional Plant Introduction Station, Washington State University, Pullman, WA, USA
| | - Jeffrey Ross-Ibarra
- Department of Evolution and Ecology, Center for Population Biology, Genome Center, University of California Davis, Davis, CA, USA.
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China. .,Hubei Hongshan Laboratory, Wuhan, China.
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23
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Yang R, Cao R, Gong X, Feng J. Cultivation has selected for a wider niche and large range shifts in maize. PeerJ 2022; 10:e14019. [PMID: 36168438 PMCID: PMC9509669 DOI: 10.7717/peerj.14019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 08/16/2022] [Indexed: 01/19/2023] Open
Abstract
Background Maize (Zea mays L.) is a staple crop cultivated on a global scale. However, its ability to feed the rapidly growing human population may be impaired by climate change, especially if it has low climatic niche and range lability. One important question requiring clarification is therefore whether maize shows high niche and range lability. Methods We used the COUE scheme (a unified terminology representing niche centroid shift, overlap, unfilling and expansion) and species distribution models to study the niche and range changes between maize and its wild progenitors using occurrence records of maize, lowland teosinte (Zea mays ssp. parviglumis) and highland teosinte (Zea mays ssp. mexicana), respectively, as well as explore the mechanisms underlying the niche and range changes. Results In contrast to maize in Mexico, maize did not conserve its niche inherited from lowland and highland teosinte at the global scale. The niche breadth of maize at the global scale was wider than that of its wild progenitors (ca. 5.21 and 3.53 times wider compared with lowland and highland teosinte, respectively). Compared with its wild progenitors, maize at global scale can survive in regions with colder, wetter climatic conditions, as well as with wider ranges of climatic variables (ca. 4.51 and 2.40 times wider compared with lowland and highland teosinte, respectively). The niche changes of maize were largely driven by human introduction and cultivation, which have exposed maize to climatic conditions different from those experienced by its wild progenitors. Small changes in niche breadth had large effects on the magnitude of range shifts; changes in niche breadth thus merit increased attention. Discussion Our results demonstrate that maize shows wide climatic niche and range lability, and this substantially expanded its realized niche and potential range. Our findings also suggest that niche and range shifts probably triggered by natural and artificial selection in cultivation may enable maize to become a global staple crop to feed the growing population and adapting to changing climatic conditions. Future analyses are needed to determine the limits of the novel conditions that maize can tolerate, especially relative to projected climate change.
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24
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Gui S, Wei W, Jiang C, Luo J, Chen L, Wu S, Li W, Wang Y, Li S, Yang N, Li Q, Fernie AR, Yan J. A pan-Zea genome map for enhancing maize improvement. Genome Biol 2022; 23:178. [PMID: 35999561 PMCID: PMC9396798 DOI: 10.1186/s13059-022-02742-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 07/27/2022] [Indexed: 12/22/2022] Open
Abstract
Background Maize (Zea mays L.) is at the vanguard facing the upcoming breeding challenges. However, both a super pan-genome for the Zea genus and a comprehensive genetic variation map for maize breeding are still lacking. Results Here, we construct an approximately 6.71-Gb pan-Zea genome that contains around 4.57-Gb non-B73 reference sequences from fragmented de novo assemblies of 721 pan-Zea individuals. We annotate a total of 58,944 pan-Zea genes and find around 44.34% of them are dispensable in the pan-Zea population. Moreover, 255,821 common structural variations are identified and genotyped in a maize association mapping panel. Further analyses reveal gene presence/absence variants and their potential roles during domestication of maize. Combining genetic analyses with multi-omics data, we demonstrate how structural variants are associated with complex agronomic traits. Conclusions Our results highlight the underexplored role of the pan-Zea genome and structural variations to further understand domestication of maize and explore their potential utilization in crop improvement. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02742-7.
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Affiliation(s)
- Songtao Gui
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wenjie Wei
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chenglin Jiang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jingyun Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lu Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shenshen Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wenqiang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuebin Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shuyan Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ning Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.,Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Qing Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.,Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Alisdair R Fernie
- Department of Molecular Physiology, Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Golm, Germany
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China. .,Hubei Hongshan Laboratory, Wuhan, 430070, China.
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An adaptive teosinte mexicana introgression modulates phosphatidylcholine levels and is associated with maize flowering time. Proc Natl Acad Sci U S A 2022; 119:e2100036119. [PMID: 35771940 PMCID: PMC9271162 DOI: 10.1073/pnas.2100036119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Native Americans domesticated maize (Zea mays ssp. mays) from lowland teosinte parviglumis (Zea mays ssp. parviglumis) in the warm Mexican southwest and brought it to the highlands of Mexico and South America where it was exposed to lower temperatures that imposed strong selection on flowering time. Phospholipids are important metabolites in plant responses to low-temperature and phosphorus availability and have been suggested to influence flowering time. Here, we combined linkage mapping with genome scans to identify High PhosphatidylCholine 1 (HPC1), a gene that encodes a phospholipase A1 enzyme, as a major driver of phospholipid variation in highland maize. Common garden experiments demonstrated strong genotype-by-environment interactions associated with variation at HPC1, with the highland HPC1 allele leading to higher fitness in highlands, possibly by hastening flowering. The highland maize HPC1 variant resulted in impaired function of the encoded protein due to a polymorphism in a highly conserved sequence. A meta-analysis across HPC1 orthologs indicated a strong association between the identity of the amino acid at this position and optimal growth in prokaryotes. Mutagenesis of HPC1 via genome editing validated its role in regulating phospholipid metabolism. Finally, we showed that the highland HPC1 allele entered cultivated maize by introgression from the wild highland teosinte Zea mays ssp. mexicana and has been maintained in maize breeding lines from the Northern United States, Canada, and Europe. Thus, HPC1 introgressed from teosinte mexicana underlies a large metabolic QTL that modulates phosphatidylcholine levels and has an adaptive effect at least in part via induction of early flowering time.
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26
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Carlson MO, Rice DP, Berg JJ, Steinrücken M. Polygenic score accuracy in ancient samples: Quantifying the effects of allelic turnover. PLoS Genet 2022; 18:e1010170. [PMID: 35522704 PMCID: PMC9116686 DOI: 10.1371/journal.pgen.1010170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 05/18/2022] [Accepted: 03/26/2022] [Indexed: 11/19/2022] Open
Abstract
Polygenic scores link the genotypes of ancient individuals to their phenotypes, which are often unobservable, offering a tantalizing opportunity to reconstruct complex trait evolution. In practice, however, interpretation of ancient polygenic scores is subject to numerous assumptions. For one, the genome-wide association (GWA) studies from which polygenic scores are derived, can only estimate effect sizes for loci segregating in contemporary populations. Therefore, a GWA study may not correctly identify all loci relevant to trait variation in the ancient population. In addition, the frequencies of trait-associated loci may have changed in the intervening years. Here, we devise a theoretical framework to quantify the effect of this allelic turnover on the statistical properties of polygenic scores as functions of population genetic dynamics, trait architecture, power to detect significant loci, and the age of the ancient sample. We model the allele frequencies of loci underlying trait variation using the Wright-Fisher diffusion, and employ the spectral representation of its transition density to find analytical expressions for several error metrics, including the expected sample correlation between the polygenic scores of ancient individuals and their true phenotypes, referred to as polygenic score accuracy. Our theory also applies to a two-population scenario and demonstrates that allelic turnover alone may explain a substantial percentage of the reduced accuracy observed in cross-population predictions, akin to those performed in human genetics. Finally, we use simulations to explore the effects of recent directional selection, a bias-inducing process, on the statistics of interest. We find that even in the presence of bias, weak selection induces minimal deviations from our neutral expectations for the decay of polygenic score accuracy. By quantifying the limitations of polygenic scores in an explicit evolutionary context, our work lays the foundation for the development of more sophisticated statistical procedures to analyze both temporally and geographically resolved polygenic scores.
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Affiliation(s)
- Maryn O. Carlson
- Committee on Genetics, Genomics, & Systems Biology, University of Chicago, Chicago, Illinois, United States of America
| | - Daniel P. Rice
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Jeremy J. Berg
- Committee on Genetics, Genomics, & Systems Biology, University of Chicago, Chicago, Illinois, United States of America
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Matthias Steinrücken
- Committee on Genetics, Genomics, & Systems Biology, University of Chicago, Chicago, Illinois, United States of America
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
- Department of Ecology & Evolution, University of Chicago, Chicago, Illinois, United States of America
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27
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Vierra BJ, Vint JM. Climate Change and the Neolithic in the American Southwest. JOURNAL OF ANTHROPOLOGICAL RESEARCH 2022. [DOI: 10.1086/717841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Bradley J. Vierra
- Department of Anthropology, New Mexico State University, Las Cruces, NM 88003, USA
- Desert Archaeology Inc., Tucson
| | - James M. Vint
- Department of Anthropology, New Mexico State University, Las Cruces, NM 88003, USA
- Desert Archaeology Inc., Tucson
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28
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Fan D, Lei S, Liang H, Yao Q, Kou Y, Cheng S, Yang Y, Qiu Y, Zhang Z. More opportunities more species: Pleistocene differentiation and northward expansion of an evergreen broad-leaved tree species Machilus thunbergii (Lauraceae) in Southeast China. BMC PLANT BIOLOGY 2022; 22:35. [PMID: 35038992 PMCID: PMC8762935 DOI: 10.1186/s12870-021-03420-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 12/28/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND The broad continuum between tropical and temperate floras in Eastern Asia (EAS) are thought to be one of the main factors responsible for a prominent species diversity anomaly of temperate plants between EAS and eastern North America (ENS). However, how the broad continuum and niche evolution between tropical and temperate floras in EAS contributes to lineage divergence and species diversity remains largely unknown. RESULTS Population genetic structure, demography, and determinants of genetic structure [i.e., isolation-by-distance (IBD), isolation-by-resistance (IBR), and isolation-by-environment (IBE)] of Machilus thunbergii Sieb. et Zucc. (Lauraceae) were evaluated by examining sequence variation of ten low-copy nuclear genes across 43 populations in southeast China. Climatic niche difference and potential distributions across four periods (Current, mid-Holocene, the last glacial maximum, the last interglacial) of two genetic clusters were determined by niche modelling. North and south clusters of populations in M. thunbergii were revealed and their demarcation line corresponds well with the northern boundary of tropical zone in China of Zhu & Wan. The divergence time between the clusters and demographic expansion of M. thunbergii occurred after the mid-Pleistocene climate transition (MPT, 0.8-1.2 Ma). Migration rates between clusters were asymmetrical, being much greater from north to south than the reverse. Significant effects of IBE, but non-significant effects of IBD and IBR on population genetic divergence were detected. The two clusters have different ecological niches and require different temperature regimes. CONCLUSIONS The north-south genetic differentiation may be common across the temperate-tropical boundary in southeast China. Divergent selection under different temperature regimes (possibly above and below freezing temperature in winter) could account for this divergence pattern. The broad continuum between tropical and temperate floras in EAS may have provided ample opportunities for tropical plant lineages to acquire freezing tolerance and to colonize the temperate regions during the late-Cenozoic global cooling. Our findings shed deeper insights into the high temperate plant species diversity in EAS.
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Affiliation(s)
- Dengmei Fan
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Shuqing Lei
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Hua Liang
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Qi Yao
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Yixuan Kou
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, Jiangxi, China.
| | - Shanmei Cheng
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Yi Yang
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Yingxiong Qiu
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zhiyong Zhang
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, Jiangxi, China.
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29
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Estrada O, Richards SM, Breen J. Discovering the Secrets of Ancient Plants: Recovery of DNA from Museum and Archaeological Plant Specimens. Methods Mol Biol 2022; 2512:261-267. [PMID: 35818010 DOI: 10.1007/978-1-0716-2429-6_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Plant DNA preserved in ancient specimens has recently gained importance as a tool in comparative genomics, allowing the investigation of evolutionary processes in plant genomes through time. However, recovering the genomic information contained in such specimens is challenging owing to the presence of secondary substances that limit DNA retrieval. In this chapter, we provide a DNA extraction protocol optimized for the recovery of DNA from degraded plant materials. The protocol is based on a commercially available DNA extraction kit that does not require handling of hazardous reagents.
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Affiliation(s)
- Oscar Estrada
- Centre for Anthropobiology and Genomics of Toulouse (CAGT), CNRS UMR 5288, Université Toulouse III - Paul Sabatier, Toulouse, France.
- Australian Centre for Ancient DNA (ACAD), School of Biological Science, The University of Adelaide, Adelaide, SA, Australia.
- Grupo de Agrobiotecnología, Instituto de Biología, Universidad de Antioquia, Medellín, Colombia.
| | - Stephen M Richards
- Australian Centre for Ancient DNA (ACAD), School of Biological Science, The University of Adelaide, Adelaide, SA, Australia
| | - James Breen
- Indigenous Genomics, Telethon Kids Institute, Adelaide, SA, Australia
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30
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Allaby RG, Stevens CJ, Kistler L, Fuller DQ. Emerging evidence of plant domestication as a landscape-level process. Trends Ecol Evol 2021; 37:268-279. [PMID: 34863580 DOI: 10.1016/j.tree.2021.11.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 11/01/2021] [Accepted: 11/02/2021] [Indexed: 01/03/2023]
Abstract
The evidence from ancient crops over the past decade challenges some of our most basic assumptions about the process of domestication. The emergence of crops has been viewed as a technologically progressive process in which single or multiple localized populations adapt to human environments in response to cultivation. By contrast, new genetic and archaeological evidence reveals a slow process that involved large populations over wide areas with unexpectedly sustained cultural connections in deep time. We review evidence that calls for a new landscape framework of crop origins. Evolutionary processes operate across vast distances of landscape and time, and the origins of domesticates are complex. The domestication bottleneck is a redundant concept and the progressive nature of domestication is in doubt.
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Affiliation(s)
- Robin G Allaby
- School of Life Sciences, University of Warwick, Coventry, UK.
| | - Chris J Stevens
- Institute of Archaeology, University College London (UCL), London, UK; School of Archaeology and Museology, Peking University, Beijing, China; McDonald Institute of Archaeology, University of Cambridge, Cambridge, UK
| | - Logan Kistler
- Department of Anthropology, Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Dorian Q Fuller
- Institute of Archaeology, University College London (UCL), London, UK; School of Cultural Heritage, Northwest University, Xi'an, Shaanxi, China
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31
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Abraham-Juárez MJ, Barnes AC, Aragón-Raygoza A, Tyson D, Kur A, Strable J, Rellán-Álvarez R. The arches and spandrels of maize domestication, adaptation, and improvement. CURRENT OPINION IN PLANT BIOLOGY 2021; 64:102124. [PMID: 34715472 DOI: 10.1016/j.pbi.2021.102124] [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: 04/06/2021] [Revised: 09/20/2021] [Accepted: 09/21/2021] [Indexed: 06/13/2023]
Abstract
People living in the Balsas River basin in southwest México domesticated maize from the bushy grass teosinte. Nine thousand years later, in 2021, Ms. Deb Haaland - a member of the Pueblo of Laguna tribe of New Mexico - wore a dress adorned with a cornstalk when she was sworn in as the Secretary of Interior of the United States of America. This choice of garment highlights the importance of the coevolution of maize and the farmers who, through careful selection over thousands of years, domesticated maize and adapted the physiology and shoot architecture of maize to fit local environments and growth habits. Some traits such as tillering were directly selected on (arches), and others such as tassel size are the by-products (spandrels) of maize evolution. Here, we review current knowledge of the underlying cellular, developmental, physiological, and metabolic processes that were selected by farmers and breeders, which have positioned maize as a top global staple crop.
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Affiliation(s)
- María Jazmín Abraham-Juárez
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), Irapuato, 36821, Mexico
| | - Allison C Barnes
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, 27695, USA
| | - Alejandro Aragón-Raygoza
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, 27695, USA; Unidad de Genómica Avanzada, Cinvestav Sede Irapuato, Km. 9.6 Libramiento Norte Carretera Irapuato-León, Guanajuato, Mexico
| | - Destiny Tyson
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, 27695, USA; Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, 27695, USA
| | - Andi Kur
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, 27695, USA
| | - Josh Strable
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, 27695, USA.
| | - Rubén Rellán-Álvarez
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, 27695, USA.
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32
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Kreiner JM, Tranel PJ, Weigel D, Stinchcombe JR, Wright SI. The genetic architecture and population genomic signatures of glyphosate resistance in Amaranthus tuberculatus. Mol Ecol 2021; 30:5373-5389. [PMID: 33853196 DOI: 10.1111/mec.15920] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 03/15/2021] [Accepted: 04/06/2021] [Indexed: 01/04/2023]
Abstract
Much of what we know about the genetic basis of herbicide resistance has come from detailed investigations of monogenic adaptation at known target-sites, despite the increasingly recognized importance of polygenic resistance. Little work has been done to characterize the broader genomic basis of herbicide resistance, including the number and distribution of genes involved, their effect sizes, allele frequencies and signatures of selection. In this work, we implemented genome-wide association (GWA) and population genomic approaches to examine the genetic architecture of glyphosate (Round-up) resistance in the problematic agricultural weed Amaranthus tuberculatus. A GWA was able to correctly identify the known target-gene but statistically controlling for two causal target-site mechanisms revealed an additional 250 genes across all 16 chromosomes associated with non-target-site resistance (NTSR). The encoded proteins had functions that have been linked to NTSR, the most significant of which is response to chemicals, but also showed pleiotropic roles in reproduction and growth. Compared to an empirical null that accounts for complex population structure, the architecture of NTSR was enriched for large effect sizes and low allele frequencies, suggesting the role of pleiotropic constraints on its evolution. The enrichment of rare alleles also suggested that the genetic architecture of NTSR may be population-specific and heterogeneous across the range. Despite their rarity, we found signals of recent positive selection on NTSR-alleles by both window- and haplotype-based statistics, and an enrichment of amino acid changing variants. In our samples, genome-wide single nucleotide polymorphisms explain a comparable amount of the total variation in glyphosate resistance to monogenic mechanisms, even in a collection of individuals where 80% of resistant individuals have large-effect TSR mutations, indicating an underappreciated polygenic contribution to the evolution of herbicide resistance in weed populations.
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Affiliation(s)
- Julia M Kreiner
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Patrick J Tranel
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - John R Stinchcombe
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
- Koffler Scientific Reserve, University of Toronto, King City, ON, Canada
| | - Stephen I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada
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33
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Zhang L, Ma X, Zhang X, Xu Y, Ibrahim AK, Yao J, Huang H, Chen S, Liao Z, Zhang Q, Niyitanga S, Yu J, Liu Y, Xu X, Wang J, Tao A, Xu J, Chen S, Yang X, He Q, Lin L, Fang P, Zhang L, Ming R, Qi J, Zhang L. Reference genomes of the two cultivated jute species. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:2235-2248. [PMID: 34170619 PMCID: PMC8541789 DOI: 10.1111/pbi.13652] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 06/08/2021] [Accepted: 06/17/2021] [Indexed: 05/10/2023]
Abstract
Cultivated jute, which comprises the two species Corchorus capsularis and C. olitorius, is the second most important natural fibre source after cotton. Here we describe chromosome-level assemblies of the genomes of both cultivated species. The C. capsularis and C. olitorius assemblies are each comprised of seven pseudo-chromosomes, with the C. capsularis assembly consisting of 336 Mb with 25,874 genes and the C. olitorius assembly containing 361 Mb with 28 479 genes. Although the two Corchorus genomes exhibit collinearity, the genome of C. olitorius contains 25 Mb of additional sequences than that of C. capsularis with 13 putative inversions, which might give a hint to the difference of phenotypic variants between the two cultivated jute species. Analysis of gene expression in isolated fibre tissues reveals candidate genes involved in fibre development. Our analysis of the population structures of 242 cultivars from C. capsularis and 57 cultivars from C. olitorius by whole-genome resequencing resulted in post-domestication bottlenecks occurred ~2000 years ago in these species. We identified hundreds of putative significant marker-trait associations (MTAs) controlling fibre fineness, cellulose content and lignin content of fibre by integrating data from genome-wide association studies (GWAS) with data from analyses of selective sweeps due to natural and artificial selection in these two jute species. Among them, we further validated that CcCOBRA1 and CcC4H1 regulate fibre quality in transgenic plants via improving the biosynthesis of the secondary cell wall. Our results yielded important new resources for functional genomics research and genetic improvement in jute and allied fibre crops.
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Affiliation(s)
- Lilan Zhang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of CropsFujian Provincial Key Laboratory of Crop Breeding by DesignFujian Agriculture and Forestry UniversityFuzhouChina
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast ChinaFujian Public Platform for Germplasm Resources of Bast Fibre CropsFujian International Science and Technology Cooperation Base for Genetics, Breeding and Multiple Utilization Development of Southern Economic CropsFujian Agriculture and Forestry UniversityFuzhouChina
- Center for Genomics and BiotechnologyHaixia Institue of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Xiaokai Ma
- Center for Genomics and BiotechnologyHaixia Institue of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Xingtan Zhang
- Center for Genomics and BiotechnologyHaixia Institue of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Yi Xu
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of CropsFujian Provincial Key Laboratory of Crop Breeding by DesignFujian Agriculture and Forestry UniversityFuzhouChina
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast ChinaFujian Public Platform for Germplasm Resources of Bast Fibre CropsFujian International Science and Technology Cooperation Base for Genetics, Breeding and Multiple Utilization Development of Southern Economic CropsFujian Agriculture and Forestry UniversityFuzhouChina
- Center for Genomics and BiotechnologyHaixia Institue of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Aminu Kurawa Ibrahim
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of CropsFujian Provincial Key Laboratory of Crop Breeding by DesignFujian Agriculture and Forestry UniversityFuzhouChina
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast ChinaFujian Public Platform for Germplasm Resources of Bast Fibre CropsFujian International Science and Technology Cooperation Base for Genetics, Breeding and Multiple Utilization Development of Southern Economic CropsFujian Agriculture and Forestry UniversityFuzhouChina
- Center for Genomics and BiotechnologyHaixia Institue of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Jiayu Yao
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of CropsFujian Provincial Key Laboratory of Crop Breeding by DesignFujian Agriculture and Forestry UniversityFuzhouChina
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast ChinaFujian Public Platform for Germplasm Resources of Bast Fibre CropsFujian International Science and Technology Cooperation Base for Genetics, Breeding and Multiple Utilization Development of Southern Economic CropsFujian Agriculture and Forestry UniversityFuzhouChina
- Center for Genomics and BiotechnologyHaixia Institue of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Huaxing Huang
- Center for Genomics and BiotechnologyHaixia Institue of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Shuai Chen
- Center for Genomics and BiotechnologyHaixia Institue of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Zhenyang Liao
- Center for Genomics and BiotechnologyHaixia Institue of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Qing Zhang
- Center for Genomics and BiotechnologyHaixia Institue of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Sylvain Niyitanga
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of CropsFujian Provincial Key Laboratory of Crop Breeding by DesignFujian Agriculture and Forestry UniversityFuzhouChina
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast ChinaFujian Public Platform for Germplasm Resources of Bast Fibre CropsFujian International Science and Technology Cooperation Base for Genetics, Breeding and Multiple Utilization Development of Southern Economic CropsFujian Agriculture and Forestry UniversityFuzhouChina
| | - Jiaxin Yu
- Center for Genomics and BiotechnologyHaixia Institue of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Yi Liu
- Center for Genomics and BiotechnologyHaixia Institue of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Xiuming Xu
- Center for Genomics and BiotechnologyHaixia Institue of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Jingjing Wang
- Center for Genomics and BiotechnologyHaixia Institue of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Aifen Tao
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of CropsFujian Provincial Key Laboratory of Crop Breeding by DesignFujian Agriculture and Forestry UniversityFuzhouChina
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast ChinaFujian Public Platform for Germplasm Resources of Bast Fibre CropsFujian International Science and Technology Cooperation Base for Genetics, Breeding and Multiple Utilization Development of Southern Economic CropsFujian Agriculture and Forestry UniversityFuzhouChina
| | - Jiantang Xu
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of CropsFujian Provincial Key Laboratory of Crop Breeding by DesignFujian Agriculture and Forestry UniversityFuzhouChina
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast ChinaFujian Public Platform for Germplasm Resources of Bast Fibre CropsFujian International Science and Technology Cooperation Base for Genetics, Breeding and Multiple Utilization Development of Southern Economic CropsFujian Agriculture and Forestry UniversityFuzhouChina
| | - Siyuan Chen
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of CropsFujian Provincial Key Laboratory of Crop Breeding by DesignFujian Agriculture and Forestry UniversityFuzhouChina
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast ChinaFujian Public Platform for Germplasm Resources of Bast Fibre CropsFujian International Science and Technology Cooperation Base for Genetics, Breeding and Multiple Utilization Development of Southern Economic CropsFujian Agriculture and Forestry UniversityFuzhouChina
| | - Xin Yang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of CropsFujian Provincial Key Laboratory of Crop Breeding by DesignFujian Agriculture and Forestry UniversityFuzhouChina
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast ChinaFujian Public Platform for Germplasm Resources of Bast Fibre CropsFujian International Science and Technology Cooperation Base for Genetics, Breeding and Multiple Utilization Development of Southern Economic CropsFujian Agriculture and Forestry UniversityFuzhouChina
| | - Qingyao He
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of CropsFujian Provincial Key Laboratory of Crop Breeding by DesignFujian Agriculture and Forestry UniversityFuzhouChina
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast ChinaFujian Public Platform for Germplasm Resources of Bast Fibre CropsFujian International Science and Technology Cooperation Base for Genetics, Breeding and Multiple Utilization Development of Southern Economic CropsFujian Agriculture and Forestry UniversityFuzhouChina
| | - Lihui Lin
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of CropsFujian Provincial Key Laboratory of Crop Breeding by DesignFujian Agriculture and Forestry UniversityFuzhouChina
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast ChinaFujian Public Platform for Germplasm Resources of Bast Fibre CropsFujian International Science and Technology Cooperation Base for Genetics, Breeding and Multiple Utilization Development of Southern Economic CropsFujian Agriculture and Forestry UniversityFuzhouChina
| | - Pingping Fang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of CropsFujian Provincial Key Laboratory of Crop Breeding by DesignFujian Agriculture and Forestry UniversityFuzhouChina
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast ChinaFujian Public Platform for Germplasm Resources of Bast Fibre CropsFujian International Science and Technology Cooperation Base for Genetics, Breeding and Multiple Utilization Development of Southern Economic CropsFujian Agriculture and Forestry UniversityFuzhouChina
| | - Liemei Zhang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of CropsFujian Provincial Key Laboratory of Crop Breeding by DesignFujian Agriculture and Forestry UniversityFuzhouChina
| | - Ray Ming
- Department of Plant Biologythe University of Illinois at Urbana‐ChampaignUrbanaILUSA
| | - Jianmin Qi
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of CropsFujian Provincial Key Laboratory of Crop Breeding by DesignFujian Agriculture and Forestry UniversityFuzhouChina
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast ChinaFujian Public Platform for Germplasm Resources of Bast Fibre CropsFujian International Science and Technology Cooperation Base for Genetics, Breeding and Multiple Utilization Development of Southern Economic CropsFujian Agriculture and Forestry UniversityFuzhouChina
| | - Liwu Zhang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of CropsFujian Provincial Key Laboratory of Crop Breeding by DesignFujian Agriculture and Forestry UniversityFuzhouChina
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast ChinaFujian Public Platform for Germplasm Resources of Bast Fibre CropsFujian International Science and Technology Cooperation Base for Genetics, Breeding and Multiple Utilization Development of Southern Economic CropsFujian Agriculture and Forestry UniversityFuzhouChina
- Center for Genomics and BiotechnologyHaixia Institue of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
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34
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Liu N, Du Y, Warburton ML, Xiao Y, Yan J. Phenotypic Plasticity Contributes to Maize Adaptation and Heterosis. Mol Biol Evol 2021; 38:1262-1275. [PMID: 33212480 PMCID: PMC8480182 DOI: 10.1093/molbev/msaa283] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Plant phenotypic plasticity describes altered phenotypic performance of an individual when grown in different environments. Exploring genetic architecture underlying plant plasticity variation may help mitigate the detrimental effects of a rapidly changing climate on agriculture, but little research has been done in this area to date. In the present study, we established a population of 976 maize F1 hybrids by crossing 488 diverse inbred lines with two elite testers. Genome-wide association study identified hundreds of quantitative trait loci associated with phenotypic plasticity variation across diverse F1 hybrids, the majority of which contributed very little variance, in accordance with the polygenic nature of these traits. We identified several quantitative trait locus regions that may have been selected during the tropical-temperate adaptation process. We also observed heterosis in terms of phenotypic plasticity, in addition to the traditional genetic value differences measured between hybrid and inbred lines, and the pattern of which was affected by genetic background. Our results demonstrate a landscape of phenotypic plasticity in maize, which will aid in the understanding of its genetic architecture, its contribution to adaptation and heterosis, and how it may be exploited for future maize breeding in a rapidly changing environment.
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Affiliation(s)
- Nannan Liu
- Horticulture Biology and Metabolomics Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.,National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yuanhao Du
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Marilyn L Warburton
- United States Department of Agriculture-Agricultural Research Service: Corn Host Plant Resistance Research Unit, Mississippi State, MS
| | - Yingjie Xiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
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35
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Blanc J, Kremling KAG, Buckler E, Josephs EB. Local adaptation contributes to gene expression divergence in maize. G3-GENES GENOMES GENETICS 2021; 11:6114460. [PMID: 33604670 PMCID: PMC8022924 DOI: 10.1093/g3journal/jkab004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 12/20/2020] [Indexed: 11/14/2022]
Abstract
Gene expression links genotypes to phenotypes, so identifying genes whose expression is shaped by selection will be important for understanding the traits and processes underlying local adaptation. However, detecting local adaptation for gene expression will require distinguishing between divergence due to selection and divergence due to genetic drift. Here, we adapt a QST−FST framework to detect local adaptation for transcriptome-wide gene expression levels in a population of diverse maize genotypes. We compare the number and types of selected genes across a wide range of maize populations and tissues, as well as selection on cold-response genes, drought-response genes, and coexpression clusters. We identify a number of genes whose expression levels are consistent with local adaptation and show that genes involved in stress response show enrichment for selection. Due to its history of intense selective breeding and domestication, maize evolution has long been of interest to researchers, and our study provides insight into the genes and processes important for in local adaptation of maize.
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Affiliation(s)
- Jennifer Blanc
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Karl A G Kremling
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.,Inari Agriculture, Cambridge, MA 02139, USA
| | - Edward Buckler
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.,Institute for Genomic Diversity, 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
| | - Emily B Josephs
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA.,Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI 48824, USA
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36
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Pérez-Escobar OA, Bellot S, Przelomska NAS, Flowers JM, Nesbitt M, Ryan P, Gutaker RM, Gros-Balthazard M, Wells T, Kuhnhäuser BG, Schley R, Bogarín D, Dodsworth S, Diaz R, Lehmann M, Petoe P, Eiserhardt WL, Preick M, Hofreiter M, Hajdas I, Purugganan M, Antonelli A, Gravendeel B, Leitch IJ, Torres Jimenez MF, Papadopulos AST, Chomicki G, Renner SS, Baker WJ. Molecular clocks and archaeogenomics of a Late Period Egyptian date palm leaf reveal introgression from wild relatives and add timestamps on the domestication. Mol Biol Evol 2021; 38:4475-4492. [PMID: 34191029 PMCID: PMC8476131 DOI: 10.1093/molbev/msab188] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The date palm, Phoenix dactylifera, has been a cornerstone of Middle Eastern and North African agriculture for millennia. It was first domesticated in the Persian Gulf, and its evolution appears to have been influenced by gene flow from two wild relatives, P. theophrasti, currently restricted to Crete and Turkey, and P. sylvestris, widespread from Bangladesh to the West Himalayas. Genomes of ancient date palm seeds show that gene flow from P. theophrasti to P. dactylifera may have occurred by ∼2,200 years ago, but traces of P. sylvestris could not be detected. We here integrate archeogenomics of a ∼2,100-year-old P. dactylifera leaf from Saqqara (Egypt), molecular-clock dating, and coalescence approaches with population genomic tests, to probe the hybridization between the date palm and its two closest relatives and provide minimum and maximum timestamps for its reticulated evolution. The Saqqara date palm shares a close genetic affinity with North African date palm populations, and we find clear genomic admixture from both P. theophrasti, and P. sylvestris, indicating that both had contributed to the date palm genome by 2,100 years ago. Molecular-clocks placed the divergence of P. theophrasti from P. dactylifera/P. sylvestris and that of P. dactylifera from P. sylvestris in the Upper Miocene, but strongly supported, conflicting topologies point to older gene flow between P. theophrasti and P. dactylifera, and P. sylvestris and P. dactylifera. Our work highlights the ancient hybrid origin of the date palms, and prompts the investigation of the functional significance of genetic material introgressed from both close relatives, which in turn could prove useful for modern date palm breeding.
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Affiliation(s)
| | - Sidonie Bellot
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK
| | - Natalia A S Przelomska
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK.,National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Jonathan M Flowers
- Center for Genomics and Systems Biology, New York University Abu Dhabi, United Arab Emirates
| | - Mark Nesbitt
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK
| | - Philippa Ryan
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK
| | | | - Muriel Gros-Balthazard
- French National Research Institute for Sustainable Development, Montpellier, BP 64501 - 34394 Cedex 5, France
| | - Tom Wells
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3QU, UK
| | | | - Rowan Schley
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK
| | - Diego Bogarín
- Lankester Botanical Garden, University of Costa Rica, San José, 302-7050, Costa Rica
| | - Steven Dodsworth
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK.,School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK
| | - Rudy Diaz
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK
| | | | - Peter Petoe
- Department of Biology, Aarhus University, 8000 Aarhus C, Denmark
| | - Wolf L Eiserhardt
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK.,Department of Biology, Aarhus University, 8000 Aarhus C, Denmark
| | - Michaela Preick
- Institute of Biochemistry and Biology, University of Potsdam, 14469 Potsdam, Germany
| | - Michael Hofreiter
- Institute of Biochemistry and Biology, University of Potsdam, 14469 Potsdam, Germany
| | - Irka Hajdas
- Department of Earth Sciences, ETH Zurich, 8092, Switzerland
| | - Michael Purugganan
- Center for Genomics and Systems Biology, New York University Abu Dhabi, United Arab Emirates
| | - Alexandre Antonelli
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK.,Department of Plant Sciences, University of Oxford, Oxford, OX1 3QU, UK.,Gothenburg Global Biodiversity Centre and Department of Biological and Environmental Sciences, University of Gothenburg, 413 19, Sweden
| | | | - Ilia J Leitch
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK
| | - Maria Fernanda Torres Jimenez
- Gothenburg Global Biodiversity Centre and Department of Biological and Environmental Sciences, University of Gothenburg, 413 19, Sweden
| | - Alexander S T Papadopulos
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, University of Bangor, Bangor LL57 2UW, UK
| | - Guillaume Chomicki
- Department of Animal and Plant Sciences, Alfred Denny Building, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Susanne S Renner
- Department of Biology, Washington University, Saint Louis, MO 63130, USA
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37
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de Vareilles A, Pelling R, Woodbridge J, Fyfe R. Archaeology and agriculture: plants, people, and past land-use. Trends Ecol Evol 2021; 36:943-954. [PMID: 34210535 DOI: 10.1016/j.tree.2021.06.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 05/27/2021] [Accepted: 06/03/2021] [Indexed: 11/29/2022]
Abstract
As a specialised branch of archaeology requiring specific field and laboratory methodologies, the contributions of archaeobotany have often been overlooked by the ecological research community. Developments in the fields of botany, chemistry, and ancient DNA analyses have greatly increased the potential for archaeobotany to contribute to topical questions relating to the Anthropocene and landscape transformations. We review the role of archaeobotany in identifying and describing past arable land use. Analytical techniques are illustrated with examples at both local and regional scales, demonstrating how archaeobotany can provide unique details of the wide array of past subsistence and land-use strategies. These data and their potential should be better recognised as important information that could underpin models seeking to evaluate or predict the effects of socioenvironmental interactions.
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Affiliation(s)
- Anne de Vareilles
- Historic England, Fort Cumberland, Fort Cumberland Road, Portsmouth P04 9LD, UK.
| | - Ruth Pelling
- Historic England, Fort Cumberland, Fort Cumberland Road, Portsmouth P04 9LD, UK
| | - Jessie Woodbridge
- School of Geography, Earth and Environmental Sciences, University of Plymouth, Drake Circus, Plymouth PL4 8AA, UK
| | - Ralph Fyfe
- School of Geography, Earth and Environmental Sciences, University of Plymouth, Drake Circus, Plymouth PL4 8AA, UK
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38
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Mural RV, Grzybowski M, Miao C, Damke A, Sapkota S, Boyles RE, Salas Fernandez MG, Schnable PS, Sigmon B, Kresovich S, Schnable JC. Meta-Analysis Identifies Pleiotropic Loci Controlling Phenotypic Trade-offs in Sorghum. Genetics 2021; 218:6294935. [PMID: 34100945 PMCID: PMC9335936 DOI: 10.1093/genetics/iyab087] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 06/07/2021] [Indexed: 01/03/2023] Open
Abstract
Community association populations are composed of phenotypically and genetically diverse accessions. Once these populations are genotyped, the resulting marker data can be reused by different groups investigating the genetic basis of different traits. Because the same genotypes are observed and scored for a wide range of traits in different environments, these populations represent a unique resource to investigate pleiotropy. Here we assembled a set of 234 separate trait datasets for the Sorghum Association Panel, a group of 406 sorghum genotypes widely employed by the sorghum genetics community. Comparison of genome wide association studies conducted with two independently generated marker sets for this population demonstrate that existing genetic marker sets do not saturate the genome and likely capture only 35-43% of potentially detectable loci controlling variation for traits scored in this population. While limited evidence for pleiotropy was apparent in cross-GWAS comparisons, a multivariate adaptive shrinkage approach recovered both known pleiotropic effects of existing loci and new pleiotropic effects, particularly significant impacts of known dwarfing genes on root architecture. In addition, we identified new loci with pleiotropic effects consistent with known trade-offs in sorghum development. These results demonstrate the potential for mining existing trait datasets from widely used community association populations to enable new discoveries from existing trait datasets as new, denser genetic marker datasets are generated for existing community association populations.
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Affiliation(s)
- Ravi V Mural
- Center for Plant Science Innovation and Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68588 USA
| | - Marcin Grzybowski
- Center for Plant Science Innovation and Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68588 USA
| | - Chenyong Miao
- Center for Plant Science Innovation and Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68588 USA
| | - Alyssa Damke
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68588 USA
| | - Sirjan Sapkota
- Advanced Plant Technology Program, Clemson University, Clemson, SC 29634 USA.,Department of Plant and Environment Sciences, Clemson University, Clemson, SC 29634 USA
| | - Richard E Boyles
- Department of Plant and Environment Sciences, Clemson University, Clemson, SC 29634 USA.,Pee Dee Research and Education Center, Clemson University, Florence, SC 29532 USA
| | | | | | - Brandi Sigmon
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68588 USA
| | - Stephen Kresovich
- Department of Plant and Environment Sciences, Clemson University, Clemson, SC 29634 USA.,Feed the Future Innovation Lab for Crop Improvement Cornell University, Ithaca, NY 14850 USA
| | - James C Schnable
- Center for Plant Science Innovation and Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68588 USA
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39
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Joint analysis of days to flowering reveals independent temperate adaptations in maize. Heredity (Edinb) 2021; 126:929-941. [PMID: 33888874 PMCID: PMC8178344 DOI: 10.1038/s41437-021-00422-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 02/07/2021] [Accepted: 02/25/2021] [Indexed: 02/02/2023] Open
Abstract
Domesticates are an excellent model for understanding biological consequences of rapid climate change. Maize (Zea mays ssp. mays) was domesticated from a tropical grass yet is widespread across temperate regions today. We investigate the biological basis of temperate adaptation in diverse structured nested association mapping (NAM) populations from China, Europe (Dent and Flint) and the United States as well as in the Ames inbred diversity panel, using days to flowering as a proxy. Using cross-population prediction, where high prediction accuracy derives from overall genomic relatedness, shared genetic architecture, and sufficient diversity in the training population, we identify patterns in predictive ability across the five populations. To identify the source of temperate adapted alleles in these populations, we predict top associated genome-wide association study (GWAS) identified loci in a Random Forest Classifier using independent temperate-tropical North American populations based on lines selected from Hapmap3 as predictors. We find that North American populations are well predicted (AUC equals 0.89 and 0.85 for Ames and USNAM, respectively), European populations somewhat well predicted (AUC equals 0.59 and 0.67 for the Dent and Flint panels, respectively) and that the Chinese population is not predicted well at all (AUC is 0.47), suggesting an independent adaptation process for early flowering in China. Multiple adaptations for the complex trait days to flowering in maize provide hope for similar natural systems under climate change.
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40
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Diepenbrock CH, Ilut DC, Magallanes-Lundback M, Kandianis CB, Lipka AE, Bradbury PJ, Holland JB, Hamilton JP, Wooldridge E, Vaillancourt B, Góngora-Castillo E, Wallace JG, Cepela J, Mateos-Hernandez M, Owens BF, Tiede T, Buckler ES, Rocheford T, Buell CR, Gore MA, DellaPenna D. Eleven biosynthetic genes explain the majority of natural variation in carotenoid levels in maize grain. THE PLANT CELL 2021; 33:882-900. [PMID: 33681994 PMCID: PMC8226291 DOI: 10.1093/plcell/koab032] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 01/26/2021] [Indexed: 05/03/2023]
Abstract
Vitamin A deficiency remains prevalent in parts of Asia, Latin America, and sub-Saharan Africa where maize (Zea mays) is a food staple. Extensive natural variation exists for carotenoids in maize grain. Here, to understand its genetic basis, we conducted a joint linkage and genome-wide association study of the US maize nested association mapping panel. Eleven of the 44 detected quantitative trait loci (QTL) were resolved to individual genes. Six of these were correlated expression and effect QTL (ceeQTL), showing strong correlations between RNA-seq expression abundances and QTL allelic effect estimates across six stages of grain development. These six ceeQTL also had the largest percentage of phenotypic variance explained, and in major part comprised the three to five loci capturing the bulk of genetic variation for each trait. Most of these ceeQTL had strongly correlated QTL allelic effect estimates across multiple traits. These findings provide an in-depth genome-level understanding of the genetic and molecular control of carotenoids in plants. In addition, these findings provide a roadmap to accelerate breeding for provitamin A and other priority carotenoid traits in maize grain that should be readily extendable to other cereals.
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Affiliation(s)
| | - Daniel C Ilut
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853
| | - Maria Magallanes-Lundback
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Catherine B Kandianis
- Present addresses: Nacre Innovations, Houston, Texas 77002 (C.B.K.); Department of Crop Sciences, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801 (A.E.L.); University of Michigan, Ann Arbor, MI 48109 (E.W.); Centro de Investigación Científica de Yucatan, CONACYT—Unidad de Biotecnologia, Merida, Yucatan 97200, Mexico (E.G.-C.); Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, Minnesota 55455 (J.C.); Bayer, Stonington, Illinois 62567 (M.M.-H.); BASF, Dawson, Georgia 39842 (B.F.O.); and Corteva Agriscience, St. Paul, Minnesota 55108 (T.T.)
| | - Alexander E Lipka
- Present addresses: Nacre Innovations, Houston, Texas 77002 (C.B.K.); Department of Crop Sciences, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801 (A.E.L.); University of Michigan, Ann Arbor, MI 48109 (E.W.); Centro de Investigación Científica de Yucatan, CONACYT—Unidad de Biotecnologia, Merida, Yucatan 97200, Mexico (E.G.-C.); Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, Minnesota 55455 (J.C.); Bayer, Stonington, Illinois 62567 (M.M.-H.); BASF, Dawson, Georgia 39842 (B.F.O.); and Corteva Agriscience, St. Paul, Minnesota 55108 (T.T.)
| | - Peter J Bradbury
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853
- United States Department of Agriculture—Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853
| | - James B Holland
- United States Department of Agriculture—Agricultural Research Service, Plant Science Research Unit, Department of Crop and Soil Sciences, North Carolina State University, Raleigh, North Carolina 27695
| | - John P Hamilton
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Edmund Wooldridge
- Present addresses: Nacre Innovations, Houston, Texas 77002 (C.B.K.); Department of Crop Sciences, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801 (A.E.L.); University of Michigan, Ann Arbor, MI 48109 (E.W.); Centro de Investigación Científica de Yucatan, CONACYT—Unidad de Biotecnologia, Merida, Yucatan 97200, Mexico (E.G.-C.); Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, Minnesota 55455 (J.C.); Bayer, Stonington, Illinois 62567 (M.M.-H.); BASF, Dawson, Georgia 39842 (B.F.O.); and Corteva Agriscience, St. Paul, Minnesota 55108 (T.T.)
| | - Brieanne Vaillancourt
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Elsa Góngora-Castillo
- Present addresses: Nacre Innovations, Houston, Texas 77002 (C.B.K.); Department of Crop Sciences, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801 (A.E.L.); University of Michigan, Ann Arbor, MI 48109 (E.W.); Centro de Investigación Científica de Yucatan, CONACYT—Unidad de Biotecnologia, Merida, Yucatan 97200, Mexico (E.G.-C.); Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, Minnesota 55455 (J.C.); Bayer, Stonington, Illinois 62567 (M.M.-H.); BASF, Dawson, Georgia 39842 (B.F.O.); and Corteva Agriscience, St. Paul, Minnesota 55108 (T.T.)
| | - Jason G Wallace
- Department of Crop and Soil Sciences, University of Georgia, Athens, Georgia 30602
| | - Jason Cepela
- Present addresses: Nacre Innovations, Houston, Texas 77002 (C.B.K.); Department of Crop Sciences, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801 (A.E.L.); University of Michigan, Ann Arbor, MI 48109 (E.W.); Centro de Investigación Científica de Yucatan, CONACYT—Unidad de Biotecnologia, Merida, Yucatan 97200, Mexico (E.G.-C.); Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, Minnesota 55455 (J.C.); Bayer, Stonington, Illinois 62567 (M.M.-H.); BASF, Dawson, Georgia 39842 (B.F.O.); and Corteva Agriscience, St. Paul, Minnesota 55108 (T.T.)
| | - Maria Mateos-Hernandez
- Present addresses: Nacre Innovations, Houston, Texas 77002 (C.B.K.); Department of Crop Sciences, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801 (A.E.L.); University of Michigan, Ann Arbor, MI 48109 (E.W.); Centro de Investigación Científica de Yucatan, CONACYT—Unidad de Biotecnologia, Merida, Yucatan 97200, Mexico (E.G.-C.); Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, Minnesota 55455 (J.C.); Bayer, Stonington, Illinois 62567 (M.M.-H.); BASF, Dawson, Georgia 39842 (B.F.O.); and Corteva Agriscience, St. Paul, Minnesota 55108 (T.T.)
| | - Brenda F Owens
- Present addresses: Nacre Innovations, Houston, Texas 77002 (C.B.K.); Department of Crop Sciences, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801 (A.E.L.); University of Michigan, Ann Arbor, MI 48109 (E.W.); Centro de Investigación Científica de Yucatan, CONACYT—Unidad de Biotecnologia, Merida, Yucatan 97200, Mexico (E.G.-C.); Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, Minnesota 55455 (J.C.); Bayer, Stonington, Illinois 62567 (M.M.-H.); BASF, Dawson, Georgia 39842 (B.F.O.); and Corteva Agriscience, St. Paul, Minnesota 55108 (T.T.)
| | - Tyler Tiede
- Present addresses: Nacre Innovations, Houston, Texas 77002 (C.B.K.); Department of Crop Sciences, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801 (A.E.L.); University of Michigan, Ann Arbor, MI 48109 (E.W.); Centro de Investigación Científica de Yucatan, CONACYT—Unidad de Biotecnologia, Merida, Yucatan 97200, Mexico (E.G.-C.); Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, Minnesota 55455 (J.C.); Bayer, Stonington, Illinois 62567 (M.M.-H.); BASF, Dawson, Georgia 39842 (B.F.O.); and Corteva Agriscience, St. Paul, Minnesota 55108 (T.T.)
| | - Edward S Buckler
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853
- United States Department of Agriculture—Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853
| | - Torbert Rocheford
- Department of Agronomy, Purdue University, West Lafayette, Indiana 47907
| | - C Robin Buell
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Michael A Gore
- Authors for correspondence: (C.H.D.), (M.A.G.), and (D.D.P.)
| | - Dean DellaPenna
- Authors for correspondence: (C.H.D.), (M.A.G.), and (D.D.P.)
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41
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Urrutia M, Blein‐Nicolas M, Prigent S, Bernillon S, Deborde C, Balliau T, Maucourt M, Jacob D, Ballias P, Bénard C, Sellier H, Gibon Y, Giauffret C, Zivy M, Moing A. Maize metabolome and proteome responses to controlled cold stress partly mimic early-sowing effects in the field and differ from those of Arabidopsis. PLANT, CELL & ENVIRONMENT 2021; 44:1504-1521. [PMID: 33410508 PMCID: PMC8248070 DOI: 10.1111/pce.13993] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/31/2020] [Indexed: 05/21/2023]
Abstract
In Northern Europe, sowing maize one-month earlier than current agricultural practices may lead to moderate chilling damage. However, studies of the metabolic responses to low, non-freezing, temperatures remain scarce. Here, genetically-diverse maize hybrids (Zea mays, dent inbred lines crossed with a flint inbred line) were cultivated in a growth chamber at optimal temperature and then three decreasing temperatures for 2 days each, as well as in the field. Leaf metabolomic and proteomic profiles were determined. In the growth chamber, 50% of metabolites and 18% of proteins changed between 20 and 16°C. These maize responses, partly differing from those of Arabidopsis to short-term chilling, were mapped on genome-wide metabolic maps. Several metabolites and proteins showed similar variation for all temperature decreases: seven MS-based metabolite signatures and two proteins involved in photosynthesis decreased continuously. Several increasing metabolites or proteins in the growth-chamber chilling conditions showed similar trends in the early-sowing field experiment, including trans-aconitate, three hydroxycinnamate derivatives, a benzoxazinoid, a sucrose synthase, lethal leaf-spot 1 protein, an allene oxide synthase, several glutathione transferases and peroxidases. Hybrid groups based on field biomass were used to search for the metabolite or protein responses differentiating them in growth-chamber conditions, which could be of interest for breeding.
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Affiliation(s)
- Maria Urrutia
- Biologie du Fruit et Pathologie, UMR 1332, Centre INRAE de Nouvelle Aquitaine‐BordeauxINRAE, Univ.Villenave d'OrnonFrance
- Present address:
Dtp. Biología Molecular y BioquímicaUniv. MálagaMálagaSpain
| | - Mélisande Blein‐Nicolas
- INRAE, CNRS, AgroParisTech, GQE‐Le MoulonUniv. Paris‐SaclayGif‐sur‐YvetteFrance
- PAPPSO, doi:10.15454/1.5572393176364355E12, GQE‐Le MoulonGif‐sur‐YvetteFrance
| | - Sylvain Prigent
- Biologie du Fruit et Pathologie, UMR 1332, Centre INRAE de Nouvelle Aquitaine‐BordeauxINRAE, Univ.Villenave d'OrnonFrance
| | - Stéphane Bernillon
- Biologie du Fruit et Pathologie, UMR 1332, Centre INRAE de Nouvelle Aquitaine‐BordeauxINRAE, Univ.Villenave d'OrnonFrance
- PMB‐Metabolome, INRAE, 2018, Bordeaux Metabolome, doi:10.15454/1.5572412770331912E12, MetaboHUB, PHENOME, IBVM, Centre INRAE de Nouvelle Aquitaine‐BordeauxVillenave d'OrnonFrance
| | - Catherine Deborde
- Biologie du Fruit et Pathologie, UMR 1332, Centre INRAE de Nouvelle Aquitaine‐BordeauxINRAE, Univ.Villenave d'OrnonFrance
- PMB‐Metabolome, INRAE, 2018, Bordeaux Metabolome, doi:10.15454/1.5572412770331912E12, MetaboHUB, PHENOME, IBVM, Centre INRAE de Nouvelle Aquitaine‐BordeauxVillenave d'OrnonFrance
| | - Thierry Balliau
- INRAE, CNRS, AgroParisTech, GQE‐Le MoulonUniv. Paris‐SaclayGif‐sur‐YvetteFrance
- PAPPSO, doi:10.15454/1.5572393176364355E12, GQE‐Le MoulonGif‐sur‐YvetteFrance
| | - Mickaël Maucourt
- Biologie du Fruit et Pathologie, UMR 1332, Centre INRAE de Nouvelle Aquitaine‐BordeauxINRAE, Univ.Villenave d'OrnonFrance
- PMB‐Metabolome, INRAE, 2018, Bordeaux Metabolome, doi:10.15454/1.5572412770331912E12, MetaboHUB, PHENOME, IBVM, Centre INRAE de Nouvelle Aquitaine‐BordeauxVillenave d'OrnonFrance
| | - Daniel Jacob
- Biologie du Fruit et Pathologie, UMR 1332, Centre INRAE de Nouvelle Aquitaine‐BordeauxINRAE, Univ.Villenave d'OrnonFrance
- PMB‐Metabolome, INRAE, 2018, Bordeaux Metabolome, doi:10.15454/1.5572412770331912E12, MetaboHUB, PHENOME, IBVM, Centre INRAE de Nouvelle Aquitaine‐BordeauxVillenave d'OrnonFrance
| | - Patricia Ballias
- Biologie du Fruit et Pathologie, UMR 1332, Centre INRAE de Nouvelle Aquitaine‐BordeauxINRAE, Univ.Villenave d'OrnonFrance
- PMB‐Metabolome, INRAE, 2018, Bordeaux Metabolome, doi:10.15454/1.5572412770331912E12, MetaboHUB, PHENOME, IBVM, Centre INRAE de Nouvelle Aquitaine‐BordeauxVillenave d'OrnonFrance
| | - Camille Bénard
- Biologie du Fruit et Pathologie, UMR 1332, Centre INRAE de Nouvelle Aquitaine‐BordeauxINRAE, Univ.Villenave d'OrnonFrance
- PMB‐Metabolome, INRAE, 2018, Bordeaux Metabolome, doi:10.15454/1.5572412770331912E12, MetaboHUB, PHENOME, IBVM, Centre INRAE de Nouvelle Aquitaine‐BordeauxVillenave d'OrnonFrance
| | | | - Yves Gibon
- Biologie du Fruit et Pathologie, UMR 1332, Centre INRAE de Nouvelle Aquitaine‐BordeauxINRAE, Univ.Villenave d'OrnonFrance
- PMB‐Metabolome, INRAE, 2018, Bordeaux Metabolome, doi:10.15454/1.5572412770331912E12, MetaboHUB, PHENOME, IBVM, Centre INRAE de Nouvelle Aquitaine‐BordeauxVillenave d'OrnonFrance
| | - Catherine Giauffret
- INRAE, Univ. Liège, Univ. Lille, Univ. Picardie Jules Verne, BioEcoAgroPeronneFrance
| | - Michel Zivy
- INRAE, CNRS, AgroParisTech, GQE‐Le MoulonUniv. Paris‐SaclayGif‐sur‐YvetteFrance
- PAPPSO, doi:10.15454/1.5572393176364355E12, GQE‐Le MoulonGif‐sur‐YvetteFrance
| | - Annick Moing
- Biologie du Fruit et Pathologie, UMR 1332, Centre INRAE de Nouvelle Aquitaine‐BordeauxINRAE, Univ.Villenave d'OrnonFrance
- PMB‐Metabolome, INRAE, 2018, Bordeaux Metabolome, doi:10.15454/1.5572412770331912E12, MetaboHUB, PHENOME, IBVM, Centre INRAE de Nouvelle Aquitaine‐BordeauxVillenave d'OrnonFrance
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42
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Boden SA. Evolution: Replicated mutation of COL2 contributed long-day flowering in common bean. Curr Biol 2021; 31:R384-R386. [PMID: 33905695 DOI: 10.1016/j.cub.2021.02.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The ability to flower without strict daylength constraints has helped spread cultivation of crop plants to new locations. The generation of daylength-insensitive common bean accessions in central and South America involved the repeated selection of mutant alleles for a key transcription factor that suppresses long-day flowering.
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Affiliation(s)
- Scott A Boden
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Glen Osmond, SA 5064, Australia.
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43
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Genotyping by Sequencing Reveals Genetic Relatedness of Southwestern U.S. Blue Maize Landraces. Int J Mol Sci 2021; 22:ijms22073436. [PMID: 33810494 PMCID: PMC8037273 DOI: 10.3390/ijms22073436] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/18/2021] [Accepted: 03/23/2021] [Indexed: 11/17/2022] Open
Abstract
Maize has played a key role in the sustenance and cultural traditions of the inhabitants of the southwestern USA for many centuries. Blue maize is an important component of the diverse landraces still cultivated in the region but the degree to which they are related is unknown. This research was designed to ascertain the genotypic, morphological, and phenotypic diversity of six representative southwestern blue maize landraces. Their genotypic diversity was examined using tunable genotyping-by-sequencing (tGBS™). A total of 81,038 high quality SNPs were identified and obtained through tGBS. A total of 45 morphological and biochemical traits were evaluated at two locations in New Mexico. The varieties Los Lunas High and Flor del Rio were genetically less related with other southwestern landraces whereas diffusion between Navajo Blue, Hopi Blue, Yoeme Blue, and Taos Blue demonstrated that these landraces were genetically related. Phenotypic variability was highest for kernel traits and least for plant traits. Plant, ear, and kernel traits were fairly consistent within and across locations. Principal component analysis and tGBS showed that Corn Belt variety ‘Ohio Blue’ was distinctly different from southwestern landraces. Genotypic analysis displayed that southwestern landraces are genetically closely related, but selection has resulted in differing phenotypes. This study has provided additional insight into the genetic relatedness of southwestern blue maize landraces.
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44
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Genome assembly and population genomic analysis provide insights into the evolution of modern sweet corn. Nat Commun 2021; 12:1227. [PMID: 33623026 PMCID: PMC7902669 DOI: 10.1038/s41467-021-21380-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 01/26/2021] [Indexed: 01/31/2023] Open
Abstract
Sweet corn is one of the most important vegetables in the United States and Canada. Here, we present a de novo assembly of a sweet corn inbred line Ia453 with the mutated shrunken2-reference allele (Ia453-sh2). This mutation accumulates more sugar and is present in most commercial hybrids developed for the processing and fresh markets. The ten pseudochromosomes cover 92% of the total assembly and 99% of the estimated genome size, with a scaffold N50 of 222.2 Mb. This reference genome completely assembles the large structural variation that created the mutant sh2-R allele. Furthermore, comparative genomics analysis with six field corn genomes highlights differences in single-nucleotide polymorphisms, structural variations, and transposon composition. Phylogenetic analysis of 5,381 diverse maize and teosinte accessions reveals genetic relationships between sweet corn and other types of maize. Our results show evidence for a common origin in northern Mexico for modern sweet corn in the U.S. Finally, population genomic analysis identifies regions of the genome under selection and candidate genes associated with sweet corn traits, such as early flowering, endosperm composition, plant and tassel architecture, and kernel row number. Our study provides a high-quality reference-genome sequence to facilitate comparative genomics, functional studies, and genomic-assisted breeding for sweet corn.
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45
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3D morphology of nematode encapsulation in snail shells, revealed by micro-CT imaging. Sci Rep 2021; 11:2523. [PMID: 33510331 PMCID: PMC7843631 DOI: 10.1038/s41598-021-82106-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 11/25/2020] [Indexed: 11/25/2022] Open
Abstract
Many parasites and hosts are embroiled in an on-going arms race that affects the evolution of each participant. One such battle is between parasitic nematodes and terrestrial gastropods which have co-evolved for 90–130 MY. Recently, snails have been shown to encase and kill invading nematodes using their shell as a defence mechanism. However, there is remarkably little known about this process in terms of understanding where, when and how nematodes are fixed within the shell. Also there has never been any attempt to observe this process using methods other than light microscopy. Therefore, we used micro CT scanning of a Cepaea nemoralis shell (a common host for nematodes) to 3D visualise encased nematode parasites and quantify morphological parameters. By taking this approach future studies could use micro CT scanning of fossil shells in conchology collections to understand nematode/snail co-evolution.
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46
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Archaeological Central American maize genomes suggest ancient gene flow from South America. Proc Natl Acad Sci U S A 2020; 117:33124-33129. [PMID: 33318213 PMCID: PMC7777085 DOI: 10.1073/pnas.2015560117] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Maize is a global food staple with great economic and cultural importance. Archaeogenomic studies have revealed a process of protracted maize domestication and multiple waves of human-mediated dispersal in the Americas. Maize first arrived in South America as a partial domesticate, where the domestication syndrome became independently fixed and improved varieties developed away from the influence of wild gene flow. We demonstrate that hybrids of some of these improved varieties were likely reintroduced back to Central America. We hypothesize that this backflow of South American genetic material may have contributed to the development of a more productive staple, which was related to the growth and aggregation of human populations, and the formation of more complex social and political structures regionally. Maize (Zea mays ssp. mays) domestication began in southwestern Mexico ∼9,000 calendar years before present (cal. BP) and humans dispersed this important grain to South America by at least 7,000 cal. BP as a partial domesticate. South America served as a secondary improvement center where the domestication syndrome became fixed and new lineages emerged in parallel with similar processes in Mesoamerica. Later, Indigenous cultivators carried a second major wave of maize southward from Mesoamerica, but it has been unclear until now whether the deeply divergent maize lineages underwent any subsequent gene flow between these regions. Here we report ancient maize genomes (2,300–1,900 cal. BP) from El Gigante rock shelter, Honduras, that are closely related to ancient and modern maize from South America. Our findings suggest that the second wave of maize brought into South America hybridized with long-established landraces from the first wave, and that some of the resulting newly admixed lineages were then reintroduced to Central America. Direct radiocarbon dates and cob morphological data from the rock shelter suggest that more productive maize varieties developed between 4,300 and 2,500 cal. BP. We hypothesize that the influx of maize from South America into Central America may have been an important source of genetic diversity as maize was becoming a staple grain in Central and Mesoamerica.
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47
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Stetter MG. Limits and constraints to crop domestication. AMERICAN JOURNAL OF BOTANY 2020; 107:1617-1621. [PMID: 33325038 DOI: 10.1002/ajb2.1585] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 10/08/2020] [Indexed: 06/12/2023]
Affiliation(s)
- Markus G Stetter
- Department of Plant Sciences, University of Cologne, Cologne, Germany, Cluster of Excellence on Plant Sciences, University of Cologne, Cologne, Germany
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48
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Latorre SM, Lang PLM, Burbano HA, Gutaker RM. Isolation, Library Preparation, and Bioinformatic Analysis of Historical and Ancient Plant DNA. ACTA ACUST UNITED AC 2020; 5:e20121. [PMID: 33211414 DOI: 10.1002/cppb.20121] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The ability to sequence DNA retrieved from ancient and historical material plays a crucial role in reinforcing evolutionary and anthropological inference. While the focus of the field is largely on analyzing DNA from ancient hominids and other animals, we have also learned from plant ancient DNA (aDNA), in particular, about human farming practices, crop domestication, environment management, species invasion, and adaptation to various environmental conditions. In the following protocols, we outline best practices for plant aDNA isolation, preparation for sequencing, bioinformatic processing, and authentication. We describe the process all the way from processing of archaeological or historical plant material to characterizing and authenticating sequencing reads. In alternative protocols, we include modifications to this process that are tailored to strongly degraded DNA. Throughout, we stress the importance of precautionary measures to successfully analyze aDNA. Finally, we discuss the evolution of the archaeogenomics field and the development of new methods, which both shaped this protocol. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Isolation of aDNA Alternate Protocol 1: Isolation of ultra-short DNA (Dabney modification) Support Protocol 1: Preparation of PTB-based mix Support Protocol 2: Preparation of binding buffer Basic Protocol 2: Preparation of genomic libraries Alternate Protocol 2: Preparation of genomic libraries with uracil removal Basic Protocol 3: Bioinformatic processing and authentication of aDNA.
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Affiliation(s)
- Sergio M Latorre
- Research Group for Ancient Genomics and Evolution, Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | | | - Hernán A Burbano
- Research Group for Ancient Genomics and Evolution, Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany.,Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Rafal M Gutaker
- Center for Genomics and Systems Biology, New York University, New York, New York.,Royal Botanic Gardens, Kew, Richmond, London, United Kingdom
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Xu G, Lyu J, Li Q, Liu H, Wang D, Zhang M, Springer NM, Ross-Ibarra J, Yang J. Evolutionary and functional genomics of DNA methylation in maize domestication and improvement. Nat Commun 2020; 11:5539. [PMID: 33139747 PMCID: PMC7606521 DOI: 10.1038/s41467-020-19333-4] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 10/08/2020] [Indexed: 12/23/2022] Open
Abstract
DNA methylation is a ubiquitous chromatin feature, present in 25% of cytosines in the maize genome, but variation and evolution of the methylation landscape during maize domestication remain largely unknown. Here, we leverage whole-genome sequencing (WGS) and whole-genome bisulfite sequencing (WGBS) data on populations of modern maize, landrace, and teosinte (Zea mays ssp. parviglumis) to estimate epimutation rates and selection coefficients. We find weak evidence for direct selection on DNA methylation in any context, but thousands of differentially methylated regions (DMRs) are identified population-wide that are correlated with recent selection. For two trait-associated DMRs, vgt1-DMR and tb1-DMR, HiChIP data indicate that the interactive loops between DMRs and respective downstream genes are present in B73, a modern maize line, but absent in teosinte. Our results enable a better understanding of the evolutionary forces acting on patterns of DNA methylation and suggest a role of methylation variation in adaptive evolution. Variation and evolution of DNA methylation during maize domestication remain largely unknown. Here, the authors generate genome and methylome sequencing data as well as HiChIP-based interactome data to investigate the adaptive and phenotypic consequences of methylation variations in maize.
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Affiliation(s)
- Gen Xu
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA.,Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - Jing Lyu
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA.,Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - Qing Li
- Department of Plant Biology, Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, MN, 55108, USA.,National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Han Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Fragrant Hill, Beijing, 100093, China
| | - Dafang Wang
- Division of Math and Sciences, Delta State University, Cleveland, MS, 38733, USA
| | - Mei Zhang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Fragrant Hill, Beijing, 100093, China
| | - Nathan M Springer
- Department of Plant Biology, Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Jeffrey Ross-Ibarra
- Department of Evolution and Ecology, Center for Population Biology and Genome Center, University of California, Davis, CA, 95616, USA
| | - Jinliang Yang
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA. .,Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA.
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50
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Cortés AJ, López-Hernández F, Osorio-Rodriguez D. Predicting Thermal Adaptation by Looking Into Populations' Genomic Past. Front Genet 2020; 11:564515. [PMID: 33101385 PMCID: PMC7545011 DOI: 10.3389/fgene.2020.564515] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 08/24/2020] [Indexed: 12/18/2022] Open
Abstract
Molecular evolution offers an insightful theory to interpret the genomic consequences of thermal adaptation to previous events of climate change beyond range shifts. However, disentangling often mixed footprints of selective and demographic processes from those due to lineage sorting, recombination rate variation, and genomic constrains is not trivial. Therefore, here we condense current and historical population genomic tools to study thermal adaptation and outline key developments (genomic prediction, machine learning) that might assist their utilization for improving forecasts of populations' responses to thermal variation. We start by summarizing how recent thermal-driven selective and demographic responses can be inferred by coalescent methods and in turn how quantitative genetic theory offers suitable multi-trait predictions over a few generations via the breeder's equation. We later assume that enough generations have passed as to display genomic signatures of divergent selection to thermal variation and describe how these footprints can be reconstructed using genome-wide association and selection scans or, alternatively, may be used for forward prediction over multiple generations under an infinitesimal genomic prediction model. Finally, we move deeper in time to comprehend the genomic consequences of thermal shifts at an evolutionary time scale by relying on phylogeographic approaches that allow for reticulate evolution and ecological parapatric speciation, and end by envisioning the potential of modern machine learning techniques to better inform long-term predictions. We conclude that foreseeing future thermal adaptive responses requires bridging the multiple spatial scales of historical and predictive environmental change research under modern cohesive approaches such as genomic prediction and machine learning frameworks.
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Affiliation(s)
- Andrés J Cortés
- Corporación Colombiana de Investigación Agropecuaria AGROSAVIA, C.I. La Selva, Rionegro, Colombia.,Departamento de Ciencias Forestales, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia - Sede Medellín, Medellín, Colombia
| | - Felipe López-Hernández
- Corporación Colombiana de Investigación Agropecuaria AGROSAVIA, C.I. La Selva, Rionegro, Colombia
| | - Daniela Osorio-Rodriguez
- Division of Geological and Planetary Sciences, California Institute of Technology (Caltech), Pasadena, CA, United States
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