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Maanju S, Jasrotia P, Yadav SS, Kashyap PL, Kumar S, Jat MK, Lal C, Sharma P, Singh G, Singh GP. Deciphering the genetic diversity and population structure of wild barley germplasm against corn leaf aphid, Rhopalosiphum maidis (Fitch). Sci Rep 2023; 13:17313. [PMID: 37828115 PMCID: PMC10570286 DOI: 10.1038/s41598-023-42717-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 09/14/2023] [Indexed: 10/14/2023] Open
Abstract
Corn-leaf aphid (CLA-Rhopalosiphum maidis) is a major insect pest of barley (Hordeum vulgare) causing yield loss upto 30% under severe infestation. Keeping in view of the availability of very few sources of CLA resistance in barley, the present investigation was framed to assess the genetic diversity and population structure of 43 wild barley (H. vulgare subsp. spontaneum) genotypes using eight microsatellite markers against R. maidis. Three statistical methods viz. multivariate-hierarchical clustering, Bayesian clustering and PCoA, unanimously grouped genotypes into three subpopulations (K = 3) with 25.58% (SubPop1-Red), 39.53% (SubPop2-Green) and 34.88% (SubPop3-Blue) genotypes including admixtures. Based on Q ≥ 66.66%, 37.20% genotypes formed a superficial "Mixed/Admixture" subpopulation. All polymorphic SSR markers generated 36 alleles, averaging to 4.5 alleles/locus (2-7 range). The PIC and H were highest in MS31 and lowest in MS28, with averages of 0.66 and 0.71. MAF and mean genetic diversity were 0.16 and 89.28%, respectively. All these parameters indicated the presence of predominant genetic diversity and population structure amongst the studied genotypes. Based on AII, only 6 genotypes were found to be R. maidis resistant. SubPop3 had 91.66% (11) of the resistant or moderately resistant genotypes. SubPop3 also had the most pure genotypes (11), the least aphid infestation (8.78), and the highest GS (0.88), indicating its suitability for future R. maidis resistance breeding initiatives.
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Affiliation(s)
- Sunny Maanju
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132001, India
- CCS Haryana Agricultural University, Hisar, Haryana, 125004, India
| | - Poonam Jasrotia
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132001, India.
| | | | - Prem Lal Kashyap
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132001, India
| | - Sudheer Kumar
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132001, India
| | - Manoj Kumar Jat
- CCS Haryana Agricultural University, Hisar, Haryana, 125004, India
| | - Chuni Lal
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132001, India
| | - Preeti Sharma
- CCS Haryana Agricultural University, Hisar, Haryana, 125004, India
| | - Gyanendra Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132001, India
| | - Gyanendra Pratap Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132001, India
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110012, India
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Rau D, Attene G, Rodriguez M, Baghino L, Pisanu AB, Sanna D, Acquadro A, Portis E, Comino C. The Population Structure of a Globe Artichoke Worldwide Collection, as Revealed by Molecular and Phenotypic Analyzes. FRONTIERS IN PLANT SCIENCE 2022; 13:898740. [PMID: 35865281 PMCID: PMC9294547 DOI: 10.3389/fpls.2022.898740] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 05/13/2022] [Indexed: 05/27/2023]
Abstract
The knowledge of the organization of the domesticated gene pool of crop species is an essential requirement to understand crop evolution, to rationalize conservation programs, and to support practical decisions in plant breeding. Here, we integrate simple sequence repeat (SSR) analysis and phenotypic characterization to investigate a globe artichoke collection that comprises most of the varieties cultivated worldwide. We show that the cultivated gene pool of globe artichoke includes five distinct genetic groups associated with the major phenotypic typologies: Catanesi (which based on our analysis corresponds to Violetti di Provenza), Spinosi, Violetti di Toscana, Romaneschi, and Macau. We observed that 17 and 11% of the molecular and phenotypic variance, respectively, is between these groups, while within groups, strong linkage disequilibrium and heterozygote excess are evident. The divergence between groups for quantitative traits correlates with the average broad-sense heritability within the groups. The phenotypic divergence between groups for both qualitative and quantitative traits is strongly and positively correlated with SSR divergence (FST) between groups. All this implies a low population size and strong bottleneck effects, and indicates a long history of clonal propagation and selection during the evolution of the domesticated gene pool of globe artichoke. Moreover, the comparison between molecular and phenotypic population structures suggests that harvest time, plant architecture (i.e., plant height, stem length), leaf spininess, head morphology (i.e., head shape, bract shape, spininess) together with the number of heads per plant were the main targets of selection during the evolution of the cultivated germplasm. We emphasize our findings in light of the potential exploitation of this collection for association mapping studies.
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Affiliation(s)
- Domenico Rau
- Dipartimento di Agraria, Sezione di Agronomia, Coltivazioni Erbacee e Genetica (SACEG), Università degli Studi di Sassari, Sassari, Italy
| | - Giovanna Attene
- Dipartimento di Agraria, Sezione di Agronomia, Coltivazioni Erbacee e Genetica (SACEG), Università degli Studi di Sassari, Sassari, Italy
| | - Monica Rodriguez
- Dipartimento di Agraria, Sezione di Agronomia, Coltivazioni Erbacee e Genetica (SACEG), Università degli Studi di Sassari, Sassari, Italy
| | - Limbo Baghino
- Agenzia AGRIS Sardegna (Servizio Ricerca sui Sistemi Colturali Erbacei, Settore Innovazione dei Modelli Gestionali e Studio Della Biodiversità Nelle Colture Intensive), Oristano, Italy
| | - Anna Barbara Pisanu
- Agenzia AGRIS Sardegna (Servizio Ricerca sui Sistemi Colturali Erbacei, Settore Innovazione dei Modelli Gestionali e Studio Della Biodiversità Nelle Colture Intensive), Oristano, Italy
| | - Davide Sanna
- Agenzia AGRIS Sardegna (Servizio Ricerca sui Sistemi Colturali Erbacei, Settore Innovazione dei Modelli Gestionali e Studio Della Biodiversità Nelle Colture Intensive), Oristano, Italy
| | - Alberto Acquadro
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari (DISAFA), Genetica Vegetale (Plant Genetics), Università degli Studi di Torino, Turin, Italy
| | - Ezio Portis
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari (DISAFA), Genetica Vegetale (Plant Genetics), Università degli Studi di Torino, Turin, Italy
| | - Cinzia Comino
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari (DISAFA), Genetica Vegetale (Plant Genetics), Università degli Studi di Torino, Turin, Italy
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Teklemariam SS, Bayissa KN, Matros A, Pillen K, Ordon F, Wehner G. The genetic diversity of Ethiopian barley genotypes in relation to their geographical origin. PLoS One 2022; 17:e0260422. [PMID: 35622864 PMCID: PMC9140232 DOI: 10.1371/journal.pone.0260422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 04/19/2022] [Indexed: 11/18/2022] Open
Abstract
Ethiopia is recognized as a center of diversity for barley, and its landraces are known for the distinct genetic features compared to other barley collections. The genetic diversity of Ethiopian barley likely results from the highly diverse topography, altitude, climate conditions, soil types, and farming systems. To get detailed information on the genetic diversity a panel of 260 accessions, comprising 239 landraces and 21 barley breeding lines, obtained from the Ethiopian biodiversity institute (EBI) and the national barley improvement program, respectively were studied for their genetic diversity using the 50k iSelect single nucleotide polymorphism (SNP) array. A total of 983 highly informative SNP markers were used for structure and diversity analysis. Three genetically distinct clusters were obtained from the structure analysis comprising 80, 71, and 109 accessions, respectively. Analysis of molecular variance (AMOVA) revealed the presence of higher genetic variation (89%) within the clusters than between the clusters (11%), with moderate genetic differentiation (PhiPT = 0.11) and five accessions were detected as first-generation migrants using Monte Carlo resampling methods. The Mantel test revealed that the genetic distance between accessions is poorly associated with their geographical distance. Despite the observed weak correlation between geographic distance and genetic differentiation, for some regions like Gonder, Jimma, Gamo-Gofa, Shewa, and Welo, more than 50% of the landraces derived from these regions are assigned to one of the three clusters.
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Affiliation(s)
- Surafel Shibru Teklemariam
- Ethiopian Institute of Agricultural Research (EIAR), Melkassa Agricultural Research Center, Melkassa, Ethiopia
| | - Kefyalew Negisho Bayissa
- Ethiopian Institute of Agricultural Research (EIAR), National Agricultural Biotechnology Research Center, Holetta, Ethiopia
| | - Andrea Matros
- Julius Kühn Institute (JKI), Federal Research Centre on Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
| | - Klaus Pillen
- Institute of Agricultural and Nutritional Sciences, Martin Luther University, Halle (Saale), Germany
| | - Frank Ordon
- Julius Kühn Institute (JKI), Federal Research Centre on Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
| | - Gwendolin Wehner
- Julius Kühn Institute (JKI), Federal Research Centre on Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
- * E-mail:
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Genetic diversity, population structure and relationship of Ethiopian barley (Hordeum vulgare L.) landraces as revealed by SSR markers. J Genet 2022. [DOI: 10.1007/s12041-021-01346-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Henningsen E, Sallam AH, Matny O, Szinyei T, Figueroa M, Steffenson BJ. Rpg7: A New Gene for Stem Rust Resistance from Hordeum vulgare ssp. spontaneum. PHYTOPATHOLOGY 2021; 111:548-558. [PMID: 32880513 DOI: 10.1094/phyto-08-20-0325-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Wheat stem rust (causal organism: Puccinia graminis f. sp. tritici) is an important fungal disease that causes significant yield losses in barley. The deployment of resistant cultivars is the most effective means of controlling this disease. Stem rust evaluations of a diverse collection of wild barley (Hordeum vulgare ssp. spontaneum) identified two Jordanian accessions (WBDC094 and WBDC238) with resistance to a virulent pathotype (P. graminis f. sp. tritici HKHJC) from the United States. To elucidate the genetics of stem rust resistance, both accessions were crossed to the susceptible landrace Hiproly. Segregation ratios of F2 and F3 progeny indicated that a single dominant gene confers resistance to P. graminis f. sp. tritici HKHJC. Molecular mapping of the resistance locus was performed in the Hiproly/WBDC238 F2 population based on 3,329 single-nucleotide polymorphism markers generated by genotyping-by-sequencing. Quantitative trait locus analysis positioned the resistance gene to the long arm of chromosome 3H between the physical/genetic positions of 683.8 Mbp/172.9 cM and 693.7 Mbp/176.0 cM. Because this resistance gene is novel, it was assigned the new gene locus symbol of Rpg7 with a corresponding allele symbol of Rpg7.i. At the seedling stage, Rpg7 confers resistance against a number of other important P. graminis f. sp. tritici pathotypes from the United States (MCCFC, QCCJB, and TTTTF) and Africa (TTKSK) as well as an isolate (92-MN-90) of the rye stem rust pathogen (P. graminis f. sp. secalis) from Minnesota. The resistance conferred by Rpg7 can be readily transferred into breeding programs because of its simple inheritance and clear phenotypic expression.
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Affiliation(s)
- Eva Henningsen
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Ahmad H Sallam
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Oadi Matny
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Tamas Szinyei
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Melania Figueroa
- Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, Canberra, ACT 2601, Australia
| | - Brian J Steffenson
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, U.S.A
- Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul, MN 55108, U.S.A
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Cortinovis G, Di Vittori V, Bellucci E, Bitocchi E, Papa R. Adaptation to novel environments during crop diversification. CURRENT OPINION IN PLANT BIOLOGY 2020; 56:203-217. [PMID: 32057695 DOI: 10.1016/j.pbi.2019.12.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 12/19/2019] [Accepted: 12/21/2019] [Indexed: 06/10/2023]
Abstract
In the context of the global challenge of climate change, mitigation strategies are needed to adapt crops to novel environments. The main goal to address this is an understanding of the genetic basis of crop adaptation to different agro-ecological conditions. The movement of crops during the Colombian Exchange that started with the travels of Columbus in 1492 is an example of rapid adaptation to novel environments. Many diversification-related traits have been characterised in multiple crop species, and association-mapping analyses have identified loci involved in these. Here, we present an overview of current knowledge regarding the molecular basis related to the complex patterns of crop adaptation and dissemination, particularly outside their centres of origin. Investigation of the genomic basis of crop expansion offers a powerful contribution to the development of tools to identify and exploit valuable genetic diversity and to improve and design novel resilient crop varieties.
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Affiliation(s)
- Gaia Cortinovis
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy
| | - Valerio Di Vittori
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy
| | - Elisa Bellucci
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy
| | - Elena Bitocchi
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy.
| | - Roberto Papa
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy.
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Hernández-Rosales HS, Castellanos-Morales G, Sánchez-de la Vega G, Aguirre-Planter E, Montes-Hernández S, Lira-Saade R, Eguiarte LE. Phylogeographic and population genetic analyses of Cucurbita moschata reveal divergence of two mitochondrial lineages linked to an elevational gradient. AMERICAN JOURNAL OF BOTANY 2020; 107:510-525. [PMID: 32072632 DOI: 10.1002/ajb2.1424] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 11/26/2019] [Indexed: 06/10/2023]
Abstract
PREMISE Domestication usually involves local adaptation to environmental conditions. Cucurbita species are a promising model for studying these processes. Cucurbita moschata is the third major crop in the genus because of its economic value and because it displays high landrace diversity, but research about its genetic diversity, population structure, and phylogeography is limited. We aimed at understanding how geography and elevation shape the distribution of genetic diversity in C. moschata landraces in Mexico. METHODS We sampled fruits from 24 localities throughout Mexico. We assessed 11 nuclear microsatellite loci, one mtDNA region, and three cpDNA regions but found no variation in cpDNA. We explored genetic structure with cluster analysis, and phylogeographic relationships with haplotype network analysis. RESULTS Mitochondrial genetic diversity was high, and nuclear genetic differentiation among localities was intermediate compared to other domesticated Cucurbita. We found high levels of inbreeding. We recovered two mitochondrial lineages: highland (associated with the Trans-Mexican Volcanic Belt) and lowland. Nuclear microsatellites show that localities from the Yucatan Peninsula constitute a well-differentiated group. CONCLUSIONS Mexico is an area of high diversity for C. moschata, and these landraces represent important plant genetic resources. In Mexico this species is characterized by divergence processes linked to an elevational gradient, which could be related to adaptation and may be of value for applications in agriculture. The Isthmus of Tehuantepec may be a partial barrier to gene flow. Morphological variation, agricultural management, and cultural differences may be related to this pattern of genetic structure, but further studies are needed.
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Affiliation(s)
- Helena S Hernández-Rosales
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior s/n Anexo al Jardín Botánico, 04510, Ciudad de México, Mexico
- Programa de Doctorado en Ciencias Biomédicas, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior s/n Anexo al Jardín Botánico, 04510, Ciudad de México, Mexico
| | - Gabriela Castellanos-Morales
- Departamento de Conservación de la Biodiversidad, El Colegio de la Frontera Sur, Villahermosa, Carretera Villahermosa-Reforma km 15.5 Ranchería El Guineo 2ª sección, 86280, Villahermosa, Tabasco, Mexico
| | - Guillermo Sánchez-de la Vega
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior s/n Anexo al Jardín Botánico, 04510, Ciudad de México, Mexico
| | - Erika Aguirre-Planter
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior s/n Anexo al Jardín Botánico, 04510, Ciudad de México, Mexico
| | - Salvador Montes-Hernández
- Campo Experimental Bajío, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarías, Km 6.5 carretera Celaya-San Miguel de Allende, C.P. 38110, Celaya, Guanajuato, México, Mexico
| | - Rafael Lira-Saade
- UBIPRO, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Av. de los Barrios #1, Col. Los Reyes Iztacala, 54090, Tlanepantla, Edo. de Mex, Mexico
| | - Luis E Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior s/n Anexo al Jardín Botánico, 04510, Ciudad de México, Mexico
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Ruelle ML, Asfaw Z, Dejen A, Tewolde-Berhan S, Nebiyu A, Tana T, Power AG. Inter- and intraspecific diversity of food legumes among households and communities in Ethiopia. PLoS One 2019; 14:e0227074. [PMID: 31869394 PMCID: PMC6927635 DOI: 10.1371/journal.pone.0227074] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 12/10/2019] [Indexed: 12/05/2022] Open
Abstract
Smallholders throughout sub-Saharan Africa produce legume crops as sources of food, fodder, and cash income, as well as to improve soil fertility. Ethiopian farmers have developed diverse legume varieties that enable adaptation to changing agroecological and sociocultural conditions. However, over the past several decades, as farm sizes declined and extension services promoted new varieties developed by plant breeders, changes in legume diversity have not been monitored. Based on interviews with smallholder farmers (n = 1296), we investigated the status of inter- and intraspecific legume diversity in major production areas of Ethiopia for five food legumes: common bean (Phaseolus vulgaris L.), field pea (Pisum sativum L.), faba bean (Vicia faba L.), groundnut (Arachis hypogaea L.) and fenugreek (Trigonella foenum-graecum L.). Legume species richness increased with altitude, relative household wealth, and land area planted to legumes. The highest numbers of varieties were found for common bean, followed by field pea, faba bean, groundnut and fenugreek. The average number of varieties planted per household was low (ranging from 1 to 2) and often much lower than the number reported in the same community or zone, which ranged from 2 to 18. For three out of the five species, the number of varieties significantly increased with total land area planted to legumes. Most varieties were rare, planted by less than 1/3 of farmers; however, informants accurately named varieties planted by others in the same community, demonstrating awareness of legume diversity at the community level. Given that the ability to plant multiple legume varieties is limited by land size, policies need to strengthen community-level conservation based on the diverse interests and needs of individual households.
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Affiliation(s)
- Morgan L. Ruelle
- Department of Ecology & Evolutionary Biology, Cornell University, Ithaca, New York, United States of America
- International Development, Community & Environment Department, Clark University, Worcester, Massachusetts, United States of America
- * E-mail:
| | - Zemede Asfaw
- Department of Plant Biology and Biodiversity Management, Addis Ababa University, Addis Ababa, Ethiopia
| | - Asmare Dejen
- Department of Agricultural Entomology, Wollo University, Dessie, Ethiopia
| | - Sarah Tewolde-Berhan
- Department of Food Science and Post-Harvest Technology, Mekelle University, Mekelle, Ethiopia
| | - Amsalu Nebiyu
- Department of Horticulture and Plant Sciences, Jimma University, Jimma, Ethiopia
| | - Tamado Tana
- School of Plant Sciences, Haramaya University, Haramaya, Ethiopia
| | - Alison G. Power
- Department of Ecology & Evolutionary Biology, Cornell University, Ithaca, New York, United States of America
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Mohd-Assaad N, McDonald BA, Croll D. The emergence of the multi-species NIP1 effector in Rhynchosporium was accompanied by high rates of gene duplications and losses. Environ Microbiol 2019; 21:2677-2695. [PMID: 30838748 DOI: 10.1111/1462-2920.14583] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 02/23/2019] [Accepted: 03/04/2019] [Indexed: 01/28/2023]
Abstract
Plant pathogens secrete effector proteins to manipulate the host and facilitate infection. Cognate hosts trigger strong defence responses upon detection of these effectors. Consequently, pathogens and hosts undergo rapid coevolutionary arms races driven by adaptive evolution of effectors and receptors. Because of their high rate of turnover, most effectors are thought to be species-specific and the evolutionary trajectories are poorly understood. Here, we investigate the necrosis-inducing protein 1 (NIP1) effector in the multihost pathogen genus Rhynchosporium. We retraced the evolutionary history of the NIP1 locus using whole-genome assemblies of 146 strains covering four closely related species. NIP1 orthologues were present in all species but the locus consistently segregated presence-absence polymorphisms suggesting long-term balancing selection. We also identified previously unknown paralogues of NIP1 that were shared among multiple species and showed substantial copy-number variation within R. commune. The NIP1A paralogue was under significant positive selection suggesting that NIP1A is the dominant effector variant coevolving with host immune receptors. Consistent with this prediction, we found that copy number variation at NIP1A had a stronger effect on virulence than NIP1B. Our analyses unravelled the origins and diversification mechanisms of a pathogen effector family shedding light on how pathogens gain adaptive genetic variation.
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Affiliation(s)
- Norfarhan Mohd-Assaad
- Plant Pathology, Institute of Integrative Biology, ETH, Zurich, 8092 Zurich, Switzerland.,School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
| | - Bruce A McDonald
- Plant Pathology, Institute of Integrative Biology, ETH, Zurich, 8092 Zurich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland
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Mohd-Assaad N, McDonald BA, Croll D. Genome-Wide Detection of Genes Under Positive Selection in Worldwide Populations of the Barley Scald Pathogen. Genome Biol Evol 2018; 10:1315-1332. [PMID: 29722810 PMCID: PMC5972619 DOI: 10.1093/gbe/evy087] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/30/2018] [Indexed: 12/29/2022] Open
Abstract
Coevolution between hosts and pathogens generates strong selection pressures to maintain resistance and infectivity, respectively. Genomes of plant pathogens often encode major effect loci for the ability to successfully infect specific host genotypes. Hence, spatial heterogeneity in host genotypes coupled with abiotic factors could lead to locally adapted pathogen populations. However, the genetic basis of local adaptation is poorly understood. Rhynchosporium commune, the pathogen causing barley scald disease, interacts at least partially in a gene-for-gene manner with its host. We analyzed global field populations of 125 R. commune isolates to identify candidate genes for local adaptation. Whole genome sequencing data showed that the pathogen is subdivided into three genetic clusters associated with distinct geographic and climatic regions. Using haplotype-based selection scans applied independently to each genetic cluster, we found strong evidence for selective sweeps throughout the genome. Comparisons of loci under selection among clusters revealed little overlap, suggesting that ecological differences associated with each cluster led to variable selection regimes. The strongest signals of selection were found predominantly in the two clusters composed of isolates from Central Europe and Ethiopia. The strongest selective sweep regions encoded protein functions related to biotic and abiotic stress responses. Selective sweep regions were enriched in genes encoding functions in cellular localization, protein transport activity, and DNA damage responses. In contrast to the prevailing view that a small number of gene-for-gene interactions govern plant pathogen evolution, our analyses suggest that the evolutionary trajectory is largely determined by spatially heterogeneous biotic and abiotic selection pressures.
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Affiliation(s)
- Norfarhan Mohd-Assaad
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Bruce A McDonald
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Switzerland
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Sakaguchi S, Horie K, Ishikawa N, Nagano AJ, Yasugi M, Kudoh H, Ito M. Simultaneous evaluation of the effects of geographic, environmental and temporal isolation in ecotypic populations of Solidago virgaurea. THE NEW PHYTOLOGIST 2017; 216:1268-1280. [PMID: 28833204 DOI: 10.1111/nph.14744] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 07/07/2017] [Indexed: 05/14/2023]
Abstract
Early stages of ecological speciation can create populations with an ecology and reproduction timing distinct from those of related populations. Landscape genetic models incorporating environmental heterogeneity and population-specific reproductive traits enable the processes of population genetic differentiation to be inferred. We investigated genome-wide genetic variation in ecotypic populations of Solidago virgaurea sensu lato, a herbaceous plant inhabiting a wide range of habitats (woodlands, serpentine barrens and alpine grasslands) and displaying remarkable variation in flowering time. Simultaneous evaluation of environmental factors revealed an overwhelming effect of soil type differences on neutral genetic differentiation, compared with elevational differences. This result probably reflects the abrupt environmental changes generated by geological boundaries, whereas mountain slopes exhibit clinal changes, facilitating gene exchange between neighbouring populations. Temporal isolation was positively associated with genetic differentiation, with some early-flowering serpentine populations having allele frequencies distinct from adjacent nonserpentine populations. Overall, this study highlights the importance of ecological processes and of evolution of flowering time to promote genetic differentiation of S. virgaurea populations in a complex landscape.
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Affiliation(s)
- Shota Sakaguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-nihonmatsu-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Kenji Horie
- Asahikawa City Northern Wild Plants Garden, Asahikawa, 071-1200, Japan
| | - Naoko Ishikawa
- Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, 153-8902, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Shiga, 520-2194, Japan
- Center for Ecological Research, Kyoto University, Otsu, Shiga, 520-2113, Japan
- JST CREST, Honcho 4-1-8, Kawaguchi, Saitama, 332-0012, Japan
| | - Masaki Yasugi
- National Institute for Basic Biology, Higashiyama 5-1, Myodaiji, Okazaki, 444-8787, Aichi, Japan
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, Otsu, Shiga, 520-2113, Japan
| | - Motomi Ito
- Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, 153-8902, Japan
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13
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Unexpected pattern of pearl millet genetic diversity among ethno-linguistic groups in the Lake Chad Basin. Heredity (Edinb) 2017; 118:491-502. [PMID: 28121310 PMCID: PMC5520532 DOI: 10.1038/hdy.2016.128] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 11/01/2016] [Accepted: 11/30/2016] [Indexed: 11/08/2022] Open
Abstract
Despite of a growing interest in considering the role of sociological factors in seed exchanges and their consequences on the evolutionary dynamics of agro-biodiversity, very few studies assessed the link between ethno-linguistic diversity and genetic diversity patterns in small-holder farming systems. This is key for optimal improvement and conservation of crop genetic resources. Here, we investigated genetic diversity at 17 SSR markers of pearl millet landraces (varieties named by farmers) in the Lake Chad Basin. 69 pearl millet populations, representing 27 landraces collected in eight ethno-linguistic farmer groups, were analyzed. We found that the farmers' local taxonomy was not a good proxy for population's genetic differentiation as previously shown at smaller scales. Our results show the existence of a genetic structure of pearl millet mainly associated with ethno-linguistic diversity in the western side of the lake Chad. It suggests there is a limit to gene flow between landraces grown by different ethno-linguistic groups. This result was rather unexpected, because of the highly outcrossing mating system of pearl millet, the high density of pearl millet fields all along the green belt of this Sahelian area and the fact that seed exchanges among ethno-linguistic groups are known to occur. In the eastern side of the Lake, the pattern of genetic diversity suggests a larger efficient circulation of pearl millet genes between ethno-linguistic groups that are less numerous, spatially intermixed and, for some of them, more prone to exogamy. Finally, other historical and environmental factors which may contribute to the observed diversity patterns are discussed.
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14
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Rau D, Rodriguez M, Rapposelli E, Murgia ML, Papa R, Brown AHD, Attene G. Spatial genetic structure in wild cardoon, the ancestor of cultivated globe artichoke: Limited gene flow, fragmentation and population history. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 253:194-205. [PMID: 27968988 DOI: 10.1016/j.plantsci.2016.09.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 09/23/2016] [Accepted: 09/26/2016] [Indexed: 06/06/2023]
Abstract
Nuclear and chloroplast markers and phenotypic characters were integrated to analyse the population genetic structure of wild cardoon, Cynara cardunculus var. sylvestris, the ancestor of cultivated globe artichoke, Cynara cardunculus var. scolymus on the island of Sardinia, Italy. The spatial scale ranged from a few metres to ∼200km. Wild cardoon appears to be genetically fragmented, with significant genetic divergence at various scales, indicating that gene flow is insufficient to counterbalance the effects of genetic drift or founder effects. Divergence between populations was higher for chloroplast (40%) than for nuclear markers (15%), suggesting that gene flow via seed was lower than via pollen. Two main genetic groups were detected; these correlated with differences in flowering time, capitula size, glossiness, and anthocyanin pigmentation. A complex population structure of wild cardoon emerged over small spatial scales, likely resulting from the interplay between gene dispersal, colonisation history and selective forces. Indeed, Sardinia appears to be a 'hybrid zone' of different gene pools. The island has unique diverse germplasm that has originated from hybridisation among different gene pools. The sampling of seeds from a few plants but from many sites is suggested as the best strategy to harvest the genetic diversity of wild cardoon.
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Affiliation(s)
- D Rau
- Dipartimento di Agraria, Università degli Studi di Sassari, Via E. De Nicola, 07100 Sassari, Italy.
| | - M Rodriguez
- Dipartimento di Agraria, Università degli Studi di Sassari, Via E. De Nicola, 07100 Sassari, Italy; Centro per la Conservazione e Valorizzazione della Biodiversità Vegetale, Università degli Studi di Sassari, Surigheddu, 07040 Alghero, Italy
| | - E Rapposelli
- AGRIS Sardegna, Servizio per la Ricerca in Arboricoltura, Via Mameli 126/D, Cagliari, Italy
| | - M L Murgia
- Dipartimento di Agraria, Università degli Studi di Sassari, Via E. De Nicola, 07100 Sassari, Italy
| | - R Papa
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali (D3A), Università Politecnica delle Marche (UNIVPM), Via Brecce Bianche, 60131 Ancona, Italy
| | - A H D Brown
- Bioversity International (Honorary Research Fellow), Via dei Tre Denari, 472/a, 00054 Maccarese, Fiumicino, Italy
| | - G Attene
- Dipartimento di Agraria, Università degli Studi di Sassari, Via E. De Nicola, 07100 Sassari, Italy; Centro per la Conservazione e Valorizzazione della Biodiversità Vegetale, Università degli Studi di Sassari, Surigheddu, 07040 Alghero, Italy
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15
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Dong G, Zhang D, Liu X, Liu F, Chen F, Jones M. Asian archaeology. Response to Comment on "Agriculture facilitated permanent human occupation of the Tibetan Plateau after 3600 B.P.". Science 2015; 348:872. [PMID: 25999500 DOI: 10.1126/science.aaa7573] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Guedes et al. have drawn attention to a mismatch between the predictions of their "thermal niche model" and the records we have published of early barley finds in the northeastern Tibetan Plateau. Here, we consider how that mismatch usefully draws our attention to the additional variables that may account for it-namely, variations in genetic expression and agricultural practice.
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Affiliation(s)
- Guanghui Dong
- Key Laboratory of Western China's Environmental Systems (Ministry of Education), Lanzhou University, Lanzhou 730000, China.
| | - Dongju Zhang
- Key Laboratory of Western China's Environmental Systems (Ministry of Education), Lanzhou University, Lanzhou 730000, China
| | - Xinyi Liu
- Department of Anthropology, Washington University in St. Louis, St. Louis, MO 63130, USA.
| | - Fengwen Liu
- Key Laboratory of Western China's Environmental Systems (Ministry of Education), Lanzhou University, Lanzhou 730000, China
| | - Fahu Chen
- Key Laboratory of Western China's Environmental Systems (Ministry of Education), Lanzhou University, Lanzhou 730000, China
| | - Martin Jones
- McDonald Institute of Archaeological Research, University of Cambridge, Cambridge CB2 3ER, UK
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16
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Genetic diversity and population structure in a legacy collection of spring barley landraces adapted to a wide range of climates. PLoS One 2014; 9:e116164. [PMID: 25541702 PMCID: PMC4277474 DOI: 10.1371/journal.pone.0116164] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2014] [Accepted: 12/04/2014] [Indexed: 01/09/2023] Open
Abstract
Global environmental change and increasing human population emphasize the urgent need for higher yielding and better adapted crop plants. One strategy to achieve this aim is to exploit the wealth of so called landraces of crop species, representing diverse traditional domesticated populations of locally adapted genotypes. In this study, we investigated a comprehensive set of 1485 spring barley landraces (Lrc1485) adapted to a wide range of climates, which were selected from one of the largest genebanks worldwide. The landraces originated from 5° to 62.5° N and 16° to 71° E. The whole collection was genotyped using 42 SSR markers to assess the genetic diversity and population structure. With an average allelic richness of 5.74 and 372 alleles, Lrc1485 harbours considerably more genetic diversity than the most polymorphic current GWAS panel for barley. Ten major clusters defined most of the population structure based on geographical origin, row type of the ear and caryopsis type – and were assigned to specific climate zones. The legacy core reference set Lrc648 established in this study will provide a long-lasting resource and a very valuable tool for the scientific community. Lrc648 is best suited for multi-environmental field testing to identify candidate genes underlying quantitative traits but also for allele mining approaches.
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17
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Charrier O, Dupont P, Pornon A, Escaravage N. Microsatellite marker analysis reveals the complex phylogeographic history of Rhododendron ferrugineum (Ericaceae) in the Pyrenees. PLoS One 2014; 9:e92976. [PMID: 24667824 PMCID: PMC3965482 DOI: 10.1371/journal.pone.0092976] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 02/27/2014] [Indexed: 11/18/2022] Open
Abstract
Genetic variation within plant species is determined by a number of factors such as reproductive mode, breeding system, life history traits and climatic events. In alpine regions, plants experience heterogenic abiotic conditions that influence the population's genetic structure. The aim of this study was to investigate the genetic structure and phylogeographic history of the subalpine shrub Rhododendron ferrugineum across the Pyrenees and the links between the populations in the Pyrenees, the Alps and Jura Mountains. We used 27 microsatellite markers to genotype 645 samples from 29 Pyrenean populations, three from the Alps and one from the Jura Mountains. These data were used to estimate population genetics statistics such as allelic richness, observed heterozygosity, expected heterozygosity, fixation index, inbreeding coefficient and number of migrants. Genetic diversity was found to be higher in the Alps than in the Pyrenees suggesting colonization waves from the Alps to the Pyrenees. Two separate genetic lineages were found in both the Alps and Pyrenees, with a substructure of five genetic clusters in the Pyrenees where a loss of genetic diversity was noted. The strong differentiation among clusters is maintained by low gene flow across populations. Moreover, some populations showed higher genetic diversity than others and presented rare alleles that may indicate the presence of alpine refugia. Two lineages of R. ferrugineum have colonized the Pyrenees from the Alps. Then, during glaciation events R. ferrugineum survived in the Pyrenees in different refugia such as lowland refugia at the eastern part of the chain and nunataks at high elevations leading to a clustered genetic pattern.
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Affiliation(s)
- Olivia Charrier
- University Toulouse III Paul Sabatier, Lab Evolution & Diversite Biologique EDB, F-31062 Toulouse, France
- CNRS, EDB, UMR 5174, F-31062 Toulouse, France
- * E-mail:
| | - Pierre Dupont
- University Toulouse III Paul Sabatier, Lab Evolution & Diversite Biologique EDB, F-31062 Toulouse, France
- CNRS, EDB, UMR 5174, F-31062 Toulouse, France
| | - André Pornon
- University Toulouse III Paul Sabatier, Lab Evolution & Diversite Biologique EDB, F-31062 Toulouse, France
- CNRS, EDB, UMR 5174, F-31062 Toulouse, France
| | - Nathalie Escaravage
- University Toulouse III Paul Sabatier, Lab Evolution & Diversite Biologique EDB, F-31062 Toulouse, France
- CNRS, EDB, UMR 5174, F-31062 Toulouse, France
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18
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Bellucci E, Bitocchi E, Rau D, Nanni L, Ferradini N, Giardini A, Rodriguez M, Attene G, Papa R. Population structure of barley landrace populations and gene-flow with modern varieties. PLoS One 2013; 8:e83891. [PMID: 24386303 PMCID: PMC3873955 DOI: 10.1371/journal.pone.0083891] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Accepted: 11/16/2013] [Indexed: 11/18/2022] Open
Abstract
Landraces are heterogeneous plant varieties that are reproduced by farmers as populations that are subject to both artificial and natural selection. Landraces are distinguished by farmers due to their specific traits, and different farmers often grow different populations of the same landrace. We used simple sequence repeats (SSRs) to analyse 12 barley landrace populations from Sardinia from two collections spanning 10 years. We analysed the population structure, and compared the population diversity of the landraces that were collected at field level (population). We used a representative pool of barley varieties for diversity comparisons and to analyse the effects of gene flow from modern varieties. We found that the Sardinian landraces are a distinct gene pool from those of both two-row and six-row barley varieties. There is also a low, but significant, mean level and population-dependent level of introgression from the modern varieties into the Sardinian landraces. Moreover, we show that the Sardinian landraces have the same level of gene diversity as the representative sample of modern commercial varieties grown in Italy in the last decades, even within population level. Thus, these populations represent crucial sources of germplasm that will be useful for crop improvement and for population genomics studies and association mapping, to identify genes, loci and genome regions responsible for adaptive variations. Our data also suggest that landraces are a source of valuable germplasm for sustainable agriculture in the context of future climate change, and that in-situ conservation strategies based on farmer use can preserve the genetic identity of landraces while allowing adaptation to local environments.
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Affiliation(s)
- Elisa Bellucci
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Ancona, Italy
| | - Elena Bitocchi
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Ancona, Italy
| | - Domenico Rau
- Dipartimento di Agraria, Università degli Studi di Sassari, Sassari, Italy
| | - Laura Nanni
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Ancona, Italy
| | - Nicoletta Ferradini
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Ancona, Italy
| | - Alessandro Giardini
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Ancona, Italy
| | - Monica Rodriguez
- Dipartimento di Agraria, Università degli Studi di Sassari, Sassari, Italy
| | - Giovanna Attene
- Dipartimento di Agraria, Università degli Studi di Sassari, Sassari, Italy
| | - Roberto Papa
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Ancona, Italy
- Consiglio per la Ricerca e Sperimentazione in Agricoltura, Cereal Research Centre (CRA-CER), Foggia, Italy
- * E-mail:
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Sexton JP, Hangartner SB, Hoffmann AA. GENETIC ISOLATION BY ENVIRONMENT OR DISTANCE: WHICH PATTERN OF GENE FLOW IS MOST COMMON? Evolution 2013; 68:1-15. [DOI: 10.1111/evo.12258] [Citation(s) in RCA: 467] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 08/19/2013] [Indexed: 12/25/2022]
Affiliation(s)
- Jason P. Sexton
- Bio21 Molecular Science Institute; The University of Melbourne; Parkville Victoria 3010 Australia
| | - Sandra B. Hangartner
- Bio21 Molecular Science Institute; The University of Melbourne; Parkville Victoria 3010 Australia
| | - Ary A. Hoffmann
- Bio21 Molecular Science Institute; The University of Melbourne; Parkville Victoria 3010 Australia
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20
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Samberg LH, Fishman L, Allendorf FW. Population genetic structure in a social landscape: barley in a traditional Ethiopian agricultural system. Evol Appl 2013; 6:1133-45. [PMID: 24478796 PMCID: PMC3901544 DOI: 10.1111/eva.12091] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Accepted: 05/31/2013] [Indexed: 11/30/2022] Open
Abstract
Conservation strategies are increasingly driven by our understanding of the processes and patterns of gene flow across complex landscapes. The expansion of population genetic approaches into traditional agricultural systems requires understanding how social factors contribute to that landscape, and thus to gene flow. This study incorporates extensive farmer interviews and population genetic analysis of barley landraces (Hordeum vulgare) to build a holistic picture of farmer-mediated geneflow in an ancient, traditional agricultural system in the highlands of Ethiopia. We analyze barley samples at 14 microsatellite loci across sites at varying elevations and locations across a contiguous mountain range, and across farmer-identified barley types and management strategies. Genetic structure is analyzed using population-based and individual-based methods, including measures of population differentiation and genetic distance, multivariate Principal Coordinate Analysis, and Bayesian assignment tests. Phenotypic analysis links genetic patterns to traits identified by farmers. We find that differential farmer management strategies lead to markedly different patterns of population structure across elevation classes and barley types. The extent to which farmer seed management appears as a stronger determinant of spatial structure than the physical landscape highlights the need for incorporation of social, landscape, and genetic data for the design of conservation strategies in human-influenced landscapes.
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Rodriguez M, Rau D, Angioi SA, Bellucci E, Bitocchi E, Nanni L, Knüpffer H, Negri V, Papa R, Attene G. European Phaseolus coccineus L. landraces: population structure and adaptation, as revealed by cpSSRs and phenotypic analyses. PLoS One 2013; 8:e57337. [PMID: 23451209 PMCID: PMC3579852 DOI: 10.1371/journal.pone.0057337] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Accepted: 01/21/2013] [Indexed: 11/18/2022] Open
Abstract
Relatively few studies have extensively analysed the genetic diversity of the runner bean through molecular markers. Here, we used six chloroplast microsatellites (cpSSRs) to investigate the cytoplasmic diversity of 331 European domesticated accessions of the scarlet runner bean (Phaseolus coccineus L.), including the botanical varieties albiflorus, bicolor and coccineus, and a sample of 49 domesticated and wild accessions from Mesoamerica. We further explored the pattern of diversity of the European landraces using 12 phenotypic traits on 262 individuals. For 158 European accessions, we studied the relationships between cpSSR polymorphisms and phenotypic traits. Additionally, to gain insights into the role of gene flow and migration, for a subset of 115 accessions, we compared and contrasted the results obtained by cpSSRs and phenotypic traits with those obtained in a previous study with 12 nuclear microsatellites (nuSSRs). Our results suggest that both demographic and selective factors have roles in the shaping of the population genetic structure of the European runner bean. In particular, we infer the existence of a moderate-to-strong cytoplasmic bottleneck that followed the expansion of the crop into Europe, and we deduce multiple domestication events for this species. We also observe an adaptive population differentiation in the phenology across a latitudinal gradient, which suggests that selection led to the diversification of the runner bean in Europe. The botanical varieties albiflorus, bicolor and coccineus, which are based solely on flower colour, cannot be distinguished based on these cpSSRs and nuSSRs, nor according to the 12 quantitative traits.
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Affiliation(s)
- Monica Rodriguez
- Dipartimento di Agraria, Sezione di Agronomia, Coltivazioni Erbacee e Genetica, Università degli Studi di Sassari, Sassari, Italy
| | - Domenico Rau
- Dipartimento di Agraria, Sezione di Agronomia, Coltivazioni Erbacee e Genetica, Università degli Studi di Sassari, Sassari, Italy
| | - Simonetta A. Angioi
- Dipartimento di Agraria, Sezione di Agronomia, Coltivazioni Erbacee e Genetica, Università degli Studi di Sassari, Sassari, Italy
| | - Elisa Bellucci
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università Politecnica delle Marche, Ancona, Italy
| | - Elena Bitocchi
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università Politecnica delle Marche, Ancona, Italy
| | - Laura Nanni
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università Politecnica delle Marche, Ancona, Italy
| | - Helmut Knüpffer
- Genebank Department, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Valeria Negri
- Dipartimento di Biologia Applicata, Università degli Studi di Perugia, Perugia, Italy
| | - Roberto Papa
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università Politecnica delle Marche, Ancona, Italy
- Cereal Research Centre, Agricultural Research Council, Foggia, Italy
| | - Giovanna Attene
- Dipartimento di Agraria, Sezione di Agronomia, Coltivazioni Erbacee e Genetica, Università degli Studi di Sassari, Sassari, Italy
- Centro per la Conservazione e Valorizzazione della Biodiversità Vegetale, Università degli Studi di Sassari, Surigheddu Alghero, Italy
- * E-mail:
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Rodriguez M, Rau D, O'Sullivan D, Brown AHD, Papa R, Attene G. Genetic structure and linkage disequilibrium in landrace populations of barley in Sardinia. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 125:171-84. [PMID: 22411093 DOI: 10.1007/s00122-012-1824-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Accepted: 02/11/2012] [Indexed: 05/14/2023]
Abstract
Multilocus digenic linkage disequilibria (LD) and their population structure were investigated in eleven landrace populations of barley (Hordeum vulgare ssp. vulgare L.) in Sardinia, using 134 dominant simple-sequence amplified polymorphism markers. The analysis of molecular variance for these markers indicated that the populations were partially differentiated (F(ST) = 0.18), and clustered into three geographic areas. Consistent with this population pattern, STRUCTURE analysis allocated individuals from a bulk of all populations into four genetic groups, and these groups also showed geographic patterns. In agreement with other molecular studies in barley, the general level of LD was low (13% of locus pairs, with P < 0.01) in the bulk of 337 lines, and decayed steeply with map distance between markers. The partitioning of multilocus associations into various components indicated that genetic drift and founder effects played a major role in determining the overall genetic makeup of the diversity in these landrace populations, but that epistatic homogenising or diversifying selection was also present. Notably, the variance of the disequilibrium component was relatively high, which implies caution in the pooling of barley lines for association studies. Finally, we compared the analyses of multilocus structure in barley landrace populations with parallel analyses in both composite crosses of barley on the one hand and in natural populations of wild barley on the other. Neither of these serves as suitable mimics of landraces in barley, which require their own study. Overall, the results suggest that these populations can be exploited for LD mapping if population structure is controlled.
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Affiliation(s)
- Monica Rodriguez
- Centro per la Conservazione e Valorizzazione della Biodiversità Vegetale, Università degli Studi di Sassari, Via E. de Nicola, 07100, Sassari, Italy.
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Newton AC, Flavell AJ, George TS, Leat P, Mullholland B, Ramsay L, Revoredo-Giha C, Russell J, Steffenson BJ, Swanston JS, Thomas WTB, Waugh R, White PJ, Bingham IJ. Crops that feed the world 4. Barley: a resilient crop? Strengths and weaknesses in the context of food security. Food Secur 2011. [DOI: 10.1007/s12571-011-0126-3] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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