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Glison N, Gaiero P, Monteverde E, Speranza PR. Breeding for reduced seed dormancy to domesticate new grass species. Genet Mol Biol 2024; 47Suppl 1:e20230262. [PMID: 38666746 PMCID: PMC11046443 DOI: 10.1590/1678-4685-gmb-2023-0262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 03/01/2024] [Indexed: 04/29/2024] Open
Abstract
Introducing new grass species into cultivation has long been proposed as beneficial to increase the sustainability and diversity of productive systems. However, wild species with potential tend to show high seed dormancy, causing slow, poor, and unsynchronized seedling emergence. Meanwhile, domesticated species, such as cereals, show lower seed dormancy, facilitating their successful establishment. In this work, we conduct a review of phenotypic variation on seed dormancy and its genetic and molecular basis. This quantitative and highly heritable trait shows phenotype plasticity which is modulated by environmental factors. The level of dormancy depends on the expression of genes associated with the metabolism and sensitivity to the hormones abscisic acid (ABA) and gibberellins (GA), along with other dormancy-specific genes. The genetic regulation of these traits is highly conserved across species. The low seed dormancy observed in cereals and some temperate forages was mostly unconsciously selected during various domestication processes. Emphasis is placed on selecting materials with low seed dormancy for warm-season forage grasses to improve their establishment and adoption. Finally, we review advances in the domestication of dallisgrass, where seed dormancy was considered a focus trait throughout the process.
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Affiliation(s)
- Nicolás Glison
- Universidad de la República, Facultad de Agronomía, Departamento de Biología Vegetal, Montevideo, Uruguay
| | - Paola Gaiero
- Universidad de la República, Facultad de Agronomía, Departamento de Biología Vegetal, Montevideo, Uruguay
| | - Eliana Monteverde
- Universidad de la República, Facultad de Agronomía, Departamento de Biología Vegetal, Montevideo, Uruguay
- University of Illinois, Department of Crop Sciences, Urbana, IL, USA
| | - Pablo R. Speranza
- Universidad de la República, Facultad de Agronomía, Departamento de Biología Vegetal, Montevideo, Uruguay
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Alam O, Purugganan MD. Domestication and the evolution of crops: variable syndromes, complex genetic architectures, and ecological entanglements. Plant Cell 2024:koae013. [PMID: 38243576 DOI: 10.1093/plcell/koae013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 12/01/2023] [Accepted: 12/14/2023] [Indexed: 01/21/2024]
Abstract
Domestication can be considered a specialized mutualism in which a domesticator exerts control over the reproduction or propagation (fitness) of a domesticated species to gain resources or services. The evolution of crops by human-associated selection provides a powerful set of models to study recent and rapid evolutionary adaptations and their genetic bases. Moreover, the domestication and dispersal of crops like rice, maize, and wheat during the Holocene transformed human social and political organization by serving as the key mechanism by which human societies fed themselves. Here we review major themes and identify emerging questions in three fundamental areas of crop domestication research: domestication phenotypes and syndromes, genetic architecture underlying crop evolution, and the ecology of domestication. Current insights on the domestication syndrome in crops largely come from research on cereal crops like rice and maize, and recent work indicates distinct domestication phenotypes can arise from different domestication histories. While early studies on the genetics of domestication often identified single large-effect loci underlying major domestication traits, emerging evidence supports polygenic bases for many canonical traits like shattering and plant architecture. Adaptation in human-constructed environments also influenced ecological traits in domesticates like resource acquisition rates and interactions with other organisms like root mycorrhizal fungi and pollinators. Understanding the ecological context of domestication will be key to developing resource-efficient crops and implementing more sustainable land management and cultivation practices.
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Affiliation(s)
- Ornob Alam
- Center for Genomics and Systems Biology, New York University, New York, NY USA 10003
| | - Michael D Purugganan
- Center for Genomics and Systems Biology, New York University, New York, NY USA 10003
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
- Institute for the Study of the Ancient World, New York University, New York, NY USA 10028
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3
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Conrady M, Lampei C, Bossdorf O, Hölzel N, Michalski S, Durka W, Bucharova A. Plants cultivated for ecosystem restoration can evolve toward a domestication syndrome. Proc Natl Acad Sci U S A 2023; 120:e2219664120. [PMID: 37155873 PMCID: PMC10193954 DOI: 10.1073/pnas.2219664120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 04/05/2023] [Indexed: 05/10/2023] Open
Abstract
The UN Decade on Ecosystem Restoration calls for upscaling restoration efforts, but many terrestrial restoration projects are constrained by seed availability. To overcome these constraints, wild plants are increasingly propagated on farms to produce seeds for restoration projects. During on-farm propagation, the plants face non-natural conditions with different selection pressures, and they might evolve adaptations to cultivation that parallel those of agricultural crops, which could be detrimental to restoration success. To test this, we compared traits of 19 species grown from wild-collected seeds to those from their farm-propagated offspring of up to four cultivation generations, produced by two European seed growers, in a common garden experiment. We found that some plants rapidly evolved across cultivated generations towards increased size and reproduction, lower within-species variability, and more synchronized flowering. In one species, we found evolution towards less seed shattering. These trait changes are typical signs of the crop domestication syndrome, and our study demonstrates that it can also occur during cultivation of wild plants, within only few cultivated generations. However, there was large variability between cultivation lineages, and the observed effect sizes were generally rather moderate, which suggests that the detected evolutionary changes are unlikely to compromise farm-propagated seeds for ecosystem restoration. To mitigate the potential negative effects of unintended selection, we recommend to limit the maximum number of generations the plants can be cultivated without replenishing the seed stock from new wild collections.
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Affiliation(s)
- Malte Conrady
- Institute of Landscape Ecology, University of Münster, 48149Münster, Germany
- Department of Biology, Philipps-University Marburg, 35043Marburg, Germany
| | - Christian Lampei
- Institute of Landscape Ecology, University of Münster, 48149Münster, Germany
- Department of Biology, Philipps-University Marburg, 35043Marburg, Germany
| | - Oliver Bossdorf
- Plant Evolutionary Ecology, Institute of Evolution & Ecology, University of Tübingen, 72076Tübingen, Germany
| | - Norbert Hölzel
- Institute of Landscape Ecology, University of Münster, 48149Münster, Germany
| | - Stefan Michalski
- Department of Community Ecology, Helmholtz Centre for Environmental Research - UFZ, 06120Halle, Germany
| | - Walter Durka
- Department of Community Ecology, Helmholtz Centre for Environmental Research - UFZ, 06120Halle, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103Leipzig, Germany
| | - Anna Bucharova
- Institute of Landscape Ecology, University of Münster, 48149Münster, Germany
- Department of Biology, Philipps-University Marburg, 35043Marburg, Germany
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Lopez-Moreno H, Basurto-Garduño AC, Torres-Meraz MA, Diaz-Valenzuela E, Arellano-Arciniega S, Zalapa J, Sawers RJH, Cibrián-Jaramillo A, Diaz-Garcia L. Genetic analysis and QTL mapping of domestication-related traits in chili pepper ( Capsicum annuum L .). Front Genet 2023; 14:1101401. [PMID: 37255716 PMCID: PMC10225550 DOI: 10.3389/fgene.2023.1101401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 03/31/2023] [Indexed: 06/01/2023] Open
Abstract
Chili pepper (Capsicum annuum L.) is one of the oldest and most phenotypically diverse pre-Columbian crops of the Americas. Despite the abundance of genetic resources, the use of wild germplasm and landraces in chili pepper breeding is limited. A better understanding of the evolutionary history in chili peppers, particularly in the context of traits of agronomic interest, can contribute to future improvement and conservation of genetic resources. In this study, an F2:3 mapping population derived from a cross between a C. annuum wild accession (Chiltepin) and a cultivated variety (Puya) was used to identify genomic regions associated with 19 domestication and agronomic traits. A genetic map was constructed consisting of 1023 single nucleotide polymorphism (SNP) markers clustered into 12 linkage groups and spanning a total of 1,263.87 cM. A reciprocal translocation that differentiates the domesticated genome from its wild ancestor and other related species was identified between chromosomes 1 and 8. Quantitative trait locus (QTL) analysis detected 20 marker-trait associations for 13 phenotypes, from which 14 corresponded to previously identified loci, and six were novel genomic regions related to previously unexplored domestication-syndrome traits, including form of unripe fruit, seedlessness, deciduous fruit, and growth habit. Our results revealed that the genetic architecture of Capsicum domestication is similar to other domesticated species with few loci with large effects, the presence of QTLs clusters in different genomic regions, and the predominance of domesticated recessive alleles. Our analysis indicates the domestication process in chili pepper has also had an effect on traits not directly related to the domestication syndrome. The information obtained in this study provides a more complete understanding of the genetic basis of Capsicum domestication that can potentially guide strategies for the exploitation of wild alleles.
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Affiliation(s)
- Hector Lopez-Moreno
- Ecological and Evolutionary Genomics Laboratory, Unidad de Genomica Avanzada (Langebio), Irapuato, Mexico
| | - Ana Celia Basurto-Garduño
- Ecological and Evolutionary Genomics Laboratory, Unidad de Genomica Avanzada (Langebio), Irapuato, Mexico
| | | | - Eric Diaz-Valenzuela
- Ecological and Evolutionary Genomics Laboratory, Unidad de Genomica Avanzada (Langebio), Irapuato, Mexico
| | - Sergio Arellano-Arciniega
- Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias Campo Experimental AGS, Pabellón de Arteaga, Mexico
| | - Juan Zalapa
- Department of Horticulture, University of WI-Madison, Madison, WI, United States
- USDA-ARS Vegetable Crops Research Unit, Department of Horticulture University of WI-Madison, Madison, WI, United States
| | - Ruairidh J. H. Sawers
- Department of Plant Science, The Pennsylvania State University, State College, PA, United States
| | - Angelica Cibrián-Jaramillo
- Ecological and Evolutionary Genomics Laboratory, Unidad de Genomica Avanzada (Langebio), Irapuato, Mexico
| | - Luis Diaz-Garcia
- Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias Campo Experimental AGS, Pabellón de Arteaga, Mexico
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Chapuis M, Leménager N, Piou C, Roumet P, Marche H, Centanni J, Estienne C, Ecarnot M, Vasseur F, Violle C, Kazakou E. Domestication provides durum wheat with protection from locust herbivory. Ecol Evol 2023; 13:e9741. [PMID: 36694552 PMCID: PMC9843534 DOI: 10.1002/ece3.9741] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 12/17/2022] [Accepted: 12/28/2022] [Indexed: 01/19/2023] Open
Abstract
Lower plant resistance to herbivores following domestication has been suggested as the main cause for higher feeding damage in crops than in wild progenitors. While herbivore compensatory feeding has also been proposed as a possible mechanism for raised damage in crops with low nutritional quality, predictions regarding the effects of plant domestication on nutritional quality for herbivores remain unclear. In particular, data on primary metabolites, even major macronutrients, measured in the organs consumed by herbivores, are scarce. In this study, we used a collection of 10 accessions of wild ancestors and 10 accessions of modern progenies of Triticum turgidum to examine whether feeding damage and selectivity by nymphs of Locusta migratoria primarily depended on five leaf traits related to structural resistance or nutrient profiles. Our results unexpectedly showed that locusts favored wild ancestors over domesticated accessions and that leaf toughness and nitrogen and soluble protein contents increased with the domestication process. Furthermore, the quantitative relationship between soluble protein and digestible carbohydrates was found to poorly meet the specific requirements of the herbivore, in all wheat accessions, both wild and modern. The increase in leaf structural resistance to herbivores in domesticated tetraploid wheat accessions suggested that resource allocation trade-offs between growth and herbivory resistance may have been disrupted by domestication in the vegetative organs of this species. Since domestication did not result in a loss of nutritional quality in the leaves of the tetraploid wheat, our results rather provides evidence for a role of the content of plants in nonnutritive nitrogenous secondary compounds, possibly deterrent or toxic, at least for grasshopper herbivores.
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Affiliation(s)
- Marie‐Pierre Chapuis
- CIRAD, CBGPMontpellierFrance,CBGP, CIRAD, Montpellier SupAgro, INRA, IRD, Univ MontpellierMontpellierFrance
| | - Nicolas Leménager
- CIRAD, CBGPMontpellierFrance,CBGP, CIRAD, Montpellier SupAgro, INRA, IRD, Univ MontpellierMontpellierFrance
| | - Cyril Piou
- CIRAD, CBGPMontpellierFrance,CBGP, CIRAD, Montpellier SupAgro, INRA, IRD, Univ MontpellierMontpellierFrance
| | - Pierre Roumet
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut AgroMontpellierFrance
| | - Héloïse Marche
- CIRAD, CBGPMontpellierFrance,CBGP, CIRAD, Montpellier SupAgro, INRA, IRD, Univ MontpellierMontpellierFrance
| | - Julia Centanni
- CEFE, Univ Montpellier, CNRS, EPHE, IRDMontpellierFrance
| | - Christophe Estienne
- CIRAD, CBGPMontpellierFrance,CBGP, CIRAD, Montpellier SupAgro, INRA, IRD, Univ MontpellierMontpellierFrance
| | - Martin Ecarnot
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut AgroMontpellierFrance
| | | | - Cyrille Violle
- CEFE, Univ Montpellier, CNRS, EPHE, IRDMontpellierFrance
| | - Elena Kazakou
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Institut AgroMontpellierFrance
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6
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Hattori M, Saito A, Nagasawa M, Kikusui T, Yamamoto S. Changes in Cat Facial Morphology Are Related to Interaction with Humans. Animals (Basel) 2022; 12:ani12243493. [PMID: 36552413 PMCID: PMC9774281 DOI: 10.3390/ani12243493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/03/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022] Open
Abstract
We aimed to clarify the changes in facial morphology of cats in relation to their interactions with humans. In Study 1, we compared the facial morphology of cats (feral mixed breed, owned domestic mixed breed, and owned domestic purebreds) with that of African wildcats. After collecting 3295 photos, we found that owned domestic cats' noses were significantly shorter than those of African wildcats and feral mixed breed, and there were no significant differences between the latter two. The eye angles were significantly more gradual in owned domestic purebreds than in the other groups. In Study 2, we examined the correlation between facial morphology and years with the owner, and found that the former is not affected by the latter. This suggests that changes in facial morphology are possibly transgenerational changes. The difference in facial morphology between wildcats and owned cats might be caused by domestication, and that between feral cats and owned cats might be due to feralization. In Study 3, we investigated whether cats' facial features affect cuteness ratings. We asked human participants to evaluate the cuteness of cats' face images and found that faces with shorter nose lengths were considered cuter. This suggests that owned domestic cats' facial morphology is preferred by humans.
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Affiliation(s)
- Madoka Hattori
- Wildlife Research Center, Kyoto University, 2-24 Tanaka-Sekiden-cho, Sakyo-ku, Kyoto 606-8203, Japan
- Department of Animal Science and Biotechnology, Azabu University, 1-17-71 Fuchinobe, Chuo-ku, Sagamihara-shi 252-5201, Japan
| | - Atsuko Saito
- Department of Psychology, Faculty of Human Sciences, Sophia University, 7-1 Kioicho, Chiyoda-ku, Tokyo 102-8554, Japan
| | - Miho Nagasawa
- Department of Animal Science and Biotechnology, Azabu University, 1-17-71 Fuchinobe, Chuo-ku, Sagamihara-shi 252-5201, Japan
| | - Takefumi Kikusui
- Department of Animal Science and Biotechnology, Azabu University, 1-17-71 Fuchinobe, Chuo-ku, Sagamihara-shi 252-5201, Japan
| | - Shinya Yamamoto
- Wildlife Research Center, Kyoto University, 2-24 Tanaka-Sekiden-cho, Sakyo-ku, Kyoto 606-8203, Japan
- Institute for Advanced Study, Kyoto University, Yoshida Ushinomiya-cho, Sakyo-ku, Kyoto 606-8501, Japan
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7
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Wilson LAB. Developmental instability in domesticated mammals. J Exp Zool B Mol Dev Evol 2022; 338:484-494. [PMID: 34813170 DOI: 10.1002/jez.b.23108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 11/04/2021] [Accepted: 11/08/2021] [Indexed: 06/13/2023]
Abstract
Measures of fluctuating asymmetry (FA) have been adopted widely as an estimate of developmental instability. Arising from various sources of stress, developmental instability is associated with an organism's capacity to maintain fitness. The process of domestication has been framed as an environmental stress with human-specified parameters, suggesting that FA may manifest to a larger degree among domesticates compared to their wild relatives. This study used three-dimensional geometric morphometric landmark data to (a) quantify the amount of FA in the cranium of six domestic mammal species and their wild relatives and, (b) provide novel assessment of the commonalities and differences across domestic/wild pairs concerning the extent to which random variation arising from the developmental system assimilates into within-population variation. The majority of domestic mammals showed greater disparity for asymmetric shape, however, only two forms (Pig, Dog) showed significantly higher disparity as well as a higher degree of asymmetry compared to their wild counterparts (Wild Boar, Wolf). Contra to predictions, most domestic and wild forms did not show a statistically significant correspondence between symmetric shape variation and FA, however, a moderate correlation value was recorded for most pairs (r-partial least squares >0.5). Within pairs, domestic and wild forms showed similar correlation magnitudes for the relationship between the asymmetric and symmetric components. In domesticates, new variation may therefore retain a general, conserved pattern in the gross structuring of the cranium, whilst also being a source for response to selection on specific features.
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Affiliation(s)
- Laura A B Wilson
- School of Archaeology and Anthropology, The Australian National University, Canberra, ACT, Australia
- School of Biological, Earth, and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
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Zhang H, Mascher M, Abbo S, Jayakodi M. Advancing Grain Legumes Domestication and Evolution Studies with Genomics. Plant Cell Physiol 2022; 63:1540-1553. [PMID: 35534441 PMCID: PMC9680859 DOI: 10.1093/pcp/pcac062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 05/03/2022] [Accepted: 05/09/2022] [Indexed: 06/14/2023]
Abstract
Grain legumes were domesticated in parallel with cereals in several regions of the world and formed the economic basis of early farming cultures. Since then, legumes have played a vital role in human and animal diets and in fostering agrobiodiversity. Increasing grain legume cultivation will be crucial to safeguard nutritional security and the resilience of agricultural ecosystems across the globe. A better understanding of the molecular underpinnings of domestication and crop evolution of grain legumes may be translated into practical approaches in modern breeding programs to stabilize yield, which is threatened by evolving pathogens and changing climates. During recent decades, domestication research in all crops has greatly benefited from the fast progress in genomic technologies. Yet still, many questions surrounding the domestication and diversification of legumes remain unanswered. In this review, we assess the potential of genomic approaches in grain legume research. We describe the centers of origin and the crucial domestication traits of grain legumes. In addition, we survey the effect of domestication on both above-ground and below-ground traits that have economic importance. Finally, we discuss open questions in grain legume domestication and diversification and outline how to bridge the gap between the preservation of historic crop diversity and their utilization in modern plant breeding.
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Affiliation(s)
- Hailin Zhang
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, Gatersleben, Seeland 06466, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, Gatersleben, Seeland 06466, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, Leipzig 04103, Germany
| | - Shahal Abbo
- The Levi Eshkol School of Agriculture, The Hebrew University of Jerusalem, POB 12, Rehovot 7610001, Israel
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Nerva L, Sandrini M, Moffa L, Velasco R, Balestrini R, Chitarra W. Breeding toward improved ecological plant-microbiome interactions. Trends Plant Sci 2022; 27:1134-1143. [PMID: 35803843 DOI: 10.1016/j.tplants.2022.06.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 06/04/2022] [Accepted: 06/09/2022] [Indexed: 06/15/2023]
Abstract
Domestication processes, amplified by breeding programs, have allowed the selection of more productive genotypes and more suitable crop lines capable of coping with the changing climate. Notwithstanding these advancements, the impact of plant breeding on the ecology of plant-microbiome interactions has not been adequately considered yet. This includes the possible exploitation of beneficial plant-microbe interactions to develop crops with improved performance and better adaptability to any environmental scenario. Here we discuss the exploitation of customized synthetic microbial communities in agricultural systems to develop more sustainable breeding strategies based on the implementation of multiple interactions between plants and their beneficial associated microorganisms.
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Affiliation(s)
- Luca Nerva
- Research Centre for Viticulture and Enology, Council for Agricultural Research and Economics (CREA-VE), Via XXVIII Aprile 26, 31015 Conegliano, (TV), Italy; National Research Council of Italy - Institute for Sustainable Plant Protection (CNR-IPSP), Strada delle Cacce, 73, 10135 Torino (TO), Italy
| | - Marco Sandrini
- Research Centre for Viticulture and Enology, Council for Agricultural Research and Economics (CREA-VE), Via XXVIII Aprile 26, 31015 Conegliano, (TV), Italy; University of Udine, Department of Agricultural, Food, Environmental and Animal Sciences, Via delle Scienze 206, 33100, Udine, (UD), Italy
| | - Loredana Moffa
- Research Centre for Viticulture and Enology, Council for Agricultural Research and Economics (CREA-VE), Via XXVIII Aprile 26, 31015 Conegliano, (TV), Italy; University of Udine, Department of Agricultural, Food, Environmental and Animal Sciences, Via delle Scienze 206, 33100, Udine, (UD), Italy
| | - Riccardo Velasco
- Research Centre for Viticulture and Enology, Council for Agricultural Research and Economics (CREA-VE), Via XXVIII Aprile 26, 31015 Conegliano, (TV), Italy
| | - Raffaella Balestrini
- National Research Council of Italy - Institute for Sustainable Plant Protection (CNR-IPSP), Strada delle Cacce, 73, 10135 Torino (TO), Italy.
| | - Walter Chitarra
- Research Centre for Viticulture and Enology, Council for Agricultural Research and Economics (CREA-VE), Via XXVIII Aprile 26, 31015 Conegliano, (TV), Italy; National Research Council of Italy - Institute for Sustainable Plant Protection (CNR-IPSP), Strada delle Cacce, 73, 10135 Torino (TO), Italy
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10
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Li Y, Fang X, Lin Z. Convergent loss of anthocyanin pigments is controlled by the same MYB gene in cereals. J Exp Bot 2022; 73:6089-6102. [PMID: 35724645 DOI: 10.1093/jxb/erac270] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 06/17/2022] [Indexed: 06/15/2023]
Abstract
Loss of anthocyanin pigments is a common transition during cereal domestication, diversification, and improvement. However, the genetic basis for this convergent transition in cereal remains largely unknown. Here, we identified a chromosomal syntenic block across different species that contained R2R3-MYB genes (c1/pl1) responsible for the convergent decoloring of anthocyanins in cereals. Quantitative trait locus (QTL) mapping identified a major QTL for aerial root color corresponding to pl1 and a major QTL for spikelet color corresponding to c1 on maize chromosomes 6 and 9, respectively. One insertion in the regulatory region that led to transcriptional down-regulation was present in maize pl1, and several insertions in the coding region resulting in loss of function occurred in maize c1. A transposable element insertion in the third exon of c1, leading to three new non-functional transcripts, was responsible for decoloring in foxtail millet. The c1/pl1 genes enhanced the transcription of the core enzyme-encoding genes, including pr1, fht1, a1, a2, bz1, and aat1 in the anthocyanin pathway, while they repressed the expression of fnsii1 in flavones, sm2 in maysin, and bx3, bx4, bx5, and bx10 in DIMBOA. Our results indicated that the convergent decoloring of these plants shared the same genetic basis across different cereal species.
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Affiliation(s)
- Yan Li
- National Maize Improvement Center; Center for Crop Functional Genomics and Molecular Breeding; Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education; Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, China Agricultural University, Beijing, China
| | - Xiaojian Fang
- National Maize Improvement Center; Center for Crop Functional Genomics and Molecular Breeding; Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education; Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, China Agricultural University, Beijing, China
| | - Zhongwei Lin
- National Maize Improvement Center; Center for Crop Functional Genomics and Molecular Breeding; Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education; Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, China Agricultural University, Beijing, China
- Sanya Institute of China Agricultural University, Sanya, Hainan, China
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11
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Amkul K, Somta P, Laosatit K, Wang L. Identification of QTLs for Domestication-Related Traits in Zombi Pea [ Vigna vexillata (L.) A. Rich], a Lost Crop of Africa. Front Genet 2020; 11:803. [PMID: 33193562 PMCID: PMC7530282 DOI: 10.3389/fgene.2020.00803] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 07/06/2020] [Indexed: 11/13/2022] Open
Abstract
Zombi pea [Vigna vexillata (L.) A. Rich] is a legume crop found in Africa. Wild zombi pea is widely distributed throughout the tropical and subtropical regions, whereas domesticated zombi pea is rarely cultivated. Plant domestication is an evolutionary process in which the phenotypes of wild species, including seed dormancy, pod shattering, organ size, and architectural and phenological characteristics, undergo changes. The molecular mechanism underlying the domestication of zombi pea is relatively unknown. In this study, the genetic basis of the following 13 domestication-related traits was investigated in an F2 population comprising 198 individuals derived from a cross between cultivated (var. macrosperma) and wild (var. vexillata) zombi pea accessions: seed dormancy, pod shattering, days-to-flowering, days-to-maturity, stem thickness, stem length, number of branches, leaf area, pod length, 100-seed weight, seed width, seed length, and seeds per pod. A genetic map containing 6,529 single nucleotide polymorphisms constructed for the F2 population was used to identify quantitative trait loci (QTLs) for these traits. A total of 62 QTLs were identified for the 13 traits, with 1-11 QTLs per trait. The major QTLs for days-to-flowering, stem length, number of branches, pod length, 100-seed weight, seed length, and seeds per pod were clustered in linkage group 5. In contrast, the major QTLs for seed dormancy and pod shattering belonged to linkage groups 3 and 11, respectively. A comparative genomic analysis with the cowpea [Vigna unguiculata (L.) Walp.] genome used as the reference sequence (i.e., the genome of the legume species most closely related to zombi pea) enabled the identification of candidate genes for the major QTLs. Thus, we revealed the genomic regions associated with domestication-related traits and the candidate genes controlling these traits in zombi pea. The data presented herein may be useful for breeding new varieties of zombi pea and other Vigna species.
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Affiliation(s)
- Kitiya Amkul
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom, Thailand
| | - Prakit Somta
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom, Thailand.,Center of Excellence on Agricultural Biotechnology: (AG-BIO/PERDO-CHE), Bangkok, Thailand
| | - Kularb Laosatit
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom, Thailand
| | - Lixia Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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12
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Ferrero V, Baeten L, Blanco-Sánchez L, Planelló R, Díaz-Pendón JA, Rodríguez-Echeverría S, Haegeman A, de la Peña E. Complex patterns in tolerance and resistance to pests and diseases underpin the domestication of tomato. New Phytol 2020; 226:254-266. [PMID: 31793000 DOI: 10.1111/nph.16353] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 11/19/2019] [Indexed: 05/26/2023]
Abstract
A frequent hypothesis explaining the high susceptibility of many crops to pests and diseases is that, in the process of domestication, crops have lost defensive genes and traits against pests and diseases. Ecological theory predicts trade-offs whereby resistance and tolerance go at the cost of each other. We used wild relatives, early domesticated varieties, traditional local landraces and cultivars of tomato (Solanum lycopersicum) to test whether resistance and tolerance trade-offs were phylogenetically structured or varied according to degree of domestication. We exposed tomato genotypes to the aphid Macrosiphum euphorbiae, the cotton leafworm Spodoptera littoralis, the root knot nematode Meloidogyne incognita and two common insect-transmitted plant viruses, and reconstructed their phylogenetic relationships using Genotyping-by-Sequencing. We found differences in the performance and effect of pest and diseases but such differences were not related with domestication degree nor genetic relatedness, which probably underlie a complex genetic basis for resistance and indicate that resistance traits appeared at different stages and in unrelated genetic lineages. Still, wild and early domesticated accessions showed greater resistance to aphids and tolerance to caterpillars, nematodes and diseases than modern cultivars. Our findings help to understand how domestication affects plant-pest interactions and underline the importance of tolerance in crop breeding.
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Affiliation(s)
- Victoria Ferrero
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, 3000-456, Coimbra, Portugal
- Institute for Subtropical and Mediterranean Horticulture, Spanish National Research Council (IHSM-UMA-CSIC), Finca Experimental La Mayora, Algarrobo-Costa, 29750, Málaga, Spain
| | - Lander Baeten
- Department of Environment, Forest & Nature Lab, Ghent University, BE-9090, Melle-Gontrode, Belgium
| | - Lidia Blanco-Sánchez
- Institute for Subtropical and Mediterranean Horticulture, Spanish National Research Council (IHSM-UMA-CSIC), Finca Experimental La Mayora, Algarrobo-Costa, 29750, Málaga, Spain
| | - Rosario Planelló
- Grupo de Biología y Toxicología Ambiental, Facultad de Ciencias, Universidad Nacional de Educación a Distancia, UNED, Paseo de la Senda del Rey 9, 28040, Madrid, Spain
| | - Juan Antonio Díaz-Pendón
- Institute for Subtropical and Mediterranean Horticulture, Spanish National Research Council (IHSM-UMA-CSIC), Finca Experimental La Mayora, Algarrobo-Costa, 29750, Málaga, Spain
| | - Susana Rodríguez-Echeverría
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, 3000-456, Coimbra, Portugal
| | - Annelies Haegeman
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Caritasstraat 39, B-9090, Melle, Belgium
| | - Eduardo de la Peña
- Institute for Subtropical and Mediterranean Horticulture, Spanish National Research Council (IHSM-UMA-CSIC), Finca Experimental La Mayora, Algarrobo-Costa, 29750, Málaga, Spain
- Department of Biology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35, B-9000, Gent, Belgium
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13
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Zeder MA. Straw Foxes: Domestication Syndrome Evaluation Comes Up Short. Trends Ecol Evol 2020; 35:647-649. [PMID: 32668211 DOI: 10.1016/j.tree.2020.03.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 02/23/2020] [Accepted: 03/02/2020] [Indexed: 02/01/2023]
Affiliation(s)
- Melinda A Zeder
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.
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14
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Abstract
Domestication of wild animals induces a set of phenotypic characteristics collectively known as the domestication syndrome. However, how this syndrome emerges is still not clear. Recently, the neural crest cell deficit hypothesis proposed that it is generated by a mildly disrupted neural crest cell developmental program, but clear support is lacking due to the difficulties of distinguishing pure domestication effects from preexisting genetic differences between farmed and wild mammals and birds. Here, we use a farmed fish as model to investigate the role of persistent changes in DNA methylation (epimutations) in the process of domestication. We show that early domesticates of sea bass, with no genetic differences with wild counterparts, contain epimutations in tissues with different embryonic origins. About one fifth of epimutations that persist into adulthood are established by the time of gastrulation and affect genes involved in developmental processes that are expressed in embryonic structures, including the neural crest. Some of these genes are differentially expressed in sea bass with lower jaw malformations, a key feature of domestication syndrome. Interestingly, these epimutations significantly overlap with cytosine-to-thymine polymorphisms after 25 years of selective breeding. Furthermore, epimutated genes coincide with genes under positive selection in other domesticates. We argue that the initial stages of domestication include dynamic alterations in DNA methylation of developmental genes that affect the neural crest. Our results indicate a role for epimutations during the beginning of domestication that could be fixed as genetic variants and suggest a conserved molecular process to explain Darwin’s domestication syndrome across vertebrates.
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Affiliation(s)
- Dafni Anastasiadi
- Institut de Ciències del Mar, Spanish National Research Council (CSIC), Barcelona, Spain.,The New Zealand Institute for Plant & Food Research, Nelson, New Zealand
| | - Francesc Piferrer
- Institut de Ciències del Mar, Spanish National Research Council (CSIC), Barcelona, Spain
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15
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Kissing Kucek L, Riday H, Rufener BP, Burke AN, Eagen SS, Ehlke N, Krogman S, Mirsky SB, Reberg-Horton C, Ryan MR, Wayman S, Wiering NP. Pod Dehiscence in Hairy Vetch ( Vicia villosa Roth). Front Plant Sci 2020; 11:82. [PMID: 32194580 PMCID: PMC7063115 DOI: 10.3389/fpls.2020.00082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 01/21/2020] [Indexed: 05/03/2023]
Abstract
Hairy vetch, Vicia villosa (Roth), is a cover crop that does not exhibit a typical domestication syndrome. Pod dehiscence reduces seed yield and creates weed problems for subsequent crops. Breeding efforts aim to reduce pod dehiscence in hairy vetch. To characterize pod dehiscence in the species, we quantified visual dehiscence and force required to cause dehiscence among 606 genotypes grown among seven environments of the United States. To identify potential secondary selection traits, we correlated pod dehiscence with various morphological pod characteristics and field measurements. Genotypes of hairy vetch exhibited wide variation in pod dehiscence, from completely indehiscent to completely dehiscent ratings. Mean force to dehiscence also varied widely, from 0.279 to 8.97 N among genotypes. No morphological traits were consistently correlated with pod dehiscence among environments where plants were grown. Results indicated that visual ratings of dehiscence would efficiently screen against genotypes with high pod dehiscence early in the breeding process. Force to dehiscence may be necessary to identify the indehiscent genotypes during advanced stages of selection.
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Affiliation(s)
| | - Heathcliffe Riday
- Dairy Forage Research Center, USDA-ARS, Madison, WI, United States
- *Correspondence: Heathcliffe Riday,
| | - Bryce P. Rufener
- Dairy Forage Research Center, USDA-ARS, Madison, WI, United States
| | - Allen N. Burke
- Sustainable Agricultural Systems Laboratory, Beltsville Agricultural Research Center, USDA-ARS, Beltsville, MD, United States
| | - Sarah Seehaver Eagen
- Crop and Soil Science, North Carolina State University, Raleigh, NC, United States
| | - Nancy Ehlke
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, United States
| | - Sarah Krogman
- Noble Research Institute, Ardmore, OK, United States
| | - Steven B. Mirsky
- Sustainable Agricultural Systems Laboratory, Beltsville Agricultural Research Center, USDA-ARS, Beltsville, MD, United States
| | - Chris Reberg-Horton
- Crop and Soil Science, North Carolina State University, Raleigh, NC, United States
| | - Matthew R. Ryan
- School of Integrated Plant Science, Cornell University, Ithaca, NY, United States
| | - Sandra Wayman
- School of Integrated Plant Science, Cornell University, Ithaca, NY, United States
| | - Nick P. Wiering
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, United States
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16
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Lord KA, Larson G, Coppinger RP, Karlsson EK. The History of Farm Foxes Undermines the Animal Domestication Syndrome. Trends Ecol Evol 2019; 35:125-136. [PMID: 31810775 DOI: 10.1016/j.tree.2019.10.011] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 10/17/2019] [Accepted: 10/18/2019] [Indexed: 12/22/2022]
Abstract
The Russian Farm-Fox Experiment is the best known experimental study in animal domestication. By subjecting a population of foxes to selection for tameness alone, Dimitry Belyaev generated foxes that possessed a suite of characteristics that mimicked those found across domesticated species. This 'domestication syndrome' has been a central focus of research into the biological pathways modified during domestication. Here, we chart the origins of Belyaev's foxes in eastern Canada and critically assess the appearance of domestication syndrome traits across animal domesticates. Our results suggest that both the conclusions of the Farm-Fox Experiment and the ubiquity of domestication syndrome have been overstated. To understand the process of domestication requires a more comprehensive approach focused on essential adaptations to human-modified environments.
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Affiliation(s)
- Kathryn A Lord
- Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01655, USA; Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Greger Larson
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK
| | - Raymond P Coppinger
- School of Cognitive Science, Hampshire College, 893 West St, Amherst, MA 01002, USA
| | - Elinor K Karlsson
- Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01655, USA; Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA; Program in Molecular Medicine, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01655, USA.
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17
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Garamszegi LZ, Temrin H, Kubinyi E, Miklósi Á, Kolm N. The role of common ancestry and gene flow in the evolution of human-directed play behaviour in dogs. J Evol Biol 2019; 33:318-328. [PMID: 31705702 DOI: 10.1111/jeb.13567] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 11/04/2019] [Indexed: 11/29/2022]
Abstract
Among-population variance of phenotypic traits is of high relevance for understanding evolutionary mechanisms that operate in relatively short timescales, but various sources of nonindependence, such as common ancestry and gene flow, can hamper the interpretations. In this comparative analysis of 138 dog breeds, we demonstrate how such confounders can independently shape the evolution of a behavioural trait (human-directed play behaviour from the Dog Mentality Assessment project). We combined information on genetic relatedness and haplotype sharing to reflect common ancestry and gene flow, respectively, and entered these into a phylogenetic mixed model to partition the among-breed variance of human-directed play behaviour while also accounting for within-breed variance. We found that 75% of the among-breed variance was explained by overall genetic relatedness among breeds, whereas 15% could be attributed to haplotype sharing that arises from gene flow. Therefore, most of the differences in human-directed play behaviour among breeds have likely been caused by constraints of common ancestry as a likely consequence of past selection regimes. On the other hand, gene flow caused by crosses among breeds has played a minor, but not negligible role. Our study serves as an example of an analytical approach that can be applied to comparative situations where the effects of shared origin and gene flow require quantification and appropriate statistical control in a within-species/among-population framework. Altogether, our results suggest that the evolutionary history of dog breeds has left remarkable signatures on the among-breed variation of a behavioural phenotype.
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Affiliation(s)
- László Zsolt Garamszegi
- Centre for Ecological Research, Institute of Ecology and Botany, Vácrátót, Hungary.,MTA-ELTE Theoretical Biology and Evolutionary Ecology Research Group, Department of Plant Systematics, Ecology and Theoretical Biology, Eötvös Loránd University, Budapest, Hungary.,Department of Evolutionary Ecology, Estación Biológica de Doñana-CSIC, Seville, Spain
| | - Hans Temrin
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Enikő Kubinyi
- Department of Ethology, Eötvös Loránd University, Budapest, Hungary
| | - Ádám Miklósi
- Department of Ethology, Eötvös Loránd University, Budapest, Hungary.,MTA-ELTE Comparative Ethology Research Group, Budapest, Hungary
| | - Niclas Kolm
- Department of Zoology, Stockholm University, Stockholm, Sweden
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18
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Brǿnnvik H, von Wettberg EJ. Bird Dispersal as a Pre-Adaptation for Domestication in Legumes: Insights for Neo-Domestication. Front Plant Sci 2019; 10:1293. [PMID: 31681385 PMCID: PMC6803499 DOI: 10.3389/fpls.2019.01293] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 09/18/2019] [Indexed: 06/10/2023]
Affiliation(s)
- Hester Brǿnnvik
- Department of Plant and Soil Science, University of Vermont, Burlington, VT, United States
| | - Eric J. von Wettberg
- Department of Plant and Soil Science, University of Vermont, Burlington, VT, United States
- Mathematical Biology and Bioinformatics Laboratory, Peter the Great St. Petersburg Polytechic University, Saint Petersburg, Russia
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19
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Abstract
The question of whether "developmental bias" can influence evolution is still controversial, despite much circumstantial evidence and a good theoretical argument. Here, I will argue that the domestication of mammalian species, which took place independently more than two dozen times, provides a particularly convincing example of developmental bias in evolution. The singular finding that underlies this claim is the repeated occurrence in domesticated mammals of a set of distinctive traits, none of which were deliberately selected. This phenomenon has been termed "the domestication syndrome". In this article, I will: (a) describe the properties of the domestication syndrome; (b) show how it can be explained in terms of the operation of a specific genetic regulatory network, that which governs neural crest cell development; and (c) discuss Dmitry Belyaev's idea of "destabilizing selection," which holds that selecting for a new behavior often entails neuroendocrine alterations that alter many aspects of development. Finally, I will argue for the potential general significance of such destabilizing selection, in combination with developmental bias, in animal evolution.
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Affiliation(s)
- Adam S Wilkins
- Institute of Theoretical Biology, Humboldt Universität zu Berlin, Berlin, Germany
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20
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Abstract
Language evolution has long been researched. I will review a number of broad, emerging research directions which arguably have the potential to contribute to our understanding of language evolution. Emerging topics in genomics and neurolinguistics are explored, and human-specific levels of braincase globularity - and the broader process of self-domestication within which globularity seems capable of being encapsulated - will be argued to be the central pillars of any satisfactory and interdisciplinary model of language evolution.
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Affiliation(s)
- Elliot Murphy
- Division of Psychology and Language Sciences, University College London, London, United Kingdom
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21
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Cortés AJ, Skeen P, Blair MW, Chacón-Sánchez MI. Does the Genomic Landscape of Species Divergence in Phaseolus Beans Coerce Parallel Signatures of Adaptation and Domestication? Front Plant Sci 2018; 9:1816. [PMID: 30619396 PMCID: PMC6306030 DOI: 10.3389/fpls.2018.01816] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 11/22/2018] [Indexed: 05/10/2023]
Abstract
Exploring the genomic architecture of species and populations divergence aids understanding how lineages evolve and adapt, and ultimately can show the repeatability of evolutionary processes. Yet, the genomic signatures associated with divergence are still relatively unexplored, leading to a knowledge gap on whether species divergence ultimately differs in its genetic architecture from divergence at other spatial scales (i.e., populations, ecotypes). Our goal in this research was to determine whether genomic islands of speciation are more prone to harbor within-species differentiation due to genomic features, suppressed recombination, smaller effective population size or increased drift, across repeated hierarchically nested levels of divergence. We used two species of Phaseolus beans with strong genepool and population sub-structure produced by multiple independent domestications each especially in Andean and Mesoamerican / Middle American geographies. We genotyped 22,531 GBS-derived SNP markers in 209 individuals of wild and cultivated Phaseolus vulgaris and Phaseolus lunatus. We identified six regions for species-associated divergence. Out of these divergence peaks, 21% were recovered in the four within-species between-genepool comparisons and in the five within-genepool wild-cultivated comparisons (some of the latter did retrieve genuine signatures of the well described multiple domestication syndromes). However, genomic regions with overall high relative differentiation (measured by FST) coincided with regions of low SNP density and regions of elevated delta divergence between-genepools (ΔDiv), independent of the scale of divergence. The divergence in chromosome Pv10 further coincided with a between-species pericentric inversion. These convergences suggest that shared variants are being recurrently fixed at replicated regions of the genome, and in a similar manner across different hierarchically nested levels of divergence, likely as result of genomic features that make certain regions more prone to accumulate islands of speciation and within-species divergence. In summary, neighboring signatures of speciation, adaptation and domestication in Phaseolus beans are influenced by ubiquitous genomic constrains, which may continue to fortuitously shape genomic differentiation at various others scales of divergence.
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Affiliation(s)
- Andrés J. Cortés
- Corporación Colombiana de Investigación Agropecuaria (Agrosavia) – Centro de Investigación La Selva, Rionegro, Colombia
- Universidad Nacional de Colombia – Sede Medellín, Facultad de Ciencias Agrarias – Departamento de Ciencias
Forestales, Medellín, Colombia
| | - Paola Skeen
- Universidad Nacional de Colombia – Bogotá, Facultad de Ciencias Agrarias – Departamento de Agronomía, Bogotá, Colombia
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Matthew W. Blair
- Department of Agricultural and Environmental Science, Tennessee State University, Nashville, TN, United States
| | - María I. Chacón-Sánchez
- Universidad Nacional de Colombia – Bogotá, Facultad de Ciencias Agrarias – Departamento de Agronomía, Bogotá, Colombia
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22
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Kantar MB, Hüber S, Herman A, Bock DG, Baute G, Betts K, Ott M, Brandvain Y, Wyse D, Stupar RM, Rieseberg LH. Neo-Domestication of an Interspecific Tetraploid Helianthus annuus × Helianthus tuberous Population That Segregates for Perennial Habit. Genes (Basel) 2018; 9:genes9090422. [PMID: 30134600 PMCID: PMC6162802 DOI: 10.3390/genes9090422] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 08/14/2018] [Accepted: 08/16/2018] [Indexed: 11/16/2022] Open
Abstract
Perennial agriculture has been proposed as an option to improve the sustainability of cropping systems, by increasing the efficiency of resource use, while also providing ecosystem services. Neo-domestication, the contemporary domestication of plants that have not previously been used in agriculture, can be used to generate new crops for these systems. Here we explore the potential of a tetraploid (2n = 4x = 68) interspecific hybrid sunflower as a perennial oilseed for use in multifunctional agricultural systems. A population of this novel tetraploid was obtained from crosses between the annual diploid oilseed crop Helianthus annuus (2n = 2x = 34) and the perennial hexaploid tuber crop Helianthus tuberosus (2n = 6x = 102). We selected for classic domestication syndrome traits for three generations. Substantial phenotypic gains were made, in some cases approaching 320%. We also analyzed the genetic basis of tuber production (i.e., perenniality), with the goal of obtaining molecular markers that could be used to facilitate future breeding in this system. Results from quantitative trait locus (QTL) mapping suggest that tuber production has an oligogenic genetic basis. Overall, this study indicates that substantial gains towards domestication goals can be achieved over contemporary time scales.
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Affiliation(s)
- Michael B Kantar
- Department of Tropical Plant & Soil Sciences, St. John Plant Science Lab, Room 102, 3190 Maile Way, Honolulu, HI 96822, USA.
- Biodiversity Research Centre and Department of Botany, University of British Columbia, 3529-6270 University Boulevard, Vancouver, British Columbia, BC V6T 1Z4, Canada.
- Department of Agronomy and Plant Genetics, University of Minnesota, 411 Borlaug Hall, 1991 Upper Buford Circle, St. Paul, MN 55108, USA.
| | - Sariel Hüber
- Biodiversity Research Centre and Department of Botany, University of British Columbia, 3529-6270 University Boulevard, Vancouver, British Columbia, BC V6T 1Z4, Canada.
- Department of Biotechnology, Tel-Hai Academic College, Upper Galilee 12210, Israel.
- MIGAL-Galilee Research Institute, Kiryat Shmona 11016, Israel.
| | - Adam Herman
- Department of Plant and Microbial Biology, 123 Snyder Hall, 1475 Gortner Ave, Saint Paul, MN 55108, USA.
| | - Dan G Bock
- Biodiversity Research Centre and Department of Botany, University of British Columbia, 3529-6270 University Boulevard, Vancouver, British Columbia, BC V6T 1Z4, Canada.
| | - Greg Baute
- Biodiversity Research Centre and Department of Botany, University of British Columbia, 3529-6270 University Boulevard, Vancouver, British Columbia, BC V6T 1Z4, Canada.
| | - Kevin Betts
- Department of Agronomy and Plant Genetics, University of Minnesota, 411 Borlaug Hall, 1991 Upper Buford Circle, St. Paul, MN 55108, USA.
| | - Matthew Ott
- Department of Agronomy and Plant Genetics, University of Minnesota, 411 Borlaug Hall, 1991 Upper Buford Circle, St. Paul, MN 55108, USA.
| | - Yaniv Brandvain
- Department of Plant and Microbial Biology, 123 Snyder Hall, 1475 Gortner Ave, Saint Paul, MN 55108, USA.
| | - Donald Wyse
- Department of Agronomy and Plant Genetics, University of Minnesota, 411 Borlaug Hall, 1991 Upper Buford Circle, St. Paul, MN 55108, USA.
| | - Robert M Stupar
- Department of Agronomy and Plant Genetics, University of Minnesota, 411 Borlaug Hall, 1991 Upper Buford Circle, St. Paul, MN 55108, USA.
| | - Loren H Rieseberg
- Biodiversity Research Centre and Department of Botany, University of British Columbia, 3529-6270 University Boulevard, Vancouver, British Columbia, BC V6T 1Z4, Canada.
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23
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Pedrosa HC, Clement CR, Schietti J. The Domestication of the Amazon Tree Grape ( Pourouma cecropiifolia) Under an Ecological Lens. Front Plant Sci 2018; 9:203. [PMID: 29593750 PMCID: PMC5861524 DOI: 10.3389/fpls.2018.00203] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 02/02/2018] [Indexed: 06/08/2023]
Abstract
Domestication studies traditionally focus on the differences in morphological characteristics between wild and domesticated populations that are under direct selection, the components of the domestication syndrome. Here, we consider that other aspects can be modified, because of the interdependence between plant characteristics and the forces of natural selection. We investigated the ongoing domestication of Pourouma cecropiifolia populations cultivated by the Ticuna people in Western Amazonia, using traditional and ecological approaches. We compared fruit characteristics between wild and domesticated populations to quantify the direct effects of domestication. To examine the characteristics that are not under direct selection and the correlated effects of human selection and natural selection, we investigated the differences in vegetative characteristics, changes in seed:fruit allometric relations and the relations of these characteristics with variation in environmental conditions summarized in a principal component analysis. Domestication generated great changes in fruit characteristics, as expected in fruit crops. The fruits of domesticated plants had 20× greater mass and twice as much edible pulp as wild fruits. The plant height:DBH ratio and wood density were, respectively, 42% and 22% smaller in domesticated populations, probably in response to greater luminosity and higher sand content of the cultivated landscapes. Seed:fruit allometry was modified by domestication: although domesticated plants have heavier seeds, the domesticated fruits have proportionally (46%) smaller seed mass compared to wild fruits. The high light availability and poor soils of cultivated landscapes may have contributed to seed mass reduction, while human selection promoted seed mass increase in correlation with fruit mass increase. These contrasting effects generated a proportionately smaller increase in seed mass in domesticated plants. In this study, it was not possible to clearly dissociate the environmental effects from the domestication effects in changes in morphological characteristics, because the environmental conditions were intensively modified by human management, showing that plant domestication is intrinsically related to landscape domestication. Our results suggest that evaluation of environmental conditions together with human selection on domesticated phenotypes provide a better understanding of the changes generated by domestication in plants.
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Affiliation(s)
- Hermísia C. Pedrosa
- Programa de Pós-Graduação em Ecologia, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
| | - Charles R. Clement
- Coordenação de Tecnologia e Inovação, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
| | - Juliana Schietti
- Programa de Pós-Graduação em Ecologia, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
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Geiger M, Sánchez-Villagra MR, Lindholm AK. A longitudinal study of phenotypic changes in early domestication of house mice. R Soc Open Sci 2018; 5:172099. [PMID: 29657805 PMCID: PMC5882729 DOI: 10.1098/rsos.172099] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 01/31/2018] [Indexed: 05/24/2023]
Abstract
Similar phenotypic changes occur across many species as a result of domestication, e.g. in pigmentation and snout size. Experimental studies of domestication have concentrated on intense and directed selection regimes, while conditions that approximate the commensal and indirect interactions with humans have not been explored. We examine long-term data on a free-living population of wild house mice that have been indirectly selected for tameness by regular exposure to humans. In the course of a decade, this mouse population exhibited significantly increased occurrence of white patches of fur and decreased head length. These phenotypic changes fit to the predictions of the 'domestication syndrome'.
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Affiliation(s)
- Madeleine Geiger
- Palaeontological Institute and Museum, University of Zurich, Karl-Schmid-Strasse 4, 8006 Zurich, Switzerland
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Marcelo R. Sánchez-Villagra
- Palaeontological Institute and Museum, University of Zurich, Karl-Schmid-Strasse 4, 8006 Zurich, Switzerland
| | - Anna K. Lindholm
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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Iriondo JM, Milla R, Volis S, Rubio de Casas R. Reproductive traits and evolutionary divergence between Mediterranean crops and their wild relatives. Plant Biol (Stuttg) 2018; 20 Suppl 1:78-88. [PMID: 28976618 DOI: 10.1111/plb.12640] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 09/27/2017] [Indexed: 05/12/2023]
Abstract
Changes in reproductive traits associated with domestication critically determine the evolutionary divergence between crops and their wild relatives, as well as the potential of crop plants to become feral. In this review, we examine the genetic mechanisms of plant domestication and the different types of selection involved, and describe the particularities of domestication of Mediterranean field crops with regard to their reproductive traits, showing illustrative examples. We also explore gene flow patterns between Mediterranean field crops and their wild relatives, along with their ecological, evolutionary and economic implications. Domestication entails multiple selective processes, including direct selection, environmental adaptation and developmental constraints. In contrast to clonal propagation in perennials, sexual reproduction and seed propagation in annuals and biennials have led to a distinct pathway of evolution of reproductive traits. Thus, the initial domestication and further breeding of Mediterranean field crops has brought about changes in reproductive traits, such as higher mean values and variance of seed and fruit sizes, reduced fruit and seed toxicity, non-shattering seeds and loss of seed dormancy. Evolution under domestication is not a linear process, and bi-directional gene flow between wild and crop taxa is a frequent phenomenon. Thus, hybridisation and introgression have played a very important role in determining the genetics of current cultivars. In turn, gene flow from crops to wild relatives can lead to introgression of crop genes into wild populations and potentially alter the characteristics of natural communities. In conclusion, plant evolution under domestication has not only changed the reproductive biology of cultivated taxa, its effects are multifaceted and have implications beyond agriculture.
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Affiliation(s)
- J M Iriondo
- Área de Biodiversidad y Conservación, Departamento de Biología, Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, Móstoles, Madrid, Spain
| | - R Milla
- Área de Biodiversidad y Conservación, Departamento de Biología, Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, Móstoles, Madrid, Spain
| | - S Volis
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - R Rubio de Casas
- Departamento de Ecología, Facultad de Ciencias, Universidad de Granada, Granada, Spain
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Chacón-Fuentes M, Parra L, Lizama M, Seguel I, Urzúa A, Quiroz A. Plant Flavonoid Content Modified by Domestication. Environ Entomol 2017; 46:1080-1089. [PMID: 28981645 DOI: 10.1093/ee/nvx126] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Indexed: 06/07/2023]
Abstract
Plant domestication can modify and weaken defensive chemical traits, reducing chemical defenses in plants and consequently their resistance against pests. We characterized and quantified the major defensive flavonols and isoflavonoids present in both wild and cultivated murtilla plants (Ugni molinae Turcz), established in a common garden. We examined their effects on the larvae of Chilesia rudis (Butler) (Lepidoptera: Arctiidae). Insect community and diversity indices were also evaluated. We hypothesized that domestication reduces flavonoid contents and modifies C. rudis preference, the insect community, and diversity. Methanolic extracts were obtained from leaves of U. molinae plants and analyzed by high performance liquid chromatography. Results showed higher insect numbers (86.48%) and damage index (1.72 ± 0.16) in cultivated plants. Four new first records of insects were found associated with U. molinae. Diversity indices, such as Simpson, Shannon, and Margalef, were higher in cultivated plants than in wild plants. Furthermore, eight isoflavonoids were identified in U. molinae leaves for the first time. The five flavonols showed higher concentrations in wild U. molinae leaves (89.8 µg/g) than in cultivated plants (75.2 µg/g); however, no differences were found in isoflavonoids between wild and cultivated plants. The larvae of C. rudis consumed more leaf material of cultivated plants than wild plants in choice (3.8 vs. 0.8 mm2) and no-choice (7.5 vs. 3.0 mm2) assays. Our study demonstrates that domestication in U. molinae reduces the amount of flavonoids in leaves, increasing the preference of C. rudis and the insect community.
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Affiliation(s)
- Manuel Chacón-Fuentes
- Doctorado en Ciencias de Recursos Naturales, Universidad de La Frontera, Av. Francisco Salazar 01145, Temuco, Chile
- Laboratorio de Química Ecológica, Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Av. Francisco Salazar 01145, Casilla 54-D, Temuco, Chile
| | - Leonardo Parra
- Laboratorio de Química Ecológica, Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Av. Francisco Salazar 01145, Casilla 54-D, Temuco, Chile
- Centro de Investigación Biotecnológica Aplicada al Medio Ambiente (CIBAMA), Universidad de La Frontera, Av. Francisco Salazar 01145, Casilla 54-D, Temuco, Chile
- Scientific and Technological Bioresources Nucleus, BIOREN -UFRO, Universidad de La Frontera, Temuco, Chile
| | - Marcelo Lizama
- Laboratorio de Química Ecológica, Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Av. Francisco Salazar 01145, Casilla 54-D, Temuco, Chile
- Centro de Investigación Biotecnológica Aplicada al Medio Ambiente (CIBAMA), Universidad de La Frontera, Av. Francisco Salazar 01145, Casilla 54-D, Temuco, Chile
| | - Ivette Seguel
- Instituto de Investigaciones Agropecuarias, Centro Regional de Investigación Carillanca, Temuco, Chile
| | - Alejandro Urzúa
- Laboratorio de Química Ecológica, Departamento de Ciencias del Ambiente, Universidad de Santiago de Chile, Av. Bernardo O' Higgins 3363, Santiago, Chile
| | - Andrés Quiroz
- Laboratorio de Química Ecológica, Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Av. Francisco Salazar 01145, Casilla 54-D, Temuco, Chile
- Centro de Investigación Biotecnológica Aplicada al Medio Ambiente (CIBAMA), Universidad de La Frontera, Av. Francisco Salazar 01145, Casilla 54-D, Temuco, Chile
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Murgia ML, Attene G, Rodriguez M, Bitocchi E, Bellucci E, Fois D, Nanni L, Gioia T, Albani DM, Papa R, Rau D. A Comprehensive Phenotypic Investigation of the "Pod-Shattering Syndrome" in Common Bean. Front Plant Sci 2017; 8:251. [PMID: 28316606 PMCID: PMC5334323 DOI: 10.3389/fpls.2017.00251] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 02/09/2017] [Indexed: 05/03/2023]
Abstract
Seed shattering in crops is a key domestication trait due to its relevance for seed dispersal, yield, and fundamental questions in evolution (e.g., convergent evolution). Here, we focused on pod shattering in common bean (Phaseolus vulgaris L.), the most important legume crop for human consuption in the world. With this main aim, we developed a methodological pipeline that comprises a thorough characterization under field conditions, including also the chemical composition and histological analysis of the pod valves. The pipeline was developed based on the assumption that the shattering trait itself can be treated in principle as a "syndrome" (i.e., a set of correlated different traits) at the pod level. We characterized a population of 267 introgression lines that were developed ad-hoc to study shattering in common bean. Three main objectives were sought: (1) to dissect the shattering trait into its "components," of level (percentage of shattering pods per plant) and mode (percentage of pods with twisting or non-twisting valves); (2) to test whether shattering is associated to the chemical composition and/or the histological characteristics of the pod valves; and (3) to test the associations between shattering and other plant traits. We can conclude the following: Very high shattering levels can be achieved in different modes; shattering resistance is mainly a qualitative trait; and high shattering levels is correlated with high carbon and lignin contents of the pod valves and with specific histological charaterstics of the ventral sheath and the inner fibrous layer of the pod wall. Our data also suggest that shattering comes with a "cost," as it is associated with low pod size, low seed weight per pod, high pod weight, and low seed to pod-valves ratio; indeed, it can be more exaustively described as a syndrome at the pod level. Our work suggests that the valve chemical composition (i.e., carbon and lignin content) can be used for a high troughput phenotyping procedures for shattering phenotyping. Finally, we believe that the application of our pipeline will greatly facilitate comparative studies among legume crops, and gene tagging.
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Affiliation(s)
- Maria L. Murgia
- Dipartimento di Agraria, Sezione di Agronomia, Colture Erbacee e Genetica, Università degli Studi di SassariSassari, Italy
| | - Giovanna Attene
- Dipartimento di Agraria, Sezione di Agronomia, Colture Erbacee e Genetica, Università degli Studi di SassariSassari, Italy
| | - Monica Rodriguez
- Dipartimento di Agraria, Sezione di Agronomia, Colture Erbacee e Genetica, Università degli Studi di SassariSassari, Italy
| | - Elena Bitocchi
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle MarcheAncona, Italy
| | - Elisa Bellucci
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle MarcheAncona, Italy
| | - Davide Fois
- Dipartimento di Agraria, Sezione di Agronomia, Colture Erbacee e Genetica, Università degli Studi di SassariSassari, Italy
| | - Laura Nanni
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle MarcheAncona, Italy
| | - Tania Gioia
- Scuola di Scienze Agrarie, Alimentari, Forestali ed Ambientali, Università degli Studi della BasilicataPotenza, Italy
| | - Diego M. Albani
- Dipartimento di Agraria, Sezione di Economia e Sistemi Arborei e Forestali, Università degli Studi di SassariSassari, Italy
| | - Roberto Papa
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle MarcheAncona, Italy
- *Correspondence: Roberto Papa
| | - Domenico Rau
- Dipartimento di Agraria, Sezione di Agronomia, Colture Erbacee e Genetica, Università degli Studi di SassariSassari, Italy
- Domenico Rau
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Macko-Podgórni A, Machaj G, Stelmach K, Senalik D, Grzebelus E, Iorizzo M, Simon PW, Grzebelus D. Characterization of a Genomic Region under Selection in Cultivated Carrot ( Daucus carota subsp. sativus) Reveals a Candidate Domestication Gene. Front Plant Sci 2017; 8:12. [PMID: 28149306 PMCID: PMC5241283 DOI: 10.3389/fpls.2017.00012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 01/04/2017] [Indexed: 05/11/2023]
Abstract
Carrot is one of the most important vegetables worldwide, owing to its capability to develop fleshy, highly nutritious storage roots. It was domesticated ca. 1,100 years ago in Central Asia. No systematic knowledge about the molecular mechanisms involved in the domestication syndrome in carrot are available, however, the ability to form a storage root is undoubtedly the essential transition from the wild Daucus carota to the cultivated carrot. Here, we expand on the results of a previous study which identified a polymorphism showing a significant signature for selection upon domestication. We mapped the region under selection to the distal portion of the long arm of carrot chromosome 2, confirmed that it had been selected, as reflected in both the lower nucleotide diversity in the cultivated gene pool, as compared to the wild (πw/πc = 7.4 vs. 1.06 for the whole genome), and the high FST (0.52 vs. 0.12 for the whole genome). We delimited the region to ca. 37 kb in length and identified a candidate domestication syndrome gene carrying three non-synonymous single nucleotide polymorphisms and one indel systematically differentiating the wild and the cultivated accessions. This gene, DcAHLc1, belongs to the AT-hook motif nuclear localized (AHL) family of plant regulatory genes which are involved in the regulation of organ development, including root tissue patterning. AHL genes work through direct interactions with other AHL family proteins and a range of other proteins that require intercellular protein movement. Based on QTL data on root thickening we speculate that DcAHLc1 might be involved in the development of the carrot storage root, as the localization of the gene overlapped with one of the QTLs. According to haplotype information we propose that the 'cultivated' variant of DcAHLc1 has been selected from wild Central Asian carrot populations upon domestication and it is highly predominant in the western cultivated carrot gene pool. However, some primitive eastern landraces and the derived B7262 purple inbred line still carry the 'wild' variant, reflecting a likely complexity of the genetic determination of the formation of carrot storage roots.
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Affiliation(s)
- Alicja Macko-Podgórni
- Institute of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in KrakowKrakow, Poland
| | - Gabriela Machaj
- Institute of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in KrakowKrakow, Poland
| | - Katarzyna Stelmach
- Institute of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in KrakowKrakow, Poland
| | - Douglas Senalik
- Vegetable Crops Research Unit, United States Department of Agriculture-Agricultural Research Service, Department of Horticulture, University of Wisconsin–Madison, MadisonWI, USA
| | - Ewa Grzebelus
- Institute of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in KrakowKrakow, Poland
| | - Massimo Iorizzo
- Plants for Human Health Institute, Department of Horticultural Science, North Carolina State University, KannapolisNC, USA
| | - Philipp W. Simon
- Vegetable Crops Research Unit, United States Department of Agriculture-Agricultural Research Service, Department of Horticulture, University of Wisconsin–Madison, MadisonWI, USA
| | - Dariusz Grzebelus
- Institute of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in KrakowKrakow, Poland
- *Correspondence: Dariusz Grzebelus,
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Pilot M, Malewski T, Moura AE, Grzybowski T, Oleński K, Kamiński S, Fadel FR, Alagaili AN, Mohammed OB, Bogdanowicz W. Diversifying Selection Between Pure-Breed and Free-Breeding Dogs Inferred from Genome-Wide SNP Analysis. G3 (Bethesda) 2016; 6:2285-98. [PMID: 27233669 DOI: 10.1534/g3.116.029678] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Domesticated species are often composed of distinct populations differing in the character and strength of artificial and natural selection pressures, providing a valuable model to study adaptation. In contrast to pure-breed dogs that constitute artificially maintained inbred lines, free-ranging dogs are typically free-breeding, i.e., unrestrained in mate choice. Many traits in free-breeding dogs (FBDs) may be under similar natural and sexual selection conditions to wild canids, while relaxation of sexual selection is expected in pure-breed dogs. We used a Bayesian approach with strict false-positive control criteria to identify FST-outlier SNPs between FBDs and either European or East Asian breeds, based on 167,989 autosomal SNPs. By identifying outlier SNPs located within coding genes, we found four candidate genes under diversifying selection shared by these two comparisons. Three of them are associated with the Hedgehog (HH) signaling pathway regulating vertebrate morphogenesis. A comparison between FBDs and East Asian breeds also revealed diversifying selection on the BBS6 gene, which was earlier shown to cause snout shortening and dental crowding via disrupted HH signaling. Our results suggest that relaxation of natural and sexual selection in pure-breed dogs as opposed to FBDs could have led to mild changes in regulation of the HH signaling pathway. HH inhibits adhesion and the migration of neural crest cells from the neural tube, and minor deficits of these cells during embryonic development have been proposed as the underlying cause of “domestication syndrome.” This suggests that the process of breed formation involved the same genetic and developmental pathways as the process of domestication.
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Abstract
BACKGROUND Domesticated animals quickly evolve docile and submissive behaviors after isolation from their wild conspecifics. Model organisms reared for prolonged periods in the laboratory also exhibit similar shifts towards these domesticated behaviors. Yet whether this divergence is due to inadvertent selection in the lab or the fixation of deleterious mutations remains unknown. RESULTS Here, we compare the genomes of lab-reared and wild-caught Drosophila melanogaster to understand the genetic basis of these recently endowed behaviors common to laboratory models. From reassembled genomes of common lab strains, we identify unique, derived variants not present in global populations (lab-specific SNPs). Decreased selective constraints across low frequency SNPs (unique to one or two lab strains) are different from patterns found in the wild and more similar to neutral expectations, suggesting an overall accumulation of deleterious mutations. However, high-frequency lab SNPs found in most or all lab strains reveal an enrichment of X-linked loci and neuro-sensory genes across large extended haplotypes. Among shared polymorphisms, we also find highly differentiated SNPs, in which the derived allele is higher in frequency in the wild (Fst*wild>lab), enriched for similar neurogenetic ontologies, indicative of relaxed selection on more active wild alleles in the lab. CONCLUSIONS Among random mutations that continuously accumulate in the laboratory, we detect common adaptive signatures in domesticated lab strains of fruit flies. Our results demonstrate that lab animals can quickly evolve domesticated behaviors via unconscious selection by humans early on a broad pool of disproportionately large neurogenetic targets followed by the fixation of accumulated deleterious mutations on functionally similar targets.
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Affiliation(s)
- Craig E Stanley
- Department of Biology, Temple University, Philadelphia, PA, USA.
| | - Rob J Kulathinal
- Department of Biology, Temple University, Philadelphia, PA, USA.
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Santos-del-Blanco L, Alía R, González-Martínez SC, Sampedro L, Lario F, Climent J. Correlated genetic effects on reproduction define a domestication syndrome in a forest tree. Evol Appl 2015; 8:403-10. [PMID: 25926884 PMCID: PMC4408150 DOI: 10.1111/eva.12252] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 02/04/2015] [Indexed: 02/03/2023] Open
Abstract
Compared to natural selection, domestication implies a dramatic change in traits linked to fitness. A number of traits conferring fitness in the wild might be detrimental under domestication, and domesticated species typically differ from their ancestors in a set of traits known as the domestication syndrome. Specifically, trade-offs between growth and reproduction are well established across the tree of life. According to allocation theory, selection for growth rate is expected to indirectly alter life-history reproductive traits, diverting resources from reproduction to growth. Here we tested this hypothesis by examining the genetic change and correlated responses of reproductive traits as a result of selection for timber yield in the tree Pinus pinaster. Phenotypic selection was carried out in a natural population, and progenies from selected trees were compared with those of control trees in a common garden experiment. According to expectations, we detected a genetic change in important life-history traits due to selection. Specifically, threshold sizes for reproduction were much higher and reproductive investment relative to size significantly lower in the selected progenies just after a single artificial selection event. Our study helps to define the domestication syndrome in exploited forest trees and shows that changes affecting developmental pathways are relevant in domestication processes of long-lived plants.
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Affiliation(s)
- Luis Santos-del-Blanco
- Department of Forest Ecology and Genetics, INIA-CIFORMadrid, Spain
- Sustainable Forest Management Research InstitutePalencia, Spain
- Department of Ecology and Evolution, University of LausanneLausanne, Switzerland
| | - Ricardo Alía
- Department of Forest Ecology and Genetics, INIA-CIFORMadrid, Spain
- Sustainable Forest Management Research InstitutePalencia, Spain
| | - Santiago C González-Martínez
- Department of Forest Ecology and Genetics, INIA-CIFORMadrid, Spain
- Sustainable Forest Management Research InstitutePalencia, Spain
| | | | - Francisco Lario
- Vivero de Maceda, Dirección Técnica, TRAGSAMaceda, Ourense, Spain
| | - José Climent
- Department of Forest Ecology and Genetics, INIA-CIFORMadrid, Spain
- Sustainable Forest Management Research InstitutePalencia, Spain
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Abstract
Seed shattering (or pod dehiscence, or fruit shedding) is essential for the propagation of their offspring in wild plants but is a major cause of yield loss in crops. In the dicot model species, Arabidopsis thaliana, pod dehiscence necessitates a development of the abscission zones along the pod valve margins. In monocots, such as cereals, an abscission layer in the pedicle is required for the seed shattering process. In the past decade, great advances have been made in characterizing the genetic contributors that are involved in the complex regulatory network in the establishment of abscission cell identity. We summarize the recent burgeoning progress in the field of genetic regulation of pod dehiscence and fruit shedding, focusing mainly on the model species A. thaliana with its close relatives and the fleshy fruit species tomato, as well as the genetic basis responsible for the parallel loss of seed shattering in domesticated crops. This review shows how these individual genes are co-opted in the developmental process of the tissues that guarantee seed shattering. Research into the genetic mechanism underlying seed shattering provides a premier prerequisite for the future breeding program for harvest in crops.
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Affiliation(s)
| | - Yin-Zheng Wang
- *Correspondence: Yin-Zheng Wang, State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing 100093, China,
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Doust AN, Lukens L, Olsen KM, Mauro-Herrera M, Meyer A, Rogers K. Beyond the single gene: How epistasis and gene-by-environment effects influence crop domestication. Proc Natl Acad Sci U S A 2014; 111:6178-83. [PMID: 24753598 DOI: 10.1073/pnas.1308940110] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Domestication is a multifaceted evolutionary process, involving changes in individual genes, genetic interactions, and emergent phenotypes. There has been extensive discussion of the phenotypic characteristics of plant domestication, and recent research has started to identify the specific genes and mutational mechanisms that control domestication traits. However, there is an apparent disconnect between the simple genetic architecture described for many crop domestication traits, which should facilitate rapid phenotypic change under selection, and the slow rate of change reported from the archeobotanical record. A possible explanation involves the middle ground between individual genetic changes and their expression during development, where gene-by-gene (epistatic) and gene-by-environment interactions can modify the expression of phenotypes and opportunities for selection. These aspects of genetic architecture have the potential to significantly slow the speed of phenotypic evolution during crop domestication and improvement. Here we examine whether epistatic and gene-by-environment interactions have shaped how domestication traits have evolved. We review available evidence from the literature, and we analyze two domestication-related traits, shattering and flowering time, in a mapping population derived from a cross between domesticated foxtail millet and its wild progenitor. We find that compared with wild progenitor alleles, those favored during domestication often have large phenotypic effects and are relatively insensitive to genetic background and environmental effects. Consistent selection should thus be able to rapidly change traits during domestication. We conclude that if phenotypic evolution was slow during crop domestication, this is more likely due to cultural or historical factors than epistatic or environmental constraints.
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Olsen KM, Wendel JF. Crop plants as models for understanding plant adaptation and diversification. Front Plant Sci 2013; 4:290. [PMID: 23914199 PMCID: PMC3729982 DOI: 10.3389/fpls.2013.00290] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 07/13/2013] [Indexed: 05/19/2023]
Abstract
Since the time of Darwin, biologists have understood the promise of crop plants and their wild relatives for providing insight into the mechanisms of phenotypic evolution. The intense selection imposed by our ancestors during plant domestication and subsequent crop improvement has generated remarkable transformations of plant phenotypes. Unlike evolution in natural settings, descendent and antecedent conditions for crop plants are often both extant, providing opportunities for direct comparisons through crossing and other experimental approaches. Moreover, since domestication has repeatedly generated a suite of "domestication syndrome" traits that are shared among crops, opportunities exist for gaining insight into the genetic and developmental mechanisms that underlie parallel adaptive evolution. Advances in our understanding of the genetic architecture of domestication-related traits have emerged from combining powerful molecular technologies with advanced experimental designs, including nested association mapping, genome-wide association studies, population genetic screens for signatures of selection, and candidate gene approaches. These studies may be combined with high-throughput evaluations of the various "omics" involved in trait transformation, revealing a diversity of underlying causative mutations affecting phenotypes and their downstream propagation through biological networks. We summarize the state of our knowledge of the mutational spectrum that generates phenotypic novelty in domesticated plant species, and our current understanding of how domestication can reshape gene expression networks and emergent phenotypes. An exploration of traits that have been subject to similar selective pressures across crops (e.g., flowering time) suggests that a diversity of targeted genes and causative mutational changes can underlie parallel adaptation in the context of crop evolution.
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Affiliation(s)
- Kenneth M. Olsen
- Biology Department, Washington UniversitySt. Louis, MO, USA
- *Correspondence: Kenneth M. Olsen, Biology Department, Washington University, Campus Box 1137, St. Louis, MO 63130-4899, USA e-mail:
| | - Jonathan F. Wendel
- Ecology, Evolution, and Organismal Biology Department, Iowa State UniversityAmes, IA, USA
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Terral JF, Tabard E, Bouby L, Ivorra S, Pastor T, Figueiral I, Picq S, Chevance JB, Jung C, Fabre L, Tardy C, Compan M, Bacilieri R, Lacombe T, This P. Evolution and history of grapevine (Vitis vinifera) under domestication: new morphometric perspectives to understand seed domestication syndrome and reveal origins of ancient European cultivars. Ann Bot 2010; 105:443-55. [PMID: 20034966 PMCID: PMC2826248 DOI: 10.1093/aob/mcp298] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2009] [Revised: 10/05/2009] [Accepted: 11/03/2009] [Indexed: 05/19/2023]
Abstract
BACKGROUND AND AIMS In spite of the abundance of archaeological, bio-archaeological, historical and genetic data, the origins, historical biogeography, identity of ancient grapevine cultivars and mechanisms of domestication are still largely unknown. Here, analysis of variation in seed morphology aims to provide accurate criteria for the discrimination between wild grapes and modern cultivars and to understand changes in functional traits in relation to the domestication process. This approach is also used to quantify the phenotypic diversity in the wild and cultivated compartments and to provide a starting point for comparing well-preserved archaeological material, in order to elucidate the history of grapevine varieties. METHODS Geometrical analysis (elliptic Fourier transform method) was applied to grapevine seed outlines from modern wild individuals, cultivars and well-preserved archaeological material from southern France, dating back to the first to second centuries. KEY RESULTS AND CONCLUSIONS Significant relationships between seed shape and taxonomic status, geographical origin (country or region) of accessions and parentage of varieties are highlighted, as previously noted based on genetic approaches. The combination of the analysis of modern reference material and well-preserved archaeological seeds provides original data about the history of ancient cultivated forms, some of them morphologically close to the current 'Clairette' and 'Mondeuse blanche' cultivars. Archaeobiological records seem to confirm the complexity of human contact, exchanges and migrations which spread grapevine cultivation in Europe and in Mediterranean areas, and argue in favour of the existence of local domestication in the Languedoc (southern France) region during Antiquity.
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Affiliation(s)
- Jean-Frédéric Terral
- Centre de Bio-Archéologie et d'Ecologie, Equipe Ressources Biologiques, Sociétés, Biodiversité-UMR 5059 CNRS/UM2/EPHE, Institut de Botanique (Université Montpellier 2), 163 Rue Auguste Broussonet, 34090 Montpellier, France.
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Weeden NF. Genetic changes accompanying the domestication of Pisum sativum: is there a common genetic basis to the ' domestication syndrome' for legumes? Ann Bot 2007; 100:1017-25. [PMID: 17660515 PMCID: PMC2759201 DOI: 10.1093/aob/mcm122] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2006] [Accepted: 05/22/2007] [Indexed: 05/16/2023]
Abstract
BACKGROUND AND AIMS The changes that occur during the domestication of crops such as maize and common bean appear to be controlled by relatively few genes. This study investigates the genetic basis of domestication in pea (Pisum sativum) and compares the genes involved with those determined to be important in common bean domestication. METHODS Quantitative trait loci and classical genetic analysis are used to investigate and identify the genes modified at three stages of the domestication process. Five recombinant inbred populations involving crosses between different lines representing different stages are examined. KEY RESULTS A minimum of 15 known genes, in addition to a relatively few major quantitative trait loci, are identified as being critical to the domestication process. These genes control traits such as pod dehiscence, seed dormancy, seed size and other seed quality characters, stem height, root mass, and harvest index. Several of the genes have pleiotropic effects that in species possessing a more rudimentary genetic characterization might have been interpreted as clusters of genes. Very little evidence for gene clustering was found in pea. When compared with common bean, pea has used a different set of genes to produce the same or similar phenotypic changes. CONCLUSIONS Similar to results for common bean, relatively few genes appear to have been modified during the domestication of pea. However, the genes involved are different, and there does not appear to be a common genetic basis to 'domestication syndrome' in the Fabaceae.
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Affiliation(s)
- Norman F Weeden
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, USA.
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Pickersgill B. Domestication of plants in the Americas: insights from Mendelian and molecular genetics. Ann Bot 2007; 100:925-40. [PMID: 17766847 PMCID: PMC2759216 DOI: 10.1093/aob/mcm193] [Citation(s) in RCA: 129] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/24/2006] [Revised: 06/04/2007] [Accepted: 07/23/2007] [Indexed: 05/17/2023]
Abstract
BACKGROUND Plant domestication occurred independently in four different regions of the Americas. In general, different species were domesticated in each area, though a few species were domesticated independently in more than one area. The changes resulting from human selection conform to the familiar domestication syndrome, though different traits making up this syndrome, for example loss of dispersal, are achieved by different routes in crops belonging to different families. GENETIC AND MOLECULAR ANALYSES OF DOMESTICATION Understanding of the genetic control of elements of the domestication syndrome is improving as a result of the development of saturated linkage maps for major crops, identification and mapping of quantitative trait loci, cloning and sequencing of genes or parts of genes, and discoveries of widespread orthologies in genes and linkage groups within and between families. As the modes of action of the genes involved in domestication and the metabolic pathways leading to particular phenotypes become better understood, it should be possible to determine whether similar phenotypes have similar underlying genetic controls, or whether human selection in genetically related but independently domesticated taxa has fixed different mutants with similar phenotypic effects. CONCLUSIONS Such studies will permit more critical analysis of possible examples of multiple domestications and of the origin(s) and spread of distinctive variants within crops. They also offer the possibility of improving existing crops, not only major food staples but also minor crops that are potential export crops for developing countries or alternative crops for marginal areas.
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