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Plestenjak E, Meglič V, Sinkovič L, Pipan B. Factors Influencing the Emergence of Heterogeneous Populations of Common Bean ( Phaseolus vulgaris L.) and Their Potential for Intercropping. PLANTS (BASEL, SWITZERLAND) 2024; 13:1112. [PMID: 38674521 PMCID: PMC11055032 DOI: 10.3390/plants13081112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/12/2024] [Accepted: 04/13/2024] [Indexed: 04/28/2024]
Abstract
The common bean is an important legume valued for its protein-rich seeds and its ability to fix nitrogen, making it a key element of crop rotation. In conventional agriculture, the emphasis is on uniformity and genetic purity to optimize crop performance and maximize yields. This is due to both the legal obligations to register varieties and the challenges of implementing breeding programs to create genetically diverse varieties. This paper focuses on the factors that influence the occurrence of heterogeneous common bean populations. The main factors contributing to this diversity have been described, including local adaptations, variable weather conditions, different pollinator species, and intricate interactions between genes controlling seed coat colour. We also discuss the benefits of intercropping common beans for organic farming systems, highlighting the improvement in resistance to diseases, and adverse environmental conditions. This paper contributes to a better understanding of common bean seed heterogeneity and the legal obligation to use heterogeneous populations.
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Affiliation(s)
- Eva Plestenjak
- Crop Science Department, Agricultural Institute of Slovenia, Hacquetova Ulica 17, 1000 Ljubljana, Slovenia; (V.M.); (L.S.); (B.P.)
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1001 Ljubljana, Slovenia
| | - Vladimir Meglič
- Crop Science Department, Agricultural Institute of Slovenia, Hacquetova Ulica 17, 1000 Ljubljana, Slovenia; (V.M.); (L.S.); (B.P.)
| | - Lovro Sinkovič
- Crop Science Department, Agricultural Institute of Slovenia, Hacquetova Ulica 17, 1000 Ljubljana, Slovenia; (V.M.); (L.S.); (B.P.)
| | - Barbara Pipan
- Crop Science Department, Agricultural Institute of Slovenia, Hacquetova Ulica 17, 1000 Ljubljana, Slovenia; (V.M.); (L.S.); (B.P.)
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2
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Arriagada O, Arévalo B, Pacheco I, Schwember AR, Meisel LA, Silva H, Márquez K, Plaza A, Pérez-Diáz R, Pico-Mendoza J, Cabeza RA, Tapia G, Fuentes C, Rodríguez-Alvarez Y, Carrasco B. A Past Genetic Bottleneck from Argentine Beans and a Selective Sweep Led to the Race Chile of the Common Bean ( Phaseolus vulgaris L.). Int J Mol Sci 2024; 25:4081. [PMID: 38612891 PMCID: PMC11012279 DOI: 10.3390/ijms25074081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/02/2024] [Accepted: 04/04/2024] [Indexed: 04/14/2024] Open
Abstract
The domestication process of the common bean gave rise to six different races which come from the two ancestral genetic pools, the Mesoamerican (Durango, Jalisco, and Mesoamerica races) and the Andean (New Granada, Peru, and Chile races). In this study, a collection of 281 common bean landraces from Chile was analyzed using a 12K-SNP microarray. Additionally, 401 accessions representing the rest of the five common bean races were analyzed. A total of 2543 SNPs allowed us to differentiate a genetic group of 165 accessions that corresponds to the race Chile, 90 of which were classified as pure accessions, such as the bean types 'Tórtola', 'Sapito', 'Coscorrón', and 'Frutilla'. Our genetic analysis indicates that the race Chile has a close relationship with accessions from Argentina, suggesting that nomadic ancestral peoples introduced the bean seed to Chile. Previous archaeological and genetic studies support this hypothesis. Additionally, the low genetic diversity (π = 0.053; uHe = 0.53) and the negative value of Tajima' D (D = -1.371) indicate that the race Chile suffered a bottleneck and a selective sweep after its introduction, supporting the hypothesis that a small group of Argentine bean genotypes led to the race Chile. A total of 235 genes were identified within haplotype blocks detected exclusively in the race Chile, most of them involved in signal transduction, supporting the hypothesis that intracellular signaling pathways play a fundamental role in the adaptation of organisms to changes in the environment. To date, our findings are the most complete investigation associated with the origin of the race Chile of common bean.
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Affiliation(s)
- Osvin Arriagada
- Centro de Estudios en Alimentos Procesados (CEAP), Av. Lircay s/n, Talca 3480094, Chile; (B.A.); (K.M.); (A.P.); (R.P.-D.); (C.F.)
| | - Bárbara Arévalo
- Centro de Estudios en Alimentos Procesados (CEAP), Av. Lircay s/n, Talca 3480094, Chile; (B.A.); (K.M.); (A.P.); (R.P.-D.); (C.F.)
| | - Igor Pacheco
- Instituto de Nutrición y Tecnología de los Alimentos (INTA), El Líbano 5524, Santiago 7830490, Chile; (I.P.); (L.A.M.)
| | - Andrés R. Schwember
- Departamento de Ciencias Vegetales, Facultad de Agronomía y Sistemas Naturales, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile; (A.R.S.); (Y.R.-A.)
| | - Lee A. Meisel
- Instituto de Nutrición y Tecnología de los Alimentos (INTA), El Líbano 5524, Santiago 7830490, Chile; (I.P.); (L.A.M.)
| | - Herman Silva
- Laboratorio de Genómica Funcional & Bioinformática, Departamento de Producción Agrícola, Facultad de Ciencias Agronómicas, Universidad de Chile, Av. Santa Rosa 11315, Santiago 8820808, Chile;
| | - Katherine Márquez
- Centro de Estudios en Alimentos Procesados (CEAP), Av. Lircay s/n, Talca 3480094, Chile; (B.A.); (K.M.); (A.P.); (R.P.-D.); (C.F.)
| | - Andrea Plaza
- Centro de Estudios en Alimentos Procesados (CEAP), Av. Lircay s/n, Talca 3480094, Chile; (B.A.); (K.M.); (A.P.); (R.P.-D.); (C.F.)
| | - Ricardo Pérez-Diáz
- Centro de Estudios en Alimentos Procesados (CEAP), Av. Lircay s/n, Talca 3480094, Chile; (B.A.); (K.M.); (A.P.); (R.P.-D.); (C.F.)
| | - José Pico-Mendoza
- Facultad de Ingeniería Agronómica, Universidad Técnica de Manabí, Portoviejo 130105, Ecuador;
| | - Ricardo A. Cabeza
- Laboratorio de Nutrición Vegetal, Departamento de Producción Agrícola, Facultad de Ciencias Agrarias, Universidad de Talca, Talca 3460000, Chile;
| | - Gerardo Tapia
- Unidad de Recursos Genéticos, Instituto de Investigaciones Agropecuarias (INIA Quilamapu), Chillán 3800062, Chile;
| | - Camila Fuentes
- Centro de Estudios en Alimentos Procesados (CEAP), Av. Lircay s/n, Talca 3480094, Chile; (B.A.); (K.M.); (A.P.); (R.P.-D.); (C.F.)
- Programa de Doctorado en Ciencias Agrarias, Facultad de Ciencias Agrarias, Universidad de Talca, Talca 3460000, Chile
| | - Yohaily Rodríguez-Alvarez
- Departamento de Ciencias Vegetales, Facultad de Agronomía y Sistemas Naturales, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile; (A.R.S.); (Y.R.-A.)
| | - Basilio Carrasco
- Centro de Estudios en Alimentos Procesados (CEAP), Av. Lircay s/n, Talca 3480094, Chile; (B.A.); (K.M.); (A.P.); (R.P.-D.); (C.F.)
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3
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Soldan R, Fusi M, Cardinale M, Homma F, Santos LG, Wenzl P, Bach-Pages M, Bitocchi E, Chacon Sanchez MI, Daffonchio D, Preston GM. Consistent effects of independent domestication events on the plant microbiota. Curr Biol 2024; 34:557-567.e4. [PMID: 38232731 DOI: 10.1016/j.cub.2023.12.056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 12/01/2023] [Accepted: 12/18/2023] [Indexed: 01/19/2024]
Abstract
The effect of plant domestication on plant-microbe interactions remains difficult to prove. In this study, we provide evidence of a domestication effect on the composition and abundance of the plant microbiota. We focused on the genus Phaseolus, which underwent four independent domestication events within two species (P. vulgaris and P. lunatus), providing multiple replicates of a process spanning thousands of years. We targeted Phaseolus seeds to identify a link between domesticated traits and bacterial community composition as Phaseolus seeds have been subject to large and consistent phenotypic changes during these independent domestication events. The seed bacterial communities of representative plant accessions from subpopulations descended from each domestication event were analyzed under controlled and field conditions. The results showed that independent domestication events led to similar seed bacterial community signatures in independently domesticated plant populations, which could be partially explained by selection for common domesticated plant phenotypes. Our results therefore provide evidence of a consistent effect of plant domestication on seed microbial community composition and abundance and offer avenues for applying knowledge of the impact of plant domestication on the plant microbiota to improve microbial applications in agriculture.
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Affiliation(s)
| | - Marco Fusi
- Center for Conservation and Restoration Science, Edinburgh Napier University, Edinburgh, UK
| | - Massimiliano Cardinale
- University of Salento, Department of Biological and Environmental Sciences and Technologies, Lecce, Italy
| | - Felix Homma
- University of Oxford, Department of Biology, Oxford, UK
| | - Luis Guillermo Santos
- The Alliance Biodiversity International and the International Center for Tropical Agriculture (CIAT), Palmira, Colombia
| | - Peter Wenzl
- The Alliance Biodiversity International and the International Center for Tropical Agriculture (CIAT), Palmira, Colombia
| | | | - Elena Bitocchi
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Ancona, Italy
| | - Maria Isabel Chacon Sanchez
- Departamento de Agronomía, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Daniele Daffonchio
- Red Sea Research Center (RSRC), 4700 King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Gail M Preston
- University of Oxford, Department of Biology, Oxford, UK.
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4
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Bellucci E, Benazzo A, Xu C, Bitocchi E, Rodriguez M, Alseekh S, Di Vittori V, Gioia T, Neumann K, Cortinovis G, Frascarelli G, Murube E, Trucchi E, Nanni L, Ariani A, Logozzo G, Shin JH, Liu C, Jiang L, Ferreira JJ, Campa A, Attene G, Morrell PL, Bertorelle G, Graner A, Gepts P, Fernie AR, Jackson SA, Papa R. Selection and adaptive introgression guided the complex evolutionary history of the European common bean. Nat Commun 2023; 14:1908. [PMID: 37019898 PMCID: PMC10076260 DOI: 10.1038/s41467-023-37332-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 03/14/2023] [Indexed: 04/07/2023] Open
Abstract
Domesticated crops have been disseminated by humans over vast geographic areas. Common bean (Phaseolus vulgaris L.) was introduced in Europe after 1492. Here, by combining whole-genome profiling, metabolic fingerprinting and phenotypic characterisation, we show that the first common bean cultigens successfully introduced into Europe were of Andean origin, after Francisco Pizarro's expedition to northern Peru in 1529. We reveal that hybridisation, selection and recombination have shaped the genomic diversity of the European common bean in parallel with political constraints. There is clear evidence of adaptive introgression into the Mesoamerican-derived European genotypes, with 44 Andean introgressed genomic segments shared by more than 90% of European accessions and distributed across all chromosomes except PvChr11. Genomic scans for signatures of selection highlight the role of genes relevant to flowering and environmental adaptation, suggesting that introgression has been crucial for the dissemination of this tropical crop to the temperate regions of Europe.
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Affiliation(s)
- Elisa Bellucci
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131, Ancona, Italy
| | - Andrea Benazzo
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121, Ferrara, Italy
| | - Chunming Xu
- Center for Applied Genetic Technologies, University of Georgia, 30602, Athens, GA, USA
| | - Elena Bitocchi
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131, Ancona, Italy
| | - Monica Rodriguez
- Department of Agriculture, University of Sassari, 07100, Sassari, Italy
- Centro per la Conservazione e Valorizzazione della Biodiversità Vegetale-CBV, Università degli Studi di Sassari, 07041, Alghero, Italy
| | - Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology (MPI-MP), 14476, Potsdam-Golm, Germany
- Center for Plant Systems Biology and Plant Biotechnology, 4000, Plovdiv, Bulgaria
| | - Valerio Di Vittori
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131, Ancona, Italy
- Max Planck Institute of Molecular Plant Physiology (MPI-MP), 14476, Potsdam-Golm, Germany
| | - Tania Gioia
- School of Agricultural, Forestry, Food and Environmental Sciences, University of Basilicata, 85100, Potenza, Italy
| | - Kerstin Neumann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Seeland, Germany
| | - Gaia Cortinovis
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131, Ancona, Italy
| | - Giulia Frascarelli
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131, Ancona, Italy
| | - Ester Murube
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131, Ancona, Italy
| | - Emiliano Trucchi
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121, Ferrara, Italy
- Department of Life and Environmental Sciences, Marche Polytechnic University, 60131, Ancona, Italy
| | - Laura Nanni
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131, Ancona, Italy
| | - Andrea Ariani
- Department of Plant Sciences, University of California, 95616-8780, Davis, CA, USA
| | - Giuseppina Logozzo
- School of Agricultural, Forestry, Food and Environmental Sciences, University of Basilicata, 85100, Potenza, Italy
| | - Jin Hee Shin
- Center for Applied Genetic Technologies, University of Georgia, 30602, Athens, GA, USA
| | - Chaochih Liu
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108-6026, USA
| | - Liang Jiang
- Max Planck Institute of Molecular Plant Physiology (MPI-MP), 14476, Potsdam-Golm, Germany
| | - Juan José Ferreira
- Regional Agrifood Research and Development Service (SERIDA), 33310, Villaviciosa, Asturias, Spain
| | - Ana Campa
- Regional Agrifood Research and Development Service (SERIDA), 33310, Villaviciosa, Asturias, Spain
| | - Giovanna Attene
- Department of Agriculture, University of Sassari, 07100, Sassari, Italy
- Centro per la Conservazione e Valorizzazione della Biodiversità Vegetale-CBV, Università degli Studi di Sassari, 07041, Alghero, Italy
| | - Peter L Morrell
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108-6026, USA
| | - Giorgio Bertorelle
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121, Ferrara, Italy
| | - Andreas Graner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Seeland, Germany
| | - Paul Gepts
- Department of Plant Sciences, University of California, 95616-8780, Davis, CA, USA
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology (MPI-MP), 14476, Potsdam-Golm, Germany
- Center for Plant Systems Biology and Plant Biotechnology, 4000, Plovdiv, Bulgaria
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, 30602, Athens, GA, USA
| | - Roberto Papa
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131, Ancona, Italy.
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5
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Catarcione G, Paolacci AR, Alicandri E, Gramiccia E, Taviani P, Rea R, Costanza MT, De Lorenzis G, Puccio G, Mercati F, Ciaffi M. Genetic Diversity and Population Structure of Common Bean ( Phaseolus vulgaris L.) Landraces in the Lazio Region of Italy. PLANTS (BASEL, SWITZERLAND) 2023; 12:744. [PMID: 36840092 PMCID: PMC9968208 DOI: 10.3390/plants12040744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/02/2023] [Accepted: 02/04/2023] [Indexed: 06/18/2023]
Abstract
Common bean cultivation has historically been a typical component of rural economies in Italy, particularly in mountainous and hilly zones along the Apennine ridge of the central and southern regions, where the production is focused on local landraces cultivated by small-scale farmers using low-input production systems. Such landraces are at risk of genetic erosion because of the recent socioeconomic changes in rural communities. One hundred fourteen accessions belonging to 66 landraces still being grown in the Lazio region were characterized using a multidisciplinary approach. This approach included morphological (seed traits), biochemical (phaseolin and phytohemagglutinin patterns), and molecular (microsatellite loci) analyses to investigate their genetic variation, structure, and distinctiveness, which will be essential for the implementation of adequate ex situ and in situ conservation strategies. Another objective of this study was to determine the original gene pool (Andean and Mesoamerican) of the investigated landraces and to evaluate the cross-hybridization events between the two ancestral gene pools in the P. vulgaris germplasm in the Lazio region. Molecular analyses on 456 samples (four for each of the 114 accessions) revealed that the P. vulgaris germplasm in the Lazio region exhibited a high level of genetic diversity (He = 0.622) and that the Mesoamerican and Andean gene pools were clearly differentiated, with the Andean gene pool prevailing (77%) and 12% of landraces representing putative hybrids between the two gene pools. A model-based cluster analysis based on the molecular markers highlighted three main groups in agreement with the phaseolin patterns and growth habit of landraces. The combined utilisation of morphological, biochemical, and molecular data allowed for the differentiation of all landraces and the resolution of certain instances of homonymy and synonymy. Furthermore, although a high level of homozygosity was found across all landraces, 32 of the 66 examined (49%) exhibited genetic variability, indicating that the analysis based on a single or few plants per landrace, as usually carried out, may provide incomplete information.
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Affiliation(s)
- Giulio Catarcione
- DIBAF, Università degli Studi della Tuscia, Via San Camillo de Lellis, 01100 Viterbo, Italy
| | - Anna Rita Paolacci
- DIBAF, Università degli Studi della Tuscia, Via San Camillo de Lellis, 01100 Viterbo, Italy
| | - Enrica Alicandri
- DIBAF, Università degli Studi della Tuscia, Via San Camillo de Lellis, 01100 Viterbo, Italy
| | - Elena Gramiccia
- DIBAF, Università degli Studi della Tuscia, Via San Camillo de Lellis, 01100 Viterbo, Italy
| | | | - Roberto Rea
- ARSIAL, Via Rodolfo Lanciani 38, 00162 Roma, Italy
| | | | | | | | | | - Mario Ciaffi
- DIBAF, Università degli Studi della Tuscia, Via San Camillo de Lellis, 01100 Viterbo, Italy
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Mutari B, Sibiya J, Shayanowako A, Chidzanga C, Matova PM, Gasura E. Genome-wide association mapping for component traits of drought tolerance in dry beans (Phaseolus vulgaris L.). PLoS One 2023; 18:e0278500. [PMID: 37200295 DOI: 10.1371/journal.pone.0278500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 04/30/2023] [Indexed: 05/20/2023] Open
Abstract
Understanding the genetic basis of traits of economic importance under drought stressed and well-watered conditions is important in enhancing genetic gains in dry beans (Phaseolus vulgaris L.). This research aims to: (i) identify markers associated with agronomic and physiological traits for drought tolerance and (ii) identify drought-related putative candidate genes within the mapped genomic regions. An andean and middle-american diversity panel (AMDP) comprising of 185 genotypes was screened in the field under drought stressed and well-watered conditions for two successive seasons. Agronomic and physiological traits, viz., days to 50% flowering (DFW), plant height (PH), days to physiological maturity (DPM), grain yield (GYD), 100-seed weight (SW), leaf temperature (LT), leaf chlorophyll content (LCC) and stomatal conductance (SC) were phenotyped. Principal component and association analysis were conducted using the filtered 9370 Diversity Arrays Technology sequencing (DArTseq) markers. The mean PH, GYD, SW, DPM, LCC and SC of the panel was reduced by 12.1, 29.6, 10.3, 12.6, 28.5 and 62.0%, respectively under drought stressed conditions. Population structure analysis revealed two sub-populations, which corresponded to the andean and middle-american gene pools. Markers explained 0.08-0.10, 0.22-0.23, 0.29-0.32, 0.43-0.44, 0.65-0.66 and 0.69-0.70 of the total phenotypic variability (R2) for SC, LT, PH, GYD, SW and DFW, respectively under drought stressed conditions. For well-watered conditions, R2 varied from 0.08 (LT) to 0.70 (DPM). Overall, 68 significant (p < 10-03) marker-trait associations (MTAs) and 22 putative candidate genes were identified across drought stressed and well-watered conditions. Most of the identified genes had known biological functions related to regulating the response to drought stress. The findings provide new insights into the genetic architecture of drought stress tolerance in common bean. The findings also provide potential candidate SNPs and putative genes that can be utilized in gene discovery and marker-assisted breeding for drought tolerance after validation.
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Affiliation(s)
- Bruce Mutari
- School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Scottsville, Pietermaritzburg, South Africa
- Department of Research and Specialist Services, Crop Breeding Institute, Harare, Zimbabwe
| | - Julia Sibiya
- School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Scottsville, Pietermaritzburg, South Africa
| | - Admire Shayanowako
- School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Scottsville, Pietermaritzburg, South Africa
| | - Charity Chidzanga
- School of Agriculture, Food and Wine, The University of Adelaide, Glen Osmond, Australia
| | | | - Edmore Gasura
- University of Zimbabwe, Mt Pleasant, Harare, Zimbabwe
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7
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Ugwuanyi S, Udengwu OS, Snowdon RJ, Obermeier C. Novel candidate loci for morpho-agronomic and seed quality traits detected by targeted genotyping-by-sequencing in common bean. FRONTIERS IN PLANT SCIENCE 2022; 13:1014282. [PMID: 36438107 PMCID: PMC9685177 DOI: 10.3389/fpls.2022.1014282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 10/18/2022] [Indexed: 06/16/2023]
Abstract
Phaseolus vulgaris L., known as common bean, is one of the most important grain legumes cultivated around the world for its immature pods and dry seeds, which are rich in protein and micronutrients. Common bean offers a cheap food and protein sources to ameliorate food shortage and malnutrition around the world. However, the genetic basis of most important traits in common bean remains unknown. This study aimed at identifying QTL and candidate gene models underlying twenty-six agronomically important traits in common bean. For this, we assembled and phenotyped a diversity panel of 200 P. vulgaris genotypes in the greenhouse, comprising determinate bushy, determinate climbing and indeterminate climbing beans. The panel included dry beans and snap beans from different breeding programmes, elite lines and landraces from around the world with a major focus on accessions of African, European and South American origin. The panel was genotyped using a cost-conscious targeted genotyping-by-sequencing (GBS) platform to take advantage of highly polymorphic SNPs detected in previous studies and in diverse germplasm. The detected single nucleotide polymorphisms (SNPs) were applied in marker-trait analysis and revealed sixty-two quantitative trait loci (QTL) significantly associated with sixteen traits. Gene model identification via a similarity-based approach implicated major candidate gene models underlying the QTL associated with ten traits including, flowering, yield, seed quality, pod and seed characteristics. Our study revealed six QTL for pod shattering including three new QTL potentially useful for breeding. However, the panel was evaluated in a single greenhouse environment and the findings should be corroborated by evaluations across different field environments. Some of the detected QTL and a number of candidate gene models only elucidate the understanding of the genetic nature of these traits and provide the basis for further studies. Finally, the study showed the possibility of using a limited number of SNPs in performing marker-trait association in common bean by applying a highly scalable targeted GBS approach. This targeted GBS approach is a cost-efficient strategy for assessment of the genetic basis of complex traits and can enable geneticists and breeders to identify novel loci and targets for marker-assisted breeding more efficiently.
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Affiliation(s)
- Samson Ugwuanyi
- Department of Plant Breeding, Justus Liebig University, Giessen, Germany
- Department of Plant Science and Biotechnology, University of Nigeria, Nsukka, Nigeria
| | - Obi Sergius Udengwu
- Department of Plant Science and Biotechnology, University of Nigeria, Nsukka, Nigeria
| | - Rod J. Snowdon
- Department of Plant Breeding, Justus Liebig University, Giessen, Germany
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8
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Rau D, Attene G, Rodriguez M, Baghino L, Pisanu AB, Sanna D, Acquadro A, Portis E, Comino C. The Population Structure of a Globe Artichoke Worldwide Collection, as Revealed by Molecular and Phenotypic Analyzes. FRONTIERS IN PLANT SCIENCE 2022; 13:898740. [PMID: 35865281 PMCID: PMC9294547 DOI: 10.3389/fpls.2022.898740] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 05/13/2022] [Indexed: 05/27/2023]
Abstract
The knowledge of the organization of the domesticated gene pool of crop species is an essential requirement to understand crop evolution, to rationalize conservation programs, and to support practical decisions in plant breeding. Here, we integrate simple sequence repeat (SSR) analysis and phenotypic characterization to investigate a globe artichoke collection that comprises most of the varieties cultivated worldwide. We show that the cultivated gene pool of globe artichoke includes five distinct genetic groups associated with the major phenotypic typologies: Catanesi (which based on our analysis corresponds to Violetti di Provenza), Spinosi, Violetti di Toscana, Romaneschi, and Macau. We observed that 17 and 11% of the molecular and phenotypic variance, respectively, is between these groups, while within groups, strong linkage disequilibrium and heterozygote excess are evident. The divergence between groups for quantitative traits correlates with the average broad-sense heritability within the groups. The phenotypic divergence between groups for both qualitative and quantitative traits is strongly and positively correlated with SSR divergence (FST) between groups. All this implies a low population size and strong bottleneck effects, and indicates a long history of clonal propagation and selection during the evolution of the domesticated gene pool of globe artichoke. Moreover, the comparison between molecular and phenotypic population structures suggests that harvest time, plant architecture (i.e., plant height, stem length), leaf spininess, head morphology (i.e., head shape, bract shape, spininess) together with the number of heads per plant were the main targets of selection during the evolution of the cultivated germplasm. We emphasize our findings in light of the potential exploitation of this collection for association mapping studies.
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Affiliation(s)
- Domenico Rau
- Dipartimento di Agraria, Sezione di Agronomia, Coltivazioni Erbacee e Genetica (SACEG), Università degli Studi di Sassari, Sassari, Italy
| | - Giovanna Attene
- Dipartimento di Agraria, Sezione di Agronomia, Coltivazioni Erbacee e Genetica (SACEG), Università degli Studi di Sassari, Sassari, Italy
| | - Monica Rodriguez
- Dipartimento di Agraria, Sezione di Agronomia, Coltivazioni Erbacee e Genetica (SACEG), Università degli Studi di Sassari, Sassari, Italy
| | - Limbo Baghino
- Agenzia AGRIS Sardegna (Servizio Ricerca sui Sistemi Colturali Erbacei, Settore Innovazione dei Modelli Gestionali e Studio Della Biodiversità Nelle Colture Intensive), Oristano, Italy
| | - Anna Barbara Pisanu
- Agenzia AGRIS Sardegna (Servizio Ricerca sui Sistemi Colturali Erbacei, Settore Innovazione dei Modelli Gestionali e Studio Della Biodiversità Nelle Colture Intensive), Oristano, Italy
| | - Davide Sanna
- Agenzia AGRIS Sardegna (Servizio Ricerca sui Sistemi Colturali Erbacei, Settore Innovazione dei Modelli Gestionali e Studio Della Biodiversità Nelle Colture Intensive), Oristano, Italy
| | - Alberto Acquadro
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari (DISAFA), Genetica Vegetale (Plant Genetics), Università degli Studi di Torino, Turin, Italy
| | - Ezio Portis
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari (DISAFA), Genetica Vegetale (Plant Genetics), Università degli Studi di Torino, Turin, Italy
| | - Cinzia Comino
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari (DISAFA), Genetica Vegetale (Plant Genetics), Università degli Studi di Torino, Turin, Italy
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9
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Abstract
This article comments on:
Williams O, Vander Schoor JK, Butler JB, Ridge S, Sussmilch FC, Hecht VFG, Weller JL. 2022. The genetic architecture of flowering time changes in pea from wild to crop. Journal of Experimental Botany 73,3978–3990.
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Affiliation(s)
- Mark A Chapman
- Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
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10
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Zia B, Shi A, Olaoye D, Xiong H, Ravelombola W, Gepts P, Schwartz HF, Brick MA, Otto K, Ogg B, Chen S. Genome-Wide Association Study and Genomic Prediction for Bacterial Wilt Resistance in Common Bean ( Phaseolus vulgaris) Core Collection. Front Genet 2022; 13:853114. [PMID: 35711938 PMCID: PMC9197503 DOI: 10.3389/fgene.2022.853114] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 04/14/2022] [Indexed: 11/30/2022] Open
Abstract
Common bean (Phaseolus vulgaris) is one of the major legume crops cultivated worldwide. Bacterial wilt (BW) of common bean (Curtobacterium flaccumfaciens pv. flaccumfaciens), being a seed-borne disease, has been a challenge in common bean producing regions. A genome-wide association study (GWAS) was conducted to identify SNP markers associated with BW resistance in the USDA common bean core collection. A total of 168 accessions were evaluated for resistance against three different isolates of BW. Our study identified a total of 14 single nucleotide polymorphism (SNP) markers associated with the resistance to BW isolates 528, 557, and 597 using mixed linear models (MLMs) in BLINK, FarmCPU, GAPIT, and TASSEL 5. These SNPs were located on chromosomes Phaseolus vulgaris [Pv]02, Pv04, Pv08, and Pv09 for isolate 528; Pv07, Pv10, and Pv11 for isolate 557; and Pv04, Pv08, and Pv10 for isolate 597. The genomic prediction accuracy was assessed by utilizing seven GP models with 1) all the 4,568 SNPs and 2) the 14 SNP markers. The overall prediction accuracy (PA) ranged from 0.30 to 0.56 for resistance against the three BW isolates. A total of 14 candidate genes were discovered for BW resistance located on chromosomes Pv02, Pv04, Pv07, Pv08, and Pv09. This study revealed vital information for developing genetic resistance against the BW pathogen in common bean. Accordingly, the identified SNP markers and candidate genes can be utilized in common bean molecular breeding programs to develop novel resistant cultivars.
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Affiliation(s)
- Bazgha Zia
- Department of Horticulture, University of Arkansas, Fayetteville, AR, United States
| | - Ainong Shi
- Department of Horticulture, University of Arkansas, Fayetteville, AR, United States
| | - Dotun Olaoye
- Department of Horticulture, University of Arkansas, Fayetteville, AR, United States
| | - Haizheng Xiong
- Department of Horticulture, University of Arkansas, Fayetteville, AR, United States
| | - Waltram Ravelombola
- Organic & Specialty Crop Breeding, Texas A&M AgriLife Research, Vernon, TX, United States
| | - Paul Gepts
- Department of Plant Sciences/MS1, University of California, Davis, Davis, CA, United States
| | - Howard F Schwartz
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, United States
| | - Mark A Brick
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, United States
| | - Kristen Otto
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, United States
| | - Barry Ogg
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, United States
| | - Senyu Chen
- Department of Plant Pathology, University of Minnesota, Minneapolis, MN, United States
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11
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Guerra‐García A, Rojas‐Barrera IC, Ross‐Ibarra J, Papa R, Piñero D. The genomic signature of wild‐to‐crop introgression during the domestication of scarlet runner bean (
Phaseolus coccineus
L.). Evol Lett 2022; 6:295-307. [PMID: 35937471 PMCID: PMC9346085 DOI: 10.1002/evl3.285] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 03/06/2022] [Accepted: 05/15/2022] [Indexed: 11/23/2022] Open
Abstract
The scarlet runner bean (Phaseolus coccineus) is one of the five domesticated Phaseolus species. It is cultivated in small‐scale agriculture in the highlands of Mesoamerica for its dry seeds and immature pods, and unlike the other domesticated beans, P. coccineus is an open‐pollinated legume. Contrasting with its close relative, the common bean, few studies focusing on its domestication history have been conducted. Demographic bottlenecks associated with domestication might reduce genetic diversity and facilitate the accumulation of deleterious mutations. Conversely, introgression from wild relatives could be a source of variation. Using Genotyping by Sequencing data (79,286 single‐nucleotide variants) from 237 cultivated and wild samples, we evaluated the demographic history of traditional varieties from different regions of Mexico and looked for evidence of introgression between sympatric wild and cultivated populations. Traditional varieties have high levels of diversity, even though there is evidence of a severe initial genetic bottleneck followed by a population expansion. Introgression from wild to domesticated populations was detected, which might contribute to the recovery of the genetic variation. Introgression has occurred at different times: constantly in the center of Mexico; recently in the North West; and anciently in the South. Several factors are acting together to increase and maintain genetic diversity in P. coccineus cultivars, such as demographic expansion and introgression. Wild relatives represent a valuable genetic resource and have played a key role in scarlet runner bean evolution via introgression into traditional varieties.
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Affiliation(s)
- Azalea Guerra‐García
- Departamento de Ecología Evolutiva, Instituto de Ecología Universidad Nacional Autónoma de México Ciudad de México 04510 México
- Department of Plant Sciences University of Saskatchewan Saskatoon SK S7N 5A2 Canada
| | - Idalia C. Rojas‐Barrera
- Departamento de Ecología Evolutiva, Instituto de Ecología Universidad Nacional Autónoma de México Ciudad de México 04510 México
- Environmental Genomics Max Planck Institute for Evolutionary Biology 24306 Plön Germany
| | - Jeffrey Ross‐Ibarra
- Department of Evolution and Ecology, Center for Population Biology, and Genome Center University of California, Davis Davis California 95616
| | - Roberto Papa
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali Università Politecnica delle Marche Ancona 60131 Italy
| | - Daniel Piñero
- Departamento de Ecología Evolutiva, Instituto de Ecología Universidad Nacional Autónoma de México Ciudad de México 04510 México
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12
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Castaingts M, Kirolinko C, Rivero C, Artunian J, Mancini Villagra U, Blanco FA, Zanetti ME. Identification of conserved and new miRNAs that affect nodulation and strain selectivity in the Phaseolus vulgaris-Rhizobium etli symbiosis through differential analysis of host small RNAs. THE NEW PHYTOLOGIST 2022; 234:1430-1447. [PMID: 35203109 DOI: 10.1111/nph.18055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 02/07/2022] [Indexed: 06/14/2023]
Abstract
Phaseolus vulgaris plants from the Mesoamerican centre of genetic diversification establish a preferential and more efficient root nodule symbiosis with sympatric Rhizobium etli strains. This is mediated by changes in host gene expression, which might occur either at the transcriptional or at the post-transcriptional level. However, the implication of small RNA (sRNA)-mediated control of gene expression in strain selectivity has remained elusive. sRNA sequencing was used to identify host microRNAs (miRNAs) differentially regulated in roots at an early stage of the symbiotic interaction, which were further characterized by applying a reverse genetic approach. In silico analysis identified known and new miRNAs that accumulated to a greater extent in the preferential and more efficient interaction. One of them, designated as Pvu-miR5924, participates in the mechanisms that determine the selection of R. etli strains that will colonize the nodules. In addition, the functional analysis of Pvu-miR390b verified that this miRNA is a negative modulator of nodule formation and bacterial infection. This study not only extended the list of miRNAs identified in P. vulgaris but also enabled the identification of miRNAs that play relevant functions in nodule formation, rhizobial infection and the selection of the rhizobial strains that will occupy the nodule.
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Affiliation(s)
- Melisse Castaingts
- Facultad de Ciencias Exactas, Instituto de Biotecnología y Biología Molecular, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata, 1900, Argentina
| | - Cristina Kirolinko
- Facultad de Ciencias Exactas, Instituto de Biotecnología y Biología Molecular, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata, 1900, Argentina
| | - Claudio Rivero
- Facultad de Ciencias Exactas, Instituto de Biotecnología y Biología Molecular, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata, 1900, Argentina
| | - Jennifer Artunian
- Facultad de Ciencias Exactas, Instituto de Biotecnología y Biología Molecular, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata, 1900, Argentina
| | - Ulises Mancini Villagra
- Facultad de Ciencias Exactas, Instituto de Biotecnología y Biología Molecular, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata, 1900, Argentina
| | - Flavio Antonio Blanco
- Facultad de Ciencias Exactas, Instituto de Biotecnología y Biología Molecular, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata, 1900, Argentina
| | - María Eugenia Zanetti
- Facultad de Ciencias Exactas, Instituto de Biotecnología y Biología Molecular, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata, 1900, Argentina
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13
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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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14
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Keller B, Ariza-Suarez D, Portilla-Benavides AE, Buendia HF, Aparicio JS, Amongi W, Mbiu J, Msolla SN, Miklas P, Porch TG, Burridge J, Mukankusi C, Studer B, Raatz B. Improving Association Studies and Genomic Predictions for Climbing Beans With Data From Bush Bean Populations. FRONTIERS IN PLANT SCIENCE 2022; 13:830896. [PMID: 35557726 PMCID: PMC9085748 DOI: 10.3389/fpls.2022.830896] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 02/25/2022] [Indexed: 05/29/2023]
Abstract
Common bean (Phaseolus vulgaris L.) has two major origins of domestication, Andean and Mesoamerican, which contribute to the high diversity of growth type, pod and seed characteristics. The climbing growth habit is associated with increased days to flowering (DF), seed iron concentration (SdFe), nitrogen fixation, and yield. However, breeding efforts in climbing beans have been limited and independent from bush type beans. To advance climbing bean breeding, we carried out genome-wide association studies and genomic predictions using 1,869 common bean lines belonging to five breeding panels representing both gene pools and all growth types. The phenotypic data were collected from 17 field trials and were complemented with 16 previously published trials. Overall, 38 significant marker-trait associations were identified for growth habit, 14 for DF, 13 for 100 seed weight, three for SdFe, and one for yield. Except for DF, the results suggest a common genetic basis for traits across all panels and growth types. Seven QTL associated with growth habits were confirmed from earlier studies and four plausible candidate genes for SdFe and 100 seed weight were newly identified. Furthermore, the genomic prediction accuracy for SdFe and yield in climbing beans improved up to 8.8% when bush-type bean lines were included in the training population. In conclusion, a large population from different gene pools and growth types across multiple breeding panels increased the power of genomic analyses and provides a solid and diverse germplasm base for genetic improvement of common bean.
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Affiliation(s)
- Beat Keller
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Daniel Ariza-Suarez
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
- Bean Program, International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | | | - Hector Fabio Buendia
- Bean Program, International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | | | - Winnyfred Amongi
- Bean Program, International Center for Tropical Agriculture (CIAT), Kampala, Uganda
| | - Julius Mbiu
- Tanzania Agricultural Research Institute (TARI), Dodoma, Tanzania
| | - Susan Nchimbi Msolla
- Department of Crop Science and Horticulture, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Phillip Miklas
- Department of Agriculture, Agriculture Research Service (USDA-ARS), Prosser, WA, United States
| | - Timothy G. Porch
- Department of Agriculture, Agriculture Research Service (USDA-ARS), Tropical Agriculture Research Station, Mayaguez, PR, United States
| | - James Burridge
- Department of Plant Science, The Pennsylvania State University, University Park, PA, United States
| | - Clare Mukankusi
- Bean Program, International Center for Tropical Agriculture (CIAT), Kampala, Uganda
| | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Bodo Raatz
- Bean Program, International Center for Tropical Agriculture (CIAT), Cali, Colombia
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15
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Hellwig T, Abbo S, Ophir R. Phylogeny and disparate selection signatures suggest two genetically independent domestication events in pea (Pisum L.). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:419-439. [PMID: 35061306 PMCID: PMC9303476 DOI: 10.1111/tpj.15678] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 01/15/2022] [Indexed: 05/25/2023]
Abstract
Domestication is considered a model of adaptation that can be used to draw conclusions about the modus operandi of selection in natural systems. Investigating domestication may give insights into how plants react to different intensities of human manipulation, which has direct implication for the continuing efforts of crop improvement. Therefore, scientists of various disciplines study domestication-related questions to understand the biological and cultural bases of the domestication process. We employed restriction site-associated DNA sequencing (RAD-seq) of 494 Pisum sativum (pea) samples from all wild and domesticated groups to analyze the genetic structure of the collection. Patterns of ancient admixture were investigated by analysis of admixture graphs. We used two complementary approaches, one diversity based and one based on differentiation, to detect the selection signatures putatively associated with domestication. An analysis of the subpopulation structure of wild P. sativum revealed five distinct groups with a notable geographic pattern. Pisum abyssinicum clustered unequivocally within the P. sativum complex, without any indication of hybrid origin. We detected 32 genomic regions putatively subjected to selection: 29 in P. sativum ssp. sativum and three in P. abyssinicum. The two domesticated groups did not share regions under selection and did not display similar haplotype patterns within those regions. Wild P. sativum is structured into well-diverged subgroups. Although Pisum sativum ssp. humile is not supported as a taxonomic entity, the so-called 'southern humile' is a genuine wild group. Introgression did not shape the variation observed within the sampled germplasm. The two domesticated pea groups display distinct genetic bases of domestication, suggesting two genetically independent domestication events.
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Affiliation(s)
- Timo Hellwig
- The Levi Eshkol School of AgricultureThe Hebrew University of JerusalemJerusalem, RehovotIsrael
- Volcani Center, Agricultural Research OrganizationRishon LeZionIsrael
- Institute of Plant Genetics, Heinrich‐Heine‐UniversityDüsseldorfGermany
| | - Shahal Abbo
- The Levi Eshkol School of AgricultureThe Hebrew University of JerusalemJerusalem, RehovotIsrael
| | - Ron Ophir
- Volcani Center, Agricultural Research OrganizationRishon LeZionIsrael
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16
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Giordani W, Gama HC, Chiorato AF, Marques JPR, Huo H, Benchimol-Reis LL, Camargo LEA, Garcia AAF, Vieira MLC. Genetic mapping reveals complex architecture and candidate genes involved in common bean response to Meloidogyne incognita infection. THE PLANT GENOME 2022; 15:e20161. [PMID: 34806826 DOI: 10.1002/tpg2.20161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 09/05/2021] [Indexed: 06/13/2023]
Abstract
Root-knot nematodes (RKNs), particularly Meloidogyne incognita, are among the most damaging and prevalent agricultural pathogens due to their ability to infect roots of almost all crops. The best strategy for their control is through the use of resistant cultivars. However, laborious phenotyping procedures make it difficult to assess nematode resistance in breeding programs. For common bean, this task is especially challenging because little has been done to discover resistance genes or markers to assist selection. We performed genome-wide association studies and quantitative trait loci mapping to explore the genetic architecture and genomic regions underlying the resistance to M. incognita and to identify candidate resistance genes. Phenotypic data were collected by a high-throughput assay, and the number of egg masses and the root-galling index were evaluated. Complex genetic architecture and independent genomic regions were associated with each trait. Single nucleotide polymorphisms on chromosomes Pv06, Pv07, Pv08, and Pv11 were associated with the number of egg masses, and SNPs on Pv01, Pv02, Pv05, and Pv10 were associated with root-galling. A total of 216 candidate genes were identified, including 14 resistance gene analogs and five differentially expressed in a previous RNA sequencing analysis. Histochemical analysis indicated that reactive oxygen species might play a role in the resistance response. Our findings open new perspectives to improve selection efficiency for RKN resistance, and the candidate genes are valuable targets for functional investigation and gene editing approaches.
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Affiliation(s)
- Willian Giordani
- "Luiz de Queiroz" College of Agriculture, Univ. of São Paulo, Piracicaba, São Paulo, 13418-900, Brazil
| | - Henrique Castro Gama
- "Luiz de Queiroz" College of Agriculture, Univ. of São Paulo, Piracicaba, São Paulo, 13418-900, Brazil
| | | | | | - Heqiang Huo
- Mid-Florida Research and Education Center, Univ. of Florida, Apopka, FL, 32703, USA
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17
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Transcriptomic analysis of Mesoamerican and Andean Phaseolus vulgaris accessions revealed mRNAs and lncRNAs associated with strain selectivity during symbiosis. Sci Rep 2022; 12:2614. [PMID: 35173231 PMCID: PMC8850587 DOI: 10.1038/s41598-022-06566-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 01/28/2022] [Indexed: 12/29/2022] Open
Abstract
Legume plants establish a nitrogen-fixing symbiosis with soil bacteria known as rhizobia. Compatibility between legumes and rhizobia is determined at species-specific level, but variations in the outcome of the symbiotic process are also influenced by the capacity of the plant to discriminate and select specific strains that are better partners. We compared the transcriptional response of two genetically diverse accessions of Phaseolus vulgaris from Mesoamerica and South Andes to Rhizobium etli strains that exhibit variable degrees of symbiotic affinities. Our results indicate that the plant genotype is the major determinant of the transcriptional reprogramming occurring in roots at early stages of the symbiotic interaction. Differentially expressed genes (DEGs) regulated in the Mesoamerican and the Andean accessions in response to specific strains are different, but they belong to the same functional categories. The common and strain-specific transcriptional responses to rhizobia involve distinct transcription factors and cis-elements present in the promoters of DEGs in each accession, showing that diversification and domestication of common bean at different geographic regions influenced the evolution of symbiosis differently in each genetic pool. Quantitative PCR analysis validated our transcriptional datasets, which constitute a valuable source of coding and non-coding candidate genes to further unravel the molecular determinants governing the mechanisms by which plants select bacterial strains that produce a better symbiotic outcome.
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18
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Shafi S, Saini DK, Khan MA, Bawa V, Choudhary N, Dar WA, Pandey AK, Varshney RK, Mir RR. Delineating meta-quantitative trait loci for anthracnose resistance in common bean ( Phaseolus vulgaris L.). FRONTIERS IN PLANT SCIENCE 2022; 13:966339. [PMID: 36092444 PMCID: PMC9453441 DOI: 10.3389/fpls.2022.966339] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/01/2022] [Indexed: 05/03/2023]
Abstract
Anthracnose, caused by the fungus Colletotrichum lindemuthianum, is one of the devastating disease affecting common bean production and productivity worldwide. Several quantitative trait loci (QTLs) for anthracnose resistance have been identified. In order to make use of these QTLs in common bean breeding programs, a detailed meta-QTL (MQTL) analysis has been conducted. For the MQTL analysis, 92 QTLs related to anthracnose disease reported in 18 different earlier studies involving 16 mapping populations were compiled and projected on to the consensus map. This meta-analysis led to the identification of 11 MQTLs (each involving QTLs from at least two different studies) on 06 bean chromosomes and 10 QTL hotspots each involving multiple QTLs from an individual study on 07 chromosomes. The confidence interval (CI) of the identified MQTLs was found 3.51 times lower than the CI of initial QTLs. Marker-trait associations (MTAs) reported in published genome-wide association studies (GWAS) were used to validate nine of the 11 identified MQTLs, with MQTL4.1 overlapping with as many as 40 MTAs. Functional annotation of the 11 MQTL regions revealed 1,251 genes including several R genes (such as those encoding for NBS-LRR domain-containing proteins, protein kinases, etc.) and other defense related genes. The MQTLs, QTL hotspots and the potential candidate genes identified during the present study will prove useful in common bean marker-assisted breeding programs and in basic studies involving fine mapping and cloning of genomic regions associated with anthracnose resistance in common beans.
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Affiliation(s)
- Safoora Shafi
- Division of Genetics and Plant Breeding, Faculty of Agriculture, SKUAST-Kashmir, Wadura, India
| | - Dinesh Kumar Saini
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Mohd Anwar Khan
- Division of Genetics and Plant Breeding, Faculty of Agriculture, SKUAST-Kashmir, Wadura, India
| | - Vanya Bawa
- Division of Genetics & Plant Breeding, Faculty of Agriculture, SKUAST-Jammu, Chatha, Jammu and Kashmir, India
| | - Neeraj Choudhary
- Division of Genetics & Plant Breeding, Faculty of Agriculture, SKUAST-Jammu, Chatha, Jammu and Kashmir, India
| | - Waseem Ali Dar
- Mountain Agriculture Research and Extension Station, SKUAST-Kashmir, Bandipora, Jammu and Kashmir, India
| | - Arun K. Pandey
- College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Rajeev Kumar Varshney
- State Agricultural Biotechnology Centre, Centre for Crop & Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
- Rajeev Kumar Varshney,
| | - Reyazul Rouf Mir
- Division of Genetics and Plant Breeding, Faculty of Agriculture, SKUAST-Kashmir, Wadura, India
- *Correspondence: Reyazul Rouf Mir,
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19
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Zsögön A, Peres LEP, Xiao Y, Yan J, Fernie AR. Enhancing crop diversity for food security in the face of climate uncertainty. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:402-414. [PMID: 34882870 DOI: 10.1111/tpj.15626] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 11/30/2021] [Accepted: 12/04/2021] [Indexed: 05/23/2023]
Abstract
Global agriculture is dominated by a handful of species that currently supply a huge proportion of our food and feed. It additionally faces the massive challenge of providing food for 10 billion people by 2050, despite increasing environmental deterioration. One way to better plan production in the face of current and continuing climate change is to better understand how our domestication of these crops included their adaptation to environments that were highly distinct from those of their centre of origin. There are many prominent examples of this, including the development of temperate Zea mays (maize) and the alteration of day-length requirements in Solanum tuberosum (potato). Despite the pre-eminence of some 15 crops, more than 50 000 species are edible, with 7000 of these considered semi-cultivated. Opportunities afforded by next-generation sequencing technologies alongside other methods, including metabolomics and high-throughput phenotyping, are starting to contribute to a better characterization of a handful of these species. Moreover, the first examples of de novo domestication have appeared, whereby key target genes are modified in a wild species in order to confer predictable traits of agronomic value. Here, we review the scale of the challenge, drawing extensively on the characterization of past agriculture to suggest informed strategies upon which the breeding of future climate-resilient crops can be based.
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Affiliation(s)
- Agustin Zsögön
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, CEP 36570-900, Viçosa, MG, Brazil
| | - Lázaro E P Peres
- Laboratory of Plant Developmental Genetics, Departamento de Ciências Biológicas, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, CP 09, 13418-900, Piracicaba, SP, Brazil
| | - Yingjie Xiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Alisdair R Fernie
- Department of Molecular Physiology, Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
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20
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Saradadevi R, Mukankusi C, Li L, Amongi W, Mbiu JP, Raatz B, Ariza D, Beebe S, Varshney RK, Huttner E, Kinghorn B, Banks R, Rubyogo JC, Siddique KHM, Cowling WA. Multivariate genomic analysis and optimal contributions selection predicts high genetic gains in cooking time, iron, zinc, and grain yield in common beans in East Africa. THE PLANT GENOME 2021; 14:e20156. [PMID: 34704366 DOI: 10.1002/tpg2.20156] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 08/09/2021] [Indexed: 06/13/2023]
Abstract
Common bean (Phaseolus vulgaris L.) is important in African diets for protein, iron (Fe), and zinc (Zn), but traditional cultivars have long cooking time (CKT), which increases the time, energy, and health costs of cooking. Genomic selection was used to predict genomic estimated breeding values (GEBV) for grain yield (GY), CKT, Fe, and Zn in an African bean panel of 358 genotypes in a two-stage analysis. In Stage 1, best linear unbiased estimates (BLUE) for each trait were obtained from 898 genotypes across 33 field trials in East Africa. In Stage 2, BLUE in a training population of 141 genotypes were used in a multivariate genomic analysis with genome-wide single nucleotide polymorphism data from the African bean panel. Moderate to high genomic heritability was found for GY (0.45 ± 0.10), CKT (0.50 ± 0.15), Fe (0.57 ± 0.12), and Zn (0.61 ± 0.13). There were significant favorable genetic correlations between Fe and Zn (0.91 ± 0.06), GY and Fe (0.66 ± 0.17), GY and Zn (0.44 ± 0.19), CKT and Fe (-0.57 ± 0.21), and CKT and Zn (-0.67 ± 0.20). Optimal contributions selection (OCS), based on economic index of weighted GEBV for each trait, was used to design crossing within four market groups relevant to East Africa. Progeny were predicted by OCS to increase in mean GY by 12.4%, decrease in mean CKT by 9.3%, and increase in mean Fe and Zn content by 6.9 and 4.6%, respectively, with low achieved coancestry of 0.032. Genomic selection with OCS will accelerate breeding of high-yielding, biofortified, and rapid cooking African common bean cultivars.
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Affiliation(s)
- Renu Saradadevi
- The UWA Institute of Agriculture, The Univ. of Western Australia, Perth, Western Australia, 6009, Australia
- UWA School of Agriculture and Environment, The Univ. of Western Australia, Perth, Western Australia, 6009, Australia
| | - Clare Mukankusi
- Alliance of Bioversity International & International Center for Tropical Agriculture (CIAT), PO Box 6247, Kampala, Uganda
| | - Li Li
- Animal Genetics and Breeding Unit, Univ. of New England, Armidale, New South Wales, 2351, Australia
| | - Winnyfred Amongi
- Alliance of Bioversity International & International Center for Tropical Agriculture (CIAT), PO Box 6247, Kampala, Uganda
| | - Julius Peter Mbiu
- Tanzania Agricultural Research Institute (TARI) Maruku, PO Box 127, Bukoba, Kagera, Tanzania
| | - Bodo Raatz
- Alliance of Bioversity International & International Center for Tropical Agriculture (CIAT), Cali, Colombia
- Current address: Vilmorin SA, la Menitré, France
| | - Daniel Ariza
- Alliance of Bioversity International & International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Steve Beebe
- Alliance of Bioversity International & International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Rajeev K Varshney
- The UWA Institute of Agriculture, The Univ. of Western Australia, Perth, Western Australia, 6009, Australia
- Centre of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Murdoch Univ., Murdoch, Western Australia, 6150, Australia
| | - Eric Huttner
- Australian Centre for International Agricultural Research, Canberra, Australian Capital Territory, 2617, Australia
| | - Brian Kinghorn
- School of Environmental and Rural Science, Univ. of New England, Armidale, New South Wales, 2351, Australia
| | - Robert Banks
- Animal Genetics and Breeding Unit, Univ. of New England, Armidale, New South Wales, 2351, Australia
| | - Jean Claude Rubyogo
- Alliance of Bioversity International & International Center for Tropical Agriculture (CIAT), Nairobi, Kenya
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture, The Univ. of Western Australia, Perth, Western Australia, 6009, Australia
- UWA School of Agriculture and Environment, The Univ. of Western Australia, Perth, Western Australia, 6009, Australia
| | - Wallace A Cowling
- The UWA Institute of Agriculture, The Univ. of Western Australia, Perth, Western Australia, 6009, Australia
- UWA School of Agriculture and Environment, The Univ. of Western Australia, Perth, Western Australia, 6009, Australia
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21
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The Role of Bioactive Peptides in Diabetes and Obesity. Foods 2021; 10:foods10092220. [PMID: 34574330 PMCID: PMC8469013 DOI: 10.3390/foods10092220] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/10/2021] [Accepted: 09/14/2021] [Indexed: 12/18/2022] Open
Abstract
Bioactive peptides are present in most soy products and eggs and have essential protective functions. Infection is a core feature of innate immunity that affects blood pressure and the glucose level, and ageing can be delayed by killing senescent cells. Food also encrypts bioactive peptides and protein sequences produced through proteolysis or food processing. Unique food protein fragments can improve human health and avoid metabolic diseases, inflammation, hypertension, obesity, and diabetes mellitus. This review focuses on drug targets and fundamental mechanisms of bioactive peptides on metabolic syndromes, namely obesity and type 2 diabetes, to provide new ideas and knowledge on the ability of bioactive peptide to control metabolic syndromes.
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22
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Persistent microbiome members in the common bean rhizosphere: an integrated analysis of space, time, and plant genotype. THE ISME JOURNAL 2021; 15:2708-2722. [PMID: 33772106 PMCID: PMC8397763 DOI: 10.1038/s41396-021-00955-5] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 02/12/2021] [Accepted: 03/01/2021] [Indexed: 02/01/2023]
Abstract
The full potential of managing microbial communities to support plant health is yet-unrealized, in part because it remains difficult to ascertain which members are most important for the plant. However, microbes that consistently associate with a plant species across varied field conditions and over plant development likely engage with the host or host environment. Here, we applied abundance-occupancy concepts from macroecology to quantify the core membership of bacterial/archaeal and fungal communities in the rhizosphere of the common bean (Phaseolus vulgaris). Our study investigated the microbiome membership that persisted over multiple dimensions important for plant agriculture, including major U.S. growing regions (Michigan, Nebraska, Colorado, and Washington), plant development, annual plantings, and divergent genotypes, and also included re-analysis of public data from beans grown in Colombia. We found 48 core bacterial taxa that were consistently detected in all samples, inclusive of all datasets and dimensions. This suggests reliable enrichment of these taxa to the plant environment and time-independence of their association with the plant. More generally, the breadth of ecologically important dimensions included in this work (space, time, host genotype, and management) provides an example of how to systematically identify the most stably-associated microbiome members, and can be applied to other hosts or systems.
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23
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de Carvalho Paulino JF, de Almeida CP, Song Q, Carbonell SAM, Chiorato AF, Benchimol-Reis LL. Genetic diversity and inter-gene pool introgression of Mesoamerican Diversity Panel in common beans. J Appl Genet 2021; 62:585-600. [PMID: 34386968 DOI: 10.1007/s13353-021-00657-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 07/15/2021] [Accepted: 08/02/2021] [Indexed: 10/20/2022]
Abstract
Brazil is among the largest producers and consumers of common bean (Phaseolus vulgaris L.) and can be considered a secondary center of diversity for the species. The aim of this study was to estimate the genetic diversity, population structure, and relationships among 288 common bean accessions in an American Diversity Panel (ADP) genotyped with 4,042 high-quality single nucleotide polymorphisms (SNPs). The results showed inter-gene pool hybridization (hybrids) between the two main gene pools (i.e., Mesoamerican and Andean), based on principal component analysis (PCA), discriminant analysis of principal components (DAPC), and STRUCTURE analysis. The genetic diversity parameters showed that the Mesoamerican group has higher values of diversity and allelic richness in comparison with the Andean group. Considering the optimal clusters (K), clustering was performed according to the type of grain (i.e., market group), the institution of origin, the period of release, and agronomic traits. A new subset was selected and named the Mesoamerican Diversity Panel (MDP), with 205 Mesoamerican accessions. Analysis of molecular variance (AMOVA) showed low genetic variance between the two panels (i.e., ADP and MDP) with the highest percentage of the limited variance among accessions in each group. The ADP showed occurrence of high genetic differentiation between populations (i.e., Mesoamerican and Andean) and introgression between gene pools in hybrids based on a set of diagnostic SNPs. The MDP showed better linkage disequilibrium (LD) decay. The availability of genetic variation from inter-gene pool hybridizations presents a potential opportunity for breeders towards the development of superior common bean cultivars.
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Affiliation(s)
| | - Caléo Panhoca de Almeida
- Common Bean Genetic Group, Natural Center of Plant Genetics, Agronomic Institute (IAC), Campinas, SP, Brazil
| | - Qijian Song
- Soybean Genomics and Improvement Lab, USDA-ARS, Beltsville, MD, USA
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24
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Wyatt GE, Hamrick JL, Trapnell DW. The role of anthropogenic dispersal in shaping the distribution and genetic composition of a widespread North American tree species. Ecol Evol 2021; 11:11515-11532. [PMID: 34429937 PMCID: PMC8366864 DOI: 10.1002/ece3.7944] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 06/22/2021] [Accepted: 06/25/2021] [Indexed: 11/19/2022] Open
Abstract
Dispersal and colonization are among the most important ecological processes for species persistence as they allow species to track changing environmental conditions. During the last glacial maximum (LGM), many cold-intolerant Northern Hemisphere plants retreated to southern glacial refugia. During subsequent warming periods, these species expanded their ranges northward. Interestingly, some tree species with limited seed dispersal migrated considerable distances after the LGM ~19,000 years before present (YBP). It has been hypothesized that indigenous peoples may have dispersed valued species, in some cases beyond the southern limits of the Laurentide Ice Sheet. To investigate this question, we employed a molecular genetics approach on a widespread North American understory tree species whose fruit was valued by indigenous peoples. Twenty putative anthropogenic (near pre-Columbian habitations) and 62 wild populations of Asimina triloba (pawpaw), which produces the largest edible fruit of any North American tree, were genetically assayed with nine microsatellite loci. Putative anthropogenic populations were characterized by reduced genetic diversity and greater excess heterozygosity relative to wild populations. Anthropogenic populations in regions that were glaciated during the LGM had profiles consistent with founder effects and reduced gene flow, and shared rare alleles with wild populations hundreds of kilometers away (mean = 723 km). Some of the most compelling evidence for human-mediated dispersal is that putative anthropogenic and wild populations sharing rare alleles were separated by significantly greater distances (mean = 695 km) than wild populations sharing rare alleles (mean = 607 km; p = .014). Collectively, the genetic data suggest that long-distance dispersal played an important role in the distribution of pawpaw and is consistent with the hypothesized role of indigenous peoples.
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Affiliation(s)
- Graham E. Wyatt
- Department of Plant BiologyUniversity of GeorgiaAthensGeorgiaUSA
| | - J. L. Hamrick
- Department of Plant BiologyUniversity of GeorgiaAthensGeorgiaUSA
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25
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Van Cauwenberghe J, Santamaría RI, Bustos P, Juárez S, Ducci MA, Figueroa Fleming T, Etcheverry AV, González V. Spatial patterns in phage-Rhizobium coevolutionary interactions across regions of common bean domestication. THE ISME JOURNAL 2021; 15:2092-2106. [PMID: 33558688 PMCID: PMC8245606 DOI: 10.1038/s41396-021-00907-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 01/14/2021] [Accepted: 01/21/2021] [Indexed: 01/30/2023]
Abstract
Bacteriophages play significant roles in the composition, diversity, and evolution of bacterial communities. Despite their importance, it remains unclear how phage diversity and phage-host interactions are spatially structured. Local adaptation may play a key role. Nitrogen-fixing symbiotic bacteria, known as rhizobia, have been shown to locally adapt to domesticated common bean at its Mesoamerican and Andean sites of origin. This may affect phage-rhizobium interactions. However, knowledge about the diversity and coevolution of phages with their respective Rhizobium populations is lacking. Here, through the study of four phage-Rhizobium communities in Mexico and Argentina, we show that both phage and host diversity is spatially structured. Cross-infection experiments demonstrated that phage infection rates were higher overall in sympatric rhizobia than in allopatric rhizobia except for one Argentinean community, indicating phage local adaptation and host maladaptation. Phage-host interactions were shaped by the genetic identity and geographic origin of both the phage and the host. The phages ranged from specialists to generalists, revealing a nested network of interactions. Our results suggest a key role of local adaptation to resident host bacterial communities in shaping the phage genetic and phenotypic composition, following a similar spatial pattern of diversity and coevolution to that in the host.
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Affiliation(s)
- Jannick Van Cauwenberghe
- Centro de Ciencias Genómicas, Universidad Nacional Autonóma de México, Mexico, Mexico.
- Department of Integrative Biology, University of California, Berkeley, CA, USA.
| | - Rosa I Santamaría
- Centro de Ciencias Genómicas, Universidad Nacional Autonóma de México, Mexico, Mexico
| | - Patricia Bustos
- Centro de Ciencias Genómicas, Universidad Nacional Autonóma de México, Mexico, Mexico
| | - Soledad Juárez
- Centro de Ciencias Genómicas, Universidad Nacional Autonóma de México, Mexico, Mexico
| | - Maria Antonella Ducci
- Instituto Nacional de Tecnología Agropecuaria, Universidad Nacional de Salta, Salta, Argentina
| | | | | | - Víctor González
- Centro de Ciencias Genómicas, Universidad Nacional Autonóma de México, Mexico, Mexico.
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Shi A, Gepts P, Song Q, Xiong H, Michaels TE, Chen S. Genome-Wide Association Study and Genomic Prediction for Soybean Cyst Nematode Resistance in USDA Common Bean ( Phaseolus vulgaris) Core Collection. FRONTIERS IN PLANT SCIENCE 2021; 12:624156. [PMID: 34163495 PMCID: PMC8215670 DOI: 10.3389/fpls.2021.624156] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 05/14/2021] [Indexed: 05/16/2023]
Abstract
Soybean cyst nematode (SCN, Heterodera glycines) has become the major yield-limiting biological factor in soybean production. Common bean is also a good host of SCN, and its production is challenged by this emerging pest in many regions such as the upper Midwest USA. The use of host genetic resistance has been the most effective and environmentally friendly method to manage SCN. The objectives of this study were to evaluate the SCN resistance in the USDA common bean core collection and conduct a genome-wide association study (GWAS) of single nucleotide polymorphism (SNP) markers with SCN resistance. A total of 315 accessions of the USDA common bean core collection were evaluated for resistance to SCN HG Type 0 (race 6). The common bean core set was genotyped with the BARCBean6K_3 Infinium BeadChips, consisting of 4,654 SNPs. Results showed that 15 accessions were resistant to SCN with a Female Index (FI) at 4.8 to 9.4, and 62 accessions were moderately resistant (10 < FI < 30) to HG Type 0. The association study showed that 11 SNP markers, located on chromosomes Pv04, 07, 09, and 11, were strongly associated with resistance to HG Type 0. GWAS was also conducted for resistance to HG Type 2.5.7 and HG Type 1.2.3.5.6.7 based on the public dataset (N = 276), consisting of a diverse set of common bean accessions genotyped with the BARCBean6K_3 chip. Six SNPs associated with HG Type 2.5.7 resistance on Pv 01, 02, 03, and 07, and 12 SNPs with HG Type 1.2.3.5.6.7 resistance on Pv 01, 03, 06, 07, 09, 10, and 11 were detected. The accuracy of genomic prediction (GP) was 0.36 to 0.49 for resistance to the three SCN HG types, indicating that genomic selection (GS) of SCN resistance is feasible. This study provides basic information for developing SCN-resistant common bean cultivars, using the USDA core germ plasm accessions. The SNP markers can be used in molecular breeding in common beans through marker-assisted selection (MAS) and GS.
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Affiliation(s)
- Ainong Shi
- Department of Horticulture, PTSC316, University of Arkansas, Fayetteville, AR, United States
| | - Paul Gepts
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Qijian Song
- United States Department of Agriculture, Agricultural Research Service, Beltsville Agricultural Research Center, Beltsville, MD, United States
| | - Haizheng Xiong
- Department of Horticulture, PTSC316, University of Arkansas, Fayetteville, AR, United States
| | - Thomas E. Michaels
- Department of Horticultural Science, University of Minnesota, St. Paul, MN, United States
| | - Senyu Chen
- Southern Research and Outreach Center, University of Minnesota, Waseca, MN, United States
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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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Nadeem MA, Yeken MZ, Shahid MQ, Habyarimana E, Yılmaz H, Alsaleh A, Hatipoğlu R, Çilesiz Y, Khawar KM, Ludidi N, Ercişli S, Aasim M, Karaköy T, Baloch FS. Common bean as a potential crop for future food security: an overview of past, current and future contributions in genomics, transcriptomics, transgenics and proteomics. BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2021.1920462] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Affiliation(s)
- Muhammad Azhar Nadeem
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Mehmet Zahit Yeken
- Department of Field Crops, Faculty of Agriculture, Bolu Abant İzzet Baysal University, Bolu, Turkey
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, PR China
| | | | - Hilal Yılmaz
- Department of Plant and Animal Production, Izmit Vocational School, Kocaeli University, Kocaeli, Turkey
| | - Ahmad Alsaleh
- Department of Food and Agriculture, Insitutue of Hemp Research, Yozgat Bozok University, 66200, Yozgat, Turkey
| | - Rüştü Hatipoğlu
- Department of Field Crops, Faculty of Agricultural, University of Cukurova, Adana, Turkey
| | - Yeter Çilesiz
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Khalid Mahmood Khawar
- Department of Field Crops, Faculty of Agriculture, Ankara University, Ankara, Turkey
| | - Ndiko Ludidi
- Department of Biotechnology and DSI-NRF Center of Excellence in Food Security, University of the Western Cape, Bellville, South Africa
| | - Sezai Ercişli
- Department of Horticulture, Faculty of Agriculture, Ataturk University, Erzurum, Turkey
| | - Muhammad Aasim
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Tolga Karaköy
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Faheem Shehzad Baloch
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
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Genome-wide association mapping reveals race-specific SNP markers associated with anthracnose resistance in carioca common beans. PLoS One 2021; 16:e0251745. [PMID: 34010322 PMCID: PMC8133444 DOI: 10.1371/journal.pone.0251745] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 04/30/2021] [Indexed: 11/24/2022] Open
Abstract
Brazil is the largest consumer of dry edible beans (Phaseolus vulgaris L.) in the world, 70% of consumption is of the carioca variety. Although the variety has high yield, it is susceptible to several diseases, among them, anthracnose (ANT) can lead to losses of up to 100% of production. The most effective strategy to overcome ANT, a disease caused by the fungus Colletotrichum lindemuthianum, is the development of resistant cultivars. For that reason, the selection of carioca genotypes resistant to multiple ANT races and the identification of loci/markers associated with genetic resistance are extremely important for the genetic breeding process. Using a carioca diversity panel (CDP) with 125 genotypes and genotyped by BeadChip BARCBean6K_3 and a carioca segregating population AM (AND-277 × IAC-Milênio) genotyped by sequencing (GBS). Multiple interval mapping (MIM) and genome-wide association studies (GWAS) were used as mapping tools for the resistance genes to the major ANT physiological races present in the country. In general, 14 single nucleotide polymorphisms (SNPs) showed high significance for resistance by GWAS, and loci associated with multiple races were also identified, as the Co-3 locus. The SNPs ss715642306 and ss715649427 in linkage disequilibrium (LD) at the beginning of chromosome Pv04 were associated with all the races used, and 16 genes known to be related to plant immunity were identified in this region. Using the resistant cultivars and the markers associated with significant quantitative resistance loci (QRL), discriminant analysis of principal components (DAPC) was performed considering the allelic contribution to resistance. Through the DAPC clustering, cultivar sources with high potential for durable anthracnose resistance were recommended. The MIM confirmed the presence of the Co-14locus in the AND-277 cultivar which revealed that it was the only one associated with resistance to ANT race 81. Three other loci were associated with race 81 on chromosomes Pv03, Pv10, and Pv11. This is the first study to identify new resistance loci in the AND-277 cultivar. Finally, the same Co-14locus was also significant for the CDP at the end of Pv01. The new SNPs identified, especially those associated with more than one race, present great potential for use in marker-assisted and early selection of inbred lines.
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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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Katuuramu DN, Wiesinger JA, Luyima GB, Nkalubo ST, Glahn RP, Cichy KA. Investigation of Genotype by Environment Interactions for Seed Zinc and Iron Concentration and Iron Bioavailability in Common Bean. FRONTIERS IN PLANT SCIENCE 2021; 12:670965. [PMID: 34040625 PMCID: PMC8141707 DOI: 10.3389/fpls.2021.670965] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 03/24/2021] [Indexed: 05/26/2023]
Abstract
Iron and zinc malnutrition are global public health concerns afflicting mostly infants, children, and women in low- and middle-income countries with widespread consumption of plant-based diets. Common bean is a widely consumed staple crop around the world and is an excellent source of protein, fiber, and minerals including iron and zinc. The development of nutrient-dense common bean varieties that deliver more bioavailable iron and zinc with a high level of trait stability requires a measurement of the contributions from genotype, environment, and genotype by environment interactions. In this research, we investigated the magnitude of genotype by environment interaction for seed zinc and iron concentration and seed iron bioavailability (FeBIO) using a set of nine test genotypes and three farmers' local check varieties. The research germplasm was evaluated for two field seasons across nine on-farm locations in three agro-ecological zones in Uganda. Seed zinc concentration ranged from 18.0 to 42.0 μg g-1 and was largely controlled by genotype, location, and the interaction between location and season [28.0, 26.2, and 14.7% of phenotypic variability explained (PVE), respectively]. Within a genotype, zinc concentration ranged on average 12 μg g-1 across environments. Seed iron concentration varied from 40.7 to 96.7 μg g-1 and was largely controlled by genotype, location, and the interaction between genotype, location, and season (25.7, 17.4, and 13.7% of PVE, respectively). Within a genotype, iron concentration ranged on average 28 μg g-1 across environments. Seed FeBIO ranged from 8 to 116% of Merlin navy control and was largely controlled by genotype (68.3% of PVE). The red mottled genotypes (Rozi Koko and Chijar) accumulated the most seed zinc and iron concentration, while the yellow (Ervilha and Cebo Cela) and white (Blanco Fanesquero) genotypes had the highest seed FeBIO and performed better than the three farmers' local check genotypes (NABE-4, NABE-15, and Masindi yellow). The genotypes with superior and stable trait performance, especially the Manteca seed class which combine high iron and zinc concentrations with high FeBIO, would serve as valuable parental materials for crop improvement breeding programs aimed at enhancing the nutritional value of the common bean.
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Affiliation(s)
- Dennis N. Katuuramu
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
- USDA – ARS, U.S. Vegetable Laboratory, Charleston, SC, United States
| | - Jason A. Wiesinger
- USDA – ARS, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, United States
| | - Gabriel B. Luyima
- Legumes Research Program, National Crops Resources Research Institute, Kampala, Uganda
| | - Stanley T. Nkalubo
- Legumes Research Program, National Crops Resources Research Institute, Kampala, Uganda
| | - Raymond P. Glahn
- USDA – ARS, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, United States
| | - Karen A. Cichy
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
- USDA – ARS, Sugarbeet and Bean Research Unit, East Lansing, MI, United States
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32
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Richard MMS, Gratias A, Alvarez Diaz JC, Thareau V, Pflieger S, Meziadi C, Blanchet S, Marande W, Bitocchi E, Papa R, Miklas PN, Geffroy V. A common bean truncated CRINKLY4 kinase controls gene-for-gene resistance to the fungus Colletotrichum lindemuthianum. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:3569-3581. [PMID: 33693665 DOI: 10.1093/jxb/erab082] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 03/05/2021] [Indexed: 05/27/2023]
Abstract
Identifying the molecular basis of resistance to pathogens is critical to promote a chemical-free cropping system. In plants, nucleotide-binding leucine-rich repeat constitute the largest family of disease resistance (R) genes, but this resistance can be rapidly overcome by the pathogen, prompting research into alternative sources of resistance. Anthracnose, caused by the fungus Colletotrichum lindemuthianum, is one of the most important diseases of common bean. This study aimed to identify the molecular basis of Co-x, an anthracnose R gene conferring total resistance to the extremely virulent C. lindemuthianum strain 100. To that end, we sequenced the Co-x 58 kb target region in the resistant JaloEEP558 (Co-x) common bean and identified KTR2/3, an additional gene encoding a truncated and chimeric CRINKLY4 kinase, located within a CRINKLY4 kinase cluster. The presence of KTR2/3 is strictly correlated with resistance to strain 100 in a diversity panel of common beans. Furthermore, KTR2/3 expression is up-regulated 24 hours post-inoculation and its transient expression in a susceptible genotype increases resistance to strain 100. Our results provide evidence that Co-x encodes a truncated and chimeric CRINKLY4 kinase probably resulting from an unequal recombination event that occurred recently in the Andean domesticated gene pool. This atypical R gene may act as a decoy involved in indirect recognition of a fungal effector.
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Affiliation(s)
- Manon M S Richard
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris Saclay (IPS2), Orsay, France
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences (SILS), University of Amsterdam, Amsterdam, The Netherlands
| | - Ariane Gratias
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris Saclay (IPS2), Orsay, France
| | - Juan C Alvarez Diaz
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris Saclay (IPS2), Orsay, France
| | - Vincent Thareau
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris Saclay (IPS2), Orsay, France
| | - Stéphanie Pflieger
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris Saclay (IPS2), Orsay, France
| | - Chouaib Meziadi
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris Saclay (IPS2), Orsay, France
| | - Sophie Blanchet
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris Saclay (IPS2), Orsay, France
| | | | - Elena Bitocchi
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Ancona, Italy
| | - Roberto Papa
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Ancona, Italy
| | - Phillip N Miklas
- USDA ARS, Grain Legume Genet & Physiol Res Unit, Prosser, WA, USA
| | - Valérie Geffroy
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris Saclay (IPS2), Orsay, France
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González AM, Vander Schoor JK, Fang C, Kong F, Wu J, Weller JL, Santalla M. Ancient relaxation of an obligate short-day requirement in common bean through loss of CONSTANS-like gene function. Curr Biol 2021; 31:1643-1652.e2. [PMID: 33609454 DOI: 10.1016/j.cub.2021.01.075] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 01/18/2021] [Accepted: 01/21/2021] [Indexed: 01/24/2023]
Abstract
Common bean (Phaseolus vulgaris L.) is a major global food staple and source of dietary protein that was domesticated independently in Mexico and Andean South America. Its subsequent development as a crop of importance worldwide has been enabled by genetic relaxation of the strict short-day requirement typical of wild forms, but the genetic basis for this change is not well understood. Recently, a loss of photoperiod sensitivity was shown to result from mutations in the phytochrome photoreceptor gene Ppd/PHYA3 that arose independently within the two major domesticated lineages. Here, we define a second major photoperiod sensitivity locus, at which recessive alleles associate with deleterious mutations affecting the CONSTANS-like gene COL2. A wider survey of sequence variation in over 800 diverse lines, including wild, landrace, and domesticated accessions, show that distinct col2 haplotypes are associated with early flowering in Andean and Mesoamerican germplasm. The relative frequencies and distributions of COL2 and PHYA3 haplotypes imply that photoperiod adaptation developed in two phases within each gene pool: an initial reduction in sensitivity through impairment of COL2 function and subsequent complete loss through PHYA3. Gene expression analyses indicate that COL2 functions downstream of PHYA3 to repress expression of FT genes and may function in parallel with PvE1, the bean ortholog of a key legume-specific flowering repressor. Collectively, these results define the molecular basis for a key phenological adaptation, reveal a striking convergence in the naturally replicated evolution of this major crop, and further emphasize the wider evolutionary lability of CONSTANS effects on flowering time control.
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Affiliation(s)
- Ana M González
- Grupo de Genética del Desarrollo de Plantas, Misión Biológica de Galicia-CSIC, PO Box 28, 36080 Pontevedra, Spain
| | | | - Chao Fang
- Innovation Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Fanjiang Kong
- Innovation Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Jing Wu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - James L Weller
- School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, TAS 7001, Australia.
| | - Marta Santalla
- Grupo de Genética del Desarrollo de Plantas, Misión Biológica de Galicia-CSIC, PO Box 28, 36080 Pontevedra, Spain.
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Parker TA, Lo S, Gepts P. Pod shattering in grain legumes: emerging genetic and environment-related patterns. THE PLANT CELL 2021; 33:179-199. [PMID: 33793864 PMCID: PMC8136915 DOI: 10.1093/plcell/koaa025] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 11/26/2020] [Indexed: 05/25/2023]
Abstract
A reduction in pod shattering is one of the main components of grain legume domestication. Despite this, many domesticated legumes suffer serious yield losses due to shattering, particularly under arid conditions. Mutations related to pod shattering modify the twisting force of pod walls or the structural strength of the dehiscence zone in pod sutures. At a molecular level, a growing body of evidence indicates that these changes are controlled by a relatively small number of key genes that have been selected in parallel across grain legume species, supporting partial molecular convergence. Legume homologs of Arabidopsis thaliana silique shattering genes play only minor roles in legume pod shattering. Most domesticated grain legume species contain multiple shattering-resistance genes, with mutants of each gene typically showing only partial shattering resistance. Hence, crosses between varieties with different genes lead to transgressive segregation of shattering alleles, producing plants with either enhanced shattering resistance or atavistic susceptibility to the trait. The frequency of these resistance pod-shattering alleles is often positively correlated with environmental aridity. The continued development of pod-shattering-related functional information will be vital for breeding crops that are suited to the increasingly arid conditions expected in the coming decades.
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Affiliation(s)
- Travis A Parker
- Department of Plant Sciences/MS1, Section of Crop & Ecosystem Sciences, University of California, 1 Shields Avenue, Davis, CA 95616-8780
| | - Sassoum Lo
- Department of Plant Sciences/MS1, Section of Crop & Ecosystem Sciences, University of California, 1 Shields Avenue, Davis, CA 95616-8780
| | - Paul Gepts
- Department of Plant Sciences/MS1, Section of Crop & Ecosystem Sciences, University of California, 1 Shields Avenue, Davis, CA 95616-8780
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35
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Rodríguez Madrera R, Campa Negrillo A, Suárez Valles B, Ferreira Fernández JJ. Phenolic Content and Antioxidant Activity in Seeds of Common Bean ( Phaseolus vulgaris L.). Foods 2021; 10:foods10040864. [PMID: 33921060 PMCID: PMC8071416 DOI: 10.3390/foods10040864] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/09/2021] [Accepted: 04/13/2021] [Indexed: 01/20/2023] Open
Abstract
Dry bean (Phaseolus vulgaris L.) is one of the most important pulses consumed in the world. Total phenolic content, total flavonoid content, total monomeric anthocyanin content and antioxidant capacity were determined, using ferric reducing antioxidant power and free radical scavenging activity, in 255 lines grown under the same environmental conditions. For all parameters analysed, there was a wide range of variability, with differences always above one order of magnitude. Phenolic compounds in beans with coloured coats were found to be more efficient antioxidants than those with completely white coats, and samples with more strongly coloured coats (red, cream, black, pink and brown) showed the highest antioxidant capacities. Based on the strong correlation detected between the variables, total phenolic content can be considered an appropriate indicator of antioxidant activity. The results provide a robust database for selecting those lines of greater functional and nutritional interest in terms of cultivation for direct consumption, for inclusions in food formulations or for use in future breeding programs.
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Affiliation(s)
- Roberto Rodríguez Madrera
- Área de Tecnología de los Alimentos, Regional Agrifood Research and Development Service (SERIDA), E-33300 Villaviciosa, Asturias, Spain;
- Correspondence: ; Tel.: +34-985890066
| | - Ana Campa Negrillo
- Área de Cultivos Hortofrutícolas y Forestales, Regional Agrifood Research and Development Service (SERIDA), E-33300 Villaviciosa, Asturias, Spain; (A.C.N.); (J.J.F.F.)
| | - Belén Suárez Valles
- Área de Tecnología de los Alimentos, Regional Agrifood Research and Development Service (SERIDA), E-33300 Villaviciosa, Asturias, Spain;
| | - Juan José Ferreira Fernández
- Área de Cultivos Hortofrutícolas y Forestales, Regional Agrifood Research and Development Service (SERIDA), E-33300 Villaviciosa, Asturias, Spain; (A.C.N.); (J.J.F.F.)
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de Almeida CP, de Carvalho Paulino JF, Bonfante GFJ, Perseguini JMKC, Santos IL, Gonçalves JGR, Patrício FRA, Taniguti CH, Gesteira GDS, Garcia AAF, Song Q, Carbonell SAM, Chiorato AF, Benchimol-Reis LL. Angular Leaf Spot Resistance Loci Associated With Different Plant Growth Stages in Common Bean. FRONTIERS IN PLANT SCIENCE 2021; 12:647043. [PMID: 33927738 PMCID: PMC8078856 DOI: 10.3389/fpls.2021.647043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 03/23/2021] [Indexed: 06/12/2023]
Abstract
Angular leaf spot (ALS) is a disease that causes major yield losses in the common bean crop. Studies based on different isolates and populations have already been carried out to elucidate the genetic mechanisms of resistance to ALS. However, understanding of the interaction of this resistance with the reproductive stages of common bean is lacking. The aim of the present study was to identify ALS resistance loci at different plant growth stages (PGS) by association and linkage mapping approaches. An BC2F3 inter-gene pool cross population (AND 277 × IAC-Milênio - AM population) profiled with 1,091 SNPs from genotyping by sequencing (GBS) was used for linkage mapping, and a carioca diversity panel (CDP) genotyped by 5,398 SNPs from BeadChip assay technology was used for association mapping. Both populations were evaluated for ALS resistance at the V2 and V3 PGSs (controlled conditions) and R8 PGS (field conditions). Different QTL (quantitative trait loci) were detected for the three PGSs and both populations, showing a different quantitative profile of the disease at different plant growth stages. For the three PGS, multiple interval mapping (MIM) identified seven significant QTL, and the Genome-wide association study (GWAS) identified fourteen associate SNPs. Several loci validated regions of previous studies, and Phg-1, Phg-2, Phg-4, and Phg-5, among the 5 loci of greatest effects reported in the literature, were detected in the CDP. The AND 277 cultivar contained both the Phg-1 and the Phg-5 QTL, which is reported for the first time in the descendant cultivar CAL143 as ALS10.1UC. The novel QTL named ALS11.1AM was located at the beginning of chromosome Pv11. Gene annotation revealed several putative resistance genes involved in the ALS response at the three PGSs, and with the markers and loci identified, new specific molecular markers can be developed, representing a powerful tool for common bean crop improvement and for gain in ALS resistance.
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Affiliation(s)
| | | | | | | | - Isabella Laporte Santos
- Centro de Pesquisa em Recursos Genéticos Vegetais, Instituto Agronômico - IAC, Campinas, Brazil
| | | | | | - Cristiane Hayumi Taniguti
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Piracicaba, Brazil
| | - Gabriel de Siqueira Gesteira
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Piracicaba, Brazil
| | - Antônio Augusto Franco Garcia
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Piracicaba, Brazil
| | - Qijian Song
- USDA-ARS, Soybean Genomics and Improvement Lab, Beltsville, MD, United States
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Ángel Martín-Rodríguez J, Ariani A, Leija A, Elizondo A, Fuentes SI, Ramirez M, Gepts P, Hernández G, Formey D. Phaseolus vulgaris MIR1511 genotypic variations differentially regulate plant tolerance to aluminum toxicity. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:1521-1533. [PMID: 33300202 DOI: 10.1111/tpj.15129] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 11/20/2020] [Accepted: 12/03/2020] [Indexed: 05/28/2023]
Abstract
The common-bean (Phaseolus vulgaris), a widely consumed legume, originated in Mesoamerica and expanded to South America, resulting in the development of two geographically distinct gene pools. Poor soil condition, including metal toxicity, are often constraints to common-bean crop production. Several P. vulgaris miRNAs, including miR1511, respond to metal toxicity. The MIR1511 gene sequence from the two P. vulgaris model sequenced genotypes revealed that, as opposed to BAT93 (Mesoamerican), the G19833 (Andean) accession displays a 58-bp deletion, comprising the mature and star miR1511 sequences. Genotyping-By-Sequencing data analysis from 87 non-admixed Phaseolus genotypes, comprising different Phaseolus species and P. vulgaris populations, revealed that all the P. vulgaris Andean genotypes and part of the Mesoamerican (MW1) genotypes analyzed displayed a truncated MIR1511 gene. The geographic origin of genotypes with a complete versus truncated MIR1511 showed a distinct distribution. The P. vulgaris ALS3 (Aluminum Sensitive Protein 3) gene, known to be important for aluminum detoxification in several plants, was experimentally validated as the miR1511 target. Roots from BAT93 plants showed decreased miR1511 and increased ALS3 transcript levels at early stages under aluminum toxicity (AlT), while G19833 plants, lacking mature miR1511, showed higher and earlier ALS3 response. Root architecture analyses evidenced higher tolerance of G19833 plants to AlT. However, G19833 plants engineered for miR1511 overexpression showed lower ALS3 transcript level and increased sensitivity to AlT. Absence of miR1511 in Andean genotypes, resulting in a diminished ALS3 transcript degradation, appears to be an evolutionary advantage to high Al levels in soils with increased drought conditions.
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Affiliation(s)
| | - Andrea Ariani
- Department of Plant Sciences, Section of Crop and Ecosystem Sciences, University of California, Davis, CA, USA
| | - Alfonso Leija
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Armando Elizondo
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Sara I Fuentes
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Mario Ramirez
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Paul Gepts
- Department of Plant Sciences, Section of Crop and Ecosystem Sciences, University of California, Davis, CA, USA
| | - Georgina Hernández
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Damien Formey
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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Di Vittori V, Bitocchi E, Rodriguez M, Alseekh S, Bellucci E, Nanni L, Gioia T, Marzario S, Logozzo G, Rossato M, De Quattro C, Murgia ML, Ferreira JJ, Campa A, Xu C, Fiorani F, Sampathkumar A, Fröhlich A, Attene G, Delledonne M, Usadel B, Fernie AR, Rau D, Papa R. Pod indehiscence in common bean is associated with the fine regulation of PvMYB26. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:1617-1633. [PMID: 33247939 PMCID: PMC7921299 DOI: 10.1093/jxb/eraa553] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 11/22/2020] [Indexed: 05/25/2023]
Abstract
In legumes, pod shattering occurs when mature pods dehisce along the sutures, and detachment of the valves promotes seed dispersal. In Phaseolus vulgaris (L)., the major locus qPD5.1-Pv for pod indehiscence was identified recently. We developed a BC4/F4 introgression line population and narrowed the major locus down to a 22.5 kb region. Here, gene expression and a parallel histological analysis of dehiscent and indehiscent pods identified an AtMYB26 orthologue as the best candidate for loss of pod shattering, on a genomic region ~11 kb downstream of the highest associated peak. Based on mapping and expression data, we propose early and fine up-regulation of PvMYB26 in dehiscent pods. Detailed histological analysis establishes that pod indehiscence is associated with the lack of a functional abscission layer in the ventral sheath, and that the key anatomical modifications associated with pod shattering in common bean occur early during pod development. We finally propose that loss of pod shattering in legumes resulted from histological convergent evolution and that it is the result of selection at orthologous loci.
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Affiliation(s)
- Valerio Di Vittori
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università Politecnica delle Marche, via Brecce Bianche, Ancona, Italy
- Max Planck Institute of Molecular Plant Physiology, Am Müehlenberg, Potsdam-Golm, Germany
| | - Elena Bitocchi
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università Politecnica delle Marche, via Brecce Bianche, Ancona, Italy
| | - Monica Rodriguez
- Dipartimento di Agraria, Università degli Studi di Sassari, Via E. De Nicola, Sassari, Italy
- Centro per la Conservazione e Valorizzazione della Biodiversità Vegetale, Università degli Studi di Sassari, SS 127bis, km 28.500 Surigheddu, Alghero, Italy
| | - Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, Am Müehlenberg, Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
| | - Elisa Bellucci
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università Politecnica delle Marche, via Brecce Bianche, Ancona, Italy
| | - Laura Nanni
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università Politecnica delle Marche, via Brecce Bianche, Ancona, Italy
| | - Tania Gioia
- Scuola di Scienze Agrarie, Forestali, Alimentari ed Ambientali, Università degli Studi della Basilicata, viale dell’Ateneo Lucano, Potenza, Italy
| | - Stefania Marzario
- Scuola di Scienze Agrarie, Forestali, Alimentari ed Ambientali, Università degli Studi della Basilicata, viale dell’Ateneo Lucano, Potenza, Italy
| | - Giuseppina Logozzo
- Scuola di Scienze Agrarie, Forestali, Alimentari ed Ambientali, Università degli Studi della Basilicata, viale dell’Ateneo Lucano, Potenza, Italy
| | - Marzia Rossato
- Dipartimento di Biotecnologie, Università degli Studi di Verona, Cà Vignal, Strada Le Grazie, Verona, Italy
| | - Concetta De Quattro
- Dipartimento di Biotecnologie, Università degli Studi di Verona, Cà Vignal, Strada Le Grazie, Verona, Italy
| | - Maria L Murgia
- Dipartimento di Agraria, Università degli Studi di Sassari, Via E. De Nicola, Sassari, Italy
| | - Juan José Ferreira
- Plant Genetics Group, Agri-Food Research and Development Regional Service (SERIDA), Asturias, Spain
| | - Ana Campa
- Plant Genetics Group, Agri-Food Research and Development Regional Service (SERIDA), Asturias, Spain
| | - Chunming Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Fabio Fiorani
- Institute of Biosciences and Geosciences (IBG-2): Plant Sciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Arun Sampathkumar
- Max Planck Institute of Molecular Plant Physiology, Am Müehlenberg, Potsdam-Golm, Germany
| | - Anja Fröhlich
- Max Planck Institute of Molecular Plant Physiology, Am Müehlenberg, Potsdam-Golm, Germany
| | - Giovanna Attene
- Dipartimento di Agraria, Università degli Studi di Sassari, Via E. De Nicola, Sassari, Italy
- Centro per la Conservazione e Valorizzazione della Biodiversità Vegetale, Università degli Studi di Sassari, SS 127bis, km 28.500 Surigheddu, Alghero, Italy
| | - Massimo Delledonne
- Dipartimento di Biotecnologie, Università degli Studi di Verona, Cà Vignal, Strada Le Grazie, Verona, Italy
| | - Björn Usadel
- Institute of Biosciences and Geosciences (IBG-2): Plant Sciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Müehlenberg, Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
| | - Domenico Rau
- Dipartimento di Agraria, Università degli Studi di Sassari, Via E. De Nicola, Sassari, Italy
| | - Roberto Papa
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università Politecnica delle Marche, via Brecce Bianche, Ancona, Italy
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Delfini J, Moda-Cirino V, dos Santos Neto J, Ruas PM, Sant’Ana GC, Gepts P, Gonçalves LSA. Population structure, genetic diversity and genomic selection signatures among a Brazilian common bean germplasm. Sci Rep 2021; 11:2964. [PMID: 33536468 PMCID: PMC7859210 DOI: 10.1038/s41598-021-82437-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 01/07/2021] [Indexed: 01/30/2023] Open
Abstract
Brazil is the world's largest producer of common bean. Knowledge of the genetic diversity and relatedness of accessions adapted to Brazilian conditions is of great importance for the conservation of germplasm and for directing breeding programs aimed at the development of new cultivars. In this context, the objective of this study was to analyze the genetic diversity, population structure, and linkage disequilibrium (LD) of a diversity panel consisting of 219 common bean accessions, most of which belonging to the Mesoamerican gene pool. Genotyping by sequencing (GBS) of these accessions allowed the identification of 49,817 SNPs with minor allele frequency > 0.05. Of these, 17,149 and 12,876 were exclusive to the Mesoamerican and Andean pools, respectively, and 11,805 SNPs could differentiate the two gene pools. Further the separation according to the gene pool, bayesian analysis of the population structure showed a subdivision of the Mesoamerican accessions based on the origin and color of the seed tegument. LD analysis revealed the occurrence of long linkage blocks and low LD decay with physical distance between SNPs (LD half decay in 249 kb, corrected for population structure and relatedness). The GBS technique could effectively characterize the Brazilian common bean germplasms, and the diversity panel used in this study may be of great use in future genome-wide association studies.
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Affiliation(s)
- Jessica Delfini
- grid.411400.00000 0001 2193 3537Agronomy Department, Universidade Estadual de Londrina (UEL), Londrina, 86051-900 Brazil ,Plant Breeding, Instituto de Desenvolvimento Rural do Paraná-Iapar-Emater (IDR-Paraná), Londrina, 86047-902 Brazil
| | - Vânia Moda-Cirino
- Plant Breeding, Instituto de Desenvolvimento Rural do Paraná-Iapar-Emater (IDR-Paraná), Londrina, 86047-902 Brazil
| | - José dos Santos Neto
- grid.411400.00000 0001 2193 3537Agronomy Department, Universidade Estadual de Londrina (UEL), Londrina, 86051-900 Brazil ,Plant Breeding, Instituto de Desenvolvimento Rural do Paraná-Iapar-Emater (IDR-Paraná), Londrina, 86047-902 Brazil
| | - Paulo Maurício Ruas
- grid.411400.00000 0001 2193 3537Biology Department, Universidade Estadual de Londrina (UEL), Londrina, 86051-900 Brazil
| | | | - Paul Gepts
- grid.27860.3b0000 0004 1936 9684Section of Crop and Ecosystem Sciences, Department of Plant Sciences, University of California, Davis, 95616-8780 USA
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Larranaga N, van Zonneveld M, Hormaza JI. Holocene land and sea-trade routes explain complex patterns of pre-Columbian crop dispersion. THE NEW PHYTOLOGIST 2021; 229:1768-1781. [PMID: 33089900 DOI: 10.1111/nph.16936] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 09/06/2020] [Indexed: 05/17/2023]
Abstract
Pre-Columbian crop movement remains poorly understood, hampering a good interpretation of the domestication and diversification of Neotropical crops. To provide new insights into pre-Columbian crop movement, we applied spatial genetics to identify and compare dispersal routes of three American crops between Mesoamerica and the Andes, two important centres of pre-Columbian crop and cultural diversity. Our analysis included georeferenced simple-sequence repeats (SSR) marker datasets of 1852 genotypes of cherimoya (Annona cherimola Mill.), a perennial fruit crop that became underutilised in the Americas after the European conquest, 770 genotypes of maize (Zea mays L.) and 476 genotypes of common bean (Phaseolus vulgaris L.). Our findings show that humans brought cherimoya from Mesoamerica to present Peru through long-distance sea-trade routes across the Pacific Ocean at least 4700 yr bp, after more ancient dispersion of maize and other crops through the Mesoamerican isthmus over land and near-coastal waters. To our knowledge, this is the first evidence of pre-Columbian crop movement between Mesoamerica and the Andes across the Pacific Ocean providing new insights into pre-Columbian crop exchange in the Americas. We propose that cherimoya represents a wider group of perennial fruit crops dispersed by humans via sea-trade routes between Mesoamerica and the Andes across the Pacific Ocean.
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Affiliation(s)
- Nerea Larranaga
- Instituto de Hortofruticultura Subtropical y Mediterranea La Mayora (IHSM La Mayora - CSIC - UMA), Algarrobo, 29750, Spain
- IMAREFI, University of Guadalajara, Jalisco, 45110, México
| | - Maarten van Zonneveld
- Genetic Resources and Seed Unit, World Vegetable Center, Shanhua, 74151, Taiwan
- Bioversity International, Turrialba, Costa Rica, 7170, Spain
| | - Jose I Hormaza
- Instituto de Hortofruticultura Subtropical y Mediterranea La Mayora (IHSM La Mayora - CSIC - UMA), Algarrobo, 29750, Spain
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Burgarella C, Berger A, Glémin S, David J, Terrier N, Deu M, Pot D. The Road to Sorghum Domestication: Evidence From Nucleotide Diversity and Gene Expression Patterns. FRONTIERS IN PLANT SCIENCE 2021; 12:666075. [PMID: 34527004 PMCID: PMC8435843 DOI: 10.3389/fpls.2021.666075] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 07/20/2021] [Indexed: 05/17/2023]
Abstract
Native African cereals (sorghum, millets) ensure food security to millions of low-income people from low fertility and drought-prone regions of Africa and Asia. In spite of their agronomic importance, the genetic bases of their phenotype and adaptations are still not well-understood. Here we focus on Sorghum bicolor, which is the fifth cereal worldwide for grain production and constitutes the staple food for around 500 million people. We leverage transcriptomic resources to address the adaptive consequences of the domestication process. Gene expression and nucleotide variability were analyzed in 11 domesticated and nine wild accessions. We documented a downregulation of expression and a reduction of diversity both in nucleotide polymorphism (30%) and gene expression levels (18%) in domesticated sorghum. These findings at the genome-wide level support the occurrence of a global reduction of diversity during the domestication process, although several genes also showed patterns consistent with the action of selection. Nine hundred and forty-nine genes were significantly differentially expressed between wild and domesticated gene pools. Their functional annotation points to metabolic pathways most likely contributing to the sorghum domestication syndrome, such as photosynthesis and auxin metabolism. Coexpression network analyzes revealed 21 clusters of genes sharing similar expression patterns. Four clusters (totaling 2,449 genes) were significantly enriched in differentially expressed genes between the wild and domesticated pools and two were also enriched in domestication and improvement genes previously identified in sorghum. These findings reinforce the evidence that the combined and intricated effects of the domestication and improvement processes do not only affect the behaviors of a few genes but led to a large rewiring of the transcriptome. Overall, these analyzes pave the way toward the identification of key domestication genes valuable for genetic resources characterization and breeding purposes.
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Affiliation(s)
- Concetta Burgarella
- CIRAD, UMR AGAP Institut, Montpellier, France
- AGAP Institut, Univ F-34398 Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- *Correspondence: Concetta Burgarella
| | - Angélique Berger
- CIRAD, UMR AGAP Institut, Montpellier, France
- AGAP Institut, Univ F-34398 Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Sylvain Glémin
- CNRS, Univ. Rennes, ECOBIO – UMR 6553, Rennes, France
- Department of Ecology and Evolution, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Jacques David
- AGAP Institut, Univ F-34398 Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Nancy Terrier
- AGAP Institut, Univ F-34398 Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Monique Deu
- CIRAD, UMR AGAP Institut, Montpellier, France
- AGAP Institut, Univ F-34398 Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - David Pot
- CIRAD, UMR AGAP Institut, Montpellier, France
- AGAP Institut, Univ F-34398 Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- David Pot
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Parker TA, de Sousa LL, de Oliveira Floriani T, Palkovic A, Gepts P. Toward the introgression of PvPdh1 for increased resistance to pod shattering in common bean. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:313-325. [PMID: 33130953 DOI: 10.1007/s00122-020-03698-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 09/29/2020] [Indexed: 06/11/2023]
Abstract
A common bean shattering-resistance allele of PvPdh1 reduces pod twists during dehiscence, shows dominance that varies by phenotyping method, is part of a selective sweep, and can be introgressed using CAPS markers. Some varieties of common bean (Phaseolus vulgaris L.) suffer from pod shattering, which can severely reduce yields, especially in arid conditions. The PvPdh1 locus on chromosome Pv03 has recently been described as a major locus controlling pod shattering in common bean and could be used to mitigate pod shattering in the future. Despite this, the role of a possible second locus on chromosome Pv08 remains unclear and patterns of dominance and epistasis between alleles of these genes have not been resolved. This information will be vital for efficient selection to decrease pod shattering. Further, the genetic diversity around the PvPdh1 gene has not yet been thoroughly explored, and there are not yet genetic screens that can be used to evaluate pod shattering in segregating populations. Here, we have developed a recombinant inbred population to determine the roles of genes implicated in pod shattering and evaluate the patterns of dominance among the relevant alleles. Our results suggest that a PvPdh1 allele reduces pod valve twisting, and its dominance varies by phenotyping method. This allele is the only genetic variant that provides environmentally stable and widespread resistance to pod shattering in Middle American common beans grown for grain. Further analyses identified a selective sweep around PvPdh1 with greater nucleotide diversity in individuals with the ancestral, shattering-susceptible allele. Finally, we developed simple, effective CAPS markers to facilitate the introgression of PvPdh1 into new varieties of common bean. These genetic resources will be critical for improving the aridity resilience of a major global staple.
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Affiliation(s)
- Travis A Parker
- Department of Plant Sciences / MS1, Section of Crop & Ecosystem Sciences, 1 Shields Avenue, Davis, CA, 95616-8780, USA
| | - Lorenna Lopes de Sousa
- Department of Plant Sciences / MS1, Section of Crop & Ecosystem Sciences, 1 Shields Avenue, Davis, CA, 95616-8780, USA
| | - Talissa de Oliveira Floriani
- Department of Plant Sciences / MS1, Section of Crop & Ecosystem Sciences, 1 Shields Avenue, Davis, CA, 95616-8780, USA
| | - Antonia Palkovic
- Department of Plant Sciences / MS1, Section of Crop & Ecosystem Sciences, 1 Shields Avenue, Davis, CA, 95616-8780, USA
| | - Paul Gepts
- Department of Plant Sciences / MS1, Section of Crop & Ecosystem Sciences, 1 Shields Avenue, Davis, CA, 95616-8780, USA.
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de Almeida CP, Paulino JFDC, Morais Carbonell SA, Chiorato AF, Song Q, Di Vittori V, Rodriguez M, Papa R, Benchimol-Reis LL. Genetic Diversity, Population Structure, and Andean Introgression in Brazilian Common Bean Cultivars after Half a Century of Genetic Breeding. Genes (Basel) 2020; 11:E1298. [PMID: 33143347 PMCID: PMC7694079 DOI: 10.3390/genes11111298] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 10/27/2020] [Accepted: 10/28/2020] [Indexed: 12/29/2022] Open
Abstract
Brazil is the largest consumer and third highest producer of common beans (Phaseolus vulgaris L.) worldwide. Since the 1980s, the commercial Carioca variety has been the most consumed in Brazil, followed by Black and Special beans. The present study evaluates genetic diversity and population structure of 185 Brazilian common bean cultivars using 2827 high-quality single-nucleotide polymorphisms (SNPs). The Andean allelic introgression in the Mesoamerican accessions was investigated, and a Carioca panel was tested using an association mapping approach. The results distinguish the Mesoamerican from the Andean accessions, with a prevalence of Mesoamerican accessions (94.6%). When considering the commercial classes, low levels of genetic differentiation were seen, and the Carioca group showed the lowest genetic diversity. However, gain in gene diversity and allelic richness was seen for the modern Carioca cultivars. A set of 1060 'diagnostic SNPs' that show alternative alleles between the pure Mesoamerican and Andean accessions were identified, which allowed the identification of Andean allelic introgression events and shows that there are putative introgression segments in regions enriched with resistance genes. Finally, genome-wide association studies revealed SNPs significantly associated with flowering time, pod maturation, and growth habit, showing that the Carioca Association Panel represents a powerful tool for crop improvements.
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Affiliation(s)
- Caléo Panhoca de Almeida
- Centro de Pesquisa em Recursos Genéticos Vegetais, Instituto Agronômico (IAC), Campinas, São Paulo 13075-630, Brazil; (J.F.d.C.P.); (L.L.B.-R.)
| | - Jean Fausto de Carvalho Paulino
- Centro de Pesquisa em Recursos Genéticos Vegetais, Instituto Agronômico (IAC), Campinas, São Paulo 13075-630, Brazil; (J.F.d.C.P.); (L.L.B.-R.)
| | | | - Alisson Fernando Chiorato
- Centro de Grãos e Fibras, Instituto Agronômico (IAC), Campinas, São Paulo 13075-630, Brazil; (S.A.M.C.); (A.F.C.)
| | - Qijian Song
- Soybean Genomics and Improvement Laboratory, US Department of Agriculture–Agricultural Research Service (USDA-ARS), Beltsville, MD 20705, USA;
| | - Valerio Di Vittori
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica dele Marche, 60131 Ancona, Italy; (V.D.V.); (R.P.)
- Max-Planck-Institute of Molecular Plant Physiology, Am Müehlenberg 1, 14476 Potsdam-Golm, Germany
| | - Monica Rodriguez
- Dipartimento di Agraria, Università degli Studi di Sassari, 07100 Sassari, Italy;
- Centro per la Cobservazione e Valorizzazione della Biodiversità Vegetale (CBV), Università degli Studi di Sassari, 07040 Alghero, Italy
| | - Roberto Papa
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica dele Marche, 60131 Ancona, Italy; (V.D.V.); (R.P.)
| | - Luciana Lasry Benchimol-Reis
- Centro de Pesquisa em Recursos Genéticos Vegetais, Instituto Agronômico (IAC), Campinas, São Paulo 13075-630, Brazil; (J.F.d.C.P.); (L.L.B.-R.)
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Banoo A, Nabi A, Rasool RS, Mahiya-Farooq, Shah MD, Ahmad M, Sofi PA, Aasiya-Nabi, Itoo H, Sharma PN, Padder BA. North-Western Himalayan Common Beans: Population Structure and Mapping of Quantitative Anthracnose Resistance Through Genome Wide Association Study. FRONTIERS IN PLANT SCIENCE 2020; 11:571618. [PMID: 33123180 PMCID: PMC7573075 DOI: 10.3389/fpls.2020.571618] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 09/04/2020] [Indexed: 08/31/2023]
Abstract
Common bean (Phaseolus vulgaris L.) is an important legume crop of north-western (NW) Himalayan region and the major disease that causes catastrophic loss to the crop is anthracnose, which is caused by Colletotrichum lindemuthianum. The pathogen is highly diverse and most of the commercial cultivars are susceptible to different races prevalent in the region. The lack of information on the genomic regions associated with anthracnose resistance in NW Himalayan common bean population prompted us to dissect Quantitative Resistance Loci (QRLs) against major anthracnose races. In this study, 188 common bean landraces collected from NW region were screened against five important anthracnose races and 113 bean genotypes showed resistance to one or multiple races. Genotyping by sequencing (GBS) was performed on a panel of 192 bean lines (4 controls plus 188 Indian beans) and 22,589 SNPs were obtained that are evenly distributed. Population structure analysis of 192 bean genotypes categorized 188 Indian beans into two major clusters representing Andean and Mesoamerican gene pools with obvious admixtures. Many QRLs associated with anthracnose resistance to Indian C. lindemuthianum virulences (race 3, 87, and 503) are located at Pv04 within the gene models that encode typical resistance gene signatures. The QRLs associated with race 73 are located on Pv08 and overlaps with Co-4 anthracnose resistance gene. A SNP located at distal end of Pv11 in a gene model Phvul.011G202300 which encodes a LRR with a typical NB-ARC domain showed association with race 73 resistance. Common bean genomic regions located at Pv03, Pv09, and Pv11 showed association with resistance to anthracnose race 2047. The present study showed presence of many novel bean genomic regions associated with anthracnose resistance. The presence of Co-4 and Co-2 genes in our material is encouraging for breeding durable anthracnose resistant cultivars for the region.
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Affiliation(s)
- Aqleema Banoo
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Srinagar, India
| | - Asha Nabi
- Directorate of Extension, SKUAST-Kashmir, Srinagar, India
| | - Rovidha S. Rasool
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Srinagar, India
| | - Mahiya-Farooq
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Srinagar, India
| | - Mehraj D. Shah
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Srinagar, India
| | - Mushtaq Ahmad
- Directorate of Extension, SKUAST-Kashmir, Srinagar, India
| | - Parvaze A. Sofi
- Division of Genetics and Plant Breeding, Faculty of Agriculture, SKUAST-Kashmir, Wadura, India
| | - Aasiya-Nabi
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Srinagar, India
| | - Hamidullah Itoo
- Ambri Apple Research Centre, SKUAST-Kashmir, Srinagar, India
| | - P. N. Sharma
- Department of Plant Pathology, CSK HPKV, Palampur, India
| | - Bilal A. Padder
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Srinagar, India
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Characterization of extractable phenolic profile of common bean seeds (Phaseolus vulgaris L.) in a Spanish diversity panel. Food Res Int 2020; 138:109713. [PMID: 33292961 DOI: 10.1016/j.foodres.2020.109713] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 08/31/2020] [Accepted: 09/07/2020] [Indexed: 11/21/2022]
Abstract
Phenolic compounds are important bioactive compounds in common bean (Phaseolus vulgaris L.). The aim of this work was the characterization of extractable phenolic profile (corresponding to 12 hydroxycinnamic acids and derivatives, 13 anthocyanins and 15 flavonols) in a bean diversity panel constituted by 220 lines, all grown under the same environmental conditions. Hydroxycinnamic derivatives were detected in all samples, while anthocyanins and flavonols were not detected in samples with completely white seed coats. In general, lines with black seeds showed higher contents of anthocyanins, followed by some red-seeded lines, while notable levels of flavonols were detected in market classes, including those with yellow, pink, and cream seed coats. However, a clear relationship between phenolic composition and seed phenotype could not be established, indicating the great influence of the genotype. This wide variability in the phenolic profiles analyzed is of particular interest for further breeding trials and the selection of varieties on the basis of this group of compounds.
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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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Reinprecht Y, Schram L, Smith TH, Pauls KP. Enhancing In-crop Diversity in Common Bean by Planting Cultivar Mixtures and Its Effect on Productivity. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2020. [DOI: 10.3389/fsufs.2020.00126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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48
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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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Herschlag R, Okada R, Alcalá-Briseño RI, de Souto ER, Valverde RA. Identification of a novel endornavirus in Geranium carolinianum and occurrence within three agroecosystems. Virus Res 2020; 288:198116. [PMID: 32795491 DOI: 10.1016/j.virusres.2020.198116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/05/2020] [Accepted: 08/06/2020] [Indexed: 10/23/2022]
Abstract
A putative endornavirus was detected in Carolina geranium (Geranium carolinianum) in Louisiana, USA. The virus was provisionally named Geranium carolinianum endornavirus 1 (GcEV1). The viral RNA was sequenced, and it consisted of 14,625 nt containing a single ORF coding a putative polyprotein of 4815 aa with conserved domains for a helicase 1, peptidase C97, glycosyl transferase GTB-type, and RNA-dependent RNA polymerase 2. The 5'end consisted of 130 nt while the 3'end consisted of 54 nt ending in nine cytosine residues. The closest relative to GcEV1 was Phaseolus vulgaris endornavirus 3. In phylogenetic analyses, GcEV1 clustered with members of the genus Alphaendornavirus. GcEV1 was detected in 57 of 60 G. carolinianum plants collected from three distinct agroecosystems. The virus was not detected in eight other species of the genus Geranium. There was no association of a particular phenotypic trait of the host with the presence or absence of the virus. GcEV1 was transmitted at a rate of 100% in seeds of a self-pollinated G. carolinianum plant.
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Affiliation(s)
- Rachel Herschlag
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA, USA
| | - Ryo Okada
- Laboratory of Molecular and Cellular Biology, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, 183-8509, Japan
| | | | - Eliezer Rodrigues de Souto
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA, USA
| | - Rodrigo A Valverde
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA, USA.
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Fiore MC, Raimondo FM, Mercati F, Digangi I, Sunseri F, Scialabba A. Preserving Biodiversity in Marginal Rural Areas: Assessment of Morphological and Genetic Variability of a Sicilian Common Bean Germplasm Collection. PLANTS (BASEL, SWITZERLAND) 2020; 9:E989. [PMID: 32759817 PMCID: PMC7463873 DOI: 10.3390/plants9080989] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 07/31/2020] [Accepted: 08/01/2020] [Indexed: 11/17/2022]
Abstract
The historical cultivation of common bean (Phaseolus vulgaris L.) has resulted in the development of local populations/cultivars in restricted Italian rural areas. Many common bean landraces, still cultivated in small mountain areas from Sicily, have become outdated and endangered due to the commercial varieties spreading. These accessions are poorly known but often represent a genetic heritage to be preserved and enhanced. The ex situ conservation of fifty-seven Sicilian common bean landraces was carried out at the "Living Plants Germplasm Bank" at Ucria (Messina, Italy), founded by the Nebrodi Regional Park, together with the "Sicilian Plant Germplasm Repository" of University of Palermo (SPGR/PA). To assess the germplasm genetic diversity, nineteen morphological traits and eight Simple Sequence Repeats (SSRs) were used. Genetic distances among landraces were calculated to construct a clustering tree by using unweighted pair group method arithmetic (UPGMA). Seed germplasm diversity of Sicilian common bean varied from 80.7% to 93.3%, based on six seed descriptors and six leaf, flower, and pod descriptors, respectively, while cluster genetic analysis depicted a clear separation among all the 57 landraces. Principal coordinates (PCoA) and STRUCTURE analyses showed a prevalent rate of admixture between Mesoamerican and Andean gene pools in Sicilian common bean collection, confirming its heterogeneity. The observed high level of diversity evidenced the needs to adopt accurate criterion to plan a definitive ex situ germplasm collection to share agrobiodiversity with local farmers and to avoid any further loss of genetic resources in rural and protected areas.
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Affiliation(s)
- Maria Carola Fiore
- Council for Agricultural Research and Economics Research Centre for Plant Protection and Certification (S.S. 113 km 245,500), 90011 Bagheria, Italy
| | | | - Francesco Mercati
- Institute of Biosciences and Bioresources (IBBR), National Research Council, Corso Calatafimi 414, 90129 Palermo, Italy;
| | - Ignazio Digangi
- Living Plants Germplasm Bank of Nebrodi, Contrada Pirato, 98060 Ucria (ME), Italy;
| | - Francesco Sunseri
- Department of Agraria, University Mediterranea of Reggio Calabria, Località Feo di Vito snc, 89124 Reggio Calabria, Italy;
| | - Anna Scialabba
- Department of Biological, Chemical and Pharmaceutical Science and Technologies (STEBICEF), University of Palermo, Via Archirafi 38, 90123 Palermo, Italy;
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