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Pieri A, Beleggia R, Gioia T, Tong H, Di Vittori V, Frascarelli G, Bitocchi E, Nanni L, Bellucci E, Fiorani F, Pecchioni N, Marzario S, De Quattro C, Limongi AR, De Vita P, Rossato M, Schurr U, David JL, Nikoloski Z, Papa R. Transcriptomic response to nitrogen availability reveals signatures of adaptive plasticity during tetraploid wheat domestication. THE PLANT CELL 2024; 36:3809-3823. [PMID: 39056474 PMCID: PMC11371143 DOI: 10.1093/plcell/koae202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 06/18/2024] [Accepted: 07/17/2024] [Indexed: 07/28/2024]
Abstract
The domestication of crops, coupled with agroecosystem development, is associated with major environmental changes and provides an ideal model of phenotypic plasticity. Here, we examined 32 genotypes of three tetraploid wheat (Triticum turgidum L.) subspecies, wild emmer, emmer, and durum wheat, which are representative of the key stages in the domestication of tetraploid wheat. We developed a pipeline that integrates RNA-Seq data and population genomics to assess gene expression plasticity and identify selection signatures under diverse nitrogen availability conditions. Our analysis revealed differing gene expression responses to nitrogen availability across primary (wild emmer to emmer) and secondary (emmer to durum wheat) domestication. Notably, nitrogen triggered the expression of twice as many genes in durum wheat compared to that in emmer and wild emmer. Unique selection signatures were identified at each stage: primary domestication mainly influenced genes related to biotic interactions, whereas secondary domestication affected genes related to amino acid metabolism, in particular lysine. Selection signatures were found in differentially expressed genes (DEGs), notably those associated with nitrogen metabolism, such as the gene encoding glutamate dehydrogenase (GDH). Overall, our study highlights the pivotal role of nitrogen availability in the domestication and adaptive responses of a major food crop, with varying effects across different traits and growth conditions.
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Affiliation(s)
- Alice Pieri
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, via Brecce Bianche, Ancona 60131, Italy
| | - Romina Beleggia
- Council for Agricultural Research and Economics (CREA), Research Centre for Cereal and Industrial Crops (CREA-CI), Foggia 71122, Italy
| | - Tania Gioia
- School of Agricultural, Forestry, Food and Environmental Sciences, University of Basilicata, Potenza 85100, Italy
| | - Hao Tong
- Bioinformatics Department, Institute of Biochemistry and Biology, University of Potsdam, Potsdam 14476, Germany
- Systems Biology and Mathematical Modeling Group, Max Planck Institute of Molecular Plant Physiology, Potsdam 14476, Germany
| | - Valerio Di Vittori
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, via Brecce Bianche, Ancona 60131, Italy
| | - Giulia Frascarelli
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, via Brecce Bianche, Ancona 60131, Italy
| | - Elena Bitocchi
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, via Brecce Bianche, Ancona 60131, Italy
| | - Laura Nanni
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, via Brecce Bianche, Ancona 60131, Italy
| | - Elisa Bellucci
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, via Brecce Bianche, Ancona 60131, Italy
| | - Fabio Fiorani
- Institute of Biosciences and Geosciences (IBG-2): Plant Sciences, Forschungszentrum Julich GmbH, Julich 52428, Germany
| | - Nicola Pecchioni
- Council for Agricultural Research and Economics (CREA), Research Centre for Cereal and Industrial Crops (CREA-CI), Foggia 71122, Italy
| | - Stefania Marzario
- School of Agricultural, Forestry, Food and Environmental Sciences, University of Basilicata, Potenza 85100, Italy
| | - Concetta De Quattro
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, Verona 37134, Italy
| | - Antonina Rita Limongi
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, Verona 37134, Italy
| | - Pasquale De Vita
- Council for Agricultural Research and Economics (CREA), Research Centre for Cereal and Industrial Crops (CREA-CI), Foggia 71122, Italy
| | - Marzia Rossato
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, Verona 37134, Italy
| | - Ulrich Schurr
- Institute of Biosciences and Geosciences (IBG-2): Plant Sciences, Forschungszentrum Julich GmbH, Julich 52428, Germany
| | - Jacques L David
- AGAP, Univ. Montpellier, CIRAD, INRAE, Institut Agro, Montpellier 34060, France
| | - Zoran Nikoloski
- Bioinformatics Department, Institute of Biochemistry and Biology, University of Potsdam, Potsdam 14476, Germany
- Systems Biology and Mathematical Modeling Group, Max Planck Institute of Molecular Plant Physiology, Potsdam 14476, Germany
| | - Roberto Papa
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, via Brecce Bianche, Ancona 60131, Italy
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Mohammadi M, Mohammadi R. Potential of tetraploid wheats in plant breeding: A review. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 346:112155. [PMID: 38885883 DOI: 10.1016/j.plantsci.2024.112155] [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: 03/22/2024] [Revised: 06/05/2024] [Accepted: 06/08/2024] [Indexed: 06/20/2024]
Abstract
Domestication syndrome, selection pressure, and modern plant breeding programs have reduced the genetic diversity of the wheat germplasm. For the genetic gains of breeding programs to be sustainable, plant breeders require a diverse gene pool to select genes for resistance to biotic stress factors, tolerance to abiotic stress factors, and improved quality and yield components. Thus, old landraces, subspecies and wild ancestors are rich sources of genetic diversity that have not yet been fully exploited, and it is possible to utilize this diversity. Compared with durum wheat, tetraploid wheat subspecies have retained much greater genetic diversity despite genetic drift and various environmental influences, and the identification and utilization of this diversity can make a greater contribution to the genetic enrichment of wheat. In addition, using the pre-breeding method, the valuable left-behind alleles in the wheat gene pool can be re-introduced through hybridization and introgressive gene flow to create a sustainable opportunity for the genetic gain of wheat. This review provides some insights about the potential of tetraploid wheats in plant breeding and the genetic gains made by them in plant breeding across past decades, and gathers the known functional information on genes/QTLs, metabolites, traits and their direct involvement in wheat resistance/tolerance to biotic/abiotic stresses.
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Affiliation(s)
- Majid Mohammadi
- Dryland Agricultural Research Institute (DARI), Sararood branch, AREEO, Kermanshah, Iran.
| | - Reza Mohammadi
- Dryland Agricultural Research Institute (DARI), Sararood branch, AREEO, Kermanshah, Iran.
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Wang Z, Miao L, Chen Y, Peng H, Ni Z, Sun Q, Guo W. Deciphering the evolution and complexity of wheat germplasm from a genomic perspective. J Genet Genomics 2023; 50:846-860. [PMID: 37611848 DOI: 10.1016/j.jgg.2023.08.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/29/2023] [Accepted: 08/09/2023] [Indexed: 08/25/2023]
Abstract
Bread wheat provides an essential fraction of the daily calorific intake for humanity. Due to its huge and complex genome, progress in studying on the wheat genome is substantially trailed behind those of the other two major crops, rice and maize, for at least a decade. With rapid advances in genome assembling and reduced cost of high-throughput sequencing, emerging de novo genome assemblies of wheat and whole-genome sequencing data are leading to a paradigm shift in wheat research. Here, we review recent progress in dissecting the complex genome and germplasm evolution of wheat since the release of the first high-quality wheat genome. New insights have been gained in the evolution of wheat germplasm during domestication and modern breeding progress, genomic variations at multiple scales contributing to the diversity of wheat germplasm, and complex transcriptional and epigenetic regulations of functional genes in polyploid wheat. Genomics databases and bioinformatics tools meeting the urgent needs of wheat genomics research are also summarized. The ever-increasing omics data, along with advanced tools and well-structured databases, are expected to accelerate deciphering the germplasm and gene resources in wheat for future breeding advances.
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Affiliation(s)
- Zihao Wang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Lingfeng Miao
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yongming Chen
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Huiru Peng
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zhongfu Ni
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Qixin Sun
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Weilong Guo
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China.
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Ouaja M, Bahri BA, Ferjaoui S, Medini M, Sripada UM, Hamza S. Unlocking the story of resistance to Zymoseptoria tritici in Tunisian old durum wheat germplasm based on population structure analysis. BMC Genomics 2023; 24:328. [PMID: 37322410 PMCID: PMC10268414 DOI: 10.1186/s12864-023-09395-1] [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: 05/01/2022] [Accepted: 05/20/2023] [Indexed: 06/17/2023] Open
Abstract
BACKGROUND Septoria tritici blotch (STB) remains a significant obstacle to durum wheat cultivation on a global scale. This disease remains a challenge for farmers, researchers, and breeders, who are collectively dedicated to reduce its damage and improve wheat resistance. Tunisian durum wheat landraces have been recognized as valuable genetic ressources that exhibit resistance to biotic and abiotic stresses and therefore play a crucial role in breeding program aimed at creating new wheat varieties resistant to fungal diseases as STB, as well as adapted to climate change constraints. RESULTS A total of 366 local durum wheat accessions were assessed for resistance to two virulent Tunisian isolates of Zymoseptoria tritici Tun06 and TM220 under field conditions. Population structure analysis of the durum wheat accessions, performed with 286 polymorphic SNPs (PIC > 0.3) covering the entire genome, identified three genetic subpopulations (GS1, GS2 and GS3) with 22% of admixed genotypes. Interestingly, all of the resistant genotypes were among GS2 or admixed with GS2. CONCLUSIONS This study revealed the population structure and the genetic distribution of the resistance to Z. tritici in the Tunisian durum wheat landraces. Accessions grouping pattern reflected the geographical origins of the landraces. We suggested that GS2 accessions were mostly derived from eastern Mediterranean populations, unlike GS1 and GS3 that originated from the west. Resistant GS2 accessions belonged to landraces Taganrog, Sbei glabre, Richi, Mekki, Badri, Jneh Khotifa and Azizi. Furthermore, we suggested that admixture contributed to transmit STB resistance from GS2 resistant landraces to initially susceptible landraces such as Mahmoudi (GS1), but also resulted in the loss of resistance in the case of GS2 susceptible Azizi and Jneh Khotifa accessions.
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Affiliation(s)
- Maroua Ouaja
- Department of agronomy and plant biotechnology, Laboratory of genetics and cereal breeding (LR14AGR01), The National Agronomic Institute of Tunisia (INAT), University of Carthage, 43 Avenue Charles-Nicolle, Tunis, 1082, Tunisia
| | - Bochra A Bahri
- Department of agronomy and plant biotechnology, Laboratory of genetics and cereal breeding (LR14AGR01), The National Agronomic Institute of Tunisia (INAT), University of Carthage, 43 Avenue Charles-Nicolle, Tunis, 1082, Tunisia
- Department of Plant Pathology, Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Griffin, GA, 30223, USA
| | - Sahbi Ferjaoui
- Field Crops Laboratory, Regional Field Crops Research Center of Beja (CRRGC), P.O. Box 350, Beja, 9000, Tunisia
| | - Maher Medini
- Banque Nationale des Gènes (BNG), Boulevard du Leader Yasser Arafat Z. I Charguia 1, Tunis, 1080, Tunisie
| | - Udupa M Sripada
- International Center for Agricultural Research in the Dry Areas (ICARDA), Avenue Hafiane Cherkaoui, Rabat, Marocco
| | - Sonia Hamza
- Department of agronomy and plant biotechnology, Laboratory of genetics and cereal breeding (LR14AGR01), The National Agronomic Institute of Tunisia (INAT), University of Carthage, 43 Avenue Charles-Nicolle, Tunis, 1082, Tunisia.
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5
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Abstract
Plant life defines the environments to which animals adapt and provides the basis of food webs. This was equally true for hunter-gatherer economies of ancestral humans, yet through the domestication of plants and the creation of agricultural ecologies based around them, human societies transformed vegetation and transported plant taxa into new geographical regions. These human-plant interactions ultimately co-evolved, increasing human population densities, technologies of farming, and the diversification of landraces and crop complexes. Research in archaeology on preserved plant remains (archaeobotany) and on the genomes of crops, including ancient genomes, has transformed our scientific understanding of the complex relationships between humans and plants that are entailed by domestication. Key realizations of recent research include the recognition that: the co-evolution of domesticates and cultures was protracted, the adaptations of plant populations were unintended results of human economies rather than intentional breeding, domestication took place in dozens of world regions involving different crops and cultures, and convergent evolution can be recognized among cropping types - such as among seed crops, tuber crops, and fruit trees. Seven general domestication pathways can be defined for plants. Lessons for the present-day include: the importance of diversity in the past; genetic diversity within species has the potential to erode over time, but also to be rescued through processes of integration; similarly, diversification within agricultural ecosystems has undergone processes of decline, including marginalised, lost and 'forgotten' crops, as well as processes of renewal resulting from trade and human mobility that brought varied crops and varieties together.
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Affiliation(s)
- Dorian Q Fuller
- Institute of Archaeology, University College London (UCL), London, UK; School of Cultural Heritage, Northwest University, Xi'an, Shaanxi, China.
| | - Tim Denham
- School of Archaeology and Anthropology, The Australian National University, Canberra, Australia
| | - Robin Allaby
- School of Life Sciences, University of Warwick, Coventry, UK
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Strejčková B, Mazzucotelli E, Čegan R, Milec Z, Brus J, Çakır E, Mastrangelo AM, Özkan H, Šafář J. Wild emmer wheat, the progenitor of modern bread wheat, exhibits great diversity in the VERNALIZATION1 gene. FRONTIERS IN PLANT SCIENCE 2023; 13:1106164. [PMID: 36684759 PMCID: PMC9853909 DOI: 10.3389/fpls.2022.1106164] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 12/16/2022] [Indexed: 06/17/2023]
Abstract
Wild emmer wheat is an excellent reservoir of genetic variability that can be utilized to improve cultivated wheat to address the challenges of the expanding world population and climate change. Bearing this in mind, we have collected a panel of 263 wild emmer wheat (WEW) genotypes across the Fertile Crescent. The genotypes were grown in different locations and phenotyped for heading date. Genome-wide association mapping (GWAS) was carried out, and 16 SNPs were associated with the heading date. As the flowering time is controlled by photoperiod and vernalization, we sequenced the VRN1 gene, the most important of the vernalization response genes, to discover new alleles. Unlike most earlier attempts, which characterized known VRN1 alleles according to a partial promoter or intron sequences, we obtained full-length sequences of VRN-A1 and VRN-B1 genes in a panel of 95 wild emmer wheat from the Fertile Crescent and uncovered a significant sequence variation. Phylogenetic analysis of VRN-A1 and VRN-B1 haplotypes revealed their evolutionary relationships and geographic distribution in the Fertile Crescent region. The newly described alleles represent an attractive resource for durum and bread wheat improvement programs.
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Affiliation(s)
- Beáta Strejčková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University Olomouc, Olomouc, Czechia
| | - Elisabetta Mazzucotelli
- Council for Agricultural Research and Economics (CREA) Research Centre for Genomics and Bioinformatics via San Protaso 302, Fiorenzuola d’Arda, Italy
| | - Radim Čegan
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, ;Czechia
| | - Zbyněk Milec
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Jan Brus
- Department of Geoinformatics, Faculty of Science, Palacký University Olomouc, Olomouc, Czechia
| | - Esra Çakır
- Department of Field Crops, Faculty of Agriculture, University of Çukurova, Adana, Turkey
| | - Anna Maria Mastrangelo
- Council for Agricultural Research and Economics (CREA) Research Centre for Cereal and Industrial Crops, Foggia, Italy
| | - Hakan Özkan
- Department of Field Crops, Faculty of Agriculture, University of Çukurova, Adana, Turkey
| | - Jan Šafář
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
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7
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Wang Z, Wang W, Xie X, Wang Y, Yang Z, Peng H, Xin M, Yao Y, Hu Z, Liu J, Su Z, Xie C, Li B, Ni Z, Sun Q, Guo W. Dispersed emergence and protracted domestication of polyploid wheat uncovered by mosaic ancestral haploblock inference. Nat Commun 2022; 13:3891. [PMID: 35794156 PMCID: PMC9259585 DOI: 10.1038/s41467-022-31581-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 06/23/2022] [Indexed: 12/15/2022] Open
Abstract
Major crops are all survivors of domestication bottlenecks. Studies have focused on the genetic loci related to the domestication syndrome, while the contribution of ancient haplotypes remains largely unknown. Here, an ancestral genomic haploblock dissection method is developed and applied to a resequencing dataset of 386 tetraploid/hexaploid wheat accessions, generating a pan-ancestry haploblock map. Together with cytoplastic evidences, we reveal that domesticated polyploid wheat emerged from the admixture of six founder wild emmer lineages, which contributed the foundation of ancestral mosaics. The key domestication-related loci, originated over a wide geographical range, were gradually pyramided through a protracted process. Diverse stable-inheritance ancestral haplotype groups of the chromosome central zone are identified, revealing the expanding routes of wheat and the trends of modern wheat breeding. Finally, an evolution model of polyploid wheat is proposed, highlighting the key role of wild-to-crop and interploidy introgression, that increased genomic diversity following bottlenecks introduced by domestication and polyploidization.
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Affiliation(s)
- Zihao Wang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Wenxi Wang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Xiaoming Xie
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Yongfa Wang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zhengzhao Yang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Huiru Peng
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China
| | - Mingming Xin
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China
| | - Yingyin Yao
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China
| | - Zhaorong Hu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China
| | - Jie Liu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China
| | - Zhenqi Su
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China
| | - Chaojie Xie
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China
| | - Baoyun Li
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China.
- Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China.
| | - Weilong Guo
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China.
- Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China.
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8
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Levy AA, Feldman M. Evolution and origin of bread wheat. THE PLANT CELL 2022; 34:2549-2567. [PMID: 35512194 PMCID: PMC9252504 DOI: 10.1093/plcell/koac130] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 03/18/2022] [Indexed: 05/12/2023]
Abstract
Bread wheat (Triticum aestivum, genome BBAADD) is a young hexaploid species formed only 8,500-9,000 years ago through hybridization between a domesticated free-threshing tetraploid progenitor, genome BBAA, and Aegilops tauschii, the diploid donor of the D subgenome. Very soon after its formation, it spread globally from its cradle in the fertile crescent into new habitats and climates, to become a staple food of humanity. This extraordinary global expansion was probably enabled by allopolyploidy that accelerated genetic novelty through the acquisition of new traits, new intergenomic interactions, and buffering of mutations, and by the attractiveness of bread wheat's large, tasty, and nutritious grain with high baking quality. New genome sequences suggest that the elusive donor of the B subgenome is a distinct (unknown or extinct) species rather than a mosaic genome. We discuss the origin of the diploid and tetraploid progenitors of bread wheat and the conflicting genetic and archaeological evidence on where it was formed and which species was its free-threshing tetraploid progenitor. Wheat experienced many environmental changes throughout its evolution, therefore, while it might adapt to current climatic changes, efforts are needed to better use and conserve the vast gene pool of wheat biodiversity on which our food security depends.
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Affiliation(s)
- Avraham A Levy
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100 Israel
| | - Moshe Feldman
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100 Israel
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9
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Bajgain P, Brandvain Y, Anderson JA. Influence of Pollen Dispersal and Mating Pattern in Domestication of Intermediate Wheatgrass, a Novel Perennial Food Crop. FRONTIERS IN PLANT SCIENCE 2022; 13:871130. [PMID: 35574146 PMCID: PMC9096613 DOI: 10.3389/fpls.2022.871130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 04/11/2022] [Indexed: 06/15/2023]
Abstract
Intermediate wheatgrass (IWG) is a perennial forage grass that is currently being domesticated as a grain crop. It is a primarily wind-pollinated outcrossing species and expresses severe inbreeding depression when self-pollinated. Characterization of pollen dispersal, mating parameters, and change in genetic diversity due to pollen movement is currently lacking in IWG. In this study, we examined pollen dispersal in an IWG selection nursery by evaluating 846 progeny from 15 mother plants and traced their parentage to 374 fathers. A set of 2,500 genomic loci was used to characterize the population. We assigned paternity to 769 (91%) progeny and the average number of fathers per mother plant was 37, from an average of 56 progeny examined per mother. An extensive number (80%) of pollination events occurred within 10 m of the mother plants. Pollination success was not correlated with trait attributes of the paternal genotypes. Mating system analysis confirmed that IWG is highly outcrossing and inbreeding was virtually absent. Neither genetic diversity nor the genome-estimated trait values of progeny were significantly affected by pollinator distance. The distance of pollinator in an IWG breeding nursery therefore was not found to be a major contributor in maintaining genetic diversity. These findings reveal the pollen dispersal model in IWG for the first time and its effect on genetic diversity, which will be valuable in designing future IWG breeding populations. Information generated and discussed in this study could be applied in understanding gene flow and genetic diversity of other open-pollinated species.
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Affiliation(s)
- Prabin Bajgain
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, United States
| | - Yaniv Brandvain
- Department of Plant Biology, University of Minnesota, Saint Paul, MN, United States
| | - James A. Anderson
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, United States
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10
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Sun L, Song R, Wang Y, Wang X, Peng J, Nevo E, Ren X, Sun D. New insights into the evolution of CAF1 family and utilization of TaCAF1Ia1 specificity to reveal the origin of the maternal progenitor for common wheat. J Adv Res 2022; 42:135-148. [PMID: 36513409 PMCID: PMC9788937 DOI: 10.1016/j.jare.2022.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 03/19/2022] [Accepted: 04/08/2022] [Indexed: 12/27/2022] Open
Abstract
INTRODUCTION Until now, the most likely direct maternal progenitor (AABB) for common wheat (AABBDD) has yet to be identified. Here, we try to solve this particular problem with the specificity of a novel gene family in wheat and by using large population of rare germplasm resources. OBJECTIVES Dissect the novelty of TaCAF1Ia subfamily in wheat. Exploit the conservative and specific characteristics of TaCAF1Ia1 to reveal the origin of the maternal progenitor for common wheat. METHODS Phylogenetic and collinear analysis of TaCAF1 genes were performed to identify the evolutionary specificity of TaCAF1Ia subfamily. The large-scale expression patterns and interaction patterns analysis of CCR4-NOT complex were used to clarify the expressed and structural specificity of TaCAF1Ia subfamily in wheat. The population resequencing and phylogeny analysis of the TaCAF1Ia1 were utilized for the traceability analysis to understand gene-pool exchanges during the transferring and subsequent development from tetraploid to hexaploidy wheat. RESULTS TaCAF1Ia is a novel non-typical CAF1 subfamily without DEDD (Asp-Glu-Asp-Asp) domain, whose members were extensively duplicated in wheat genome. The replication events had started and constantly evolved from ancestor species. Specifically, it was found that a key member CAF1Ia1 was highly specialized and only existed in the subB genome and S genome. Unlike CAF1s reported in other plants, TaCAF1Ia genes may be new factors for anther development. These atypical TaCAF1s could also form CCR4-NOT complex in wheat but with new interaction sites. Utilizing the particular but conserved characteristics of the TaCAF1Ia1 gene, the comparative analysis of haplotypes composition for TaCAF1Ia1 were identified among wheat populations with different ploidy levels. Based on this, the dual-lineages origin model of maternal progenitor for common wheat and potential three-lineages domestication model for cultivated tetraploid wheat were proposed. CONCLUSION This study brings fresh insights for revealing the origin of wheat and the function of CAF1 in plants.
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Affiliation(s)
- Longqing Sun
- Hubei Hongshan Laboratory, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, Hubei, China,Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Ruilian Song
- Hubei Hongshan Laboratory, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yixiang Wang
- Hubei Hongshan Laboratory, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Xiaofang Wang
- Hubei Hongshan Laboratory, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Junhua Peng
- Germplasm Enhancement Department, Huazhi Biotech Institute, Changsa, Hunan, China
| | - Eviatar Nevo
- Institute of Evolution, University of Haifa, Mount Carmel, Haifa, Israel
| | - Xifeng Ren
- Hubei Hongshan Laboratory, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, Hubei, China,Corresponding authors.
| | - Dongfa Sun
- Hubei Hongshan Laboratory, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, Hubei, China,Corresponding authors.
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11
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Badaeva ED, Konovalov FA, Knüpffer H, Fricano A, Ruban AS, Kehel Z, Zoshchuk SA, Surzhikov SA, Neumann K, Graner A, Hammer K, Filatenko A, Bogaard A, Jones G, Özkan H, Kilian B. Genetic diversity, distribution and domestication history of the neglected GGA tA t genepool of wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:755-776. [PMID: 34283259 PMCID: PMC8942905 DOI: 10.1007/s00122-021-03912-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 07/07/2021] [Indexed: 05/03/2023]
Abstract
We present a comprehensive survey of cytogenetic and genomic diversity of the GGAtAt genepool of wheat, thereby unlocking these plant genetic resources for wheat improvement. Wheat yields are stagnating around the world and new sources of genes for resistance or tolerances to abiotic traits are required. In this context, the tetraploid wheat wild relatives are among the key candidates for wheat improvement. Despite its potential huge value for wheat breeding, the tetraploid GGAtAt genepool is largely neglected. Understanding the population structure, native distribution range, intraspecific variation of the entire tetraploid GGAtAt genepool and its domestication history would further its use for wheat improvement. The paper provides the first comprehensive survey of genomic and cytogenetic diversity sampling the full breadth and depth of the tetraploid GGAtAt genepool. According to the results obtained, the extant GGAtAt genepool consists of three distinct lineages. We provide detailed insights into the cytogenetic composition of GGAtAt wheats, revealed group- and population-specific markers and show that chromosomal rearrangements play an important role in intraspecific diversity of T. araraticum. The origin and domestication history of the GGAtAt lineages is discussed in the context of state-of-the-art archaeobotanical finds. We shed new light on the complex evolutionary history of the GGAtAt wheat genepool and provide the basis for an increased use of the GGAtAt wheat genepool for wheat improvement. The findings have implications for our understanding of the origins of agriculture in southwest Asia.
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Affiliation(s)
- Ekaterina D Badaeva
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia.
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
| | - Fedor A Konovalov
- Independent Clinical Bioinformatics Laboratory, Moscow, Russia
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Helmut Knüpffer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Agostino Fricano
- Council for Agricultural Research and Economics - Research Centre for Genomics & Bioinformatics, Fiorenzuola d'Arda (PC), Italy
| | - Alevtina S Ruban
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
- KWS SAAT SE & Co. KGaA, Einbeck, Germany
| | - Zakaria Kehel
- International Center for the Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
| | - Svyatoslav A Zoshchuk
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Sergei A Surzhikov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Kerstin Neumann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Andreas Graner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Karl Hammer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Anna Filatenko
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
- Independent Researcher, St. Petersburg, Russia
| | | | - Glynis Jones
- Department of Archaeology, University of Sheffield, Sheffield, UK
| | - Hakan Özkan
- Department of Field Crops, Faculty of Agriculture, University of Çukurova, Adana, Turkey
| | - Benjamin Kilian
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
- Global Crop Diversity Trust, Bonn, Germany
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12
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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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13
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Sharma S, Schulthess AW, Bassi FM, Badaeva ED, Neumann K, Graner A, Özkan H, Werner P, Knüpffer H, Kilian B. Introducing Beneficial Alleles from Plant Genetic Resources into the Wheat Germplasm. BIOLOGY 2021; 10:982. [PMID: 34681081 PMCID: PMC8533267 DOI: 10.3390/biology10100982] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 09/24/2021] [Accepted: 09/24/2021] [Indexed: 12/02/2022]
Abstract
Wheat (Triticum sp.) is one of the world's most important crops, and constantly increasing its productivity is crucial to the livelihoods of millions of people. However, more than a century of intensive breeding and selection processes have eroded genetic diversity in the elite genepool, making new genetic gains difficult. Therefore, the need to introduce novel genetic diversity into modern wheat has become increasingly important. This review provides an overview of the plant genetic resources (PGR) available for wheat. We describe the most important taxonomic and phylogenetic relationships of these PGR to guide their use in wheat breeding. In addition, we present the status of the use of some of these resources in wheat breeding programs. We propose several introgression schemes that allow the transfer of qualitative and quantitative alleles from PGR into elite germplasm. With this in mind, we propose the use of a stage-gate approach to align the pre-breeding with main breeding programs to meet the needs of breeders, farmers, and end-users. Overall, this review provides a clear starting point to guide the introgression of useful alleles over the next decade.
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Affiliation(s)
- Shivali Sharma
- Global Crop Diversity Trust, Platz der Vereinten Nationen 7, D-53113 Bonn, Germany; (S.S.); (P.W.)
| | - Albert W. Schulthess
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstr. 3, D-06466 Seeland, Germany; (A.W.S.); (K.N.); (A.G.); (H.K.)
| | - Filippo M. Bassi
- International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat 10112, Morocco;
| | - Ekaterina D. Badaeva
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia;
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), 630090 Novosibirsk, Russia
| | - Kerstin Neumann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstr. 3, D-06466 Seeland, Germany; (A.W.S.); (K.N.); (A.G.); (H.K.)
| | - Andreas Graner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstr. 3, D-06466 Seeland, Germany; (A.W.S.); (K.N.); (A.G.); (H.K.)
| | - Hakan Özkan
- Department of Field Crops, Faculty of Agriculture, University of Çukurova, Adana 01330, Turkey;
| | - Peter Werner
- Global Crop Diversity Trust, Platz der Vereinten Nationen 7, D-53113 Bonn, Germany; (S.S.); (P.W.)
| | - Helmut Knüpffer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstr. 3, D-06466 Seeland, Germany; (A.W.S.); (K.N.); (A.G.); (H.K.)
| | - Benjamin Kilian
- Global Crop Diversity Trust, Platz der Vereinten Nationen 7, D-53113 Bonn, Germany; (S.S.); (P.W.)
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14
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Civáň P, Drosou K, Armisen-Gimenez D, Duchemin W, Salse J, Brown TA. Episodes of gene flow and selection during the evolutionary history of domesticated barley. BMC Genomics 2021; 22:227. [PMID: 33794767 PMCID: PMC8015183 DOI: 10.1186/s12864-021-07511-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 03/05/2021] [Indexed: 02/08/2023] Open
Abstract
Background Barley is one of the founder crops of Neolithic agriculture and is among the most-grown cereals today. The only trait that universally differentiates the cultivated and wild subspecies is ‘non-brittleness’ of the rachis (the stem of the inflorescence), which facilitates harvesting of the crop. Other phenotypic differences appear to result from facultative or regional selective pressures. The population structure resulting from these regional events has been interpreted as evidence for multiple domestications or a mosaic ancestry involving genetic interaction between multiple wild or proto-domesticated lineages. However, each of the three mutations that confer non-brittleness originated in the western Fertile Crescent, arguing against multiregional origins for the crop. Results We examined exome data for 310 wild, cultivated and hybrid/feral barley accessions and showed that cultivated barley is structured into six genetically-defined groups that display admixture, resulting at least in part from two or more significant passages of gene flow with distinct wild populations. The six groups are descended from a single founding population that emerged in the western Fertile Crescent. Only a few loci were universally targeted by selection, the identity of these suggesting that changes in seedling emergence and pathogen resistance could represent crucial domestication switches. Subsequent selection operated on a regional basis and strongly contributed to differentiation of the genetic groups. Conclusions Identification of genetically-defined groups provides clarity to our understanding of the population history of cultivated barley. Inference of population splits and mixtures together with analysis of selection sweeps indicate descent from a single founding population, which emerged in the western Fertile Crescent. This founding population underwent relatively little genetic selection, those changes that did occur affecting traits involved in seedling emergence and pathogen resistance, indicating that these phenotypes should be considered as ‘domestication traits’. During its expansion out of the western Fertile Crescent, the crop underwent regional episodes of gene flow and selection, giving rise to a modern genetic signature that has been interpreted as evidence for multiple domestications, but which we show can be rationalized with a single origin. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07511-7.
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Affiliation(s)
- Peter Civáň
- Department of Earth and Environmental Sciences, Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, UK.,INRA-Université Clermont-Auvergne, UMR 1095 GDEC, 5 Chemin de Beaulieu, 63000, Clermont-Ferrand, France
| | - Konstantina Drosou
- Department of Earth and Environmental Sciences, Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, UK.,KNH Centre for Biomedical Egyptology, Faculty of Biology, Medicine and Health, University of Manchester, 99 Oxford Road, Manchester, M13 9PG, UK
| | - David Armisen-Gimenez
- INRA-Université Clermont-Auvergne, UMR 1095 GDEC, 5 Chemin de Beaulieu, 63000, Clermont-Ferrand, France.,Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, 69364, Lyon, France
| | - Wandrille Duchemin
- INRA-Université Clermont-Auvergne, UMR 1095 GDEC, 5 Chemin de Beaulieu, 63000, Clermont-Ferrand, France.,Center for Scientific Computing (sciCORE), University of Basel, Basel, Switzerland
| | - Jérôme Salse
- INRA-Université Clermont-Auvergne, UMR 1095 GDEC, 5 Chemin de Beaulieu, 63000, Clermont-Ferrand, France
| | - Terence A Brown
- Department of Earth and Environmental Sciences, Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, UK.
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15
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Oliveira HR, Jacocks L, Czajkowska BI, Kennedy SL, Brown TA. Multiregional origins of the domesticated tetraploid wheats. PLoS One 2020; 15:e0227148. [PMID: 31968001 PMCID: PMC6975532 DOI: 10.1371/journal.pone.0227148] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 12/12/2019] [Indexed: 12/21/2022] Open
Abstract
We used genotyping-by-sequencing (GBS) to investigate the evolutionary history of domesticated tetraploid wheats. With a panel of 189 wild and domesticated wheats, we identified 1,172,469 single nucleotide polymorphisms (SNPs) with a read depth ≥3. Principal component analyses (PCAs) separated the Triticum turgidum and Triticum timopheevii accessions, as well as wild T. turgidum from the domesticated emmers and the naked wheats, showing that SNP typing by GBS is capable of providing robust information on the genetic relationships between wheat species and subspecies. The PCAs and a neighbour-joining analysis suggested that domesticated tetraploid wheats have closest affinity with wild emmers from the northern Fertile Crescent, consistent with the results of previous genetic studies on the origins of domesticated wheat. However, a more detailed examination of admixture and allele sharing between domesticates and different wild populations, along with genome-wide association studies (GWAS), showed that the domesticated tetraploid wheats have also received a substantial genetic input from wild emmers from the southern Levant. Taking account of archaeological evidence that tetraploid wheats were first cultivated in the southern Levant, we suggest that a pre-domesticated crop spread from this region to southeast Turkey and became mixed with a wild emmer population from the northern Fertile Crescent. Fixation of the domestication traits in this mixed population would account for the allele sharing and GWAS results that we report. We also propose that feralization of the component of the pre-domesticated population that did not acquire domestication traits has resulted in the modern wild population from southeast Turkey displaying features of both the domesticates and wild emmer from the southern Levant, and hence appearing to be the sole progenitor of domesticated tetraploids when the phylogenetic relationships are studied by methods that assume a treelike pattern of evolution.
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Affiliation(s)
- Hugo R Oliveira
- School of Earth and Environmental Sciences, Manchester Institute of Biotechnology, University of Manchester, Manchester, England, United Kingdom
| | - Lauren Jacocks
- School of Earth and Environmental Sciences, Manchester Institute of Biotechnology, University of Manchester, Manchester, England, United Kingdom
| | - Beata I Czajkowska
- School of Earth and Environmental Sciences, Manchester Institute of Biotechnology, University of Manchester, Manchester, England, United Kingdom
| | - Sandra L Kennedy
- School of Earth and Environmental Sciences, Manchester Institute of Biotechnology, University of Manchester, Manchester, England, United Kingdom
| | - Terence A Brown
- School of Earth and Environmental Sciences, Manchester Institute of Biotechnology, University of Manchester, Manchester, England, United Kingdom
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16
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Scott MF, Botigué LR, Brace S, Stevens CJ, Mullin VE, Stevenson A, Thomas MG, Fuller DQ, Mott R. A 3,000-year-old Egyptian emmer wheat genome reveals dispersal and domestication history. NATURE PLANTS 2019; 5:1120-1128. [PMID: 31685951 PMCID: PMC6858886 DOI: 10.1038/s41477-019-0534-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 09/22/2019] [Indexed: 05/05/2023]
Abstract
Tetraploid emmer wheat (Triticum turgidum ssp. dicoccon) is a progenitor of the world's most widely grown crop, hexaploid bread wheat (Triticum aestivum), as well as the direct ancestor of tetraploid durum wheat (T. turgidum subsp. turgidum). Emmer was one of the first cereals to be domesticated in the old world; it was cultivated from around 9700 BC in the Levant1,2 and subsequently in south-western Asia, northern Africa and Europe with the spread of Neolithic agriculture3,4. Here, we report a whole-genome sequence from a museum specimen of Egyptian emmer wheat chaff, 14C dated to the New Kingdom, 1130-1000 BC. Its genome shares haplotypes with modern domesticated emmer at loci that are associated with shattering, seed size and germination, as well as within other putative domestication loci, suggesting that these traits share a common origin before the introduction of emmer to Egypt. Its genome is otherwise unusual, carrying haplotypes that are absent from modern emmer. Genetic similarity with modern Arabian and Indian emmer landraces connects ancient Egyptian emmer with early south-eastern dispersals, whereas inferred gene flow with wild emmer from the Southern Levant signals a later connection. Our results show the importance of museum collections as sources of genetic data to uncover the history and diversity of ancient cereals.
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Affiliation(s)
- Michael F Scott
- Genetics Institute, Research Department of Genetics, Evolution and Environment, University College London, London, UK.
| | - Laura R Botigué
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Selina Brace
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Chris J Stevens
- Institute of Archaeology, University College London, London, UK
| | | | - Alice Stevenson
- Institute of Archaeology, University College London, London, UK
| | - Mark G Thomas
- Genetics Institute, Research Department of Genetics, Evolution and Environment, University College London, London, UK
- Research Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Dorian Q Fuller
- Institute of Archaeology, University College London, London, UK
| | - Richard Mott
- Genetics Institute, Research Department of Genetics, Evolution and Environment, University College London, London, UK.
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17
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Pont C, Leroy T, Seidel M, Tondelli A, Duchemin W, Armisen D, Lang D, Bustos-Korts D, Goué N, Balfourier F, Molnár-Láng M, Lage J, Kilian B, Özkan H, Waite D, Dyer S, Letellier T, Alaux M, Russell J, Keller B, van Eeuwijk F, Spannagl M, Mayer KFX, Waugh R, Stein N, Cattivelli L, Haberer G, Charmet G, Salse J. Tracing the ancestry of modern bread wheats. Nat Genet 2019; 51:905-911. [PMID: 31043760 DOI: 10.1038/s41588-019-0393-z] [Citation(s) in RCA: 154] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 03/13/2019] [Indexed: 11/10/2022]
Abstract
For more than 10,000 years, the selection of plant and animal traits that are better tailored for human use has shaped the development of civilizations. During this period, bread wheat (Triticum aestivum) emerged as one of the world's most important crops. We use exome sequencing of a worldwide panel of almost 500 genotypes selected from across the geographical range of the wheat species complex to explore how 10,000 years of hybridization, selection, adaptation and plant breeding has shaped the genetic makeup of modern bread wheats. We observe considerable genetic variation at the genic, chromosomal and subgenomic levels, and use this information to decipher the likely origins of modern day wheats, the consequences of range expansion and the allelic variants selected since its domestication. Our data support a reconciled model of wheat evolution and provide novel avenues for future breeding improvement.
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Affiliation(s)
- Caroline Pont
- INRA-Université Clermont Auvergne, Clermont-Ferrand, France
| | - Thibault Leroy
- INRA-Université de Bordeaux, Cestas, France.,ISEM, Université de Montpellier, CNRS, IRD, EPHE, Place Eugène Bataillon, Montpellier, France
| | | | - Alessandro Tondelli
- Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
| | | | - David Armisen
- INRA-Université Clermont Auvergne, Clermont-Ferrand, France
| | - Daniel Lang
- PGSB, Helmholtz Center Munich, Neuherberg, Germany
| | - Daniela Bustos-Korts
- Wageningen University & Research, Biometris, Applied Statistics, Wageningen, the Netherlands
| | - Nadia Goué
- INRA-Université Clermont Auvergne, Clermont-Ferrand, France.,Plateforme Auvergne Bioinformatique, Mésocentre, Université Clermont Auvergne, Aubière, France
| | | | - Márta Molnár-Láng
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Hungary
| | | | - Benjamin Kilian
- Global Crop Diversity Trust, Bonn, Germany.,Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Hakan Özkan
- University of Çukurova, Faculty of Agriculture, Department of Field Crops, Adana, Turkey
| | - Darren Waite
- Earlham Institute, Norwich Research Park, Norwich, UK
| | | | | | - Michael Alaux
- URGI, INRA, Université Paris-Saclay, Versailles, France
| | | | | | - Beat Keller
- Department of Plant and Microbial Biology, University of Zurich, Zürich, Switzerland
| | - Fred van Eeuwijk
- Wageningen University & Research, Biometris, Applied Statistics, Wageningen, the Netherlands
| | | | - Klaus F X Mayer
- PGSB, Helmholtz Center Munich, Neuherberg, Germany.,School of Life Sciences, Technical University Munich, Weihenstephan, Germany
| | - Robbie Waugh
- The James Hutton Institute, Invergowrie, Dundee, UK.,The University of Dundee, Division of Plant Sciences, School of Life Sciences, Dundee, UK.,School of Agriculture, Food and Wine, University of Adelaide, Adelaide, South Australia, Australia
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
| | | | - Gilles Charmet
- INRA-Université Clermont Auvergne, Clermont-Ferrand, France
| | - Jérôme Salse
- INRA-Université Clermont Auvergne, Clermont-Ferrand, France.
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18
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A discriminatory test for the wheat B and G genomes reveals misclassified accessions of Triticum timopheevii and Triticum turgidum. PLoS One 2019; 14:e0215175. [PMID: 30969996 PMCID: PMC6457550 DOI: 10.1371/journal.pone.0215175] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Accepted: 03/27/2019] [Indexed: 11/22/2022] Open
Abstract
The tetraploid wheat species Triticum turgidum and Triticum timopheevii are morphologically similar, and misidentification of material collected from the wild is possible. We compared published sequences for the Ppd-A1, Ppd-B1 and Ppd-G1 genes from multiple accessions of T. turgidum and T. timopheevii and devised a set of four polymerase chain reactions (PCRs), two specific for Ppd-B1 and two for Ppd-G1. We used these PCRs with 51 accessions of T. timopheevii and 20 of T. turgidum. Sixty of these accessions gave PCR products consistent with their taxon identifications, but the other eleven accessions gave anomalous results: ten accessions that were classified as T. turgidum were identified as T. timopheevii by the PCRs, and one T. timopheevii accession was typed as T. turgidum. We believe that these anomalies are not due to errors in the PCR tests because the results agree with a more comprehensive analysis of genome-wide single nucleotide polymorphisms, which similarly suggest that these eleven accessions have been misclassified. Our results therefore show that the accepted morphological tests for discrimination between T. turgidum and T. timopheevii might not be entirely robust, but that species identification can be made cheaply and quickly by PCRs directed at the Ppd-1 gene.
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19
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Haas M, Schreiber M, Mascher M. Domestication and crop evolution of wheat and barley: Genes, genomics, and future directions. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:204-225. [PMID: 30414305 DOI: 10.1111/jipb.12737] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 10/27/2018] [Indexed: 05/02/2023]
Abstract
Wheat and barley are two of the founder crops of the agricultural revolution that took place 10,000 years ago in the Fertile Crescent and both crops remain among the world's most important crops. Domestication of these crops from their wild ancestors required the evolution of traits useful to humans, rather than survival in their natural environment. Of these traits, grain retention and threshability, yield improvement, changes to photoperiod sensitivity and nutritional value are most pronounced between wild and domesticated forms. Knowledge about the geographical origins of these crops and the genes responsible for domestication traits largely pre-dates the era of next-generation sequencing, although sequencing will lead to new insights. Molecular markers were initially used to calculate distance (relatedness), genetic diversity and to generate genetic maps which were useful in cloning major domestication genes. Both crops are characterized by large, complex genomes which were long thought to be beyond the scope of whole-genome sequencing. However, advances in sequencing technologies have improved the state of genomic resources for both wheat and barley. The availability of reference genomes for wheat and some of its progenitors, as well as for barley, sets the stage for answering unresolved questions in domestication genomics of wheat and barley.
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Affiliation(s)
- Matthew Haas
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, 06466 Seeland, Germany
| | - Mona Schreiber
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, 06466 Seeland, Germany
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, 06466 Seeland, Germany
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
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20
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Hunt HV, Rudzinski A, Jiang H, Wang R, Thomas MG, Jones MK. Genetic evidence for a western Chinese origin of broomcorn millet ( Panicum miliaceum). THE HOLOCENE 2018; 28:1968-1978. [PMID: 30542237 PMCID: PMC6236650 DOI: 10.1177/0959683618798116] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 07/27/2018] [Indexed: 05/10/2023]
Abstract
Broomcorn millet (Panicum miliaceum) is a key domesticated cereal that has been associated with the north China centre of agricultural origins. Early archaeobotanical evidence for this crop has generated two major debates. First, its contested presence in pre-7000 cal. BP sites in eastern Europe has admitted the possibility of a western origin. Second, its occurrence in the 7th and 8th millennia cal. BP in diverse regions of northern China is consistent with several possible origin foci, associated with different Neolithic cultures. We used microsatellite and granule-bound starch synthase I (GBSSI) genotype data from 341 landrace samples across Eurasia, including 195 newly genotyped samples from China, to address these questions. A spatially explicit discriminative modelling approach favours an eastern Eurasian origin for the expansion of broomcorn millet. This is consistent with recent archaeobotanical and chronological re-evaluations, and stable isotopic data. The same approach, together with the distribution of GBSSI alleles, is also suggestive that the origin of broomcorn millet expansion was in western China. This second unexpected finding stimulates new questions regarding the ecology of wild millet and vegetation dynamics in China prior to the mid-Holocene domestication of millet. The chronological relationship between population expansion and domestication is unclear, but our analyses are consistent with the western Loess Plateau being at least one region of primary domestication of broomcorn millet. Patterns of genetic variation indicate that this region was the source of populations to the west in Eurasia, which broomcorn probably reached via the Inner Asia Mountain Corridor from the 3rd millennium BC. A secondary westward expansion along the steppe may have taken place from the 2nd millennium BC.
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Affiliation(s)
- Harriet V Hunt
- McDonald Institute for Archaeological
Research, University of Cambridge, UK
| | - Anna Rudzinski
- Research Department of Genetics,
Evolution and Environment, University College London, UK
| | - Hongen Jiang
- Department of Archaeology and
Anthropology, University of Chinese Academy of Sciences, China
| | - Ruiyun Wang
- College of Agriculture, Shanxi
Agricultural University, China
- Institute of Crop Germplasm Resources of
Shanxi Academy of Agricultural Sciences, Key Laboratory of Crop Gene Resources and
Germplasm Enhancement on Loess Plateau, Ministry of Agriculture, Shanxi Key
Laboratory of Genetic Resources and Genetic Improvement of Minor Crops, China
| | - Mark G Thomas
- Research Department of Genetics,
Evolution and Environment, University College London, UK
- UCL Genetics Institute, University
College London, UK
| | - Martin K Jones
- Department of Archaeology and
Anthropology, University of Cambridge, UK
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21
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Trněný O, Brus J, Hradilová I, Rathore A, Das RR, Kopecký P, Coyne CJ, Reeves P, Richards C, Smýkal P. Molecular Evidence for Two Domestication Events in the Pea Crop. Genes (Basel) 2018; 9:genes9110535. [PMID: 30404223 PMCID: PMC6265838 DOI: 10.3390/genes9110535] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 10/25/2018] [Accepted: 10/29/2018] [Indexed: 12/02/2022] Open
Abstract
Pea, one of the founder crops from the Near East, has two wild species: Pisum sativum subsp. elatius, with a wide distribution centered in the Mediterranean, and P. fulvum, which is restricted to Syria, Lebanon, Israel, Palestine and Jordan. Using genome wide analysis of 11,343 polymorphic single nucleotide polymorphisms (SNPs) on a set of wild P. elatius (134) and P. fulvum (20) and 74 domesticated accessions (64 P. sativum landraces and 10 P. abyssinicum), we demonstrated that domesticated P. sativum and the Ethiopian pea (P. abyssinicum) were derived from different P. elatius genepools. Therefore, pea has at least two domestication events. The analysis does not support a hybrid origin of P. abyssinicum, which was likely introduced into Ethiopia and Yemen followed by eco-geographic adaptation. Both P. sativum and P. abyssinicum share traits that are typical of domestication, such as non-dormant seeds. Non-dormant seeds were also found in several wild P. elatius accessions which could be the result of crop to wild introgression or natural variation that may have been present during pea domestication. A sub-group of P. elatius overlaps with P. sativum landraces. This may be a consequence of bidirectional gene-flow or may suggest that this group of P. elatius is the closest extant wild relative of P. sativum.
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Affiliation(s)
- Oldřich Trněný
- Agricultural Research Ltd., 66441 Troubsko, Czech Republic.
| | - Jan Brus
- Department of Geoinformatics, Palacký University, 783 71 Olomouc, Czech Republic.
| | - Iveta Hradilová
- Department of Botany, Palacký University, 783 71 Olomouc, Czech Republic.
| | - Abhishek Rathore
- The International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, Telangana 502324, India.
| | - Roma R Das
- The International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, Telangana 502324, India.
| | - Pavel Kopecký
- Crop Research Institute, The Centre of the Region Haná for biotechnological and Agricultural Research, 783 71 Olomouc, Czech Republic.
| | - Clarice J Coyne
- United States Department of Agriculture, Washington State University, Pullman, WA 99164-6402, USA.
| | - Patrick Reeves
- United States Department of Agriculture, National Laboratory for Genetic Resources Preservation, Fort Collins, CO 80521, USA.
| | - Christopher Richards
- United States Department of Agriculture, National Laboratory for Genetic Resources Preservation, Fort Collins, CO 80521, USA.
| | - Petr Smýkal
- Department of Botany, Palacký University, 783 71 Olomouc, Czech Republic.
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Abstract
Humans have domesticated hundreds of plant and animal species as sources of food, fiber, forage, and tools over the past 12,000 years, with manifold effects on both human society and the genetic structure of the domesticated species. The outcomes of crop domestication were shaped by selection driven by human preferences, cultivation practices, and agricultural environments, as well as other population genetic processes flowing from the ensuing reduction in effective population size. It is obvious that any selection imposes a reduction of diversity, favoring preferred genotypes, such as nonshattering seeds or increased palatability. Furthermore, agricultural practices greatly reduced effective population sizes of crops, allowing genetic drift to alter genotype frequencies. Current advances in molecular technologies, particularly of genome sequencing, provide evidence of human selection acting on numerous loci during and after crop domestication. Population-level molecular analyses also enable us to clarify the demographic histories of the domestication process itself, which, together with expanded archaeological studies, can illuminate the origins of crops. Domesticated plant species are found in 160 taxonomic families. Approximately 2500 species have undergone some degree of domestication, and 250 species are considered to be fully domesticated. The evolutionary trajectory from wild to crop species is a complex process. Archaeological records suggest that there was a period of predomestication cultivation while humans first began the deliberate planting of wild stands that had favorable traits. Later, crops likely diversified as they were grown in new areas, sometimes beyond the climatic niche of their wild relatives. However, the speed and level of human intentionality during domestication remains a topic of active discussion. These processes led to the so-called domestication syndrome, that is, a group of traits that can arise through human preferences for ease of harvest and growth advantages under human propagation. These traits included reduced dispersal ability of seeds and fruits, changes to plant structure, and changes to plant defensive characteristics and palatability. Domestication implies the action of selective sweeps on standing genetic variation, as well as new genetic variation introduced via mutation or introgression. Furthermore, genetic bottlenecks during domestication or during founding events as crops moved away from their centers of origin may have further altered gene pools. To date, a few hundred genes and loci have been identified by classical genetic and association mapping as targets of domestication and postdomestication divergence. However, only a few of these have been characterized, and for even fewer is the role of the wild-type allele in natural populations understood. After domestication, only favorable haplotypes are retained around selected genes, which creates a genetic valley with extremely low genetic diversity. These “selective sweeps” can allow mildly deleterious alleles to come to fixation and may create a genetic load in the cultivated gene pool. Although the population-wide genomic consequences of domestication offer several predictions for levels of the genetic diversity in crops, our understanding of how this diversity corresponds to nutritional aspects of crops is not well understood. Many studies have found that modern cultivars have lower levels of key micronutrients and vitamins. We suspect that selection for palatability and increased yield at domestication and during postdomestication divergence exacerbated the low nutrient levels of many crops, although relatively little work has examined this question. Lack of diversity in modern germplasm may further limit our capacity to breed for higher nutrient levels, although little effort has gone into this beyond a handful of staple crops. This is an area where an understanding of domestication across many crop taxa may provide the necessary insight for breeding more nutritious crops in a rapidly changing world.
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Allaby RG, Stevens C, Lucas L, Maeda O, Fuller DQ. Geographic mosaics and changing rates of cereal domestication. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0429. [PMID: 29061901 DOI: 10.1098/rstb.2016.0429] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/02/2017] [Indexed: 11/12/2022] Open
Abstract
Domestication is the process by which plants or animals evolved to fit a human-managed environment, and it is marked by innovations in plant morphology and anatomy that are in turn correlated with new human behaviours and technologies for harvesting, storage and field preparation. Archaeobotanical evidence has revealed that domestication was a protracted process taking thousands of plant generations. Within this protracted process there were changes in the selection pressures for domestication traits as well as variation across a geographic mosaic of wild and cultivated populations. Quantitative data allow us to estimate the changing selection coefficients for the evolution of non-shattering (domestic-type seed dispersal) in Asian rice (Oryza sativa L.), barley (Hordeum vulgare L.), emmer wheat (Triticum dicoccon (Shrank) Schübl.) and einkorn wheat (Triticum monococcum L.). These data indicate that selection coefficients tended to be low, but also that there were inflection points at which selection increased considerably. For rice, selection coefficients of the order of 0.001 prior to 5500 BC shifted to greater than 0.003 between 5000 and 4500 BC, before falling again as the domestication process ended 4000-3500 BC. In barley and the two wheats selection was strongest between 8500 and 7500 BC. The slow start of domestication may indicate that initial selection began in the Pleistocene glacial era.This article is part of the themed issue 'Process and pattern in innovations from cells to societies'.
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Affiliation(s)
- Robin G Allaby
- School of Life Sciences, University of Warwick, Warwick, UK
| | | | | | - Osamu Maeda
- Institute for Comparative Research in Human and Social Sciences, University of Tsukuba, Tsukuba, Japan
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24
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Pankin A, Altmüller J, Becker C, von Korff M. Targeted resequencing reveals genomic signatures of barley domestication. THE NEW PHYTOLOGIST 2018; 218:1247-1259. [PMID: 29528492 PMCID: PMC5947139 DOI: 10.1111/nph.15077] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 02/05/2018] [Indexed: 05/18/2023]
Abstract
Barley (Hordeum vulgare) is an established model to study domestication of the Fertile Crescent cereals. Recent molecular data suggested that domesticated barley genomes consist of the ancestral blocks descending from multiple wild barley populations. However, the relationship between the mosaic ancestry patterns and the process of domestication itself remained unclear. To address this knowledge gap, we identified candidate domestication genes using selection scans based on targeted resequencing of 433 wild and domesticated barley accessions. We conducted phylogenetic, population structure, and ancestry analyses to investigate the origin of the domesticated barley haplotypes separately at the neutral and candidate domestication loci. We discovered multiple selective sweeps that occurred on all barley chromosomes during domestication in the background of several ancestral wild populations. The ancestry analyses demonstrated that, although the ancestral blocks of the domesticated barley genomes were descended from all over the Fertile Crescent, the candidate domestication loci originated specifically in its eastern and western parts. These findings provided the first molecular evidence implicating multiple wild or protodomesticated lineages in the process of barley domestication initiated in the Levantine and Zagros clusters of the origin of agriculture.
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Affiliation(s)
- Artem Pankin
- Institute of Plant GeneticsHeinrich‐Heine‐University40225DüsseldorfGermany
- Max Planck Institute for Plant Breeding Research50829CologneGermany
| | - Janine Altmüller
- Cologne Center for Genomics (CCG)University of Cologne50931CologneGermany
| | - Christian Becker
- Cologne Center for Genomics (CCG)University of Cologne50931CologneGermany
| | - Maria von Korff
- Institute of Plant GeneticsHeinrich‐Heine‐University40225DüsseldorfGermany
- Max Planck Institute for Plant Breeding Research50829CologneGermany
- Cluster of Excellence on Plant Sciences ‘From Complex Traits towards Synthetic Modules’Heinrich‐Heine‐University40225DüsseldorfGermany
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25
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Luo G, Song S, Zhao L, Shen L, Song Y, Wang X, Yu K, Liu Z, Li Y, Yang W, Li X, Zhan K, Zhang A, Liu D. Mechanisms, origin and heredity of Glu-1Ay silencing in wheat evolution and domestication. THEORETICAL AND APPLIED GENETICS 2018; 131:1561-1575. [PMID: 29696298 DOI: 10.1007/s00122-018-3098-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 04/13/2018] [Indexed: 01/10/2023]
Abstract
KEY MESSAGE Allotetraploidization drives Glu-1Ay silencing in polyploid wheat. The high-molecular-weight glutenin subunit gene, Glu-1Ay, is always silenced in common wheat via elusive mechanisms. To investigate its silencing and heredity during wheat polyploidization and domestication, the Glu-1Ay gene was characterized in 1246 accessions containing diploid and polyploid wheat worldwide. Eight expressed Glu-1Ay alleles (in 71.81% accessions) and five silenced alleles with a premature termination codon (PTC) were identified in Triticum urartu; 4 expressed alleles (in 41.21% accessions), 13 alleles with PTCs and 1 allele with a WIS 2-1A retrotransposon were present in wild tetraploid wheat; and only silenced alleles with PTC or WIS 2-1A were in cultivated tetra- and hexaploid wheat. Both the PTC number and position in T. urartu Glu-1Ay alleles (one in the N-terminal region) differed from its progeny wild tetraploid wheat (1-5 PTCs mainly in the repetitive domain). The WIS 2-1A insertion occurred ~ 0.13 million years ago in wild tetraploid wheat, much later than the allotetraploidization event. The Glu-1Ay alleles with PTCs or WIS 2-1A that arose in wild tetraploid wheat were fully succeeded to cultivated tetraploid and hexaploid wheat. In addition, the Glu-1Ay gene in wild einkorn inherited to cultivated einkorn. Our data demonstrated that the silencing of Glu-1Ay in tetraploid and hexaploid wheat was attributed to the new PTCs and WIS 2-1A insertion in wild tetraploid wheat, and most silenced alleles were delivered to the cultivated tetraploid and hexaploid wheat, providing a clear evolutionary history of the Glu-1Ay gene in the wheat polyploidization and domestication processes.
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Affiliation(s)
- Guangbin Luo
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuyi Song
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101, China.,College of Agronomy, The Collaborative Innovation Center of Grain Crops in Henan, Henan Agricultural University, 63 Nongye Road, Zhengzhou, 450002, China
| | - Liru Zhao
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lisha Shen
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanhong Song
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101, China.,College of Agronomy, The Collaborative Innovation Center of Grain Crops in Henan, Henan Agricultural University, 63 Nongye Road, Zhengzhou, 450002, China
| | - Xin Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kang Yu
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101, China.,Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Fragrant Hill, Beijing, 100093, China
| | - Zhiyong Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101, China
| | - Yiwen Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101, China
| | - Wenlong Yang
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101, China
| | - Xin Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101, China
| | - Kehui Zhan
- College of Agronomy, The Collaborative Innovation Center of Grain Crops in Henan, Henan Agricultural University, 63 Nongye Road, Zhengzhou, 450002, China
| | - Aimin Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101, China. .,College of Agronomy, The Collaborative Innovation Center of Grain Crops in Henan, Henan Agricultural University, 63 Nongye Road, Zhengzhou, 450002, China.
| | - Dongcheng Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101, China.
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26
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Regional diversity on the timing for the initial appearance of cereal cultivation and domestication in southwest Asia. Proc Natl Acad Sci U S A 2018; 113:14001-14006. [PMID: 27930348 DOI: 10.1073/pnas.1612797113] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recent studies have broadened our knowledge regarding the origins of agriculture in southwest Asia by highlighting the multiregional and protracted nature of plant domestication. However, there have been few archaeobotanical data to examine whether the early adoption of wild cereal cultivation and the subsequent appearance of domesticated-type cereals occurred in parallel across southwest Asia, or if chronological differences existed between regions. The evaluation of the available archaeobotanical evidence indicates that during Pre-Pottery Neolithic A (PPNA) cultivation of wild cereal species was common in regions such as the southern-central Levant and the Upper Euphrates area, but the plant-based subsistence in the eastern Fertile Crescent (southeast Turkey, Iran, and Iraq) focused on the exploitation of plants such as legumes, goatgrass, fruits, and nuts. Around 10.7-10.2 ka Cal BP (early Pre-Pottery Neolithic B), the predominant exploitation of cereals continued in the southern-central Levant and is correlated with the appearance of significant proportions (∼30%) of domesticated-type cereal chaff in the archaeobotanical record. In the eastern Fertile Crescent exploitation of legumes, fruits, nuts, and grasses continued, and in the Euphrates legumes predominated. In these two regions domesticated-type cereal chaff (>10%) is not identified until the middle and late Pre-Pottery Neolithic B (10.2-8.3 ka Cal BP). We propose that the cultivation of wild and domesticated cereals developed at different times across southwest Asia and was conditioned by the regionally diverse plant-based subsistence strategies adopted by Pre-Pottery Neolithic groups.
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27
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Lundström M, Leino MW, Hagenblad J. Evolutionary history of the NAM-B1 gene in wild and domesticated tetraploid wheat. BMC Genet 2017; 18:118. [PMID: 29262777 PMCID: PMC5738170 DOI: 10.1186/s12863-017-0566-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 11/09/2017] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND The NAM-B1 gene in wheat has for almost three decades been extensively studied and utilized in breeding programs because of its significant impact on grain protein and mineral content and pleiotropic effects on senescence rate and grain size. First detected in wild emmer wheat, the wild-type allele of the gene has been introgressed into durum and bread wheat. Later studies have, however, also found the presence of the wild-type allele in some domesticated subspecies. In this study we trace the evolutionary history of the NAM-B1 in tetraploid wheat species and evaluate it as a putative domestication gene. RESULTS Genotyping of wild and landrace tetraploid accessions showed presence of only null alleles in durum. Domesticated emmer wheats contained both null alleles and the wild-type allele while wild emmers, with one exception, only carried the wild-type allele. One of the null alleles consists of a deletion that covers several 100 kb. The other null-allele, a one-basepair frame-shift insertion, likely arose among wild emmer. This allele was the target of a selective sweep, extending over several 100 kb. CONCLUSIONS The NAM-B1 gene fulfils some criteria for being a domestication gene by encoding a trait of domestication relevance (seed size) and is here shown to have been under positive selection. The presence of both wild-type and null alleles in domesticated emmer does, however, suggest the gene to be a diversification gene in this species. Further studies of genotype-environment interactions are needed to find out under what conditions selection on different NAM-B1 alleles have been beneficial.
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Affiliation(s)
- Maria Lundström
- Linköping University, IFM Biology, SE-581 83, Linköping, Sweden
| | - Matti W Leino
- Linköping University, IFM Biology, SE-581 83, Linköping, Sweden.,Nordiska museet, Swedish Museum of Cultural History, Box 27820, SE-115 93, Stockholm, Sweden.,The Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Jenny Hagenblad
- Linköping University, IFM Biology, SE-581 83, Linköping, Sweden.
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28
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Jorgensen C, Luo MC, Ramasamy R, Dawson M, Gill BS, Korol AB, Distelfeld A, Dvorak J. A High-Density Genetic Map of Wild Emmer Wheat from the Karaca Dağ Region Provides New Evidence on the Structure and Evolution of Wheat Chromosomes. FRONTIERS IN PLANT SCIENCE 2017; 8:1798. [PMID: 29104581 PMCID: PMC5655018 DOI: 10.3389/fpls.2017.01798] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 10/03/2017] [Indexed: 05/05/2023]
Abstract
Wild emmer (Triticum turgidum ssp. dicoccoides) is a progenitor of all cultivated wheat grown today. It has been hypothesized that emmer was domesticated in the Karaca Dağ region in southeastern Turkey. A total of 445 recombinant inbred lines of T. turgidum ssp. durum cv. 'Langdon' x wild emmer accession PI 428082 from this region was developed and genotyped with the Illumina 90K single nucleotide polymorphism Infinium assay. A genetic map comprising 2,650 segregating markers was constructed. The order of the segregating markers and an additional 8,264 co-segregating markers in the Aegilops tauschii reference genome sequence was used to compare synteny of the tetraploid wheat with the Brachypodium distachyon, rice, and sorghum. These comparisons revealed the presence of 15 structural chromosome rearrangements, in addition to the already known 4A-5A-7B rearrangements. The most common type was an intra-chromosomal translocation in which the translocated segment was short and was translocated only a short distance along the chromosome. A large reciprocal translocation, one small non-reciprocal translocation, and three large and one small paracentric inversions were also discovered. The use of inversions for a phylogeny reconstruction in the Triticum-Aegilops alliance was illustrated. The genetic map was inconsistent with the current model of evolution of the rearranged chromosomes 4A-5A-7B. Genetic diversity in the rearranged chromosome 4A showed that the rearrangements might have been contemporary with wild emmer speciation. A selective sweep was found in the centromeric region of chromosome 4A in Karaca Dağ wild emmer but not in 4A of T. aestivum. The absence of diversity from a large portion of chromosome 4A of wild emmer, believed to be ancestral to all domesticated wheat, is puzzling.
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Affiliation(s)
- Chad Jorgensen
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Ramesh Ramasamy
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Mathew Dawson
- Department of Statistics, University of California, Davis, Davis, CA, United States
| | - Bikram S. Gill
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | | | - Assaf Distelfeld
- Institute for Cereal Crops Improvement, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Jan Dvorak
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
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29
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High-precision chronology for Central American maize diversification from El Gigante rockshelter, Honduras. Proc Natl Acad Sci U S A 2017; 114:9026-9031. [PMID: 28784803 DOI: 10.1073/pnas.1705052114] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The first steps toward maize (Zea mays subspecies mays) domestication occurred in the Balsas region of Mexico by ∼9,000 calendar years B.P. (cal B.P.), but it remains unclear when maize was productive enough to be a staple grain in the Americas. Molecular and microbotanical data provide a partial picture of the timing and nature of morphological change, with genetic data indicating that alleles for some domestication traits were not yet fixed by 5,300 cal B.P. in the highlands of Mexico. Here, we report 88 radiocarbon dates on the botanical remains from El Gigante rockshelter (Honduras) to establish a Bayesian chronology over the past ∼11,000 y spanning the transition to maize-based food production. Botanical remains are remarkably well preserved and include over 10,000 maize macrofossils. We directly dated 37 maize cobs to establish the appearance and local change of maize at the site. Cobs are common in deposits dating between 4,340 and 4,020 cal B.P., and again between 2,350 and 980 cal B.P. The earliest cobs appear robustly domesticated, having 10-14 rows, suggesting strong selection for increased yield. The later cobs are comparable to these earliest ones, but show clear emergence of diverse traits, including increased cob width, rachis segment length, and cupule width. Our results indicate that domesticated landraces of maize productive enough to be a staple grain existed in Central America by 4,300 cal B.P.
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Civáň P, Brown TA. A novel mutation conferring the nonbrittle phenotype of cultivated barley. THE NEW PHYTOLOGIST 2017; 214:468-472. [PMID: 28092403 PMCID: PMC5347957 DOI: 10.1111/nph.14377] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 11/03/2016] [Indexed: 05/07/2023]
Abstract
The nonbrittle rachis, resulting in a seed head which does not shatter at maturity, is one of the key phenotypes that distinguishes domesticated barley from its wild relatives. The phenotype is associated with two loci, Btr1 and Btr2, with all domesticated barleys thought to have either a 1 bp deletion in Btr1 or an 11 bp deletion in Btr2. We used a PCR genotyping method with 380 domesticated barley landraces to identify those with the Btr1 deletion and those with the Btr2 deletion. We discovered two landraces, from Serbia and Greece, that had neither deletion. Instead these landraces possess a novel point mutation in Btr1, changing a leucine to a proline in the protein product. We confirmed that plants carrying this mutation have the nonbrittle phenotype and identified wild haplotypes from the Gaziantep region of southeast Turkey as the closest wild relatives of these two landraces. The presence of a third mutation conferring the nonbrittle phenotype of domesticated barley shows that the origin of this trait is more complex than previously thought, and is consistent with recent models that view the transition to agriculture in southwest Asia as a protracted and multiregional process.
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Affiliation(s)
- Peter Civáň
- School of Earth and Environmental SciencesManchester Institute of BiotechnologyUniversity of ManchesterManchesterM1 7DNUK
| | - Terence A. Brown
- School of Earth and Environmental SciencesManchester Institute of BiotechnologyUniversity of ManchesterManchesterM1 7DNUK
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Pankin A, von Korff M. Co-evolution of methods and thoughts in cereal domestication studies: a tale of barley (Hordeum vulgare). CURRENT OPINION IN PLANT BIOLOGY 2017; 36:15-21. [PMID: 28011443 DOI: 10.1016/j.pbi.2016.12.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 11/20/2016] [Accepted: 12/02/2016] [Indexed: 05/02/2023]
Abstract
Five major cereals such as wheat, rice, maize, barley and sorghum were among the first Neolithic crops that facilitated the establishment of the early agricultural societies. Since then they have remained the staple source of calories for the majority of the human population. Ample archaeological and molecular evidence has provided important insights into the domestication history of cereals but the debates on the origin of cereal crops are still far from resolved. Here, we review the recent advances in applying genome sequencing technologies for deciphering the history of cereal domestication. As a model example, we demonstrate that the evolution of thoughts on barley domestication closely followed the development of views on the rise of agriculture in the Near East in general and greatly accelerated with the advent of the genomic technologies and resources available for barley research.
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Affiliation(s)
- Artem Pankin
- Institute of Plant Genetics, Heinrich-Heine-University, 40225 Düsseldorf, Germany; Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany; Cluster of Excellence on Plant Sciences "From Complex Traits towards Synthetic Modules", 40225 Düsseldorf, Germany.
| | - Maria von Korff
- Institute of Plant Genetics, Heinrich-Heine-University, 40225 Düsseldorf, Germany; Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany; Cluster of Excellence on Plant Sciences "From Complex Traits towards Synthetic Modules", 40225 Düsseldorf, Germany.
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Lv GY, Guo XG, Xie LP, Xie CG, Zhang XH, Yang Y, Xiao L, Tang YY, Pan XL, Guo AG, Xu H. Molecular Characterization, Gene Evolution, and Expression Analysis of the Fructose-1, 6-bisphosphate Aldolase (FBA) Gene Family in Wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2017; 8:1030. [PMID: 28659962 PMCID: PMC5470051 DOI: 10.3389/fpls.2017.01030] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 05/29/2017] [Indexed: 05/17/2023]
Abstract
Fructose-1, 6-bisphosphate aldolase (FBA) is a key plant enzyme that is involved in glycolysis, gluconeogenesis, and the Calvin cycle. It plays significant roles in biotic and abiotic stress responses, as well as in regulating growth and development processes. In the present paper, 21 genes encoding TaFBA isoenzymes were identified, characterized, and categorized into three groups: class I chloroplast/plastid FBA (CpFBA), class I cytosol FBA (cFBA), and class II chloroplast/plastid FBA. By using a prediction online database and genomic PCR analysis of Chinese Spring nulli-tetrasomic lines, we have confirmed the chromosomal location of these genes in 12 chromosomes of four homologous groups. Sequence and genomic structure analysis revealed the high identity of the allelic TaFBA genes and the origin of different TaFBA genes. Numerous putative environment stimulus-responsive cis-elements have been identified in 1,500-bp regions of TaFBA gene promoters, of which the most abundant are the light-regulated elements (LREs). Phylogenetic reconstruction using the deduced protein sequence of 245 FBA genes indicated an independent evolutionary pathway for the class I and class II groups. Although, earlier studies have indicated that class II FBA only occurs in prokaryote and fungi, our results have demonstrated that a few class II CpFBAs exist in wheat and other closely related species. Class I TaFBA was predicted to be tetramers and class II to be dimers. Gene expression analysis based on microarray and transcriptome databases suggested the distinct role of TaFBAs in different tissues and developmental stages. The TaFBA 4-9 genes were highly expressed in leaves and might play important roles in wheat development. The differential expression patterns of the TaFBA genes in light/dark and a few abiotic stress conditions were also analyzed. The results suggested that LRE cis-elements of TaFBA gene promoters were not directly related to light responses. Most TaFBA genes had higher expression levels in the roots than in the shoots when under various stresses. Class I cytosol TaFBA genes, particularly TaFBA10/12/18 and TaFBA13/16, and three class II TaFBA genes are involved in responses to various abiotic stresses. Class I CpFBA genes in wheat are apparently sensitive to different stress conditions.
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Affiliation(s)
- Geng-Yin Lv
- College of Life Sciences, Northwest A & F UniversityYangling, China
| | - Xiao-Guang Guo
- College of Life Sciences, Northwest A & F UniversityYangling, China
| | - Li-Ping Xie
- College of Life Sciences, Northwest A & F UniversityYangling, China
| | - Chang-Gen Xie
- College of Life Sciences, Northwest A & F UniversityYangling, China
- State Key Laboratory of Crop Stress Biology for Arid AreasYangling, China
| | - Xiao-Hong Zhang
- College of Life Sciences, Northwest A & F UniversityYangling, China
| | - Yuan Yang
- College of Life Sciences, Northwest A & F UniversityYangling, China
| | - Lei Xiao
- College of Life Sciences, Northwest A & F UniversityYangling, China
| | - Yu-Ying Tang
- College of Life Sciences, Northwest A & F UniversityYangling, China
| | - Xing-Lai Pan
- Department of Food Crop Science, Cotton Research Institute, Shanxi Academy of Agricultural Sciences (CAAS)Yuncheng, China
| | - Ai-Guang Guo
- College of Life Sciences, Northwest A & F UniversityYangling, China
- State Key Laboratory of Crop Stress Biology for Arid AreasYangling, China
| | - Hong Xu
- College of Life Sciences, Northwest A & F UniversityYangling, China
- State Key Laboratory of Crop Stress Biology for Arid AreasYangling, China
- *Correspondence: Hong Xu
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Gourds and squashes (Cucurbita spp.) adapted to megafaunal extinction and ecological anachronism through domestication. Proc Natl Acad Sci U S A 2015; 112:15107-12. [PMID: 26630007 DOI: 10.1073/pnas.1516109112] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The genus Cucurbita (squashes, pumpkins, gourds) contains numerous domesticated lineages with ancient New World origins. It was broadly distributed in the past but has declined to the point that several of the crops' progenitor species are scarce or unknown in the wild. We hypothesize that Holocene ecological shifts and megafaunal extinctions severely impacted wild Cucurbita, whereas their domestic counterparts adapted to changing conditions via symbiosis with human cultivators. First, we used high-throughput sequencing to analyze complete plastid genomes of 91 total Cucurbita samples, comprising ancient (n = 19), modern wild (n = 30), and modern domestic (n = 42) taxa. This analysis demonstrates independent domestication in eastern North America, evidence of a previously unknown pathway to domestication in northeastern Mexico, and broad archaeological distributions of taxa currently unknown in the wild. Further, sequence similarity between distant wild populations suggests recent fragmentation. Collectively, these results point to wild-type declines coinciding with widespread domestication. Second, we hypothesize that the disappearance of large herbivores struck a critical ecological blow against wild Cucurbita, and we take initial steps to consider this hypothesis through cross-mammal analyses of bitter taste receptor gene repertoires. Directly, megafauna consumed Cucurbita fruits and dispersed their seeds; wild Cucurbita were likely left without mutualistic dispersal partners in the Holocene because they are unpalatable to smaller surviving mammals with more bitter taste receptor genes. Indirectly, megafauna maintained mosaic-like landscapes ideal for Cucurbita, and vegetative changes following the megafaunal extinctions likely crowded out their disturbed-ground niche. Thus, anthropogenic landscapes provided favorable growth habitats and willing dispersal partners in the wake of ecological upheaval.
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Resilience at the Transition to Agriculture: The Long-Term Landscape and Resource Development at the Aceramic Neolithic Tell Site of Chogha Golan (Iran). BIOMED RESEARCH INTERNATIONAL 2015; 2015:532481. [PMID: 26345115 PMCID: PMC4544718 DOI: 10.1155/2015/532481] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 05/24/2015] [Indexed: 11/17/2022]
Abstract
The evidence for the slow development from gathering and cultivation of wild species to the use of domesticates in the Near East, deriving from a number of Epipalaeolithic and aceramic Neolithic sites with short occupational stratigraphies, cannot explain the reasons for the protracted development of agriculture in the Fertile Crescent. The botanical and faunal remains from the long stratigraphic sequence of Chogha Golan, indicate local changes in environmental conditions and subsistence practices that characterize a site-specific pathway into emerging agriculture.
Our multidisciplinary approach demonstrates a long-term subsistence strategy of several hundred years on wild cereals and pulses as well as on hunting a variety of faunal species that were based on relatively favorable and stable environmental conditions. Fluctuations in the availability of resources after around 10.200 cal BP may have been caused by small-scale climatic fluctuations. The temporary depletion of resources was managed through a shift to other species which required minor technological changes to make these resources accessible and by intensification of barley cultivation which approached its domestication. After roughly 200 years, emmer domestication is apparent, accompanied by higher contribution of cattle in the diet, suggesting long-term intensification of resource management.
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Abstract
Genomic analysis of barley paints a picture of diffuse origins of this crop, with different regional wild populations contributing putative adaptive variations.
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Affiliation(s)
- Robin G Allaby
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK.
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36
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Poets AM, Fang Z, Clegg MT, Morrell PL. Barley landraces are characterized by geographically heterogeneous genomic origins. Genome Biol 2015. [PMID: 26293830 DOI: 10.1186/s13059‐015‐0712‐3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The genetic provenance of domesticated plants and the routes along which they were disseminated in prehistory have been a long-standing source of debate. Much of this debate has focused on identifying centers of origins for individual crops. However, many important crops show clear genetic signatures of multiple domestications, inconsistent with geographically circumscribed centers of origin. To better understand the genetic contributions of wild populations to domesticated barley, we compare single nucleotide polymorphism frequencies from 803 barley landraces to 277 accessions from wild populations. RESULTS We find that the genetic contribution of individual wild populations differs across the genome. Despite extensive human movement and admixture of barley landraces since domestication, individual landrace genomes indicate a pattern of shared ancestry with geographically proximate wild barley populations. This results in landraces with a mosaic of ancestry from multiple source populations rather than discrete centers of origin. We rule out recent introgression, suggesting that these contributions are ancient. The over-representation in landraces of genomic segments from local wild populations suggests that wild populations contributed locally adaptive variation to primitive varieties. CONCLUSIONS This study increases our understanding of the evolutionary process associated with the transition from wild to domesticated barley. Our findings indicate that cultivated barley is comprised of multiple source populations with unequal contributions traceable across the genome. We detect putative adaptive variants and identify the wild progenitor conferring those variants.
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Affiliation(s)
- Ana M Poets
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA.
| | - Zhou Fang
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA. .,Current address, Bayer CropScience, 407 Davis Drive, Morrisville, NC, 27560, USA.
| | - Michael T Clegg
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92697, USA.
| | - Peter L Morrell
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA.
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Poets AM, Fang Z, Clegg MT, Morrell PL. Barley landraces are characterized by geographically heterogeneous genomic origins. Genome Biol 2015; 16:173. [PMID: 26293830 PMCID: PMC4546095 DOI: 10.1186/s13059-015-0712-3] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 07/01/2015] [Indexed: 11/23/2022] Open
Abstract
Background The genetic provenance of domesticated plants and the routes along which they were disseminated in prehistory have been a long-standing source of debate. Much of this debate has focused on identifying centers of origins for individual crops. However, many important crops show clear genetic signatures of multiple domestications, inconsistent with geographically circumscribed centers of origin. To better understand the genetic contributions of wild populations to domesticated barley, we compare single nucleotide polymorphism frequencies from 803 barley landraces to 277 accessions from wild populations. Results We find that the genetic contribution of individual wild populations differs across the genome. Despite extensive human movement and admixture of barley landraces since domestication, individual landrace genomes indicate a pattern of shared ancestry with geographically proximate wild barley populations. This results in landraces with a mosaic of ancestry from multiple source populations rather than discrete centers of origin. We rule out recent introgression, suggesting that these contributions are ancient. The over-representation in landraces of genomic segments from local wild populations suggests that wild populations contributed locally adaptive variation to primitive varieties. Conclusions This study increases our understanding of the evolutionary process associated with the transition from wild to domesticated barley. Our findings indicate that cultivated barley is comprised of multiple source populations with unequal contributions traceable across the genome. We detect putative adaptive variants and identify the wild progenitor conferring those variants. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0712-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ana M Poets
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA.
| | - Zhou Fang
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA. .,Current address, Bayer CropScience, 407 Davis Drive, Morrisville, NC, 27560, USA.
| | - Michael T Clegg
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92697, USA.
| | - Peter L Morrell
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA.
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38
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Poets AM, Fang Z, Clegg MT, Morrell PL. Barley landraces are characterized by geographically heterogeneous genomic origins. Genome Biol 2015. [PMID: 26293830 DOI: 10.1186/s13059-015-071-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023] Open
Abstract
BACKGROUND The genetic provenance of domesticated plants and the routes along which they were disseminated in prehistory have been a long-standing source of debate. Much of this debate has focused on identifying centers of origins for individual crops. However, many important crops show clear genetic signatures of multiple domestications, inconsistent with geographically circumscribed centers of origin. To better understand the genetic contributions of wild populations to domesticated barley, we compare single nucleotide polymorphism frequencies from 803 barley landraces to 277 accessions from wild populations. RESULTS We find that the genetic contribution of individual wild populations differs across the genome. Despite extensive human movement and admixture of barley landraces since domestication, individual landrace genomes indicate a pattern of shared ancestry with geographically proximate wild barley populations. This results in landraces with a mosaic of ancestry from multiple source populations rather than discrete centers of origin. We rule out recent introgression, suggesting that these contributions are ancient. The over-representation in landraces of genomic segments from local wild populations suggests that wild populations contributed locally adaptive variation to primitive varieties. CONCLUSIONS This study increases our understanding of the evolutionary process associated with the transition from wild to domesticated barley. Our findings indicate that cultivated barley is comprised of multiple source populations with unequal contributions traceable across the genome. We detect putative adaptive variants and identify the wild progenitor conferring those variants.
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Affiliation(s)
- Ana M Poets
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA.
| | - Zhou Fang
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA.
- Current address, Bayer CropScience, 407 Davis Drive, Morrisville, NC, 27560, USA.
| | - Michael T Clegg
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92697, USA.
| | - Peter L Morrell
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA.
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Badaeva ED, Keilwagen J, Knüpffer H, Waßermann L, Dedkova OS, Mitrofanova OP, Kovaleva ON, Liapunova OA, Pukhalskiy VA, Özkan H, Graner A, Willcox G, Kilian B. Chromosomal passports provide new insights into diffusion of emmer wheat. PLoS One 2015; 10:e0128556. [PMID: 26024381 PMCID: PMC4449015 DOI: 10.1371/journal.pone.0128556] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Accepted: 04/28/2015] [Indexed: 12/27/2022] Open
Abstract
Emmer wheat, Triticum dicoccon schrank (syn. T. dicoccum (schrank) schÜbl.), is one of the earliest domesticated crops, harboring a wide range of genetic diversity and agronomically valuable traits. The crop, however, is currently largely neglected. We provide a wealth of karyotypic information from a comprehensive collection of emmer wheat and related taxa. In addition to C-banding polymorphisms, we identified 43 variants of chromosomal rearrangements in T. dicoccon; among them 26 (60.4%) were novel. The T7A:5B translocation was most abundant in Western Europe and the Mediterranean. The plant genetic resources investigated here might become important in the future for wheat improvement. Based on cluster analysis four major karyotypic groups were discriminated within the T. dicoccon genepool, each harboring characteristic C-banding patterns and translocation spectra: the balkan, asian, european and ethiopian groups. We postulate four major diffusion routes of the crop and discuss their migration out of the Fertile Crescent considering latest archaeobotanical findings.
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Affiliation(s)
- Ekaterina D. Badaeva
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina street 3, Moscow 119991, Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova street 32, Moscow 119991, Russia
| | - Jens Keilwagen
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Erwin-Baur-Straße 27, 06484 Quedlinburg, Germany
| | - Helmut Knüpffer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, D-06466 Stadt Seeland OT Gatersleben, Germany
| | - Louise Waßermann
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Erwin-Baur-Straße 27, 06484 Quedlinburg, Germany
| | - Olga S. Dedkova
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina street 3, Moscow 119991, Russia
| | - Olga P. Mitrofanova
- N.I. Vavilov Institute of Plant Industry (VIR), Russian Academy of Agricultural Sciences, Bolshaya Morskaya street 44, St. Petersburg 190000, Russia
| | - Olga N. Kovaleva
- N.I. Vavilov Institute of Plant Industry (VIR), Russian Academy of Agricultural Sciences, Bolshaya Morskaya street 44, St. Petersburg 190000, Russia
| | - Olga A. Liapunova
- N.I. Vavilov Institute of Plant Industry (VIR), Russian Academy of Agricultural Sciences, Bolshaya Morskaya street 44, St. Petersburg 190000, Russia
| | - Vitaly A. Pukhalskiy
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina street 3, Moscow 119991, Russia
| | - Hakan Özkan
- University of Cukurova, Faculty of Agriculture, Department of Field Crops. 01330 Adana, Turkey
| | - Andreas Graner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, D-06466 Stadt Seeland OT Gatersleben, Germany
| | - George Willcox
- Archéorient CNRS UMR 5133, Université de Lyon II, Antenne d’Archéorient, Jalés, Berrias, F-07460 St-Paul-le-Jeune, France
| | - Benjamin Kilian
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, D-06466 Stadt Seeland OT Gatersleben, Germany
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Abstract
An ordered draft sequence of the 17-gigabase hexaploid bread wheat (Triticum aestivum) genome has been produced by sequencing isolated chromosome arms. We have annotated 124,201 gene loci distributed nearly evenly across the homeologous chromosomes and subgenomes. Comparative gene analysis of wheat subgenomes and extant diploid and tetraploid wheat relatives showed that high sequence similarity and structural conservation are retained, with limited gene loss, after polyploidization. However, across the genomes there was evidence of dynamic gene gain, loss, and duplication since the divergence of the wheat lineages. A high degree of transcriptional autonomy and no global dominance was found for the subgenomes. These insights into the genome biology of a polyploid crop provide a springboard for faster gene isolation, rapid genetic marker development, and precise breeding to meet the needs of increasing food demand worldwide.
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