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Nasar S, Ostevik K, Murtaza G, Rausher MD. Morphological and molecular characterization of variation in common bean (Phaseolus vulgaris L.) germplasm from Azad Jammu and Kashmir, Pakistan. PLoS One 2022; 17:e0265817. [PMID: 35472209 PMCID: PMC9041810 DOI: 10.1371/journal.pone.0265817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 03/08/2022] [Indexed: 11/18/2022] Open
Abstract
Phaseolus vulgaris, an essential food and source of protein, is cultivated across the world. This study was carried out to investigate the diversity and population structure of 34 P. vulgaris landrace accessions collected from the Azad Jammu and Kashmir (AJ&K) regions of Pakistan. The samples were analyzed both morphologically and using genetic variation identified through RNA sequencing. Our results indicated that most genetic variation occurs among local accessions, with little genetic variation occurring between geographical regions. In addition, the accessions fell into two major genetic groups. Morphological analysis revealed that these two genetic groups differ in a number of quantitative traits, including seed length, seed width, and seed weight. One accession, DUD-11, appears to be a mixture of the two major groups genetically as well as morphologically. Among the other accessions, DUD-8, RWK-2, and NGD-1 depicted particularly high seed weight along with higher seed length, seed width, and seed yield per plant. We suggest focusing on these accessions in future breeding programs. More generally, our results provide baseline data that will be useful for crop improvement and effective cultivation practices in Pakistan.
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Affiliation(s)
- Sidra Nasar
- Department of Botany, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Kate Ostevik
- Department of Biology, Duke University, Durham, North Carolina, United States of America
- Department of Evolution, Ecology, and Organismal Biology, University of California Riverside, Riverside, California, United States of America
| | - Ghulam Murtaza
- Department of Botany, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Mark D. Rausher
- Department of Biology, Duke University, Durham, North Carolina, United States of America
- * E-mail:
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Kaplin VG. Distribution and Biology of Invasive Species of Bean Bruchid Acanthoscelides obtectus (Insecta, Coleoptera, Bruchidae). RUSSIAN JOURNAL OF BIOLOGICAL INVASIONS 2022. [DOI: 10.1134/s2075111722010064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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DISTRIBUTION AND BIOLOGY OF INVASIVE SPECIES OF BEAN BRUCHID <i>ACANTHOSCELIDES OBTECTUS</i> (INSECTA, COLEOPTERA, BRUCHIDAE). RUSSIAN JOURNAL OF BIOLOGICAL INVASIONS 2021. [DOI: 10.35885/1996-1499-2021-14-4-54-76] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The review of literary sources on ecology, biology, distribution of bean bruchid ( Acanthoscelides obtectus ) and its main food plant - Phaseolus vulgaris in North and South America; Europe, Africa, Asia, Australia and more details in Russia; the influence of abiotic, biotic and anthropogenic factors on the invasive process, phytosanitary condition of common bean crops in Russia is presented. Some aspects of the invader management are shown. The main stages and areas of cultivation of common bean and invasion of bean bruchid from their primary habitat in South America and in the south of North America are traced; the vectors and reasons causing them are considered. In Russia, the economic importance of bean bruchid has increased since the mid-1980s, which coincided with the climate warming; there was an expansion of its distribution in the eastern and north-western directions. At the last decades of the 20th century, it had penetrated in Smolensk and in the south part of the Tver and the Tomsk regions. With the increase in production of beans in Russia, the lack of systemic protection from bean bruchid and further increase of climate warming will contribute to the extension of its range to the north in the European part of Russia and the Urals to 57-58° N. Lat., where the conditions of the summer period are favorable for development of common bean and bean bruchid. To the east, it may spread to Tyva, Buryatia, the Trans-Baikal territory, the Amur region, the Jewish Autonomous region, and the southern part of the Khabarovsk territory. With the introduction of strict internal quarantine and a system of protection of common bean from this pest, which prevents the spread of infected dry bean, on the contrary, it is possible to reduce the distribution range of the bean bruchid, with its disappearance in the Siberian, Ural districts, Bashkortostan and Tatarstan.
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Elias JCF, Gonçalves-Vidigal MC, Ariani A, Valentini G, Martiniano-Souza MDC, Vaz Bisneta M, Gepts P. Genome-Environment Association Analysis for Bio-Climatic Variables in Common Bean ( Phaseolus vulgaris L.) from Brazil. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10081572. [PMID: 34451617 PMCID: PMC8399474 DOI: 10.3390/plants10081572] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/23/2021] [Accepted: 07/26/2021] [Indexed: 05/08/2023]
Abstract
Abiotic stress is a limiting factor for common bean (Phaseolus vulgaris L.) production globally. The study of the genotypic, phenotypic, and bio-climatic variables in a broad set of accessions may assist the identification of genomic regions involved in the climatic adaptation of the common bean. We conducted a genotyping-by-sequencing analysis using 28,823 SNPs on 110 georeferenced common bean accessions from Brazil to discover associations between SNPs and bio-climatic indexes. The population structure analysis clustered the accessions into two groups corresponding to the Andean and Mesoamerican gene pools. Of the 19 bioclimatic variables, 17 exhibited a significant association with SNPs on chromosomes Pv01, Pv02, Pv03, Pv04, Pv06, Pv09, Pv10, and Pv11 of common bean. Ten candidate genes were associated with specific bio-climatic variables related to temperature and precipitation. The candidate genes associated with this significant Pv09 region encode a Platz transcription factor family protein previously reported to be an essential regulator of drought stress. The SNP markers and candidate genes associated with the bio-climatic variables should be validated in segregating populations for water stress, which could further be used for marker-assisted selection. As a result, bean breeding programs may be able to provide advances in obtaining drought-tolerant cultivars.
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Affiliation(s)
- Júlio Cesar F. Elias
- Departamento de Agronomia, Universidade Estadual de Maringá-UEM, Av. Colombo 5790, Maringá 87020-900, Brazil; (J.C.F.E.); (M.d.C.M.-S.); (M.V.B.)
| | - Maria Celeste Gonçalves-Vidigal
- Departamento de Agronomia, Universidade Estadual de Maringá-UEM, Av. Colombo 5790, Maringá 87020-900, Brazil; (J.C.F.E.); (M.d.C.M.-S.); (M.V.B.)
- Correspondence: ; Tel.:+55-449-9908-8186
| | | | - Giseli Valentini
- Soybean Genomics and Improvement Laboratory USDA-ARS, 10300 Baltimore Avenue, Beltsville, MD 20705, USA;
| | - Maria da Conceição Martiniano-Souza
- Departamento de Agronomia, Universidade Estadual de Maringá-UEM, Av. Colombo 5790, Maringá 87020-900, Brazil; (J.C.F.E.); (M.d.C.M.-S.); (M.V.B.)
| | - Mariana Vaz Bisneta
- Departamento de Agronomia, Universidade Estadual de Maringá-UEM, Av. Colombo 5790, Maringá 87020-900, Brazil; (J.C.F.E.); (M.d.C.M.-S.); (M.V.B.)
| | - Paul Gepts
- Department of Plant Sciences, Section of Crop and Ecosystem Sciences, University of California, Davis, CA 95161-8780, USA;
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Chacón-Sánchez MI, Martínez-Castillo J, Duitama J, Debouck DG. Gene Flow in Phaseolus Beans and Its Role as a Plausible Driver of Ecological Fitness and Expansion of Cultigens. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.618709] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The genus Phaseolus, native to the Americas, is composed of more than eighty wild species, five of which were domesticated in pre-Columbian times. Since the beginning of domestication events in this genus, ample opportunities for gene flow with wild relatives have existed. The present work reviews the extent of gene flow in the genus Phaseolus in primary and secondary areas of domestication with the aim of illustrating how this evolutionary force may have conditioned ecological fitness and the widespread adoption of cultigens. We focus on the biological bases of gene flow in the genus Phaseolus from a spatial and time perspective, the dynamics of wild-weedy-crop complexes in the common bean and the Lima bean, the two most important domesticated species of the genus, and the usefulness of genomic tools to detect inter and intraspecific introgression events. In this review we discuss the reproductive strategies of several Phaseolus species, the factors that may favor outcrossing rates and evidence suggesting that interspecific gene flow may increase ecological fitness of wild populations. We also show that wild-weedy-crop complexes generate genetic diversity over which farmers are able to select and expand their cultigens outside primary areas of domestication. Ultimately, we argue that more studies are needed on the reproductive biology of the genus Phaseolus since for most species breeding systems are largely unknown. We also argue that there is an urgent need to preserve wild-weedy-crop complexes and characterize the genetic diversity generated by them, in particular the genome-wide effects of introgressions and their value for breeding programs. Recent technological advances in genomics, coupled with agronomic characterizations, may make a large contribution.
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Paulino JFDC, de Almeida CP, Bueno CJ, Song Q, Fritsche-Neto R, Carbonell SAM, Chiorato AF, Benchimol-Reis LL. Genome-Wide Association Study Reveals Genomic Regions Associated with Fusarium Wilt Resistance in Common Bean. Genes (Basel) 2021; 12:765. [PMID: 34069884 PMCID: PMC8157364 DOI: 10.3390/genes12050765] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/13/2021] [Accepted: 05/13/2021] [Indexed: 12/31/2022] Open
Abstract
Fusarium wilt (Fusarium oxysporum f. sp. phaseoli, Fop) is one of the main fungal soil diseases in common bean. The aim of the present study was to identify genomic regions associated with Fop resistance through genome-wide association studies (GWAS) in a Mesoamerican Diversity Panel (MDP) and to identify potential common bean sources of Fop's resistance. The MDP was genotyped with BARCBean6K_3BeadChip and evaluated for Fop resistance with two different monosporic strains using the root-dip method. Disease severity rating (DSR) and the area under the disease progress curve (AUDPC), at 21 days after inoculation (DAI), were used for GWAS performed with FarmCPU model. The p-value of each SNP was determined by resampling method and Bonferroni test. For UFV01 strain, two significant single nucleotide polymorphisms (SNPs) were mapped on the Pv05 and Pv11 for AUDPC, and the same SNP (ss715648096) on Pv11 was associated with AUDPC and DSR. Another SNP, mapped on Pv03, showed significance for DSR. Regarding IAC18001 strain, significant SNPs on Pv03, Pv04, Pv05, Pv07 and on Pv01, Pv05, and Pv10 were observed. Putative candidate genes related to nucleotide-binding sites and carboxy-terminal leucine-rich repeats were identified. The markers may be important future tools for genomic selection to Fop disease resistance in beans.
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Affiliation(s)
| | - Caléo Panhoca de Almeida
- Centro de Recursos Genéticos Vegetais, Instituto Agronômico, Campinas 13075-630, SP, Brazil; (J.F.d.C.P.); (C.P.d.A.)
| | - César Júnior Bueno
- Centro Avançado de Pesquisa em Proteção de Plantas e Saúde Animal, Instituto Biológico, Campinas 13101-680, SP, Brazil;
| | - Qijian Song
- Soybean Genomics and Improvement Laboratory, US Department of Agriculture, Agricultural Research Service (USDA-ARS), Beltsville, MD 20705, USA;
| | - Roberto Fritsche-Neto
- Department of Genetics, ‘Luiz de Queiroz’ Agriculture College, University of Sao Paulo, Piracicaba 13418-900, SP, Brazil;
| | | | - Alisson Fernando Chiorato
- Centro de Grãos e Fibras, Instituto Agronômico, Campinas 13075-630, SP, Brazil; (S.A.M.C.); (A.F.C.)
| | - Luciana Lasry Benchimol-Reis
- Centro de Recursos Genéticos Vegetais, Instituto Agronômico, Campinas 13075-630, SP, Brazil; (J.F.d.C.P.); (C.P.d.A.)
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Wilker J, Humphries S, Rosas-Sotomayor JC, Gómez Cerna M, Torkamaneh D, Edwards M, Navabi A, Pauls KP. Genetic Diversity, Nitrogen Fixation, and Water Use Efficiency in a Panel of Honduran Common Bean ( Phaseolus vulgaris L.) Landraces and Modern Genotypes. PLANTS 2020; 9:plants9091238. [PMID: 32961677 PMCID: PMC7569834 DOI: 10.3390/plants9091238] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/10/2020] [Accepted: 09/11/2020] [Indexed: 01/09/2023]
Abstract
Common bean (Phaseolus vulgaris L.) provides critical nutrition and a livelihood for millions of smallholder farmers worldwide. Beans engage in symbiotic nitrogen fixation (SNF) with Rhizobia. Honduran hillside farmers farm marginal land and utilize few production inputs; therefore, bean varieties with high SNF capacity and environmental resiliency would be of benefit to them. We explored the diversity for SNF, agronomic traits, and water use efficiency (WUE) among 70 Honduran landrace, participatory bred (PPB), and conventionally bred bean varieties (HON panel) and 6 North American check varieties in 3 low-N field trials in Ontario, Canada and Honduras. Genetic diversity was measured with a 6K single nucleotide polymorphism (SNP) array, and phenotyping for agronomic, SNF, and WUE traits was carried out. STRUCTURE analysis revealed two subpopulations with admixture between the subpopulations. Nucleotide diversity was greater in the landraces than the PPB varieties across the genome, and multiple genomic regions were identified where population genetic differentiation between the landraces and PPB varieties was evident. Significant differences were found between varieties and breeding categories for agronomic traits, SNF, and WUE. Landraces had above average SNF capacity, conventional varieties showed higher yields, and PPB varieties performed well for WUE. Varieties with the best SNF capacity could be used in further participatory breeding efforts.
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Affiliation(s)
- Jennifer Wilker
- Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada; (J.W.); (D.T.); (M.E.)
| | - Sally Humphries
- Department of Sociology and Anthropology, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | - Juan Carlos Rosas-Sotomayor
- Departamento de Ciencia y Producción Agropecuaria, Escuela Agrícola Panamericana, Zamorano, Tegucigalpa 11101, Honduras;
| | - Marvin Gómez Cerna
- Fundación para la Investigación Participativa con Agricultores de Honduras, La Ceiba, Atlántida 561, Honduras;
| | - Davoud Torkamaneh
- Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada; (J.W.); (D.T.); (M.E.)
| | - Michelle Edwards
- Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada; (J.W.); (D.T.); (M.E.)
| | - Alireza Navabi
- Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada; (J.W.); (D.T.); (M.E.)
| | - K. Peter Pauls
- Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada; (J.W.); (D.T.); (M.E.)
- Correspondence: ; Tel.: +1-519-824-4120 (ext. 54136)
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Carvalho MS, de Oliveira Moulin Carias CM, Silva MA, da Silva Ferreira MF, de Souza TLPO, Posse SCP, Ferreira A. Genetic diversity and structure of landrace accessions, elite lineages and cultivars of common bean estimated with SSR and SNP markers. Mol Biol Rep 2020; 47:6705-6715. [PMID: 32803507 DOI: 10.1007/s11033-020-05726-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 08/08/2020] [Indexed: 11/26/2022]
Abstract
Common bean (Phaseolus vulgaris L.) is an important source of proteins, fibers and minerals for humans, being grown mainly in developing countries and representing a source of income for small farmers. In this work, a set of 206 Brazilian landraces and 59 elite lineages and cultivars were genotyped with 23 SSR (Simple Sequence Repeats) and 251 SNPs (Single-Nucleotide Polymorphism) markers. The ideal number of groups, according to STRUCTURE, was K = 2 for both SNPs and SSRs. This could be expected considering the two original gene pools-Andean (AND) and Mesoamerican (MES). The matrices of genetic simple matching dissimilarity for SSRs and SNPs were highly correlated; therefore, the allelic data of the markers was combined and analyzed to understand the genetic relationships of the studied collection. The neighbor-joining analysis considering the genetic distance of simple matching grouped the 265 genotypes into 17 subgroups. The markers SSR and SNP presented high power to discriminate among the genotypes. The ample genetic diversity observed in the work collection makes it a valuable source for the conservation, sustainable management and exploration in breeding programs of the crop.
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Affiliation(s)
- Marina Santos Carvalho
- Laboratório de Genética e Melhoramento Vegetal, Departamento de Agronomia, Centro de Ciências Agrárias e Engenharias, Universidade Federal Do Espírito Santo, Alegre, ES, 29500-000, Brazil
| | - Cintia Machado de Oliveira Moulin Carias
- Laboratório de Genética e Melhoramento Vegetal, Departamento de Agronomia, Centro de Ciências Agrárias e Engenharias, Universidade Federal Do Espírito Santo, Alegre, ES, 29500-000, Brazil
| | - Matheus Alves Silva
- Laboratório de Genética e Melhoramento Vegetal, Departamento de Agronomia, Centro de Ciências Agrárias e Engenharias, Universidade Federal Do Espírito Santo, Alegre, ES, 29500-000, Brazil
| | - Marcia Flores da Silva Ferreira
- Laboratório de Genética e Melhoramento Vegetal, Departamento de Agronomia, Centro de Ciências Agrárias e Engenharias, Universidade Federal Do Espírito Santo, Alegre, ES, 29500-000, Brazil.
| | | | | | - Adesio Ferreira
- Laboratório de Genética e Melhoramento Vegetal, Departamento de Agronomia, Centro de Ciências Agrárias e Engenharias, Universidade Federal Do Espírito Santo, Alegre, ES, 29500-000, Brazil
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Lei L, Wang L, Wang S, Wu J. Marker-Trait Association Analysis of Seed Traits in Accessions of Common Bean ( Phaseolus vulgaris L.) in China. Front Genet 2020; 11:698. [PMID: 32714377 PMCID: PMC7344293 DOI: 10.3389/fgene.2020.00698] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 06/08/2020] [Indexed: 01/22/2023] Open
Abstract
Seed weight and seed size are the key agronomic traits that determine yield in common bean. To investigate the genetic architecture of four seed traits (100-seed weight, seed length, seed width, and seed height) of common bean in China, marker-trait association analysis of these seed traits was performed in a nationwide population of 395 common bean accessions using 116 polymorphic SSR markers. The four seed traits were evaluated in six trials across three environments. Seed size varied among the environments. Population structure was evaluated based on SSR markers and phaseolin, which divided the accessions into two main subpopulations representing the two known gene pools. Seed weight and seed size had a strong relationship with population clustering. In addition, in a Genome-wide association studies (GWAS), 21 significantly associated markers were identified for the four seed traits with two models, namely, general linear model (GLM) and mixed linear model (MLM). Some markers had pleiotropic effects, i.e., controlled more than one trait. The significant quantitative trait loci identified in this study could be used in marker-assisted breeding to accelerate the genetic improvement of yield in common bean.
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Affiliation(s)
- Lei Lei
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lanfen Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shumin Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jing Wu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Beijing, China
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Zitnick-Anderson K, Oladzadabbasabadi A, Jain S, Modderman C, Osorno JM, McClean PE, Pasche JS. Sources of Resistance to Fusarium solani and Associated Genomic Regions in Common Bean Diversity Panels. Front Genet 2020; 11:475. [PMID: 32612633 PMCID: PMC7308507 DOI: 10.3389/fgene.2020.00475] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 04/16/2020] [Indexed: 11/21/2022] Open
Abstract
Common bean (Phaseolus vulgaris L.) production worldwide is hampered by Fusarium root rot (FRR), which is caused by Fusarium solani. Screening for FRR resistance on a large scale is notoriously difficult and often yields inconsistent results due to variability within the environment and pathogen biology. A greenhouse screening assay was developed incorporating multiple isolates of F. solani to improve assay reproducibility. The Andean (ADP; n = 270) and Middle American (MDP; n = 280) Diversity Panels were screened in the greenhouse to identify genetic factors associated with FRR resistance. Forty-seven MDP and 34 ADP lines from multiple market classes were identified as resistant to FRR. Greenhouse phenotyping repeatability was confirmed via five control lines. Genome-wide association mapping using ∼200k SNPs was performed on standard phenotyping score 1–9, as well as binary and polynomial transformation of score data. Sixteen and seven significant genomic regions were identified for ADP and MDP, respectively, using all three classes of phenotypic data. Most candidate genes were associated with plant immune/defense mechanisms. For the ADP population, ortholog of glucan synthase-like enzyme, senescence-associated genes, and NAC domain protein, associated with peak genomic region Pv08:0.04–0.18 Mbp, were the most significant candidate genes. For the MDP population, the peak SNPs Pv07:15.29 Mbp and Pv01:51 Mbp mapped within gene models associated with ethylene response factor 1 and MAC/Perforin domain-containing gene respectively. The research provides a basis for bean improvement through the use of resistant genotypes and genomic regions for more durable root rot resistance.
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Affiliation(s)
| | | | - Shalu Jain
- Department of Pathology and Entomology, Syngenta, Stanton, MN, United States
| | - Chryseis Modderman
- Department of Soil, Water, and Climate, University of Minnesota, Morris, Morris, MN, United States
| | - Juan M Osorno
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Phillip E McClean
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Julie S Pasche
- Department of Plant Pathology, North Dakota State University, Fargo, ND, United States
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MacQueen AH, White JW, Lee R, Osorno JM, Schmutz J, Miklas PN, Myers J, McClean PE, Juenger TE. Genetic Associations in Four Decades of Multienvironment Trials Reveal Agronomic Trait Evolution in Common Bean. Genetics 2020; 215:267-284. [PMID: 32205398 PMCID: PMC7198278 DOI: 10.1534/genetics.120.303038] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 03/12/2020] [Indexed: 11/18/2022] Open
Abstract
Multienvironment trials (METs) are widely used to assess the performance of promising crop germplasm. Though seldom designed to elucidate genetic mechanisms, MET data sets are often much larger than could be duplicated for genetic research and, given proper interpretation, may offer valuable insights into the genetics of adaptation across time and space. The Cooperative Dry Bean Nursery (CDBN) is a MET for common bean (Phaseolus vulgaris) grown for > 70 years in the United States and Canada, consisting of 20-50 entries each year at 10-20 locations. The CDBN provides a rich source of phenotypic data across entries, years, and locations that is amenable to genetic analysis. To study stable genetic effects segregating in this MET, we conducted genome-wide association studies (GWAS) using best linear unbiased predictions derived across years and locations for 21 CDBN phenotypes and genotypic data (1.2 million SNPs) for 327 CDBN genotypes. The value of this approach was confirmed by the discovery of three candidate genes and genomic regions previously identified in balanced GWAS. Multivariate adaptive shrinkage (mash) analysis, which increased our power to detect significant correlated effects, found significant effects for all phenotypes. Mash found two large genomic regions with effects on multiple phenotypes, supporting a hypothesis of pleiotropic or linked effects that were likely selected on in pursuit of a crop ideotype. Overall, our results demonstrate that statistical genomics approaches can be used on MET phenotypic data to discover significant genetic effects and to define genomic regions associated with crop improvement.
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Affiliation(s)
- Alice H MacQueen
- Integrative Biology, The University of Texas at Austin, Texas 78712
| | - Jeffrey W White
- U.S. Arid Land Agricultural Research Center, U.S. Department of Agriculture-Agricultural Research Service, Maricopa, Arizona 85239
| | - Rian Lee
- Genomics and Bioinformatics Program, North Dakota State University, Fargo, North Dakota 58102
| | - Juan M Osorno
- Genomics and Bioinformatics Program, North Dakota State University, Fargo, North Dakota 58102
| | - Jeremy Schmutz
- Hudson-Alpha Institute for Biotechnology, Huntsville, Alabama 35806
| | - Phillip N Miklas
- Grain Legume Genetics and Physiology Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Prosser, Washington 99350
| | - Jim Myers
- Department of Horticulture, Oregon State University, Corvallis, Oregon 97331
| | - Phillip E McClean
- Genomics and Bioinformatics Program, North Dakota State University, Fargo, North Dakota 58102
| | - Thomas E Juenger
- Integrative Biology, The University of Texas at Austin, Texas 78712
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Cortinovis G, Frascarelli G, Di Vittori V, Papa R. Current State and Perspectives in Population Genomics of the Common Bean. PLANTS (BASEL, SWITZERLAND) 2020; 9:E330. [PMID: 32150958 PMCID: PMC7154925 DOI: 10.3390/plants9030330] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 02/27/2020] [Accepted: 03/03/2020] [Indexed: 11/17/2022]
Abstract
* Correspondence: r [...].
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Affiliation(s)
| | | | | | - Roberto Papa
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali (D3A), Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy; (G.C.); (G.F.); (V.D.V.)
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Berny Mier y Teran JC, Konzen ER, Medina V, Palkovic A, Ariani A, Tsai SM, Gilbert ME, Gepts P. Root and shoot variation in relation to potential intermittent drought adaptation of Mesoamerican wild common bean (Phaseolus vulgaris L.). ANNALS OF BOTANY 2019; 124:917-932. [PMID: 30596881 PMCID: PMC6881220 DOI: 10.1093/aob/mcy221] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Accepted: 11/14/2018] [Indexed: 05/09/2023]
Abstract
BACKGROUND Wild crop relatives have been potentially subjected to stresses on an evolutionary time scale prior to domestication. Among these stresses, drought is one of the main factors limiting crop productivity and its impact is likely to increase under current scenarios of global climate change. We sought to determine to what extent wild common bean (Phaseolus vulgaris) exhibited adaptation to drought stress, whether this potential adaptation is dependent on the climatic conditions of the location of origin of individual populations, and to what extent domesticated common bean reflects potential drought adaptation. METHODS An extensive and diverse set of wild beans from across Mesoamerica, along with a set of reference Mesoamerican domesticated cultivars, were evaluated for root and shoot traits related to drought adaptation. A water deficit experiment was conducted by growing each genotype in a long transparent tube in greenhouse conditions so that root growth, in addition to shoot growth, could be monitored. RESULTS Phenotypic and landscape genomic analyses, based on single-nucleotide polymorphisms, suggested that beans originating from central and north-west Mexico and Oaxaca, in the driest parts of their distribution, produced more biomass and were deeper-rooted. Nevertheless, deeper rooting was correlated with less root biomass production relative to total biomass. Compared with wild types, domesticated types showed a stronger reduction and delay in growth and development in response to drought stress. Specific genomic regions were associated with root depth, biomass productivity and drought response, some of which showed signals of selection and were previously related to productivity and drought tolerance. CONCLUSIONS The drought tolerance of wild beans consists in its stronger ability, compared with domesticated types, to continue growth in spite of water-limited conditions. This study is the first to relate bean response to drought to environment of origin for a diverse selection of wild beans. It provides information that needs to be corroborated in crosses between wild and domesticated beans to make it applicable to breeding programmes.
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Affiliation(s)
- Jorge C Berny Mier y Teran
- University of California, Department of Plant Sciences/Mail Stop 1, Section of Crop & Ecosystem Sciences, Davis, CA, USA
| | - Enéas R Konzen
- University of California, Department of Plant Sciences/Mail Stop 1, Section of Crop & Ecosystem Sciences, Davis, CA, USA
- Centro de Energia Nuclear na Agricultura (CENA), Universidade de São Paulo, Piracicaba, SP, Brasil
| | - Viviana Medina
- University of California, Department of Plant Sciences/Mail Stop 1, Section of Crop & Ecosystem Sciences, Davis, CA, USA
| | - Antonia Palkovic
- University of California, Department of Plant Sciences/Mail Stop 1, Section of Crop & Ecosystem Sciences, Davis, CA, USA
| | - Andrea Ariani
- University of California, Department of Plant Sciences/Mail Stop 1, Section of Crop & Ecosystem Sciences, Davis, CA, USA
| | - Siu M Tsai
- Centro de Energia Nuclear na Agricultura (CENA), Universidade de São Paulo, Piracicaba, SP, Brasil
| | - Matthew E Gilbert
- University of California, Department of Plant Sciences/Mail Stop 1, Section of Crop & Ecosystem Sciences, Davis, CA, USA
| | - P Gepts
- University of California, Department of Plant Sciences/Mail Stop 1, Section of Crop & Ecosystem Sciences, Davis, CA, USA
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14
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Genotyping-by-Sequencing Reveals Molecular Genetic Diversity in Italian Common Bean Landraces. DIVERSITY 2019. [DOI: 10.3390/d11090154] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The common bean (Phaseolus vulgaris L.) is one of the main legumes worldwide and represents a valuable source of nutrients. Independent domestication events in the Americas led to the formation of two cultivated genepools, namely Mesoamerican and Andean, to which European material has been brought back. In this study, Italian common bean landraces were analyzed for their genetic diversity and structure, using single nucleotide polymorphism (SNP) markers derived from genotyping-by-sequencing (GBS) technology. After filtering, 11,866 SNPs were obtained and 798 markers, pruned for linkage disequilibrium, were used for structure analysis. The most probable number of subpopulations (K) was two, consistent with the presence of the two genepools, identified through the phaseolin diagnostic marker. Some landraces were admixed, suggesting probable hybridization events between Mesoamerican and Andean material. When increasing the number of possible Ks, the Andean germplasm appeared to be structured in two or three subgroups. The subdivision within the Andean material was also observed in a principal coordinate analysis (PCoA) plot and a dendrogram based on genetic distances. The Mesoamerican landraces showed a higher level of genetic diversity compared to the Andean landraces. Calculation of the fixation index (FST) at individual SNPs between the Mesoamerican and Andean genepools and within the Andean genepool evidenced clusters of highly divergent loci in specific chromosomal regions. This work may help to preserve landraces of the common bean from genetic erosion, and could represent a starting point for the identification of interesting traits that determine plant adaptation.
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15
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Wilker J, Navabi A, Rajcan I, Marsolais F, Hill B, Torkamaneh D, Pauls KP. Agronomic Performance and Nitrogen Fixation of Heirloom and Conventional Dry Bean Varieties Under Low-Nitrogen Field Conditions. FRONTIERS IN PLANT SCIENCE 2019; 10:952. [PMID: 31404343 PMCID: PMC6676800 DOI: 10.3389/fpls.2019.00952] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 07/09/2019] [Indexed: 05/26/2023]
Abstract
Common beans (Phaseolus vulgaris) form a relationship with nitrogen-fixing rhizobia and through a process termed symbiotic nitrogen fixation (SNF) which provides them with a source of nitrogen. However, beans are considered poor nitrogen fixers, and modern production practices involve routine use of N fertilizer, which leads to the down-regulation of SNF. High-yielding, conventionally bred bean varieties are developed using conventional production practices and selection criteria, typically not including SNF efficiency, and may have lost this trait over decades of modern breeding. In contrast, heirloom bean genotypes were developed before the advent of modern production practices and may represent an underutilized pool of genetics which could be used to improve SNF. This study compared the SNF capacity under low-N field conditions, of collections of heirloom varieties with and conventionally bred dry bean varieties. The heirloom-conventional panel (HCP) consisted of 42 genotypes from various online seed retailers or from the University of Guelph Bean Breeding program seedbank. The HCP was genotyped using a single nucleotide polymorphism (SNP) array to investigate genetic relatedness within the panel. Field trials were conducted at three locations in ON, Canada from 2014 to 2015 and various agronomic and seed composition traits were measured, including capacity for nitrogen fixation (using the natural abundance method to measure seed N isotope ratios). Significant variation for SNF was found in the panel. However, on average, heirloom genotypes did not fix significantly more nitrogen than conventionally bred varieties. However, five heirloom genotypes fixed >60% of their nitrogen from the atmosphere. Yield (kg ha-1) was not significantly different between heirloom and conventional genotypes, suggesting that incorporating heirloom genotypes into a modern breeding program would not negatively impact yield. Nitrogen fixation was significantly higher among Middle American genotypes than among Andean genotypes, confirming previous findings. The best nitrogen fixing line was Coco Sophie, a European heirloom white bean whose genetic makeup is admixed between the Andean and Middle American genepools. Heirloom genotypes represent a useful source of genetics to improve SNF in modern bean breeding.
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Affiliation(s)
- Jennifer Wilker
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
| | - Alireza Navabi
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
| | - Istvan Rajcan
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
| | - Frédéric Marsolais
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, ON, Canada
| | - Brett Hill
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB, Canada
| | - Davoud Torkamaneh
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
| | - K. Peter Pauls
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
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16
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Oladzad A, Zitnick-Anderson K, Jain S, Simons K, Osorno JM, McClean PE, Pasche JS. Genotypes and Genomic Regions Associated With Rhizoctonia solani Resistance in Common Bean. FRONTIERS IN PLANT SCIENCE 2019; 10:956. [PMID: 31396253 PMCID: PMC6667560 DOI: 10.3389/fpls.2019.00956] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 07/09/2019] [Indexed: 05/11/2023]
Abstract
Rhizoctonia solani Kühn (teleomorph Thanatephorus cucumeris) is an important root rot pathogen of common bean (Phaseolus vulgaris L.). To uncover genetic factors associated with resistance to the pathogen, the Andean (ADP; n = 273) and Middle American (MDP; n = 279) diversity panels, which represent much of the genetic diversity known in cultivated common bean, were screened in the greenhouse using R. solani anastomosis group 2-2. Repeatability of the assay was confirmed by the response of five control genotypes. The phenotypic data for both panels were normally distributed. The resistance responses of ∼10% of the ADP (n = 28) and ∼6% of the MDP (n = 18) genotypes were similar or higher than that of the resistant control line VAX 3. A genome-wide association study (GWAS) was performed using ∼200k single nucleotide polymorphisms to discover genomic regions associated with resistance in each panel, For GWAS, the raw phenotypic score, and polynomial and binary transformation of the scores, were individually used as the input data. A major QTL peak was observed on Pv02 in the ADP, while a major QTL was observed on Pv01 with the MDP. These regions were associated with clusters of TIR-NB_ARC-LRR (TNL) gene models encoding proteins similar to known disease resistance genes. Other QTL, unique to each panel, were mapped within or adjacent to a gene model or cluster of related genes associated with disease resistance. This is a first case study that provides evidence for major as well as minor genes involved in resistance to R. solani in common bean. This information will be useful to integrate more durable root rot resistance in common bean breeding programs and to study the genetic mechanisms associated with root diseases in this important societal legume.
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Affiliation(s)
- Atena Oladzad
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | | | - Shalu Jain
- Department of Plant Pathology, North Dakota State University, Fargo, ND, United States
| | - Kristin Simons
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
- Department of Plant Pathology, North Dakota State University, Fargo, ND, United States
| | - Juan M. Osorno
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Phillip E. McClean
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Julie S. Pasche
- Department of Plant Pathology, North Dakota State University, Fargo, ND, United States
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Perez de Souza L, Scossa F, Proost S, Bitocchi E, Papa R, Tohge T, Fernie AR. Multi-tissue integration of transcriptomic and specialized metabolite profiling provides tools for assessing the common bean (Phaseolus vulgaris) metabolome. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:1132-1153. [PMID: 30480348 PMCID: PMC6850281 DOI: 10.1111/tpj.14178] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 11/15/2018] [Accepted: 11/23/2018] [Indexed: 05/02/2023]
Abstract
Common bean (Phaseolus vulgaris L.) is an important legume species with a rich natural diversity of landraces that originated from the wild forms following multiple independent domestication events. After the publication of its genome, several resources for this relevant crop have been made available. A comprehensive characterization of specialized metabolism in P. vulgaris, however, is still lacking. In this study, we used a metabolomics approach based on liquid chromatography-mass spectrometry to dissect the chemical composition at a tissue-specific level in several accessions of common bean belonging to different gene pools. Using a combination of literature search, mass spectral interpretation, 13 C-labeling, and correlation analyses, we were able to assign chemical classes and/or putative structures for approximately 39% of all measured metabolites. Additionally, we integrated this information with transcriptomics data and phylogenetic inference from multiple legume species to reconstruct the possible metabolic pathways and identify sets of candidate genes involved in the biosynthesis of specialized metabolites. A particular focus was given to flavonoids, triterpenoid saponins and hydroxycinnamates, as they represent metabolites involved in important ecological interactions and they are also associated with several health-promoting benefits when integrated into the human diet. The data are presented here in the form of an accessible resource that we hope will set grounds for further studies on specialized metabolism in legumes.
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Affiliation(s)
| | - Federico Scossa
- Max‐Planck‐Institute of Molecular Plant PhysiologyAm Müehlenberg 1Potsdam‐Golm14476Germany
- Consiglio per la ricerca in agricoltura e l′analisi dell′economia agrariaCREA‐OFAVia di Fioranello 5200134RomeItaly
| | - Sebastian Proost
- Max‐Planck‐Institute of Molecular Plant PhysiologyAm Müehlenberg 1Potsdam‐Golm14476Germany
| | - Elena Bitocchi
- Department of Agricultural, Food, and Environmental SciencesUniversità Politecnica delle Marche60131AnconaItaly
| | - Roberto Papa
- Department of Agricultural, Food, and Environmental SciencesUniversità Politecnica delle Marche60131AnconaItaly
| | - Takayuki Tohge
- Max‐Planck‐Institute of Molecular Plant PhysiologyAm Müehlenberg 1Potsdam‐Golm14476Germany
- Graduate School of Biological SciencesNara Institute of Science and TechnologyIkoma, Nara630‐0192Japan
| | - Alisdair R. Fernie
- Max‐Planck‐Institute of Molecular Plant PhysiologyAm Müehlenberg 1Potsdam‐Golm14476Germany
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18
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Jain S, Poromarto S, Osorno JM, McClean PE, Nelson BD. Genome wide association study discovers genomic regions involved in resistance to soybean cyst nematode (Heterodera glycines) in common bean. PLoS One 2019; 14:e0212140. [PMID: 30730982 PMCID: PMC6366866 DOI: 10.1371/journal.pone.0212140] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 01/28/2019] [Indexed: 12/25/2022] Open
Abstract
Common bean (Phaseolus vulgaris L.) is an important high protein crop grown worldwide. North Dakota and Minnesota are the largest producers of common beans in the USA, but crop production is threatened by soybean cyst nematode (SCN; Heterodera glycines Ichinohe) because most current cultivars are susceptible. Greenhouse screening data using SCN HG type 0 from 317 plant introductions (PI's) from the USDA core collection was used to conduct a genome wide association study (GWAS). These lines were divided into two subpopulations based on principal component analysis (Middle American vs. Andean). Phenotypic results based on the female index showed that accessions could be classified as highly resistant (21% and 27%), moderately resistant (51% and 48%), moderately susceptible (27% and 22%) and highly susceptible (1% and 3%) for Middle American and Andean gene pools, respectively. Mixed models with two principal components (PCs) and kinship matrix for Middle American genotypes and Andean genotypes were used in the GWAS analysis using 3,985 and 4,811 single nucleotide polymorphic (SNP) markers, respectively which were evenly distributed across all 11 chromosomes. Significant peaks on Pv07, and Pv11 in Middle American and on Pv07, Pv08, Pv09 and Pv11 in Andean group were found to be associated with SCN resistance. Homologs of soybean rhg1, a locus which confers resistance to SCN in soybean, were identified on chromosomes Pv01 and Pv08 in the Middle American and Andean gene pools, respectively. These genomic regions may be the key to develop SCN-resistant common bean cultivars.
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Affiliation(s)
- Shalu Jain
- Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, United States of America
| | - Susilo Poromarto
- Department of Agrotechnology, Sebelas Maret University, Surakarta, Jawa Tengah, Indonesia
| | - Juan M. Osorno
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, United States of America
| | - Phillip E. McClean
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, United States of America
| | - Berlin D. Nelson
- Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, United States of America
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19
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Nadeem MA, Habyarimana E, Çiftçi V, Nawaz MA, Karaköy T, Comertpay G, Shahid MQ, Hatipoğlu R, Yeken MZ, Ali F, Ercişli S, Chung G, Baloch FS. Characterization of genetic diversity in Turkish common bean gene pool using phenotypic and whole-genome DArTseq-generated silicoDArT marker information. PLoS One 2018; 13:e0205363. [PMID: 30308006 PMCID: PMC6181364 DOI: 10.1371/journal.pone.0205363] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Accepted: 09/20/2018] [Indexed: 12/31/2022] Open
Abstract
Turkey presents a great diversity of common bean landraces in farmers' fields. We collected 183 common bean accessions from 19 different Turkish geographic regions and 5 scarlet runner bean accessions to investigate their genetic diversity and population structure using phenotypic information (growth habit, and seed weight, flower color, bracteole shape and size, pod shape and leaf shape and color), geographic provenance and 12,557 silicoDArT markers. A total of 24.14% markers were found novel. For the entire population (188 accessions), the expected heterozygosity was 0.078 and overall gene diversity, Fst and Fis were 0.14, 0.55 and 1, respectively. Using marker information, model-based structure, principal coordinate analysis (PCoA) and unweighted pair-group method with arithmetic means (UPGMA) algorithms clustered the 188 accessions into two main populations A (predominant) and B, and 5 unclassified genotypes, representing 3 meaningful heterotic groups for breeding purposes. Phenotypic information clearly distinguished these populations; population A and B, respectively, were bigger (>40g/100 seeds) and smaller (<40g/100 seeds) seed-sized. The unclassified population was pure and only contained climbing genotypes with 100 seed weight 2-3 times greater than populations A and B. Clustering was mainly based on A: seed weight, B: growth habit, C: geographical provinces and D: flower color. Mean kinship was generally low, but population B was more diverse than population A. Overall, a useful level of gene and genotypic diversity was observed in this work and can be used by the scientific community in breeding efforts to develop superior common bean strains.
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Affiliation(s)
- Muhammad Azhar Nadeem
- Department of field crops, Faculty of Agricultural and Natural Science, Abant Izzet Baysal University, Bolu, Turkey
| | - Ephrem Habyarimana
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria–Centro di ricerca cerealicoltura e colture industriali, Bologna, Italy
| | - Vahdettin Çiftçi
- Department of field crops, Faculty of Agricultural and Natural Science, Abant Izzet Baysal University, Bolu, Turkey
| | - Muhammad Amjad Nawaz
- Department of Biotechnology, Chonnam National University, Chonnam, Republic of Korea
| | - Tolga Karaköy
- Organic Agriculture Program, Vocational School of Sivas, University of Cumhuriyet, Sivas, Turkey
| | - Gonul Comertpay
- Eastern Mediterranean Agricultural Research Institute, Turkey
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bio resources, South China Agricultural University, Guangzhou, China
| | - Rüştü Hatipoğlu
- Department of Field Crops, Faculty of Agricultural, University of Cukurova, Adana, Turkey
| | - Mehmet Zahit Yeken
- Department of field crops, Faculty of Agricultural and Natural Science, Abant Izzet Baysal University, Bolu, Turkey
| | - Fawad Ali
- Department of field crops, Faculty of Agricultural and Natural Science, Abant Izzet Baysal University, Bolu, Turkey
| | - Sezai Ercişli
- Department of Horticulture, Faculty of Agriculture, Ataturk University, Erzurum, Turkey
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Chonnam, Republic of Korea
| | - Faheem Shehzad Baloch
- Department of field crops, Faculty of Agricultural and Natural Science, Abant Izzet Baysal University, Bolu, Turkey
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20
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McClean PE, Bett KE, Stonehouse R, Lee R, Pflieger S, Moghaddam SM, Geffroy V, Miklas P, Mamidi S. White seed color in common bean (Phaseolus vulgaris) results from convergent evolution in the P (pigment) gene. THE NEW PHYTOLOGIST 2018; 219:1112-1123. [PMID: 29897103 DOI: 10.1111/nph.15259] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 04/20/2018] [Indexed: 05/10/2023]
Abstract
The presence of seed color in common bean (Phaseolus vulgaris) requires the dominant-acting P (pigment) gene, and white seed is a recessive phenotype in all domesticated races of the species. P was classically associated with seed size, thus describing it as the first genetic marker for a quantitative trait. The molecular structure of P was characterized to understand the selection of white seeds during bean diversification and the relationship of P to seed weight. P was identified by homology searches, a genome-wide association study (GWAS) and gene remodeling, and confirmed by gene silencing. Allelic variation was assessed by a combination of resequencing and marker development, and the relationship between P and seed weight was assessed by a GWAS study. P is a member of clade B of subclass IIIf of plant basic helix-loop-helix (bHLH) proteins. Ten race-specific P alleles conditioned the white seed phenotype, and each causative mutation affected at least one bHLH domain required for color expression. GWAS analysis confirmed the classic association of P with seed weight. In common bean, white seeds are the result of convergent evolution and, among plant species, orthologous convergence on a single transcription factor gene was observed.
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Affiliation(s)
- Phillip E McClean
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
- Genomics and Bioinformatics Program, North Dakota State University, Fargo, ND, 58108, USA
| | - Kirstin E Bett
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
| | - Robert Stonehouse
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
| | - Rian Lee
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Stephanie Pflieger
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, Orsay, 91405, France
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, Orsay, 91405, France
| | | | - Valerie Geffroy
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, Orsay, 91405, France
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, Orsay, 91405, France
| | - Phil Miklas
- USDA-ARS, Grain Legumes Genetics and Physiology Research Unit, Prosser, WA, 99350, USA
| | - Sujan Mamidi
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
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21
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Watling J, Shock MP, Mongeló GZ, Almeida FO, Kater T, De Oliveira PE, Neves EG. Direct archaeological evidence for Southwestern Amazonia as an early plant domestication and food production centre. PLoS One 2018; 13:e0199868. [PMID: 30044799 PMCID: PMC6059402 DOI: 10.1371/journal.pone.0199868] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 06/14/2018] [Indexed: 11/19/2022] Open
Abstract
Southwestern Amazonia is considered an early centre of plant domestication in the New World, but most of the evidence for this hypothesis comes from genetic data since systematic archaeological fieldwork in the area is recent. This paper provides first-hand archaeobotanical evidence of food production from early and middle Holocene (ca. 9,000-5000 cal. BP) deposits at Teotonio, an open-air site located on a 40 m-high bluff on the south bank of the Madeira river. Such evidence includes the presence of local and exotic domesticates such as manioc (Manihot esculenta), squash (Cucurbita sp.) and beans (Phaseolus sp.), alongside edible fruits such as pequiá (Caryocar sp.) and guava (Psidium sp.) that point to the beginnings of landscape domestication. The results contribute to an ever-growing number of studies that posit southwest Amazonia as an important centre for early crop domestication and experimentation, and which highlight the longue-durée of human impacts on tropical forest biodiversity around the world.
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Affiliation(s)
- Jennifer Watling
- Museum of Archaeology and Ethnology, University of São Paulo, São Paulo, Brazil
| | - Myrtle P. Shock
- Anthropology and Archaeology Program, Institute of Social Science, Federal University of Western Pará, Santarém, Pará, Brazil
| | | | - Fernando O. Almeida
- Department of Archaeology, Federal University of Sergipe, Aracajú, Sergipe, Brazil
| | - Thiago Kater
- Department of Archaeology, Federal University of Sergipe, Aracajú, Sergipe, Brazil
| | - Paulo E. De Oliveira
- Institute of Geosciences, University of São Paulo, São Paulo, Brazil
- Department of Botany, The Field Museum of Natural History, Chicago, Illinois, United States of America
| | - Eduardo G. Neves
- Museum of Archaeology and Ethnology, University of São Paulo, São Paulo, Brazil
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22
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Lobaton JD, Miller T, Gil J, Ariza D, de la Hoz JF, Soler A, Beebe S, Duitama J, Gepts P, Raatz B. Resequencing of Common Bean Identifies Regions of Inter-Gene Pool Introgression and Provides Comprehensive Resources for Molecular Breeding. THE PLANT GENOME 2018; 11. [PMID: 30025029 DOI: 10.3835/plantgenome2017.08.0068] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Common bean ( L.) is the most important grain legume for human consumption and is a major nutrition source in the tropics. Because bean production is reduced by both abiotic and biotic constraints, current breeding efforts are focused on the development of improved varieties with tolerance to these stresses. We characterized materials from different breeding programs spanning three continents to understand their sequence diversity and advance the development of molecular breeding tools. For this, 37 varieties belonging to , (A. Gray), and L. were sequenced by whole-genome sequencing, identifying more than 40 million genomic variants. Evaluation of nuclear DNA content and analysis of copy number variation revealed important differences in genomic content not only between and the two other domesticated species, but also within , affecting hundreds of protein-coding genomic regions. A large number of inter-gene pool introgressions were identified. Furthermore, interspecific introgressions for disease resistance in breeding lines were mapped. Evaluation of newly developed single nucleotide polymorphism markers within previously discovered quantitative trait loci for common bacterial blight and angular leaf spot provides improved specificity to tag sources of resistance to these diseases. We expect that this dataset will provide a deeper molecular understanding of breeding germplasm and deliver molecular tools for germplasm development, aiming to increase the efficiency of bean breeding programs.
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Yeken MZ, Kantar F, Çancı H, Özer G, Çiftçi V. Breeding of Dry Bean Cultivars Using Phaseolus vulgaris Landraces in Turkey. ULUSLARARASI TARIM VE YABAN HAYATI BILIMLERI DERGISI 2018. [DOI: 10.24180/ijaws.408794] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Chacón-Sánchez MI, Martínez-Castillo J. Testing Domestication Scenarios of Lima Bean ( Phaseolus lunatus L.) in Mesoamerica: Insights from Genome-Wide Genetic Markers. FRONTIERS IN PLANT SCIENCE 2017; 8:1551. [PMID: 28955351 PMCID: PMC5601060 DOI: 10.3389/fpls.2017.01551] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 08/24/2017] [Indexed: 05/03/2023]
Abstract
Plant domestication can be seen as a long-term process that involves a complex interplay among demographic processes and evolutionary forces. Previous studies have suggested two domestication scenarios for Lima bean in Mesoamerica: two separate domestication events, one from gene pool MI in central-western Mexico and another one from gene pool MII in the area Guatemala-Costa Rica, or a single domestication from gene pool MI in central-western Mexico followed by post-domestication gene flow with wild populations. In this study we evaluated the genetic structure of the wild gene pool and tested these two competing domestication scenarios of Lima bean in Mesoamerica by applying an ABC approach to a set of genome-wide SNP markers. The results confirm the existence of three gene pools in wild Lima bean, two Mesoamerican gene pools (MI and MII) and the Andean gene pool (AI), and suggest the existence of another gene pool in central Colombia. The results indicate that although both domestication scenarios may be supported by genetic data, higher statistical support was given to the single domestication scenario in central-western Mexico followed by admixture with wild populations. Domestication would have involved strong founder effects reflected in loss of genetic diversity and increased LD levels in landraces. Genomic regions affected by selection were detected and these may harbor candidate genes related to domestication.
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Affiliation(s)
- María I. Chacón-Sánchez
- Departamento de Agronomía, Facultad de Ciencias Agrarias, Universidad Nacional de ColombiaBogotá, Colombia
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Valdisser PAMR, Pereira WJ, Almeida Filho JE, Müller BSF, Coelho GRC, de Menezes IPP, Vianna JPG, Zucchi MI, Lanna AC, Coelho ASG, de Oliveira JP, Moraes ADC, Brondani C, Vianello RP. In-depth genome characterization of a Brazilian common bean core collection using DArTseq high-density SNP genotyping. BMC Genomics 2017; 18:423. [PMID: 28558696 PMCID: PMC5450071 DOI: 10.1186/s12864-017-3805-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 05/17/2017] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Common bean is a legume of social and nutritional importance as a food crop, cultivated worldwide especially in developing countries, accounting for an important source of income for small farmers. The availability of the complete sequences of the two common bean genomes has dramatically accelerated and has enabled new experimental strategies to be applied for genetic research. DArTseq has been widely used as a method of SNP genotyping allowing comprehensive genome coverage with genetic applications in common bean breeding programs. RESULTS Using this technology, 6286 SNPs (1 SNP/86.5 Kbp) were genotyped in genic (43.3%) and non-genic regions (56.7%). Genetic subdivision associated to the common bean gene pools (K = 2) and related to grain types (K = 3 and K = 5) were reported. A total of 83% and 91% of all SNPs were polymorphic within the Andean and Mesoamerican gene pools, respectively, and 26% were able to differentiate the gene pools. Genetic diversity analysis revealed an average H E of 0.442 for the whole collection, 0.102 for Andean and 0.168 for Mesoamerican gene pools (F ST = 0.747 between gene pools), 0.440 for the group of cultivars and lines, and 0.448 for the group of landrace accessions (F ST = 0.002 between cultivar/line and landrace groups). The SNP effects were predicted with predominance of impact on non-coding regions (77.8%). SNPs under selection were identified within gene pools comparing landrace and cultivar/line germplasm groups (Andean: 18; Mesoamerican: 69) and between the gene pools (59 SNPs), predominantly on chromosomes 1 and 9. The LD extension estimate corrected for population structure and relatedness (r2SV) was ~ 88 kbp, while for the Andean gene pool was ~ 395 kbp, and for the Mesoamerican was ~ 130 kbp. CONCLUSIONS For common bean, DArTseq provides an efficient and cost-effective strategy of generating SNPs for large-scale genome-wide studies. The DArTseq resulted in an operational panel of 560 polymorphic SNPs in linkage equilibrium, providing high genome coverage. This SNP set could be used in genotyping platforms with many applications, such as population genetics, phylogeny relation between common bean varieties and support to molecular breeding approaches.
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Affiliation(s)
- Paula A. M. R. Valdisser
- Embrapa Arroz e Feijão (CNPAF), Santo Antônio de Goiás, Goiânia, GO Brazil
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Estadual de Campinas (UNICAMP), Campinas, SP Brazil
| | - Wendell J. Pereira
- Programa de Pós-Graduação em Biologia Molecular, Universidade de Brasília (UnB), Brasília, DF Brazil
| | - Jâneo E. Almeida Filho
- Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, Rio de Janeiro, RJ Brazil
| | - Bárbara S. F. Müller
- Programa de Pós-Graduação em Biologia Molecular, Universidade de Brasília (UnB), Brasília, DF Brazil
| | | | - Ivandilson P. P. de Menezes
- Laboratório de Genética e Biologia Molecular, Departamento de Biologia, Instituto Federal Goiano (IF Goiano), Urutaí, GO Brazil
| | - João P. G. Vianna
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Estadual de Campinas (UNICAMP), Campinas, SP Brazil
| | - Maria I. Zucchi
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Estadual de Campinas (UNICAMP), Campinas, SP Brazil
| | - Anna C. Lanna
- Embrapa Arroz e Feijão (CNPAF), Santo Antônio de Goiás, Goiânia, GO Brazil
| | | | | | | | - Claudio Brondani
- Embrapa Arroz e Feijão (CNPAF), Santo Antônio de Goiás, Goiânia, GO Brazil
| | - Rosana P. Vianello
- Embrapa Arroz e Feijão (CNPAF), Santo Antônio de Goiás, Goiânia, GO Brazil
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Li X, Jian Y, Xie C, Wu J, Xu Y, Zou C. Fast diffusion of domesticated maize to temperate zones. Sci Rep 2017; 7:2077. [PMID: 28522839 PMCID: PMC5437101 DOI: 10.1038/s41598-017-02125-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 04/06/2017] [Indexed: 11/09/2022] Open
Abstract
Adaptation to a temperate climate was a prerequisite for the spread of maize across a broad geographical range. To explicitly explore the demographic process underlying maize adaptation, we used a diffusion-based method to model the differentiation between temperate and tropical populations using the Non-Stiff Stalk group as a proxy for temperate maize. Based on multiple sequential Markovian coalescent approaches, we estimate that tropical and temperate maize diverged approximately 3'000 to 5'000 years ago and the population size shrank after the split. Using composite likelihood approaches, we identified a distinct tropical-temperate divergence event initiated 4'958 years ago (95% confidence interval (CI): 4'877-5'039) from an ancestral population whose effective size was 24,162 (95% CI: 23,914-24,409). We found that continuous gene flow between tropical and temperate maize accompanied the differentiation of temperate maize. Long identical-by-descent tracts shared by tropical and temperate inbred lines have been identified, which might be the result of gene flow between tropical and temperate maize or artificial selection during domestication and crop improvement. Understanding the demographic history of maize diffusion not only provides evidence for population dynamics of maize, but will also assist the identification of regions under selection and the genetic basis of complex traits of agronomic importance.
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Affiliation(s)
- Xiaolong Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yinqiao Jian
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chuanxiao Xie
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jun Wu
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yunbi Xu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
- International Maize and Wheat Improvement Center (CIMMYT), El Batán, 56130, Texcoco, Mexico.
| | - Cheng Zou
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Bitocchi E, Rau D, Bellucci E, Rodriguez M, Murgia ML, Gioia T, Santo D, Nanni L, Attene G, Papa R. Beans ( Phaseolus ssp.) as a Model for Understanding Crop Evolution. FRONTIERS IN PLANT SCIENCE 2017; 8:722. [PMID: 28533789 PMCID: PMC5420584 DOI: 10.3389/fpls.2017.00722] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Accepted: 04/19/2017] [Indexed: 05/03/2023]
Abstract
Here, we aim to provide a comprehensive and up-to-date overview of the most significant outcomes in the literature regarding the origin of Phaseolus genus, the geographical distribution of the wild species, the domestication process, and the wide spread out of the centers of origin. Phaseolus can be considered as a unique model for the study of crop evolution, and in particular, for an understanding of the convergent phenotypic evolution that occurred under domestication. The almost unique situation that characterizes the Phaseolus genus is that five of its ∼70 species have been domesticated (i.e., Phaseolus vulgaris, P. coccineus, P. dumosus, P. acutifolius, and P. lunatus), and in addition, for P. vulgaris and P. lunatus, the wild forms are distributed in both Mesoamerica and South America, where at least two independent and isolated episodes of domestication occurred. Thus, at least seven independent domestication events occurred, which provides the possibility to unravel the genetic basis of the domestication process not only among species of the same genus, but also between gene pools within the same species. Along with this, other interesting features makes Phaseolus crops very useful in the study of evolution, including: (i) their recent divergence, and the high level of collinearity and synteny among their genomes; (ii) their different breeding systems and life history traits, from annual and autogamous, to perennial and allogamous; and (iii) their adaptation to different environments, not only in their centers of origin, but also out of the Americas, following their introduction and wide spread through different countries. In particular for P. vulgaris this resulted in the breaking of the spatial isolation of the Mesoamerican and Andean gene pools, which allowed spontaneous hybridization, thus increasing of the possibility of novel genotypes and phenotypes. This knowledge that is associated to the genetic resources that have been conserved ex situ and in situ represents a crucial tool in the hands of researchers, to preserve and evaluate this diversity, and at the same time, to identify the genetic basis of adaptation and to develop new improved varieties to tackle the challenges of climate change, and food security and sustainability.
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Affiliation(s)
- Elena Bitocchi
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic UniversityAncona, Italy
| | - Domenico Rau
- Department of Agriculture, University of SassariSassari, Italy
| | - Elisa Bellucci
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic UniversityAncona, Italy
| | | | - Maria L. Murgia
- Department of Agriculture, University of SassariSassari, Italy
| | - Tania Gioia
- School of Agricultural, Forestry, Food and Environmental Sciences, University of BasilicataPotenza, Italy
| | - Debora Santo
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic UniversityAncona, Italy
| | - Laura Nanni
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic UniversityAncona, Italy
| | - Giovanna Attene
- Department of Agriculture, University of SassariSassari, Italy
| | - Roberto Papa
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic UniversityAncona, Italy
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Bitocchi E, Rau D, Benazzo A, Bellucci E, Goretti D, Biagetti E, Panziera A, Laidò G, Rodriguez M, Gioia T, Attene G, McClean P, Lee RK, Jackson SA, Bertorelle G, Papa R. High Level of Nonsynonymous Changes in Common Bean Suggests That Selection under Domestication Increased Functional Diversity at Target Traits. FRONTIERS IN PLANT SCIENCE 2017; 7:2005. [PMID: 28111584 PMCID: PMC5216878 DOI: 10.3389/fpls.2016.02005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Accepted: 12/16/2016] [Indexed: 05/05/2023]
Abstract
Crop species have been deeply affected by the domestication process, and there have been many efforts to identify selection signatures at the genome level. This knowledge will help geneticists to better understand the evolution of organisms, and at the same time, help breeders to implement successful breeding strategies. Here, we focused on domestication in the Mesoamerican gene pool of Phaseolus vulgaris by sequencing 49 gene fragments from a sample of 45 P. vulgaris wild and domesticated accessions, and as controls, two accessions each of the closely related species Phaseolus coccineus and Phaseolus dumosus. An excess of nonsynonymous mutations within the domesticated germplasm was found. Our data suggest that the cost of domestication alone cannot explain fully this finding. Indeed, the significantly higher frequency of polymorphisms in the coding regions observed only in the domesticated plants (compared to noncoding regions), the fact that these mutations were mostly nonsynonymous and appear to be recently derived mutations, and the investigations into the functions of their relative genes (responses to biotic and abiotic stresses), support a scenario that involves new functional mutations selected for adaptation during domestication. Moreover, consistent with this hypothesis, selection analysis and the possibility to compare data obtained for the same genes in different studies of varying sizes, data types, and methodologies allowed us to identify four genes that were strongly selected during domestication. Each selection candidate is involved in plant resistance/tolerance to abiotic stresses, such as heat, drought, and salinity. Overall, our study suggests that domestication acted to increase functional diversity at target loci, which probably controlled traits related to expansion and adaptation to new agro-ecological growing conditions.
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Affiliation(s)
- Elena Bitocchi
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle MarcheAncona, Italy
| | - Domenico Rau
- Department of Agriculture, Università degli Studi di SassariSassari, Italy
| | - Andrea Benazzo
- Department of Life Sciences and Biotechnology, Università degli Studi di FerraraFerrara, Italy
| | - Elisa Bellucci
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle MarcheAncona, Italy
| | - Daniela Goretti
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle MarcheAncona, Italy
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå UniversityUmeå, Sweden
| | - Eleonora Biagetti
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle MarcheAncona, Italy
| | - Alex Panziera
- Department of Life Sciences and Biotechnology, Università degli Studi di FerraraFerrara, Italy
| | - Giovanni Laidò
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Centro di Ricerca per la CerealicolturaFoggia, Italy
| | - Monica Rodriguez
- Department of Agriculture, Università degli Studi di SassariSassari, Italy
| | - Tania Gioia
- Scuola di Scienze Agrarie, Forestali, Alimentari ed Ambientali, Università degli Studi della BasilicataPotenza, Italy
| | - Giovanna Attene
- Department of Agriculture, Università degli Studi di SassariSassari, Italy
| | - Phillip McClean
- Department of Plant Sciences, North Dakota State UniversityFargo, ND, USA
| | - Rian K. Lee
- Department of Plant Sciences, North Dakota State UniversityFargo, ND, USA
| | - Scott A. Jackson
- Center for Applied Genetic Technologies, University of GeorgiaAthens, GA, USA
| | - Giorgio Bertorelle
- Department of Life Sciences and Biotechnology, Università degli Studi di FerraraFerrara, Italy
| | - Roberto Papa
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle MarcheAncona, Italy
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Moghaddam SM, Mamidi S, Osorno JM, Lee R, Brick M, Kelly J, Miklas P, Urrea C, Song Q, Cregan P, Grimwood J, Schmutz J, McClean PE. Genome-Wide Association Study Identifies Candidate Loci Underlying Agronomic Traits in a Middle American Diversity Panel of Common Bean. THE PLANT GENOME 2016; 9. [PMID: 27902795 DOI: 10.3835/plantgenome2016.02.0012] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Common bean ( L.) breeding programs aim to improve both agronomic and seed characteristics traits. However, the genetic architecture of the many traits that affect common bean production are not completely understood. Genome-wide association studies (GWAS) provide an experimental approach to identify genomic regions where important candidate genes are located. A panel of 280 modern bean genotypes from race Mesoamerica, referred to as the Middle American Diversity Panel (MDP), were grown in four US locations, and a GWAS using >150,000 single-nucleotide polymorphisms (SNPs) (minor allele frequency [MAF] ≥ 5%) was conducted for six agronomic traits. The degree of inter- and intrachromosomal linkage disequilibrium (LD) was estimated after accounting for population structure and relatedness. The LD varied between chromosomes for the entire MDP and among race Mesoamerica and Durango-Jalisco genotypes within the panel. The LD patterns reflected the breeding history of common bean. Genome-wide association studies led to the discovery of new and known genomic regions affecting the agronomic traits at the entire population, race, and location levels. We observed strong colocalized signals in a narrow genomic interval for three interrelated traits: growth habit, lodging, and canopy height. Overall, this study detected ∼30 candidate genes based on a priori and candidate gene search strategies centered on the 100-kb region surrounding a significant SNP. These results provide a framework from which further research can begin to understand the actual genes controlling important agronomic production traits in common bean.
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Li LF, Olsen KM. To Have and to Hold: Selection for Seed and Fruit Retention During Crop Domestication. Curr Top Dev Biol 2016; 119:63-109. [PMID: 27282024 DOI: 10.1016/bs.ctdb.2016.02.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Crop domestication provides a useful model system to characterize the molecular and developmental bases of morphological variation in plants. Among the most universal changes resulting from selection during crop domestication is the loss of seed and fruit dispersal mechanisms, which greatly facilitates harvesting efficiency. In this review, we consider the molecular genetic and developmental bases of the loss of seed shattering and fruit dispersal in six major crop plant families, three of which are primarily associated with seed crops (Poaceae, Brassicaceae, Fabaceae) and three of which are associated with fleshy-fruited crops (Solanaceae, Rosaceae, Rutaceae). We find that the developmental basis of the loss of seed/fruit dispersal is conserved in a number of independently domesticated crops, indicating the widespread occurrence of developmentally convergent evolution in response to human selection. With regard to the molecular genetic approaches used to characterize the basis of this trait, traditional biparental quantitative trait loci mapping remains the most commonly used strategy; however, recent advances in next-generation sequencing technologies are now providing new avenues to map and characterize loss of shattering/dispersal alleles. We anticipate that continued application of these approaches, together with candidate gene analyses informed by known shattering candidate genes from other crops, will lead to a rapid expansion of our understanding of this critical domestication trait.
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Affiliation(s)
- L-F Li
- Washington University in St. Louis, St. Louis, MO, United States; Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, PR China.
| | - K M Olsen
- Washington University in St. Louis, St. Louis, MO, United States.
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Gros-Balthazard M, Newton C, Ivorra S, Pierre MH, Pintaud JC, Terral JF. The Domestication Syndrome in Phoenix dactylifera Seeds: Toward the Identification of Wild Date Palm Populations. PLoS One 2016; 11:e0152394. [PMID: 27010707 PMCID: PMC4807022 DOI: 10.1371/journal.pone.0152394] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 03/14/2016] [Indexed: 11/19/2022] Open
Abstract
Investigating crop origins is a priority to understand the evolution of plants under domestication, develop strategies for conservation and valorization of agrobiodiversity and acquire fundamental knowledge for cultivar improvement. The date palm (Phoenix dactylifera L.) belongs to the genus Phoenix, which comprises 14 species morphologically very close, sometimes hardly distinguishable. It has been cultivated for millennia in the Middle East and in North Africa and constitutes the keystone of oasis agriculture. Yet, its origins remain poorly understood as no wild populations are identified. Uncultivated populations have been described but they might represent feral, i.e. formerly cultivated, abandoned forms rather than truly wild populations. In this context, this study based on morphometrics applied to 1625 Phoenix seeds aims to (1) differentiate Phoenix species and (2) depict the domestication syndrome observed in cultivated date palm seeds using other Phoenix species as a "wild" reference. This will help discriminate truly wild from feral forms, thus providing new insights into the evolutionary history of this species. Seed size was evaluated using four parameters: length, width, thickness and dorsal view surface. Seed shape was quantified using outline analyses based on the Elliptic Fourier Transform method. The size and shape of seeds allowed an accurate differentiation of Phoenix species. The cultivated date palm shows distinctive size and shape features, compared to other Phoenix species: seeds are longer and elongated. This morphological shift may be interpreted as a domestication syndrome, resulting from the long-term history of cultivation, selection and human-mediated dispersion. Based on seed attributes, some uncultivated date palms from Oman may be identified as wild. This opens new prospects regarding the possible existence and characterization of relict wild populations and consequently for the understanding of the date palm origins. Finally, we here describe a pipeline for the identification of the domestication syndrome in seeds that could be used in other crops.
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Affiliation(s)
- Muriel Gros-Balthazard
- Institut des Sciences de l’Evolution, Université - Montpellier, UMR 5554 CNRS / Université de Montpellier / IRD / EPHE, CC065, Equipe Dynamique de la Biodiversité, Anthropo-écologie, Place Eugène Bataillon, 34095, Montpellier Cedex 5, France
- UMR DIADE, équipe DYNADIV, Institut de Recherche pour le Développement, 911 avenue Agropolis, 34394, Montpellier cedex 5, France
| | - Claire Newton
- Institut des Sciences de l’Evolution, Université - Montpellier, UMR 5554 CNRS / Université de Montpellier / IRD / EPHE, CC065, Equipe Dynamique de la Biodiversité, Anthropo-écologie, Place Eugène Bataillon, 34095, Montpellier Cedex 5, France
- Laboratoire d’Archéologie et de Patrimoine, Université du Québec à Rimouski, 300 Allée des Ursulines, Rimouski (Qc), G5L 3AI, Canada
| | - Sarah Ivorra
- Institut des Sciences de l’Evolution, Université - Montpellier, UMR 5554 CNRS / Université de Montpellier / IRD / EPHE, CC065, Equipe Dynamique de la Biodiversité, Anthropo-écologie, Place Eugène Bataillon, 34095, Montpellier Cedex 5, France
| | - Marie-Hélène Pierre
- Institut des Sciences de l’Evolution, Université - Montpellier, UMR 5554 CNRS / Université de Montpellier / IRD / EPHE, CC065, Equipe Dynamique de la Biodiversité, Anthropo-écologie, Place Eugène Bataillon, 34095, Montpellier Cedex 5, France
| | - Jean-Christophe Pintaud
- UMR DIADE, équipe DYNADIV, Institut de Recherche pour le Développement, 911 avenue Agropolis, 34394, Montpellier cedex 5, France
| | - Jean-Frédéric Terral
- Institut des Sciences de l’Evolution, Université - Montpellier, UMR 5554 CNRS / Université de Montpellier / IRD / EPHE, CC065, Equipe Dynamique de la Biodiversité, Anthropo-écologie, Place Eugène Bataillon, 34095, Montpellier Cedex 5, France
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Vlasova A, Capella-Gutiérrez S, Rendón-Anaya M, Hernández-Oñate M, Minoche AE, Erb I, Câmara F, Prieto-Barja P, Corvelo A, Sanseverino W, Westergaard G, Dohm JC, Pappas GJ, Saburido-Alvarez S, Kedra D, Gonzalez I, Cozzuto L, Gómez-Garrido J, Aguilar-Morón MA, Andreu N, Aguilar OM, Garcia-Mas J, Zehnsdorf M, Vázquez MP, Delgado-Salinas A, Delaye L, Lowy E, Mentaberry A, Vianello-Brondani RP, García JL, Alioto T, Sánchez F, Himmelbauer H, Santalla M, Notredame C, Gabaldón T, Herrera-Estrella A, Guigó R. Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes. Genome Biol 2016; 17:32. [PMID: 26911872 PMCID: PMC4766624 DOI: 10.1186/s13059-016-0883-6] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Accepted: 01/22/2016] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Legumes are the third largest family of angiosperms and the second most important crop class. Legume genomes have been shaped by extensive large-scale gene duplications, including an approximately 58 million year old whole genome duplication shared by most crop legumes. RESULTS We report the genome and the transcription atlas of coding and non-coding genes of a Mesoamerican genotype of common bean (Phaseolus vulgaris L., BAT93). Using a comprehensive phylogenomics analysis, we assessed the past and recent evolution of common bean, and traced the diversification of patterns of gene expression following duplication. We find that successive rounds of gene duplications in legumes have shaped tissue and developmental expression, leading to increased levels of specialization in larger gene families. We also find that many long non-coding RNAs are preferentially expressed in germ-line-related tissues (pods and seeds), suggesting that they play a significant role in fruit development. Our results also suggest that most bean-specific gene family expansions, including resistance gene clusters, predate the split of the Mesoamerican and Andean gene pools. CONCLUSIONS The genome and transcriptome data herein generated for a Mesoamerican genotype represent a counterpart to the genomic resources already available for the Andean gene pool. Altogether, this information will allow the genetic dissection of the characters involved in the domestication and adaptation of the crop, and their further implementation in breeding strategies for this important crop.
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Affiliation(s)
- Anna Vlasova
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Salvador Capella-Gutiérrez
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
- Yeast and Basidiomycete Research Group, CBS Fungal Biodiversity Centre, Uppsalalaan 8, 3584 LT, Utrecht, The Netherlands
| | - Martha Rendón-Anaya
- Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav-Irapuato, CP 36821, Irapuato, Guanajuato, Mexico
| | - Miguel Hernández-Oñate
- Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav-Irapuato, CP 36821, Irapuato, Guanajuato, Mexico
| | - André E Minoche
- Garvan Institute of Medical Research, 384 Victoria Street, Sydney, NSW, 2010, Australia
| | - Ionas Erb
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Francisco Câmara
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Pablo Prieto-Barja
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - André Corvelo
- New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA
| | - Walter Sanseverino
- IRTA, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, 08193 Bellaterra, Barcelona, Catalonia, Spain
| | - Gastón Westergaard
- Instituto de Agrobiotecnología Rosario (INDEAR), Rosario, Santa Fe, 2000, Argentina
| | - Juliane C Dohm
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190, Vienna, Austria
| | - Georgios J Pappas
- Department of Cellular Biology, University of Brasilia, Biological Science Institute, Brasília, DF, 70790-160, Brazil
| | - Soledad Saburido-Alvarez
- Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav-Irapuato, CP 36821, Irapuato, Guanajuato, Mexico
| | - Darek Kedra
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Irene Gonzalez
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
- Genomics Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Catalonia, Spain
| | - Luca Cozzuto
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Jessica Gómez-Garrido
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - María A Aguilar-Morón
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
- Genomics Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Catalonia, Spain
| | - Nuria Andreu
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
- Genomics Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Catalonia, Spain
| | - O Mario Aguilar
- Instituto de Biotecnología y Biología Molecular (IBBM), UNLP-CONICET, 1900, La Plata, Argentina
| | - Jordi Garcia-Mas
- IRTA, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, 08193 Bellaterra, Barcelona, Catalonia, Spain
| | - Maik Zehnsdorf
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
- Genomics Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Catalonia, Spain
| | - Martín P Vázquez
- Instituto de Agrobiotecnología Rosario (INDEAR), Rosario, Santa Fe, 2000, Argentina
| | - Alfonso Delgado-Salinas
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Luis Delaye
- Departamento de Ingeniería Genética, Unidad Irapuato, Cinvestav, 36821, Irapuato, Guanajuato, Mexico
| | - Ernesto Lowy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Alejandro Mentaberry
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (UBA), C1428EGA, Buenos Aires, Argentina
| | | | - José Luís García
- Environmental Biology Department, Centro de Investigaciones Biológicas, (CSIC), 28040, Madrid, Spain
| | - Tyler Alioto
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Federico Sánchez
- Depto. de Biología Molecular de Plantas, Instituto Biotecnología, Universidad Nacional Autónoma de México, 62210, Cuernavaca, Morelos, Mexico
| | - Heinz Himmelbauer
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190, Vienna, Austria
| | - Marta Santalla
- Mision Biológica de Galicia (MBG)-National Spanish Research Council (CSIC), 36080, Pontevedra, Spain
| | - Cedric Notredame
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Toni Gabaldón
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010, Barcelona, Spain.
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav-Irapuato, CP 36821, Irapuato, Guanajuato, Mexico.
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain.
- IMIM (Hospital del Mar Medical Research Institute), 08003, Barcelona, Spain.
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Dwivedi SL, Ceccarelli S, Blair MW, Upadhyaya HD, Are AK, Ortiz R. Landrace Germplasm for Improving Yield and Abiotic Stress Adaptation. TRENDS IN PLANT SCIENCE 2016; 21:31-42. [PMID: 26559599 DOI: 10.1016/j.tplants.2015.10.012] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 09/24/2015] [Accepted: 10/15/2015] [Indexed: 05/19/2023]
Abstract
Plant landraces represent heterogeneous, local adaptations of domesticated species, and thereby provide genetic resources that meet current and new challenges for farming in stressful environments. These local ecotypes can show variable phenology and low-to-moderate edible yield, but are often highly nutritious. The main contributions of landraces to plant breeding have been traits for more efficient nutrient uptake and utilization, as well as useful genes for adaptation to stressful environments such as water stress, salinity, and high temperatures. We propose that a systematic landrace evaluation may define patterns of diversity, which will facilitate identifying alleles for enhancing yield and abiotic stress adaptation, thus raising the productivity and stability of staple crops in vulnerable environments.
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Affiliation(s)
- Sangam L Dwivedi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, India
| | | | - Matthew W Blair
- Department of Agriculture and Natural Sciences, Lawson Hall, Tennessee State University, 3500 John A. Merritt Boulevard, Nashville, TN, USA
| | - Hari D Upadhyaya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, India
| | - Ashok K Are
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, India
| | - Rodomiro Ortiz
- Swedish University of Agricultural Sciences, Department of Plant Breeding, Sundsvagen, 14 Box 101, 23053 Alnarp, Sweden.
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Villordo-Pineda E, González-Chavira MM, Giraldo-Carbajo P, Acosta-Gallegos JA, Caballero-Pérez J. Identification of novel drought-tolerant-associated SNPs in common bean (Phaseolus vulgaris). FRONTIERS IN PLANT SCIENCE 2015; 6:546. [PMID: 26257755 PMCID: PMC4508514 DOI: 10.3389/fpls.2015.00546] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 07/06/2015] [Indexed: 05/05/2023]
Abstract
Common bean (Phaseolus vulgaris L.) is a leguminous in high demand for human nutrition and a very important agricultural product. Production of common bean is constrained by environmental stresses such as drought. Although conventional plant selection has been used to increase production yield and stress tolerance, drought tolerance selection based on phenotype is complicated by associated physiological, anatomical, cellular, biochemical, and molecular changes. These changes are modulated by differential gene expression. A common method to identify genes associated with phenotypes of interest is the characterization of Single Nucleotide Polymorphims (SNPs) to link them to specific functions. In this work, we selected two drought-tolerant parental lines from Mesoamerica, Pinto Villa, and Pinto Saltillo. The parental lines were used to generate a population of 282 families (F3:5) and characterized by 169 SNPs. We associated the segregation of the molecular markers in our population with phenotypes including flowering time, physiological maturity, reproductive period, plant, seed and total biomass, reuse index, seed yield, weight of 100 seeds, and harvest index in three cultivation cycles. We observed 83 SNPs with significant association (p < 0.0003 after Bonferroni correction) with our quantified phenotypes. Phenotypes most associated were days to flowering and seed biomass with 58 and 44 associated SNPs, respectively. Thirty-seven out of the 83 SNPs were annotated to a gene with a potential function related to drought tolerance or relevant molecular/biochemical functions. Some SNPs such as SNP28 and SNP128 are related to starch biosynthesis, a common osmotic protector; and SNP18 is related to proline biosynthesis, another well-known osmotic protector.
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Affiliation(s)
- Emiliano Villordo-Pineda
- Campo Experimental Bajío-Instituto Nacional de Investigaciones Forestales, Agrícolas y PecuariasCelaya, México
- Unidad de Genética, Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Politécnica de MadridMadrid, Spain
| | - Mario M. González-Chavira
- Campo Experimental Bajío-Instituto Nacional de Investigaciones Forestales, Agrícolas y PecuariasCelaya, México
| | - Patricia Giraldo-Carbajo
- Unidad de Genética, Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Politécnica de MadridMadrid, Spain
| | - Jorge A. Acosta-Gallegos
- Campo Experimental Bajío-Instituto Nacional de Investigaciones Forestales, Agrícolas y PecuariasCelaya, México
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Dussert Y, Snirc A, Robert T. Inference of domestication history and differentiation between early- and late-flowering varieties in pearl millet. Mol Ecol 2015; 24:1387-402. [PMID: 25705965 DOI: 10.1111/mec.13119] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 02/12/2015] [Accepted: 02/13/2015] [Indexed: 02/04/2023]
Abstract
Pearl millet (Pennisetum glaucum) is a staple crop in Sahelian Africa. Farmers usually grow varieties with different cycle lengths and complementary functions in Sahelian agrosystems. Both the level of genetic differentiation of these varieties and the domestication history of pearl millet have been poorly studied. We investigated the neutral genetic diversity and population genetic structure of early- and late-flowering domesticated and wild pearl millet populations using 18 microsatellite loci and 8 nucleotide sequences. Strikingly, early- and late-flowering domesticated varieties were not differentiated over their whole distribution area, despite a clear difference in their isolation-by-distance pattern. Conversely, our data brought evidence for two well-differentiated genetic pools in wild pearl millet, allowing us to test scenarios with different numbers and origins of domestication using approximate Bayesian computation (ABC). The ABC analysis showed the likely existence of asymmetric migration between wild and domesticated populations. The model choice procedure indicated that a single domestication from the eastern wild populations was the more likely scenario to explain the polymorphism patterns observed in cultivated pearl millet.
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Affiliation(s)
- Y Dussert
- Ecologie, Systématique et Evolution, UMR 8079 CNRS, Université Paris-Sud, 91405, Orsay, France; Sorbonne Universités, UPMC Univ Paris06, IFD, 4 Place Jussieu, 75252, Paris Cedex 05, France
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Hart JP, Griffiths PD. Genotyping-by-Sequencing Enabled Mapping and Marker Development for the By-2 Potyvirus Resistance Allele in Common Bean. THE PLANT GENOME 2015; 8:eplantgenome2014.09.0058. [PMID: 33228290 DOI: 10.3835/plantgenome2014.09.0058] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 11/25/2014] [Indexed: 05/24/2023]
Abstract
Since its emergence in 2001, an aphid-transmitted virus disease complex has caused substantial economic losses to snap bean (Phaseolus vulgaris L.) production and processing in the Great Lakes Region of the United States. The general ineffectiveness of chemical control measures for nonpersistently transmitted viruses established an urgent need for the development and deployment of cultivars with resistance to the component viruses. Our objectives were to further characterize the inheritance of resistance to Bean yellow mosaic virus (BYMV), which is conditioned by the By-2 allele, to adapt genotyping-by-sequencing (GBS) to common bean to discover and genotype genome-wide single nucleotide polymorphisms (SNPs) in a set of recombinant inbred lines (RILs) derived from an introgression program, and to enable and validate marker-assisted selection for By-2. We optimized ApeKI for GBS in common bean and retained 7530 high-quality SNPs that segregated in our introgression RILs. A case-control genome-wide association study (GWAS) was used to discover 44 GBS SNPs that were strongly associated with the resistance phenotype and which delimited a 974 kb physical interval on the distal portion of chromosome 2. Seven of these SNPs were converted to single-marker Kompetitive Allele-Specific Polymerase chain reaction (KASP) assays and were demonstrated to be tightly linked to BYMV resistance in an F2 population of 185 individuals. This research enables marker-assisted selection of By-2, provides enhanced resolution for fine mapping, and demonstrates the potential of GBS as a highly efficient, high-throughput genotyping platform for common bean breeding and genetics.
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Affiliation(s)
- John P Hart
- USDA-ARS, Tropical Agriculture Res. Stn. (TARS), 2200 P.A. Campos Ave., Suite 201, Mayagüez, PR 00680-5470
| | - Phillip D Griffiths
- School of Integrative Plant Science, Plant Breeding and Genetics Section, Cornell Univ., 314 Hedrick Hall, Geneva, NY, 14456
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Schmutz J, McClean PE, Mamidi S, Wu GA, Cannon SB, Grimwood J, Jenkins J, Shu S, Song Q, Chavarro C, Torres-Torres M, Geffroy V, Moghaddam SM, Gao D, Abernathy B, Barry K, Blair M, Brick MA, Chovatia M, Gepts P, Goodstein DM, Gonzales M, Hellsten U, Hyten DL, Jia G, Kelly JD, Kudrna D, Lee R, Richard MMS, Miklas PN, Osorno JM, Rodrigues J, Thareau V, Urrea CA, Wang M, Yu Y, Zhang M, Wing RA, Cregan PB, Rokhsar DS, Jackson SA. A reference genome for common bean and genome-wide analysis of dual domestications. Nat Genet 2014; 46:707-13. [PMID: 24908249 PMCID: PMC7048698 DOI: 10.1038/ng.3008] [Citation(s) in RCA: 705] [Impact Index Per Article: 70.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 05/15/2014] [Indexed: 01/13/2023]
Abstract
Common bean (Phaseolus vulgaris L.) is the most important grain legume for human consumption and has a role in sustainable agriculture owing to its ability to fix atmospheric nitrogen. We assembled 473 Mb of the 587-Mb genome and genetically anchored 98% of this sequence in 11 chromosome-scale pseudomolecules. We compared the genome for the common bean against the soybean genome to find changes in soybean resulting from polyploidy. Using resequencing of 60 wild individuals and 100 landraces from the genetically differentiated Mesoamerican and Andean gene pools, we confirmed 2 independent domestications from genetic pools that diverged before human colonization. Less than 10% of the 74 Mb of sequence putatively involved in domestication was shared by the two domestication events. We identified a set of genes linked with increased leaf and seed size and combined these results with quantitative trait locus data from Mesoamerican cultivars. Genes affected by domestication may be useful for genomics-enabled crop improvement.
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Affiliation(s)
- Jeremy Schmutz
- US Department of Energy Joint Genome Institute, Walnut Creek, California USA
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama USA
| | - Phillip E McClean
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota USA
| | - Sujan Mamidi
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota USA
| | - G Albert Wu
- US Department of Energy Joint Genome Institute, Walnut Creek, California USA
| | - Steven B Cannon
- US Department of Agriculture–Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, Iowa USA
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama USA
| | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama USA
| | - Shengqiang Shu
- US Department of Energy Joint Genome Institute, Walnut Creek, California USA
| | - Qijian Song
- US Department of Agriculture–Agricultural Research Service, Soybean Genomics and Improvement Laboratory, Beltsville, Maryland USA
| | - Carolina Chavarro
- Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia USA
| | | | - Valerie Geffroy
- CNRS, Université Paris–Sud, Institut de Biologie des Plantes, UMR 8618, Saclay Plant Sciences (SPS), Orsay, France
- Institut National de la Recherche Agronomique (INRA), Université Paris–Sud, Unité Mixte de Recherche de Génétique Végétale, Gif-sur-Yvette, France
| | - Samira Mafi Moghaddam
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota USA
| | - Dongying Gao
- Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia USA
| | - Brian Abernathy
- Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia USA
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, Walnut Creek, California USA
| | - Matthew Blair
- Department of Agricultural and Natural Sciences, Tennessee State University, Nashville, Tennessee USA
| | - Mark A Brick
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado USA
| | - Mansi Chovatia
- US Department of Energy Joint Genome Institute, Walnut Creek, California USA
| | - Paul Gepts
- Department of Plant Sciences, University of California, Davis, Davis, California USA
| | - David M Goodstein
- US Department of Energy Joint Genome Institute, Walnut Creek, California USA
| | - Michael Gonzales
- Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia USA
| | - Uffe Hellsten
- US Department of Energy Joint Genome Institute, Walnut Creek, California USA
| | - David L Hyten
- US Department of Agriculture–Agricultural Research Service, Soybean Genomics and Improvement Laboratory, Beltsville, Maryland USA
- Present Address: Present addresses: Pioneer Hi-Bred International, Inc., Johnston, Iowa, USA (D.L.H.) and Genética e Melhoramento, Federal University of Viçosa, Viçosa, Brazil (J.R.).,
| | - Gaofeng Jia
- US Department of Agriculture–Agricultural Research Service, Soybean Genomics and Improvement Laboratory, Beltsville, Maryland USA
| | - James D Kelly
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan USA
| | - Dave Kudrna
- Arizona Genomics Institute, University of Arizona, Tucson, Arizona USA
| | - Rian Lee
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota USA
| | - Manon M S Richard
- CNRS, Université Paris–Sud, Institut de Biologie des Plantes, UMR 8618, Saclay Plant Sciences (SPS), Orsay, France
| | - Phillip N Miklas
- US Department of Agriculture–Agricultural Research Service, Vegetable and Forage Crop Research Unit, Prosser, Washington USA
| | - Juan M Osorno
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota USA
| | - Josiane Rodrigues
- US Department of Agriculture–Agricultural Research Service, Soybean Genomics and Improvement Laboratory, Beltsville, Maryland USA
- Present Address: Present addresses: Pioneer Hi-Bred International, Inc., Johnston, Iowa, USA (D.L.H.) and Genética e Melhoramento, Federal University of Viçosa, Viçosa, Brazil (J.R.).,
| | - Vincent Thareau
- CNRS, Université Paris–Sud, Institut de Biologie des Plantes, UMR 8618, Saclay Plant Sciences (SPS), Orsay, France
| | - Carlos A Urrea
- Panhandle Research and Extension Center, University of Nebraska, Scottsbluff, Nebraska USA
| | - Mei Wang
- US Department of Energy Joint Genome Institute, Walnut Creek, California USA
| | - Yeisoo Yu
- Arizona Genomics Institute, University of Arizona, Tucson, Arizona USA
| | - Ming Zhang
- US Department of Energy Joint Genome Institute, Walnut Creek, California USA
| | - Rod A Wing
- Arizona Genomics Institute, University of Arizona, Tucson, Arizona USA
| | - Perry B Cregan
- US Department of Agriculture–Agricultural Research Service, Soybean Genomics and Improvement Laboratory, Beltsville, Maryland USA
| | - Daniel S Rokhsar
- US Department of Energy Joint Genome Institute, Walnut Creek, California USA
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia USA
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Moghaddam SM, Song Q, Mamidi S, Schmutz J, Lee R, Cregan P, Osorno JM, McClean PE. Developing market class specific InDel markers from next generation sequence data in Phaseolus vulgaris L. FRONTIERS IN PLANT SCIENCE 2014; 5:185. [PMID: 24860578 PMCID: PMC4026720 DOI: 10.3389/fpls.2014.00185] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Accepted: 04/19/2014] [Indexed: 05/09/2023]
Abstract
Next generation sequence data provides valuable information and tools for genetic and genomic research and offers new insights useful for marker development. This data is useful for the design of accurate and user-friendly molecular tools. Common bean (Phaseolus vulgaris L.) is a diverse crop in which separate domestication events happened in each gene pool followed by race and market class diversification that has resulted in different morphological characteristics in each commercial market class. This has led to essentially independent breeding programs within each market class which in turn has resulted in limited within market class sequence variation. Sequence data from selected genotypes of five bean market classes (pinto, black, navy, and light and dark red kidney) were used to develop InDel-based markers specific to each market class. Design of the InDel markers was conducted through a combination of assembly, alignment and primer design software using 1.6× to 5.1× coverage of Illumina GAII sequence data for each of the selected genotypes. The procedure we developed for primer design is fast, accurate, less error prone, and higher throughput than when they are designed manually. All InDel markers are easy to run and score with no need for PCR optimization. A total of 2687 InDel markers distributed across the genome were developed. To highlight their usefulness, they were employed to construct a phylogenetic tree and a genetic map, showing that InDel markers are reliable, simple, and accurate.
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Affiliation(s)
- Samira Mafi Moghaddam
- Genomics and Bioinformatics Program, North Dakota State UniversityFargo, ND, USA
- Department of Plant Sciences, North Dakota State UniversityFargo, ND, USA
| | - Qijian Song
- Soybean Genomics and Improvement Laboratory, United States Department of Agriculture, Agricultural Research ServiceBeltsville, MD, USA
| | - Sujan Mamidi
- Genomics and Bioinformatics Program, North Dakota State UniversityFargo, ND, USA
- Department of Plant Sciences, North Dakota State UniversityFargo, ND, USA
| | | | - Rian Lee
- Department of Plant Sciences, North Dakota State UniversityFargo, ND, USA
| | - Perry Cregan
- Soybean Genomics and Improvement Laboratory, United States Department of Agriculture, Agricultural Research ServiceBeltsville, MD, USA
| | - Juan M. Osorno
- Department of Plant Sciences, North Dakota State UniversityFargo, ND, USA
| | - Phillip E. McClean
- Genomics and Bioinformatics Program, North Dakota State UniversityFargo, ND, USA
- Department of Plant Sciences, North Dakota State UniversityFargo, ND, USA
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40
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Gerbault P, Allaby RG, Boivin N, Rudzinski A, Grimaldi IM, Pires JC, Climer Vigueira C, Dobney K, Gremillion KJ, Barton L, Arroyo-Kalin M, Purugganan MD, Rubio de Casas R, Bollongino R, Burger J, Fuller DQ, Bradley DG, Balding DJ, Richerson PJ, Gilbert MTP, Larson G, Thomas MG. Storytelling and story testing in domestication. Proc Natl Acad Sci U S A 2014; 111:6159-64. [PMID: 24753572 PMCID: PMC4035932 DOI: 10.1073/pnas.1400425111] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The domestication of plants and animals marks one of the most significant transitions in human, and indeed global, history. Traditionally, study of the domestication process was the exclusive domain of archaeologists and agricultural scientists; today it is an increasingly multidisciplinary enterprise that has come to involve the skills of evolutionary biologists and geneticists. Although the application of new information sources and methodologies has dramatically transformed our ability to study and understand domestication, it has also generated increasingly large and complex datasets, the interpretation of which is not straightforward. In particular, challenges of equifinality, evolutionary variance, and emergence of unexpected or counter-intuitive patterns all face researchers attempting to infer past processes directly from patterns in data. We argue that explicit modeling approaches, drawing upon emerging methodologies in statistics and population genetics, provide a powerful means of addressing these limitations. Modeling also offers an approach to analyzing datasets that avoids conclusions steered by implicit biases, and makes possible the formal integration of different data types. Here we outline some of the modeling approaches most relevant to current problems in domestication research, and demonstrate the ways in which simulation modeling is beginning to reshape our understanding of the domestication process.
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Affiliation(s)
| | - Robin G. Allaby
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Nicole Boivin
- Research Laboratory for Archaeology and the History of Art, School of Archaeology, Oxford OX1 3QY, United Kingdom
| | - Anna Rudzinski
- Research Department of Genetics, Evolution, and Environment and
| | - Ilaria M. Grimaldi
- Research Laboratory for Archaeology and the History of Art, School of Archaeology, Oxford OX1 3QY, United Kingdom
| | - J. Chris Pires
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211
| | | | - Keith Dobney
- Department of Archaeology, University of Aberdeen, Aberdeen AB24 3UF, United Kingdom
| | | | - Loukas Barton
- Department of Anthropology, Center for Comparative Archaeology, University of Pittsburgh, Pittsburgh, PA 15260
| | - Manuel Arroyo-Kalin
- Institute of Archaeology, University College London, London WC1H 0PY, United Kingdom
| | - Michael D. Purugganan
- Department of Biology, New York University, New York, NY 10003-6688
- Center for Genomics and Systems Biology, New York University Abu Dhabi Research Institute, Abu Dhabi, United Arab Emirates
| | | | - Ruth Bollongino
- Institute of Anthropology, Johannes Gutenberg University, D-55099 Mainz, Germany
| | - Joachim Burger
- Institute of Anthropology, Johannes Gutenberg University, D-55099 Mainz, Germany
| | - Dorian Q. Fuller
- Institute of Archaeology, University College London, London WC1H 0PY, United Kingdom
| | | | - David J. Balding
- University College London Genetics Institute, University College London, London WC1E 6BT, United Kingdom
| | - Peter J. Richerson
- Department of Environmental Science and Policy, University of California, Davis, CA 95616
| | - M. Thomas P. Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; and
| | - Greger Larson
- Durham Evolution and Ancient DNA, Department of Archaeology, Durham University, Durham DH1 3LE, United Kingdom
| | - Mark G. Thomas
- Research Department of Genetics, Evolution, and Environment and
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Gepts P. The contribution of genetic and genomic approaches to plant domestication studies. CURRENT OPINION IN PLANT BIOLOGY 2014; 18:51-9. [PMID: 24631844 DOI: 10.1016/j.pbi.2014.02.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Revised: 02/04/2014] [Accepted: 02/09/2014] [Indexed: 05/25/2023]
Abstract
The application of genomic approaches to the phenomenon of plant domestication promises a better understanding of the origins of agriculture, but also of the way plant genomes in general are organized and expressed. Building on earlier genetic research, more detailed information has become available on the organization of genetic diversity at the genome level and the effects of gene flow on diversity in different regions of the genome. In addition, putative domestication genes have been identified through population genomics approaches (selective sweeps or divergence scanning). Further information has been obtained on the origin of domestication syndrome mutations and the dispersal and adaptation of crops after domestication. For the future, increasingly multidisciplinary approaches using combinations of genomics and other approaches will prevail.
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Affiliation(s)
- Paul Gepts
- University of California, Department of Plant Sciences/MS 1, Section of Crop and Ecosystem Sciences, 1 Shields Avenue, Davis, CA 95616, United States of America.
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Mamidi S, Rossi M, Moghaddam SM, Annam D, Lee R, Papa R, McClean PE. Demographic factors shaped diversity in the two gene pools of wild common bean Phaseolus vulgaris L. Heredity (Edinb) 2013; 110:267-76. [PMID: 23169559 PMCID: PMC3668653 DOI: 10.1038/hdy.2012.82] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Revised: 05/31/2012] [Accepted: 06/29/2012] [Indexed: 11/09/2022] Open
Abstract
Wild common bean (Phaseolus vulgaris L.) is distributed throughout the Americas from Mexico to northern Argentina. Within this range, the species is divided into two gene pools (Andean and Middle American) along a latitudinal gradient. The diversity of 24 wild common bean genotypes from throughout the geographic range of the species was described by using sequence data from 13 loci. An isolation-migration model was evaluated using a coalescent analysis to estimate multiple demographic parameters. Using a Bayesian approach, Andean and Middle American subpopulations with high percentage of parentages were observed. Over all loci, the Middle American gene pool was more diverse than the Andean gene pool (π(sil)=0.0089 vs 0.0068). The two subpopulations were strongly genetically differentiated over all loci (F(st)=0.29). It is estimated that the two current wild gene pools diverged from a common ancestor ∼111 000 years ago. Subsequently, each gene pool underwent a bottleneck immediately after divergence and lasted ∼40 000 years. The Middle American bottleneck population size was ∼46% of the ancestral population size, whereas the Andean was 26%. Continuous asymmetric gene flow was detected between the two gene pools with a larger number of migrants entering Middle American gene pool from the Andean gene pool. These results suggest that because of the complex population structure associated with the ancestral divergence, subsequent bottlenecks in each gene pool, gene pool-specific domestication and intense selection within each gene pool by breeders; association mapping would best be practised within each common bean gene pool.
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Affiliation(s)
- S Mamidi
- Genomics and Bioinformatics Program, North Dakota State University, Fargo, ND, USA
- Department of Plant Sciences, North Dakota State University, Fargo, ND, USA
| | - M Rossi
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Ancona, Italy
| | - S M Moghaddam
- Genomics and Bioinformatics Program, North Dakota State University, Fargo, ND, USA
- Department of Plant Sciences, North Dakota State University, Fargo, ND, USA
| | - D Annam
- Department of Statistics, North Dakota State University, Fargo, ND, USA
| | - R Lee
- Genomics and Bioinformatics Program, North Dakota State University, Fargo, ND, USA
- Department of Plant Sciences, North Dakota State University, Fargo, ND, USA
| | - R Papa
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Ancona, Italy
- Cereal Research Centre, Agricultural Research Council (CRA-CER), Foggia, Italy
| | - P E McClean
- Genomics and Bioinformatics Program, North Dakota State University, Fargo, ND, USA
- Department of Plant Sciences, North Dakota State University, Fargo, ND, USA
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Bitocchi E, Bellucci E, Giardini A, Rau D, Rodriguez M, Biagetti E, Santilocchi R, Spagnoletti Zeuli P, Gioia T, Logozzo G, Attene G, Nanni L, Papa R. Molecular analysis of the parallel domestication of the common bean (Phaseolus vulgaris) in Mesoamerica and the Andes. THE NEW PHYTOLOGIST 2013; 197:300-313. [PMID: 23126683 DOI: 10.1111/j.1469-8137.2012.04377.x] [Citation(s) in RCA: 131] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Accepted: 09/07/2012] [Indexed: 05/03/2023]
Abstract
We have studied the nucleotide diversity of common bean, Phaseolus vulgaris, which is characterized by two independent domestications in two geographically distinct areas: Mesoamerica and the Andes. This provides an important model, as domestication can be studied as a replicate experiment. We used nucleotide data from five gene fragments characterized by large introns to analyse 214 accessions (102 wild and 112 domesticated). The wild accessions represent a cross-section of the entire geographical distribution of P. vulgaris. A reduction in genetic diversity in both of these gene pools was found, which was three-fold greater in Mesoamerica compared with the Andes. This appears to be a result of a bottleneck that occurred before domestication in the Andes, which strongly impoverished this wild germplasm, leading to the minor effect of the subsequent domestication bottleneck (i.e. sequential bottleneck). These findings show the importance of considering the evolutionary history of crop species as a major factor that influences their current level and structure of genetic diversity. Furthermore, these data highlight a single domestication event within each gene pool. Although the findings should be interpreted with caution, this evidence indicates the Oaxaca valley in Mesoamerica, and southern Bolivia and northern Argentina in South America, as the origins of common bean domestication.
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Affiliation(s)
- Elena Bitocchi
- 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
| | - Alessandro Giardini
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Domenico Rau
- Dipartimento di Agraria, Università degli Studi di Sassari, Via de Nicola, 07100, Sassari, Italy
| | - Monica Rodriguez
- Dipartimento di Agraria, Università degli Studi di Sassari, Via de Nicola, 07100, Sassari, Italy
| | - Eleonora Biagetti
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Rodolfo Santilocchi
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Pierluigi Spagnoletti Zeuli
- Scuola di Scienze Agrarie, Forestali, Alimentari ed Ambientali, Università degli Studi della Basilicata, via dell'Ateneo Lucano, 10, 85100, Potenza, Italy
| | - Tania Gioia
- Scuola di Scienze Agrarie, Forestali, Alimentari ed Ambientali, Università degli Studi della Basilicata, via dell'Ateneo Lucano, 10, 85100, Potenza, Italy
| | - Giuseppina Logozzo
- Scuola di Scienze Agrarie, Forestali, Alimentari ed Ambientali, Università degli Studi della Basilicata, via dell'Ateneo Lucano, 10, 85100, Potenza, Italy
| | - Giovanna Attene
- Dipartimento di Agraria, Università degli Studi di Sassari, Via de Nicola, 07100, Sassari, Italy
| | - Laura Nanni
- 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
- Cereal Research Centre, Agricultural Research Council (CRA-CER), S.S. 16, Km 675, 71122, Foggia, Italy
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Cavalieri A, Merchant A, van Volkenburgh E. Why not beans? FUNCTIONAL PLANT BIOLOGY : FPB 2011; 38:iii-vi. [PMID: 32480950 DOI: 10.1071/fpv38n12_fo] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Changes in climate and urbanisation rapidly affecting human livelihood are particularly threatening to developing nations in tropical regions. Food production crises have focused the global development agenda on agricultural research, a proven approach for increasing crop yield. A few crops benefit from private investment, but improvement of most crops will rely on limited public funding that must be deployed strategically, pushing forward both proven approaches and new ideas. Why not invest in beans? More than 300 million people rely on this crop, considered to be the most important grain legume for human consumption. Yet the yield of beans, especially in poor regions or marginal soils, is reduced by abiotic stresses such as phosphorus deficiency, aluminum toxicity and especially drought. Is it possible to assemble resources, including genetic diversity in beans, breeding expertise, genomic information and tools, and physiological insight to generate rapid progress in developing new lines of beans more tolerant to abiotic stress? A workshop to address this question was held in November 2010 at the International Center for Tropical Agriculture (CIAT) in Colombia. The resulting 'call to action' is presented in this issue which also includes research papers focused on tolerance of beans to stress.
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Affiliation(s)
- Anthony Cavalieri
- International Centre for Tropical Agriculture (CIAT), Palmira 6713, Colombia
| | - Andrew Merchant
- Faculty of Agriculture, Food and Natural Resources, The University of Sydney, Sydney, NSW 2006, Australia
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