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Civáň P, Fricano A, Russell J, Pont C, Özkan H, Kilian B, Brown TA. Genetic erosion in domesticated barley and a hypothesis of a North African centre of diversity. Ecol Evol 2024; 14:e70068. [PMID: 39114174 PMCID: PMC11303984 DOI: 10.1002/ece3.70068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 06/27/2024] [Accepted: 07/10/2024] [Indexed: 08/10/2024] Open
Abstract
Barley is one of the founder crops of the Neolithic transition in West Asia. While recent advances in genomics have provided a rather detailed picture of barley domestication, there are contradictory views on how the domestication process affected genetic diversity. We set out to revisit this question by integrating public DNA sequencing data from ancient barley and wide collections of extant wild and domesticated accessions. Using two previously overlooked approaches - analyses of chloroplast genomes and genome-wide proportions of private variants - we found that the barley cultivated six millennia ago was genetically unique and more diverse when compared to extant landraces and cultivars. Moreover, the chloroplast genomes revealed a link between the ancient barley, an obscure wild genotype from north-eastern Libya, and a distinct population of barley cultivated in Ethiopia/Eritrea. Based on these results, we hypothesize past existence of a wider North African population that included both wild and cultivated types and suffered from genetic erosion in the past six millennia, likely due to a rapid desertification that ended the Holocene African humid period. Besides providing clues about the origin of Ethiopian landraces, the hypothesis explains the post-domestication loss of diversity observed in barley. Analyses of additional samples will be necessary to resolve the history of African barley and its contribution to the extant cultivated gene pool.
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Affiliation(s)
- Peter Civáň
- INRAE/UCA UMR 1095, GDECClermont FerrandFrance
| | - Agostino Fricano
- Council for Agricultural Research and Economics – Research Centre for Genomics and BioinformaticsFiorenzuola d'Arda (PC)Italy
| | | | | | - Hakan Özkan
- Department of Field Crops, Faculty of AgricultureUniversity of ÇukurovaAdanaTurkey
| | | | - Terence A. Brown
- Department of Earth and Environmental Sciences, Manchester Institute of BiotechnologyUniversity of ManchesterManchesterUK
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Dougherty L, Borejsza-Wysocka E, Miaule A, Wang P, Zheng D, Jansen M, Brown S, Piñeros M, Dardick C, Xu K. A single amino acid substitution in MdLAZY1A dominantly impairs shoot gravitropism in Malus. PLANT PHYSIOLOGY 2023; 193:1142-1160. [PMID: 37394917 DOI: 10.1093/plphys/kiad373] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 06/15/2023] [Accepted: 06/16/2023] [Indexed: 07/04/2023]
Abstract
Plant architecture is 1 of the most important factors that determines crop yield potential and productivity. In apple (Malus domestica), genetic improvement of tree architecture has been challenging due to a long juvenile phase and growth as complex trees composed of a distinct scion and a rootstock. To better understand the genetic control of apple tree architecture, the dominant weeping growth phenotype was investigated. We report the identification of MdLAZY1A (MD13G1122400) as the genetic determinant underpinning the Weeping (W) locus that largely controls weeping growth in Malus. MdLAZY1A is 1 of the 4 paralogs in apple that are most closely related to AtLAZY1 involved in gravitropism in Arabidopsis (Arabidopsis thaliana). The weeping allele (MdLAZY1A-W) contains a single nucleotide mutation c.584T>C that leads to a leucine to proline (L195P) substitution within a predicted transmembrane domain that colocalizes with Region III, 1 of the 5 conserved regions in LAZY1-like proteins. Subcellular localization revealed that MdLAZY1A localizes to the plasma membrane and nucleus in plant cells. Overexpressing the weeping allele in apple cultivar Royal Gala (RG) with standard growth habit impaired its gravitropic response and altered the growth to weeping-like. Suppressing the standard allele (MdLAZY1A-S) by RNA interference (RNAi) in RG similarly changed the branch growth direction to downward. Overall, the L195P mutation in MdLAZY1A is genetically causal for weeping growth, underscoring not only the crucial roles of residue L195 and Region III in MdLAZY1A-mediated gravitropic response but also a potential DNA base editing target for tree architecture improvement in Malus and other crops.
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Affiliation(s)
- Laura Dougherty
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell Agritech, Geneva, NY 14456, USA
| | - Ewa Borejsza-Wysocka
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell Agritech, Geneva, NY 14456, USA
| | - Alexandre Miaule
- School of Integrative Plant Sciences, Plant Biology Section, Cornell University, Ithaca, NY 14853, USA
| | - Ping Wang
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell Agritech, Geneva, NY 14456, USA
| | - Desen Zheng
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell Agritech, Geneva, NY 14456, USA
| | - Michael Jansen
- United States Department of Agriculture-Agricultural Research Service, Systematic Entomology Laboratory, Electron and Confocal Microscopy Unit, Beltsville, MD 20705, USA
| | - Susan Brown
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell Agritech, Geneva, NY 14456, USA
| | - Miguel Piñeros
- School of Integrative Plant Sciences, Plant Biology Section, Cornell University, Ithaca, NY 14853, USA
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Ithaca, NY 14853, USA
| | - Christopher Dardick
- United States Department of Agriculture-Agricultural Research Service, Appalachian Fruit Research Station, Kearneysville, WV 25430, USA
| | - Kenong Xu
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell Agritech, Geneva, NY 14456, USA
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Qiu CW, Ma Y, Liu W, Zhang S, Wang Y, Cai S, Zhang G, Chater CCC, Chen ZH, Wu F. Genome resequencing and transcriptome profiling reveal molecular evidence of tolerance to water deficit in barley. J Adv Res 2023; 49:31-45. [PMID: 36170948 PMCID: PMC10334146 DOI: 10.1016/j.jare.2022.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 09/17/2022] [Accepted: 09/19/2022] [Indexed: 11/27/2022] Open
Abstract
INTRODUCTION Frequent climate change-induced drought events are detrimental environmental stresses affecting global crop production and ecosystem health. Several efforts have facilitated crop breeding for resilient varieties to counteract stress. However, progress is hampered due to the complexity of drought tolerance; a greater variety of novel genes are required across varying environments. Tibetan annual wild barley is a unique and precious germplasm that is well adapted to abiotic stress and can provide elite genes for crop improvement in drought tolerance. OBJECTIVES To identify the genetic basis and unique mechanisms for drought tolerance in Tibetan wild barley. METHODS Whole genome resequencing and comparative RNA-seq approaches were performed to identify candidate genes associated with drought tolerance via investigating the genetic diversity and transcriptional variation between cultivated and Tibetan wild barley. Bioinformatics, population genetics, and gene silencing were conducted to obtain insights into ecological adaptation in barley and functions of key genes. RESULTS Over 20 million genetic variants and a total of 15,361 significantly affected genes were identified in our dataset. Combined genomic, transcriptomic, evolutionary, and experimental analyses revealed 26 water deficit resilience-associated genes in the drought-tolerant wild barley XZ5 with unique genetic variants and expression patterns. Functional prediction revealed Tibetan wild barley employs effective regulators to activate various responsive pathways with novel genes, such as Zinc-Induced Facilitator-Like 2 (HvZIFL2) and Peroxidase 11 (HvPOD11), to adapt to water deficit conditions. Gene silencing and drought tolerance evaluation in a natural barley population demonstrated that HvZIFL2 and HvPOD11 positively regulate drought tolerance in barley. CONCLUSION Our findings reveal functional genes that have been selected across barley's complex history of domestication to thrive in water deficit environments. This will be useful for molecular breeding and provide new insights into drought-tolerance mechanisms in wild relatives of major cereal crops.
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Affiliation(s)
- Cheng-Wei Qiu
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Yue Ma
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
| | - Wenxing Liu
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Shuo Zhang
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Yizhou Wang
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
| | - Shengguan Cai
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
| | - Guoping Zhang
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
| | - Caspar C C Chater
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK; School of Biosciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Zhong-Hua Chen
- School of Science, Western Sydney University, Penrith, NSW, Australia; Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia.
| | - Feibo Wu
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China.
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Yadav IS, Singh N, Wu S, Raupp J, Wilson DL, Rawat N, Gill BS, Poland J, Tiwari VK. Exploring genetic diversity of wild and related tetraploid wheat species Triticum turgidum and Triticum timopheevii. J Adv Res 2023; 48:47-60. [PMID: 36084813 PMCID: PMC10248793 DOI: 10.1016/j.jare.2022.08.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/25/2022] [Accepted: 08/31/2022] [Indexed: 11/27/2022] Open
Abstract
INTRODUCTION The domestication bottleneck has reduced genetic diversity inwheat, necessitating the use of wild relatives in breeding programs. Wild tetraploid wheat are widely used in the breeding programs but with morphological characters, it is difficult to distinguish these, resulting in misclassification/mislabeling or duplication of accessions in the Gene bank. OBJECTIVES The study aims to exploreGenotyping by sequencing (GBS) to characterize wild and domesticated tetraploid wheat accessions to generate a core set of accessions to be used in the breeding program. METHODS TASSEL-GBS pipeline was used for SNP discovery, fastStructure was used to determine the population structure and PowerCore was used to generate a core sets. Nucleotide diversity matrices of Nie's and F-statistics (FST) index were used to determine the center of genetic diversity. RESULTS We found 65 % and 47 % duplicated accessions in Triticum timopheevii and T. turgidum respectively. Genome-wide nucleotide diversity and FST scan uncovered a lower intra and higher inter-species differentiation. Distinct FST regions were identified in genomic regions belonging to domestication genes: non-brittle rachis (Btr1) and vernalization (VRN-1).Our results suggest that Israel, Jordan, Syria, and Lebanonas the hub of genetic diversity of wild emmer;Turkey, and Georgia for T. durum; and Iraq, Azerbaijan, and Armenia for theT. timopheevii. Identified core set accessions preserved more than 93 % of the available genetic diversity. Genome wide association study (GWAS) indicated the potential chromosomal segment for resistance to leaf rust in T. timopheevii. CONCLUSION The present study explored the potential of GBS technology in data reduction while maintaining the significant genetic diversity of the species. Wild germplasm showed more differentiation than domesticated accessions, indicating the availability of sufficient diversity for crop improvement. With reduced complexity, the core set preserves the genetic diversity of the gene bank collections and will aid in a more robust characterization of wild germplasm.
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Affiliation(s)
- Inderjit S. Yadav
- Department of Plant Sciences and Landscape Architecture, University of Maryland, College Park, MD 20742, USA
| | | | - Shuangye Wu
- Department of Plant Pathology and Wheat Genetics Resource Center, Kansas State University, 1712 Claflin Road, Manhattan, KS 66506, USA
| | - Jon Raupp
- Department of Plant Pathology and Wheat Genetics Resource Center, Kansas State University, 1712 Claflin Road, Manhattan, KS 66506, USA
| | - Duane L. Wilson
- Department of Plant Pathology and Wheat Genetics Resource Center, Kansas State University, 1712 Claflin Road, Manhattan, KS 66506, USA
| | - Nidhi Rawat
- Department of Plant Sciences and Landscape Architecture, University of Maryland, College Park, MD 20742, USA
| | - Bikram S. Gill
- Department of Plant Pathology and Wheat Genetics Resource Center, Kansas State University, 1712 Claflin Road, Manhattan, KS 66506, USA
| | - Jesse Poland
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, 4700 KAUST, Thuwal 23955-6900, Saudi Arabia
| | - Vijay K. Tiwari
- Department of Plant Sciences and Landscape Architecture, University of Maryland, College Park, MD 20742, USA
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Pourkheirandish M, Komatsuda T. Grain Disarticulation in Wild Wheat and Barley. PLANT & CELL PHYSIOLOGY 2022; 63:1584-1591. [PMID: 35765920 PMCID: PMC9680857 DOI: 10.1093/pcp/pcac091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 06/17/2022] [Accepted: 08/04/2022] [Indexed: 05/26/2023]
Abstract
Our industrial-scale crop monocultures, which are necessary to provide grain for large-scale food and feed production, are highly vulnerable to biotic and abiotic stresses. Crop wild relatives have adapted to harsh environmental conditions over millennia; thus, they are an important source of genetic variation and crop diversification. Despite several examples where significant yield increases have been achieved through the introgression of genomic regions from wild relatives, more detailed understanding of the differences between wild and cultivated species for favorable and unfavorable traits is still required to harness these valuable resources. Recently, as an alternative to the introgression of beneficial alleles from the wild into domesticated species, a radical suggestion is to domesticate wild relatives to generate new crops. A first and critical step for the domestication of cereal wild relatives would be to prevent grain disarticulation from the inflorescence at maturity. Discovering the molecular mechanisms and understanding the network of interactions behind grain retention/disarticulation would enable the implementation of approaches to select for this character in targeted species. Brittle rachis 1 and Brittle rachis 2 are major genes responsible for grain disarticulation in the wild progenitors of wheat and barley that were the target of mutations during domestication. These two genes are only found in the Triticeae tribe and are hypothesized to have evolved by a duplication followed by neo-functionalization. Current knowledge gaps include the molecular mechanisms controlling grain retention in cereals and the genomic consequences of strong selection for this essential character.
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Affiliation(s)
| | - Takao Komatsuda
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong 250100, China
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Crain J, Larson S, Dorn K, DeHaan L, Poland J. Genetic architecture and QTL selection response for Kernza perennial grain domestication traits. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2769-2784. [PMID: 35763029 PMCID: PMC9243872 DOI: 10.1007/s00122-022-04148-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 05/31/2022] [Indexed: 06/15/2023]
Abstract
Analysis of multi-year breeding program data revealed that the genetic architecture of an intermediate wheatgrass population was highly polygenic for both domestication and agronomic traits, supporting the use of genomic selection for new crop domestication. Perennial grains have the potential to provide food for humans and decrease the negative impacts of annual agriculture. Intermediate wheatgrass (IWG, Thinopyrum intermedium, Kernza®) is a promising perennial grain candidate that The Land Institute has been breeding since 2003. We evaluated four consecutive breeding cycles of IWG from 2016 to 2020 with each cycle containing approximately 1100 unique genets. Using genotyping-by-sequencing markers, quantitative trait loci (QTL) were mapped for 34 different traits using genome-wide association analysis. Combining data across cycles and years, we found 93 marker-trait associations for 16 different traits, with each association explaining 0.8-5.2% of the observed phenotypic variance. Across the four cycles, only three QTL showed an FST differentiation > 0.15 with two corresponding to a decrease in floret shattering. Additionally, one marker associated with brittle rachis was 216 bp from an ortholog of the btr2 gene. Power analysis and quantitative genetic theory were used to estimate the effective number of QTL, which ranged from a minimum of 33 up to 558 QTL for individual traits. This study suggests that key agronomic and domestication traits are under polygenic control and that molecular methods like genomic selection are needed to accelerate domestication and improvement of this new crop.
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Affiliation(s)
- Jared Crain
- Department of Plant Pathology, Kansas State University, 4024 Throckmorton Plant Sciences Center, Manhattan, KS, 66506, USA
| | - Steve Larson
- USDA-ARS, Forage and Range Research, Utah State University, Logan, UT, 84322, USA
| | - Kevin Dorn
- USDA-ARS, Soil Management and Sugarbeet Research, Fort Collins, CO, 80526, USA
| | - Lee DeHaan
- The Land Institute, 2440 E. Water Well Rd, Salina, KS, 67401, USA
| | - Jesse Poland
- Department of Plant Pathology, Kansas State University, 4024 Throckmorton Plant Sciences Center, Manhattan, KS, 66506, USA.
- Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.
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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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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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DeHaan L, Larson S, López-Marqués RL, Wenkel S, Gao C, Palmgren M. Roadmap for Accelerated Domestication of an Emerging Perennial Grain Crop. TRENDS IN PLANT SCIENCE 2020; 25:525-537. [PMID: 32407693 DOI: 10.1016/j.tplants.2020.02.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 02/03/2020] [Accepted: 02/06/2020] [Indexed: 05/14/2023]
Abstract
Shifting the life cycle of grain crops from annual to perennial would usher in a new era of agriculture that is more environmentally friendly, resilient to climate change, and capable of soil carbon sequestration. Despite decades of work, transforming the annual grain crop wheat (Triticum aestivum) into a perennial has yet to be realized. Direct domestication of wild perennial grass relatives of wheat, such as Thinopyrum intermedium, is an alternative approach. Here we highlight protein coding sequences in the recently released T. intermedium genome sequence that may be orthologous to domestication genes identified in annual grain crops. Their presence suggests a roadmap for the accelerated domestication of this plant using new breeding technologies.
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Affiliation(s)
- Lee DeHaan
- The Land Institute, 2440 E. Water Well Road, Salina, KS 67401, USA
| | - Steve Larson
- United States Department of Agriculture, Agriculture Research Service, Forage and Range Research, Utah State University, Logan, UT 84322-6300, USA
| | - Rosa L López-Marqués
- NovoCrops Center, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Stephan Wenkel
- NovoCrops Center, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Michael Palmgren
- NovoCrops Center, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark.
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Nave M, Avni R, Çakır E, Portnoy V, Sela H, Pourkheirandish M, Ozkan H, Hale I, Komatsuda T, Dvorak J, Distelfeld A. Wheat domestication in light of haplotype analyses of the Brittle rachis 1 genes (BTR1-A and BTR1-B). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 285:193-199. [PMID: 31203884 DOI: 10.1016/j.plantsci.2019.05.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 05/08/2019] [Accepted: 05/15/2019] [Indexed: 06/09/2023]
Abstract
Wheat domestication was a milestone in the rise of agrarian societies in the Fertile Crescent. As opposed to the freely dispersing seeds of its tetraploid progenitor wild emmer, the hallmark trait of domesticated wheat is intact, harvestable spikes. During domestication, wheat acquired recessive loss-of-function mutations in the Brittle Rachis 1 genes, both in the A genome (BTR1-A) and B genome (BTR1-B). In this study, we probe the geographical provenances of these mutations via haplotype analyses of a collection of wild and domesticated accessions. Our results show that the precursor of the domesticated haplotype of BTR1-A was detected in 32% of the wild accessions gathered throughout the Levant, from central Israel to central Turkey. In contrast, the precursor of the domesticated haplotype of BTR1-B, which carries a distinct 11 bp deletion in the promoter region, was found in only 10% of the tested wild accessions, all from the Southern Levant. Moreover, we identified of a single wild emmer accession in Southern Levant that carries the progenitor haplotypes for both BTR1-A and BTR1-B genes. These observations suggest that at least part of the emmer domestication process occurred in Southern Levant, contrary to the widely held view that the northern part of the Fertile Crescent was the center of wheat domestication.
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Affiliation(s)
- Moran Nave
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Raz Avni
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Esra Çakır
- Department of Field Crops, Faculty of Agriculture, Cukurova University, Adana, Turkey
| | - Vitaly Portnoy
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Hanan Sela
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Mohammad Pourkheirandish
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria, Australia
| | - Hakan Ozkan
- Department of Field Crops, Faculty of Agriculture, Cukurova University, Adana, Turkey
| | - Iago Hale
- Department of Agriculture, Nutrition, and Food Systems, University of New Hampshire, Durham, NH, USA
| | - Takao Komatsuda
- National Institute of Agrobiological Sciences, Tsukuba, Japan; Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Jan Dvorak
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Assaf Distelfeld
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel.
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11
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Radchuk V, Sharma R, Potokina E, Radchuk R, Weier D, Munz E, Schreiber M, Mascher M, Stein N, Wicker T, Kilian B, Borisjuk L. The highly divergent Jekyll genes, required for sexual reproduction, are lineage specific for the related grass tribes Triticeae and Bromeae. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 98:961-974. [PMID: 31021020 PMCID: PMC6851964 DOI: 10.1111/tpj.14363] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 03/27/2019] [Accepted: 04/04/2019] [Indexed: 05/26/2023]
Abstract
Phylogenetically related groups of species contain lineage-specific genes that exhibit no sequence similarity to any genes outside the lineage. We describe here that the Jekyll gene, required for sexual reproduction, exists in two much diverged allelic variants, Jek1 and Jek3. Despite low similarity, the Jek1 and Jek3 proteins share identical signal peptides, conserved cysteine positions and direct repeats. The Jek1/Jek3 sequences are located at the same chromosomal locus and inherited in a monogenic Mendelian fashion. Jek3 has a similar expression as Jek1 and complements the Jek1 function in Jek1-deficient plants. Jek1 and Jek3 allelic variants were almost equally distributed in a collection of 485 wild and domesticated barley accessions. All domesticated barleys harboring the Jek1 allele belong to single haplotype J1-H1 indicating a genetic bottleneck during domestication. Domesticated barleys harboring the Jek3 allele consisted of three haplotypes. Jekyll-like sequences were found only in species of the closely related tribes Bromeae and Triticeae but not in other Poaceae. Non-invasive magnetic resonance imaging revealed intrinsic grain structure in Triticeae and Bromeae, associated with the Jekyll function. The emergence of Jekyll suggests its role in the separation of the Bromeae and Triticeae lineages within the Poaceae and identifies the Jekyll genes as lineage-specific.
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Affiliation(s)
- Volodymyr Radchuk
- Leibniz‐Institute of Plant Genetics and Crop Plant Research (IPK)06466GaterslebenGermany
| | - Rajiv Sharma
- Leibniz‐Institute of Plant Genetics and Crop Plant Research (IPK)06466GaterslebenGermany
- Present address:
Division of Plant SciencesSchool of Life SciencesUniversity of DundeeThe James Hutton InstituteInvergowrie, DundeeDD2 5DAUK
| | - Elena Potokina
- Leibniz‐Institute of Plant Genetics and Crop Plant Research (IPK)06466GaterslebenGermany
- Vavilov Institute of Plant Genetic Resources (VIR)St. Petersburg190000Russian Federation
| | - Ruslana Radchuk
- Leibniz‐Institute of Plant Genetics and Crop Plant Research (IPK)06466GaterslebenGermany
| | - Diana Weier
- Leibniz‐Institute of Plant Genetics and Crop Plant Research (IPK)06466GaterslebenGermany
| | - Eberhard Munz
- Leibniz‐Institute of Plant Genetics and Crop Plant Research (IPK)06466GaterslebenGermany
- Department of Experimental Physics 5University of WürzburgWürzburgGermany
| | | | - Martin Mascher
- Leibniz‐Institute of Plant Genetics and Crop Plant Research (IPK)06466GaterslebenGermany
| | - Nils Stein
- Leibniz‐Institute of Plant Genetics and Crop Plant Research (IPK)06466GaterslebenGermany
| | - Thomas Wicker
- Department of Plant and Microbial BiologyUniversity of ZürichZürichSwitzerland
| | - Benjamin Kilian
- Leibniz‐Institute of Plant Genetics and Crop Plant Research (IPK)06466GaterslebenGermany
- Present address:
Global Crop Diversity Trust53113BonnGermany
| | - Ljudmilla Borisjuk
- Leibniz‐Institute of Plant Genetics and Crop Plant Research (IPK)06466GaterslebenGermany
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12
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The complex geography of domestication of the African rice Oryza glaberrima. PLoS Genet 2019; 15:e1007414. [PMID: 30845217 PMCID: PMC6424484 DOI: 10.1371/journal.pgen.1007414] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 03/19/2019] [Accepted: 02/08/2019] [Indexed: 11/19/2022] Open
Abstract
While the domestication history of Asian rice has been extensively studied, details of the evolution of African rice remain elusive. The inner Niger delta has been suggested as the center of origin but molecular data to support this hypothesis is lacking. Here, we present a comprehensive analysis of the evolutionary and domestication history of African rice. By analyzing whole genome re-sequencing data from 282 individuals of domesticated African rice Oryza glaberrima and its progenitor O. barthii, we hypothesize a non-centric (i.e. multiregional) domestication origin for African rice. Our analyses showed genetic structure within O. glaberrima that has a geographical association. Furthermore, we have evidence that the previously hypothesized O. barthii progenitor populations in West Africa have evolutionary signatures similar to domesticated rice and carried causal domestication mutations, suggesting those progenitors were either mislabeled or may actually represent feral wild-domesticated hybrids. Phylogeographic analysis of genes involved in the core domestication process suggests that the origins of causal domestication mutations could be traced to wild progenitors in multiple different locations in West and Central Africa. In addition, measurements of panicle threshability, a key early domestication trait for seed shattering, were consistent with the gene phylogeographic results. We suggest seed non-shattering was selected from multiple genotypes, possibly arising from different geographical regions. Based on our evidence, O. glaberrima was not domesticated from a single centric location but was a result of diffuse process where multiple regions contributed key alleles for different domestication traits. For many crops it is not clear how they were domesticated from their wild progenitors. Transition from a wild to domesticated state required a series of genetic changes, and studying the evolutionary origin of these domestication-causing mutations are key to understanding the domestication origins of a crop. Moreover, population comparisons provide insight into the relationship between wild and cultivated populations and the evolutionary history of domestication. In this study, we investigated the domestication history of Oryza glaberrima, a rice species that was domesticated in West Africa independent from the Asian rice species O. sativa. Using genome-wide data from a large sample of domesticated and wild African rice samples we did not find evidence that supported the established domestication model for O. glaberrima—a single domestication origin. Rather, our evidence suggests the domestication process for African rice was initiated in multiple regions of West Africa, caused potentially by the local environments and cultivation preference of people. Hence domestication of African rice was a multi-regional process.
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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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14
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Lister DL, Jones H, Oliveira HR, Petrie CA, Liu X, Cockram J, Kneale CJ, Kovaleva O, Jones MK. Barley heads east: Genetic analyses reveal routes of spread through diverse Eurasian landscapes. PLoS One 2018; 13:e0196652. [PMID: 30020920 PMCID: PMC6051582 DOI: 10.1371/journal.pone.0196652] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 04/17/2018] [Indexed: 11/19/2022] Open
Abstract
One of the world’s most important crops, barley, was domesticated in the Near East around 11,000 years ago. Barley is a highly resilient crop, able to grown in varied and marginal environments, such as in regions of high altitude and latitude. Archaeobotanical evidence shows that barley had spread throughout Eurasia by 2,000 BC. To further elucidate the routes by which barley cultivation was spread through Eurasia, simple sequence repeat (SSR) analysis was used to determine genetic diversity and population structure in three extant barley taxa: domesticated barley (Hordeum vulgare L. subsp. vulgare), wild barley (H. vulgare subsp. spontaneum) and a six-rowed brittle rachis form (H. vulgare subsp. vulgare f. agriocrithon (Åberg) Bowd.). Analysis of data using the Bayesian clustering algorithm InStruct suggests a model with three ancestral genepools, which captures a major split in the data, with substantial additional resolution provided under a model with eight genepools. Our results indicate that H. vulgare subsp. vulgare f. agriocrithon accessions and Tibetan Plateau H. vulgare subsp. spontaneum are closely related to the H. vulgare subsp. vulgare in their vicinity, and are therefore likely to be feral derivatives of H. vulgare subsp. vulgare. Under the eight genepool model, cultivated barley is split into six ancestral genepools, each of which has a distinct distribution through Eurasia, along with distinct morphological features and flowering time phenotypes. The distribution of these genepools and their phenotypic characteristics is discussed together with archaeological evidence for the spread of barley eastwards across Eurasia.
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Affiliation(s)
- Diane L. Lister
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, United Kingdom
- * E-mail:
| | - Huw Jones
- The John Bingham Laboratory, NIAB, Cambridge, United Kingdom
| | - Hugo R. Oliveira
- Manchester Institute of Biotechnology, School of Earth and Environmental Sciences, University of Manchester, Manchester, United Kingdom
| | - Cameron A. Petrie
- Department of Archaeology, University of Cambridge, Cambridge, United Kingdom
| | - Xinyi Liu
- Department of Anthropology, Washington University in St. Louis, St. Louis, MO, United States of America
| | - James Cockram
- The John Bingham Laboratory, NIAB, Cambridge, United Kingdom
| | - Catherine J. Kneale
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, United Kingdom
| | - Olga Kovaleva
- N.I. Vavilov Research Institute of Plant Industry, St. Petersburg, Russia
| | - Martin K. Jones
- Department of Archaeology, University of Cambridge, Cambridge, United Kingdom
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15
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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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16
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Pournosrat R, Kaya S, Shaaf S, Kilian B, Ozkan H. Geographical and environmental determinants of the genetic structure of wild barley in southeastern Anatolia. PLoS One 2018; 13:e0192386. [PMID: 29420597 PMCID: PMC5805283 DOI: 10.1371/journal.pone.0192386] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Accepted: 01/21/2018] [Indexed: 11/29/2022] Open
Abstract
Despite the global value of barley, compared to its wild progenitor, genetic variation in this crop has been drastically reduced due to the process of domestication, selection and improvement. In the medium term, this will negatively impact both the vulnerability and yield stability of barley against biotic and abiotic stresses under climate change. Returning to the crop wild relatives (CWR) as sources of new and beneficial alleles is a clear option for enhancing the resilience of diversity and adaptation to climate change. Southeastern Anatolia constitutes an important part of the natural distribution of wild barley in the Fertile Crescent where important crops were initially domesticated. In this study, we investigated genetic diversity in a comprehensive collection of 281 geo-referenced wild barley individuals from 92 collection sites with sample sizes ranging from 1 to 9 individuals per site, collected from southeastern Anatolia and 131 domesticated genotypes from 49 different countries using 40 EST-SSR markers. A total of 375 alleles were detected across entire collection, of which 283 were carried by domesticated genotypes and 316 alleles were present in the wild gene pool. The number of unique alleles in the wild and in the domesticated gene pool was 92 and 59, respectively. The population structure at K = 3 suggested two groups of wild barley namely G1-W consisting wild barley genotypes from the western part and G1-E comprising those mostly from the eastern part of the study area, with a sharp separation from the domesticated gene pool. The geographic and climatic factors jointly showed significant effects on the distribution of wild barley. Using a Latent Factor Mixed Model, we identified four candidate loci potentially involved in adaptation of wild barley to three environmental factors: temperature seasonality, mean temperature of driest quarter, and precipitation of coldest quarter. These loci are probably the targets of genomic regions, with potential roles against abiotic stresses.
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Affiliation(s)
- Reza Pournosrat
- Department of Agronomy and Plant Breeding, College of Agriculture and Natural Resources, Sanandaj Branch, Islamic Azad University, Sanandaj, Iran
| | - Selma Kaya
- University of Çukurova, Faculty of Agriculture, Department of Field Crops, Adana, Turkey
| | - Salar Shaaf
- Department of Agronomy and Plant Breeding, College of Agriculture and Natural Resources, Sanandaj Branch, Islamic Azad University, Sanandaj, Iran
- * E-mail: (HO); (BK); (SS)
| | - Benjamin Kilian
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Genebank Department, Genome Diversity Group, Seeland, Germany
- * E-mail: (HO); (BK); (SS)
| | - Hakan Ozkan
- University of Çukurova, Faculty of Agriculture, Department of Field Crops, Adana, Turkey
- * E-mail: (HO); (BK); (SS)
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17
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Pourkheirandish M, Dai F, Sakuma S, Kanamori H, Distelfeld A, Willcox G, Kawahara T, Matsumoto T, Kilian B, Komatsuda T. On the Origin of the Non-brittle Rachis Trait of Domesticated Einkorn Wheat. FRONTIERS IN PLANT SCIENCE 2018; 8:2031. [PMID: 29354137 PMCID: PMC5758593 DOI: 10.3389/fpls.2017.02031] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 11/14/2017] [Indexed: 05/20/2023]
Abstract
Einkorn and emmer wheat together with barley were among the first cereals domesticated by humans more than 10,000 years ago, long before durum or bread wheat originated. Domesticated einkorn wheat differs from its wild progenitor in basic morphological characters such as the grain dispersal system. This study identified the Non-brittle rachis 1 (btr1) and Non-brittle rachis 2 (btr2) in einkorn as homologous to barley. Re-sequencing of the Btr1 and Btr2 in a collection of 53 lines showed that a single non-synonymous amino acid substitution (alanine to threonine) at position 119 at btr1, is responsible for the non-brittle rachis trait in domesticated einkorn. Tracing this haplotype variation back to wild einkorn samples provides further evidence that the einkorn progenitor came from the Northern Levant. We show that the geographical origin of domesticated haplotype coincides with the non-brittle domesticated barley haplotypes, which suggest the non-brittle rachis phenotypes of einkorn and barley were fixed in same geographic area in today's South-east Turkey.
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Affiliation(s)
- Mohammad Pourkheirandish
- National Institute of Agrobiological Sciences, Tsukuba, Japan
- Plant Breeding Institute, The University of Sydney, Cobbitty, NSW, Australia
| | - Fei Dai
- National Institute of Agrobiological Sciences, Tsukuba, Japan
| | - Shun Sakuma
- National Institute of Agrobiological Sciences, Tsukuba, Japan
| | | | - Assaf Distelfeld
- The Institute for Cereal Crops Improvement, Tel Aviv University, Tel Aviv, Israel
| | - George Willcox
- Centre National de la Recherche Scientifique, Saint-André-de-Cruzières, France
| | - Taihachi Kawahara
- Plant Germplasm Institute, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | | | | | - Takao Komatsuda
- National Institute of Agrobiological Sciences, Tsukuba, Japan
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Japan
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18
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Barley Developmental Mutants: The High Road to Understand the Cereal Spike Morphology. DIVERSITY-BASEL 2017. [DOI: 10.3390/d9020021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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